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Title: Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

Abstract

Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transportmore » and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. In conclusion, these data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as well as the rapid responses of indigenous microbial species in the degradation of marine particulate organic matter (POM) in situ in the ocean's interior.« less

Authors:
 [1];  [2];  [3];  [4];  [2]
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  2. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Univ. of Hawaii, Honolulu, HI (United States)
  3. Univ. of Hawaii, Honolulu, HI (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  4. Univ. of Hawaii, Honolulu, HI (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF)
OSTI Identifier:
1259661
Alternate Identifier(s):
OSTI ID: 1418923
Report Number(s):
LLNL-JRNL-735612
Journal ID: ISSN 1664-302X
Grant/Contract Number:  
EF0424599; 329108; 3777; 3794; AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; metagenomics; marineparticles; sedimenttrap; biological pump; microbiology; 54 ENVIRONMENTAL SCIENCES

Citation Formats

Fontanez, Kristina M., Eppley, John M., Samo, Ty J., Karl, David M., and DeLong, Edward F.. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. United States: N. p., 2015. Web. doi:10.3389/fmicb.2015.00469.
Fontanez, Kristina M., Eppley, John M., Samo, Ty J., Karl, David M., & DeLong, Edward F.. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. United States. doi:10.3389/fmicb.2015.00469.
Fontanez, Kristina M., Eppley, John M., Samo, Ty J., Karl, David M., and DeLong, Edward F.. Tue . "Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre". United States. doi:10.3389/fmicb.2015.00469. https://www.osti.gov/servlets/purl/1259661.
@article{osti_1259661,
title = {Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre},
author = {Fontanez, Kristina M. and Eppley, John M. and Samo, Ty J. and Karl, David M. and DeLong, Edward F.},
abstractNote = {Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. In conclusion, these data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as well as the rapid responses of indigenous microbial species in the degradation of marine particulate organic matter (POM) in situ in the ocean's interior.},
doi = {10.3389/fmicb.2015.00469},
journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {5}
}

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Works referenced in this record:

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides
journal, October 2010

  • Vaaje-Kolstad, Gustav; Westereng, Bjørge; Horn, Svein J.
  • Science, Vol. 330, Issue 6001, p. 219-222
  • DOI: 10.1126/science.1192231