Deciphering Metabolic Currencies That Support Marine Microbial Networks

Durham, Bryndan P.

doi:10.1128/msystems.00763-21

Cited by 11 publications

(4 citation statements)

References 25 publications

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“…Given the many thousands of individual microbial species and metabolites present in seawater communities, it has been challenging to connect specific metabolic processes to the microbial taxa responsible (Cavaco et al, 2022;Paoli et al, 2022). Advances in molecular and chemical tools have improved resolution and identification of microbially cycled metabolites in seawater communities (Moran et al, 2016;Durham, 2021;Vallet et al, 2021;Raina et al, 2022). Genome-based studies of marine microbial plankton have been useful in reconstructing potential metabolisms, ecological functions, and evolutionary relationships of taxonomic groups.…”

Section: Introductionmentioning

confidence: 99%

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

et al. 2022

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Most biological diversity on Earth is contained within microbial communities. In the ocean, these communities dominate processes related to carbon fixation and nutrient recycling. Yet, specific factors that determine community composition and metabolic activity are difficult to resolve in complex microbial populations, complicating predictions of microbial processes in a changing ocean. Microbial metabolism generates small organic molecules that reflect both the biochemical and physiological diversity as well as the taxonomic specificity of these biological processes. These small molecules serve as the conduit for taxon-specific signaling and exchange. Here, we use liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to taxonomically categorize 111 metabolites that include small molecules in central and secondary metabolism across 42 taxa representing numerically dominant and metabolically important lineages of microbial autotrophs and heterotrophs. Patterns in metabolite presence-absence broadly reflected taxonomic lineages. A subset of metabolites that includes osmolytes, sulfurcontaining metabolites, sugars, and amino acid derivatives provided chemotaxonomic information among phytoplankton taxa. A variety of phytohormones and signaling molecules were predominantly found in the heterotrophic bacteria and archaea, expanding knowledge of metabolites implicated in modulating interactions between microbes. This chemotaxonomic inventory of marine microbial metabolites is a key step in deciphering metabolic networks that influence ocean biogeochemical cycles.

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Section: Introductionmentioning

confidence: 99%

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

et al. 2022

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“…Modelling of metabolism is also useful to explore communities of organisms (Vázquez‐Castellanos et al ., 2019). This family of approaches is particularly timely because we are beginning to understand, through the study of seawater, what metabolic ‘currencies’ are shared by the millions of microbes that coexist in this environment (Durham, 2021). Microbial co‐cultures have been studied using FBA, with interesting observations involving cross‐feeding (Konstantinidis et al ., 2021).…”

Section: Synthetic Biology In Silicomentioning

confidence: 99%

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

Danchin

2021

Microbial Biotechnology

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Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computeraided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

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confidence: 99%

“…Interactions between microbial species and other organisms guarantee ecosystem functions by contributing to community structure, activity, and resistance to environmental changes (Amin et al, 2012;Bjorbaekmo et al, 2020;Durham, 2021;Farnelid et al, 2021);. The most common interactions include competition, mutualism, and parasitism (Amin et al, 2012;Faust and Raes, 2012;Bjorbaekmo et al, 2020;Durham, 2021). Co-occurrence network analyses can assess the importance of biotic interactions (Milici et al, 2016;Brisson et al, 2019;Anderson and Harvey, 2020;Hoshino et al, 2020), which have been recognized as powerful tools to study how microorganisms are involved in the functioning of the ecosystem in sediments (Hoshino et al, 2020) and marine water (Cui et al, 2019;Hou et al, 2020).…”

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confidence: 99%

Co-occurrence and diversity patterns of benthonic and planktonic communities in a shallow marine ecosystem

et al. 2022

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Marine microorganisms are involved in a variety of biogeochemical cycles and live in diverse ecological communities where they interact with each other and with other organisms to guarantee ecosystem functions. The present study focused on a shallow marine environment located in Ría de Vigo (NW, Spain), where sediment and size-fractionated plankton samples were collected from 2016 to 2018. DNA metabarcoding was used to describe the eukaryote and prokaryote composition and diversity in sediments and plankton and to depict possible associations among the most frequent and abundant organisms by co-occurrence network analysis. High eukaryote and prokaryote diversity indices were obtained in all compartments. Significant differences among eukaryote and prokaryote communities were found between sediment and plankton samples, with a high percentage of exclusive operational taxonomic units (OTUs) associated with each compartment, especially from sediment. Despite these differences, shared taxa between water and sediment were also obtained, suggesting a relatively meaningful exchange of organisms between both environmental compartments. Significant co-occurrences were mainly obtained between prokaryotes (41%), followed by eukaryotes–prokaryotes (32%) and between eukaryotes (27%). The abundant and strong positive correlations between organisms, including representatives from the sediment and the water column, suggested an essential role of biotic interactions as community-structuring factors in shallow waters where beneficial associations likely prevail. This study provides a novel approach for the detailed description of the eukaryote and prokaryote diversity and co-occurrence patterns in a shallow marine area, including both the sediment and different water-size fractions. The high diversity obtained and the detection of predominantly coexisting interactions among organisms from sediment and the overlying water column suggest a movement of species between both habitats and therefore confirm the importance of integratively studying shallow marine ecosystems.

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Deciphering Metabolic Currencies That Support Marine Microbial Networks

Cited by 11 publications

References 25 publications

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

Co-occurrence and diversity patterns of benthonic and planktonic communities in a shallow marine ecosystem

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