scholarly journals Disturbance and recovery: a synthesis of microbial community reassembly following disturbance across realms

2021 ◽  
Author(s):  
Stephanie Jurburg ◽  
Shane Blowes ◽  
Ashley Shade ◽  
Nico Eisenhauer ◽  
Jonathan Chase
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
Disturbance And Recovery ◽  
Microbial Community Assembly ◽  
Community Reassembly ◽  
Over Time

Disturbances alter the diversity and composition of microbial communities, but whether microbiomes from different environments exhibit similar degrees of resistance or rates of recovery has not been evaluated. Here, we synthesized 86 time series of disturbed mammalian, aquatic, and soil microbiomes to examine how the recovery of microbial richness and community composition differed after disturbance. We found no general patterns in compositional variance (i.e., dispersion) in any microbiomes over time. Only mammalian microbiomes consistently exhibited decreases in richness following disturbance. Importantly, they tended to recover this richness, but not their composition, over time. In contrast, aquatic microbiomes tended to diverge from their pre-disturbance composition following disturbance. By synthesizing microbiome responses across environments, our study aids in the reconciliation of disparate microbial community assembly frameworks, and highlights the role of the environment in microbial community reassembly following disturbance.

scholarly journals Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

2020 ◽  
Author(s):  
Qing-Lin Chen ◽  
Hang-Wei Hu ◽  
Zhen-Zhen Yan ◽  
Chao-Yu Li ◽  
Bao-Anh Thi Nguyen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Fungal Community ◽  
Community Assembly ◽  
Distance Decay ◽  
Termite Mounds ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

scholarly journals A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Daliang Ning ◽  
Mengting Yuan ◽  
Linwei Wu ◽  
Ya Zhang ◽  
Xue Guo ◽  
...  
Keyword(s):  
Animal Ecology ◽  
Microbial Community ◽  
Community Assembly ◽  
Null Model ◽  
High Accuracy ◽  
Relative Importance ◽  
Experimental Warming ◽  
Community Based ◽  
Microbial Community Assembly ◽  
Over Time

Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), and specificity (0.95–0.98) on simulated communities, which are 10–160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and ‘drift’ (59%). Interestingly, warming decreases ‘drift’ over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.

scholarly journals Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 285 ◽  
Author(s):  
Mengxin Zhao ◽  
Jing Cong ◽  
Jingmin Cheng ◽  
Qi Qi ◽  
Yuyu Sheng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Community Assembly ◽  
Soil Microbial Community ◽  
Southern China ◽  
Microbial Community Composition ◽  
Nitrogen And Phosphorus ◽  
Soil Microbial ◽  
Microbial Community Assembly ◽  
Microbial Functional Gene

Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.

scholarly journals Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

2013 ◽  
Vol 7 (11) ◽  
pp. 2116-2125 ◽  
Author(s):  
Jonathan McCafferty ◽  
Marcus Mühlbauer ◽  
Raad Z Gharaibeh ◽  
Janelle C Arthur ◽  
Ernesto Perez-Chanona ◽  
...  
Keyword(s):  
Microbial Community ◽  
Mouse Model ◽  
Community Assembly ◽  
Founder Effects ◽  
Changes Over Time ◽  
Microbial Community Assembly ◽  
Cage Effects ◽  
Over Time

scholarly journals Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

2020 ◽  
Author(s):  
Oskar Modin ◽  
Raquel Liebana ◽  
Soroush Saheb-Alam ◽  
Britt-Marie Wilén ◽  
Carolina Suarez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Null Model ◽  
Amplicon Sequencing ◽  
Null Models ◽  
Marker Genes ◽  
Experimental Systems ◽  
Microbial Community Assembly ◽  
The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

scholarly journals Hierarchical control of microbial community assembly

2021 ◽  
Author(s):  
Sammy Pontrelli ◽  
Rachel Szabo ◽  
Shaul Pollak ◽  
Julia A Schwartzman ◽  
Daniela Ledezma-Tejeida ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Resource Availability ◽  
Community Assembly ◽  
Hierarchical Control ◽  
Complex Forms ◽  
Chain Lengths ◽  
Changes Over Time ◽  
Microbial Community Assembly ◽  
Over Time

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders control the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical crossfeeding structure that allows biopolymer degraders to shape the dynamics of community assembly.

scholarly journals Divergent role of abiotic factors in shaping microbial community assembly of paocai brine during aging process

2020 ◽  
Vol 137 ◽  
pp. 109559
Author(s):  
Nan Zhao ◽  
Bo Yang ◽  
Wenwei Lu ◽  
Xiaoming Liu ◽  
Jianxin Zhao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Aging Process ◽  
Abiotic Factors ◽  
Microbial Community Assembly

scholarly journals A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Daniel Aguirre de Cárcer
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Phylogenetic Signal ◽  
A Priori ◽  
Amplicon Sequencing ◽  
Bioinformatic Analysis ◽  
Microbial Ecosystems ◽  
And Function ◽  
Microbial Community Assembly

Abstract Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs’ identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

scholarly journals Emergence Shapes the Structure of the Seed Microbiota

2014 ◽  
Vol 81 (4) ◽  
pp. 1257-1266 ◽  
Author(s):  
Matthieu Barret ◽  
Martial Briand ◽  
Sophie Bonneau ◽  
Anne Préveaux ◽  
Sophie Valière ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Practical Applications ◽  
Bacterial Marker ◽  
Species Specific ◽  
Diversity Studies

ABSTRACTSeeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment ofgyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

scholarly journals Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

2020 ◽  
Author(s):  
Samir Giri ◽  
Leonardo Oña ◽  
Silvio Waschina ◽  
Shraddha Shitut ◽  
Ghada Yousif ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Bacterial Species ◽  
Exchange Interactions ◽  
Structure And Function ◽  
Phylogenetic Distance ◽  
And Function ◽  
Microbial Community Assembly ◽  
Feeding Interactions

AbstractThe exchange of metabolites among different bacterial genotypes is key for determining the structure and function of microbial communities. However, the factors that govern the establishment of these cross-feeding interactions remain poorly understood. While kin selection theory predicts that individuals should direct benefits preferentially to close relatives, the potential benefits resulting from a metabolic exchange may be larger for more distantly related species. Here we distinguish between these two possibilities by performing pairwise cocultivation experiments between auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients were able to grow in the vast majority of pairs tested (78%), suggesting that metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient as well as the dissimilarity of their metabolic networks was positively associated with the growth of auxotrophic recipients. Finally, this result was corroborated in an in-silico analysis of a co-growth of species from a gut microbial community. Together, these findings suggest metabolic cross-feeding interactions are more likely to establish between strains that are metabolically more dissimilar. Thus, our work identifies a new rule of microbial community assembly, which can help predict, understand, and manipulate natural and synthetic microbial systems.SignificanceMetabolic cross-feeding is critical for determining the structure and function of natural microbial communities. However, the rules that determine the establishment of these interactions remain poorly understood. Here we systematically analyze the propensity of different bacterial species to engage in unidirectional cross-feeding interactions. Our results reveal that synergistic growth was prevalent in the vast majority of cases analyzed. Moreover, both phylogenetic and metabolic dissimilarity between donors and recipients favored a successful establishment of metabolite exchange interactions. This work identifies a new rule of microbial community assembly that can help predict, understand, and manipulate microbial communities for diverse applications.

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