Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

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A network-based approach to deciphering a dynamic microbiome’s response to a subtle perturbation

Scientific Reports ◽

10.1038/s41598-020-73920-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Grace Tzun-Wen Shaw ◽

An-Chi Liu ◽

Chieh-Yin Weng ◽

Yi-Chun Chen ◽

Cheng-Yu Chen ◽

...

Keyword(s):

Microbial Communities ◽

Ecosystem Functioning ◽

Environmental Changes ◽

Ecosystem Dynamics ◽

Environmental Research ◽

Human Society ◽

The Past ◽

Environmental Perturbations ◽

Before And After ◽

Occurrence Patterns

Abstract Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

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Putative functions and co-occurrence patterns of the microbial communities in natural and engineered ecosystems

10.21203/rs.3.rs-510082/v1 ◽

2021 ◽

Author(s):

Yu Xia ◽

Na Li ◽

Yiyun Chen ◽

Weijia Li ◽

Xuwen He ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Wastewater Treatment Plants ◽

Rrna Gene ◽

Natural Environments ◽

Anaerobic Digesters ◽

Network Analyses ◽

Wb Network ◽

Almost All ◽

Occurrence Patterns

Abstract Understanding functions and co-occurrence patterns of microbial communities in various ecosystems enriches the knowledge on ecosystem characteristics and microbial ecology. However, such analyses have rarely been reported. Herein, functions and inter-taxa correlations of microbial communities in a set of natural environments (farmland (SA), forest soil (SB) and Caspian Sea sediments (CSS)) and engineered ecosystems (wastewater treatment plants (FW, WA and WB) and anaerobic digesters (AD)) were studied based on FAPROTAX and network analyses, respectively, by a collection of 115 samples from seven published 16S rRNA gene datasets generated by high-throughput sequencing. The results show that chemoheterotrophy related populations were the most abundant in almost all the communities. Their relative abundances (RAs) in the AD systems were the highest (43.7%±4.2%), followed by those of the soil environments (40.2%±1.9% in SA and 36.4%±2.0% in SB). For each ecosystem, the indicative community and overall community showed differentiations in several function categories. For example, the SA and SB indicative communities showed higher RAs in aerobic chemoheterotrophy, the CSS indicative community showed higher RAs in sulfate respiration, the AD indicative community showed higher RAs in fermentation, and the WB indicative community included higher RAs of predatory/exoparasitic bacteria. Three molecular ecological networks of the communities from the AD, WB and SB datasets were constructed, respectively. The WB network showed the highest proportion of negative correlations (70.4%), possibly attributed to the environmental pressure which aggravated microbial competition. The positively correlated taxa showed lower phylogenetic distances than the negatively correlated taxa on average in each network.

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Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Scientific Reports ◽

10.1038/s41598-018-23931-0 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 46

Author(s):

Dinka Mandakovic ◽

Claudia Rojas ◽

Jonathan Maldonado ◽

Mauricio Latorre ◽

Dante Travisany ◽

...

Keyword(s):

Environmental Stress ◽

Microbial Communities ◽

Ecological Factors ◽

Occurrence Patterns

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A Network-Based Approach to Deciphering A Dynamic Microbiome’s Response to A Subtle Perturbation

10.21203/rs.3.rs-27654/v1 ◽

2020 ◽

Author(s):

Grace Tzun-Wen Shaw ◽

An-Chi Liu ◽

Chieh-Yin Weng ◽

Yi-Chun Chen ◽

Cheng-Yu Chen ◽

...

Keyword(s):

Microbial Communities ◽

Environmental Changes ◽

Swine Manure ◽

Ecosystem Dynamics ◽

Environmental Research ◽

Human Society ◽

Environmental Perturbations ◽

Key Species ◽

Before And After ◽

Occurrence Patterns

Abstract Background: Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Declines in biodiversity lead to more than just species loss. The exponentially growing human population and its exploitation of natural resources affect the environment from local to global scales via climate change, global warming, and other human-driven environmental problems. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to moderate or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations.Results: Recent studies have proven that co-occurrence patterns are effective for measuring responses to subtle perturbations. In this study, we mimicked dynamic microbial ecosystems under pressure from subtle perturbations by adding a key microbial species and comparing network topologies. The present study is a comprehensive investigation of how a network-oriented method can be used to track microbiome dynamics after a key species, S. acidaminiphila, is added into anaerobic digestion reactors of swine manure. Microbial networks before and after bioaugmentation with S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes.Conclusions: This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

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Using network analysis to explore co-occurrence patterns in soil microbial communities

The ISME Journal ◽

10.1038/ismej.2011.119 ◽

2011 ◽

Vol 6 (2) ◽

pp. 343-351 ◽

Cited By ~ 838

Author(s):

Albert Barberán ◽

Scott T Bates ◽

Emilio O Casamayor ◽

Noah Fierer

Keyword(s):

Network Analysis ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Occurrence Patterns

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Global-scale structure of the eelgrass microbiome

10.1101/089797 ◽

2016 ◽

Cited By ~ 3

Author(s):

Ashkaan K Fahimipour ◽

Melissa R Kardish ◽

Jonathan A Eisen ◽

Jenna M Lang ◽

Jessica L Green ◽

...

Keyword(s):

Microbial Communities ◽

Spatial Scales ◽

Metabolic Modeling ◽

Global Scale ◽

Functional Roles ◽

Spatial Turnover ◽

Sulfur Oxidizing ◽

And Performance ◽

Occurrence Patterns ◽

Root Surfaces

AbstractPlant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial plant species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrassZostera marinathroughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of their surrounding seawater and sediment communities, we uncovered the structure, composition and variability of microbial communities associated withZ. marina. We also investigated hypotheses about the mechanisms driving assembly of the eelgrass microbiome using a whole-genomic metabolic modeling approach. Our results reveal aboveground leaf communities displaying high variability and spatial turnover, that strongly mirror their adjacent coastal seawater microbiomes. In contrast, roots showed relatively low spatial turnover and were compositionally distinct from surrounding sediment communities — a result largely driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Metabolic modeling of enriched taxa was consistent with an assembly process whereby similarity in resource use drives taxonomic co-occurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a coreZ. marinaroot microbiome with putative functional roles and highlights potentially disparate processes influencing microbiome assembly on different plant compartments.

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