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 »
- Authors:
-
- Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
- Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Univ. of Hawaii, Honolulu, HI (United States)
- Univ. of Hawaii, Honolulu, HI (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Univ. of Hawaii, Honolulu, HI (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (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:
- 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. https://doi.org/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. https://doi.org/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},
number = ,
volume = 6,
place = {United States},
year = {Tue May 19 00:00:00 EDT 2015},
month = {Tue May 19 00:00:00 EDT 2015}
}
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