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

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. 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.Gordon and Betty Moore Foundation (Grant 3777)Agouron Institute (AI-MO9.12.1)National Science Foundation (U.S.). Center for Microbial Oceanography: Research and Education (EF0424599)Simons Foundation (Award 329108)National Science Foundation (U.S.) (Postdoctoral Research Fellowship in Biology DBI-1202684

Major Role of Microbes in Carbon Fluxes during Austral Winter in the Southern Drake Passage

Carbon cycling in Southern Ocean is a major issue in climate change, hence the need to understand the role of biota in the regulation of carbon fixation and cycling. Southern Ocean is a heterogeneous system, characterized by a strong seasonality, due to long dark winter. Yet, currently little is known about biogeochemical dynamics during this season, particularly in the deeper part of the ocean. We studied bacterial communities and processes in summer and winter cruises in the southern Drake Passage. Here we show that in winter, when the primary production is greatly reduced, Bacteria and Archaea become the major producers of biogenic particles, at the expense of dissolved organic carbon drawdown. Heterotrophic production and chemoautotrophic CO2 fixation rates were substantial, also in deep water, and bacterial populations were controlled by protists and viruses. A dynamic food web is also consistent with the observed temporal and spatial variations in archaeal and bacterial communities that might exploit various niches. Thus, Southern Ocean microbial loop may substantially maintain a wintertime food web and system respiration at the expense of summer produced DOC as well as regenerate nutrients and iron. Our findings have important implications for Southern Ocean ecosystem functioning and carbon cycle and its manipulation by iron enrichment to achieve net sequestration of atmospheric CO2

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

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. 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 in situ in the ocean’s interior

List of GenBank accession number and closest relative to 16S rDNA bacterial sequences obtained from DGGE.

*<p>phylotypes found in both seasons. Ref. = References of the closest relative.</p

List and parameters of stations sampled for bacterial community analysis.

*<p>positive temperatures in summer at surface, in winter at depth.</p

Areal data from summer 2004 and winter 2006 cruises.

<p>All parameters for the summer cruise have been integrated over the entire euphotic layer (1% incident PAR at surface; it was similar to the mixed layer depth or deeper). The winter PP has been integrated over the euphotic layer while other parameters have been integrated over the mixed layer depth (epipelagic) and from there down to 750 m (mesopelagic layer). Averages and standard deviation in parenthesis.</p><p>PP = primary production; BCP = bacterial carbon production; Summer excess DOC = summer dissolved organic carbon values minus average winter constant value (36.5±2.8 µM C s.d.); BCD = bacterial carbon demand (BCP/bacterial growth efficiency); N.D. = not determined.</p>*<p>BCD calculated using a bacterial growth efficiency derived by the curve in ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006941#pone.0006941-Rivkin1" target="_blank">[20]</a> (∼36% in summer and 39% in winter).</p>**<p>BCD calculated using bacterial growth efficiency of 13% in summer and 6.2% in winter (averaging all data for summer and only HNLC for winter from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006941#pone.0006941-Obernosterer1" target="_blank">[12]</a>).</p>§<p>no s.d. reported because the value is derived from a single depth profile.</p>°<p>DOC data for winter are not reported, since they are considered as constant refractory DOC values, and have been used to determine summer excess DOC.</p