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Title: Phylogenetically conserved resource partitioning in the coastal microbial loop

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.
Authors:
ORCiD logo [1] ;  [2] ;  [3] ;  [4] ;  [4] ;  [2] ;  [2] ;  [4] ;  [1]
  1. Oregon State Univ., Corvallis, OR (United States). Dept. of Microbiology
  2. Univ. of Tennessee, Knoxville, TN (United States). Graduate School of Genome Science and Technology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Publication Date:
Grant/Contract Number:
AC05-00OR22725; AC52-07NA27344; GBMF3302
Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 11; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Research Org:
Oregon State Univ., Corvallis, OR (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Gordon and Betty Moore Foundation (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1394611

Bryson, Samuel, Li, Zhou, Chavez, Francisco, Weber, Peter K., Pett-Ridge, Jennifer, Hettich, Robert L., Pan, Chongle, Mayali, Xavier, and Mueller, Ryan S.. Phylogenetically conserved resource partitioning in the coastal microbial loop. United States: N. p., Web. doi:10.1038/ismej.2017.128.
Bryson, Samuel, Li, Zhou, Chavez, Francisco, Weber, Peter K., Pett-Ridge, Jennifer, Hettich, Robert L., Pan, Chongle, Mayali, Xavier, & Mueller, Ryan S.. Phylogenetically conserved resource partitioning in the coastal microbial loop. United States. doi:10.1038/ismej.2017.128.
Bryson, Samuel, Li, Zhou, Chavez, Francisco, Weber, Peter K., Pett-Ridge, Jennifer, Hettich, Robert L., Pan, Chongle, Mayali, Xavier, and Mueller, Ryan S.. 2017. "Phylogenetically conserved resource partitioning in the coastal microbial loop". United States. doi:10.1038/ismej.2017.128. https://www.osti.gov/servlets/purl/1394611.
@article{osti_1394611,
title = {Phylogenetically conserved resource partitioning in the coastal microbial loop},
author = {Bryson, Samuel and Li, Zhou and Chavez, Francisco and Weber, Peter K. and Pett-Ridge, Jennifer and Hettich, Robert L. and Pan, Chongle and Mayali, Xavier and Mueller, Ryan S.},
abstractNote = {Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.},
doi = {10.1038/ismej.2017.128},
journal = {The ISME Journal},
number = ,
volume = 11,
place = {United States},
year = {2017},
month = {8}
}

Works referenced in this record:

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340