Strengthening Insights in Microbial Ecological Networks from Theory to Applications

ABSTRACT Networks encode the interactions between the components in complex systems and play an essential role in understanding complex systems. Microbial ecological networks provide a system-level insight for comprehensively understanding complex microbial interactions, which play important roles in microbial community assembly. However, microbial ecological networks are in their infancy of both network inference and biological interpretation. In this perspective, we articulate the theory gaps and limitations in building and interpreting microbial ecological networks, emphasize developing tools for evaluating the predicted microbial interaction relationships, and predict the potential applications of microbial ecological networks in the long run.

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Interrogation of Internal Workings in Microbial Community Assembly: Play a Game through a Behavioral Network?

mSystems ◽

10.1128/msystems.00550-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 1

Author(s):

Qian Wang ◽

Xinjuan Liu ◽

Libo Jiang ◽

Yige Cao ◽

Xiang Zhan ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Behavioral Ecology ◽

Community Assembly ◽

Association Studies ◽

Microbial Interactions ◽

Genome Wide Association Studies ◽

Rule Of Thumb ◽

Starting Point ◽

Microbial Community Assembly

ABSTRACTIncreasing evidence shows that the influence of microbiota on biogeochemical cycling, plant development, and human health is executed through a complex network of microbe-microbe interactions. However, characterizing how microbes interact and work together within closely packed and highly heterogeneous microbial ecosystems is extremely challenging. Here, we describe a rule-of-thumb framework for visualizing polymicrobial interactions and extracting general principles that underlie microbial communities. We integrate elements of metabolic ecology, behavioral ecology, and game theory to quantify the interactive strategies by which microbes at any taxonomic level compete for resources and cooperate symbiotically with each other to form and stabilize ecological communities. We show how the framework can chart an omnidirectional landscape of microbial cooperation and competition that may drive various natural processes. This framework can be implemented into genome-wide association studies to unravel the genetic mechanisms underlying microbial interaction networks and their evolutionary consequences along spatiotemporal gradients.IMPORTANCEIdentifying general biological rules that underlie the complexity and heterogeneity of microbial communities has proven to be highly challenging. We present a rule-of-thumb framework for studying and characterizing how microbes interact with each other across different taxa to determine community behavior and dynamics. This framework is computationally simple but conceptually meaningful, and it can provide a starting point to generate novel biological hypotheses about microbial interactions and explore internal workings of microbial community assembly in depth.

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Unraveling negative biotic interactions determining soil microbial community assembly and functioning

The ISME Journal ◽

10.1038/s41396-021-01076-9 ◽

2021 ◽

Author(s):

Sana Romdhane ◽

Aymé Spor ◽

Julie Aubert ◽

David Bru ◽

Marie-Christine Breuil ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Soil Microbial Community ◽

Biotic Interactions ◽

Microbial Interactions ◽

Relative Fitness ◽

Soil Microbiome ◽

Soil Microbial ◽

Microbial Community Assembly

AbstractMicrobial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.

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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

Biochemical Society Transactions ◽

10.1042/bst20190172 ◽

2020 ◽

Vol 48 (2) ◽

pp. 399-409

Author(s):

Baizhen Gao ◽

Rushant Sabnis ◽

Tommaso Costantini ◽

Robert Jinkerson ◽

Qing Sun

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Environmental Remediation ◽

Real Life ◽

Design Principles ◽

Microbial Interactions ◽

Potential Applications ◽

New Gene ◽

Global Biogeochemical Cycles ◽

Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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Faculty Opinions recommendation of Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732864671.793571177 ◽

2020 ◽

Author(s):

Stanislav Kopriva

Keyword(s):

Microbial Community ◽

Community Assembly ◽

Root Exudate ◽

Substrate Preferences ◽

Microbial Community Assembly ◽

Rhizosphere Microbial Community

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Faculty Opinions recommendation of Emergent simplicity in microbial community assembly.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733755101.793554292 ◽

2018 ◽

Author(s):

Søren Sørensen

Keyword(s):

Microbial Community ◽

Community Assembly ◽

Microbial Community Assembly

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Historical contingency impacts on community assembly and ecosystem function in chemosynthetic marine ecosystems

Scientific Reports ◽

10.1038/s41598-021-92613-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dimitri Kalenitchenko ◽

Erwan Peru ◽

Pierre E. Galand

Keyword(s):

Community Assembly ◽

Sea Water ◽

Marine Ecosystem ◽

Marine Ecosystems ◽

Metagenomic Sequencing ◽

Historical Contingency ◽

Historical Events ◽

Species Sorting ◽

Environmental Selection ◽

Microbial Community Assembly

AbstractPredicting ecosystem functioning requires an understanding of the mechanisms that drive microbial community assembly. Many studies have explored microbial diversity extensively and environmental factors are thought to be the principal drivers of community composition. Community assembly is, however, also influenced by past conditions that might affect present-day assemblages. Historical events, called legacy effects or historical contingencies, remain poorly studied in the sea and their impact on the functioning of the communities is not known. We tested the influence, if any, of historical contingencies on contemporary community assembly and functions in a marine ecosystem. To do so, we verified if different inoculum communities colonizing the same substrate led to communities with different compositions. We inoculated wood with sea water microbes from different marine environments that differ in ecological and evolutionary history. Using 16S rRNA and metagenomic sequencing, it was demonstrated that historical contingencies change the composition and potential metabolisms of contemporary communities. The effect of historical events was transient, dominated by environmental selection as, over time, species sorting was a more important driver of community assembly. Our study shows not only that historical contingencies affect marine ecosystems but takes the analysis a step further by characterizing this effect as strong but transient.

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