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Bibliography on: Long Term Ecological Research

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 29 Sep 2023 at 01:51 Created: 

Long Term Ecological Research

The LTER Network: The US. long-term ecological research network consists of 28 sites with a rich history of ecological inquiry, collaboration across a wide range of research topics, and engagement with students, educators, and community members. Bringing together diverse groups of researchers with sustained data collection, ecosystem manipulation experiments, and modeling, these sites allow scientists to apply new tools and explore new questions in systems where the context is well understood, shared, and thoroughly documented.

Created with PubMed® Query: ( LTER OR ("Long Term Ecological Research") ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2023-09-28

Nativ H, Galili O, Almuly R, et al (2023)

New Record of Dendronephthya sp. (Family: Nephtheidae) from Mediterranean Israel: Evidence for Tropicalization?.

Biology, 12(9): pii:biology12091220.

Bio-invasions have the potential to provoke cascade effects that can disrupt natural ecosystems and cause ecological regime shifts. The Mediterranean Sea is particularly prone to bio-invasions as the changing water conditions, evoked by climate change, are creating advantageous conditions for Lessepsian migrants from the Red Sea. Recently, in May 2023, a new alien species was documented in the Mediterranean Sea-a soft coral of the genus Dendronephthya. This discovery was made by divers conducting 'Long-Term Ecological Research' surveys, along the coast of Israel, at a depth of 42 m. Genetic and morphological testing suggest that the species identity may be Dendronepthya hemprichi, an Indo-Pacific coral, common in the Red Sea. According to life history traits of this species, such as accelerated attachment to available surfaces and fast growth, we expect it to rapidly expand its distribution and abundance across the Mediterranean Sea.

RevDate: 2023-09-11

Rodenhizer H, Natali SM, Mauritz M, et al (2023)

Abrupt permafrost thaw drives spatially heterogeneous soil moisture and carbon dioxide fluxes in upland tundra.

Global change biology [Epub ahead of print].

Permafrost thaw causes the seasonally thawed active layer to deepen, causing the Arctic to shift toward carbon release as soil organic matter becomes susceptible to decomposition. Ground subsidence initiated by ice loss can cause these soils to collapse abruptly, rapidly shifting soil moisture as microtopography changes and also accelerating carbon and nutrient mobilization. The uncertainty of soil moisture trajectories during thaw makes it difficult to predict the role of abrupt thaw in suppressing or exacerbating carbon losses. In this study, we investigated the role of shifting soil moisture conditions on carbon dioxide fluxes during a 13-year permafrost warming experiment that exhibited abrupt thaw. Warming deepened the active layer differentially across treatments, leading to variable rates of subsidence and formation of thermokarst depressions. In turn, differential subsidence caused a gradient of moisture conditions, with some plots becoming consistently inundated with water within thermokarst depressions and others exhibiting generally dry, but more variable soil moisture conditions outside of thermokarst depressions. Experimentally induced permafrost thaw initially drove increasing rates of growing season gross primary productivity (GPP), ecosystem respiration (Reco), and net ecosystem exchange (NEE) (higher carbon uptake), but the formation of thermokarst depressions began to reverse this trend with a high level of spatial heterogeneity. Plots that subsided at the slowest rate stayed relatively dry and supported higher CO2 fluxes throughout the 13-year experiment, while plots that subsided very rapidly into the center of a thermokarst feature became consistently wet and experienced a rapid decline in growing season GPP, Reco , and NEE (lower carbon uptake or carbon release). These findings indicate that Earth system models, which do not simulate subsidence and often predict drier active layer conditions, likely overestimate net growing season carbon uptake in abruptly thawing landscapes.

RevDate: 2023-09-05
CmpDate: 2023-09-05

Aneaus S, Rashid I, Srivastava PK, et al (2023)

Quantifying the landscape changes within and outside the Dachigam National Park, Kashmir Himalaya, India using observations and models.

Environmental monitoring and assessment, 195(10):1139.

Protected areas are the cornerstone of biodiversity and serve as a haven for biodiversity conservation. However, due to immense anthropic pressures and ongoing changes in climate, the protected reserves are under immense threat. Human interference through land system changes is a major precusor of fragmentation of landscapes resulting in the decline of Himalayan biodiversity. In this context, this research assessed land use land cover changes (LULCCs) and fragmentation within and outside the Dachigam National Park (DNP) using remote sensing data, GIS-based models and ground truth over the past 55 years (1965-2020). Landscape Fragmentation Tool (LFT) helped to compute edge effect, patchiness, perforation and core areas. The Land Change Modeller (LCM) of IDRISI TerrSet was used for simulating the future LULC for the years 2030, 2050, 2700 and 2100. The analysis of LULCCs showed that built-up and aquatic vegetation expanded by 326% and 174%, respectively in the vicinity of the DNP. The area under agriculture, scrub and pasture decreased primarily due to intensified land use activities. Within the DNP, the area under forest cover declined by 7%. A substantial decrease was observed in the core zone both within (39%) and outside (30%) the DNP indicative of fragmentation of natural habitats. LCM analysis projected 10% increase in the built-up extents besides forests, shrublands and pastures. This knowledge generated in this study shall form an important baseline for understanding and characterising the human-wildlife relationship, initiating long-term ecological research (LTER) on naturally vegetated and aquatic ecosystems (primarily Dal Lake) of the region.

RevDate: 2023-09-07

Gallitelli L, D'Agostino M, Battisti C, et al (2023)

Dune plants as a sink for beach litter: The species-specific role and edge effect on litter entrapment by plants.

The Science of the total environment, 904:166756 pii:S0048-9697(23)05381-0 [Epub ahead of print].

Anthropogenic litter accumulates along coasts worldwide. In addition to the flowing litter load, wind, sea currents, geomorphology and vegetation determine the distribution of litter trapped on the sandy coasts. Although some studies highlighted the role of dune plants in trapping marine litter, little is known about their efficiency as sinks and about the small-scale spatial distribution of litter across the dune area. Here, we explore these gaps by analysing six plant species widespread in Mediterranean coastal habitats, namely Echinophora spinosa, Limbarda crithmoides, Anthemis maritima, Pancratium maritimum, Thinopyrum junceum, and Salsola kali. The present study analyses for the first time the capture of litter by dune vegetation at a multi-species level, considering their morphological structure. Data on plastic accumulation on dune plants were compared with unvegetated control plots located at embryo-dune and foredune belts. We found that dunal plants mainly entrapped macrolitter (> 0.5 cm). Particularly, E. spinosa, L. crithmoides, A. maritima and P. maritimum mostly accumulated litter in the embryo dune while T. junceum and S. kali entrapped more in the foredune area. Moreover, beach litter was mainly blocked at the edge of the plant patches rather than in the core, highlighting the 'Plant-edge litter effect'. As A. maritima and S. kali entrapped respectively more litter in embryo and foredune habitats, these species could be used to monitor and recollect litter. In this light, our findings provide further insight into the role of dune plants in the beach litter dynamics, suppling useful information for beach clean-up actions.

RevDate: 2023-09-02

Niu F, Pierce NA, Okin GS, et al (2023)

Sandblasting promotes shrub encroachment in arid grasslands.

The New phytologist [Epub ahead of print].

Shrub encroachment is a common ecological state transition in global drylands and has myriad adverse effects on grasslands and the services they provide. This physiognomic shift is often ascribed to changes in climate (e.g. precipitation) and disturbance regimes (e.g. grazing and fire), but this remains debated. Aeolian processes are known to impact resource distribution in drylands, but their potential role in grassland-to-shrubland state changes has received little attention. We quantified the effects of 'sandblasting' (abrasive damage by wind-blown soil) on the ecophysiology of dryland grass vs shrub functional types using a portable wind tunnel to test the hypothesis that grasses would be more susceptible to sandblasting than shrubs and, thus, reinforce transitions to shrub dominance in wind-erodible grasslands when climate- or disturbance-induced reductions in ground cover occur. Grasses and shrubs responded differently to sandblasting, wherein water-use efficiency declined substantially in grasses, but only slightly in shrubs, owing to grasses having greater increases in day/nighttime leaf conductance and transpiration. The differential ecophysiological response to sandblasting exhibited by grass and shrub functional types could consequently alter the vegetation dynamics in dryland grasslands in favour of the xerophytic shrubs. Sandblasting could thus be an overlooked driver of shrub encroachment in wind-erodible grasslands.

RevDate: 2023-08-08

Vaca-Sánchez MS, Cuevas-Reyes P, Munck I, et al (2023)

Patterns in Wing Morphology and Fluctuating Asymmetry in Eulaema nigrita along an Altitudinal Gradient in the Brazilian Rupestrian Grassland.

Neotropical entomology [Epub ahead of print].

Mountain ecosystems experience abrupt abiotic changes that represent environmental filters for many organisms, shaping their phenotypic expressions. However, little is known about the morphological and symmetric adjustments of native bees along altitudinal gradients. We evaluated the changes on wing morphology, wing size, and vein fluctuating asymmetry (FA) of Eulaema nigrita Lepeletier (Apidae: Euglossini) associated with climatic variables along an altitudinal gradient in the rupestrian grassland (known also as campo rupestre or rupestrian field) of Serra do Cipó, Brazil. Seven sampling points along the altitudinal gradient were selected and distributed among 800 and 1400 m.a.s.l., and then, 40 individuals of E. nigrita were collected per each altitudinal point to determine the FA levels and the morphological changes using geometric morphometric techniques. We found that the wing size of E. nigrita decreased with increasing altitude. At the highest altitudes, the levels of FA of the wing veins were greater compared to bees from lower altitudes. We detected significant changes in wing morphology along the altitudinal gradient; bees of lower altitudes showed longer and wider wings than bees of higher altitudes, which had narrower and less elongated wings. Our results show a set of morphological adjustments and phenotypic expressions in E. nigrita associated with the variation in environmental conditions along the altitudinal gradient. We highlight the importance of environmental variables as insect-stressor factors, and that FA and geometric morphometric can be excellent tools for monitoring and evaluating environmental stresses.

RevDate: 2023-07-18

Perez-Quezada JF, Barichivich J, Urrutia-Jalabert R, et al (2023)

Warming and drought weaken the carbon sink capacity of an endangered paleoendemic temperate rainforest in South America.

Journal of geophysical research. Biogeosciences, 128(4):2022jg007258.

Measurements of ecosystem carbon (C) fluxes in temperate forests are concentrated in the Northern Hemisphere, leaving the functionally diverse temperate forests in the Southern Hemisphere underrepresented. Here, we report three years (February 2018-January 2021) of C fluxes, studied with eddy-covariance and closed chamber techniques, in an endangered temperate evergreen rainforest of the long-lived paleoendemic South American conifer Fitzroya cupressoides. Using classification and regression trees we analyzed the most relevant drivers and thresholds of daily net ecosystem exchange (NEE) and soil respiration. The annual NEE showed that the forest was a moderate C sink during the period analyzed (-287±38 g C m[-2] year [-1]). We found that the capacity to capture C of the Fitzroya rainforests in the Coastal Range of southern Chile is optimal under cool and rainy conditions in the early austral spring (October-November) and decreases rapidly towards the summer dry season (January-February) and autumn. Although the studied forest type has a narrow geographical coverage, the gross primary productivity measured at the tower was highly representative of Fitzroya and other rainforests in the region. Our results suggest that C fluxes in paleoendemic cool F. cupressoides forests may be negatively affected by the warming and drying predicted by climate change models, reinforcing the importance of maintaining this and other long-term ecological research sites in the Southern Hemisphere.

RevDate: 2023-07-12

Tennies NK, F Alberto (2023)

A tool for detecting giant kelp canopy biomass decline in the Californias.

Journal of phycology [Epub ahead of print].

Kelp species provide many ecosystem services associated with their three-dimensional structures. Among these, fast-growth, canopy-forming species, like giant kelp Macrocystis pyrifera, are the foundation of kelp forests across many temperate reefs. Giant kelp populations have experienced regional declines in different parts of the world. Giant kelp canopy is very dynamic and can take years to recover from disturbance, challenging comparisons of standing biomass with historical baselines. The Santa Barbara Coastal LTER (SBC LTER), curates a time series of Landsat sensed surface cover and biomass for giant kelp in the west coast of North America. In the last decade, this resource has been fundamental to understanding the species' population dynamics and drivers. However, simple ready-to-use summary statistics aimed at classifying regional kelp decline or recovery are not readily available to stakeholders and coastal managers. To this end, we describe here two simple metrics made available through the R package kelpdecline. First, the proportion of Landsat pixels in decline (PPD), in which current biomass is compared with a historical baseline, and second, a pixel occupancy trend (POT), in which current year pixel occupancy is compared to the time-series long probability of occupancy. The package produces raster maps and output tables summarizing kelp decline and trends over a 0.25 × 0.25° scale. Using kelpdecline, we show how sensitivity analysis on PPD parameter variation can increase the confidence of kelp decline estimates.

RevDate: 2023-09-15

Hardison SB, McGlathery KJ, MCN Castorani (2023)

Effects of seagrass restoration on coastal fish abundance and diversity.

Conservation biology : the journal of the Society for Conservation Biology [Epub ahead of print].

Restoration is accelerating to reverse global declines of key habitats and recover lost ecosystem functions, particularly in coastal ecosystems. However, there is high uncertainty about the long-term capacity of restored ecosystems to provide habitat and increase biodiversity and the degree to which these ecosystem services are mediated by spatial and temporal environmental variability. We addressed these gaps by sampling fishes biannually for 5-7 years (2012-2018) at 16 sites inside and outside a rapidly expanding restored seagrass meadow in coastal Virginia (USA). Despite substantial among-year variation in abundance and species composition, seine catches in restored seagrass beds were consistently larger (6.4 times more fish, p < 0.001) and more speciose (2.6 times greater species richness, p < 0.001; 3.1 times greater Hill-Shannon diversity, p = 0.03) than seine catches in adjacent unvegetated areas. Catches were particularly larger during summer than autumn (p < 0.01). Structural equation modeling revealed that depth and water residence time interacted to control seagrass presence, leading to higher fish abundance and richness in shallow, well-flushed areas that supported seagrass. Together, our results indicate that seagrass restoration yields large and consistent benefits for many coastal fishes, but that restoration and its benefits are sensitive to the dynamic seascapes in which restoration is conducted. Consideration of how seascape-scale environmental variability affects the success of habitat restoration and subsequent ecosystem function will improve restoration outcomes and the provisioning of ecosystem services.

RevDate: 2023-07-01

Holzer JM, DE Orenstein (2023)

Organizational transformation for greater sustainability impact: recent changes in a scientific research infrastructure in Europe.

Landscape ecology [Epub ahead of print].

CONTEXT: Scholars across holistic, transdisciplinary, place-based fields of research, such as landscape ecology and social ecology, have increasingly called for an 'all-hands-on-deck' approach for transformations toward greater sustainability of social-ecological systems. This Perspective showcases organizational transformation toward sustainability in the context of a research network dedicated to place-based, social-ecological research in Europe.

OBJECTIVES: Using the European LTER research infrastructure (eLTER RI) as a case, we analyze recent organizational-level shifts motivated by desires to increase sustainability impact. These shifts include knowledge integration between the natural and social sciences, stakeholder engagement, and a reformulation of administrative guidelines and practices.

METHODS: Following a program evaluation, new conversations led to new initiatives in the eLTER RI. As researchers who were involved in the program evaluation and the development of new initiatives, we rely on our professional experience and participant observation to provide insights about this process and its developments.

RESULTS: Recommendations from a recent assessment that critiqued and provided recommendations for the research infrastructure have recently been implemented in the eLTER RI. eLTER has leveraged a unique and timely opportunity-formal recognition and project funding by the EU-to upscale and standardize its infrastructure by creating novel protocols and enacting steps towards implementation.

CONCLUSIONS: This Perspective demonstrates how eLTER's research agenda and related protocols have evolved to better integrate multiple knowledge types, promote stakeholder integration into research, and foster greater equity and reflexivity in doing science, all of which are considered necessary to increase sustainability impact. We conclude by considering current and potential future challenges.

RevDate: 2023-07-01

Hansen FA, James DK, Anderson JP, et al (2023)

Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert.

Frontiers in microbiology, 14:1135800.

INTRODUCTION: Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert.

METHODS: This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity.

RESULTS: Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations.

DISCUSSION: Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.

RevDate: 2023-09-01
CmpDate: 2023-09-01

Volf M, Leong JV, de Lima Ferreira P, et al (2023)

Contrasting levels of β-diversity and underlying phylogenetic trends indicate different paths to chemical diversity in highland and lowland willow species.

Ecology letters, 26(9):1559-1571.

Diverse specialised metabolites contributed to the success of vascular plants in colonising most terrestrial habitats. Understanding how distinct aspects of chemical diversity arise through heterogeneous environmental pressures can help us understand the effects of abiotic and biotic stress on plant evolution and community assembly. We examined highland and lowland willow species within a phylogenetic framework to test for trends in their chemical α-diversity (richness) and β-diversity (variation among species sympatric in elevation). We show that differences in chemistry among willows growing at different elevations occur mainly through shifts in chemical β-diversity and due to convergence or divergence among species sharing their elevation level. We also detect contrasting phylogenetic trends in concentration and α-diversity of metabolites in highland and lowland willow species. The resulting elevational patterns contribute to the chemical diversity of willows and suggest that variable selective pressure across ecological gradients may, more generally, underpin complex changes in plant chemistry.

RevDate: 2023-08-29
CmpDate: 2023-08-28

Kumar J, Coffin AW, Baffaut C, et al (2023)

Quantitative Representativeness and Constituency of the Long-Term Agroecosystem Research Network and Analysis of Complementarity with Existing Ecological Networks.

Environmental management, 72(4):705-726.

Studies conducted at sites across ecological research networks usually strive to scale their results to larger areas, trying to reach conclusions that are valid throughout larger enclosing regions. Network representativeness and constituency can show how well conditions at sampling locations represent conditions also found elsewhere and can be used to help scale-up results over larger regions. Multivariate statistical methods have been used to design networks and select sites that optimize regional representation, thereby maximizing the value of datasets and research. However, in networks created from already established sites, an immediate challenge is to understand how well existing sites represent the range of environments in the whole area of interest. We performed an analysis to show how well sites in the USDA Long-Term Agroecosystem Research (LTAR) Network represent all agricultural working lands within the conterminous United States (CONUS). Our analysis of 18 LTAR sites, based on 15 climatic and edaphic characteristics, produced maps of representativeness and constituency. Representativeness of the LTAR sites was quantified through an exhaustive pairwise Euclidean distance calculation in multivariate space, between the locations of experiments within each LTAR site and every 1 km cell across the CONUS. Network representativeness is from the perspective of all CONUS locations, but we also considered the perspective from each LTAR site. For every LTAR site, we identified the region that is best represented by that particular site-its constituency-as the set of 1 km grid locations best represented by the environmental drivers at that particular LTAR site. Representativeness shows how well the combination of characteristics at each CONUS location was represented by the LTAR sites' environments, while constituency shows which LTAR site was the closest match for each location. LTAR representativeness was good across most of the CONUS. Representativeness for croplands was higher than for grazinglands, probably because croplands have more specific environmental criteria. Constituencies resemble ecoregions but have their environmental conditions "centered" on those at particular existing LTAR sites. Constituency of LTAR sites can be used to prioritize the locations of experimental research at or even within particular sites, or to identify the extents that can likely be included when generalizing knowledge across larger regions of the CONUS. Sites with a large constituency have generalist environments, while those with smaller constituency areas have more specialized environmental combinations. These "specialist" sites are the best representatives for smaller, more unusual areas. The potential of sharing complementary sites from the Long-Term Ecological Research (LTER) Network and the National Ecological Observatory Network (NEON) to boost representativeness was also explored. LTAR network representativeness would benefit from borrowing several NEON sites and the Sevilleta LTER site. Later network additions must include such specialist sites that are targeted to represent unique missing environments. While this analysis exhaustively considered principal environmental characteristics related to production on working lands, we did not consider the focal agronomic systems under study, or their socio-economic context.

RevDate: 2023-09-01

Perales KM, MJ Vander Zanden (2023)

Lakeshore residential development as a driver of aquatic habitat and littoral fish communities: A cross-system study.

Ecological applications : a publication of the Ecological Society of America, 33(6):e2896.

Lakeshore riparian habitats have undergone intensive residential development in many parts of the world. Lakeshore residential development (LRD) is associated with aquatic habitat loss/alteration, including altered macrophyte communities and reduced coarse woody habitat. Yet habitat-mediated and other generalized effects of LRD on lake biotic communities are not well understood. We used two approaches to examine the relationships among LRD, habitat, and fish community in a set of 57 northern Wisconsin lakes. First, we examined how LRD affected aquatic habitat using mixed linear effects models. Second, we evaluated how LRD affected fish abundance and community structure at both whole-lake and site-level spatial scales using generalized linear mixed-effects models. We found that LRD did not have a significant relationship with the total abundance (all species combined) of fish at either scale. However, there were significant species-specific responses to LRD at the whole-lake scale. Species abundances varied across the LRD gradient, with bluegill (Lepomis macrochirus) and mimic shiners (Notropis volucellus) responding positively along the gradient and walleye (Sander vitreus) having the most negative response. We also quantified site-level habitat associations for each fish species. We found that habitat associations did not inform a species' overall response to LRD, as illustrated by species with similar responses to LRD having vastly different habitat associations. Finally, even with the inclusion of littoral habitat information in models, LRD still had significant effects on species abundances, reflecting a role of LRD in shaping littoral fish communities independent of our measure of littoral habitat alteration. Our results indicated that LRD altered littoral fish communities at the whole-lake scale through both habitat and non-habitat-mediated drivers.

RevDate: 2023-07-27
CmpDate: 2023-07-27

Besser AC, Manlick PJ, Blevins CM, et al (2023)

Variation in gut microbial contribution of essential amino acids to host protein metabolism in a wild small mammal community.

Ecology letters, 26(8):1359-1369.

Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ[13] C) and nitrogen (δ[15] N) isotope analysis, we estimated the proportional contributions of essential amino acids (AAESS) synthesized by gut microbes to five co-occurring desert rodents representing herbivorous, omnivorous and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (Dipodomys spp.) routed a substantial proportion (~40%-50%) of their AAESS from gut microbes, while higher trophic level omnivores (Peromyscus spp.) and insectivores (Onychomys arenicola) obtained most of their AAESS (~58%) from plant-based energy channels but still received ~20% of their AAESS from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals.

RevDate: 2023-07-02
CmpDate: 2023-06-30

Thompson GL, Bray N, Groffman PM, et al (2023)

Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes.

Oecologia, 202(2):337-351.

Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.

RevDate: 2023-06-07

Dutta A, Connors E, Trinh R, et al (2023)

Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula.

Frontiers in microbiology, 14:1168507.

The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.

RevDate: 2023-08-31
CmpDate: 2023-06-15

Gou X, Reich PB, Qiu L, et al (2023)

Leguminous plants significantly increase soil nitrogen cycling across global climates and ecosystem types.

Global change biology, 29(14):4028-4043.

Leguminous plants are an important component of terrestrial ecosystems and significantly increase soil nitrogen (N) cycling and availability, which affects productivity in most ecosystems. Clarifying whether the effects of legumes on N cycling vary with contrasting ecosystem types and climatic regions is crucial for understanding and predicting ecosystem processes, but these effects are currently unknown. By conducting a global meta-analysis, we revealed that legumes increased the soil net N mineralization rate (Rmin) by 67%, which was greater than the recently reported increase associated with N deposition (25%). This effect was similar for tropical (53%) and temperate regions (81%) but was significantly greater in grasslands (151%) and forests (74%) than in croplands (-3%) and was greater in in situ incubation (101%) or short-term experiments (112%) than in laboratory incubation (55%) or long-term experiments (37%). Legumes significantly influenced the dependence of Rmin on N fertilization and experimental factors. The Rmin was significantly increased by N fertilization in the nonlegume soils, but not in the legume soils. In addition, the effects of mean annual temperature, soil nutrients and experimental duration on Rmin were smaller in the legume soils than in the nonlegume soils. Collectively, our results highlighted the significant positive effects of legumes on soil N cycling, and indicated that the effects of legumes should be elucidated when addressing the response of soils to plants.

RevDate: 2023-06-19
CmpDate: 2023-06-19

Battisti C, Fanelli G, Gallitelli L, et al (2023)

Dunal plants as sink for anthropogenic marine litter: The entrapping role of Salsola kali L. (1753) in a Mediterranean remote beach (Sardinia, Italy).

Marine pollution bulletin, 192:115033.

The ability to retain anthropogenic marine litter by a halo-psammophilous plant formation dominated by a single prostrate species (Salsola kali) on a Sardinian beach was measured. We hypothesized that the anthropogenic litter (i) is trapped by plants to a greater extent than in control areas, and (ii) has more elongated size, mimicking the organic Posidonia wrack, largely occurring locally as 'banquettes'. Salsola kali patches show an apparently higher anthropogenic litter density than control sites without vegetation. Salsola kali plants trap litter items significantly longer and a larger number of size length categories than control plots. These effects may be due to the prostrate structure of the plant with small thorns at the apex. Also, litter entrapped by plants can interfere with the mechanisms of dune deposition and structuration, in turn affecting food chains by decreasing the availability of organic material for pedofauna.

RevDate: 2023-05-04
CmpDate: 2023-05-02

Henschke N, Espinasse B, Stock CA, et al (2023)

The role of water mass advection in staging of the Southern Ocean Salpa thompsoni populations.

Scientific reports, 13(1):7088.

Salpa thompsoni is an important grazer in the Southern Ocean. Their abundance in the western Antarctic Peninsula is highly variable, varying by up to 5000-fold inter-annually. Here, we use a particle-tracking model to simulate the potential dispersal of salp populations from a source location in the Antarctic Circumpolar Current (ACC) to the Palmer Long Term Ecological Research (PAL LTER) study area. Tracking simulations are run from 1998 to 2015, and compared against both a stationary salp population model simulated at the PAL LTER study area and observations from the PAL LTER program. The tracking simulation was able to recreate closely the long-term trend and the higher abundances at the slope stations. The higher abundances observed at slope stations are likely due to the advection of salp populations from a source location in the ACC, highlighting the significant role of water mass circulation in the distribution and abundance of Southern Ocean salp populations.

RevDate: 2023-06-26
CmpDate: 2023-06-26

Haubrock PJ, Pilotto F, Soto I, et al (2023)

Long-term trends in abundances of non-native species across biomes, realms, and taxonomic groups in Europe.

The Science of the total environment, 884:163808.

Rates of biological invasion have increased over recent centuries and are expected to increase in the future. Whereas increasing rates of non-native species incursions across realms, taxonomic groups, and regions are well-reported, trends in abundances within these contexts have lacked analysis due to a paucity of long-term data at large spatiotemporal scales. These knowledge gaps impede prioritisation of realms, regions, and taxonomic groups for management. We analysed 180 biological time series (median 15 ± 12.8 sampling years) mainly from Long-Term Ecological Research (LTER) sites comprising abundances of marine, freshwater, and terrestrial non-native species in Europe. A high number (150; 83,3 %) of these time series were invaded by at least one non-native species. We tested whether (i) local long-term abundance trends of non-native species are consistent among environmental realms, taxonomic groups, and regions, and (ii) if any detected trend can be explained by climatic conditions. Our results indicate that abundance trends at local scales are highly variable, with evidence of declines in marine and freshwater long-term monitoring sites, despite non-native species reports increasing rapidly since the late 1970s. These declines were driven mostly by abundance trends in non-native fish, birds, and invertebrate species in three biogeographic regions (Continental, Atlantic, and the North Sea). Temperature and precipitation were important predictors of observed abundance trends across Europe. Yet, the response was larger for species with already declining trends and differed among taxa. Our results indicate that trends in biological invasions, especially across different taxonomic groups, are context-dependent and require robust local data to understand long-term trends across contexts at large scales. While the process of biological invasion is spatiotemporally broad, economic or ecological impacts are generally realised on the local level. Accordingly, we urge proactive and coordinated management actions from local to large scales, as invasion impacts are substantial and dynamics are prone to change.

RevDate: 2023-04-30

Pozojević I, Dorić V, Miliša M, et al (2023)

Defining Patterns and Rates of Natural vs. Drought Driven Aquatic Community Variability Indicates the Ongoing Need for Long Term Ecological Research.

Biology, 12(4):.

Most ecologists have used climate change, as an omnipresent pressure, to support their findings in researching the vulnerability of specific taxa, communities, or ecosystems. However, there is a widespread lack of long-term biological, biocoenological, or community data of periods longer than several years to ascertain patterns as to how climate change affects communities. Since the 1950s, southern Europe has faced an ongoing trend of drying and loss of precipitation. A 13-year research program in the Dinaric karst ecoregion of Croatia aimed to comprehensively track emergence patterns of freshwater insects (true flies: Diptera) in a pristine aquatic environment. Three sites, spring, upper, and lower tufa barriers (calcium carbonate barriers on a barrage lake system that act as natural damns), were sampled monthly over 154 months. This coincided with a severe drought event in 2011/2012. This was the most significant drought (very low precipitation rates for an extended period of time) in the Croatian Dinaric ecoregion since the start of detailed records in the early 20th century. Significant shifts in dipteran taxa occurrence were determined using indicator species analysis. Patterns of seasonal and yearly dynamics were presented as Euclidian distance metrics of similarity in true fly community composition compared at increasing time intervals, to ascertain the degree of temporal variability of similarity within the community of a specific site and to define patterns of similarity change over time. Analyses detected significant shifts in community structure linked to changes in discharge regimes, especially to the drought period.

RevDate: 2023-05-08
CmpDate: 2023-05-08

Hartline DK, Cieslak MC, Castelfranco AM, et al (2023)

De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes.

Scientific data, 10(1):242.

This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. 'Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study's primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.

RevDate: 2023-06-09
CmpDate: 2023-06-08

Rypel AL (2023)

Ecosystem size filters life-history strategies to shape community assembly in lakes.

The Journal of animal ecology, 92(6):1161-1175.

Enhancing understanding of community assembly rules hinges on shared conceptualizations that operate across scales and levels of ecological organization. Knowledge of the biogeography of life-history strategies is especially limited but crucial for building fundamental information on the relationships between trait diversity and species richness. The goals of this study were to (i) demonstrate how life histories can be classified using a previously identified triangular continuum of evolutionary trade-offs; (ii) test whether spatial and temporal heterogeneity in species abundances is linked to life-history strategy; (iii) compare species-area relationships across the primary life-history strategist groups and (iv) explore how species life-history niche spaces are shaped by ecosystem size and landscape architecture. Fish communities were sampled in 40 lakes that varied widely in volume; 11 lakes were sampled annually for 28 or 42 years. Seventy-one species were classified as equilibrium, periodic or opportunistic strategists, and species-area curves were quantified and compared among strategy types. As predicted by life-history theory, relative abundances of opportunistic strategists were extremely variable over space and time, whereas abundances of equilibrium and periodic strategists were more stable. Small lakes were often dominated by only one species, usually an opportunistic strategist. Species richness increased with ecosystem size, but larger ecosystems were increasingly inhabited by equilibrium, and then, periodic strategists. Richness of periodic species increased with ecosystem size at a faster rate compared with opportunistic species showing that colonization-extinction points fundamentally vary by strategy. Similarly, life-history niche space increased with ecosystem size in accord with species-area relationships but showed saturation behaviour. Niche space became increasingly crowded in large lakes, particularly in lakes with higher hydrologic connectance. Ecosystem size mediates the assembly of communities through effects on environmental stability, hydrology and life-history filtering. This finding provides novel insights into community assembly at multiple scales and has broad conservation applications. Because ecosystem size filters towards orthogonal and inverse life histories, conservation actions (e.g. fish stockings) that do not consider life-history and community filtering rules will probably fail.

RevDate: 2023-05-10
CmpDate: 2023-04-19

Sidhu C, Kirstein IV, Meunier CL, et al (2023)

Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom.

Microbiome, 11(1):77.

BACKGROUND: Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that collectively remineralize gigatons of algal biomass on a global scale. This biomass is largely composed of distinct polysaccharides, and the microbial decomposition of these polysaccharides is therefore a process of prime importance.

RESULTS: In 2020, we sampled a complete biphasic spring bloom in the German Bight over a 90-day period. Bacterioplankton metagenomes from 30 time points allowed reconstruction of 251 metagenome-assembled genomes (MAGs). Corresponding metatranscriptomes highlighted 50 particularly active MAGs of the most abundant clades, including many polysaccharide degraders. Saccharide measurements together with bacterial polysaccharide utilization loci (PUL) expression data identified β-glucans (diatom laminarin) and α-glucans as the most prominent and actively metabolized dissolved polysaccharide substrates. Both substrates were consumed throughout the bloom, with α-glucan PUL expression peaking at the beginning of the second bloom phase shortly after a peak in flagellate and the nadir in bacterial total cell counts.

CONCLUSIONS: We show that the amounts and composition of dissolved polysaccharides, in particular abundant storage polysaccharides, have a pronounced influence on the composition of abundant bacterioplankton members during phytoplankton blooms, some of which compete for similar polysaccharide niches. We hypothesize that besides the release of algal glycans, also recycling of bacterial glycans as a result of increased bacterial cell mortality can have a significant influence on bacterioplankton composition during phytoplankton blooms. Video Abstract.

RevDate: 2023-07-01
CmpDate: 2023-06-23

Chase AB, Bogdanov A, Demko AM, et al (2023)

Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments.

The ISME journal, 17(7):976-983.

While the field of microbial biogeography has largely focused on the contributions of abiotic factors to community patterns, the potential influence of biotic interactions in structuring microbial communities, such as those mediated by the production of specialized metabolites, remains largely unknown. Here, we examined the relationship between microbial community structure and specialized metabolism at local spatial scales in marine sediment samples collected from the Long-Term Ecological Research (LTER) site in Moorea, French Polynesia. By employing a multi-omic approach to characterize the taxonomic, functional, and specialized metabolite composition within sediment communities, we find that biogeographic patterns were driven by local scale processes (e.g., biotic interactions) and largely independent of dispersal limitation. Specifically, we observed high variation in biosynthetic potential (based on Bray-Curtis dissimilarity) between samples, even within 1 m[2] plots, that reflected uncharacterized chemical space associated with site-specific metabolomes. Ultimately, connecting biosynthetic potential to community metabolomes facilitated the in situ detection of natural products and revealed new insights into the complex metabolic dynamics associated with sediment microbial communities. Our study demonstrates the potential to integrate biosynthetic genes and metabolite production into assessments of microbial community dynamics.

RevDate: 2023-05-25
CmpDate: 2023-05-25

Matthews TJ, Wayman JP, Whittaker RJ, et al (2023)

A global analysis of avian island diversity-area relationships in the Anthropocene.

Ecology letters, 26(6):965-982.

Research on island species-area relationships (ISAR) has expanded to incorporate functional (IFDAR) and phylogenetic (IPDAR) diversity. However, relative to the ISAR, we know little about IFDARs and IPDARs, and lack synthetic global analyses of variation in form of these three categories of island diversity-area relationship (IDAR). Here, we undertake the first comparative evaluation of IDARs at the global scale using 51 avian archipelagic data sets representing true and habitat islands. Using null models, we explore how richness-corrected functional and phylogenetic diversity scale with island area. We also provide the largest global assessment of the impacts of species introductions and extinctions on the IDAR. Results show that increasing richness with area is the primary driver of the (non-richness corrected) IPDAR and IFDAR for many data sets. However, for several archipelagos, richness-corrected functional and phylogenetic diversity changes linearly with island area, suggesting that the dominant community assembly processes shift along the island area gradient. We also find that archipelagos with the steepest ISARs exhibit the biggest differences in slope between IDARs, indicating increased functional and phylogenetic redundancy on larger islands in these archipelagos. In several cases introduced species seem to have 're-calibrated' the IDARs such that they resemble the historic period prior to recent extinctions.

RevDate: 2023-03-14

Bregman G, Lalzar M, Livne L, et al (2023)

Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea.

Frontiers in microbiology, 14:1027804.

Sharks, as apex predators, play an essential ecological role in shaping the marine food web and maintaining healthy and balanced marine ecosystems. Sharks are sensitive to environmental changes and anthropogenic pressure and demonstrate a clear and rapid response. This designates them a "keystone" or "sentinel" group that may describe the structure and function of the ecosystem. As a meta-organism, sharks offer selective niches (organs) for microorganisms that can provide benefits for their hosts. However, changes in the microbiota (due to physiological or environmental changes) can turn the symbiosis into a dysbiosis and may affect the physiology, immunity and ecology of the host. Although the importance of sharks within the ecosystem is well known, relatively few studies have focused on the microbiome aspect, especially with long-term sampling. Our study was conducted at a site of coastal development in Israel where a mixed-species shark aggregation (November-May) is observed. The aggregation includes two shark species, the dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) which segregate by sex (females and males, respectively). In order to characterize the bacterial profile and examine the physiological and ecological aspects, microbiome samples were collected from different organs (gills, skin, and cloaca) from both shark species over 3 years (sampling seasons: 2019, 2020, and 2021). The bacterial composition was significantly different between the shark individuals and the surrounding seawater and between the shark species. Additionally, differences were apparent between all the organs and the seawater, and between the skin and gills. The most dominant groups for both shark species were Flavobacteriaceae, Moraxellaceae, and Rhodobacteraceae. However, specific microbial biomarkers were also identified for each shark. An unexpected difference in the microbiome profile and diversity between the 2019-2020 and 2021 sampling seasons, revealed an increase in the potential pathogen Streptococcus. The fluctuations in the relative abundance of Streptococcus between the months of the third sampling season were also reflected in the seawater. Our study provides initial information on shark microbiome in the Eastern Mediterranean Sea. In addition, we demonstrated that these methods were also able to describe environmental episodes and the microbiome is a robust measure for long-term ecological research.

RevDate: 2023-04-25
CmpDate: 2023-04-25

Ferri V, Crescia P, C Battisti (2023)

Discarded bottles entrap endemic small mammals species in a large Mediterranean island.

Environmental science and pollution research international, 30(19):57164-57173.

We examined the entrapment effect of discarded bottles on small mammals, along a road network located in North-Western Sardinia (Italy). On 162 bottles, 49 (> 30%) contained at least one animal specimen (invertebrate or vertebrate) and 26 (16%) entrapped 151 small mammals: insectivorous shrews (Soricomorpha) were more frequently recorded. Larger bottles (66 cl.) showed a higher number of entrapped mammals, but difference was not significant when compared to smaller bottles (33 cl.). Our data highlighted as abandoned bottles represent a threatening factor for small mammals on a large Mediterranean island with over-represented endemic shrews (predators of high trophic level) attracted by insects entrapped in bottles. Correspondence analysis suggest a weak segregation between bottles of different size, related to the abundance of the most entrapped species, the Mediterranean shrew (Crocidura pachyura). This still neglected type of litter, reducing number and biomass of insectivorous mammals of high trophic level and high ecological value may affect the food web in terrestrial insular communities, yet impoverished for biogeographical reasons. However, discarded bottles may represent as low-cost surrogate pitfall traps useful to improve knowledge in poor studied areas. Following the DPSIR (Driving force, Pressure, State, Impact, Response) approach as a framework to select indicator, we suggest as the effectiveness of removal clean-ups could be monitored using both the density of discarded bottles (as indicator of threat pressure) and the abundance of entrapped animals (as indicator of impact on small mammals).

RevDate: 2023-04-16
CmpDate: 2023-03-31

Propster JR, Schwartz E, Hayer M, et al (2023)

Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming.

Applied and environmental microbiology, 89(3):e0154322.

Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using [18]O-labeled water, from which taxon-specific rates of [18]O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.

RevDate: 2023-04-17

Battisti C, Cento M, Circosta A, et al (2023)

Resurrecting seasonal dynamics in waterbirds after wetland restoration: before-after monitoring highlights the role of a single dominant species.

Wetlands ecology and management, 31(2):203-211.

We compared a set of uni-varied diversity metrics of a guild of water-related birds (hereafter 'waterbirds') before and after a wetland restoration carried out on uncultivated (reclaimed) lands. Over a period of five years, we observed a restart of seasonal waterbirds dynamics after wetland restoration by flooding of abandoned croplands, with a significant increase in all metrics of diversity, more evident in autumn-winter periods. Seasonal thresholds were evident before (2017-2018) and after (2018-2019) the flooding. These dynamics appeared irregular, probably for a different inter-annual suitability of the flooded meadows due to local ecological factors (e.g., change in meteorological regime and in rush-bed vegetation cover). Rarefaction curves, both for richness and diversity, showed how the waterbird community moved towards a greater complexity. Flooded meadow restoration, particularly favoured wintering species in Mediterranean sites, which explained the strong fluctuations in total abundance. At the species level, Northern Lapwing (Vanellus vanellus), absent before restoration, was the most abundant species after flooding, using flooded meadows with its gregarious behaviour. This 'crowding' may be explained also for a lack of similar habitats in the surrounding. Other dominant species (Anas platyrhynchos, Ardea cinerea, Egretta garzetta) showed a significant increase after restoration. Standardized before-after monitoring on medium term time periods seem suitable to evidence inter-annual season dynamics in diversity metrics of waterbird assemblages.

RevDate: 2023-05-29
CmpDate: 2023-04-06

Solokas MA, Feiner ZS, Al-Chokachy R, et al (2023)

Shrinking body size and climate warming: Many freshwater salmonids do not follow the rule.

Global change biology, 29(9):2478-2492.

Declining body size is believed to be a universal response to climate warming and has been documented in numerous studies of marine and anadromous fishes. The Salmonidae are a family of coldwater fishes considered to be among the most sensitive species to climate warming; however, whether the shrinking body size response holds true for freshwater salmonids has yet to be examined at a broad spatial scale. We compiled observations of individual fish lengths from long-term surveys across the Northern Hemisphere for 12 species of freshwater salmonids and used linear mixed models to test for spatial and temporal trends in body size (fish length) spanning recent decades. Contrary to expectations, we found a significant increase in length overall but with high variability in trends among populations and species. More than two-thirds of the populations we examined increased in length over time. Secondary regressions revealed larger-bodied populations are experiencing greater increases in length than smaller-bodied populations. Mean water temperature was weakly predictive of changes in body length but overall minimal influences of environmental variables suggest that it is difficult to predict an organism's response to changing temperatures by solely looking at climatic factors. Our results suggest that declining body size is not universal, and the response of fishes to climate change may be largely influenced by local factors. It is important to know that we cannot assume the effects of climate change are predictable and negative at a large spatial scale.

RevDate: 2023-05-26
CmpDate: 2023-03-22

Pallin LJ, Kellar NM, Steel D, et al (2023)

A surplus no more? Variation in krill availability impacts reproductive rates of Antarctic baleen whales.

Global change biology, 29(8):2108-2121.

The krill surplus hypothesis of unlimited prey resources available for Antarctic predators due to commercial whaling in the 20th century has remained largely untested since the 1970s. Rapid warming of the Western Antarctic Peninsula (WAP) over the past 50 years has resulted in decreased seasonal ice cover and a reduction of krill. The latter is being exacerbated by a commercial krill fishery in the region. Despite this, humpback whale populations have increased but may be at a threshold for growth based on these human-induced changes. Understanding how climate-mediated variation in prey availability influences humpback whale population dynamics is critical for focused management and conservation actions. Using an 8-year dataset (2013-2020), we show that inter-annual humpback whale pregnancy rates, as determined from skin-blubber biopsy samples (n = 616), are positively correlated with krill availability and fluctuations in ice cover in the previous year. Pregnancy rates showed significant inter-annual variability, between 29% and 86%. Our results indicate that krill availability is in fact limiting and affecting reproductive rates, in contrast to the krill surplus hypothesis. This suggests that this population of humpback whales may be at a threshold for population growth due to prey limitations. As a result, continued warming and increased fishing along the WAP, which continue to reduce krill stocks, will likely impact this humpback whale population and other krill predators in the region. Humpback whales are sentinel species of ecosystem health, and changes in pregnancy rates can provide quantifiable signals of the impact of environmental change at the population level. Our findings must be considered paramount in developing new and more restrictive conservation and management plans for the Antarctic marine ecosystem and minimizing the negative impacts of human activities in the region.

RevDate: 2023-02-24
CmpDate: 2023-02-24

Griffin-Nolan RJ, Felton AJ, Slette IJ, et al (2023)

Traits that distinguish dominant species across aridity gradients differ from those that respond to soil moisture.

Oecologia, 201(2):311-322.

Many plant traits respond to changes in water availability and might be useful for understanding ecosystem properties such as net primary production (NPP). This is especially evident in grasslands where NPP is water-limited and primarily determined by the traits of dominant species. We measured root and shoot morphology, leaf hydraulic traits, and NPP of four dominant North American prairie grasses in response to four levels of soil moisture in a greenhouse experiment. We expected that traits of species from drier regions would be more responsive to reduced water availability and that this would make these species more resistant to low soil moisture than species from wetter regions. All four species grew taller, produced more biomass, and increased total root length in wetter treatments. Each species reduced its leaf turgor loss point (TLP) in drier conditions, but only two species (one xeric, one mesic) maintained leaf water potential above TLP. We identified a suite of traits that clearly distinguished species from one another, but, surprisingly, these traits were relatively unresponsive to reduced soil moisture. Specifically, more xeric species produced thinner roots with higher specific root length and had a lower root mass fraction. This suggest that root traits are critical for distinguishing species from one another but might not respond strongly to changing water availability, though this warrants further investigation in the field. Overall, we found that NPP of these dominant grass species responded similarly to varying levels of soil moisture despite differences in species morphology, physiology, and habitat of origin.

RevDate: 2023-02-08
CmpDate: 2023-02-08

Gallitelli L, Battisti C, M Scalici (2023)

Dunal plants intercepting macrolitter: Implications for beach clean-ups.

Marine pollution bulletin, 187:114585.

Coastal vegetation intercepts macroplastics and, consequently, it may represent a reservoir of anthropogenic litter and organic wrack. We aimed at investigating (i) the abundance variation of macrolitter from the beach to foredune and backdune (three cross-shore plots over 20 long-shore sectors) and (ii) the role of the halo-psammophilous plants and Phragmites australis reedbed in intercepting the macrolitter, respectively, in the foredunes and backdunes. The vegetation in the foredunes (mainly halo-psammophilous species) acted as a first interception belt for macrolitter, while the bigger litter reached the backdunes. Our results might be of great concern with implications for beach clean-ups - which must also be mainly focused in foredunes and backdunes, however warning operators in advance that they could damage the vegetation by trampling on.

RevDate: 2023-05-26
CmpDate: 2023-03-14

Ueyama M, Knox SH, Delwiche KB, et al (2023)

Modeled production, oxidation, and transport processes of wetland methane emissions in temperate, boreal, and Arctic regions.

Global change biology, 29(8):2313-2334.

Wetlands are the largest natural source of methane (CH4) to the atmosphere. The eddy covariance method provides robust measurements of net ecosystem exchange of CH4 , but interpreting its spatiotemporal variations is challenging due to the co-occurrence of CH4 production, oxidation, and transport dynamics. Here, we estimate these three processes using a data-model fusion approach across 25 wetlands in temperate, boreal, and Arctic regions. Our data-constrained model-iPEACE-reasonably reproduced CH4 emissions at 19 of the 25 sites with normalized root mean square error of 0.59, correlation coefficient of 0.82, and normalized standard deviation of 0.87. Among the three processes, CH4 production appeared to be the most important process, followed by oxidation in explaining inter-site variations in CH4 emissions. Based on a sensitivity analysis, CH4 emissions were generally more sensitive to decreased water table than to increased gross primary productivity or soil temperature. For periods with leaf area index (LAI) of ≥20% of its annual peak, plant-mediated transport appeared to be the major pathway for CH4 transport. Contributions from ebullition and diffusion were relatively high during low LAI (<20%) periods. The lag time between CH4 production and CH4 emissions tended to be short in fen sites (3 ± 2 days) and long in bog sites (13 ± 10 days). Based on a principal component analysis, we found that parameters for CH4 production, plant-mediated transport, and diffusion through water explained 77% of the variance in the parameters across the 19 sites, highlighting the importance of these parameters for predicting wetland CH4 emissions across biomes. These processes and associated parameters for CH4 emissions among and within the wetlands provide useful insights for interpreting observed net CH4 fluxes, estimating sensitivities to biophysical variables, and modeling global CH4 fluxes.

RevDate: 2023-05-26
CmpDate: 2023-03-07

Tang B, Rocci KS, Lehmann A, et al (2023)

Nitrogen increases soil organic carbon accrual and alters its functionality.

Global change biology, 29(7):1971-1983.

Nitrogen (N) availability has been considered as a critical factor for the cycling and storage of soil organic carbon (SOC), but effects of N enrichment on the SOC pool appear highly variable. Given the complex nature of the SOC pool, recent frameworks suggest that separating this pool into different functional components, for example, particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), is of great importance for understanding and predicting SOC dynamics. Importantly, little is known about how these N-induced changes in SOC components (e.g., changes in the ratios among these fractions) would affect the functionality of the SOC pool, given the differences in nutrient density, resistance to disturbance, and turnover time between POC and MAOC pool. Here, we conducted a global meta-analysis of 803 paired observations from 98 published studies to assess the effect of N addition on these SOC components, and the ratios among these fractions. We found that N addition, on average, significantly increased POC and MAOC pools by 16.4% and 3.7%, respectively. In contrast, both the ratios of MAOC to SOC and MAOC to POC were remarkably decreased by N enrichment (4.1% and 10.1%, respectively). Increases in the POC pool were positively correlated with changes in aboveground plant biomass and with hydrolytic enzymes. However, the positive responses of MAOC to N enrichment were correlated with increases in microbial biomass. Our results suggest that although reactive N deposition could facilitate soil C sequestration to some extent, it might decrease the nutrient density, turnover time, and resistance to disturbance of the SOC pool. Our study provides mechanistic insights into the effects of N enrichment on the SOC pool and its functionality at global scale, which is pivotal for understanding soil C dynamics especially in future scenarios with more frequent and severe perturbations.

RevDate: 2023-01-11
CmpDate: 2023-01-05

Battisti C, Gallitelli L, Vanadia S, et al (2023)

General macro-litter as a proxy for fishing lines, hooks and nets entrapping beach-nesting birds: Implications for clean-ups.

Marine pollution bulletin, 186:114502.

Fishing lines, hooks and nets represent a sub-category of macro-litter potentially entrapping plover birds nesting on sandy beaches. Here, during a winter period, the accumulation pattern of both general beach litter and fishing lines, hooks and nets was analysed on four central Italy beaches. Despite the active monthly litter removal by clean-ups, there was not a decrease in its density during the winter period, due to the continuous accumulation by frequent winter storms. However, the entrapping litter was very low (<2.5 % of the general litter) and appeared directly correlated to the general litter density. Following a DPSIR approach, the general litter can act as an indirect pressure indicator (proxy) of the amount of entrapping litter. Therefore, an increase in general macro-litter should alarm those involved in the conservation of entanglement-sensitive bird species, such as plovers, suggesting that they should implement high-frequency clean-up activities aimed at removing it.

RevDate: 2022-12-21

Beck M, Billoir E, Felten V, et al (2022)

Lessons from linking bio- and ecological traits to stoichiometric traits in stream macroinvertebrates.

Ecology and evolution, 12(12):e9605.

Ecologists rely on various functional traits when investigating the functioning of ecological systems and its responses to global changes. Changing nutrient levels, for example, can affect taxa expressing different trait combinations in various ways, e.g., favoring small, fast-growing species under high phosphorus conditions. Stoichiometric traits, describing the elemental composition of organism body tissues, can help in understanding the mechanisms behind such functional shifts. So far, mainly life-history traits have been related to body stoichiometry (e.g., the growth rate hypothesis) on a limited number of taxa, and there is little knowledge of the general link between stoichiometric and other functional traits on a taxonomically large scale. Here, we highlight this link in the freshwater macroinvertebrates, testing predictions from underlying trait-based and Ecological Stoichiometry Theory (EST) in >200 taxa belonging to eight larger taxonomic groups. We applied a series of multivariate analyses on six of their stoichiometric traits (%C, %N, %P, C:N, C:P, and N:P) and 23 biological and ecological traits. We found significant relationships between stoichiometric traits and other types of traits when analyzing single-trait and multi-trait profiles. Patterns found within traits related to organism development or nutrient cycling were in line with our assumptions based on EST, e.g., traits describing predators were associated with high %N; traits suggesting a fast development (small maximum body size and high molting frequency) with high %P. Associations between ecological traits and body stoichiometry could be explained by the longitudinal stream gradient: Taxa preferring headwater habitats (i.e., high altitude, coarse substrate, and cold temperature) exhibited high %N and %P. Demonstrating the link between stoichiometric and both bio- and ecological traits on a large diversity of taxa underlines the potential of integrating stoichiometric traits into ecological analyses to improve our understanding of taxonomic and functional responses of communities-and ecosystems-to changing environmental conditions worldwide.

RevDate: 2023-01-11
CmpDate: 2022-11-28

Pallin LJ, Botero-Acosta N, Steel D, et al (2022)

Variation in blubber cortisol levels in a recovering humpback whale population inhabiting a rapidly changing environment.

Scientific reports, 12(1):20250.

Glucocorticoids are regularly used as biomarkers of relative health for individuals and populations. Around the Western Antarctic Peninsula (WAP), baleen whales have and continue to experience threats, including commercial harvest, prey limitations and habitat change driven by rapid warming, and increased human presence via ecotourism. Here, we measured demographic variation and differences across the foraging season in blubber cortisol levels of humpback whales (Megaptera novaeangliae) over two years around the WAP. Cortisol concentrations were determined from 305 biopsy samples of unique individuals. We found no significant difference in the cortisol concentration between male and female whales. However, we observed significant differences across demographic groups of females and a significant decrease in the population across the feeding season. We also assessed whether COVID-19-related reductions in tourism in 2021 along the WAP correlated with lower cortisol levels across the population. The decline in vessel presence in 2021 was associated with a significant decrease in humpback whale blubber cortisol concentrations at the population level. Our findings provide critical contextual data on how these hormones vary naturally in a population over time, show direct associations between cortisol levels and human presence, and will enable comparisons among species experiencing different levels of human disturbance.

RevDate: 2023-02-06
CmpDate: 2023-02-06

Bearzi G, Bonizzoni S, Fanesi F, et al (2023)

Seabirds pecking polystyrene items in offshore Adriatic Sea waters.

Environmental science and pollution research international, 30(3):8338-8346.

A number of seabird species have been known to peck, displace, and ingest various plastic items including expanded polystyrene, for reasons that remain largely conjectural. Ingestion of polystyrene parts potentially causes lethal or sublethal effects on birds. Pecking can also result in the damage of polystyrene items, resulting in increased market turnover and environmental build-up, or economic consequences for stakeholders. In January and February, 2022, fishers in a portion of the western Adriatic Sea coast reported pecking damage caused by gulls (Laridae) to polystyrene buoys used to float, signal, and retrieve static fishing nets and traps. We investigated the magnitude of this phenomenon in four fishing harbours of Italy by scoring damage to 470 buoys and interviewing 29 fishers (encompassing 42% of the relevant fleet). Information was complemented by opportunistic observations at sea. Our preliminary assessment suggests that offshore polystyrene pecking increases in winter months, and it occurs sporadically among years. The overall economic damage to the static net fishery appeared generally modest (approximately 3-4 Euro to replace one buoy), with wide variations in the extent of reported damage. We reviewed the hypotheses behind polystyrene pecking, but none of them provide a clear explanation for the observed behaviour. Finally, we discuss potential effects on seabirds and advocate monitoring to investigate causal factors and mitigate damage to seabirds, fisheries, and marine environment.

RevDate: 2023-01-23
CmpDate: 2023-01-23

Cordeiro CAMM, Aued AW, Barros F, et al (2022)

Long-term monitoring projects of Brazilian marine and coastal ecosystems.

PeerJ, 10:e14313.

Biodiversity assessment is a mandatory task for sustainable and adaptive management for the next decade, and long-term ecological monitoring programs are a cornerstone for understanding changes in ecosystems. The Brazilian Long-Term Ecological Research Program (PELD) is an integrated effort model supported by public funds that finance ecological studies at 34 locations. By interviewing and compiling data from project coordinators, we assessed monitoring efforts, targeting biological groups and scientific production from nine PELD projects encompassing coastal lagoons to mesophotic reefs and oceanic islands. Reef environments and fish groups were the most often studied within the long-term projects. PELD projects covered priority areas for conservation but missed sensitive areas close to large cities, as well as underrepresenting ecosystems on the North and Northeast Brazilian coast. Long-term monitoring projects in marine and coastal environments in Brazil are recent (<5 years), not yet integrated as a network, but scientifically productive with considerable relevance for academic and human resources training. Scientific production increased exponentially with project age, despite interruption and shortage of funding during their history. From our diagnosis, we recommend some actions to fill in observed gaps, such as: enhancing projects' collaboration and integration; focusing on priority regions for new projects; broadening the scope of monitored variables; and, maintenance of funding for existing projects.

RevDate: 2023-04-15
CmpDate: 2022-11-29

Waterton J, Hammond M, JA Lau (2022)

Evolutionary effects of nitrogen are not easily predicted from ecological responses.

American journal of botany, 109(11):1741-1756.

PREMISE: Anthropogenic nitrogen (N) addition alters the abiotic and biotic environment, potentially leading to changes in patterns of natural selection (i.e., trait-fitness relationships) and the opportunity for selection (i.e., variance in relative fitness). Because N addition favors species with light acquisition strategies (e.g., tall species), we predicted that N would strengthen selection favoring those same traits. We also predicted that N could alter the opportunity for selection via its effects on mean fitness and/or competitive asymmetries.

METHODS: We quantified the strength of selection and the opportunity for selection in replicated populations of the annual grass Setaria faberi (giant foxtail) growing in a long-term N addition experiment. We also correlated these population-level parameters with community-level metrics to identify the proximate causes of N-mediated evolutionary effects.

RESULTS: N addition increased aboveground productivity, light asymmetry, and reduced species diversity. Contrary to expectations, N addition did not strengthen selection for trait values associated with higher light acquisition such as greater height and specific leaf area (SLA); rather, it strengthened selection favoring lower SLA. Light asymmetry and species diversity were associated with selection for height and SLA, suggesting a role for these factors in driving N-mediated selection. The opportunity for selection was not influenced by N addition but was negatively associated with species diversity.

CONCLUSIONS: Our results indicate that anthropogenic N enrichment can affect evolutionary processes, but that evolutionary changes in plant traits within populations are unlikely to parallel the shifts in plant traits observed at the community level.

RevDate: 2023-04-18
CmpDate: 2023-04-18

Hsieh HY, Vandermeer J, I Perfecto (2022)

Surprising effects of cascading higher order interactions.

Scientific reports, 12(1):19378.

Most species are embedded in multi-interaction networks. Consequently, theories focusing on simple pair-wise interactions cannot predict ecological and/or evolutionary outcomes. This study explores how cascading higher-order interactions (HOIs) would affect the population dynamics of a focal species. Employing a system that involves a myrmecophylic beetle, a parasitic wasp that attacks the beetle, an ant, and a parasitic fly that attacks the ant, the study explores how none, one, and two HOIs affect the parasitism and the sex ratio of the beetle. We conducted mesocosm experiments to examine these HOIs on beetle survival and sex ratio and found that the 1st degree HOI does not change the beetle's survival rate or sex ratio. However, the 2nd degree HOI significantly reduces the beetle's survival rate and changes its sex ratio from even to strongly female-biased. We applied Bayes' theorem to analyze the per capita survival probability of female vs. male beetles and suggested that the unexpected results might arise from complex eco-evolutionary dynamics involved with the 1st and 2nd degree HOIs. Field data suggested the HOIs significantly regulate the sex ratio of the beetle. As the same structure of HOIs appears in other systems, we believe the complexity associated with the 2nd degree HOI would be more common than known and deserve more scientific attention.

RevDate: 2022-11-11
CmpDate: 2022-11-11

Barbosa FG, M Lanari (2022)

Bibliometric analysis of peer-reviewed literature on the Patos Lagoon, southern Brazil.

Anais da Academia Brasileira de Ciencias, 94(3):e20210861 pii:S0001-37652022000501008.

Coastal lagoons provide several ecological resources and services with their functioning being mainly investigated in temperate areas. The Patos Lagoon, a subtropical system in southern Brazil, is one of the largest chocked coastal lagoons in the world. It provides habitat for numerous organisms and a range of ecosystem services. We performed a bibliometric analysis to identify and analyze the characteristics of studies carried out in the Patos Lagoon based on articles published in peer-reviewed journals indexed in the Science Citation Index Expanded database of Clarivate Analytics Web of Science and Scopus database. We found 360 articles published between 1965 and 2019 in 150 journals. The number of articles has increased in the last decades mainly resulting from national collaborative efforts. Most articles were published by Brazilian research institutions. Most studies were performed in the Patos Lagoon estuary, a Long-term Ecological Research program´s study site. Our study thus highlights the importance of long-term projects to the comprehension of subtropical coastal lagoons functioning and indicates knowledge gaps that must be addressed in future studies.

RevDate: 2023-01-23
CmpDate: 2023-01-17

Liang Y, Gustafson EJ, He HS, et al (2023)

What is the role of disturbance in catalyzing spatial shifts in forest composition and tree species biomass under climate change?.

Global change biology, 29(4):1160-1177.

Mounting evidence suggests that climate change will cause shifts of tree species range and abundance (biomass). Abundance changes under climate change are likely to occur prior to a detectable range shift. Disturbances are expected to directly affect tree species abundance and composition, and could profoundly influence tree species spatial distribution within a geographical region. However, how multiple disturbance regimes will interact with changing climate to alter the spatial distribution of species abundance remains unclear. We simulated such forest demographic processes using a forest landscape succession and disturbance model (LANDIS-II) parameterized with forest inventory data in the northeastern United States. Our study incorporated climate change under a high-emission future and disturbance regimes varying with gradients of intensities and spatial extents. The results suggest that disturbances catalyze changes in tree species abundance and composition under a changing climate, but the effects of disturbances differ by intensity and extent. Moderate disturbances and large extent disturbances have limited effects, while high-intensity disturbances accelerate changes by removing cohorts of mid- and late-successional species, creating opportunities for early-successional species. High-intensity disturbances result in the northern movement of early-successional species and the southern movement of late-successional species abundances. Our study is among the first to systematically investigate how disturbance extent and intensity interact to determine the spatial distribution of changes in species abundance and forest composition.

RevDate: 2023-09-18

Speed JDM, Evankow AM, Petersen TK, et al (2022)

A regionally coherent ecological fingerprint of climate change, evidenced from natural history collections.

Ecology and evolution, 12(11):e9471.

Climate change has dramatic impacts on ecological systems, affecting a range of ecological factors including phenology, species abundance, diversity, and distribution. The breadth of climate change impacts on ecological systems leads to the occurrence of fingerprints of climate change. However, climate fingerprints are usually identified across broad geographical scales and are potentially influenced by publication biases. In this study, we used natural history collections spanning over 250 years, to quantify a range of ecological responses to climate change, including phenology, abundance, diversity, and distributions, across a range of taxa, including vertebrates, invertebrates, plants, and fungi, within a single region, Central Norway. We tested the hypotheses that ecological responses to climate change are apparent and coherent at a regional scale, that longer time series show stronger trends over time and in relation to temperature, and that ecological responses change in trajectory at the same time as shifts in temperature. We identified a clear regional coherence in climate signal, with decreasing abundances of limnic zooplankton (on average by 7691 individuals m[-3] °C[-1]) and boreal forest breeding birds (on average by 1.94 territories km[-2] °C[-1]), and earlier plant flowering phenology (on average 2 days °C[-1]) for every degree of temperature increase. In contrast, regional-scale species distributions and species diversity were largely stable. Surprisingly, the effect size of ecological response did not increase with study duration, and shifts in responses did not occur at the same time as shifts in temperature. This may be as the long-term studies include both periods of warming and temperature stability, and that ecological responses lag behind warming. Our findings demonstrate a regional climate fingerprint across a long timescale. We contend that natural history collections provide a unique window on a broad spectrum of ecological responses at timescales beyond most ecological monitoring programs. Natural history collections are thus an essential source for long-term ecological research.

RevDate: 2022-11-08
CmpDate: 2022-11-08

Behera SK, Behera MD, Tuli R, et al (2022)

Atmospheric temperature and humidity demonstrated strong correlation with productivity in tropical moist deciduous forests.

Environmental monitoring and assessment, 195(1):69 pii:10.1007/s10661-022-10668-7.

Tropical forests sequester six times higher carbon than that released by humans annually into the atmosphere. These biodiversity-rich tropical forests have high net primary productivity (NPP), which differs among constituent plant communities. Tropical moist deciduous forests occupy 179,335 km[2] of India's geographical area and constitute 44% of the country's total protected area (PA) forests. The productivity of these forests has neither been estimated specifically nor precisely. We measured the annual NPP of three predominant distinct community types, viz., mixed (DM), sal (SM), and teak (TP), in a tropical moist deciduous forest in northern India. The NPP was estimated from tree biomass data collected from nine long-term ecological research (LTER) plots of 1 ha each representing the above three community types. The estimated annual NPP were 10.28, 6.25, and 9.79 Mg ha[-1] year[-1] in DM; 8.93, 7.09, and 10.59 Mg ha[-1] year[-1] in SM; and 14.57, 7.14, and 13.56 Mg ha[-1] year[-1] in TP for the years 2010, 2011, and 2012, respectively. The NPP was correlated with tree density, height and DBH, species richness, diversity, microclimatic and edaphic variables, and leaf area index (LAI) using principal component analysis (PCA) and generalized linear modeling (GLM). Air temperature and humidity were strongly related to NPP in all the community types, while "complementarity" and "selection effects" contributed to the NPP in both the sal and mixed forest communities with equal importance, and the NPP in teak plantation ould point to "dominance effect."

RevDate: 2022-11-25
CmpDate: 2022-11-25

Ladouceur E, Blowes SA, Chase JM, et al (2022)

Linking changes in species composition and biomass in a globally distributed grassland experiment.

Ecology letters, 25(12):2699-2712.

Global change drivers, such as anthropogenic nutrient inputs, are increasing globally. Nutrient deposition simultaneously alters plant biodiversity, species composition and ecosystem processes like aboveground biomass production. These changes are underpinned by species extinction, colonisation and shifting relative abundance. Here, we use the Price equation to quantify and link the contributions of species that are lost, gained or that persist to change in aboveground biomass in 59 experimental grassland sites. Under ambient (control) conditions, compositional and biomass turnover was high, and losses (i.e. local extinctions) were balanced by gains (i.e. colonisation). Under fertilisation, the decline in species richness resulted from increased species loss and decreases in species gained. Biomass increase under fertilisation resulted mostly from species that persist and to a lesser extent from species gained. Drivers of ecological change can interact relatively independently with diversity, composition and ecosystem processes and functions such as aboveground biomass due to the individual contributions of species lost, gained or persisting.

RevDate: 2022-10-22
CmpDate: 2022-10-21

Brown JA, Lerman SB, Basile AJ, et al (2022)

No fry zones: How restaurant distribution and abundance influence avian communities in the Phoenix, AZ metropolitan area.

PloS one, 17(10):e0269334.

Urbanization is one of the most widespread and extreme examples of habitat alteration. As humans dominate landscapes, they introduce novel elements into environments, including artificial light, noise pollution, and anthropogenic food sources. One understudied form of anthropogenic food is refuse from restaurants, which can alter wildlife populations and, in turn, entire wildlife communities by providing a novel and stable food source. Using data from the Maricopa Association of Governments and the Central Arizona-Phoenix Long Term Ecological Research (CAP LTER) project, we investigated whether and how the distribution of restaurants influences avian communities. The research aimed to identify restaurants, and thus the associated food they may provide, as the driver of potential patterns by controlling for other influences of urbanization, including land cover and the total number of businesses. Using generalized linear mixed models, we tested whether the number of restaurants within 1 km of bird monitoring locations predict avian community richness and abundance and individual species abundance and occurrence patterns. Results indicate that restaurants may decrease avian species diversity and increase overall abundance. Additionally, restaurants may be a significant predictor of the overall abundance of urban-exploiting species, including rock pigeon (Columba livia), mourning dove (Zenaida macroura), and Inca dove (Columbina Inca). Understanding how birds utilize anthropogenic food sources can inform possible conservation or wildlife management practices. As this study highlights only correlations, we suggest further experimental work to address the physiological ramifications of consuming anthropogenic foods provided by restaurants and studies to quantify how frequently anthropogenic food sources are used compared to naturally occurring sources.

RevDate: 2022-09-28

Amoussou N, Thomas M, Pasquet A, et al (2022)

Finding the Best Match: A Ranking Procedure of Fish Species Combinations for Polyculture Development.

Life (Basel, Switzerland), 12(9):.

Polyculture is a potentially interesting rearing practice for future aquaculture developments. Nevertheless, it may result in beneficial as well as detrimental consequences for fish production. One way to maximize the benefits of polyculture is to combine species with high levels of compatibility and complementarity. This requires the development of a ranking procedure, based on a multi-trait assessment, that highlights the most suitable species combinations for polyculture. Moreover, in order to ensure the relevance of such a procedure, it is important to integrate the socio-economic expectations by assigning relative weights to each trait according to the stakeholder priorities. Here, we proposed a ranking procedure of candidate fish polycultures (i.e., species combinations that could be potentially interesting for aquaculture) based on a multi-trait assessment approach and the stakeholder priorities. This procedure aims at successively (i) weighting evaluation results obtained for each candidate polyculture according to stakeholder priorities; (ii) assessing differentiation between candidate species combinations based on these weighted results; and (iii) ranking differentiated candidate polycultures. We applied our procedure on three test cases of fish polycultures in recirculated aquaculture systems. These test cases each focused on a target species (two on Sander lucioperca and one on Carassius auratus), which were reared in two or three different alternative candidate fish polycultures. For each test case, our procedure aimed at ranking alternative combinations according to their benefits for production and/or welfare of the target species. These benefits were evaluated based on survival rate as well as morphology, behavioral, and physiological traits. Three scenarios of stakeholder priorities were considered for weighting evaluation results: placing a premium on production, welfare, or both for the target species. A comparison of our procedure results between these scenarios showed that the ranking changed for candidate polycultures in two test cases. This highlights the need to carefully consider stakeholder priorities when choosing fish polycultures.

RevDate: 2023-01-10
CmpDate: 2022-10-04

Kim H, McComb BC, Frey SJK, et al (2022)

Forest microclimate and composition mediate long-term trends of breeding bird populations.

Global change biology, 28(21):6180-6193.

Climate change is contributing to biodiversity redistributions and species declines. However, cooler microclimate conditions provided by old-growth forest structures compared with surrounding open or younger forests have been hypothesized to provide thermal refugia for species that are sensitive to climate warming and dampen the negative effects of warming on population trends of animals (i.e., the microclimate buffering hypothesis). In addition to thermal refugia, the compositional and structural diversity of old-growth forest vegetation itself may provide resources to species that are less available in forests with simpler structure (i.e., the insurance hypothesis). We used 8 years of breeding bird abundance data from a forested watershed, accompanied with sub-canopy temperature data, and ground- and LiDAR-based vegetation data to test these hypotheses and identify factors influencing bird population changes from 2011 to 2018. After accounting for imperfect detection, we found that for 5 of 20 bird species analyzed, abundance trends tended to be less negative or neutral at sites with cooler microclimates, which supports the microclimate buffering hypothesis. Negative effects of warming on two species were also reduced in locations with greater forest compositional diversity supporting the insurance hypothesis. We provide the first empirical evidence that complex forest structure and vegetation diversity confer microclimatic advantages to some animal populations in the face of climate change. Conservation of old-growth forests, or their characteristics in managed forests, could help slow the negative effects of climate warming on some breeding bird populations via microclimate buffering and possibly insurance effects.

RevDate: 2022-12-07
CmpDate: 2022-09-23

Banchi E, Manna V, Fonti V, et al (2022)

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing.

Environmental science and pollution research international, 29(44):67466-67482.

The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.

RevDate: 2022-09-10

Hudson AR, Peters DPC, Blair JM, et al (2022)

Cross-Site Comparisons of Dryland Ecosystem Response to Climate Change in the US Long-Term Ecological Research Network.

Bioscience, 72(9):889-907.

Long-term observations and experiments in diverse drylands reveal how ecosystems and services are responding to climate change. To develop generalities about climate change impacts at dryland sites, we compared broadscale patterns in climate and synthesized primary production responses among the eight terrestrial, nonforested sites of the United States Long-Term Ecological Research (US LTER) Network located in temperate (Southwest and Midwest) and polar (Arctic and Antarctic) regions. All sites experienced warming in recent decades, whereas drought varied regionally with multidecadal phases. Multiple years of wet or dry conditions had larger effects than single years on primary production. Droughts, floods, and wildfires altered resource availability and restructured plant communities, with greater impacts on primary production than warming alone. During severe regional droughts, air pollution from wildfire and dust events peaked. Studies at US LTER drylands over more than 40 years demonstrate reciprocal links and feedbacks among dryland ecosystems, climate-driven disturbance events, and climate change.

RevDate: 2022-08-29

Jones JA, CT Driscoll (2022)

Long-Term Ecological Research on Ecosystem Responses to Climate Change.

Bioscience, 72(9):814-826 pii:biac021.

In this article marking the 40th anniversary of the US National Science Foundation's Long Term Ecological Research (LTER) Network, we describe how a long-term ecological research perspective facilitates insights into an ecosystem's response to climate change. At all 28 LTER sites, from the Arctic to Antarctica, air temperature and moisture variability have increased since 1930, with increased disturbance frequency and severity and unprecedented disturbance types. LTER research documents the responses to these changes, including altered primary production, enhanced cycling of organic and inorganic matter, and changes in populations and communities. Although some responses are shared among diverse ecosystems, most are unique, involving region-specific drivers of change, interactions among multiple climate change drivers, and interactions with other human activities. Ecosystem responses to climate change are just beginning to emerge, and as climate change accelerates, long-term ecological research is crucial to understand, mitigate, and adapt to ecosystem responses to climate change.

RevDate: 2022-09-08
CmpDate: 2022-09-08

Chaumet B, Probst JL, Payré-Suc V, et al (2022)

Pond mitigation in dissolved and particulate pesticide transfers: Influence of storm events and seasonality (Auradé agricultural catchment, SW-France).

Journal of environmental management, 320:115911.

In agricultural headwater catchments, wetlands such as ponds are numerous and well known to partly dissipate contamination. Most of the pesticides are transferred from soils to the aquatic environment during flood events. This study reports the annual/seasonal behaviour of 6 pesticides (metolachlor, boscalid, epoxiconazole, tebuconazole, aclonifen and pendimethalin) in such an environment. Because it is rarely considered, the study focussed on the high frequency of the distribution of pesticides between dissolved and particulate phases, as well as the main controlling factors of their upstream-downstream transfer. The pond removal rate was calculated to evaluate the wetland efficiency in pesticide mitigation. We conducted a one-year high frequency hydrochemical survey, with particular emphasis on flood events, in the upper Auradé catchment (SW-France), an area of long-term conventional agriculture on highly erosive carbonated soils. The inlet and outlet of the pond were instrumented for water level measurements and water sampling. The highest concentrations were observed for tebuconazole and, in general, the presence of the molecules during the year depended on the season. The pond showed satisfactory efficiency in pesticide attenuation for the six molecules considered, although the removal rate depended on the molecule and the bearing phase (from 28.4% for boscalid to 89.4% for aclonifen in the dissolved phase and from 22.1% for pendimethalin to 96.8% for metolachlor in the particulate fraction). Interestingly, the more hydrophilic the molecule (low LogKOW), the more efficient the pesticide removal rate was for its particulate fraction, and the opposite for hydrophobic molecules (high LogKOW). Flood events carried a large amount of Total Suspended Solid (TSS) bearing hydrophobic molecules from a major legacy of upper catchment soils, although 52% of the pesticides were transported by the dissolved fraction. Significant resuspension of TSS from the pond was evidenced by the annual mass balance with four tons of TSS released, while the positive rate of pesticide removal involved other effective mechanisms such as exchange and complexation. Although these constructed wetlands may be beneficial for pesticide mitigation, the results highlighted the need for improved land management in the upstream catchment during the different seasons to avoid bare soils that pose a risk of high surface water contamination, especially due to the presence of hydrophobic molecules in combination with a high erosive context.

RevDate: 2022-08-13

Percopo I, Ruggiero MV, Sarno D, et al (2022)

Phenological segregation suggests speciation by time in the planktonic diatom Pseudo-nitzschia allochrona sp. nov.

Ecology and evolution, 12(8):e9155.

The processes leading to the emergence of new species are poorly understood in marine plankton, where weak physical barriers and homogeneous environmental conditions limit spatial and ecological segregation. Here, we combine molecular and ecological information from a long-term time series and propose Pseudo-nitzschia allochrona, a new cryptic planktonic diatom, as a possible case of speciation by temporal segregation. The new species differs in several genetic markers (18S, 28S and ITS rDNA fragments and rbcL) from its closest relatives, which are morphologically very similar or identical, and is reproductively isolated from its sibling species P. arenysensis. Data from a long-term plankton time series show P. allochrona invariably occurring in summer-autumn in the Gulf of Naples, where its closely related species P. arenysensis, P. delicatissima, and P. dolorosa are instead found in winter-spring. Temperature and nutrients are the main factors associated with the occurrence of P. allochrona, which could have evolved in sympatry by switching its phenology and occupying a new ecological niche. This case of possible speciation by time shows the relevance of combining ecological time series with molecular information to shed light on the eco-evolutionary dynamics of marine microorganisms.

RevDate: 2023-02-09
CmpDate: 2022-09-23

Wurtzer S, Levert M, Dhenain E, et al (2022)

From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater.

The Science of the total environment, 848:157740.

Throughout the COVID-19 pandemic, new variants have continuously emerged and spread in populations. Among these, variants of concern (VOC) have been the main culprits of successive epidemic waves, due to their transmissibility, pathogenicity or ability to escape the immune response. Quantification of the SARS-CoV-2 genomes in raw wastewater is a reliable approach well-described and widely deployed worldwide to monitor the spread of SARS-CoV-2 in human populations connected to sewage systems. Discrimination of VOCs in wastewater is also a major issue and can be achieved by genome sequencing or by detection of specific mutations suggesting the presence of VOCs. This study aimed to date the emergence of these VOCs (from Alpha to Omicron BA.2) by monitoring wastewater from the greater Paris area, France, but also to model the propagation dynamics of these VOCs and to characterize the replacement kinetics of the prevalent populations. These dynamics were compared to various individual-centered public health data, such as regional incidence and the proportions of VOCs identified by sequencing of strains isolated from patient. The viral dynamics in wastewater highlighted the impact of the vaccination strategy on the viral circulation within human populations but also suggested its potential effect on the selection of variants most likely to be propagated in immunized populations. Normalization of concentrations to capture population movements appeared statistically more reliable using variations in local drinking water consumption rather than using PMMoV concentrations because PMMoV fecal shedding was subject to variability and was not sufficiently relevant in this study. The dynamics of viral spread was observed earlier (about 13 days on the wave related to Omicron VOC) in raw wastewater than the regional incidence alerting to a possible risk of decorrelation between incidence and actual virus circulation probably resulting from a lower severity of infection in vaccinated populations.

RevDate: 2022-08-17
CmpDate: 2022-07-18

Xu H, Lian X, Slette IJ, et al (2022)

Rising ecosystem water demand exacerbates the lengthening of tropical dry seasons.

Nature communications, 13(1):4093.

Precipitation-based assessments show a lengthening of tropical dry seasons under climate change, without considering simultaneous changes in ecosystem water demand. Here, we compare changes in tropical dry season length and timing when dry season is defined as the period when precipitation is less than: its climatological average, potential evapotranspiration, or actual evapotranspiration. While all definitions show more widespread tropical drying than wetting for 1983-2016, we find the largest fraction (48.7%) of tropical land probably experiencing longer dry seasons when dry season is defined as the period when precipitation cannot meet the need of actual evapotranspiration. Southern Amazonia (due to delayed end) and central Africa (due to earlier onset and delayed end) are hotspots of dry season lengthening, with greater certainty when accounting for water demand changes. Therefore, it is necessary to account for changing water demand when characterizing changes in tropical dry periods and ecosystem water deficits.

RevDate: 2022-08-04
CmpDate: 2022-08-04

Cesarini G, Secco S, Battisti C, et al (2022)

Temporal changes of plastic litter and associated encrusting biota: Evidence from Central Italy (Mediterranean Sea).

Marine pollution bulletin, 181:113890.

We investigated the temporal changes from spring to summer of the stranded litter and the composition of plastic encrusting biota along an Italian beach. Our findings highlight a higher quantity of litter (average value 1510.67 ± 581.27 items) in spring, particularly plastic material with a composition driven by currents, winds and waves transported from rivers to sea. During summer the source was caused by anti-social behaviours (e.g. cigarettes). Regarding the plastic size, the most is macroplastic (85.96 %), followed by mesoplastic (13.74 %) and megaplastic (0.30 %) overall, and no seasonal trend was observed. Concerning the encrusting biota, Mollusca was the most frequent phylum found on plastic beach litter, whereas Porifera the most abundant overall. During spring a greater abundance of individuals was recorded compared to summer. The trend of taxa richness was decreasing from spring to summer. Arthropoda, Porifera and Mollusca phyla were significantly more abundant in spring, while Algae in summer.

RevDate: 2022-07-27
CmpDate: 2022-07-27

Collins CG, Elmendorf SC, Smith JG, et al (2022)

Global change re-structures alpine plant communities through interacting abiotic and biotic effects.

Ecology letters, 25(8):1813-1826.

Global change is altering patterns of community assembly, with net outcomes dependent on species' responses to the abiotic environment, both directly and mediated through biotic interactions. Here, we assess alpine plant community responses in a 15-year factorial nitrogen addition, warming and snow manipulation experiment. We used a dynamic competition model to estimate the density-dependent and -independent processes underlying changes in species-group abundances over time. Density-dependent shifts in competitive interactions drove long-term changes in abundance of species-groups under global change while counteracting environmental drivers limited the growth response of the dominant species through density-independent mechanisms. Furthermore, competitive interactions shifted with the environment, primarily with nitrogen and drove non-linear abundance responses across environmental gradients. Our results highlight that global change can either reshuffle species hierarchies or further favour already-dominant species; predicting which outcome will occur requires incorporating both density-dependent and -independent mechanisms and how they interact across multiple global change factors.

RevDate: 2022-07-29
CmpDate: 2022-07-26

Hirsch SL, Ribes D, S Inman (2022)

Sedimentary legacy and the disturbing recurrence of the human in long-term ecological research.

Social studies of science, 52(4):561-580.

Even as new elements of a research infrastructure are added, older parts continue to exert persistent and consequential influence. We introduce the concept of sedimentary legacy to describe the relationship between infrastructure and research objects. Contrary to common accounts of legacy infrastructure that underscore lock-in, static, or constraining outcomes, sedimentary legacy emphasizes how researchers adapt infrastructure to support the investigation of new research objects, even while operating under constraining legacies. To illustrate the implications of sedimentary legacy, we track shifting objects of investigation across the history of the Long-Term Ecological Research (LTER) Network, focusing especially on recurrent ecological investigations of 'human disturbance' as researchers shift to study socioecological objects. We examine the relationship between scientific objects and the resources collected and preserved to render such objects tractable to scientific investigations, and show how the resources of a long-term research infrastructure support the assembly of certain objects of investigation, even while foreclosing others.

RevDate: 2022-07-16

Aoki LR, Brisbin MM, Hounshell AG, et al (2022)

Preparing Aquatic Research for an Extreme Future: Call for Improved Definitions and Responsive, Multidisciplinary Approaches.

Bioscience, 72(6):508-520.

Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.

RevDate: 2022-08-30
CmpDate: 2022-08-09

Gallitelli L, Battisti C, Pietrelli L, et al (2022)

Anthropogenic particles in coypu (Myocastor coypus; Mammalia, Rodentia)' faeces: first evidence and considerations about their use as track for detecting microplastic pollution.

Environmental science and pollution research international, 29(36):55293-55301.

Anthropogenic plastic litter is widespread in all environments, with particular emphasis on aquatic habitats. Specifically, although freshwater mammals are important as they are at the top of food web, research mainly focus on marine animals, while only few studies have been carried out on freshwater mammals. The main gap is that microplastics (MP) are completely understudied in freshwater mammals. Here, we reported the first evidence of the presence of anthropogenic particles (including MP) in coypu (Myocastor coypus)' faeces. Coypu is a rodent mammal inhabiting rivers and wetland areas, and we discussed our preliminary data suggesting the use of these tracks as possible future bioindicator of MP pollution in wetlands and freshwaters. We collected 30 coypu's faeces in "Torre Flavia wetland" nature reserve. Then, in laboratory, faeces were digested in 30 ml hydrogen peroxide (30%) for a week a 20 °C and analysed under stereoscope. All the suspected found MP were isolated in a petri dish, using FT-IR analysis to confirm the polymers. Overall, we recorded 444 natural and anthropogenic particles with most of items being fibres. FT-IR analysis of the 10% of the particles recovered revealed that 72% of them was not MP (mainly, polyethylene, polyethylene terephthalate, and polyamide). Also, the number of anthropogenic particles is not correlated with the faecal weight. Given that alien species, such as coypu, are widespread species, our results might have a great importance as these species and MP in faecal tracks may be used as undirect proxy of environmental bioavailability of MP pollution.

RevDate: 2023-04-11
CmpDate: 2022-12-02

Rastetter EB, Kwiatkowski BL, Kicklighter DW, et al (2022)

N and P constrain C in ecosystems under climate change: Role of nutrient redistribution, accumulation, and stoichiometry.

Ecological applications : a publication of the Ecological Society of America, 32(8):e2684.

We use the Multiple Element Limitation (MEL) model to examine responses of 12 ecosystems to elevated carbon dioxide (CO2), warming, and 20% decreases or increases in precipitation. Ecosystems respond synergistically to elevated CO2 , warming, and decreased precipitation combined because higher water-use efficiency with elevated CO2 and higher fertility with warming compensate for responses to drought. Response to elevated CO2 , warming, and increased precipitation combined is additive. We analyze changes in ecosystem carbon (C) based on four nitrogen (N) and four phosphorus (P) attribution factors: (1) changes in total ecosystem N and P, (2) changes in N and P distribution between vegetation and soil, (3) changes in vegetation C:N and C:P ratios, and (4) changes in soil C:N and C:P ratios. In the combined CO2 and climate change simulations, all ecosystems gain C. The contributions of these four attribution factors to changes in ecosystem C storage varies among ecosystems because of differences in the initial distributions of N and P between vegetation and soil and the openness of the ecosystem N and P cycles. The net transfer of N and P from soil to vegetation dominates the C response of forests. For tundra and grasslands, the C gain is also associated with increased soil C:N and C:P. In ecosystems with symbiotic N fixation, C gains resulted from N accumulation. Because of differences in N versus P cycle openness and the distribution of organic matter between vegetation and soil, changes in the N and P attribution factors do not always parallel one another. Differences among ecosystems in C-nutrient interactions and the amount of woody biomass interact to shape ecosystem C sequestration under simulated global change. We suggest that future studies quantify the openness of the N and P cycles and changes in the distribution of C, N, and P among ecosystem components, which currently limit understanding of nutrient effects on C sequestration and responses to elevated CO2 and climate change.

RevDate: 2023-09-16

Gaiser EE, Kominoski JS, McKnight DM, et al (2022)

Long-term ecological research and the COVID-19 anthropause: A window to understanding social-ecological disturbance.

Ecosphere (Washington, D.C), 13(4):e4019.

The period of disrupted human activity caused by the COVID-19 pandemic, coined the "anthropause," altered the nature of interactions between humans and ecosystems. It is uncertain how the anthropause has changed ecosystem states, functions, and feedback to human systems through shifts in ecosystem services. Here, we used an existing disturbance framework to propose new investigation pathways for coordinated studies of distributed, long-term social-ecological research to capture effects of the anthropause. Although it is still too early to comprehensively evaluate effects due to pandemic-related delays in data availability and ecological response lags, we detail three case studies that show how long-term data can be used to document and interpret changes in air and water quality and wildlife populations and behavior coinciding with the anthropause. These early findings may guide interpretations of effects of the anthropause as it interacts with other ongoing environmental changes in the future, particularly highlighting the importance of long-term data in separating disturbance impacts from natural variation and long-term trends. Effects of this global disturbance have local to global effects on ecosystems with feedback to social systems that may be detectable at spatial scales captured by nationally to globally distributed research networks.

RevDate: 2022-03-29

Wheeler MM, Collins SL, Grimm NB, et al (2021)

Water and nitrogen shape winter annual plant diversity and community composition in near-urban Sonoran Desert preserves.

Ecological monographs, 91(3):1-19.

Increased nitrogen (N) deposition threatens global biodiversity, but its effects in arid urban ecosystems are not well studied. In addition to altered N availability, urban environments also experience increases in other pollutants, decreased population connectivity, and altered biotic interactions, which can further impact biodiversity. In deserts, annual plant communities make up most of the plant diversity, support wildlife, and contribute to nutrient cycling and ecosystem processes. Functional tradeoffs allowing coexistence of a diversity of annual plant species are well established, but maintenance of diversity in urban conditions and with increased availability of limiting nutrients has not been explored. We conducted a 13-year N and phosphorus (P) addition experiment in Sonoran Desert preserves in and around Phoenix, AZ, to test how nutrient availability interacts with growing season precipitation, urban location, and microhabitat to affect winter annual plant diversity. Using structural equation modeling and generalized linear mixed modeling, we found that annual plant taxonomic diversity was significantly reduced in N-enriched and urban plots. Water availability in both current and previous growing seasons impacted annual plant diversity, with significant interaction effects showing increased diversity in wetter years and greater responsiveness of the community to water following a wet year. However, there were no significant interactions between N enrichment and water availability, urban location, or microhabitat. Lowered diversity in urban preserves may be partly attributable to increased urban N deposition. Changes in biodiversity of showy species like annual wildflowers in urban preserves can have important implications for connections between urban residents and nature, and reduced diversity and community restructuring with N enrichment represents a challenge for future preservation of aridland biodiversity.

RevDate: 2022-07-21
CmpDate: 2022-03-29

Santangelo JS, Ness RW, Cohan B, et al (2022)

Global urban environmental change drives adaptation in white clover.

Science (New York, N.Y.), 375(6586):1275-1281.

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

RevDate: 2022-07-16
CmpDate: 2022-02-16

Schaeffer B, Salls W, Coffer M, et al (2022)

Merging of the Case 2 Regional Coast Colour and Maximum-Peak Height chlorophyll-a algorithms: validation and demonstration of satellite-derived retrievals across US lakes.

Environmental monitoring and assessment, 194(3):179.

Water quality monitoring is relevant for protecting the designated, or beneficial uses, of water such as drinking, aquatic life, recreation, irrigation, and food supply that support the economy, human well-being, and aquatic ecosystem health. Managing finite water resources to support these designated uses requires information on water quality so that managers can make sustainable decisions. Chlorophyll-a (chl-a, µg L[-1]) concentration can serve as a proxy for phytoplankton biomass and may be used as an indicator of increased anthropogenic nutrient stress. Satellite remote sensing may present a complement to in situ measures for assessments of water quality through the retrieval of chl-a with in-water algorithms. Validation of chl-a algorithms across US lakes improves algorithm maturity relevant for monitoring applications. This study compares performance of the Case 2 Regional Coast Colour (C2RCC) chl-a retrieval algorithm, a revised version of the Maximum-Peak Height (MPH(P)) algorithm, and three scenarios merging these two approaches. Satellite data were retrieved from the MEdium Resolution Imaging Spectrometer (MERIS) and the Ocean and Land Colour Instrument (OLCI), while field observations were obtained from 181 lakes matched with U.S. Water Quality Portal chl-a data. The best performance based on mean absolute multiplicative error (MAEmult) was demonstrated by the merged algorithm referred to as C15-M10 (MAEmult = 1.8, biasmult = 0.97, n = 836). In the C15-M10 algorithm, the MPH(P) chl-a value was retained if it was > 10 µg L[-1]; if the MPH(P) value was ≤ 10 µg L[-1], the C2RCC value was selected, as long as that value was < 15 µg L[-1]. Time-series and lake-wide gradients compared against independent assessments from Lake Champlain and long-term ecological research stations in Wisconsin were used as complementary examples supporting water quality reporting requirements. Trophic state assessments for Wisconsin lakes provided examples in support of inland water quality monitoring applications. This study presents and assesses merged adaptations of chl-a algorithms previously reported independently. Additionally, it contributes to the transition of chl-a algorithm maturity by quantifying error statistics for a number of locations and times.

RevDate: 2022-08-30
CmpDate: 2022-06-02

Sonti NF, Groffman PM, Nowak DJ, et al (2022)

Urban net primary production: Concepts, field methods, and Baltimore, Maryland, USA case study.

Ecological applications : a publication of the Ecological Society of America, 32(4):e2562.

Given the large and increasing amount of urban, suburban, and exurban land use on Earth, there is a need to accurately assess net primary productivity (NPP) of urban ecosystems. However, the heterogeneous and dynamic urban mosaic presents challenges to the measurement of NPP, creating landscapes that may appear more similar to a savanna than to the native landscape replaced. Studies of urban biomass have tended to focus on one type of vegetation (e.g., lawns or trees). Yet a focus on the ecology of the city should include the entire urban ecosystem rather than the separate investigation of its parts. Furthermore, few studies have attempted to measure urban aboveground NPP (ANPP) using field-based methods. Most studies project growth rates from measurements of tree diameter to estimate annual ANPP or use remote sensing approaches. In addition, field-based methods for measuring NPP do not address any special considerations for adapting such field methods to urban landscapes. Frequent planting and partial or complete removal of herbaceous and woody plants can make it difficult to accurately quantify increments and losses of plant biomass throughout an urban landscape. In this study, we review how ANPP of urban landscapes can be estimated based on field measurements, highlighting the challenges specific to urban areas. We then estimated ANPP of woody and herbaceous vegetation over a 15-year period for Baltimore, MD, USA using a combination of plot-based field data and published values from the literature. Baltimore's citywide ANPP was estimated to be 355.8 g m[-2] , a result that we then put into context through comparison with other North American Long-Term Ecological Research (LTER) sites and mean annual precipitation. We found our estimate of Baltimore citywide ANPP to be only approximately half as much (or less) than ANPP at forested LTER sites of the eastern United States, and more comparable to grassland, oldfield, desert, or boreal forest ANPP. We also found that Baltimore had low productivity for its level of precipitation. We conclude with a discussion of the significance of accurate assessment of primary productivity of urban ecosystems and critical future research needs.

RevDate: 2022-05-08
CmpDate: 2022-04-05

Adelizzi R, O'Brien EA, Hoellrich M, et al (2022)

Disturbance to biocrusts decreased cyanobacteria, N-fixer abundance, and grass leaf N but increased fungal abundance.

Ecology, 103(4):e3656.

Interactions between plants and soil microbes influence plant nutrient transformations, including nitrogen (N) fixation, nutrient mineralization, and resource exchanges through fungal networks. Physical disturbances to soils can disrupt soil microbes and associated processes that support plant and microbial productivity. In low resource drylands, biological soil crusts ("biocrusts") occupy surface soils and house key autotrophic and diazotrophic bacteria, non-vascular plants, or lichens. Interactions among biocrusts, plants, and fungal networks between them are hypothesized to drive carbon and nutrient dynamics; however, comparisons across ecosystems are needed to generalize how soil disturbances alter microbial communities and their contributions to N pools and transformations. To evaluate linkages among plants, fungi, and biocrusts, we disturbed all unvegetated surfaces with human foot trampling twice yearly from 2013-2019 in dry conditions in cyanobacteria-dominated biocrusts in the Chihuahuan Desert grassland and shrubland ecosystems. After 5 years, disturbance decreased the abundances of cyanobacteria (especially Microcoleus steenstrupii clade) and N-fixers (Scytonema sp., and Schizothrix sp.) by >77% and chlorophyll a by up to 55% but, conversely, increased soil fungal abundance by 50% compared with controls. Responses of root-associated fungi differed between the two dominant plant species and ecosystem types, with a maximum of 80% more aseptate hyphae in disturbed than in control plots. Although disturbance did not affect [15] N tracer transfer from biocrusts to the dominant grass, Bouteloua eriopoda, disturbance increased available soil N by 65% in the shrubland, and decreased leaf N of B. eriopoda by up to 16%, suggesting that, although rapid N transfer during peak production was not affected by disturbance, over the long-term plant nutrient content was disrupted. Altogether, the shrubland may be more resilient to detrimental changes due to disturbance than grassland, and these results demonstrated that disturbances to soil microbial communities have the potential to cause substantial changes in N pools by reducing and reordering biocrust taxa.

RevDate: 2022-08-30
CmpDate: 2022-06-02

Nevison C, Goodale C, Hess P, et al (2022)

Nitrification and denitrification in the Community Land Model compared with observations at Hubbard Brook Forest.

Ecological applications : a publication of the Ecological Society of America, 32(4):e2530.

Models of terrestrial system dynamics often include nitrogen (N) cycles to better represent N limitations on terrestrial carbon (C) uptake, but simulating the fate of N in ecosystems has proven challenging. Here, key soil N fluxes and flux ratios from the Community Land Model version 5.0 (CLM5.0) are compared with an extensive set of observations from the Hubbard Brook Forest Long-Term Ecological Research site in New Hampshire. Simulated fluxes include microbial immobilization and plant uptake, which compete with nitrification and denitrification, respectively, for available soil ammonium (NH4 [+]) and nitrate (NO3 [-]). In its default configuration, CLM5.0 predicts that both plant uptake and immobilization are strongly dominated by NH4 [+] over NO3 [-] , and that the model ratio of nitrification:denitrification is ~1:1. In contrast, Hubbard Brook observations suggest that NO3 [-] plays a more significant role in plant uptake and that nitrification could exceed denitrification by an order of magnitude. Modifications to the standard CLM5.0 at Hubbard Brook indicate that a simultaneous increase in the competitiveness of nitrifying microbes for NH4 [+] and reduction in the competitiveness of denitrifying bacteria for NO3 [-] are needed to bring soil N flux ratios into better agreement with observations. Such adjustments, combined with evaluation against observations, may help to improve confidence in present and future simulations of N limitation on the C cycle, although C fluxes, such as gross primary productivity and net primary productivity, are less sensitive to the model modifications than soil N fluxes.

RevDate: 2022-04-05
CmpDate: 2022-04-04

Ross Brown A, Lilley MKS, Shutler J, et al (2022)

Harmful Algal Blooms and their impacts on shellfish mariculture follow regionally distinct patterns of water circulation in the western English Channel during the 2018 heatwave.

Harmful algae, 111:102166.

Harmful algal blooms (HABs) can have severe ecological, societal and economic impacts upon marine ecosystems, human health and the seafood industry. We evaluated changes in marine plankton communities with prevailing physico-chemical conditions throughout an exceptionally warm summer (2018), to elucidate key factors governing HABs and their impacts on shellfish mariculture in the western English Channel. Despite warm, stable weather conditions and widespread seasonal stratification throughout the summer, divergent plankton community compositions were observed at two rope-grown mussel (Mytilus edulis) farms (St Austell Bay and Lyme Bay) and a long-term ecological research LTER site (Plymouth L4). There were significant differences between sites in the abundances of HAB species, including Dinophysis spp. and Karenia mikimotoi, whose cell counts bloomed in excess of UK Food Standards Agency (FSA) advisory 'trigger' levels at Plymouth L4 and St Austell Bay, but not at the Lyme Bay site. The K. mikimotoi bloom occurred over two weeks in August and comprised up to 88% of the standing phytoplankton biomass in St Austell Bay. Dinophysis spp. also bloomed here from May to September, constituting up to 28% of phytoplankton biomass. This protracted bloom resulted in concentrations of Dinophysis toxins 1 & 2 and pectenotoxins and okadaic acid in shellfish, which closed shellfish harvesting operations on farms located in St Austell Bay, and other shellfish sites in the west of the western English Channel (but not in the east of the region). Inter-site differences in the abundances of these and other HAB species were associated with variations in water circulation and co-occurring phytoplankton and zooplankton communities. Furthermore, plankton monitoring data obtained from the L4 site over the past 3 decades showed HAB species (including Dinophysis spp.) with abundances commonly occurring above advisory trigger levels during warmer periods, such as that coinciding with our study. Under projected climate warming these blooms are likely to continue to be governed by regionally distinct patterns of water circulation, which need to be taken into account in marine spatial planning, when assessing the suitability of new shellfish mariculture sites.

RevDate: 2022-03-16
CmpDate: 2022-03-16

Cáliz J, Subirats J, Triadó-Margarit X, et al (2022)

Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions.

Environment international, 160:107077.

Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.

RevDate: 2022-12-07
CmpDate: 2022-01-10

Cluzel N, Courbariaux M, Wang S, et al (2022)

A nationwide indicator to smooth and normalize heterogeneous SARS-CoV-2 RNA data in wastewater.

Environment international, 158:106998.

Since many infected people experience no or few symptoms, the SARS-CoV-2 epidemic is frequently monitored through massive virus testing of the population, an approach that may be biased and may be difficult to sustain in low-income countries. Since SARS-CoV-2 RNA can be detected in stool samples, quantifying SARS-CoV-2 genome by RT-qPCR in wastewater treatment plants (WWTPs) has been carried out as a complementary tool to monitor virus circulation among human populations. However, measuring SARS-CoV-2 viral load in WWTPs can be affected by many experimental and environmental factors. To circumvent these limits, we propose here a novel indicator, the wastewater indicator (WWI), that partly reduces and corrects the noise associated with the SARS-CoV-2 genome quantification in wastewater (average noise reduction of 19%). All data processing results in an average correlation gain of 18% with the incidence rate. The WWI can take into account the censorship linked to the limit of quantification (LOQ), allows the automatic detection of outliers to be integrated into the smoothing algorithm, estimates the average measurement error committed on the samples and proposes a solution for inter-laboratory normalization in the absence of inter-laboratory assays (ILA). This method has been successfully applied in the context of Obépine, a French national network that has been quantifying SARS-CoV-2 genome in a representative sample of French WWTPs since March 5th 2020. By August 26th, 2021, 168 WWTPs were monitored in the French metropolitan and overseas territories of France. We detail the process of elaboration of this indicator, show that it is strongly correlated to the incidence rate and that the optimal time lag between these two signals is only a few days, making our indicator an efficient complement to the incidence rate. This alternative approach may be especially important to evaluate SARS-CoV-2 dynamics in human populations when the testing rate is low.

RevDate: 2021-12-17
CmpDate: 2021-12-17

Fadini RF, Brocardo CR, Rosa C, et al (2021)

Long-term standardized ecological research in an Amazonian savanna: a laboratory under threat.

Anais da Academia Brasileira de Ciencias, 93(suppl 4):e20210879 pii:S0001-37652021000801012.

A few decades ago, researchers from the National Institute for Amazonian Research (INPA) started a pilot study to integrate the ecological studies of several organisms using monitoring plots, which then became the embryo for the creation of the RAPELD (Rapid Assessments and Long-term Ecological Research) system used by the Program for Biodiversity Research (PPBio) and the Long-term ecological research site POPA (PELD Western Pará). They installed and maintained permanent plots in an Amazonian-savanna patch near to the village of Alter do Chão. Amazonian savannas constitute a threatened ecosystem comprising only 6% of the Amazon biome. Most of the studies focused on three main long-term ecological research questions, but the site was also of importance for other inquiries and for the training of young researchers, contributing 71 articles so far and 32 masters and doctorate theses. Here, we present the experimental design and results of standardized studies in the savannas and forest fragments near Alter do Chão that have been carried out over the years. We discuss the future prospects and local threats to the area (e.g. soy crops and land speculation), and highlight the need to incorporate Alter do Chão villagers in land-use planning in the region.

RevDate: 2022-12-21
CmpDate: 2022-01-20

Wurtzer S, Waldman P, Levert M, et al (2022)

SARS-CoV-2 genome quantification in wastewaters at regional and city scale allows precise monitoring of the whole outbreaks dynamics and variants spreading in the population.

The Science of the total environment, 810:152213.

SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe complications. Until today several "waves" of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission. To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020. In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification. Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave. All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.

RevDate: 2022-04-01
CmpDate: 2022-03-30

Roeder KA, Benson BR, Weiser MD, et al (2022)

Testing the role of body size and litter depth on invertebrate diversity across six forests in North America.

Ecology, 103(2):e03601.

Ecologists search for rules by which traits dictate the abundance and distribution of species. Here we search for rules that apply across three common taxa of litter invertebrates in six North American forests from Panama to Oregon. We use image analysis to quantify the abundance and body size distributions of mites, springtails, and spiders in 21 1-m[2] plots per forest. We contrast three hypotheses: two of which focus on trait-abundance relationships and a third linking abundance to species richness. Despite three orders of magnitude variation in size, the predicted negative relationship between mean body size and abundance per area occurred in only 18% of cases, never for large bodied taxa like spiders. We likewise found only 18% of tests supported our prediction that increasing litter depth allows for high abundance; two-thirds of which occurred at a single deciduous forest in Massachusetts. In contrast, invertebrate abundance constrained species richness 76% of the time. Our results suggest that body size and habitat volume in brown food webs are rarely good predictors of variation in abundance, but that variation in diversity is generally well predicted by abundance.

RevDate: 2023-02-08
CmpDate: 2022-01-14

Juyal A, Guber A, Oerther M, et al (2021)

Pore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topography.

Scientific reports, 11(1):21998.

Bioenergy cropping systems can substantially contribute to climate change mitigation. However, limited information is available on how they affect soil characteristics, including pores and particulate organic matter (POM), both essential components of the soil C cycle. The objective of this study was to determine effects of bioenergy systems and field topography on soil pore characteristics, POM, and POM decomposition under new plant growth. We collected intact soil cores from two systems: monoculture switchgrass (Panicum virgatum L.) and native prairie, at two contrasting topographical positions (depressions and slopes), planting half of the cores with switchgrass. Pore and POM characteristics were obtained using X-ray computed micro-tomography (μCT) (18.2 µm resolution) before and after new switchgrass growth. Diverse prairie vegetation led to higher soil C than switchgrass, with concomitantly higher volumes of 30-90 μm radius pores and greater solid-pore interface. Yet, that effect was present only in the coarse-textured soils on slopes and coincided with higher root biomass of prairie vegetation. Surprisingly, new switchgrass growth did not intensify decomposition of POM, but even somewhat decreased it in monoculture switchgrass as compared to non-planted controls. Our results suggest that topography can play a substantial role in regulating factors driving C sequestration in bioenergy systems.

RevDate: 2021-12-14
CmpDate: 2021-12-07

Gallitelli L, Battisti C, Olivieri Z, et al (2021)

Carpobrotus spp. patches as trap for litter: Evidence from a Mediterranean beach.

Marine pollution bulletin, 173(Pt B):113029.

Dunal plants may affect the patterns of deposition of beach litter. In this study, we aimed at evaluating if Carpobrotus spp. patches may act as a litter trap in coastal dune systems. To do so, we counted the number of macrolitter occurring in both Carpobrotus and control (embryo dune vegetation) patches classifying each item into categories according to the Marine Strategy. Totally, we observed a significant difference between litter trapped in Carpobrotus (331 items, representing 62.4% of the total beach litter) and control (199, 37.6%). Plastic fragments were the most trapped items by both Carpobrotus (46.2%) and control patches (47.2%). We also calculated the item co-occurrence, obtaining a random aggregated 'litter community'. The main emerging output is that Carpobrotus patches act as filter in respect to different anthropogenic materials (overall plastics), suggesting that alien plant management actions may contribute to solve beach litter issues as well.

RevDate: 2021-10-23
CmpDate: 2021-10-22

Trubl G, Kimbrel JA, Liquet-Gonzalez J, et al (2021)

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil.

Microbiome, 9(1):208.

BACKGROUND: Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures).

RESULTS: We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H2[18]O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up [18]O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients.

CONCLUSIONS: Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.

RevDate: 2022-01-07
CmpDate: 2022-01-07

Triadó-Margarit X, Cáliz J, EO Casamayor (2022)

A long-term atmospheric baseline for intercontinental exchange of airborne pathogens.

Environment international, 158:106916.

The atmosphere is a potential pathway for global-scale and long-range dispersal of viable microorganisms, promoting biological interconnections among the total environment. We aimed to provide relevant baseline information for long-range long-term intercontinental exchange of potentially infectious airborne microorganisms of major interest in environmental and health-related disciplines. We used an interannual survey (7-y) with wet depositions fortnightly collected above the boundary layer (free troposphere) at a remote high-elevation LTER (Long-Term-Ecological-Research) site, analyzed by 16S and 18S rRNA genes, and compared to a database of 475 well-known pathogens. We applied a conservative approach on close relatives of pathogenic species (>98% identity) standing their theoretical upper limit for atmospheric baseline relative abundances. We identified c. 2-3% of the total airborne microbiota as potential pathogens. Their most frequent environmental origins were soil, aquatic, and anthropogenic sources. Phytopathogens (mostly fungi) were the potential infectious agents most widely present. We uncovered consistent interannual dynamics with taxa foreseeable over time (i.e., predictable seasonal behavior) and under recurrent environmental scenarios (e.g., Saharan dust intrusions), respectively, being highly valuable microbial forensic environmental indicators. Up to 8 bacterial and 21 fungal genera consistently showed temporal abundances and recurrences unevenly distributed. Incidence of allergenic fungi was lower in summer, and significantly higher in spring. Close relatives to Coccidioides posadasii consistently showed higher signals (i.e., high specificity and high fidelity) in winter, whereas Cryptococcus neoformans had a significant signal in spring. Along Saharan dust intrusions, the bacterial phytopathogens Acidovorax avenae and Agrobacterium tumefaciens and the fungal phytopathogens Pseudozyma hubeiensis and Peniophora sp. consistently showed higher signals. Potential human pathogens showed low proportion, being mostly fungal allergens. Microorganisms related to obligated human, amphibian and fish pathogens were commonly found in winter. More studies in remote field sites above the boundary layer will unveil whether or not a similar trend is found globally.

RevDate: 2022-12-21
CmpDate: 2021-11-03

Le Guernic A, Palos Ladeiro M, Boudaud N, et al (2022)

First evidence of SARS-CoV-2 genome detection in zebra mussel (Dreissena polymorpha).

Journal of environmental management, 301:113866.

The uses of bivalve molluscs in environmental biomonitoring have recently gained momentum due to their ability to indicate and concentrate human pathogenic microorganisms. In the context of the health crisis caused by the COVID-19 epidemic, the objective of this study was to determine if the SARS-CoV-2 ribonucleic acid genome can be detected in zebra mussels (Dreissena polymorpha) exposed to raw and treated urban wastewaters from two separate plants to support its interest as bioindicator of the SARS-CoV-2 genome contamination in water. The zebra mussels were exposed to treated wastewater through caging at the outlet of two plants located in France, as well as to raw wastewater in controlled conditions. Within their digestive tissues, our results showed that SARS-CoV-2 genome was detected in zebra mussels, whether in raw and treated wastewaters. Moreover, the detection of the SARS-CoV-2 genome in such bivalve molluscans appeared even with low concentrations in raw wastewaters. This is the first detection of the SARS-CoV-2 genome in the tissues of a sentinel species exposed to raw and treated urban wastewaters. Despite the need for development for quantitative approaches, these results support the importance of such invertebrate organisms, especially zebra mussel, for the active surveillance of pathogenic microorganisms and their indicators in environmental waters.

RevDate: 2021-11-15
CmpDate: 2021-11-15

Radujković D, Verbruggen E, Seabloom EW, et al (2021)

Soil properties as key predictors of global grassland production: Have we overlooked micronutrients?.

Ecology letters, 24(12):2713-2725.

Fertilisation experiments have demonstrated that nutrient availability is a key determinant of biomass production and carbon sequestration in grasslands. However, the influence of nutrients in explaining spatial variation in grassland biomass production has rarely been assessed. Using a global dataset comprising 72 sites on six continents, we investigated which of 16 soil factors that shape nutrient availability associate most strongly with variation in grassland aboveground biomass. Climate and N deposition were also considered. Based on theory-driven structural equation modelling, we found that soil micronutrients (particularly Zn and Fe) were important predictors of biomass and, together with soil physicochemical properties and C:N, they explained more unique variation (32%) than climate and N deposition (24%). However, the association between micronutrients and biomass was absent in grasslands limited by NP. These results highlight soil properties as key predictors of global grassland biomass production and point to serial co-limitation by NP and micronutrients.

RevDate: 2021-11-12
CmpDate: 2021-11-12

Lin SY, Hameed A, Tsai CF, et al (2021)

Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field.

Antonie van Leeuwenhoek, 114(12):2101-2111.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501[T], harboring xenobiotic- and allelochemical-metabolizing genes, isolated from a long-term ecological research field in Taiwan. Cells of strain CC-CFT501[T] were catalase- and oxidase-positive, non-motile and short rods. Optimal growth occurred at 30 °C, pH 8 and 1% NaCl. Strain CC-CFT501[T] was found to share high 16S rRNA gene sequence similarity with the members of genera Quisquiliibacterium (94.3%, n = 1), Pandoraea (93.4-94.0%, n = 23) and Paraburkholderia (93.3-94.0%, n = 9), affiliated to the family Burkholderiaceae. Strain CC-CFT501[T] shared 76.4% orthologous average nucleotide identity (OrthoANI) and 20.9% digital DNA-DNA hybridization (dDDH) values with Quisquiliibacterium transsilvanicum DSM 29781[T]. Draft genome sequence (3.83 Mb) of strain CC-CFT501[T] revealed several genes encoding the proteins involved in biphenyl and phenolic acid metabolism. Fatty acid profile contained C16:0, C18:0, C10:0 3-OH, C16:1 ω7c/C16:1 ω6c and C18:1 ω7c/C18:1 ω6c in predominant amounts. The polar lipid profile consisted of phosphatidylethanolamine, thirteen unidentified amino lipids, two unidentified phospholipids and two unidentified glycolipids. The major polyamine was spermidine and ubiquinone Q-8 was the sole respiratory quinone. The DNA G + C content was 70.0 mol%. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT501[T] is considered to represent a novel genus and species of the family Burkholderiaceae, for which the name Zeimonas arvi gen. nov., sp. nov. is proposed. The type strain of the type species is CC-CFT501[T] (= BCRC 81218[T] = JCM 33506[T]).

RevDate: 2021-09-30

Henschel JR (2021)

Long-Term Population Dynamics of Namib Desert Tenebrionid Beetles Reveal Complex Relationships to Pulse-Reserve Conditions.

Insects, 12(9):.

Noy-Meir's paradigm concerning desert populations being predictably tied to unpredictable productivity pulses was tested by examining abundance trends of 26 species of flightless detritivorous tenebrionid beetles (Coleoptera, Tenebrionidae) in the hyper-arid Namib Desert (MAP = 25 mm). Over 45 years, tenebrionids were continuously pitfall trapped on a gravel plain. Species were categorised according to how their populations increased after 22 effective rainfall events (>11 mm in a week), and declined with decreasing detritus reserves (97.7-0.2 g m[-2]), while sustained by nonrainfall moisture. Six patterns of population variation were recognised: (a) increases triggered by effective summer rainfalls, tracking detritus over time (five species, 41% abundance); (b) irrupting upon summer rainfalls, crashing a year later (three, 18%); (c) increasing gradually after series of heavy (>40 mm) rainfall years, declining over the next decade (eight, 15%); (d) triggered by winter rainfall, population fluctuating moderately (two, 20%); (e) increasing during dry years, declining during wet (one, 0.4%); (f) erratic range expansions following heavy rain (seven, 5%). All species experienced population bottlenecks during a decade of scant reserves, followed by the community cycling back to its earlier composition after 30 years. By responding selectively to alternative configurations of resources, Namib tenebrionids showed temporal patterns and magnitudes of population fluctuation more diverse than predicted by Noy-Meir's original model, underpinning high species diversity.

RevDate: 2021-11-17
CmpDate: 2021-11-17

Atkinson ST, Cale D, Pinder A, et al (2021)

Substantial long-term loss of alpha and gamma diversity of lake invertebrates in a landscape exposed to a drying climate.

Global change biology, 27(23):6263-6279.

Many regions across the globe are shifting to more arid climates. For shallow lakes, decreasing rainfall volume and timing, changing regional wind patterns and increased evaporation rates alter water regimes so that dry periods occur more frequently and for longer. Drier conditions may affect fauna directly and indirectly through altered physicochemical conditions in lakes. Although many studies have predicted negative effects of such changes on aquatic biodiversity, empirical studies demonstrating these effects are rare. Global warming has caused severe climatic drying in southwestern Australia since the 1970s, so we aimed to determine whether lakes in this region showed impacts on lake hydroperiod, water quality, and α, β and γ diversity of lake invertebrates from 1998 to 2011. Seventeen lakes across a range of salinities were sampled biennially in spring in the Wheatbelt and Great Southern regions of Western Australia. Multivariate analyses were used to identify changes in α, β and γ diversity and examine patterns in physicochemical data. Salinity and average rainfall partially explained patterns in invertebrate richness and assemblage composition. Climatic drying was associated with significant declines in lake depth, increased frequency of dry periods, and reduced α and γ diversity (γ declined from ~300 to ~100 taxa from 1998 to 2011 in the 17 wetlands). In contrast, β diversity remained consistently high, because each lake retained a distinct fauna. Mean α diversity per-lake declined both in lakes that dried and lakes that did not dry out, but lakes which retained a greater proportion of their maximum depth retained more α diversity. Accumulated losses in α diversity caused the decline in γ diversity likely through shrinking habitat area, fewer stepping stones for dispersal and loss of specific habitat types. Biodiversity loss is thus likely from lakes in drying regions globally. Management actions will need to sustain water depth in lakes to prevent biodiversity loss.

RevDate: 2021-09-07

Grosse M, Ahlborn MC, W Hierold (2021)

Metadata of agricultural long-term experiments in Europe exclusive of Germany.

Data in brief, 38:107322.

Agricultural long-term experiments (LTEs) are an important research infrastructure for agriculture, plant and soil sciences. The aim of this metadata compilation is to make LTEs easier to find and to facilitate networking. LTEs are here defined as agricultural experiments with a minimum duration of 20 years and research in the context of soil and yield. An extensive literature review was conducted to identify LTEs in Europe exclusive of Germany, because Germany's LTEs were published before. Sources were scientific papers as well as other articles, books, trial guides and websites. The following information was searched for and compiled in this dataset, if available: site and name of the LTE, start and end (if appropriate), holding institution, type of land use (e.g. field crops or grassland), research theme, website (if available), participation in networks, measured parameters, farming category (i.e. conventional or organic), size of the LTE area, longitude and latitude of the LTE, experimental setup including factors, treatments, randomization and replication, number of plots, size of the plots, crop rotation, soil type, substrate, texture, literature which was written in the context of the LTE data, and AGROVOC keywords. LTE from the following countries are included: Austria, Belarus, Belgium, Bulgaria, Czech Republic, Denmark, Estonia, Finland, France, Great Britain, Hungary, Italy, Moldova, Norway, Poland, Romania, Serbia, Slovenia, Spain, Sweden, Switzerland, Ukraine. In total, 186 LTEs could be identified. The LTEs were classified according to the following research themes: fertilization, tillage, crop rotation, other. The majority of LTEs have the research theme "fertilization" (n = 125). Thirty LTEs have the research theme "crop rotation", 26 LTEs have the research theme "tillage", and 26 LTEs have "other" research themes. The following networks could be identified: GLTEN (Global long-term experiment network), ILTER (International long-term ecological research), IOSDV (International Organic Nitrogen Fertilization Experiment), NLFT (National Long-term Fertilization Trials, Hungary), RetiBio 2 (Italy). The oldest LTE was set up 1843, but the largest number of LTEs was established in the second half of the 20th century. Most of the LTEs are held by a scientific institution, i.e. 88 LTEs are held by a non-university scientific institution and 81 LTEs are held by a university or university of applied sciences. The link to the holding institution is provided whenever possible to facilitate contacting.

RevDate: 2021-12-23
CmpDate: 2021-12-23

Manlick PJ, Maldonado K, SD Newsome (2021)

Competition shapes individual foraging and survival in a desert rodent ensemble.

The Journal of animal ecology, 90(12):2806-2818.

Intraspecific variation, including individual diet variation, can structure populations and communities, but the causes and consequences of individual foraging strategies are often unclear. Interactions between competition and resources are thought to dictate foraging strategies (e.g. specialization vs. generalization), but classical paradigms such as optimal foraging and niche theory offer contrasting predictions for individual consumers. Furthermore, both paradigms assume that individual foraging strategies maximize fitness, yet this prediction is rarely tested. We used repeated stable isotope measurements (δ[13] C, δ[15] N; N = 3,509) and 6 years of capture-mark-recapture data to quantify the relationship between environmental variation, individual foraging and consumer fitness among four species of desert rodents. We tested the relative effects of intraspecific competition, interspecific competition, resource abundance and resource diversity on the foraging strategies of 349 individual animals, and then quantified apparent survival as function of individual foraging strategies. Consistent with niche theory, individuals contracted their trophic niches and increased foraging specialization in response to both intraspecific and interspecific competition, but this effect was offset by resource availability and individuals generalized when plant biomass was high. Nevertheless, individual specialists obtained no apparent fitness benefit from trophic niche contractions as the most specialized individuals exhibited a 10% reduction in monthly survival compared to the most generalized individuals. Ultimately, this resulted in annual survival probabilities nearly 4× higher for generalists compared to specialists. These results indicate that competition is the proximate driver of individual foraging strategies, and that diet-mediated fitness variation regulates population and community dynamics in stochastic resource environments. Furthermore, our findings show dietary generalism is a fitness maximizing strategy, suggesting that plastic foraging strategies may play a key role in species' ability to cope with environmental change.

RevDate: 2021-10-27
CmpDate: 2021-10-27

Cresta E, C Battisti (2021)

Anthropogenic litter along a coastal-wetland gradient: Reed-bed vegetation in the backdunes may act as a sink for expanded polystyrene.

Marine pollution bulletin, 172:112829.

We investigated the accumulation of litter along a transition gradient from the dunal beaches (B), to the backdunes (BD), to the channels of a coastal wetland (W), considering both the total litter and a sub-category represented by expanded polystyrene (EPS). Using a removal sampling technique carried out in spring (April and May), we hypothesized that: (i) the total accumulation of litter decreases progressively from the dunes to the backdunes to wet environments while (ii) the lighter polystyrene concentrates in the BD-W fringe where the Phragmites australis reedbeds can have a sink role for this polymer. The total litter density showed a significant decrease along the gradient B-BD-W in both months, with an evident collapse between BD and W. Analogously, EPS showed a significant difference in density along the B-BD-W gradient in both months, although with a different pattern: a maximum in the BD and a significant collapse between BD and W. The presence of backdune hygrophilous vegetation (Phragmites australis' reedbeds) may act as a sink trapping all types of litter in both cases (total litter and EPS). The different accumulation pattern between total litter and the EPS is due to the lower specific weight of the latter polymer: while the generic litter tends to decrease quantitatively moving away from the sea, the lighter EPS is removed by the winds and pushed towards the land, beyond the dune, where it is trapped by the vegetation, thus showing a peak in density in the backdunes. No significant differences were observed between the litter density in the two months (before and after the removal) either considering the total litter and only EPS. This may suggest a continuous supply of litter from the sea, highlighting how clean-ups actions should be carried out with a higher frequency rather than monthly. This may be even more valid in the period of greater frequency of intense weather-marine events (autumn-winter) when a greater quantity of litter is deposited. These are the first data for the Mediterranean regarding a specific role of wetland hygrophilous vegetation as a sink for anthropogenic litter, mainly expanded polystyrene.

RevDate: 2021-09-29
CmpDate: 2021-09-29

Cesarini G, Cera A, Battisti C, et al (2021)

Is the weight of plastic litter correlated with vegetal wrack? A case study from a Central Italian beach.

Marine pollution bulletin, 171:112794.

This study analyzes the occurrence and distribution of plastic litter and the entrapment of plastic by wrack beached on a natural reserve. Large microplastics (2.5 - 5 mm) were the most abundant plastic size category detected. The main color and shape were white and fragment, respectively. The plastics entrapped by egagropiles were mainly transparent fibers. We analyzed the correlation between the weights of plastic litter and vegetal wrack in two transects, selected for their different environmental characteristics. The transect closer to a breakwater showed a significant positive correlation between the weights of plastics and wrack, while the other transect suggested a casual pattern of plastic deposition on the beach. Further research is suggested to focus on the role of breakwaters in altering marine currents and enhancing plastic beaching.

RevDate: 2023-09-20
CmpDate: 2021-12-09

Pilla RM, Mette EM, Williamson CE, et al (2021)

Global data set of long-term summertime vertical temperature profiles in 153 lakes.

Scientific data, 8(1):200.

Climate change and other anthropogenic stressors have led to long-term changes in the thermal structure, including surface temperatures, deepwater temperatures, and vertical thermal gradients, in many lakes around the world. Though many studies highlight warming of surface water temperatures in lakes worldwide, less is known about long-term trends in full vertical thermal structure and deepwater temperatures, which have been changing less consistently in both direction and magnitude. Here, we present a globally-expansive data set of summertime in-situ vertical temperature profiles from 153 lakes, with one time series beginning as early as 1894. We also compiled lake geographic, morphometric, and water quality variables that can influence vertical thermal structure through a variety of potential mechanisms in these lakes. These long-term time series of vertical temperature profiles and corresponding lake characteristics serve as valuable data to help understand changes and drivers of lake thermal structure in a time of rapid global and ecological change.

RevDate: 2021-08-06

Wohner C, Ohnemus T, Zacharias S, et al (2021)

Assessing the biogeographical and socio-ecological representativeness of the ILTER site network.

Ecological indicators, 127:107785.

The challenges posed by climate and land use change are increasingly complex, with rising and accelerating impacts on the global environmental system. Novel environmental and ecosystem research needs to properly interpret system changes and derive management recommendations across scales. This largely depends on advances in the establishment of an internationally harmonised, long-term operating and representative infrastructure for environmental observation. This paper presents an analysis evaluating 743 formally accredited sites of the International Long-Term Ecological Research (ILTER) network in 47 countries with regard to their spatial distribution and related biogeographical and socio-ecological representativeness. "Representedness" values were computed from six global datasets. The analysis revealed a dense coverage of Northern temperate regions and anthropogenic zones most notably in the US, Europe and East Asia. Significant gaps are present in economically less developed and anthropogenically less impacted hot and barren regions like Northern and Central Africa and inner-continental parts of South America. These findings provide the arguments for our recommendations regarding the geographic expansion for the further development of the ILTER network.

RevDate: 2023-02-05
CmpDate: 2021-09-30

De Falco N, Tal-Berger R, Hjazin A, et al (2021)

Geodiversity impacts plant community structure in a semi-arid region.

Scientific reports, 11(1):15259.

Geodiversity refers to the variety of geological and physical elements as well as to geomorphological processes of the earth surface. Heterogeneity of the physical environment has an impact on plant diversity. In recent years, the relations between geodiversity and biodiversity has gained attention in conservation biology, especially in the context of climate change. In this study, we assessed the spatial and temporal change in plant's community structure in a semi-arid region, Sayeret Shaked Long Term Ecosystem Research (LTER) station, Israel. Vegetation surveys were conducted on different hillslopes, either with or without rock covers in order to study the spatial trends of hillslope geodiversity. The surveys were conducted for two consecutive years (2016 and 2017), of which the second year was drier and hotter and therefore permitted to investigate the temporal change of plant's community structure. The results of the spatial trends show that (1) geodiversity increases vegetation biodiversity and promotes perennial plants and those of the temporal change show that (2) the positive effect of geodiversity on plants' community structure and species richness is greater in the drier year than that in a wetter year. The main insight is that in these drylands, hillslopes with higher geodiversity appear to buffer the effect of drier years, and supported a more diverse plant community than lower geodiversity hillslopes.

RevDate: 2021-09-20
CmpDate: 2021-09-20

Seabloom EW, Borer ET, Hobbie SE, et al (2021)

Soil nutrients increase long-term soil carbon gains threefold on retired farmland.

Global change biology, 27(19):4909-4920.

Abandoned agricultural lands often accumulate soil carbon (C) following depletion of soil C by cultivation. The potential for this recovery to provide significant C storage benefits depends on the rate of soil C accumulation, which, in turn, may depend on nutrient supply rates. We tracked soil C for almost four decades following intensive agricultural soil disturbance along an experimentally imposed gradient in nitrogen (N) added annually in combination with other macro- and micro-nutrients. Soil %C accumulated over the course of the study in unfertilized control plots leading to a gain of 6.1 Mg C ha[-1] in the top 20 cm of soil. Nutrient addition increased soil %C accumulation leading to a gain of 17.8 Mg C ha[-1] in fertilized plots, nearly a threefold increase over the control plots. These results demonstrate that substantial increases in soil C in successional grasslands following agricultural abandonment occur over decadal timescales, and that C gain is increased by high supply rates of soil nutrients. In addition, soil %C continued to increase for decades under elevated nutrient supply, suggesting that short-term nutrient addition experiments underestimate the effects of soil nutrients on soil C accumulation.

RevDate: 2021-11-11
CmpDate: 2021-11-11

Meng B, Li J, Maurer GE, et al (2021)

Nitrogen addition amplifies the nonlinear drought response of grassland productivity to extended growing-season droughts.

Ecology, 102(11):e03483.

Understanding the response of grassland production and carbon exchange to intra-annual variation in precipitation and nitrogen addition is critical for sustainable grassland management and ecosystem restoration. We introduced growing-season drought treatments of different lengths (15, 30, 45 and 60 d drought) by delaying growing-season precipitation in a long-term nitrogen addition experiment in a low diversity meadow steppe in northeast China. Response variables included aboveground biomass (AGB), ecosystem net carbon exchange (NEE), and leaf net carbon assimilation rate (A). In unfertilized plots drought decreased AGB by 13.7% after a 45-d drought and 31.7% after a 60-d drought (47.6% in fertilized plots). Progressive increases in the drought response of NEE were also observed. The effects of N addition on the drought response of productivity increased as drought duration increased, and these responses were a function of changes in AGB and biomass allocation, particularly root to shoot ratio. However, no significant effects of drought occurred in fertilized or unfertilized plots in the growing season a year after the experiment, N addition did limit the recovery of AGB from severe drought during the remainder of the current growing season. Our results imply that chronic N enrichment could exacerbate the effects of growing-season drought on grassland productivity caused by altered precipitation seasonality under climate change, but that these effects do not carry over to the next growing season.

RevDate: 2021-09-09
CmpDate: 2021-09-09

O'Connell JL, Mishra DR, Alber M, et al (2021)

BERM: a Belowground Ecosystem Resiliency Model for estimating Spartina alterniflora belowground biomass.

The New phytologist, 232(1):425-439.

Spatiotemporal patterns of Spartina alterniflora belowground biomass (BGB) are important for evaluating salt marsh resiliency. To solve this, we created the BERM (Belowground Ecosystem Resiliency Model), which estimates monthly BGB (30-m spatial resolution) from freely available data such as Landsat-8 and Daymet climate summaries. Our modeling framework relied on extreme gradient boosting, and used field observations from four Georgia salt marshes as ground-truth data. Model predictors included estimated tidal inundation, elevation, leaf area index, foliar nitrogen, chlorophyll, surface temperature, phenology, and climate data. The final model included 33 variables, and the most important variables were elevation, vapor pressure from the previous four months, Normalized Difference Vegetation Index (NDVI) from the previous five months, and inundation. Root mean squared error for BGB from testing data was 313 g m[-2] (11% of the field data range), explained variance (R[2]) was 0.62-0.77. Testing data results were unbiased across BGB values and were positively correlated with ground-truth data across all sites and years (r = 0.56-0.82 and 0.45-0.95, respectively). BERM can estimate BGB within Spartina alterniflora salt marshes where environmental parameters are within the training data range, and can be readily extended through a reproducible workflow. This provides a powerful approach for evaluating spatiotemporal BGB and associated ecosystem function.

RevDate: 2021-05-26

Arismendi I, Bury G, Zatkos L, et al (2021)

A method to evaluate body length of live aquatic vertebrates using digital images.

Ecology and evolution, 11(10):5497-5502.

Traditional methods to measure body lengths of aquatic vertebrates rely on anesthetics, and extended handling times. These procedures can increase stress, potentially affecting the animal's welfare after its release. We developed a simple procedure using digital images to estimate body lengths of coastal cutthroat trout (Oncorhynchus clarkii clarkii) and larval coastal giant salamander (Dicamptodon tenebrosus). Images were postprocessed using ImageJ2. We measured more than 900 individuals of these two species from 200 pool habitats along 9.6 river kilometers. The percent error (mean ± SE) of our approach compared to the use of a traditional graded measuring board was relatively small for all length metrics of the two species. Total length of trout was -2.2% ± 1.0. Snout-vent length and total length of larval salamanders was 3.5% ± 3.3 and -0.6% ± 1.7, respectively. We cross-validated our results by two independent observers that followed our protocol to measure the same animals and found no significant differences (p > .7) in body size distributions for all length metrics of the two species. Our procedure provides reliable information of body size reducing stress and handling time in the field. The method is transferable across taxa and the inclusion of multiple animals per image increases sampling efficiency with stored images that can be reviewed multiple times. This practical tool can improve data collection of animal size over large sampling efforts and broad spatiotemporal contexts.

RevDate: 2022-12-17
CmpDate: 2021-05-18

Wurtzer S, Waldman P, Ferrier-Rembert A, et al (2021)

Several forms of SARS-CoV-2 RNA can be detected in wastewaters: Implication for wastewater-based epidemiology and risk assessment.

Water research, 198:117183.

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health emergency of international concern. Although SARS-CoV-2 is considered to be mainly transmitted by inhalation of contaminated droplets and aerosols, SARS-CoV-2 is also detected in human feces and to a less extent in urine, and in raw wastewaters (to date viral RNA only) suggesting that other routes of infection may exist. Monitoring SARS-CoV-2 genomes in wastewaters has been proposed as a complementary approach for tracing the dynamics of virus transmission within human population connected to wastewater network. The understanding on SARS-CoV-2 transmission through wastewater surveillance, the development of epidemic modeling and the evaluation of SARS-CoV-2 transmission from contaminated wastewater are largely limited by our knowledge on viral RNA genome persistence and virus infectivity preservation in such an environment. Using an integrity based RT-qPCR assay this study led to the discovery that SARS-CoV-2 RNA can persist under several forms in wastewaters, which provides important information on the presence of SARS-CoV-2 in raw wastewaters and associated risk assessment.

RevDate: 2021-05-25
CmpDate: 2021-05-25

Li Z, AM Cupples (2021)

Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices.

Applied microbiology and biotechnology, 105(10):4309-4327.

Nitrogen fertilizer results in the release of nitrous oxide (N2O), a concern because N2O is an ozone-depleting substance and a greenhouse gas. Although the reduction of N2O to nitrogen gas can control emissions, the factors impacting the enzymes involved have not been fully explored. The current study investigated the abundance and diversity of genes involved in nitrogen cycling (primarily denitrification) under four agricultural management practices (no tillage [NT], conventional tillage [CT], reduced input, biologically-based). The work involved examining soil shotgun sequencing data for nine genes (napA, narG, nirK, nirS, norB, nosZ, nirA, nirB, nifH). For each gene, relative abundance values, diversity and richness indices, and taxonomic classification were determined. Additionally, the genes associated with nitrogen metabolism (defined by the KEGG hierarchy) were examined. The data generated were statistically compared between the four management practices. The relative abundance of four genes (nifH, nirK, nirS, and norB) were significantly lower in the NT treatment compared to one or more of the other soils. The abundance values of napA, narG, nifH, nirA, and nirB were not significantly different between NT and CT. The relative abundance of nirS was significantly higher in the CT treatment compared to the others. Diversity and richness values were higher for four of the nine genes (napA, narG, nirA, nirB). Based on nirS/nirK ratios, CT represents the highest N2O consumption potential in four soils. In conclusion, the microbial communities involved in nitrogen metabolism were sensitive to different agricultural practices, which in turn, likely has implications for N2O emissions. KEY POINTS: • Four genes were less abundant in NT compared to one or more of the others soils (nifH, nirK, nirS, norB). • The most abundant sequences for many of the genes classified within the Proteobacteria. • Higher diversity and richness indices were observed for four genes (napA, narG, nirA, nirB). • Based on nirS/nirK ratios, CT represents the highest N2O consumption potential.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.


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This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

Electronic Scholarly Publishing
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Bellingham, WA 98226

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )