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Bibliography on: Microbial Ecology

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ESP: PubMed Auto Bibliography 22 Jan 2021 at 01:43 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.

Created with PubMed® Query: "microbial ecology" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2021-01-21

Mariani N, Borsini A, Cecil CAM, et al (2021)

Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project.

PloS one, 16(1):e0245475 pii:PONE-D-20-19577.

INTRODUCTION: Depression, cardiovascular diseases and diabetes are among the major non-communicable diseases, leading to significant disability and mortality worldwide. These diseases may share environmental and genetic determinants associated with multimorbid patterns. Stressful early-life events are among the primary factors associated with the development of mental and physical diseases. However, possible causative mechanisms linking early life stress (ELS) with psycho-cardio-metabolic (PCM) multi-morbidity are not well understood. This prevents a full understanding of causal pathways towards the shared risk of these diseases and the development of coordinated preventive and therapeutic interventions.

METHODS AND ANALYSIS: This paper describes the study protocol for EarlyCause, a large-scale and inter-disciplinary research project funded by the European Union's Horizon 2020 research and innovation programme. The project takes advantage of human longitudinal birth cohort data, animal studies and cellular models to test the hypothesis of shared mechanisms and molecular pathways by which ELS shapes an individual's physical and mental health in adulthood. The study will research in detail how ELS converts into biological signals embedded simultaneously or sequentially in the brain, the cardiovascular and metabolic systems. The research will mainly focus on four biological processes including possible alterations of the epigenome, neuroendocrine system, inflammatome, and the gut microbiome. Life-course models will integrate the role of modifying factors as sex, socioeconomics, and lifestyle with the goal to better identify groups at risk as well as inform promising strategies to reverse the possible mechanisms and/or reduce the impact of ELS on multi-morbidity development in high-risk individuals. These strategies will help better manage the impact of multi-morbidity on human health and the associated risk.

RevDate: 2021-01-20

Fernandes NM, Campello-Nunes PH, Paiva TS, et al (2021)

Correction to: Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.

RevDate: 2021-01-20

Borruso L, Checcucci A, Torti V, et al (2021)

I Like the Way You Eat It: Lemur (Indri indri) Gut Mycobiome and Geophagy.

Microbial ecology [Epub ahead of print].

Here, we investigated the possible linkages among geophagy, soil characteristics, and gut mycobiome of indri (Indri indri), an endangered lemur species able to survive only in wild conditions. The soil eaten by indri resulted in enriched secondary oxide-hydroxides and clays, together with a high concentration of specific essential micronutrients. This could partially explain the role of the soil in detoxification and as a nutrient supply. Besides, we found that soil subject to geophagy and indris' faeces shared about 8.9% of the fungal OTUs. Also, several genera (e.g. Fusarium, Aspergillus and Penicillium) commonly associated with soil and plant material were found in both geophagic soil and indri samples. On the contrary, some taxa with pathogenic potentials, such as Cryptococcus, were only found in indri samples. Further, many saprotrophs and plant-associated fungal taxa were detected in the indri faeces. These fungal species may be involved in the digestion processes of leaves and could have a beneficial role in their health. In conclusion, we found an intimate connection between gut mycobiome and soil, highlighting, once again, the potential consequent impacts on the wider habitat.

RevDate: 2021-01-20

Kim MS, Kim KH, Hwang SJ, et al (2021)

Role of Algal Community Stability in Harmful Algal Blooms in River-Connected Lakes.

Microbial ecology [Epub ahead of print].

Harmful algal blooms (HABs) in freshwater produce toxins that pose a threat to public health and aquatic ecosystems. Although algal communities have been studied globally to understand the characteristics of HABs, the occurrence of toxic cyanobacteria in freshwater ecosystems is rarely understood. Unlike abiotic factors, the effects of biotic factors (e.g., interaction, dominance, and variability) on the occurrence of toxic cyanobacteria were overlooked due to the intricate interaction of microorganisms under different environmental conditions. To address this problem, a comprehensive ecological concept stability, which encompasses variations in species or communities due to changing biological interactions or environmental fluctuations, was applied in this study. The algal communities in six river-connected lakes in the North Han River, South Korea, were classified into high and low stability groups. The algal species belonging to diatoms and green algae groups played a major role in the interaction within the algal community in highly stable lakes, but the frequency of Microcystis led the interaction within the algal community at the center of the network in low-stability lakes. These results indicate that the interaction within the cluster is easily changed by Microcystis, where the abundance explosively increases in lakes with low algal community stability. Water quality is more strongly associated with the occurrence of toxic cyanobacteria (Microcystis and Dolichospermum). In low-stability lakes, more diverse water quality indicators are correlated with the development of toxic algae than in high-stability lakes. This paper is the first report on the importance of algal community stability in freshwater in the occurrence of toxic cyanobacteria and offers a new perspective on Microcystis monitoring and management.

RevDate: 2021-01-20

Fu S, Yang Q, Wang Q, et al (2021)

Continuous Genomic Surveillance Monitored the In Vivo Evolutionary Trajectories of Vibrio parahaemolyticus and Identified a New Virulent Genotype.

mSystems, 6(1):.

Our ability to predict evolutionary trajectories of pathogens is one of the promising leverages to fight against the pandemic disease, yet few studies have addressed this question in situ, due to the difficulty in monitoring the milestone evolutionary events for a given pathogen and in understanding the evolutionary strategies. In this study, we monitored the real-time evolution of Vibrio parahaemolyticus in response to successive antibiotic treatment in three shrimp farms in North China from 2011 to 2018 by whole-genome sequencing. Results showed that the stepwise emergence of resistance was associated with the antibiotic usage. Genomic analysis of resistant isolates showed that the acquisition of the resistant mobile genetic elements flanked by an insertion sequence (ISVal1) closely mirrored the antibiotics used in shrimp farms since 2014. Next, we also identified 50 insertion sites of ISVal1 in the chromosome, which facilitated the formation of pathogenicity islands (PAIs) and fitness islands in the following years. Further, horizontal transfers of a virulent trh-nik-ure genomic island (GI) and two GIs improving the fitness have been observed in two farms since 2016. In this case study, we proposed that the insertion sequence triggered four major evolutionary events during the outbreaks of shrimp disease in three farms, including horizontal transfer of transposon (HTT) (stage 1), the formation of resistance islands (stage 2) and the PAIs (stage 3), and horizontal transfer of the PAIs (stage 4). This study presented the first in vivo evolutionary trajectories for a given bacterial pathogen, which helps us to understand the emergence mechanisms of new genotypes.IMPORTANCE Most human infectious diseases originate from animals. Thus, how to reduce or prevent pandemic zoonoses before they emerge in people is becoming a critical issue. Continuous genomic surveillance of the evolutionary trajectories of potential human pathogens on farms is a promising strategy to realize early warning. Here, we conducted an 8-year surveillance of Vibrio parahaemolyticus in three shrimp farms. The results showed that the use of antibiotics and horizontal transfer of transposons (HTT) drove the evolution of V. parahaemolyticus, which could be divided into four stages: HTT, formation of resistance islands, formation of pathogenicity islands (PAIs), and horizontal transfer of PAIs. This study presented the first in vivo monitoring of evolutionary trajectories for a given bacterial pathogen, providing valuable information for the prevention of pandemic zoonoses.

RevDate: 2021-01-20

Rubbens P, R Props (2021)

Computational Analysis of Microbial Flow Cytometry Data.

mSystems, 6(1):.

Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.

RevDate: 2021-01-20

Chang J, Shi S, Tian L, et al (2021)

Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere.

Microorganisms, 9(1): pii:microorganisms9010175.

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.

RevDate: 2021-01-19

Moroenyane I, Mendes L, Tremblay J, et al (2021)

Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome.

Microbial ecology [Epub ahead of print].

Understanding the dynamics of plant-associated microbial communities within agriculture is well documented. However, the ecological processes that assemble the plant microbiome are not well understood. This study elucidates the relative dominance of assembly processes across plant compartments (root, stem, and leaves) and developmental stages (emergence, growth, flowering, and maturation). Bacterial community composition and assembly processes were assessed using 16S rRNA gene amplicon sequencing. Null models that couple phylogenetic community composition and species distribution models were used to evaluate ecological assembly processes of bacterial communities. All models highlighted that the balance between the assembly process was modulated by compartments and developmental stages. Dispersal limitation dominated amongst the epiphytic communities and at the maturation stage. Homogeneous selection dominated assembly across plant compartments and development stages. Overall, both sets of models were mostly in agreement in predicting the prevailing assembly processes. Our results show, for the first time, that even though niche-based processes dominate in the plant environment, the relative influence of dispersal limitation in community assembly is important.

RevDate: 2021-01-17

Takano SI, Gotoh Y, T Hayashi (2021)

"Candidatus Mesenet longicola": Novel Endosymbionts of Brontispa longissima that Induce Cytoplasmic Incompatibility.

Microbial ecology [Epub ahead of print].

Intracellular bacteria that are mainly transmitted maternally affect their arthropod hosts' biology in various ways. One such effect is known as cytoplasmic incompatibility (CI), and three bacterial species are known to induce CI: Wolbachia, Cardinium hertigii, and a recently found alphaproteobacterial symbiont. To clarify the taxonomic status and provide the foundation for future studies to reveal CI mechanisms and other phenotypes, we investigated genetic and morphological properties of the third CI inducer that we have previously reported inducing CI in the coconut beetle Brontispa longissima. The draft genome of the bacteria was obtained from the oocytes of two isofemale lines of B. longissima infected with the bacteria: one from Japan (GL2) and the other from Vietnam (L5). Genome features of the symbionts (sGL2 and sL5) were highly similar, showing 1.3 Mb in size, 32.1% GC content, and 99.83% average nucleotide sequence. A phylogenetic study based on 43 universal and single-copy phylogenetic marker genes indicates that they formed a distinct clade in the family Anaplasmataceae. 16S rRNA gene sequences indicate that they are different from the closest known relatives, at least at the genus level. Therefore, we propose a new genus and species, "Candidatus Mesenet longicola", for the symbionts of B. longissima. Morphological analyses showed that Ca. M. longicola is an intracellular bacterium that is ellipsoidal to rod-shaped and 0.94 ± 0.26 μm (mean ± SD) in length, and accumulated in the anterior part of the oocyte. Candidates for the Ca. M. longicola genes responsible for CI induction are also described.

RevDate: 2021-01-18

Xiao R, Ni BJ, Liu S, et al (2021)

Impacts of organics on the microbial ecology of wastewater anammox processes: Recent advances and meta-analysis.

Water research, 191:116817 pii:S0043-1354(21)00015-4 [Epub ahead of print].

Anaerobic ammonium oxidation (anammox) represents a promising technology for wastewater nitrogen removal. Organics management is critical to achieving efficient and stable performance of anammox or integrated processes, e.g., denitratation-anammox. The aim of this systematic review is to synthesize the state-of-the-art knowledge on the multifaceted impacts of organics on wastewater anammox community structure and function. Both exogenous and endogenous organics are discussed with respect to their effects on the biofilm/granule structure and function, as well as the interactions between anammox bacteria (AnAOB) and a broad range of coexisting functional groups. A global core community consisting of 19 taxa is identified and a co-occurrence network is constructed by meta-analysis on the 16S rDNA sequences of 149 wastewater anammox samples. Correlations between core taxa, keystone taxa, and environmental factors, including COD, nitrogen loading rate (NLR) and C/N ratio are obtained. This review provides a holistic understanding of the microbial responses to different origins and types of organics in wastewater anammox reactors, which will facilitate the design and operation of more efficient anammox-based wastewater nitrogen removal process.

RevDate: 2021-01-18

Arias A, Selander E, Saiz E, et al (2021)

Predator Chemical Cue Effects on the Diel Feeding Behaviour of Marine Protists.

Microbial ecology [Epub ahead of print].

We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6-6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats.

RevDate: 2021-01-18

Kumar M, Sodhi KK, DK Singh (2021)

Addressing the potential role of curcumin in the prevention of COVID-19 by targeting the Nsp9 replicase protein through molecular docking.

Archives of microbiology [Epub ahead of print].

The pandemics have always been a destructive carrier to living organisms. Humans are the ultimate victims, as now we are facing the SARS CoV-2 virus caused COVID-19 since its emergence in Dec 2019, at Wuhan (China). Due to the new coronavirus' unexplored nature, we shed light on curcumin for its potential role against the disease. The Nsp9 replicase protein, which plays an essential role in virus replication, was extracted online, followed by 3D PDB model prediction with its validation. The in silico molecular docking of curcumin with the replicase enzyme gave insights into the preventive measures against the virus as curcumin showed multiple interactions with Nsp9 replicase. The current study showed the use of curcumin against the coronavirus and its possible role in developing medicine against it.

RevDate: 2021-01-18

DeLong EF (2021)

Genome-enabled exploration of microbial ecology and evolution in the sea: A rising tide lifts all boats.

Environmental microbiology [Epub ahead of print].

As a young bacteriologist just launching my career during the early days of the "microbial revolution" in the 1980s, I was fortunate to participate and collaborate in some early discoveries, and the development of cross-disciplinary methodological approaches. These are facilitating engagement in more holistic studies more linking reductionist laboratory studies with more holistic observational studies in the field. My early scientific career focused on applying phylogenetic and genomic approaches to characterize "wild" bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. My central interests have not changed very much over the past three decades, but knowledge, methodological advances, and new theoretical perspectives about the microbial world certainly have. In this invited "How we did it" perspective, I trace some of the trajectory of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene and genome approaches, and application of genome-enabled, cultivation-independent functional characterization of novel enzymes, pathways and their relationship to in situ biogeochemistry. Throughout this short review I have tried to acknowledge the mentors, students, postdocs, and collaborators who enabled all this research. Inevitably, this brief autobiographical review cannot be fully comprehensive, so sincere apologies to any of my great colleagues are not explicitly mentioned herein, I salute you all as well! This article is protected by copyright. All rights reserved.

RevDate: 2021-01-16

Dahl MB, Peršoh D, Jentsch A, et al (2021)

Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions.

Microbial ecology [Epub ahead of print].

Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.

RevDate: 2021-01-16

Bergo NM, Bendia AG, Ferreira JCN, et al (2021)

Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.

Microbial ecology [Epub ahead of print].

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

RevDate: 2021-01-16

Vingiani GM, Gasulla F, Barón-Sola Á, et al (2021)

Physiological and Molecular Alterations of Phycobionts of Genus Trebouxia and Coccomyxa Exposed to Cadmium.

Microbial ecology [Epub ahead of print].

Several studies on aeroterrestrial microalgae are unravelling their resistance mechanisms to different abiotic stressors, including hazardous metals, pointing to their future role as bioremediation microorganisms. In the present study, physiological and molecular alterations of four phycobionts of genus Trebouxia (T. TR1 and T. TR9) and Coccomyxa (C. subellipsoidea and C. simplex) exposed to Cd were studied. Cd accumulation and subcellular distribution, cell wall structure, production of biothiols (GSH and phytochelatins), reactive oxygen species (ROS) formation, expression of key antioxidant genes and ROS-related enzymes were evaluated to determine the physiological differences among the four microalgae, with the aim to identify the most suitable microorganism for further biotechnological applications. After 7 days of Cd exposure, Coccomyxa algae showed higher capacity of Cd intake than Trebouxia species, with C. subellipsoidea being the highest Cd accumulator at both intracellular and, especially, cell wall level. Cd induced ROS formation in the four microalgae, but to a greater extent in both Coccomyxa algae. Trebouxia TR9 showed the lowest Cd-dependent oxidative stress probably due to glutathione reductase induction. All microalgae synthetized phytochelatins in response to Cd but in a species-specific and a dose-dependent manner. Results from this study agree with the notion that each microalga has evolved a distinct strategy to detoxify hazardous metals like Cd and to cope with oxidative stress associated with them. Coccomyxa subellipsoidea and Trebouxia TR9 appear as the most interesting candidates for further applications.

RevDate: 2021-01-16

Hansen ML, He Z, Wibowo M, et al (2021)

A Whole-Cell Biosensor for Detection of 2,4-Diacetylphloroglucinol (DAPG)-Producing Bacteria from Grassland Soil.

Applied and environmental microbiology, 87(3):.

Fluorescent Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere, as they can control phytopathogens and contribute to disease suppression. DAPG can also trigger a systemic resistance response in plants and stimulate root exudation and branching as well as induce plant-beneficial activities in other rhizobacteria. While studies of DAPG-producing Pseudomonas have predominantly focused on rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk soil and grassland, where the level of DAPG producers are predicted to be low. In this study, we constructed a whole-cell biosensor for detection of DAPG and DAPG-producing bacteria from environmental samples. The constructed biosensor contains a phlF response module and either lacZ or lux genes as output modules assembled on a pSEVA plasmid backbone for easy transfer to different host species and to enable easy future genetic modifications. We show that the sensor is highly specific toward DAPG, with a sensitivity in the low nanomolar range (>20 nM). This sensitivity is comparable to the DAPG levels identified in rhizosphere samples by chemical analysis. The biosensor enables guided isolation of DAPG-producing Pseudomonas Using the biosensor, we probed the same grassland soil sampling site to isolate genetically related DAPG-producing Pseudomonas kilonensis strains over a period of 12 months. Next, we used the biosensor to determine the frequency of DAPG-producing pseudomonads within three different grassland soil sites and showed that DAPG producers can constitute part of the Pseudomonas population in the range of 0.35 to 17% at these sites. Finally, we showed that the biosensor enables detection of DAPG produced by non-Pseudomonas species. Our study shows that a whole-cell biosensor for DAPG detection can facilitate isolation of bacteria that produce this important secondary metabolite and provide insight into the population dynamics of DAPG producers in natural grassland soil.IMPORTANCE The interest in bacterial biocontrol agents as biosustainable alternatives to pesticides to increase crop yields has grown. To date, we have a broad knowledge of antimicrobial compounds, such as DAPG, produced by bacteria growing in the rhizosphere surrounding plant roots. However, compared to the rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk and grassland soil. Currently, we are restricted to chemical methods with detection limits and time-consuming PCR-based and probe hybridization approaches to detect DAPG and its respective producer. In this study, we developed a whole-cell biosensor, which can circumvent the labor-intensive screening process as well as increase the sensitivity at which DAPG can be detected. This enables quantification of relative amounts of DAPG producers, which, in turn, increases our understanding of the dynamics and ecology of these producers in natural soil environments.

RevDate: 2021-01-16

Coe GL, Pinkham NV, Celis AI, et al (2021)

Dynamic Gut Microbiome Changes in Response to Low-Iron Challenge.

Applied and environmental microbiology, 87(3):.

Iron is an essential micronutrient for life. In mammals, dietary iron is absorbed primarily in the small intestine. Currently, the impacts of dietary iron on the taxonomic structure and function of the gut microbiome and reciprocal effects on the animal host are not well understood. Here, we establish a mouse model of low-iron challenge in which intestinal biomarkers and reduced fecal iron reveal iron stress while serum iron and mouse behavioral markers indicate maintenance of iron homeostasis. We show that the diversity of the gut microbiome in conventional C57BL/6 mice changes dramatically during 2 weeks on a low-iron diet. We also show the effects of a low-iron diet on microbiome diversity are long lasting and not easily recovered when iron is returned to the diet. Finally, after optimizing taxon association methods, we show that some bacteria are unable to fully recover after the low-iron challenge and appear to be extirpated from the gut entirely. In particular, operational taxonomic units (OTUs) from the Prevotellaceae and Porphyromonadaceae families and Bacteroidales order are highly sensitive to low-iron conditions, while other seemingly insensitive OTUs recover. These results provide new insights into the iron requirements of gut microbiome members and add to the growing understanding of mammalian iron cycling.IMPORTANCE All cells need iron. Both too much and too little iron lead to diseases and unwanted outcomes. Although the impact of dietary iron on human cells and tissues has been well studied, there is currently a lack of understanding about how different levels of iron influence the abundant and diverse members of the human microbiome. This study develops a well-characterized mouse model for studying low-iron levels and identifies key groups of bacteria that are most affected. We found that the microbiome undergoes large changes when iron is removed from the diet but that many individual bacteria are able to rebound when iron levels are changed back to normal. That said, a select few members, referred to as iron-sensitive bacteria, seem to be lost. This study begins to identify individual members of the mammalian microbiome most affected by changes in dietary iron levels.

RevDate: 2021-01-15

Zai X, Luo W, Bai W, et al (2021)

Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.

Microbial ecology [Epub ahead of print].

The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.

RevDate: 2021-01-15

Moraes LC, Lang PM, Arcanjo RA, et al (2020)

Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections.

International endodontic journal, 53(12):1603-1617.

AIM: To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections.

METHODOLOGY: Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb = no antibiotics [n = 6]; Atb = antibiotics [n = 6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME.

RESULTS: Twelve patients aged from 22 to 56 years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3 days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P < 0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples.

CONCLUSION: The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.

RevDate: 2021-01-15

Lories B, Belpaire TER, Yssel A, et al (2020)

Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility.

Biofilm, 2:100022 pii:S2590-2075(20)30004-6.

Salmonella biofilms are a common cause of contaminations in the food or feed industry. In a screening for novel compounds to combat biofilm-associated foodborne outbreaks, we identified agaric acid as a Salmonella Typhimurium biofilm inhibitor that does not affect planktonic growth. Importantly, the remaining biofilm cells after preventive treatment with agaric acid were significantly more sensitive to the common disinfectant hydrogen peroxide. Screening of a GFP-promoter fusion library of biofilm related genes revealed that agaric acid downregulates the transcription of genes responsible for flagellar motility. Concurrently, swimming motility was completely abrogated in the presence of agaric acid, indicating that biofilm inhibition occurs via interference with the motility phenotype. Moreover, agaric acid also reduced biofilm formation of Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Agaric acid thus shows potential as an anti-virulence compound that inhibits both motility and biofilm formation.

RevDate: 2021-01-15

Payne AT, Davidson AJ, Kan J, et al (2020)

Widespread cryptic viral infections in lotic biofilms.

Biofilm, 2:100016 pii:S2590-2075(19)30016-4.

Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.

RevDate: 2021-01-15

Li M, Shao D, Zhou J, et al (2020)

Signatures within esophageal microbiota with progression of esophageal squamous cell carcinoma.

Chinese journal of cancer research = Chung-kuo yen cheng yen chiu, 32(6):755-767.

Objective: Esophageal squamous cell carcinoma (ESCC) is one of the dominant malignances worldwide, but currently there is less focus on the microbiota with ESCC and its precancerous lesions.

Methods: Paired esophageal biopsy and swab specimens were obtained from 236 participants in Linzhou, China. Data from 16S ribosomal RNA gene sequencing were processed using quantitative insights into microbial ecology (QIIME2) and R Studio to evaluate differences. The Wilcoxon rank sum test and Kruskal-Wallis rank sum test were used to compare diversity and characteristic genera by specimens and participant groups. Ordinal logistic regression model was used to build microbiol prediction model.

Results: Microbial diversity was similar between biopsy and swab specimens, including operational taxonomic unit (OTU) numbers and Shannon index. There were variations and similarities of esophageal microbiota among different pathological characteristics of ESCC. Top 10 relative abundance genera in all groups include Streptococcus, Prevotella, Veillonella, Actinobacillus, Haemophilus, Neisseria, Alloprevotella, Rothia, Gemella and Porphyromonas. Genus Streptococcus, Haemophilus, Neisseria and Porphyromonas showed significantly difference in disease groups when compared to normal control, whereas Streptococcus showed an increasing tendency with the progression of ESCC and others showed a decreasing tendency. About models based on all combinations of characteristic genera, only taken Streptococcus and Neisseria into model, the prediction performance was the ideal one, of which the area under the curve (AUC) was 0.738.

Conclusions: Esophageal biopsy and swab specimens could yield similar microbial characterization. The combination of Streptococcus and Neisseria has the potential to predict the progression of ESCC, which is needed to confirm by large-scale, prospective cohort studies.

RevDate: 2021-01-15

McGill SL, Yung Y, Hunt KA, et al (2021)

Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy.

Scientific reports, 11(1):1457.

Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an 'overflow' metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as 'reverse diauxie'. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence including its potentially, mutualistic interactions with microorganisms found commonly in the environment and in medical infections.

RevDate: 2021-01-15

Berger C, Rückert C, Blom J, et al (2021)

Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.

Scientific reports, 11(1):1370.

The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.

RevDate: 2021-01-14

González-Martínez A, Muñoz-Palazon B, Kruglova A, et al (2021)

Performance and microbial community structure of a full-scale ANITATMMox bioreactor for treating reject water located in Finland.

Chemosphere, 271:129526 pii:S0045-6535(20)33724-3 [Epub ahead of print].

The aim of this work was to study the operational performance and the microbial community dynamics during the start-up of ANITATMMox technology implemented at full-scale wastewater treatment plant in Finland to treat reject water from anaerobic digesters. The average ammonium removal in the studied setup reached around 90%, withstanding ammonium loads up to 0.13 g N m-2h-1. The nitrite concentration in the effluent did not exceed 10 mg L-1, and there was a slight accumulation of NO3--N during the operation which was controlled. Thus, the result showed a robust success to high ammonium loading in presence of organic matter. The sequencing showed a heterogeneous microbial population where Methanosaeta, WCHA1-57 genus, Sphingobacteriia, Chlorobia and diverse unknown fungi were found as dominant phylotypes. Moreover, members of the Brocadiaceae family were dominant in the adhered biomass, mostly represented by Candidatus Scalindua, rarely reported in WWTPs. Overall, the results demonstrated a drastic effect of region-specific operational conditions on carrier biofilm microbial communities as it was demonstrated by the microbial studies.

RevDate: 2021-01-14

Yang Y, Herbold CW, Jung MY, et al (2020)

Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.

Water research, 191:116798 pii:S0043-1354(20)31331-2 [Epub ahead of print].

Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.

RevDate: 2021-01-14

Kerkhof LJ (2021)

Is oxford nanopore sequencing ready for analyzing complex microbiomes?.

FEMS microbiology ecology pii:6098400 [Epub ahead of print].

This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65-96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis, and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.

RevDate: 2021-01-14

Hugoni M, Nunan N, Thioulouse J, et al (2021)

Small-Scale Variability in Bacterial Community Structure in Different Soil Types.

Microbial ecology [Epub ahead of print].

Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.

RevDate: 2021-01-14

Mutnale MC, Reddy GS, K Vasudevan (2021)

Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.

Microbial ecology [Epub ahead of print].

Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.

RevDate: 2021-01-14

Qin Y, Puppe D, Zhang L, et al (2021)

How Does Sphagnum Growing Affect Testate Amoeba Communities and Corresponding Protozoic Si Pools? Results from Field Analyses in SW China.

Microbial ecology [Epub ahead of print].

The policy and practice of ecological restoration and conservation in China obtained some remarkable results. For example, Sphagnum moss growing on abandoned farmland, which was peatland before agricultural use, has rapidly expanded the wetland area in SW China. Microorganisms such as testate amoebae are sensitive to environmental change and thus have been widely used as ecological indicators in various habitats. We analyzed differently aged Sphagnum growing plots on a Sphagnum growing farmland and natural Sphagnum plots in SW China to examine how Sphagnum-dwelling testate amoeba communities and corresponding protozoic silicon (Si) pools respond to ecological restoration practice. We found that abundance, taxon richness, and diversity of testate amoebae were higher in Sphagnum growing farmland plots compared to natural Sphagnum plots. Protozoic Si pools showed an increase with Sphagnum growing time representing increased Si accumulation by idiosomic testate amoeba shells. However, protozoic Si pools were negatively correlated with taxon richness and diversity of testate amoebae. Our results showed that (i) natural Sphagnum plots were not characterized by the expected higher biodiversity of testate amoebae compared to Sphagnum growing plots and (ii) consequently protozoic Si pool quantity in natural Sphagnum plots was less driven by biodiversity of testate amoebae than expected. We concluded our results to underline the value of (i) environmental restoration policy in general and (ii) testate amoeba communities and corresponding protozoic Si pools for Si cycling in restoration areas of peatlands in particular. Based on our results, we recommend a sustainable cultivation of Sphagnum moss and an additional establishment of protected areas, where no Sphagnum harvesting occurs. These protected Sphagnum areas might represent hot spots of undisturbed testate amoeba communities and corresponding protozoic Si pools and thus of microbial Si cycling.

RevDate: 2021-01-14

Fritts RK, McCully AL, JB McKinlay (2021)

Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.

Microbiology and molecular biology reviews : MMBR, 85(1):.

SUMMARYThe transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.

RevDate: 2021-01-14

Hu J, Jin VL, Konkel JYM, et al (2021)

Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity.

mSphere, 6(1):.

Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N2O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.

RevDate: 2021-01-13

Zhong Q, Cruz-Paredes C, Zhang S, et al (2021)

Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?.

Journal of hazardous materials, 411:124962 pii:S0304-3894(20)32953-8 [Epub ahead of print].

Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.

RevDate: 2021-01-13

Shen J, Wyness AJ, Claire MW, et al (2021)

Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.

Microbial ecology [Epub ahead of print].

Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.

RevDate: 2021-01-13

Petrén H, Gloder G, Posledovich D, et al (2021)

Innate preference hierarchies coupled with adult experience, rather than larval imprinting or transgenerational acclimation, determine host plant use in Pieris rapae.

Ecology and evolution, 11(1):242-251 pii:ECE37018.

The evolution of host range drives diversification in phytophagous insects, and understanding the female oviposition choices is pivotal for understanding host specialization. One controversial mechanism for female host choice is Hopkins' host selection principle, where females are predicted to increase their preference for the host species they were feeding upon as larvae. A recent hypothesis posits that such larval imprinting is especially adaptive in combination with anticipatory transgenerational acclimation, so that females both allocate and adapt their offspring to their future host. We study the butterfly Pieris rapae, for which previous evidence suggests that females prefer to oviposit on host individuals of similar nitrogen content as the plant they were feeding upon as larvae, and where the offspring show higher performance on the mother's host type. We test the hypothesis that larval experience and anticipatory transgenerational effects influence female host plant acceptance (no-choice) and preference (choice) of two host plant species (Barbarea vulgaris and Berteroa incana) of varying nitrogen content. We then test the offspring performance on these hosts. We found no evidence of larval imprinting affecting female decision-making during oviposition, but that an adult female experience of egg laying in no-choice trials on the less-preferred host Be. incana slightly increased the P. rapae propensity to oviposit on Be. incana in subsequent choice trials. We found no transgenerational effects on female host acceptance or preference, but negative transgenerational effects on larval performance, because the offspring of P. rapae females that had developed on Be. incana as larvae grew slower on both hosts, and especially on Be. incana. Our results suggest that among host species, preferences are guided by hard-wired preference hierarchies linked to species-specific host traits and less affected by larval experience or transgenerational effects, which may be more important for females evaluating different host individuals of the same species.

RevDate: 2021-01-13

Fu S, Wang Q, Zhang Y, et al (2021)

Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms.

mSystems, 6(1):.

Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments.IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.

RevDate: 2021-01-13

Meier DV, Imminger S, Gillor O, et al (2021)

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community.

mSystems, 6(1):.

Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.

RevDate: 2021-01-13

Wang H, Beier N, Boedeker C, et al (2021)

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif.

mSystems, 6(1):.

Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that Dinoroseobacter shibae, a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (ter). The peak of coverage was located at dif, a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-dif-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in D. shibae is coupled to cell division. The footprint of the FtsK-dif-XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions.IMPORTANCE Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in Dinoroseobacter shibae, a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.

RevDate: 2021-01-13

Cohen Kadosh K, Muhardi L, Parikh P, et al (2021)

Nutritional Support of Neurodevelopment and Cognitive Function in Infants and Young Children-An Update and Novel Insights.

Nutrients, 13(1): pii:nu13010199.

Proper nutrition is crucial for normal brain and neurocognitive development. Failure to optimize neurodevelopment early in life can have profound long-term implications for both mental health and quality of life. Although the first 1000 days of life represent the most critical period of neurodevelopment, the central and peripheral nervous systems continue to develop and change throughout life. All this time, development and functioning depend on many factors, including adequate nutrition. In this review, we outline the role of nutrients in cognitive, emotional, and neural development in infants and young children with special attention to the emerging roles of polar lipids and high quality (available) protein. Furthermore, we discuss the dynamic nature of the gut-brain axis and the importance of microbial diversity in relation to a variety of outcomes, including brain maturation/function and behavior are discussed. Finally, the promising therapeutic potential of psychobiotics to modify gut microbial ecology in order to improve mental well-being is presented. Here, we show that the individual contribution of nutrients, their interaction with other micro- and macronutrients and the way in which they are organized in the food matrix are of crucial importance for normal neurocognitive development.

RevDate: 2021-01-12

Nguyen TTT, Foysal MJ, Fotedar R, et al (2021)

The Effect of Two Dietary Protein Sources on Water Quality and the Aquatic Microbial Communities in Marron (Cherax cainii) Culture.

Microbial ecology [Epub ahead of print].

Feeding freshwater crayfish species with different diets not only affects the water quality but also induces the abundance of various microbial communities in their digestive tracts. In this context, very limited research has been undertaken to understand the impacts of various protein incorporated aqua-diets on the characteristics of water and its microbial communities. In this study, we have critically analysed the water quality parameters including pH, dissolved oxygen, nitrate, nitrite, ammonia and phosphorus, as well as bacterial communities under marron (Cherax cainii) aquaculture, fed fishmeal (FM) and poultry by-product meal (PBM)-based diets for 60 days. The results unveiled that over the time, feeding has significant impacts on organic waste accumulation, especially ammonia, nitrate, nitrite and phosphate, while no effects were observed on pH and dissolved oxygen. Analysis of 16S rRNA sequence data of water sample indicated significant (P < 0.05) shift of microbial abundance in post-fed FM and PBM water with the evidence of microbial transmission from the gut of marron. Post-fed marron resulted in a significant correlation of Hafnia, Enterobacter, Candidatus Bacilloplasma and Aquitella with the quality and microbial population of water. The results of this study generated valuable knowledge database of microbes-water relationship for better health management practices and production of marron aquaculture fed with FM and PBM diets in under restricted feeding regime with the feeding ratios provided.

RevDate: 2021-01-12

Rozman V, Accetto T, Duncan SH, et al (2020)

Type IV pili are widespread among non-pathogenic Gram-positive gut bacteria with diverse carbohydrate utilization patterns.

Environmental microbiology [Epub ahead of print].

Type IV pili (T4P) are bacterial surface-exposed appendages that have been extensively studied in Gram-negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non-pathogenic anaerobic Gram-positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram-positive species are associated with growth on cellulose, suggesting possible associations of T4P with substrate utilization patterns. In the present study, genome sequences of 118 taxonomically diverse, mainly Gram-positive, bacterial strains isolated from anaerobic (gastrointestinal) environments, have been analysed. The genes likely to be associated with T4P biogenesis were analysed and grouped according to T4P genetic organization. In parallel, consortia of Carbohydrate Active enZYmes (CAZymes) were also analysed and used to predict carbohydrate utilization abilities of selected strains. The predictive power of this approach was additionally confirmed by experimental assessment of substrate-related growth patterns of selected strains. Our analysis revealed that T4P systems with diverse genetic organization are widespread among Gram-positive anaerobic non-pathogenic bacteria isolated from different environments, belonging to two phylogenetically distantly related phyla: Firmicutes and Actinobacteria.

RevDate: 2021-01-11

Fu Y, Wang F, Sheng H, et al (2021)

Removal of extracellular antibiotic resistance genes using magnetic biochar/quaternary phosphonium salt in aquatic environments: A mechanistic study.

Journal of hazardous materials, 411:125048 pii:S0304-3894(21)00012-1 [Epub ahead of print].

The proliferation and spread of antibiotic resistance genes (ARGs) is becoming a worldwide crisis. Extracellular DNA encoding ARGs (eARGs) in aquatic environment plays a critical role in the dispersion of antimicrobial resistance genes. Strategies to control the dissemination of eARGs are urgently required for ecological safety and human health. Towards this goal, magnetic biochar/quaternary phosphonium salt (MBQ), was used to investigate the efficiency and removal mechanism for eARGs. Magnetic biochar modified by quaternary phosphonium salt enhanced the adsorption capacity of extracellular DNA to approximately 9 folds, compared to that of the unmodified. DNA adsorption by MBQ was mainly dominated by chemisorption in heterogeneous systems and was promoted in acidic and low-salt environment. The generation of •OH and MBQ colloid jointly cleaved DNA into fragments, facilitating the adsorption of the phosphate backbone of DNA onto MBQ through electrostatic force as well as the conformational transition of DNA. Furthermore, quantification of extracellular DNA after MBQ was applied in water demonstrated that over 92.7% of resistance genes were removed, indicating a significantly reduced risk of propagation of antimicrobial resistance in aquatic environments. These findings have a practical significance in the application of MBQ in mitigating the spread of ARGs in aquatic environment.

RevDate: 2021-01-11

Forés E, Bofill-Mas S, Itarte M, et al (2021)

Evaluation of two rapid ultrafiltration-based methods for SARS-CoV-2 concentration from wastewater.

The Science of the total environment, 768:144786 pii:S0048-9697(20)38319-4 [Epub ahead of print].

Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples seeded with murine hepatitis virus (MHV), a member of the Coronaviridae family, and the bacteriophage MS2, were used to characterize and compare two ultrafiltration-based methods: a centrifugal ultrafiltration device (Centricon® Plus-70) and the automated concentrating pipette CP-Select™. Based on the recovery efficiencies, significant differences were observed for MHV, with Centricon® Plus-70 (24%) being the most efficient method. Nevertheless, concentrations of naturally occurring SARS-CoV-2, Human adenoviruses and JC polyomaviruses in these samples did not result in significant differences between methods suggesting that testing naturally occurring viruses may complement the evaluation of viral concentration methodologies. Based on the virus adsorption to solids and the necessity of a pre-centrifugation step to remove larger particles and avoid clogging when using ultrafiltration methods, we assessed the percentage of viruses not quantified after ultrafiltration. Around 23% of the detected SARS-CoV-2 would be discarded during the debris removal step. The CP-Select™ provided the highest concentration factor (up to 333×) and the lowest LoD (6.19 × 103 GC/l) for MHV and proved to be fast, automatic, highly reproducible and suitable to work under BSL-2 measures.

RevDate: 2021-01-11

Laursen MF, Bahl MI, TR Licht (2021)

Settlers of our inner surface - Factors shaping the gut microbiota from birth to toddlerhood.

FEMS microbiology reviews pii:6081092 [Epub ahead of print].

During the first three years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth, and the availability of nutrients needed by the intestinal microbes.

RevDate: 2021-01-11

Figueroa-Gonzalez PA, Bornemann TLV, Adam PS, et al (2020)

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.

Frontiers in microbiology, 11:587782.

Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.

RevDate: 2021-01-10

Vázquez-Blanco R, Arias-Estévez M, Bååth E, et al (2020)

Comparing the effect of Cu-based fungicides and pure Cu salts on microbial biomass, microbial community structure and bacterial community tolerance to Cu.

Journal of hazardous materials, 409:124960 pii:S0304-3894(20)32951-4 [Epub ahead of print].

The effect of Cu on three different microbial endpoints was studied using different Cu sources, in order to check the usefulness of pure Cu salts to estimate the toxicity of commercial Cu fungicides on soil microbes. Cu additions caused similar dose-response curves of substrate induced respiration (SIR) decreases regardless of Cu source, i.e. the use of pure Cu salts to estimate the effect of Cu fungicides on microbial biomass using SIR may be useful. Phospholipid fatty acid (PLFA) analysis showed that the Cu source was more important for the microbial community structure than Cu concentration. Thus, the use of Cu salts to infer the effects of Cu fungicides on microbial community structure using PLFA analysis is not recommended, since effects of Cu concentration will be confounded with Cu source. Analyzing pollution induced community tolerance (PICT) to Cu showed that the use of pure Cu salts may overestimate Cu effects if Cu salt additions modified the soil pH. The highest doses of Cu salts increased bacterial community tolerance to Cu between 300 and 600 times, while commercial Cu fungicide increases were between 20 and 160 times. Therefore, the use of pure Cu salts to estimate the Cu fungicides effects on soil microbes is not recommended for PLFAs analyses, not suitable for PICT at high Cu concentrations, while useful for SIR.

RevDate: 2021-01-09

Doliwa A, Dunthorn M, Rassoshanska E, et al (2021)

Identifying Potential Hosts of Short-Branch Microsporidia.

Microbial ecology [Epub ahead of print].

Microsporidia are obligate parasites that are closely related to Fungi. While the widely known "long-branch" Microsporidia infect mostly metazoans, the hosts of "short-branch" Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, and Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.

RevDate: 2021-01-09

García Hernández E, Berg MP, Van Oosten AR, et al (2021)

Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations.

Microbial ecology [Epub ahead of print].

The digestive tract of animals harbors microbiota important for the host's fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus' digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal-bacteria interactions and provides insights into the resilience of the O. gammarellus-associated bacteria to increased flooding frequency.

RevDate: 2021-01-09

Win PM, Matsumura E, K Fukuda (2021)

Effects of Pesticides on the Diversity of Endophytic Fungi in Tea Plants.

Microbial ecology [Epub ahead of print].

We examined the effects of agrochemicals on the endophytic fungal community associated with tea plants. Endophytic fungi were isolated from four different tea plant tissues (bark, xylem, old leaves, new leaves) collected from pesticide-treated and untreated plots. In pesticide-treated plot, the acaricides, fungicides, and insecticides are typically applied 3 times each year. The infection rate was slightly lower in the pesticide-treated plot, but the difference between plots was not statistically significant. Colletotrichum camelliae, Phyllosticta capitalensis, and Pleosporales sp. were common endophytes in both plots. Among a total of 41 fungal species, only 21 were considered common endophytes. Colletotrichum pseudomajus was the predominant endophyte in the bark tissue in the untreated plot, whereas C. camelliae was predominant in the pesticide-treated plot. Paraphaeosphaeria neglecta and Phoma bellendis were predominant in the xylem tissues of samples from the untreated and treated plots, respectively. Colletotrichum camelliae was the most commonly found species in leaf tissues in both plots, but the colonization frequency was significantly lower in the pesticide-treated plot. Species richness was not affected by pesticide treatment. The community structure of endophytic fungi in stem tissues (bark and xylem) differed significantly between plots, but leaf tissue endophytic fungal community structure was not significantly influenced by pesticide treatment.

RevDate: 2021-01-09

Eraqi WA, ElRakaiby MT, Megahed SA, et al (2021)

Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis.

Microbial ecology [Epub ahead of print].

Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.

RevDate: 2021-01-08

Moossavi S, Fontes ME, Rossi L, et al (2021)

Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study.

FEMS microbiology letters pii:6070652 [Epub ahead of print].

Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimised and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for two weeks (short-term frozen). Long-term samples were stored at -20°C for more than six months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria including Streptococcus, Staphylococcus, and Bifidobacterium from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.

RevDate: 2021-01-08

Rogiers T, Claesen J, Gompel AV, et al (2021)

Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution.

Environmental microbiology [Epub ahead of print].

Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long-term co-contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation-dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long-term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co-metal-radionuclide contaminated sites. This article is protected by copyright. All rights reserved.

RevDate: 2021-01-08

Colin Y, Berthe T, Molbert N, et al (2021)

Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads.

Microbial ecology [Epub ahead of print].

Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

RevDate: 2021-01-08

Shi Y, Yang H, Chu M, et al (2021)

Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China.

Microbial ecology [Epub ahead of print].

This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.

RevDate: 2021-01-08

Verdera AB, Montecillo AD, MCM Obusan (2021)

Draft Genome Sequence of Streptomyces sp. Isolate H28 from the Meycauayan River, Philippines.

Microbiology resource announcements, 10(1):.

In this paper, we report the draft genome sequence of Streptomyces sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability to utilize and degrade both high-density polyethylene (HDPE) and low-density polyethylene (LDPE).

RevDate: 2021-01-08

Mori JF, RA Kanaly (2021)

Complete Genome Sequence of Sphingobium barthaii KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Soil Bacterium.

Microbiology resource announcements, 10(1):.

Sphingobium barthaii KK22T is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.

RevDate: 2021-01-08

Riber L, LH Hansen (2021)

Epigenetic Memories: The Hidden Drivers of Bacterial Persistence?.

Trends in microbiology pii:S0966-842X(20)30322-X [Epub ahead of print].

Epigenetic modifications, including DNA methylation, stably alter gene expression without modifying genomic sequences. Recent evidence suggests that epigenetic regulation coupled with a long-term 'memory' effect plays a major role within bacterial persistence formation. Today, emerging high-resolution, single-molecule sequencing technologies allow an increased focus on DNA modifications as regulatory epigenetic marks, which presents a unique opportunity to identify possible epigenetic drivers of bacterial persistence.

RevDate: 2021-01-08

Clodoveo ML, Hbaieb RH, Kotti F, et al (2014)

Mechanical Strategies to Increase Nutritional and Sensory Quality of Virgin Olive Oil by Modulating the Endogenous Enzyme Activities.

Comprehensive reviews in food science and food safety, 13(2):135-154.

This monograph is a critical review of the biological activities that occur during virgin olive oil (VOO) extraction process. Strategic choices of plant engineering systems and of processing technologies should be made to condition the enzymatic activities, in order to modulate the nutritional and the sensory quality of the product toward the consumer expectations. "Modulation" of the product quality properties has the main aim to predetermine the quantity and the quality of 2 classes of substances: polyphenols and volatile compounds responsible of VOO nutritional and sensory characteristics. In the 1st section, a systematic analysis of the literature has been carried out to investigate the main olive enzymatic activities involved in the complex biotransformation that occurs during the mechanical extraction process. In the 2nd section, a critical and interpretative discussion of the influence of each step of the extraction process on the polyphenols and the volatile compounds has been performed. The effect of the different mechanical devices that are part of the extraction process is analyzed and recommendations, strategies, and possible avenues for future researches are suggested.

RevDate: 2021-01-07

Wang B, Ma J, Zhang L, et al (2020)

The synergistic strategy and microbial ecology of the anaerobic co-digestion of food waste under the regulation of domestic garbage classification in China.

The Science of the total environment, 765:144632 pii:S0048-9697(20)38163-8 [Epub ahead of print].

With the implementation of new domestic garbage classification policy in China, attention is growing to improve the treatment efficiency of municipal 'wet' waste. Combing with the new regulation, the synergistic strategy and the microbial ecology of the anaerobic co-digestion (AcoD) of cooked food waste (CFW), uncooked food waste (UCFW) and rice straw (RS) were analyzed in current study. Results showed that the maximum cumulative methane yield (CMY) and synergic index were obtained when CFW and UCFW were mixed at the ratio of 1:1 (based on volatile solid content). The highest CMY 452.94 ± 0.99 mL/g-VS was obtained when the ratio of CFW, UCFW and RS was 0.81:0.09:0.10, which was 16.29%, 36.20% and 121.84% higher than their mono-digestion, respectively. The AcoD promoted the methane potential by prolonging the release time of organic matter and slowing down the hydrolysis rate. Furthermore, the AcoD increased the species diversification and relative abundance of fermentation bacteria in digesters, and Methanosaeta predominated the methanogen communities. This study demonstrated a clean and sustainable AcoD strategy for safe disposal of urban food waste and revealed the variation of microbial community, which can provide a base for efficient bioenergy recovery from urban domestic garbage.

RevDate: 2021-01-07

Chakraborty P, Paul P, Kumari M, et al (2021)

Attenuation of Pseudomonas aeruginosa biofilm by thymoquinone: an individual and combinatorial study with tetrazine-capped silver nanoparticles and tryptophan.

Folia microbiologica [Epub ahead of print].

Microbial biofilm indicates a cluster of microorganisms having the capability to display drug resistance property, thereby increasing its proficiency in spreading diseases. In the present study, the antibiofilm potential of thymoquinone, a black seed-producing natural molecule, was contemplated against the biofilm formation by Pseudomonas aeruginosa. Substantial antimicrobial activity was exhibited by thymoquinone against the test organism wherein the minimum inhibitory concentration of the compound was found to be 20 μg/mL. Thereafter, an array of experiments (crystal violet staining, protein count, and microscopic observation, etc.) were carried out by considering the sub-MIC doses of thymoquinone (5 and 10 μg/mL), each of which confirmed the biofilm attenuating capacity of thymoquinone. However, these concentrations did not show any antimicrobial activity. Further explorations on understanding the underlying mechanism of the same revealed that thymoquinone accumulated reactive oxygen species (ROS) and also inhibited the expression of the quorum sensing gene (lasI) in Pseudomonas aeruginosa. Furthermore, by taking up a combinatorial approach with two other reported antibiofilm agents (tetrazine-capped silver nanoparticles and tryptophan), the antibiofilm efficiency of thymoquinone was expanded. In this regard, the highest antibiofilm activity was observed when thymoquinone, tryptophan, and tetrazine-capped silver nanoparticles were applied together against Pseudomonas aeruginosa. These combinatorial applications of antibiofilm molecules were found to accumulate ROS in cells that resulted in the inhibition of biofilm formation. Thus, the combinatorial study of these antibiofilm molecules could be applied to control biofilm threats as the tested antibiofilm molecules alone or in combinations showed negligible or very little cytotoxicity.

RevDate: 2021-01-07

Oita S, Carey J, Kline I, et al (2021)

Methodological Approaches Frame Insights into Endophyte Richness and Community Composition.

Microbial ecology [Epub ahead of print].

Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.

RevDate: 2021-01-07

Rodrigues LA, da Silva DKA, AM Yano-Melo (2021)

Arbuscular Mycorrhizal Fungal Assemblages in Conservation Unit of Atlantic Forest Areas Under Native Vegetation and Natural Regeneration.

Microbial ecology [Epub ahead of print].

Arbuscular mycorrhizal fungi (AMF) play an important role in the dynamic of plant community in the south American Atlantic Rainforest biome. Even in protected areas, this biome is under several anthropic impacts, which can cause shifts in the soil microbiota, including AMF. This study aimed to determine the structure and composition of AMF community in areas of native Atlantic Forest and in natural regeneration and to identify which abiotic factors are influencing this community in these areas. Soil samples were collected at Monte Pascoal National and Historical Park, in Southern Bahia, in native and natural regeneration areas of Atlantic Forest in two seasons (rainy and dry). Greater number of glomerospores and richness and diversity of AMF were found in the area under regeneration, with differences between seasons being observed only for the number of glomerospores. Seventy-seven species of AMF were recorded, considering all areas and seasons, with Acaulospora and Glomus being the most representative genera. Greater abundance of species of the genera Acaulospora, Claroideoglomus, and Septoglomus was found in the regeneration area. The AMF community differed between the study areas, but not between seasons, with soil attributes (pH, K, Al, Mg, m, and clay) structuring factors for this difference in the AMF community. Atlantic Forest areas in natural regeneration and the soil edaphic factors provide changes in the structure and composition of the AMF community, increasing the richness and diversity of these fungi in conservation units.

RevDate: 2021-01-07

St James AR, Lin J, RE Richardson (2021)

Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.

Microbial ecology [Epub ahead of print].

Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.

RevDate: 2021-01-07

Li W, KE Nelson (2021)

Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.

Microbial ecology [Epub ahead of print].

In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.

RevDate: 2021-01-07

Tan MH, Loke S, Croft LJ, et al (2021)

First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.

Microbial ecology [Epub ahead of print].

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C's actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.

RevDate: 2021-01-07

Luo Y, Wang H, Liang J, et al (2021)

Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China.

Microbial ecology [Epub ahead of print].

To understand the environmental reservoirs of Vibrio cholerae and their public health significance, we surveyed freshwater samples from rivers in two cities (Jiaxing [JX] and Jiande [JD]) in Zhejiang, China. A total of 26 sampling locations were selected, and river water was sampled 456 times from 2015 to 2016 yielding 200 V. cholerae isolates, all of which were non-O1/non-O139. The average isolation rate was 47.3% and 39.1% in JX and JD, respectively. Antibiotic resistance profiles of the V. cholerae isolates were examined with nonsusceptibility to cefazolin (68.70%, 79/115) being most common, followed by ampicillin (47.83%, 55/115) and imipenem (27.83%, 32/115). Forty-two isolates (36.52%, 42/115) were defined as multidrug resistant (MDR). The presence of virulence genes was also determined, and the majority of the isolates were positive for toxR (198/200, 99%) and hlyA (196/200, 98%) with few other virulence genes observed. The population structure of the V. cholerae non-O1/non-O139 sampled was examined using multilocus sequence typing (MLST) with 200 isolates assigned to 128 STs and 6 subpopulations. The non-O1/non-O139 V. cholerae population in JX was more varied than in JD. By clonal complexes (CCs), 31 CCs that contained isolates from this study were shared with other parts of China and/or other countries, suggesting widespread presence of some non-O1/non-O139 clones. Drug resistance profiles differed between subpopulations. The findings suggest that non-O1/non-O139 V. cholerae in the freshwater environment is a potential source of human infections. Routine surveillance of non-O1/non-O139 V. cholerae in freshwater rivers will be of importance to public health.

RevDate: 2021-01-07

Hutchinson MI, Bell TAS, Gallegos-Graves V, et al (2021)

Merging Fungal and Bacterial Community Profiles via an Internal Control.

Microbial ecology [Epub ahead of print].

Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.

RevDate: 2021-01-07

Gomez JA, TP Primm (2021)

A Slimy Business: the Future of Fish Skin Microbiome Studies.

Microbial ecology [Epub ahead of print].

Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.

RevDate: 2021-01-07

Riva A, Kolimár D, Spittler A, et al (2020)

Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota.

Frontiers in microbiology, 11:585428.

The gut microbiota plays a pivotal role in the conversion of dietary flavonoids, which can affect their bioavailability and bioactivity and thereby their health-promoting properties. The ability of flavonoids to metabolically-activate the microbiota has, however, not been systematically evaluated. In the present study, we used a fluorescence-based single-cell activity measure [biorthogonal non-canonical ammino acid-tagging (BONCAT)] combined with fluorescence activated cell sorting (FACS) to determine which microorganisms are metabolically-active after amendment of the flavonoid rutin. We performed anaerobic incubations of human fecal microbiota amended with rutin and in the presence of the cellular activity marker L-azidohomoalanine (AHA) to detect metabolically-active cells. We found that 7.3% of cells in the gut microbiota were active after a 6 h incubation and 26.9% after 24 h. We then sorted BONCAT-positive cells and observed an enrichment of Lachnospiraceae (Lachnoclostridium and Eisenbergiella), Enterobacteriaceae, Tannerellaceae, and Erysipelotrichaceae species in the rutin-responsive fraction of the microbiota. There was marked inter-individual variability in the appearance of rutin conversion products after incubation with rutin. Consistent with this, there was substantial variability in the abundance of rutin-responsive microbiota among different individuals. Specifically, we observed that Enterobacteriaceae were associated with conversion of rutin into quercetin-3-glucoside (Q-glc) and Lachnospiraceae were associated with quercetin (Q) production. This suggests that individual microbiotas differ in their ability to metabolize rutin and utilize different conversion pathways.

RevDate: 2021-01-07

Meisner A, Snoek BL, Nesme J, et al (2021)

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.

The ISME journal [Epub ahead of print].

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.

RevDate: 2021-01-07

Mayta-Apaza AC, García-Cano I, Dabrowski K, et al (2021)

Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation.

Microorganisms, 9(1): pii:microorganisms9010100.

The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.

RevDate: 2021-01-06

Kanzaki N, Ekino T, Hamaguchi K, et al (2021)

Three Seinura species from Japan with a description of S. shigaensis n. sp. (Tylenchomorpha: Aphelenchoididae).

PloS one, 16(1):e0244653 pii:PONE-D-20-34242.

A preliminary survey of Seinura spp. was conducted in the Kyoto area, Western Japan. The survey yielded four new strains of Seinura spp., including two strains of S. caverna, a strain of S. italiensis, and a strain of an undescribed species. Molecularly, the two strains of S. caverna were nearly identical to the type strain but showed some minor variations, particularly in the mitochondrial cytochrome oxidase subunit I gene. The small subunit and D2-D3 large subunit sequences of the Japanese strain of S. italiensis were nearly identical and identical to its original description, respectively, and the difference in the small subunit was due to mis-reading of the sequences. The new species, S. shigaensis n. sp., was phylogenetically close to S. caverna and S. persica, although these three species were clearly different phylogenetically. The new species was typologically similar or nearly identical to several other Seinura spp., including S. chertkovi, S. christiei, S. italiensis, S. steineri, and S. tenuicaudata, but it can be distinguished from those species by the morphometric values. Because the new species is phylogenetically very close to S. caverna, it could be a good comparative system for S. caverna as a potential satellite model for the predatory nematode.

RevDate: 2021-01-06

Álvarez-Pérez S, Tsuji K, Donald M, et al (2021)

Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.

Microbial ecology [Epub ahead of print].

Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.

RevDate: 2021-01-06

Shar S, Reith F, Ball AS, et al (2021)

Long-term Impact of Gold and Platinum on Microbial Diversity in Australian Soils.

Microbial ecology [Epub ahead of print].

The effects of platinum (Pt) and gold (Au) and on the soil bacterial community was evaluated in four different Australian soil types (acidic Burn Grounds (BGR), organic matter-rich Fox Lane, high silt/metal Pinpinio (PPN), and alkali Minnipa (MNP) spiked with either Pt or Au at 1, 25, and 100 mg kg-1 using a next-generation sequencing approach (amplicon-based, MiSeq). Soil type and metal concentrations were observed to be key drivers of Pt and Au effects on soil microbial community structure. Different trends were therefore observed in the response of the bacterial community to Pt and Au amendments; however in each soil type, Pt and Au amendment caused a detectable shift in community structure that in most samples was positively correlated with increasing metal concentrations. New dominant groups were only observed in BGR and PPN soils at 100 mg kg-1 (Kazan-3B-28 and Verrucomicrobia groups (BGR, Pt) and Firmicutes and Caldithrix groups (PPN, Pt) and WS2 (BGR, Au). The effects of Pt on soil microbial diversity were largely adverse at 100 mg kg-1 and were pronounced in acidic, basic, and metal/silt-rich soils. However, this effect was concentration-related; Au appeared to be more toxic to soil bacterial communities than Pt at 25 mg kg-1 but Pt was more toxic at 100 mg kg-1. More bacterial groups such as those belonging to Burkholderiales/Burkholderiaceae, Alicyclobacillaceae, Rubrobacteraceae, Cytophagaceae, Oxalobacteraceae were selectively enriched by Pt compared to Au (Sphingomonadaceae and Rhodospirillaceae) amendments irrespective of soil type. The research outcomes have important implications in the management (remediation) of Pt- and Au-contaminated environments.

RevDate: 2021-01-06

Leiva D, Fernández-Mendoza F, Acevedo J, et al (2021)

The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate.

Microbial ecology [Epub ahead of print].

Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.

RevDate: 2021-01-06

Ogaki MB, Pinto OHB, Vieira R, et al (2021)

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding.

Microbial ecology [Epub ahead of print].

We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA by metabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550 m and 250 m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463 m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.

RevDate: 2021-01-06

Liu Y, Anastacio GR, Ishangulyyeva G, et al (2021)

Mutualistic Ophiostomatoid Fungi Equally Benefit from Both a Bark Beetle Pheromone and Host Tree Volatiles as Nutrient Sources.

Microbial ecology [Epub ahead of print].

Interactions between mutualistic bark beetles and ophiostomatoid fungi have received considerable attention in recent years. Studies have shown how volatile organic compounds emitted from mutualist fungi affect the behaviors of several bark beetle species. However, we currently lack sufficient knowledge regarding whether bark beetle pheromones can influence mutualist fungi. Here, we measured growth and biomass of two mutualistic fungi of the mountain pine beetle in response to headspace of a beetle pheromone (trans-verbenol), a blend of host tree volatiles, the combination of both, or control (no volatile source) in vitro experiments consisting of a nitrogen-based medium. The surface area and ergosterol content of the mycelia were used as surrogates for fungal growth and biomass respectively. We found that both growth and biomass of Grosmannia clavigera and Ophiostoma montium were greater in medium exposed to any type of volatile sources than the control. While growth and ergosterol content of G. clavigera were highest in the combination treatment, there were no differences in growth or biomass among the types of volatiles introduced for O. montium. These results suggest that both mutualistic fungi can utilize both bark beetle pheromone and host tree volatiles as nutrient sources. Overall, these results support the on-going studies on the role of volatile organic compounds mediating mutualistic bark beetle-fungi interactions.

RevDate: 2021-01-06

Savadova-Ratkus K, Mazur-Marzec H, Karosienė J, et al (2021)

Interplay of Nutrients, Temperature, and Competition of Native and Alien Cyanobacteria Species Growth and Cyanotoxin Production in Temperate Lakes.

Toxins, 13(1): pii:toxins13010023.

Global warming and eutrophication contribute to formation of HABs and distribution of alien cyanobacteria northward. The current study assessed how alien to Europe Sphaerospermopsis aphanizomenoides and Chrysosporum bergii will co-occur with dominant native Planktothrix agardhii and Aphanizomenon gracile species under changing conditions in temperate freshwaters. The experiments were carried out to examine the effect of nutrients and temperature on the growth rate of cyanobacteria, production of cyanotoxins, and interspecies competition. The highest growth rate was determined for A. gracile (0.43 day-1) and S. aphanizomenoides (0.40 day-1) strains at all the tested nutrient concentrations (IP and IN were significant factors). S. aphanizomenoides adapted to the wide range of nutrient concentrations and temperature due to high species ecological plasticity; however, A. gracile was able to suppress its dominance under changing conditions. Regularity between tested variables and STX concentration in A. gracile was not found, but IP concentration negatively correlated with the amount of dmMC-RR and other non-ribosomal peptides (NRPs) in P. agardhii strains. The relative concentration of NRPs in nontoxic P. agardhii strain was up to 3-fold higher than in MC-producing strain. Our study indicated that nutrients, temperature, and species had significant effects on interspecies competition. A. gracile had a negative effect on biomass of both alien species and P. agardhii.

RevDate: 2021-01-05

Aguero CM, Eyer PA, Crippen TL, et al (2021)

Reduced Environmental Microbial Diversity on the Cuticle and in the Galleries of a Subterranean Termite Compared to Surrounding Soil.

Microbial ecology [Epub ahead of print].

Termites are intimately tied to the microbial world, as they utilize their gut microbiome for the conversion of plant cellulose into necessary nutrients. Subterranean termites must also protect themselves from the vast diversity of harmful microbes found in soil. However, not all soil microbes are harmful, such as Streptomyces and methanotrophic bacteria that some species of termites harbor in complex nest structures made of fecal material. The eastern subterranean termite, Reticulitermes flavipes, has a simple nest structure consisting of fecal lined galleries. We tested the hypothesis that R. flavipes maintains a select microbial community in its nests to limit the penetration of harmful soilborne pathogens and favor the growth of beneficial microbes. Using Illumina sequencing, we characterized the bacterial and fungal communities in the surrounding soil, in the nest galleries, and on the cuticle of workers. We found that the galleries provide a more beneficial microbial community than the surrounding soil. Bacterial and fungal diversity was highest in the soil, lower in the galleries, and least on the cuticle. Bacterial communities clustered together according to the substrate from which they were sampled, but this clustering was less clear in fungal communities. Most of the identified bacterial and fungal taxa were unique to one substrate, but the soil and gallery communities had very similar phylum-level taxonomic profiles. Notably, the galleries of R. flavipes also harbored both the potentially beneficial Streptomyces and the methanotrophic Methylacidiphilales, indicating that these microbial associations in fecal material pre-date the emergence of complex fecal nest structures. Surprisingly, several pathogenic groups were relatively abundant in the galleries and on the cuticle, suggesting that pathogens may accumulate within termite nests over time while putatively remaining at enzootic level during the lifetime of the colony.

RevDate: 2021-01-05

Shih CM, Ophine L, LL Chao (2021)

Molecular Detection and Genetic Identification of Wolbachia Endosymbiont in Wild-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Sumatera Utara, Indonesia.

Microbial ecology [Epub ahead of print].

The genetic identity of Wolbachia endosymbiont in wild-caught Culex quinquefasciatus was determined for the first time in Indonesia. A total of 314 Cx. quinquefasciatus were examined for Wolbachia by PCR assay targeting the Wolbachia surface protein (wsp) gene. The prevalence of Wolbachia infection was detected in 29.94% of Cx. specimens (45.86% female and 8.27% male). The group-specific infection was detected with an infection rate of 0.32%, 28.98%, and 0.64% in groups A, B, and A&B, respectively. Phylogenetic analysis revealed all Wolbachia strains from Indonesia were genetically affiliated to the supergroup A and B with the high sequence similarity of 97.9-100% and 99.7-100%, respectively. Phylogenetic relationships can be easily distinguished by neighbor-joining analysis and were congruent by maximum likelihood method. The genetic distance (GD) values of intra- and inter-group analysis indicated a lower level (GD < 0.007 for group A and GD < 0.003 for group B) within the Indonesia strains and a higher level (GD > 1.125 for group A and GD > 1.129 for group B) as compared with other Wolbachia strains. Our results provide the first genetic identification of Wolbachia endosymbiont in Cx. quinquefasciatus collected from Indonesia, and the phylogenetic analysis revealed a new discovery of group A Wolbachia in wild-caught Cx. quinquefasciatus mosquitoes.

RevDate: 2021-01-05

Asha K, P Bhadury (2021)

Myceligenerans indicum sp. nov., an actinobacterium isolated from mangrove sediment of Sundarbans, India.

Archives of microbiology [Epub ahead of print].

A new actinobacterial species of the genus Myceligenerans has been isolated from the intertidal sediment of Indian Sundarbans mangrove ecosystem. The isolate has been characterized based on polyphasic approaches. The isolate exhibit well-developed substrate mycelia along with the presence of cocci- and rod-shaped elements. The organism can grow across a wide range of temperature, salinity, and pH as well as on different carbon sources. Phylogenetic analyses based on 16S rRNA showed that this isolate is closely related to Myceligenerans salitolerans XHU 5031 (99% identity; 100% coverage). Presence of ketosynthase domain representing polyketide synthases in the isolate provides evidence of its potential ability to produce secondary metabolites. Multigene phylogeny based on atpD and rpoB gene sequences confirmed it as a new species within the family Promicromonosporaceae (Phylum Actinobacteria). The DNA G + C content of the isolate has been determined as 72 mol%. The peptidoglycan type was A4α and the whole-cell hydrolysates contained glucose, galactose, and mannose. The polar lipids were represented by diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. Major fatty acids present in the isolate are anteiso-C15, iso-C15, iso-C16, and anteiso-C17. Whole-genome sequence indicates the size of genome is ~ 5 Mbp. GGDC (%), orthoANIu (%), and AAI of I2 genome indicated 28.9%, 77.44% and 0.859 identity with the genome of Myceligenerans xiligouense strain DSM 15,700. The isolate I2 has been proposed as a new species, Myceligenerans indicum sp. nov. The genome sequence has been deposited to GenBank/ENA/DDBJ under the accession number JABBYC000000000.

RevDate: 2021-01-05

Marco ML, Sanders ME, Gänzle M, et al (2021)

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods.

Nature reviews. Gastroenterology & hepatology [Epub ahead of print].

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.

RevDate: 2021-01-05

Kuramae EE, Dimitrov MR, da Silva GHR, et al (2020)

On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.

Microorganisms, 9(1): pii:microorganisms9010075.

Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.

RevDate: 2021-01-04

Oliveira MM, Proenca AM, Moreira-Silva E, et al (2021)

Biofilms of Pseudomonas and Lysinibacillus Marine Strains on High-Density Polyethylene.

Microbial ecology [Epub ahead of print].

Environmental pollution by plastic debris is estimated on a scale of 100 million metric tons, a portion of which is fragmented into micro- and nanoplastics. These fragments are often colonized by bacterial species in marine environments, possibly contributing to the biodegradation of such materials. However, further investigations are necessary to determine the impact of abiotic polymer weathering on biofilm adhesion, as well as the specific biofilm formation strategies employed by marine isolates. Here, we evaluate deep-sea sediment bacterial isolates for biofilm adhesion, extracellular matrix production, and polymer degradation ability. Our study focuses on high-density polyethylene (HDPE) fragments for their high durability and environmental persistence, subjecting fragments to abiotic weathering prior to bacterial colonization. Marine isolates identified as Pseudomonas sp. and Lysinibacillus sp. exhibited decreasing biofilm formation on weathered HDPE, especially over the first 24 h of incubation. This effect was countered by increased extracellular matrix production, likely improving cell adhesion to surfaces roughened by abiotic degradation. These adhesion strategies were contrasted with a reference Pseudomonas aeruginosa strain, which displayed high levels of biofilm formation on non-weathered HDPE and lower extracellular matrix production over the first 24 h of incubation. Furthermore, our results suggest that an increase in biofilm biomass correlated with changes to HDPE structure, indicating that these strains have a potential for biodegradation of plastic fragments. Therefore, this work provides a detailed account of biofilm formation strategies and bacteria-plastic interactions that represent crucial steps in the biodegradation of plastic fragments in marine environments.

RevDate: 2021-01-04

do Carmo Linhares D, Saia FT, Duarte RTD, et al (2021)

Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil.

Microbial ecology [Epub ahead of print].

Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.

RevDate: 2021-01-04

Vega L, Jaimes J, Morales D, et al (2021)

Microbial Communities' Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing.

Microbial ecology [Epub ahead of print].

Microbial communities in surface waters used for recreational purposes are indicators of contamination and risk of contact with human pathogens. Hence, monitoring microbial communities in recreational waters is important for potential public health threats to humans. Such monitoring is rare in Colombia, even in its capital, Bogotá, the most populous city in the country. This city encompasses metropolitan and linear parks with recreational water bodies that are used frequently by the public, and the presence of pathogens can compromise the health of the citizens. Therefore, we examined the bacterial, and eukaryotic communities in urban recreational lakes (URL) in four metropolitan parks in Bogotá, Colombia. Samples from four metropolitan parks (Los Novios, Simon Bolivar, El Tunal, and Timiza) and one stream contaminated with sewage from a linear park (El Virrey) were collected. We used amplicon next-generation sequencing of the 16S-rRNA gene and 18S-rRNA gene to characterize microbial communities followed by bioinformatics analyses. In addition, general water quality parameters-pH, hardness, acidity, alkalinity, dissolved oxygen, and nitrites-were recorded using a commercial kit. Genera of pathogens, including Legionella, Pseudomonas, Mycobacterium, Candida, and Naegleria, were found in lake waters. The stream El Virrey was, however, the only surface water that showed an abundance of fecal bacteria, often associated with low oxygen concentrations. All water bodies showed a predominance of fungal phyla, except for the lake at Timiza. This lake showed the highest pH, and its ecological dynamics are likely different from other water bodies. Likewise, some URLs displayed a greater abundance of cyanobacteria, including toxin-producing species. Algal genera associated with eutrophication were predominant among primary producing microorganisms. This study shows for the first time the description of the bacterial and eukaryotic communities of some URLs and a stream in Bogotá. The URLs and the stream harbored various pathogens that might pose a risk to the citizen's health.

RevDate: 2021-01-04

Cerruti M, Stevens B, Ebrahimi S, et al (2020)

Enrichment and Aggregation of Purple Non-sulfur Bacteria in a Mixed-Culture Sequencing-Batch Photobioreactor for Biological Nutrient Removal From Wastewater.

Frontiers in bioengineering and biotechnology, 8:557234.

Mixed-culture biotechnologies are widely used to capture nutrients from wastewater. Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest for their ability to directly assimilate nutrients in the biomass. One challenge targets the aggregation and accumulation of PNSB biomass to separate it from the treated water. Our aim was to enrich and produce a concentrated, fast-settling PNSB biomass with high nutrient removal capacity in a 1.5-L, stirred-tank, anaerobic sequencing-batch photobioreactor (SBR). PNSB were rapidly enriched after inoculation with activated sludge at 0.1 gVSS L-1 in a first batch of 24 h under continuous irradiance of infrared (IR) light (>700 nm) at 375 W m-2, with Rhodobacter reaching 54% of amplicon sequencing read counts. SBR operations with decreasing hydraulic retention times (48 to 16 h, i.e., 1-3 cycles d-1) and increasing volumetric organic loading rates (0.2-1.3 kg COD d-1 m-3) stimulated biomass aggregation, settling, and accumulation in the system, reaching as high as 3.8 g VSS L-1. The sludge retention time (SRT) increased freely from 2.5 to 11 days. Acetate, ammonium, and orthophosphate were removed up to 96% at a rate of 1.1 kg COD d-1 m-3, 77% at 113 g N d-1 m-3, and 73% at 15 g P d-1 m-3, respectively, with COD:N:P assimilation ratio of 100:6.7:0.9 m/m/m. SBR regime shifts sequentially selected for Rhodobacter (90%) under shorter SRT and non-limiting concentration of acetate during reaction phases, for Rhodopseudomonas (70%) under longer SRT and acetate limitation during reaction, and Blastochloris (10%) under higher biomass concentrations, underlying competition for substrate and photons in the PNSB guild. With SBR operations we produced a fast-settling biomass, highly (>90%) enriched in PNSB. A high nutrient removal was achieved by biomass assimilation, reaching the European nutrient discharge limits. We opened further insights on the microbial ecology of PNSB-based processes for water resource recovery.

RevDate: 2021-01-04

Kroetsch SA, Kidd KA, Monk WA, et al (2020)

The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates.

Ecology and evolution, 10(24):14000-14019 pii:ECE36993.

Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.

RevDate: 2021-01-04

Fu S, Ni P, Yang Q, et al (2020)

Delineating the key virulence factors and intraspecies divergence of Vibrio harveyi via whole-genome sequencing.

Canadian journal of microbiology [Epub ahead of print].

Vibrio harveyi is one of the major pathogens in aquaculture. To identify the key virulence factors affecting pathogenesis of V. harveyi towards fish, we conducted a field investigation for three representative fish farms infected with V. harveyi. Multilocus sequence typing (MLST) and whole-genome sequencing were conducted to delineate the phylogenetic relationship and genetic divergence of V. harveyi. A total of 25 V. harveyi strains were isolated from the diseased fish and groundwater and were subtyped into 12 sequence types by MLST. Five virulence genes, mshB, pilA, hutR, ureB, and ureG, were variably presented in the sequenced strains. The virulence gene profiles strongly correlated with the distinct pathogenicity of V. harveyi strains, with a strain harboring all five genes exhibiting the highest virulence towards fish. Phenotype assay confirmed that reduced virulence correlated with decreased motility and biofilm formation ability. Additionally, three types of type VI secretion system, namely T6SS1, T6SS2, and T6SS3, were identified in V. harveyi strains, which can be classified into six, four, and 12 subtypes, respectively. In conclusion, the results indicated that the virulence level of V. harveyi is mainly determined by the above virulence genes, which may play vital roles in environmental adaptation for V. harveyi.

RevDate: 2021-01-03

Saona LA, Soria M, Durán-Toro V, et al (2021)

Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes.

Microbial ecology [Epub ahead of print].

Arsenic (As) is a metalloid present in the earth's crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that form microbial mats, evaporites, and microbialites inhabiting Andean lakes, puquios, or salt flats. In this work, we characterize the biological role of As and the effect of phosphate in AMEs from the Laguna Tebenquiche (Atacama Desert, Chile). Using micro X-ray fluorescence, the distribution of As in microbial mat samples was mapped. Taxonomic and inferred functional profiles were obtained from enriched cultures of microbial mats incubated under As stress and different phosphate conditions. Additionally, representative microorganisms highly resistant to As and able to grow under low phosphate concentration were isolated and studied physiologically. Finally, the genomes of the isolated Salicola sp. and Halorubrum sp. were sequenced to analyze genes related to both phosphate metabolism and As resistance. The results revealed As as a key component of the microbial mat ecosystem: (i) As was distributed across all sections of the microbial mat and represented a significant weight percentage of the mat (0.17 %) in comparison with P (0.40%); (ii) Low phosphate concentration drastically changed the microbial community in microbial mat samples incubated under high salinity and high As concentrations; (iii) Archaea and Bacteria isolated from the microbial mat were highly resistant to arsenate (up to 500 mM), even under low phosphate concentration; (iv) The genomes of the two isolates were predicted to contain key genes in As metabolism (aioAB and arsC/acr3) and the genes predicted to encode the phosphate-specific transport operon (pstSCAB-phoU) are next to the arsC gene, suggesting a functional relationship between these two elements.

RevDate: 2021-01-02

Bossaert S, Winne V, Van Opstaele F, et al (2020)

Description of the temporal dynamics in microbial community composition and beer chemistry in sour beer production via barrel ageing of finished beers.

International journal of food microbiology, 339:109030 pii:S0168-1605(20)30524-9 [Epub ahead of print].

Currently, there is a strong interest in barrel ageing of finished, conventionally fermented beers, as a novel way to produce sour beers with a rich and complex flavour profile. The production process, however, remains largely a process of trial and error, often resulting in profit losses and inconsistency in quality. To improve product quality and consistency, a better understanding of the interactions between microorganisms, wood and maturing beer is needed. The aim of this study was to describe the temporal dynamics in microbial community composition, beer chemistry and sensory characteristics during barrel ageing of three conventionally fermented beers that differed in parameters like alcohol content and bitterness. Beers were matured for 38 weeks in new (two types of wood) and used (one type of wood) oak barrels. Beer samples were taken at the start of the maturation and after 2, 12 and 38 weeks. Microbial community composition, determined using amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 region, beer chemistry and sensory characteristics substantially changed throughout the maturation process. Likewise, total bacterial and fungal population densities generally increased during maturation. PerMANOVA revealed significant differences in the bacterial and fungal community composition of the three beers and across time points, but not between the different wood types. By contrast, significant differences in beer chemistry were found across the different beers, wood types and sampling points. Results also indicated that the outcome of the maturation process likely depends on the initial beer properties. Specifically, results suggested that beer bitterness may restrain the bacterial community composition, thereby having an impact on beer souring. While the bacterial community composition of moderately-hopped beers shifted to a dominance of lactic acid bacteria, the bacterial community of the high-bitterness beer remained fairly constant, with low population densities. Bacterial community composition of the moderate-bitterness beers also resembled those of traditional sours like lambic beers, hosting typical lambic brewing species like Pediococcus damnosus, Lactobacillus brevis and Acetobacter sp. Furthermore, results suggested that alcohol level may have affected the fungal community composition and extraction of wood compounds. More specifically, the concentration of wood compounds like cis-3-methyl-4-octanolide, trans-3-methyl-4-octanolide, eugenol and total polyphenols was higher in beers with a high alcohol content. Altogether, our results provide novel insights into the barrel ageing process of beer, and may pave the way for a new generation of sour beers.

RevDate: 2021-01-01

Park Y, Yu J, Nguyen VK, et al (2020)

Understanding complete ammonium removal mechanism in single-chamber microbial fuel cells based on microbial ecology.

The Science of the total environment, 764:144231 pii:S0048-9697(20)37762-7 [Epub ahead of print].

The removal of organics and ammonium from domestic wastewater was successfully achieved by a flat-panel air-cathode microbial fuel cell (FA-MFC). To elucidate the reason for complete ammonium removal in the single-chamber MFCs, microbial communities were analyzed in biofilms on the surface of each anode, separator, and cathode of separator-electrode assemblies (SEAs). The spatial distribution of bacterial families related to the nitrogen cycle varied based on local conditions. Since oxygen diffusing from the air-cathode created a locally aerobic condition, ammonia-oxidizing bacteria (AOB) Nitrosomonadacea and nitrite-oxidizing bacteria (NOB) Nitrospiraceae were present near the cathode. NOB (~12.1%) was more abundant than AOB (~4.4%), suggesting that the nitrate produced by NOB may be reduced back to nitrite by heterotrophic denitrifiers such as Rhodocyclaceae (~21.7%) and Comamonadaceae (~5%) in the anoxic zone close to the NOB layer. Near that zone, the "nitrite loop" also substantially enriched two nitrite-reducing bacterial families: Ignavibacteriaceae (~18.1%), facultative heterotrophs, and Brocadiaceae (~11.2%), anaerobic ammonium oxidizing autotrophs. A larger inner area of biofilm contained abundant heterotrophic denitrifiers and fermentation bacteria. These results indicate that the large-surface SEA of FA-MFC allows counter-diffusion between substrates and oxygen, resulting in interactions of bacteria involved in the nitrogen cycle for complete ammonium removal.

RevDate: 2021-01-02

Amacker N, Gao Z, Agaras BC, et al (2020)

Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads.

Frontiers in microbiology, 11:614194.

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.

RevDate: 2021-01-02

Assis JM, Abreu F, Villela HMD, et al (2020)

Delivering Beneficial Microorganisms for Corals: Rotifers as Carriers of Probiotic Bacteria.

Frontiers in microbiology, 11:608506.

The use of Beneficial Microorganisms for Corals (BMCs) to increase the resistance of corals to environmental stress has proven to be effective in laboratory trials. Because direct inoculation of BMCs in larger tanks or in the field can be challenging, a delivery mechanism is needed for efficient transmission of the BMC consortium. Packaged delivery mechanisms have been successfully used to transmit probiotics to other organisms, including humans, lobsters, and fish. Here, we tested a method for utilizing rotifers of the species Brachionus plicatilis for delivery of BMCs to corals of the species Pocillopora damicornis. Epifluorescence microscopy combined with a live/dead cell staining assay was used to evaluate the viability of the BMCs and monitor their in vivo uptake by the rotifers. The rotifers efficiently ingested BMCs, which accumulated in the digestive system and on the body surface after 10 min of interaction. Scanning electron microscopy confirmed the adherence of BMCs to the rotifer surfaces. BMC-enriched rotifers were actively ingested by P. damicornis corals, indicating that this is a promising technique for administering coral probiotics in situ. Studies to track the delivery of probiotics through carriers such as B. plicatilis, and the provision or establishment of beneficial traits in corals are the next proof-of-concept research priorities.

RevDate: 2020-12-31

Lequime S, Dehecq JS, Matheus S, et al (2020)

Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus.

PLoS pathogens, 16(12):e1009068 pii:PPATHOGENS-D-20-00924.

Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus' vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level.

RevDate: 2020-12-31

Kirchner N, Cano-Prieto C, Schulz-Fincke AC, et al (2020)

Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining.

Journal of natural products [Epub ahead of print].

Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.

RevDate: 2020-12-31

Yu Z, Schwarz C, Zhu L, et al (2020)

Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization.

Environmental science & technology [Epub ahead of print].

Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm2 in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.

RevDate: 2020-12-30

Metze D, Popp D, Schwab L, et al (2020)

Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer.

FEMS microbiology ecology pii:6055686 [Epub ahead of print].

High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediments sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate an increasing loss of ecosystem functioning, functional redundancy, and resilience, at higher temperatures, whereas 80°C results in a collapse of the ecosystem integrity.

RevDate: 2020-12-30

Afolayan AO, FA Ayeni (2020)

Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.

Journal of infection in developing countries, 14(12):.

INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.

METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.

RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.

CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.

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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.

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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.

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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.

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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.

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

ESP Plans

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

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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.

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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).

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Selected Bibliographies

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