Strengthening Insights in Microbial Ecological Networks from Theory to Applications

Lv, Xiaofei; Zhao, Kankan; Xue, Ran; Liu, Yuanhui; Xu, Jianming; Ma, Bin

doi:10.1128/msystems.00124-19

Cited by 40 publications

(27 citation statements)

References 14 publications

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“…To address and overcome this challenge, we developed a combined bioinformatics pipeline and network theory approach that was applied to a large, geographically diverse 16S rRNA dataset of four extreme aquatic environments to determine the ecological relevance of the unknown organisms in these communities. Although correlation-based microbial networks cannot infer the nature of ecological relationships, such as syntrophy or competition, they are indicative of social interactions within the community and can serve as important focal points for downstream analyses [54]. Our analysis clearly showed that the unclassified and uncultured taxa were prevalent and represented a significant proportion of the microbial diversity in all ecosystems examined, and therefore, should not be overlooked when examining community dynamics.…”

Section: Discussionmentioning

confidence: 78%

A network approach to elucidate and prioritize microbial dark matter in microbial communities

Foster²,

et al. 2020

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Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as “microbial dark matter,” represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment. Here, we establish a method to study the ecological significance of “microbial dark matter” by building microbial co-occurrence networks from publicly available 16S rRNA gene sequencing data of four extreme aquatic habitats. For each environment, we constructed networks including and excluding unknown organisms at multiple taxonomic levels and used network centrality measures to quantitatively compare networks. When the Unknown taxa were excluded from the networks, a significant reduction in degree and betweenness was observed for all environments. Strikingly, Unknown taxa occurred as top hubs in all environments, suggesting that “microbial dark matter” play necessary ecological roles within their respective communities. In addition, novel adaptation-related genes were detected after using 16S rRNA gene sequences from top-scoring hub taxa as probes to blast metagenome databases. This work demonstrates the broad applicability of network metrics to identify and prioritize key Unknown taxa and improve understanding of ecosystem structure across diverse habitats.

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Section: Discussionmentioning

confidence: 78%

A network approach to elucidate and prioritize microbial dark matter in microbial communities

Foster²,

et al. 2020

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“…The field of microbial networks is relatively new and should be developed based on the years of experience in studying plant and animal communities (52, . However, we still lack strong evidence of the ecological interpretation that exists in network inference, which needs more experimental verification in the future (54).…”

mentioning

confidence: 92%

Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

et al. 2020

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Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.

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“…These networks could be used to identify alternative community regimes, species interactions, and keystone species. However, their interpretation is not straightforward; while they represent an adequate tool to explore ecological associations, the implications of such associations are uncertain, and it is disputed to which degree biotic interactions can be recapitulated using available methods [70] , [71] , [72] .…”

Section: Methodsmentioning

confidence: 99%

Experimental and computational approaches to unravel microbial community assembly

Cárcer

2020

Computational and Structural Biotechnology Journal

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Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.

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Strengthening Insights in Microbial Ecological Networks from Theory to Applications

Cited by 40 publications

References 14 publications

A network approach to elucidate and prioritize microbial dark matter in microbial communities

A network approach to elucidate and prioritize microbial dark matter in microbial communities

Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

Experimental and computational approaches to unravel microbial community assembly

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