A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology

Tang, Yushi; Dai, Tianjiao; Su, Zhiguo; Hasegawa, Kohei; Tian, Jinfeng; Chen, Lüjun; Wen, Donghui

doi:10.1007/s00248-019-01421-8

Cited by 8 publications

(4 citation statements)

References 69 publications

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“…Similarly, phosphorus (P) has been recognized as one of the critical factors limiting the growth of microbes (Beck et al, 2017), and P‐related indices have been determined across thousands of sites (Figure 7b). Other physicochemical properties, such as total organic carbon (TOC), heavy metals, chemical oxygen demand (COD), salinity, and sulfates, are also critical to shaping microbial communities (J. Chen, Wang, et al, 2019; Y. Li et al, 2019; Peng et al, 2020; Tang et al, 2020). However, these parameters have been far less investigated than the aforementioned physicochemical properties (Figure 7b).…”

Section: Physicochemical Properties Examined In Riverine Microbial Re...mentioning

confidence: 99%

“…Other physicochemical properties, such as total organic carbon (TOC), heavy metals, chemical oxygen demand (COD), salinity, and sulfates, are also critical to shaping microbial communities (J. Chen, Wang, et al, 2019;Peng et al, 2020;Tang et al, 2020). However, these parameters have been far less investigated than the aforementioned physicochemical properties (Figure 7b).…”

Section: Physicochemical Properties Examined In Riverine Microbial Re...mentioning

confidence: 99%

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Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

et al. 2021

WIREs Water

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Microbial abundance and diversity in river ecosystems are being increasingly investigated, yet a synthesized understanding is still lacking. Here, studies of microbial abundance and diversity along global rivers are systematically reviewed based on 814 investigations performed across 8376 sites. We found that riverine microbial investigations are extremely heterogeneous regarding the spatiotemporal distribution of the sampling sites, the environmental media concerned, the microbial groups and indices targeted, the methods used, and the physicochemical properties examined. More than 72.23% of the studies were performed in the last 8 years, with most studies conducted in Europe, China, and the United States, while other regions were poorly investigated. Most studies have examined microbes in water, but very few studies have systematically investigated microbes in water, sediments, and riparian soils. Bacteria are the most studied microbial taxonomic groups; microbes with resistance genes and nitrogen cycling genes are the most studied microbial functional groups.High-throughput sequencing has greatly expanded our understanding of microbial diversity along rivers. Nevertheless, the ecological implications of microbial diversity are still poorly understood. Regarding physicochemical properties, researchers tend to examine environmental parameters that are critical for shaping microbial communities, such as pH, nitrogen, and phosphorus. Future research should pay more attention to rivers that have not been well studied, especially large rivers. Additionally, microbial studies along rivers should be conducted in a more systematic way, taking the underinvestigated environmental media, microbial groups, microbial indices, and physicochemical properties into consideration. Advanced microbiology techniques, such as multiple omics technologies, should be increasingly applied.

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Section: Physicochemical Properties Examined In Riverine Microbial Re...mentioning

confidence: 99%

Section: Physicochemical Properties Examined In Riverine Microbial Re...mentioning

confidence: 99%

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

et al. 2021

WIREs Water

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“…Other resources like Microbe Directory [41], Web of Microbes (WoM) [42], and Microbial Interaction Network Database (MIND) [43] focus on microbial environmental conditions, metabolite interactions with microbes and microbe-microbe interactions, respectively. In addition, taking advantage of aforementioned resources, novel pipelines, e.g., [44], are emerging with the aim to explore the network associations of who (microbial taxa) is performing what (microbial processes) and where (environments) directly using graph theory [45]. These analyses and resources are important because microbiologists can enrich their data to explore hypotheses but also to identify potential gaps in knowledge regarding these associations [46].…”

Section: Introductionmentioning

confidence: 99%

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

et al. 2022

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To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.

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“…Abundance and connection advantages are other factors that gives the SAR11 group has a better chance of interacting with other community members (Tang et al, 2020).…”

Section: Ld12 Is a Keystone Organism In A Tropical Quarry Lake Systemmentioning

confidence: 99%

Development of novel molecular tools to study the dynamics of individual SAR11 phylotypes in microbial communities

Poorna¹

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A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology

Cited by 8 publications

References 69 publications

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

Development of novel molecular tools to study the dynamics of individual SAR11 phylotypes in microbial communities

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