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Bibliography on: Microbial Ecology

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 May 2023 at 01:42 Created: 

Microbial Ecology

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

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Citations The Papers (from PubMed®)


RevDate: 2023-05-27

Mattelin V, Verfaille L, Kundu K, et al (2023)

A New Colorimetric Test for Accurate Determination of Plastic Biodegradation.

Polymers, 15(10): pii:polym15102311.

As plastic waste is accumulating in both controlled waste management settings and natural settings, much research is devoted to search for solutions, also in the field of biodegradation. However, determining the biodegradability of plastics in natural environments remains a big challenge due to the often very low biodegradation rates. Many standardised test methods for biodegradation in natural environments exist. These are often based on mineralisation rates in controlled conditions and are thus indirect measurements of biodegradation. It is of interest for both researchers and companies to have tests that are more rapid, easier, and more reliable to screen different ecosystems and/or niches for their plastic biodegradation potential. In this study, the goal is to validate a colorimetric test, based on carbon nanodots, to screen biodegradation of different types of plastics in natural environments. After introducing carbon nanodots into the matrix of the target plastic, a fluorescent signal is released upon plastic biodegradation. The in-house-made carbon nanodots were first confirmed regarding their biocompatibility and chemical and photostability. Subsequently, the effectivity of the developed method was evaluated positively by an enzymatic degradation test with polycaprolactone with Candida antarctica lipase B. Finally, validation experiments were performed with enriched microorganisms and real environmental samples (freshwater and seawater), of which the results were compared with parallel, frequently used biodegradation measures such as O2 and CO2, dissolved organic carbon, growth and pH, to assess the reliability of the test. Our results indicate that this colorimetric test is a good alternative to other methods, but a combination of different methods gives the most information. In conclusion, this colorimetric test is a good fit to screen, in high throughput, the depolymerisation of plastics in natural environments and under different conditions in the lab.

RevDate: 2023-05-26

Malard LA, A Guisan (2023)

Into the microbial niche.

Trends in ecology & evolution pii:S0169-5347(23)00120-9 [Epub ahead of print].

The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.

RevDate: 2023-05-26

Anderson AG, Bedford MR, CM Parsons (2023)

Effects of adaptation diet and exogenous enzymes on true metabolizable energy and cecal microbial ecology, short-chain fatty acid profile, and enzyme activity in roosters fed barley and rye diets.

Poultry science, 102(7):102768 pii:S0032-5791(23)00287-0 [Epub ahead of print].

Three experiments evaluated effects of adaptation diet and exogenous β-glucanase and xylanase on TMEn of barley and rye. Single Comb White Leghorn roosters were fed adaptation diets based on corn/soybean meal (SBM), barley/SBM with and without β-glucanase, or rye/corn/SBM with and without xylanase for 4 wk. In Experiments 1 and 2, after the adaptation period, TMEn was determined using a 48 h precision-fed rooster assay for 100% barley or 100% rye diets with or without β-glucanase or xylanase, respectively. Experiment 3 consisted only of feeding adaptation diets for 4 wk. Cecal samples were collected at the end of experiments for microbial ecology, short-chain fatty acid (SCFA) profiles, and enzyme activity analyses. In Experiments 1 and 2, β-glucanase increased (P < 0.05) TMEn of barley, and there was no significant effect of adaptation diet on TMEn values. Total cecal Eubacteria and Ruminococcaceae were decreased (P < 0.05) and Escherichia coli were increased (P < 0.05) at the end of the TMEn assay compared with the end of the adaptation period (with no TMEn assay). There was a large decrease (P < 0.05) for most cecal SCFA at the end of the TMEn assay compared with the end of the adaptation period. Both cecal β-glucanase and xylanase activity were increased for birds fed adaptation diets containing the respective enzyme. In Experiment 3, there were no consistent effects of adaptation diet on cecal microbial profiles or SCFA but cecal β-glucanase activity was increased (P < 0.05) by exogenous β-glucanase for barley and cecal xylanase activity was increased (P < 0.05) by exogenous xylanase for rye. Overall, the results indicated that TMEn of barley was increased by exogenous β-glucanase, adaptation diet did not significantly influence the TMEn response to the dietary enzymes, and cecal fermentation (based on cecal SCFA) was greatly reduced by the TMEn assay. Cecal β-glucanase and xylanase activity, however, were often increased by feeding high barley and high rye diets containing exogenous enzymes.

RevDate: 2023-05-26

Esteves SM, Jadoul A, Iacono F, et al (2023)

Natural variation of nutrient homeostasis among laboratory and field strains in Chlamydomonas reinhardtii.

Journal of experimental botany pii:7180789 [Epub ahead of print].

Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macro-nutrients have a wide range of functions in photosynthetic organisms and mineral nutrition plays thus a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, twenty-four Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared to autotrophy and 9 deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, -S) and micronutrients (-Cu, -Fe, -Mn, -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.

RevDate: 2023-05-26

Gomes TC, Conrado R, Oliveira RC, et al (2023)

Effect of Monocerin, a Fungal Secondary Metabolite, on Endothelial Cells.

Toxins, 15(5): pii:toxins15050344.

This study reports the isolation and identification of the endophytic fungus Exserohilum rostratum through molecular and morphological analysis using optical and transmission electron microscopy (TEM), as well as the procurement of its secondary metabolite monocerin, an isocoumarin derivative. Considering the previously observed biological activities of monocerin, this study was performed on human umbilical vein endothelial cells (HUVECs) that are widely used as an in vitro model for several different purposes. Important parameters, such as cell viability, senescence-associated β-galactosidase, cellular proliferation by using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE), apoptosis analysis with annexin, cellular morphology through scanning electron microscopy (SEM), and laser confocal analysis were evaluated after exposing the cells to monocerin. After 24 h of exposure to monocerin at 1.25 mM, there was more than 80% of cell viability and a low percentage of cells in the early and late apoptosis and necrosis. Monocerin increased cell proliferation and did not induce cell senescence. Morphological analysis showed cellular integrity. The study demonstrates aspects of the mechanism of action of monocerin on endothelial cell proliferation, suggesting the possibility of its pharmaceutical application, such as in regenerative medicine.

RevDate: 2023-05-26

Sarrocco S, Herrera-Estrella A, DB Collinge (2023)

Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.

Frontiers in microbiology, 14:1203870.

RevDate: 2023-05-26

Leonhardt F, Keller A, Arranz Aveces C, et al (2023)

From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian.

Microbial ecology [Epub ahead of print].

Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.

RevDate: 2023-05-25

Haskell-Ramsay CF, Dodd FL, Smith D, et al (2022)

Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults.

The Journal of nutrition, 152(12):2778-2788.

BACKGROUND: Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study.

OBJECTIVES: The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults.

METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30 g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18-49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2).

RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M = 92.2% compared with NUTS M = 94.5%; P = 0.019) and speed of response (placebo M = 788 ms compared with NUTS M = 757 ms; P = 0.004) on a picture recognition task. No significant changes to bacterial community α or β diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P = 0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome.

CONCLUSIONS: These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.

RevDate: 2023-05-25

Bossolani JW, Leite MFA, Momesso L, et al (2023)

Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence.

The Science of the total environment pii:S0048-9697(23)02968-6 [Epub ahead of print].

The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity on the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.

RevDate: 2023-05-25

Zou J, Cai L, Lin J, et al (2023)

Anaerobic fermentation of aerobic granular sludge: Insight into the effect of granule size and sludge structure on hydrolysis and acidification.

Journal of environmental management, 343:118202 pii:S0301-4797(23)00990-8 [Epub ahead of print].

Aerobic granular sludge (AGS) has different physicochemical properties and microbial communities compared to conventional activated sludge (CAS), which may result in different behaviors during anaerobic fermentation and require further investigation. This study investigated the effect of granule size and sludge structure on the hydrolysis and acidification of AGS. Experimental results show that AGS exhibited significantly higher soluble chemical oxygen demand (SCOD) dissolution and total volatile fatty acids (TVFA) production (330.6-430.3 mg/gVSS and 231.0-312.5 mgCOD/gVSS) compared to conventional activated sludge (CAS) (167.0 mg/gVSS and 133.3 mgCOD/gVSS). This is because AGS (90.6-96.9 mg/gVSS) had higher extracellular polymeric substances (EPS) content than CAS (81.2 mg/gVSS). EPS can not only serve as substrates but also release the trapped hydrolases. Moreover, the relative abundances of hydrolytic/acidogenic bacteria and genes were higher in AGS (0.46%-3.60% and 3.01 × 10[-3]%-4.04 × 10[-3]%) than in CAS (0.30% and 1.23 × 10[-3]%). The optimal granule size for AGS fermentation was found to be 500-1600 μm. The crushing of granule structure promoted the dissolution of small amounts of EPS and the release of some trapped hydrolases, thereby potentially enhancing the enzyme-substrate contacts and bacteria-substrate interactions. Therefore, the highest SCOD dissolution (510.6 mg/gVSS) and TVFA production (352.1 mgCOD/gVSS) from crushed 500-1600 μm AGS were observed. Overall, the findings of this study provide valuable insights into the recovery of organic carbon from AGS via anaerobic fermentation.

RevDate: 2023-05-25

S Camargo T, A Nickele M, Reis Filho W, et al (2023)

Correction to: Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: A Search for Potential Biocontrol Agents.

RevDate: 2023-05-24

Tao F, Huang Y, Hungate BA, et al (2023)

Microbial carbon use efficiency promotes global soil carbon storage.

Nature [Epub ahead of print].

Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

RevDate: 2023-05-24

Elston KM, Phillips LE, Leonard SP, et al (2023)

The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.

ISME communications, 3(1):49.

Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.

RevDate: 2023-05-24

Przybylska MS, Violle C, Vile D, et al (2023)

AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.

Scientific data, 10(1):314.

Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.

RevDate: 2023-05-24

Venbrux M, Crauwels S, H Rediers (2023)

Current and emerging trends in techniques for plant pathogen detection.

Frontiers in plant science, 14:1120968.

Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.

RevDate: 2023-05-24

Broman E, Abdelgadir M, Bonaglia S, et al (2023)

Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.

Microbial ecology [Epub ahead of print].

Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.

RevDate: 2023-05-24

Korpita TM, Muths EL, Watry MK, et al (2023)

Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities.

Microbial ecology [Epub ahead of print].

Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.

RevDate: 2023-05-24

Rodríguez MF, Gomez AP, Parra-Giraldo CM, et al (2023)

Proteomics and Genetic Approaches Elucidate the Circulation of Low Variability Staphylococcus aureus Strains on Colombian Dairy Farms.

Microbial ecology [Epub ahead of print].

Staphylococcus aureus is one of the most prevalent pathogens causing bovine mastitis in the world, in part because of its ease of adaptation to various hosts and the environment. This study aimed to determine the prevalence of S. aureus in Colombian dairy farms and its relationship with the causal network of subclinical mastitis. From thirteen dairy farms enrolled, 1288 quarter milk samples (QMS) and 330 teat samples were taken from cows with positive (70.1%) and negative California Mastitis Test (CMT). In addition, 126 samples from the milking parlor environment and 40 from workers (nasal) were collected. On each dairy farm, a survey was conducted, and the milking process was monitored on the day of sampling. S. aureus was identified in 176 samples, i.e., 138 QMS, 20 from teats, 8 from the milking parlor environment, and 10 from workers' nasal swabs. Isolates identified as S. aureus underwent proteomics (clustering of mass spectrum) and molecular (tuf, coa, spa Ig, clfA, and eno genes) analysis. Regarding proteomics results, isolates were distributed into three clusters, each with members from all sources and all farms. Concerning molecular analysis, the virulence-related genes clfA and eno were identified in 41.3% and 37.8% of S. aureus isolates, respectively. We provide evidence on the circulation of S. aureus strains with limited variability among animals, humans, and the environment. The parameters with the lowest compliance in the farms which may be implicated in the transmission of S. aureus are the lack of handwashing and abnormal milk handling.

RevDate: 2023-05-24

Liu B, Wang Y, Zhang H, et al (2023)

The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains.

Microbial ecology [Epub ahead of print].

The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.

RevDate: 2023-05-24

Malesevic M, Stanisavljevic N, Matijasevic D, et al (2023)

Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia.

Microbial ecology [Epub ahead of print].

The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.

RevDate: 2023-05-23

Djotan AKG, Matsushita N, K Fukuda (2023)

Correction to: Paired root-soil samples and metabarcoding reveal taxon-based colonization strategies in arbuscular mycorrhizal fungi communities in Japanese cedar and cypress stands.

RevDate: 2023-05-23

Carr EC, Barton Q, Grambo S, et al (2023)

Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.

G3 (Bethesda, Md.) pii:7176444 [Epub ahead of print].

Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primarily yeast form. These fungi grow in xeric, nutrient deplete environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community is not well understood. We have isolated two novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e., E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin that can potentially provide UV resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.

RevDate: 2023-05-22

Cao Y, Almeida-Silva F, Zhang WP, et al (2023)

Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).

Molecular biology and evolution pii:7175457 [Epub ahead of print].

When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes, and its only congeneric species, P. strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics, and the driving forces underneath the incipient speciation of the two Platycarya lineages.

RevDate: 2023-05-22

Díaz M, Monfort-Lanzas P, Quiroz-Moreno C, et al (2023)

The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.

Frontiers in microbiology, 14:1154815.

A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.

RevDate: 2023-05-22

Wu SY, Ou CC, Lee ML, et al (2023)

Polysaccharide of Ganoderma lucidum Ameliorates Cachectic Myopathy Induced by the Combination Cisplatin plus Docetaxel in Mice.

Microbiology spectrum [Epub ahead of print].

Cachexia is a lethal muscle-wasting syndrome associated with cancer and chemotherapy use. Mounting evidence suggests a correlation between cachexia and intestinal microbiota, but there is presently no effective treatment for cachexia. Whether the Ganoderma lucidum polysaccharide Liz-H exerts protective effects on cachexia and gut microbiota dysbiosis induced by the combination cisplatin plus docetaxel (cisplatin + docetaxel) was investigated. C57BL/6J mice were intraperitoneally injected with cisplatin + docetaxel, with or without oral administration of Liz-H. Body weight, food consumption, complete blood count, blood biochemistry, and muscle atrophy were measured. Next-generation sequencing was also performed to investigate changes to gut microbial ecology. Liz-H administration alleviated the cisplatin + docetaxel-induced weight loss, muscle atrophy, and neutropenia. Furthermore, upregulation of muscle protein degradation-related genes (MuRF-1 and Atrogin-1) and decline of myogenic factors (MyoD and myogenin) after treatment of cisplatin and docetaxel were prevented by Liz-H. Cisplatin and docetaxel treatment resulted in reducing comparative abundances of Ruminococcaceae and Bacteroides, but Liz-H treatment restored these to normal levels. This study indicates that Liz-H is a good chemoprotective reagent for cisplatin + docetaxel-induced cachexia. IMPORTANCE Cachexia is a multifactorial syndrome driven by metabolic dysregulation, anorexia, systemic inflammation, and insulin resistance. Approximately 80% of patients with advanced cancer have cachexia, and cachexia is the cause of death in 30% of cancer patients. Nutritional supplementation has not been shown to reverse cachexia progression. Thus, developing strategies to prevent and/or reverse cachexia is urgent. Polysaccharide is a major biologically active compound in the fungus Ganoderma lucidum. This study is the first to report that G. lucidum polysaccharides could alleviate chemotherapy-induced cachexia via reducing expression of genes that are known to drive muscle wasting, such as MuRF-1 and Atrogin-1. These results suggest that Liz-H is an effective treatment for cisplatin + docetaxel-induced cachexia.

RevDate: 2023-05-21

Liu Y, Wang H, Qian X, et al (2023)

Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.

Microbiome, 11(1):109.

BACKGROUND: Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.

RESULTS: Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.

CONCLUSIONS: Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.

RevDate: 2023-05-21

Yokoyama D, J Kikuchia (2023)

Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.

Environmental research pii:S0013-9351(23)01003-4 [Epub ahead of print].

Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.

RevDate: 2023-05-20

Kostešić E, Mitrović M, Kajan K, et al (2023)

Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia.

Microbial ecology [Epub ahead of print].

Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.

RevDate: 2023-05-19

Jin Z, Shen M, Wang L, et al (2023)

Antibacterial and immunoregulatory activity of an antimicrobial peptide hepcidin in loach (Misgurnus anguillicaudatus).

International journal of biological macromolecules pii:S0141-8130(23)01727-0 [Epub ahead of print].

Antimicrobial peptides (AMPs) are members of humoral immunity and particpate in resisting microbial invasion. In this study, an AMP gene hepcidin was obtained from the oriental loach Misgurnus anguillicaudatus and named Ma-Hep. This Ma-Hep encodes a peptide of 90 amino acids, with a predicted active peptide segment (Ma-sHep) of 25 amino acids at C terminus. Stimulation by a bacterial pathogen Aeromonas hydrophila resulted in significant up-regulation of Ma-Hep transcripts in loach midgut, head kidney, and gill. Ma-Hep and Ma-sHep proteins were expressed in Pichia pastoris and their antibacterial activity was examined. Results showed that Ma-sHep possessed stronger antibacterial activity against various Gram-positive and Gram-negative bacteria, compared to Ma-Hep. Scanning electron microscopy showed that Ma-sHep might kill bacteria by destroying bacterial cell membranes. Moreover, we found that Ma-sHep had an inhibitory effect on blood cell apoptosis induced by A. hydrophila and facilitated the bacterial phagocytosis and clearance in loach. Histopathological analysis indicated Ma-sHep could protect liver and gut of loach from bacterial infection. Ma-sHep has high thermal stability and PH stability, which is conducive to further feed addition. Feed supplemented with Ma-sHep expressing yeast improved the intestinal flora of loach by increasing the dominant bacteria and decreasing the harmful bacteria. Feed supplemented with Ma-sHep expressing yeast also regulated the expression of inflammatory related factors in various tissues of loach and reduced the mortality of loach upon bacterial infection. These findings show that the antibacterial peptide Ma-sHep is involved in the antibacterial defense of loach and can be used as a candidate for new antimicrobial agents in aquaculture.

RevDate: 2023-05-19

Rasmussen KL, Stamps BW, Vanzin GF, et al (2023)

Spatial and temporal dynamics at an actively silicifying hydrothermal system.

Frontiers in microbiology, 14:1172798.

Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.

RevDate: 2023-05-19

Van de Walle A, Kim M, Alam MK, et al (2023)

Greywater reuse as a key enabler for improving urban wastewater management.

Environmental science and ecotechnology, 16:100277 pii:S2666-4984(23)00042-X.

Sustainable water management is essential to guaranteeing access to safe water and addressing the challenges posed by climate change, urbanization, and population growth. In a typical household, greywater, which includes everything but toilet waste, constitutes 50-80% of daily wastewater generation and is characterized by low organic strength and high volume. This can be an issue for large urban wastewater treatment plants designed for high-strength operations. Segregation of greywater at the source for decentralized wastewater treatment is therefore necessary for its proper management using separate treatment strategies. Greywater reuse may thus lead to increased resilience and adaptability of local water systems, reduction in transport costs, and achievement of fit-for-purpose reuse. After covering greywater characteristics, we present an overview of existing and upcoming technologies for greywater treatment. Biological treatment technologies, such as nature-based technologies, biofilm technologies, and membrane bioreactors (MBR), conjugate with physicochemical treatment methods, such as membrane filtration, sorption and ion exchange technologies, and ultraviolet (UV) disinfection, may be able to produce treated water within the allowable parameters for reuse. We also provide a novel way to tackle challenges like the demographic variance of greywater quality, lack of a legal framework for greywater management, monitoring and control systems, and the consumer perspective on greywater reuse. Finally, benefits, such as the potential water and energy savings and sustainable future of greywater reuse in an urban context, are discussed.

RevDate: 2023-05-19

Rattray JB, Kramer PJ, Gurney J, et al (2023)

The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts.

Microbiology (Reading, England), 169(5):.

Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.

RevDate: 2023-05-18

He Y, Xu M, Lu S, et al (2023)

Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice.

Microbial pathogenesis pii:S0882-4010(23)00192-4 [Epub ahead of print].

Gastrointestinal (GI) disease is a common digestive tract disease effects health of millions of human globally each year, thus the role of intestinal microflora had been emphasized. Seaweed polysaccharides featured a wide range of pharmacological activities, such as antioxidant activity and pharmacological action, but whether they can alleviate the dysbiosis of gut microbial ecology caused by lipopolysaccharide (LPS) exposure has not been well conducted. In this study, we investigated the effects of different concentration of seaweed polysaccharides on LPS-induced intestinal disorder by using microscope and 16S rRNA high-throughput sequencing. Histopathological results indicated that the intestinal structure in the LPS-induced group was damaged. Furthermore, LPS exposure not only reduced the intestinal microbial diversity in mice but also induced momentous transformation in its composition, including a significantly increased in some pathogenic bacteria (Helicobacter, Citrobacter and Mucispirillum) and decreased in several beneficial bacteria (Firmicutes, Lactobacillus, Akkermansia and Parabacteroides). Nonetheless, seaweed polysaccharide administration could recover the gut microbial dysbiosis and the loss of gut microbial diversity induced by LPS exposure. In summary, seaweed polysaccharides were effective against LPS-induced intestinal damage in mice via the modulation of intestinal microecology.

RevDate: 2023-05-18

Pascual J, Lepleux C, Methner A, et al (2023)

Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater.

International journal of systematic and evolutionary microbiology, 73(5):.

A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2[T], was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2[T] was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2[T] was closely related to Arcobacter lekithochrous LFT 1.7[T] and Arcobacter caeni RW17-10[T](95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2[T] was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2[T] represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2[T] as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2[T] (DSM 29169[T]=KCTC 52423[T]).

RevDate: 2023-05-17

Farrell ML, Chueiri A, O'Connor L, et al (2023)

Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms.

The Science of the total environment pii:S0048-9697(23)02822-X [Epub ahead of print].

Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) in recreational water users (WU) and matched controls. A total of 411 adult participants (199 WU, 212 controls) submitted at least one faecal sample between September 2020 - October 2021. In total, 80 Enterobacterales were isolated from 73 participants. ESBL-PE were detected in 29 (7.1 %) participants (7 WU, 22 controls), and CRE were detected in nine (2.2 %) participants (4 WU, 5 controls). No carbapenemase-producing Enterobacterales (CPE) were detected. WU were significantly less likely to harbour ESBL-PE than controls (risk ratio = 0.34, 95 % CI 0.148 to 0.776, χ[2] 7.37, p = 0.007). This study demonstrates the occurrence of ESBL-PE and CRE in healthy participants in Ireland. Recreational exposure to bathing water in Ireland was associated with a decreased prevalence of colonisation with ESBL-PE and CRE.

RevDate: 2023-05-17

Lin B, Tan B, Zhang Q, et al (2023)

Unraveling the nexus of Cr (Ⅵ), Aniline, and Microbial Ecology on aniline-degrading biosystem: Removal efficiency, sludge type, microbial ecology.

Bioresource technology pii:S0960-8524(23)00611-9 [Epub ahead of print].

In order to explore the stress principle of Cr (Ⅵ) on aniline biodegradation system, a control group and experimental groups with the concentration of Cr (Ⅵ) at 2, 5, 8 mg/L were set up. The results demonstrated that Cr (Ⅵ) had minimal effects on the degradation efficiency of aniline but significantly inhibited nitrogen removal function. When Cr (Ⅵ) concentration was below 5 mg/L, the nitrification performance recovered spontaneously, while denitrification performance was severely impaired. Furthermore, the secretion of extracellular polymeric substances (EPS) and its fluorescence substance concentration were strongly inhibited with increasing Cr (Ⅵ) concentration. High-throughput sequencing revealed that the experimental groups were enriched with Leucobacter and Cr (Ⅵ)-reducing bacteria, but the abundance of nitrifiers and denitrifiers was significantly decreased compared to the control group. Overall, the effects of Cr (Ⅵ) stress at different concentrations on nitrogen removal performance were more significant than those on aniline degradation.

RevDate: 2023-05-17

Xu Y, Teng Y, Wang X, et al (2023)

Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.

Environment international, 176:107962 pii:S0160-4120(23)00235-0 [Epub ahead of print].

Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of [13]C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.

RevDate: 2023-05-16

Delbaere K, Roegiers I, Bron A, et al (2023)

The small intestine: dining table of host-microbiota meetings.

FEMS microbiology reviews pii:7165754 [Epub ahead of print].

Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.

RevDate: 2023-05-16

Zhao J, Fan D, Guo W, et al (2023)

Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands.

Microbial ecology [Epub ahead of print].

Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.

RevDate: 2023-05-16

Yang Y, Suyamud B, Liang S, et al (2023)

Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere.

Environmental microbiology [Epub ahead of print].

The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.

RevDate: 2023-05-15

Moeller FU, Herbold CW, Schintlmeister A, et al (2023)

Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.

The ISME journal [Epub ahead of print].

Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

RevDate: 2023-05-15

Harder CB, Hesling E, Botnen SS, et al (2023)

Mycena species can be opportunist-generalist plant root invaders.

Environmental microbiology [Epub ahead of print].

Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of [13] C/[15] N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published [13] C/[15] N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.

RevDate: 2023-05-15

Liao Q, Ye Y, Li Z, et al (2023)

Prediction of miRNA-disease associations in microbes based on graph convolutional networks and autoencoders.

Frontiers in microbiology, 14:1170559.

MicroRNAs (miRNAs) are short RNA molecular fragments that regulate gene expression by targeting and inhibiting the expression of specific RNAs. Due to the fact that microRNAs affect many diseases in microbial ecology, it is necessary to predict microRNAs' association with diseases at the microbial level. To this end, we propose a novel model, termed as GCNA-MDA, where dual-autoencoder and graph convolutional network (GCN) are integrated to predict miRNA-disease association. The proposed method leverages autoencoders to extract robust representations of miRNAs and diseases and meantime exploits GCN to capture the topological information of miRNA-disease networks. To alleviate the impact of insufficient information for the original data, the association similarity and feature similarity data are combined to calculate a more complete initial basic vector of nodes. The experimental results on the benchmark datasets demonstrate that compared with the existing representative methods, the proposed method has achieved the superior performance and its precision reaches up to 0.8982. These results demonstrate that the proposed method can serve as a tool for exploring miRNA-disease associations in microbial environments.

RevDate: 2023-05-15

Woksepp H, Camara F, J Bonnedahl (2023)

High prevalence of blaCTX-M-15 type extended-spectrum beta-lactamases in Gambian hooded vultures (Necrosyrtes monachus): A threatened species with substantial human interaction.

MicrobiologyOpen, 12(2):e1349.

One hundred fecal samples from hooded vultures in the Gambia (Banjul area) were investigated for the presence of bacteria with extended-spectrum cephalosporin- (ESBL/AmpC), carbapenemases, and colistin resistance. No Enterobacteriales carrying carbapenemases or resistance against colistin were detected. Fifty-four ESBL-producing Escherichia coli and five ESBL-producing Klebsiella pneumoniae isolates were identified in 52 of the samples, of which 52 E. coli and 4 K. pneumoniae yielded passed sequencing results. Fifty of the E. coli had ESBL phenotype and genotype harboring blaCTX-M genes, of which 88.5% (n = 46) were the blaCTX-M-15 gene, commonly found on the African continent. Furthermore, the genetic context around blaCTX-M-15 was similar between isolates, being colocalized with ISKpn19. In contrast, cgMLST analysis of the E. coli harboring ESBL genes revealed a genetic distribution over a large fraction of the currently known existing E. coli populations in the Gambia. Hooded vultures in the Gambia thus have a high ESBL E. coli-prevalence (>50%) with low diversity regarding key resistance genes. Furthermore, given the urban presence and frequent interactions between hooded vultures and humans, data from this study implies hooded vultures as potential vectors contributing to the further dissemination of antibiotic-resistance genes.

RevDate: 2023-05-15

Li J, Liu T, McIlroy SJ, et al (2023)

Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings.

ISME communications, 3(1):39.

The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m[3]/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.

RevDate: 2023-05-15

Sänger PA, Knüpfer M, Kegel M, et al (2023)

Regulation and Functionality of a Holin/Endolysin Pair Involved in Killing of Galleria mellonella and Caenorhabditis elegans by Yersinia enterocolitica.

Applied and environmental microbiology [Epub ahead of print].

The insecticidal toxin complex (Tc) proteins are produced by several insect-associated bacteria, including Yersinia enterocolitica strain W22703, which oscillates between two distinct pathogenicity phases in invertebrates and humans. The mechanism by which this high-molecular-weight toxin is released into the extracellular surrounding, however, has not been deciphered. In this study, we investigated the regulation and functionality of a phage-related holin/endolysin (HE) cassette located within the insecticidal pathogenicity island Tc-PAIYe of W22703. Using the Galleria mellonella infection model and luciferase reporter fusions, we revealed that quorum sensing contributes to the insecticidal activity of W22703 upon influencing the transcription of tcaR2, which encodes an activator of the tc and HE genes. In contrast, a lack of the Yersinia modulator, YmoA, stimulated HE gene transcription, and mutant W22703 ΔymoA exhibited a stronger toxicity toward insect larvae than did W22703. A luciferase reporter fusion demonstrated transcriptional activation of the HE cassette in vivo, and a significantly larger extracellular amount of subunit TcaA was found in W22703 ΔymoA relative to its ΔHE mutant. Using competitive growth assays, we demonstrated that at least in vitro, the TcaA release upon HE activity is not mediated by cell lysis of a significant part of the population. Oral infection of Caenorhabditis elegans with a HE deletion mutant attenuated the nematocidal activity of the wild type, similar to the case with a mutant lacking a Tc subunit. We conclude that the dual holin/endolysin cassette of yersiniae is a novel example of a phage-related function adapted for the release of a bacterial toxin. IMPORTANCE Members of the genus Yersinia cause gastroenteritis in humans but also exhibit toxicity toward invertebrates. A virulence factor required for this environmental life cycle stage is the multisubunit toxin complex (Tc), which is distinct from the insecticidal toxin of Bacillus thuringiensis and has the potential to be used in pest control. The mechanism by which this high-molecular-weight Tc is secreted from bacterial cells has not been uncovered. Here, we show that a highly conserved phage-related holin/endolysin pair, which is encoded by the genes holY and elyY located between the Tc subunit genes, is essential for the insecticidal activity of Y. enterocolitica and that its activation increases the amount of Tc subunits in the supernatant. Thus, the dual holY-elyY cassette of Y. enterocolitica constitutes a new example for a type 10 secretion system to release bacterial toxins.

RevDate: 2023-05-14

Refisch A, Sen ZD, Klassert TE, et al (2023)

Microbiome and immuno-metabolic dysregulation in patients with major depressive disorder with atypical clinical presentation.

Neuropharmacology pii:S0028-3908(23)00158-2 [Epub ahead of print].

Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression disorder (MDD), suggesting different manifestations of underlying pathophysiological mechanisms. Poorer treatment outcomes to first-line antidepressants were reported in MDD patients endorsing an "atypical" symptom profile that is characterized by preserved reactivity in mood, increased appetite, hypersomnia, a heavy sensation in the limbs, and interpersonal rejection sensitivity. In recent years, evidence has emerged that immunometabolic biological dysregulation is an important underlying pathophysiological mechanism in depression, which maps more consistently to atypical features. In the last few years human microbial residents have emerged as a key influencing variable associated with immunometabolic dysregulations in depression. The microbiome plays a critical role in the training and development of key components of the host's innate and adaptive immune systems, while the immune system orchestrates the maintenance of key features of the host-microbe symbiosis. Moreover, by being a metabolically active ecosystem commensal microbes may have a huge impact on signaling pathways, involved in underlying mechanisms leading to atypical depressive symptoms. In this review, we discuss the interplay between the microbiome and immunometabolic imbalance in the context of atypical depressive symptoms. Although research in this field is in its infancy, targeting biological determinants in more homogeneous clinical presentations of MDD may offer new avenues for the development of novel therapeutic strategies for treatment-resistant depression.

RevDate: 2023-05-14

Huang W, Li S, Li S, et al (2023)

Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian.

Frontiers in microbiology, 14:1151768.

The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.

RevDate: 2023-05-13

Nandni , Rani S, Chopra G, et al (2023)

Deciphering the Potential of Sulphur-Oxidizing Bacteria for Sulphate Production Correlating with pH Change.

Microbial ecology [Epub ahead of print].

Sulphur, available in the form of sulphate, is one of the essential nutrients that is required by plants. Bacteria capable of oxidizing reduced forms of sulphur to sulphate play an important role in sulphur nutrition for plants. The present study was conducted to isolate, screen, and characterize sulphur-oxidizing bacteria from different soil samples collected from mustard rhizosphere and fly ash mixed soil. A total of 33 sulphur-oxidizing bacterial isolates (HMSOB1-33) were retrieved from soil and further screened for sulphur-oxidizing ability. Maximum solubilization index (3.76), pH reduction (3.93), and sulphate production (173.61 µg/ml) were observed for the isolate HMSOB2 which on the basis of 16S rDNA sequencing was identified as Pantoea dispersa with sequence similarity 98.22%. Four other selected bacterial isolates were identified as Bacillus megaterium, Bacillus tropicus, Bacillus velezensis, and Bacillus cereus. Sulphate solubilization index (SSI) correlated positively (r = 0.91) with sulphate production; however, pH showed negative correlation (r = - 0.82) with SSI as well as sulphate production after 120 h of incubation. These promising bacterial isolates could be further explored as bioinoculant after assessing plant growth traits.

RevDate: 2023-05-13

Bier RL, Mosher JJ, Kaplan LA, et al (2023)

Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America.

Environmental microbiology [Epub ahead of print].

A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.

RevDate: 2023-05-12

Pan X, Raaijmakers JM, VJ Carrión (2023)

Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning.

Trends in microbiology pii:S0966-842X(23)00107-5 [Epub ahead of print].

Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.

RevDate: 2023-05-12

Krebs NF, Belfort MB, Meier PP, et al (2023)

Infant factors that impact the ecology of human milk secretion and composition-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 3.

The American journal of clinical nutrition, 117 Suppl 1:S43-S60.

Infants drive many lactation processes and contribute to the changing composition of human milk through multiple mechanisms. This review addresses the major topics of milk removal; chemosensory ecology for the parent-infant dyad; the infant's inputs into the composition of the human milk microbiome; and the impact of disruptions in gestation on the ecology of fetal and infant phenotypes, milk composition, and lactation. Milk removal, which is essential for adequate infant intake and continued milk synthesis through multiple hormonal and autocrine/paracrine mechanisms, should be effective, efficient, and comfortable for both the lactating parent and the infant. All 3 components should be included in the evaluation of milk removal. Breastmilk "bridges" flavor experiences in utero with postweaning foods, and the flavors become familiar and preferred. Infants can detect flavor changes in human milk resulting from parental lifestyle choices, including recreational drug use, and early experiences with the sensory properties of these recreational drugs impact subsequent behavioral responses. Interactions between the infant's own developing microbiome, that of the milk, and the multiple environmental factors that are drivers-both modifiable and nonmodifiable-in the microbial ecology of human milk are explored. Disruptions in gestation, especially preterm birth and fetal growth restriction or excess, impact the milk composition and lactation processes such as the timing of secretory activation, adequacy of milk volume and milk removal, and duration of lactation. Research gaps are identified in each of these areas. To assure a sustained and robust breastfeeding ecology, these myriad infant inputs must be systematically considered.

RevDate: 2023-05-11

Conners R, León-Quezada RI, McLaren M, et al (2023)

Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.

Nature communications, 14(1):2724.

Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.

RevDate: 2023-05-11

Weber M, Göpfert B, von Wezyk S, et al (2023)

Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.

Microbial ecology [Epub ahead of print].

The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.

RevDate: 2023-05-11

Zeng Z, Yang Z, Yang A, et al (2023)

Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants.

Microbial ecology [Epub ahead of print].

To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.

RevDate: 2023-05-10

Cai P, Zhang W, Duan X, et al (2023)

First Report of Powdery Mildew Caused by Golovinomyces bolayi on Veronica persica in Central China.

Plant disease [Epub ahead of print].

Veronica persica, Persian speedwell, is a flowering plant belonging to the family Plantaginaceae. Due to its showy flowers, this plant is widely planted in many home gardens, city parks and universities in China. From April to June 2021, signs and symptoms of powdery mildew were found on leaves of V. persica growing on the campus of Henan Normal University, Henan Province, China. Signs initially appeared as thin white colonies and subsequently white powdery masses were abundant on the adaxial and abaxial surfaces of leaves and covered up to 99 % of the leaf area. The infected leaves showed chlorotic, deformed or senescence features. About 150 V. persica plants were monitored and more than 90 % of the plants showed these signs and symptoms. Conidiophores (n = 20) were 108 to 220 × 10 to 13 μm and composed of foot cells, followed by short cells and conidia. Conidia were hyaline, doliiform-subcylindrical shaped, 21 to 37 × 15 to 22 μm, and showed distinct fibrosin bodies. Conidial germ tubes were produced at the perihilar position. No chasmothecia were observed. The observed morphological characteristics were consistent with those of previously documented Golovinomyces bolayi (Braun and Cook 2012). To further confirm the powdery mildew fungus, structures of the pathogen were harvested and total genomic DNA was isolated using the method previously described by Zhu et al. (2019, 2021). Using the primers ITS1/ITS4, the internal transcribed spacer (ITS) region of rDNA was amplified (White et al. 1990) and the amplicon was sequenced. The resulting sequence was deposited into GenBank under Accession No. MZ343575 and was 100 % identical (592/592 bp) to G. bolayi on Kalanchoe blossfeldiana (LC417096) (Braun et al. 2019). The additional phylogenetic analysis clearly illustrated that the identified fungus and G. bolayi were clustered in the same branch (Zhu et al. 2022a; Zhu et al. 2022b). To test pathogenicity, healthy V. persica plants were collected from the campus of Henan Normal University and leaf surfaces of three plants were inoculated by dusting fungal conidia from mildew-infested leaves using pressurized air. Three plants without inoculation served as a control. The spore-treated and non-treated plants were separately placed in two growth chambers (temperature, 18℃; humidity, 60%; light/dark, 16h/8h). Seven- to eight-days post-inoculation, pathogen signs were noticeable on inoculated plants, whereas control plants remained healthy. Similar results were obtained by conducting the pathogenicity assays twice. Therefore, based on the analysis, G. bolayi was identified and confirmed as the causal agent of the powdery mildew. This pathogen has been reported on V. persica in Iran (Golmohammadi et al. 2019). However, to our best knowledge, there is no report concerning the powdery mildew caused by G. bolayi on V. persica in China. Recently, G. bolayi was segregated from species clades of G. orontii complex (Braun et al. 2019). Our record of the molecular characterization of G. bolayi will support the further phylogeny and taxonomy analysis of the G. orontii complex. The sudden outbreak of powdery mildew caused by G. bolayi on V. persica may detract from plant health and ornamental value. The identification and confirmation of this disease expands the understanding of this causal agent and will offer support for future powdery mildew control.

RevDate: 2023-05-10

Cruz-Paredes C, Tájmel D, J Rousk (2023)

Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers.

Applied and environmental microbiology [Epub ahead of print].

Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.

RevDate: 2023-05-10

Talukdar D, Bandopadhyay P, Ray Y, et al (2023)

Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19.

Gut pathogens, 15(1):22.

BACKGROUND: Severe coronavirus disease 2019 (COVID-19) is associated with systemic hyper-inflammation. An adaptive interaction between gut microbiota and host immune systems is important for intestinal homeostasis and systemic immune regulation. The association of gut microbial composition and functions with COVID-19 disease severity is sparse, especially in India. We analysed faecal microbial diversity and abundances in a cohort of Indian COVID-19 patients to identify key signatures in the gut microbial ecology in patients with severe COVID-19 disease as well as in response to different therapies. The composition of the gut microbiome was characterized using 16Sr RNA gene sequences of genomic DNA extracted from faecal samples of 52 COVID-19 patients. Metabolic pathways across the groups were predicted using PICRUSt2. All statistical analyses were done using Vegan in the R environment. Plasma cytokine abundance at recruitment was measured in a multiplex assay.

RESULTS: The gut microbiome composition of mild and severe patients was found to be significantly different. Immunomodulatory commensals, viz. Lachnospiraceae family members and Bifidobacteria producing butyrate and short-chain fatty acids (SCFAs), were under represented in patients with severe COVID-19, with an increased abundance of opportunistic pathogens like Eggerthella. The higher abundance of Lachnoclostridium in severe disease was reduced in response to convalescent plasma therapy. Specific microbial genera showed distinctive trends in enriched metabolic pathways, strong correlations with blood plasma cytokine levels, and associative link to disease outcomes.

CONCLUSION: Our study indicates that, along with SARS-CoV-2, a dysbiotic gut microbial community may also play an important role in COVID-19 severity through modulation of host immune responses.

RevDate: 2023-05-09

Bi S, Lai H, Guo D, et al (2023)

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats.

BMC ecology and evolution, 23(1):16.

BACKGROUND: Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.

RESULTS: The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.

CONCLUSIONS: This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

RevDate: 2023-05-08

Banaszkiewicz S, Tabiś A, Wałecki B, et al (2023)

spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar.

Microbial ecology [Epub ahead of print].

Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.

RevDate: 2023-05-08

Gomez-Alvarez V, Siponen S, Kauppinen A, et al (2023)

A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.

Water research, 229:119495.

The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.

RevDate: 2023-05-08

Pan Q, Shikano I, Liu TX, et al (2023)

Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.

Microbial ecology [Epub ahead of print].

Insect-associated bacteria can mediate the intersection of insect and plant immunity. In this study, we aimed to evaluate the effects of single isolates or communities of gut-associated bacteria of Helicoverpa zea larvae on herbivore-induced defenses in tomato. We first identified bacterial isolates from the regurgitant of field-collected H. zea larvae by using a culture-dependent method and 16S rRNA gene sequencing. We identified 11 isolates belonging to the families Enterobacteriaceae, Streptococcaceae, Yersiniaceae, Erwiniaceae, and unclassified Enterobacterales. Seven different bacterial isolates, namely Enterobacteriaceae-1, Lactococcus sp., Klebsiella sp. 1, Klebsiella sp. 3, Enterobacterales, Enterobacteriaceae-2, and Pantoea sp., were selected based on their phylogenetic relationships to test their impacts on insect-induced plant defenses. We found that the laboratory population of H. zea larvae inoculated with individual isolates did not induce plant anti-herbivore defenses, whereas larvae inoculated with a bacterial community (combination of the 7 bacterial isolates) triggered increased polyphenol oxidase (PPO) activity in tomato, leading to retarded larval development. Additionally, field-collected H. zea larvae with an unaltered bacterial community in their gut stimulated higher plant defenses than the larvae with a reduced gut microbial community. In summary, our findings highlight the importance of the gut microbial community in mediating interactions between herbivores and their host plants.

RevDate: 2023-05-08

Rasmussen TS, Mentzel CMJ, Danielsen MR, et al (2023)

Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice.

Gut microbes, 15(1):2208504.

Probiotics are intended to improve gastrointestinal health when consumed. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome. Here, we investigate the use of fecal virome transplantation (FVT, sterile filtrated feces) as a mean to alter the gut microbiome composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs from 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, LGG+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT donor material originated from mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p < 0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of propagating the existing commensal "probiotics" that have already permanently colonized the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p < 0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating interactions between the gut microbiome and fertility.

RevDate: 2023-05-07

Hu D, Li S, Liu X, et al (2023)

Kinetic model derivation for design, building and operation of solid waste treatment unit based on system dynamics and computer simulation.

Waste management (New York, N.Y.), 166:58-69 pii:S0956-053X(23)00328-8 [Epub ahead of print].

Solid waste disposal is significantly important to maintaining normal operation of both natural and artificial ecosystems. In this study, a kinetic model of solid waste treatment unit (SWTU) was upfront developed based on microbial ecology, system dynamics, cybernetics and digital simulation, which accurately described the relationships and interactions between solid waste decomposition (SWD) processes and biotic/abiotic factors. Then a specific SWTU prototype was designed and built from this kinetic model. A 370-day experiment demonstrated that SWTU maintained normal operation with robust stability and desired dynamic behaviors, and effectively disposed the solid waste. Therefore, this kinetic model was highly valid due to its high structural and behavioral similarity with the prototype. This research could lay a strong theoretical foundation for further closed-loop control as well as optimization of SWTU, and provide scientific guidance to environmental management as well as sustainable development.

RevDate: 2023-05-07

Pjevac P, Bartosik T, Schneider S, et al (2023)

Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples.

RevDate: 2023-05-06

Kharshandi F, H Kayang (2023)

Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric.

Archives of microbiology, 205(6):221.

The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.

RevDate: 2023-05-06

Li Y, Kuramae EE, Nasir F, et al (2023)

Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting: Construction the complex co-degradation system.

Bioresource technology pii:S0960-8524(23)00558-8 [Epub ahead of print].

To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.

RevDate: 2023-05-06

Burgess WL, CD Bishop (2023)

Bacterial Diversity in Egg Capsular Fluid of the Spotted Salamander Ambystoma maculatum Decreases with Embryonic Development.

Microbial ecology [Epub ahead of print].

Egg capsules within egg masses of the spotted salamander Ambystoma maculatum host a symbiosis with the unicellular green alga Oophila amblystomatis. However, this alga is not the only microbe to inhabit those capsules, and the significance of these additional taxa for the symbiosis is unknown. Spatial and temporal patterns of bacterial diversity in egg capsules of A. maculatum have recently begun to be characterized, but patterns of bacterial diversity as a function of embryonic development are unknown. We sampled fluid from individual capsules in egg masses over a large range of host embryonic development in 2019 and 2020. We used 16S rRNA gene amplicon sequencing to examine how diversity and relative abundance of bacteria changed with embryonic development. In general, bacterial diversity decreased as embryos developed; significant differences were observed (depending on the metric) by embryonic development, pond, and year, and there were interaction effects. The function of bacteria in what is thought of as a bipartite symbiosis calls for further research.

RevDate: 2023-05-06

Gazulla CR, Cabello AM, Sánchez P, et al (2023)

A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs.

Microbial ecology [Epub ahead of print].

Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.

RevDate: 2023-05-05

Todorović I, Abrouk D, Kyselková M, et al (2023)

Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov.

Systematic and applied microbiology, 46(4):126425 pii:S0723-2020(23)00034-6 [Epub ahead of print].

Pseudomonas strains IT-194P, IT-215P, IT-P366[T] and IT-P374[T] were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366[T] and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611[T], and another species containing strains IT-P374[T] and IT-215P and clustering next to P. koreensis LMG21318[T]. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366[T] (compared with P. umsongensis DSM16611[T]) and IT-P374[T] (compared with P. koreensis LMG21318[T]). Unlike P. umsongensis DSM16611[T], strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318[T], strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366[T] (=CFBP 9060 [T] = LMG 32732 [T] = EML 1791 [T]) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374[T] (=CFBP 9061 [T] = LMG 32734 [T] = EML 1792 [T]). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).

RevDate: 2023-05-05

Fiskal A, Shuster J, Fischer S, et al (2023)

Microbially influenced corrosion and rust tubercle formation on sheet piles in freshwater systems.

Environmental microbiology [Epub ahead of print].

The extent of how complex natural microbial communities contribute to metal corrosion is still not fully resolved, especially not for freshwater environments. In order to elucidate the key processes, we investigated rust tubercles forming massively on sheet piles along the river Havel (Germany) applying a complementary set of techniques. In-situ microsensor profiling revealed steep gradients of O2 , redox potential and pH within the tubercle. Micro-computed tomography and scanning electron microscopy showed a multi-layered inner structure with chambers and channels and various organisms embedded in the mineral matrix. Using Mössbauer spectroscopy we identified typical corrosion products including electrically conductive iron (Fe) minerals. Determination of bacterial gene copy numbers and sequencing of 16S rRNA and 18S rRNA amplicons supported a densely populated tubercle matrix with a phylogenetically and metabolically diverse microbial community. Based on our results and previous models of physic(electro)chemical reactions, we propose here a comprehensive concept of tubercle formation highlighting the crucial reactions and microorganisms involved (such as phototrophs, fermenting bacteria, dissimilatory sulphate and Fe(III) reducers) in metal corrosion in freshwaters.

RevDate: 2023-05-04

Paul P, Sarkar S, Dastidar DG, et al (2023)

1, 4-naphthoquinone efficiently facilitates the disintegration of pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.

Folia microbiologica [Epub ahead of print].

1, 4-naphthoquinone, a plant-based quinone derivative, has gained much attention for its effectiveness against several biofilm-linked diseases. The biofilm inhibitory effect of 1, 4-naphthoquinone against Staphylococcus aureus has already been reported in our previous study. We observed that the extracellular DNA (eDNA) could play an important role in holding the structural integrity of the biofilm. Hence, in this study, efforts have been directed to examine the possible interactions between 1, 4-naphthoquinone and DNA. An in silico analysis indicated that 1, 4-naphthoquinone could interact with DNA through intercalation. To validate the same, UV-Vis spectrophotometric analysis was performed in which a hypochromic shift was observed when the said molecule was titrated with calf-thymus DNA (CT-DNA). Thermal denaturation studies revealed a change of 8℃ in the melting temperature (Tm) of CT-DNA when complexed with 1, 4-naphthoquinone. The isothermal calorimetric titration (ITC) assay revealed a spontaneous intercalation between CT-DNA and 1, 4-naphthoquinone with a binding constant of 0.95 ± 0.12 × 10[8]. Furthermore, DNA was run through an agarose gel electrophoresis with a fixed concentration of ethidium bromide and increasing concentrations of 1, 4-naphthoquinone. The result showed that the intensity of ethidium bromide-stained DNA got reduced concomitantly with the gradual increase of 1, 4-naphthoquinone suggesting its intercalating nature. To gain further confidence, the pre-existing biofilm was challenged with ethidium bromide wherein we observed that it could also show biofilm disintegration. Therefore, the results suggested that 1, 4-naphthoquinone could exhibit disintegration of the pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.

RevDate: 2023-05-04

Mukorako P, St-Pierre DH, Flamand N, et al (2023)

Hypoabsorptive surgeries cause limb-dependent changes in the gut endocannabinoidome and microbiome in association with beneficial metabolic effects.

International journal of obesity (2005) [Epub ahead of print].

OBJECTIVE: To determine whether the metabolic benefits of hypoabsorptive surgeries are associated with changes in the gut endocannabinoidome (eCBome) and microbiome.

METHODS: Biliopancreatic diversion with duodenal switch (BPD-DS) and single anastomosis duodeno-ileal bypass with sleeve gastrectomy (SADI-S) were performed in diet-induced obese (DIO) male Wistar rats. Control groups fed a high-fat diet (HF) included sham-operated (SHAM HF) and SHAM HF-pair-weighed to BPD-DS (SHAM HF-PW). Body weight, fat mass gain, fecal energy loss, HOMA-IR, and gut-secreted hormone levels were measured. The levels of eCBome lipid mediators and prostaglandins were quantified in different intestinal segments by LC-MS/MS, while expression levels of genes encoding eCBome metabolic enzymes and receptors were determined by RT-qPCR. Metataxonomic (16S rRNA) analysis was performed on residual distal jejunum, proximal jejunum, and ileum contents.

RESULTS: BPD-DS and SADI-S reduced fat gain and HOMA-IR, while increasing glucagon-like peptide-1 (GLP-1) and peptide tyrosine tyrosine (PYY) levels in HF-fed rats. Both surgeries induced potent limb-dependent alterations in eCBome mediators and in gut microbial ecology. In response to BPD-DS and SADI-S, changes in gut microbiota were significantly correlated with those of eCBome mediators. Principal component analyses revealed connections between PYY, N-oleoylethanolamine (OEA), N-linoleoylethanolamine (LEA), Clostridium, and Enterobacteriaceae_g_2 in the proximal and distal jejunum and in the ileum.

CONCLUSIONS: BPD-DS and SADI-S caused limb-dependent changes in the gut eCBome and microbiome. The present results indicate that these variables could significantly influence the beneficial metabolic outcome of hypoabsorptive bariatric surgeries.

RevDate: 2023-05-04

Sorouri B, Rodriguez CI, Gaut BS, et al (2023)

Variation in Sphingomonas traits across habitats and phylogenetic clades.

Frontiers in microbiology, 14:1146165.

Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.

RevDate: 2023-05-04

Yin H, Zhao M, Pan G, et al (2023)

Effects of Bacillus subtilis or Lentilactobacillus buchneri on aerobic stability, and the microbial community in aerobic exposure of whole plant corn silage.

Frontiers in microbiology, 14:1177031.

This study aimed to evaluate the effects of Bacillus subtilis or Lentilactobacillus buchneri on the fermentation quality, aerobic stability, and bacterial and fungal communities of whole plant corn silage during aerobic exposure. Whole plant corn was harvested at the wax maturity stage, which chopped to a length of approximately 1 cm, and treated with the following: distilled sterile water control, 2.0 × 10[5] CFU/g of Lentilactobacillus buchneri (LB) or 2.0 × 10[5] CFU/g of Bacillus subtilis (BS) for 42 days silage. Then, the samples were exposed to air (23-28[°]C) after opening and sampled at 0, 18 and 60 h, to investigate fermentation quality, bacterial and fungal communities, and aerobic stability. Inoculation with LB or BS increased the pH value, acetic acid, and ammonia nitrogen content of silage (P < 0.05), but it was still far below the threshold of inferior silage, the yield of ethanol was reduced (P < 0.05), and satisfactory fermentation quality was achieved. With the extension of the aerobic exposure time, inoculation with LB or BS prolonged the aerobic stabilization time of silage, attenuated the trend of pH increase during aerobic exposure, and increased the residues of lactic acid and acetic acid. The bacterial and fungal alpha diversity indices gradually declined, and the relative abundance of Basidiomycota and Kazachstania gradually increased. The relative abundance of Weissella and unclassified_f_Enterobacteria was higher and the relative abundance of Kazachstania was lower after inoculation with BS compared to the CK group. According to the correlation analysis, Bacillus and Kazachstania are bacteria and fungi that are more closely related to aerobic spoilage and inoculation with LB or BS could inhibit spoilage. The FUNGuild predictive analysis indicated that the higher relative abundance of fungal parasite-undefined saprotroph in the LB or BS groups at AS2, may account for its good aerobic stability. In conclusion, silage inoculated with LB or BS had better fermentation quality and improved aerobic stability by effectively inhibiting the microorganisms that induce aerobic spoilage.

RevDate: 2023-05-03

Donohue ME, Hert ZL, Karrick CE, et al (2023)

Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat.

Microbial ecology [Epub ahead of print].

Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.

RevDate: 2023-05-03

Saikrishna K, Talukdar D, Das S, et al (2023)

Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.

Microbial ecology [Epub ahead of print].

Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.

RevDate: 2023-05-03

Wu L, Wang XW, Tao Z, et al (2023)

Data-driven prediction of colonization outcomes for complex microbial communities.

bioRxiv : the preprint server for biology pii:2023.04.19.537502.

Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence of Enterococcus faecalis inhibits the invasion of E. faecium . The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.

RevDate: 2023-05-02

Onyango LA, Ngonga FA, Karanja EN, et al (2023)

The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers.

Scientific reports, 13(1):7156.

Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.

RevDate: 2023-05-02

Farr AD, Pesce D, Das SG, et al (2023)

The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations.

mBio [Epub ahead of print].

Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes. IMPORTANCE The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable. To this end, competition experiments were performed with a combinatorially complete set of mutants of a β-lactamase gene subject to subinhibitory concentrations of the antibiotic cefotaxime. While some mutations confer on their hosts high resistance to cefotaxime, in competition these mutations do not always confer a selective advantage. Specifically, high-resistance mutants had equivalent fitnesses despite different resistance levels and even had selective disadvantages under conditions involving spatial structure. Together, our findings suggest that the relationship between resistance level and fitness at subinhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.

RevDate: 2023-05-02

Vandeweyer D, Lievens B, L Van Campenhout (2020)

Identification of bacterial endospores and targeted detection of foodborne viruses in industrially reared insects for food.

Nature food, 1(8):511-516.

With edible insects being increasingly produced, food safety authorities have called for the determination of microbiological challenges posed to human health. Here, we find that the bacterial endospore fraction in industrially reared mealworm and cricket samples is largely comprised of Bacillus cereus group members that can pose insect or human health risks. Hepatitis A virus, hepatitis E virus and norovirus genogroup II were not detected in the sample collection, indicating a low food safety risk from these viral pathogens.

RevDate: 2023-05-01

Mosquera KD, Nilsson LKJ, de Oliveira MR, et al (2023)

Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.

Parasites & vectors, 16(1):156.

BACKGROUND: The neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.

METHODS: Larvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.

RESULTS: We found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.

CONCLUSIONS: Our findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito-microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.

RevDate: 2023-05-01

Liu YC, Ramiro-Garcia J, Paulo LM, et al (2023)

Psychrophilic and mesophilic anaerobic treatment of synthetic dairy wastewater with long chain fatty acids: Process performances and microbial community dynamics.

Bioresource technology pii:S0960-8524(23)00550-3 [Epub ahead of print].

Facilitating the anaerobic degradation of long chain fatty acids (LCFA) is the key to unlock the energy potential of lipids-rich wastewater. In this study, the feasibility of psychrophilic anaerobic treatment of LCFA-containing dairy wastewater was assessed and compared to mesophilic anaerobic treatment. The results showed that psychrophilic treatment at 15 ℃ was feasible for LCFA-containing dairy wastewater, with high removal rates of soluble COD (>90%) and LCFA (∼100%). However, efficient long-term treatment required prior acclimation of the biomass to psychrophilic temperatures. The microbial community analysis revealed that putative syntrophic fatty acid bacteria and Methanocorpusculum played a crucial role in LCFA degradation during both mesophilic and psychrophilic treatments. Additionally, a fungal-bacterial biofilm was found to be important during the psychrophilic treatment. Overall, these findings demonstrate the potential of psychrophilic anaerobic treatment for industrial wastewaters and highlight the importance of understanding the microbial communities involved in the process.

RevDate: 2023-05-01

Kearns PJ, Winter AS, Woodhams DC, et al (2023)

The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior.

Microbial ecology [Epub ahead of print].

Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.

RevDate: 2023-05-01

Miao Y, Colosimo F, Mouser PJ, et al (2023)

Editorial: Emerging microbiological processes and tools that shine in pilot- and field-scale environmental engineering applications.

Frontiers in microbiology, 14:1194772.

RevDate: 2023-05-01

Esquivel-Hernández DA, Martínez-López YE, Sánchez-Castañeda JP, et al (2023)

A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort.

Frontiers in endocrinology, 14:1128767.

INTRODUCTION: The human gut microbiota (GM) is a dynamic system which ecological interactions among the community members affect the host metabolism. Understanding the principles that rule the bidirectional communication between GM and its host, is one of the most valuable enterprise for uncovering how bacterial ecology influences the clinical variables in the host.

METHODS: Here, we used SparCC to infer association networks in 16S rRNA gene amplicon data from the GM of a cohort of Mexican patients with type 2 diabetes (T2D) in different stages: NG (normoglycemic), IFG (impaired fasting glucose), IGT (impaired glucose tolerance), IFG + IGT (impaired fasting glucose plus impaired glucose tolerance), T2D and T2D treated (T2D with a 5-year ongoing treatment).

RESULTS: By exploring the network topology from the different stages of T2D, we observed that, as the disease progress, the networks lose the association between bacteria. It suggests that the microbial community becomes highly sensitive to perturbations in individuals with T2D. With the purpose to identify those genera that guide this transition, we computationally found keystone taxa (driver nodes) and core genera for a Mexican T2D cohort. Altogether, we suggest a set of genera driving the progress of the T2D in a Mexican cohort, among them Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, Alistipes, Anaerostipes, and Terrisporobacter.

DISCUSSION: Based on a network approach, this study suggests a set of genera that can serve as a potential biomarker to distinguish the distinct degree of advances in T2D for a Mexican cohort of patients. Beyond limiting our conclusion to one population, we present a computational pipeline to link ecological networks and clinical stages in T2D, and desirable aim to advance in the field of precision medicine.

RevDate: 2023-04-30

Gounari Z, Bonatsou S, Ferrocino I, et al (2023)

Exploring yeast diversity of dry-salted naturally black olives from Greek retail outlets with culture dependent and independent molecular methods.

International journal of food microbiology, 398:110226 pii:S0168-1605(23)00142-3 [Epub ahead of print].

In the present study, the physicochemical (pH, water activity, moisture content, salt concentration) classical plate counts (total viable counts, yeasts, lactic acid bacteria, Staphylococcus aureus, Pseudomonas spp., Enterobacteriaceae) and amplicon sequencing of naturally black dry-salted olives obtained from different retail outlets of the Greek market were investigated. According to the results, the values of the physicochemical characteristics presented great variability among the samples. Specifically, pH and water activity (aw) values ranged between 4.0 and 5.0, as well as between 0.58 and 0.91, respectively. Moisture content varied between 17.3 and 56.7 % (g Η2Ο/100 g of olive pulp), whereas salt concentration ranged from 5.26 to 9.15 % (g NaCl/100 g of olive pulp). No lactic acid bacteria, S. aureus, Pseudomonas spp. and Enterobacteriaceae were detected. The mycobiota consisted of yeasts that were further characterized and identified by culture-dependent (rep-PCR, ITS-PCR, and RFLP) and amplicon target sequencing (ATS). Pichia membranifaciens, Candida sorbosivorans, Citeromyces nyonsensis, Candida etchelsii, Wickerhamomyces subpelliculosus, Candida apicola, Wickerhamomyces anomalus, Torulaspora delbrueckii and Candida versatilis were the dominant species according to ITS sequencing (culture-dependent), while ATS revealed the dominance of C. etchelsii, Pichia triangularis, P. membranifaciens, and C. versatilis among samples. The results of this study demonstrated considerable variability in quality attributes among the different commercial samples of dry-salted olives, reflecting a lack of standardization in the processing of this commercial style. However, the majority of the samples were characterized by satisfactory microbiological and hygienic quality and complied with the requirements of the trade standard for table olives of the International Olive Council (IOC) for this processing style in terms of salt concentration. In addition, the diversity of yeast species was elucidated for the first time in commercially available products, increasing our knowledge on the microbial ecology of this traditional food. Further investigation into the technological and multifunctional traits of the dominant yeast species may result in better control during dry-salting and enhance the quality and shelf-life of the final product.

RevDate: 2023-04-29

Ha AD, Moniruzzaman M, FO Aylward (2023)

Assessing the biogeography of marine giant viruses in four oceanic transects.

ISME communications, 3(1):43.

Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.

RevDate: 2023-04-29

Goswami V, Deepika S, Diwakar S, et al (2023)

Arbuscular mycorrhizas amplify the risk of heavy metal transfer to human food chain from fly ash ameliorated agricultural soils.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(23)00735-2 [Epub ahead of print].

Soil contaminants threaten global food security by posing threats to food safety through food chain pollution. Fly ash is a potential agent of soil contamination that contains heavy metals and hazardous pollutants. However, being rich in macro- and micronutrients that have direct beneficial effects on plant growth, fly ash has been recommended as a low-cost soil ameliorant in agriculture in countries of the Global South. Arbuscular mycorrhizal fungi (AMF), ubiquitous in agricultural soils, enhance efficiency of plant nutrient uptake from soils but can equally increase uptake of toxic pollutants from fly ash ameliorated soils to edible crop tissues. We investigated AMF-mediated amplification of nutrient and heavy metal uptake from fly ash amended soils to shoots, roots and grains of barley. We used a microcosm-based experiment to analyse the impacts of fly ash amendments to soil in concentrations of 0 (control), 15, 30 or 50% respectively, on root colonization by AMF Rhizophagus irregularis and AMF-mediated transfer of N, P and heavy metals: Ni, Co, Pb and Cr to barley tissues. These concentrations of fly ash are equivalent to 0, 137, 275 and 458 t ha[-1] respectively, in soil. Root AMF colonization correlated negatively with fly ash concentration and was not detected at 50% fly ash amendment. Shoots, roots and grains of mycorrhizal barley grown with 15, 30 and 50% fly ash amendments had significantly higher concentrations of Ni, Co, Pb and Cr compared to the control and their respective non-mycorrhizal counterparts. Presence of heavy metals in barley plants grown with fly ash amended soil and their increased AMF-mediated translocation to edible grains may significantly enhance the volume of heavy metals entering the human food chain. We recommend careful assessment of manipulation of agricultural soils with fly ash as heavy metal accumulation in agricultural soils and human tissues may cause irreversible damage.

RevDate: 2023-04-28

Woo AYM, Aguilar Ramos MA, Narayan R, et al (2023)

Targeting the human gut microbiome with small-molecule inhibitors.

Nature reviews. Chemistry [Epub ahead of print].

The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.

RevDate: 2023-04-28

Camargo TS, Nickele MA, Filho WR, et al (2023)

Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: a Search for Potential Biocontrol Agents.

Microbial ecology [Epub ahead of print].

The leaf-cutting ant Acromyrmex crassispinus is considered an important pest in forest plantations in southern Brazil. This work aimed to study the fungal community associated with A. crassispinus colonies, subjected to treatments with subdoses of granulated baits (sulfluramid), which might reduce the ability of the ants to care for their symbiotic fungus and other fungi (maybe biocontrol fungi) would take over, to prospect for potential biological control agents. Samplings of fungus gardens and dead ants allowed the identification of 195 fungal isolates, distributed in 29 families, 36 genera, and 53 species. The most frequent genera were Trichoderma (49.2%), Penicillium (13.8%), Chaetomium (6.2%), and Fusarium (3.6%). This is the first study that conducted a survey of antagonistic and entomopathogenic fungi to A. crassispinus and its symbiotic fungus, reporting for the first time the occurrence of potential biological control agents. Escovopsis weberi, Fusarium oxysporum, Rhizomucor variabilis, Trichoderma atroviride, Trichoderma harzianum, Trichoderma koningiopsis, and Trichoderma spirale are considered some of the potential biocontrol organisms.

RevDate: 2023-04-28

Djotan AKG, Matsushita N, K Fukuda (2023)

Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands.

Microbial ecology [Epub ahead of print].

Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.

RevDate: 2023-04-28

Berman TS, Weinberg M, Moreno KR, et al (2023)

In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.

Frontiers in immunology, 14:1152107.

INTRODUCTION: Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown.

METHODS: Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge.

RESULTS: We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities.

CONCLUSION: Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.

RevDate: 2023-04-28

Crognale S, Massimi A, Sbicego M, et al (2023)

Ecology of food waste chain-elongating microbiome.

Frontiers in bioengineering and biotechnology, 11:1157243.

Microbial chain elongation has emerged as a valuable bioprocess for obtaining marketable products, such as medium chain fatty acids usable in several industrial applications, from organic waste. The understanding of the microbiology and microbial ecology in these systems is crucial to apply these microbiomes in reliable production processes controlling microbial pathways to promote favourable metabolic processes, which will in turn increase product specificity and yields. In this research, the dynamics, cooperation/competition and potentialities of bacterial communities involved in the long-term lactate-based chain elongation process from food waste extract were evaluated under different operating conditions by DNA/RNA amplicon sequencing and functional profile prediction. The feeding strategies and the applied organic loading rates strongly affected the microbial community composition. The use of food waste extract promoted the selection of primary fermenters (i.e., Olsenella, Lactobacillus) responsible for the in situ production of electron donors (i.e., lactate). The discontinuous feeding and the organic loading rate 15 gCOD L[-1] d[-1] selected the best performing microbiome in which microbes coexist and cooperate to complete the chain elongation process. Both at DNA and RNA level, this microbiome was composed by the lactate producer Olsenella, the short chain fatty acids producers Anaerostipes, Clostridium sensu stricto 7, C. sensu stricto 12, Corynebacterium, Erysipelotrichaceae UCG-004, F0332, Leuconostoc, and the chain elongator Caproiciproducens. This microbiome also showed the highest predicted abundance of short-chain acyl-CoA dehydrogenase, the functional enzyme responsible for the chain elongation process. The combined approach herein used allowed to study the microbial ecology of chain elongation process from food waste by identifying the main functional groups, establishing the presence of potential biotic interactions within the microbiomes, and predicting metabolic potentialities. This study provided pivotal indications for the selection of high-performance microbiome involved in caproate production from food waste that can serve as a basis for further improving system performance and engineering the process scale-up.

RevDate: 2023-04-28

Turzynski V, Griesdorn L, Moraru C, et al (2023)

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition.

Viruses, 15(4): pii:v15040910.

Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

RevDate: 2023-04-28

Wong MCS, Zhang L, Ching JYL, et al (2023)

Effects of Gut Microbiome Modulation on Reducing Adverse Health Outcomes among Elderly and Diabetes Patients during the COVID-19 Pandemic: A Randomised, Double-Blind, Placebo-Controlled Trial (IMPACT Study).

Nutrients, 15(8): pii:nu15081982.

Gut microbiota is believed to be a major determinant of health outcomes. We hypothesised that a novel oral microbiome formula (SIM01) can reduce the risk of adverse health outcomes in at-risk subjects during the coronavirus disease 2019 (COVID-19) pandemic. In this single-centre, double-blind, randomised, placebo-controlled trial, we recruited subjects aged ≥65 years or with type two diabetes mellitus. Eligible subjects were randomised in a 1:1 ratio to receive three months of SIM01 or placebo (vitamin C) within one week of the first COVID-19 vaccine dose. Both the researchers and participants were blinded to the groups allocated. The rate of adverse health outcomes was significantly lower in the SIM01 group than the placebo at one month (6 [2.9%] vs. 25 [12.6], p < 0.001) and three months (0 vs. 5 [3.1%], p = 0.025). At three months, more subjects who received SIM01 than the placebo reported better sleep quality (53 [41.4%] vs. 22 [19.3%], p < 0.001), improved skin condition (18 [14.1%] vs. 8 [7.0%], p = 0.043), and better mood (27 [21.2%] vs. 13 [11.4%], p = 0.043). Subjects who received SIM01 showed a significant increase in beneficial Bifidobacteria and butyrate-producing bacteria in faecal samples and strengthened the microbial ecology network. SIM01 reduced adverse health outcomes and restored gut dysbiosis in elderly and diabetes patients during the COVID-19 pandemic.

RevDate: 2023-04-28

Maimone G, Azzaro M, Placenti F, et al (2023)

A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).

Microorganisms, 11(4): pii:microorganisms11041019.

A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.

RevDate: 2023-04-28

Zhou T, Zhao F, K Xu (2023)

Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration.

Microorganisms, 11(4): pii:microorganisms11040949.

The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.

RevDate: 2023-04-28

Lashani E, Amoozegar MA, Turner RJ, et al (2023)

Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments.

Microorganisms, 11(4): pii:microorganisms11040891.

Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.

RevDate: 2023-04-28

Thomas P, Knox OGG, Powell JR, et al (2023)

The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?.

Microorganisms, 11(4): pii:microorganisms11040835.

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe-plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host-microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.


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.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

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 )