Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

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Community coalescence: an eco-evolutionary perspective

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0252 ◽

2020 ◽

Vol 375 (1798) ◽

pp. 20190252 ◽

Cited By ~ 7

Author(s):

Meaghan Castledine ◽

Pawel Sierocinski ◽

Daniel Padfield ◽

Angus Buckling

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Ecology ◽

Evolutionary Dynamics ◽

Species Interaction ◽

Evolutionary Perspective ◽

Theme Issue ◽

Microbial Community Ecology ◽

And Function ◽

Crucial Characteristic

Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities—the type of species interaction that dominates the community—might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

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Application of Bioinformatics in Microbial Ecology

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.955-959.276 ◽

2014 ◽

Vol 955-959 ◽

pp. 276-280

Author(s):

Rui Fang Du ◽

Jing Yu Li ◽

Jian Li Liu ◽

Ji Zhao Zhao

Keyword(s):

Microbial Communities ◽

Microbial Ecology ◽

High Throughput Sequencing ◽

Structure And Function ◽

Genomic Information ◽

Major Goal ◽

Β Diversity ◽

Bioinformatics Software ◽

And Function ◽

Diversity Studies

The major goal of microbial ecology is to study the structure and function of complex microbial communities. Various bioinformatics software were employed to handle a large number of genomic information emerged by using high throughput sequencing. This paper summarizes application of bioinformatics in microbial ecology and their corresponding software used in α, β-diversity studies; and finally expounds the important roles in establishment of four synthesis databases.

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Loss of a Single Plant Functional Group in Litter Had Marginal Impacts on Microbial Community Diversity and Composition in a Tibet Fir Forest

10.21203/rs.3.rs-693895/v1 ◽

2021 ◽

Author(s):

Qianwei Li ◽

Lifeng Wang ◽

Yamei Chen ◽

Li Guo ◽

Chengming You ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

High Throughput Sequencing ◽

Driving Forces ◽

Community Diversity ◽

Plant Functional Groups ◽

Plant Residues ◽

Microbial Composition ◽

Ecological Processes ◽

And Function

Abstract Aim The decomposition of plant residues is a fundamental process of soil organic matter accumulation. The loss of plant functional groups (PFGs) could affect this process by producing litter of different qualities in the soil. Microorganisms are one of the indispensable driving forces of ecological processes, but the mechanisms by microbial communities respond to aboveground PFG changes are still unclear, which limits our understanding of biogeochemical cycle changes under PFG loss.Methods We assessed the microbial taxonomic and functional composition of six typical single PFGs (evergreen conifer, evergreen shrubs, deciduous shrub, graminoid, forb and fern), random loss of a single PFG (SPFG) from litter mixtures and total mixture of six PFGs in a Tibetan fir forest by a high-throughput sequencing method.Results The microbial composition and function did not change with loss of a SPFG in litter, and microbial communities were mainly determined by the carbon and nitrogen ratio (C:N), carbon and phosphorus ratio (C:P), N and lignin, and bacterial functional pathways and fungal functional guilds were both determined by N, C:N and C:P ratios. Bacterial diversity was positively related while fungal diversity was negatively related to N and cellulose concentrations.Conclusion We speculated that the difference in initial litter qualities (especially C:N) between different PFGs, rather than a decreased number of PFGs, is a determinant of microbial composition and function. As the loss of PFG does not change litter quality, the microbial community can resist the loss of PFG, which maintains alpine ecosystem carbon and nutrient cycling stability.

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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽

10.3390/d11120234 ◽

2019 ◽

Vol 11 (12) ◽

pp. 234 ◽

Cited By ~ 2

Author(s):

Eric A. Griffin ◽

Joshua G. Harrison ◽

Melissa K. McCormick ◽

Karin T. Burghardt ◽

John D. Parker

Keyword(s):

Phylogenetic Diversity ◽

Large Scale ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tree Diversity ◽

Trophic Levels ◽

Community Diversity ◽

And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

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Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake

10.1101/244657 ◽

2018 ◽

Author(s):

Maozhen Han ◽

Melissa Dsouza ◽

Chunyu Zhou ◽

Hongjun Li ◽

Junqian Zhang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Physicochemical Properties ◽

Microbial Communities ◽

Microbial Ecology ◽

Agricultural Pollution ◽

Agricultural Activities ◽

Sediment Samples ◽

Water And Sediment ◽

Honghu Lake

AbstractBackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.MethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.ResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.ConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.

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Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

mSystems ◽

10.1128/msystems.00201-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 28

Author(s):

Isabelle Laforest-Lapointe ◽

Marie-Claire Arrieta

Keyword(s):

Microbial Communities ◽

Microbial Ecology ◽

High Throughput Sequencing ◽

Sequencing Technology ◽

Human Gut ◽

Microbial Eukaryotes ◽

Host Health ◽

High Level ◽

Eukaryotic Organisms ◽

New Evidence

ABSTRACTHuman-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

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Predation by protists influences the temperature response of microbial communities

10.1101/2021.04.08.439073 ◽

2021 ◽

Author(s):

Jennifer D Rocca ◽

Andrea Yammine ◽

Marie Simonin ◽

Jean Gibert

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Microbial Community Structure ◽

Temperature Response ◽

Global Carbon Cycle ◽

Structure And Function ◽

And Function ◽

Global Carbon

Temperature strongly influences microbial community structure and function, which in turn contributes to the global carbon cycle that can fuel further warming. Recent studies suggest that biotic interactions amongst microbes may play an important role in determining the temperature responses of these communities. However, how microbial predation regulates these communities under future climates is still poorly understood. Here we assess whether predation by one of the most important bacterial consumers globally, protists, influences the temperature response of a freshwater microbial community structure and function. To do so, we exposed these microbial communities to two cosmopolitan species of protists at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to shifts in microbial community structure, these responses changed over time and in the presence of protist predators. Protists influenced microbial biomass and function through effects on community structure, and predation actually reduced microbial respiration rate at elevated temperature. Indicator species and threshold indicator taxa analyses showed that these predation effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities, but also demonstrates that predation can mediate these responses to warming, with important consequences for the global carbon cycle and future warming.

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Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds

Frontiers in Microbiology ◽

10.3389/fmicb.2021.790554 ◽

2022 ◽

Vol 12 ◽

Author(s):

Edward Higgins ◽

Thomas B. Parr ◽

Caryn C. Vaughn

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Canopy Cover ◽

Freshwater Mussel ◽

Local Conditions ◽

Individual Organism ◽

Mussel Shells ◽

Landscape Scales ◽

And Function

Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.

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Mechanism of differential expression of β-glucosidase genes in functional microbial communities in response to carbon catabolite repression

Biotechnology for Biofuels and Bioproducts ◽

10.1186/s13068-021-02101-x ◽

2022 ◽

Vol 15 (1) ◽

Author(s):

Xinyue Zhang ◽

Xiehui Chen ◽

Shanshan Li ◽

Ayodeji Bello ◽

Jiawen Liu ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Differential Expression ◽

Carbon Metabolism ◽

Catabolite Repression ◽

Carbon Catabolite Repression ◽

Regulatory Mechanism ◽

Glucose Tolerant ◽

And Function ◽

Functional Microbial Community

Abstract Background β-Glucosidase is the rate-limiting enzyme of cellulose degradation. It has been stipulated and established that β-glucosidase-producing microbial communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes. However, it is still unknown if this differential expression of functional microbial community happens accidentally or as a general regulatory mechanism, and of what biological significance it has. To investigate the composition and function of microbial communities and how they respond to different carbon metabolism pressures and the transcriptional regulation of functional genes, the different carbon metabolism pressure was constructed by setting up the static chamber during composting. Results The composition and function of functional microbial communities demonstrated different behaviors under the carbon metabolism pressure. Functional microbial community up-regulated glucose tolerant β-glucosidase genes expression to maintain the carbon metabolism rate by enhancing the transglycosylation activity of β-glucosidase to compensate for the decrease of hydrolysis activity under carbon catabolite repression (CCR). Micrococcales play a vital role in the resistance of functional microbial community under CCR. The transcription regulation of GH1 family β-glucosidase genes from Proteobacteria showed more obvious inhibition than other phyla under CCR. Conclusion Microbial functional communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes under CCR, which is a general regulatory mechanism, not accidental. Furthermore, the differentially expressed β-glucosidase gene exhibited species characteristics at the phylogenetic level.

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Evaluation of DESS as a storage medium for microbial community analysis

10.7287/peerj.preprints.27041v1 ◽

2018 ◽

Author(s):

Kevin M Lee ◽

Madison Adams ◽

Jonathan L Klassen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Ecology ◽

Microbial Community Structure ◽

Community Analysis ◽

Microbial Community Analysis ◽

Ant Colonies ◽

And Storage ◽

Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

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