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

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

FEMS Microbiology Ecology ◽

10.1093/femsec/fiy230 ◽

2018 ◽

Vol 95 (2) ◽

Cited By ~ 3

Author(s):

M A Wadud Khan ◽

Brendan J M Bohannan ◽

Klaus Nüsslein ◽

James M Tiedje ◽

Susannah G Tringe ◽

...

Keyword(s):

Microbial Communities ◽

Occurrence Patterns

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A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field

Canadian Journal of Microbiology ◽

10.1139/m86-063 ◽

1986 ◽

Vol 32 (4) ◽

pp. 319-325 ◽

Cited By ~ 19

Author(s):

Thomas W. Federle ◽

Robert J. Livingston ◽

Loretta E. Wolfe ◽

David C. White

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Structure ◽

Ecological Factors ◽

Estuarine Sediments ◽

Physical Factors ◽

Multivariate Statistical ◽

Apalachicola Bay ◽

Sound Experiment

Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow of the Apalachicola River. In the St. George Sound experiment, microbial communities in the microcosms differed from those in the field after only 2 weeks, and the degree of this difference increased substantially as time progressed. In the Apalachicola Bay experiment, although microbial communities in the microcosms were detectably different from those in the field, the degree of this difference was not large nor did it increase with time. This differential behavior of sediment communities from different sites may be related to the different ecological factors regulating community composition at these sites.

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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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Differential microbial communities in paddy soils between Guiyang plateaus and Chengdu basins drive the incidence of rice bacterial diseases

Plant Disease ◽

10.1094/pdis-09-21-1974-re ◽

2022 ◽

Author(s):

Yajiao Wang ◽

Shuping Tian ◽

Nan Wu ◽

Wenwen Liu ◽

Li Li ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Chemical Properties ◽

Ecological Factors ◽

Severity Index ◽

Paddy Soils ◽

Bacterial Diseases ◽

Soil Microbial

Southwest China has the most complex rice-growing regions in China. With great differences in topography, mainly consisting of basins and plateaus, ecological factors in above region differ greatly. In this study, bulk paddy soils collected from a long-term rice field in Chengdu (basins) and in Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared more than 70% of the dominant genera (abundance > 1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively related with the higher incidence of rice bacterial foot rot in Guiyang, while temperature had a greater effect on soil microbial functions and positively related with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.

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Demonstration of facilitation between microalgae to face environmental stress

Scientific Reports ◽

10.1038/s41598-019-52450-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Emna Krichen ◽

Alain Rapaport ◽

Emilie Le Floc’h ◽

Eric Fouilland

Keyword(s):

Environmental Stress ◽

Microbial Communities ◽

Ammonia Nitrogen ◽

High Rate ◽

Ammonia Toxicity ◽

Algal Community ◽

Positive Interactions ◽

Pioneer Species ◽

Freshwater Microalgae ◽

Ecological Interaction

Abstract Positive interactions such as facilitation play an important role during the biological colonization and species succession in harsh or changing environments. However, the direct evidence of such ecological interaction in microbial communities remains rare. Using common freshwater microalgae isolated from a High Rate Algal Pond HRAP treating wastewaters, we investigated with both experimental and modeling approaches the direct facilitation between two algal strains during the colonization phase. Our results demonstrate that the first colonization by microalgae under a severe chemical condition arose from the rapid growth of pioneer species such as Chlorella sorokiniana, which facilitated the subsequent colonization of low growth specialists such as Scenedesmus pectinatus. The pioneer species rapidly depleted the total available ammonia nitrogen favoring the specialist species initially inhibited by free ammonia toxicity. This latter species ultimately dominated the algal community through competitive exclusion under low nutrient conditions. We show that microbial successions are not only regulated by climatic conditions but also by interactions between species based on the ability to modify their growth conditions. We suggest that facilitation within the aquatic microbial communities is a widespread ecological interaction under a vast range of environmental stress.

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Impact of Environmental Stress-Tolerant Transgenic Potato on Genotypic Diversity of Microbial Communities and Soil Enzyme Activities under Stress Conditions

Microbes and Environments ◽

10.1264/jsme2.23.221 ◽

2008 ◽

Vol 23 (3) ◽

pp. 221-228 ◽

Cited By ~ 4

Author(s):

Makiko Mimura ◽

Kipkorir E. Lelmen ◽

Takayoshi Shimazaki ◽

Akira Kikuchi ◽

Kazuo N. Watanabe

Keyword(s):

Environmental Stress ◽

Microbial Communities ◽

Enzyme Activities ◽

Genotypic Diversity ◽

Transgenic Potato ◽

Soil Enzyme ◽

Stress Conditions ◽

Soil Enzyme Activities

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Authentic soil microbial communities in primeval forest ecosystems of Uzhanskyi National Nature Park

Fundamental and Applied Soil Science ◽

10.15421/041715 ◽

2017 ◽

Vol 18 (3-4) ◽

pp. 51-56

Author(s):

L. Yu. Symochko ◽

A. I. Fizer

Keyword(s):

Microbial Communities ◽

Functional Diversity ◽

Soil Microorganisms ◽

Soil Microbial Communities ◽

Ecological Factors ◽

Human Welfare ◽

Soil Microbiota ◽

High Productivity ◽

Soil Microbial ◽

Biomass Influence

The article presents the modern aspects of studying and evaluating the biodiversity of soil microbiocenoses in the Carpathian region. The purpose of the work was to investigate the soil microbiota of virgin ecosystems, namely the structure of microbial communities, the number of major ecological trophic groups; to analyze the successional processes occurring in the soil microbiocenosis due to the influence of endogenous and exogenous factors. Anthropogenic impact: soil compaction, sanitary felling has led to changes in the groups of soil microorganisms, reduced their numbers and functional diversity. The primeval forests as etalon ecosystems better combine above resistance and stability with high productivity of biomass. Influence of ecological factors caused changes in the community of soil organisms, varied their abundance and functional diversity. Soil microorganisms have been largely ignored by conservation efforts. However, their role in biogeochemical processes, their diversity and abundance, and their potential as repositories of valuable genetic information and metabolic products make them as important as animals and plants to the biosphere and human welfare. Study of authentic soil microbiota creates the necessary prerequisites for the conservation of microbial diversity and forming the base of the eco-microbiological monitoring.

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Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions

PeerJ ◽

10.7717/peerj.8217 ◽

2019 ◽

Vol 7 ◽

pp. e8217 ◽

Cited By ~ 6

Author(s):

Tuomas Aivelo ◽

Anna Norberg ◽

Barbara Tschirren

Keyword(s):

Microbial Communities ◽

Ixodes Ricinus ◽

Ecological Factors ◽

Environmental Variation ◽

Swiss Alps ◽

Small Scale ◽

Human Pathogens ◽

Environmental Preferences ◽

Bacterial Microbiota

Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.

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