TY - JOUR
T1 - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions
AU - Zoccarato, Luca
AU - Sher, Daniel
AU - Miki, Takeshi
AU - Segrè, Daniel
AU - Grossart, Hans Peter
N1 - © 2022. The Author(s).
PY - 2022/3/28
Y1 - 2022/3/28
N2 - Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3–8%) and different B vitamins (57–70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
AB - Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3–8%) and different B vitamins (57–70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
KW - Bacteria/metabolism
KW - Ecology
KW - Microbial Interactions
KW - Microbiota/genetics
KW - Phytoplankton/genetics
UR - http://www.scopus.com/inward/record.url?scp=85127259807&partnerID=8YFLogxK
U2 - https://doi.org/10.1038/s42003-022-03184-4
DO - https://doi.org/10.1038/s42003-022-03184-4
M3 - Article
C2 - 35347228
SN - 2399-3642
VL - 5
SP - 276
JO - Communications Biology
JF - Communications Biology
IS - 1
M1 - 276
ER -