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Whalefall microbes

Whale-falls represent localized areas of extreme organic enrichment in an otherwise oligotrophic deep-sea environment. We currently have two projects investigating the diversity and temporal evolution of microbes in sediments under deep-sea whale-falls in Monterey Canyon (CA). We have a unique opportunity to study natural and implanted whale falls that are well defined, accessible, and routinely sampled. Whale falls have been studied in the past, but never at such a temporal and spatial scale, with so many in one region, at one time, at so many depths. In these studies, we combine culture-independent molecular analyses with geochemical measurements in order to characterize changes in the distribution and activities of the microbial community, compared to the surrounding deep-sea sediments.

1) Methane cycling and phylogenetic diversity of archaea

Anaerobic remineralization within these habitats is typically portrayed as sulfidogenic, however, we have realized that these systems are also favorable for diverse methane-producing archaeal assemblages, representing up to 40% of total cell counts. Chemical analyses revealed elevated methane and depleted sulfate concentrations in sediments under the whale-fall, as compared to surrounding sediments. Carbon is enriched (up to 3.5%) in whale-fall sediments, as well as the surrounding seafloor to at least 10 m, forming a "bulls-eye" of elevated carbon. The diversity of sedimentary archaea associated with the 2893 m whale-fall in Monterey Canyon (California) varies both spatially and temporally, including methanogenic members of the Methanomicrobiales and Methanosarcinales. Interestingly, temporal changes in the archaeal community include the early establishment of methylotrophic methanogens followed by development of methanogens thought to be hydrogenotrophic, as well as members related to the newly described methanotrophic lineage, ANME-3. In comparison, archaeal assemblages in 'reference' sediments collected 10 m from the whale-fall primarily consisted of Crenarchaeota affiliated with marine group 1 and marine benthic group B. Overall, our results indicate that whale-falls can favor the establishment of metabolically and phylogenetically diverse methanogen assemblages resulting in an active near seafloor methane cycle in the deep sea. We plan to build on these initial observations to further understand the local physico-chemical environment supporting enhanced microbial activity and methane production in this unusual seafloor environment.

Goffredi, S., R.Wilpiszeski, R. Lee, V. J. Orphan (2008). Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale fall in Monterey Canyon (CA). The ISME Journal. 2: 204-220.

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2) The role of fermentative bacteria in carbon degradation in marine sediments

We suspect that active fermentation provides a surplus of H2 and supports the establishment of hydrogenotrophic methanogens (described above). Degradation of organic matter results from the cooperation of many microbial groups; much like an assembly line of bacteria performing a variety of functions. Heterotrophic bacteria involved in the early stages of organic carbon breakdown in marine sediments are thought to significantly influence the ecology of many other microbial groups, including fermenters, and terminal sulfate reducers and methanogens. Their breakdown of organic matter results in smaller compounds that are biologically available to lower trophic groups. In turn, these groups, by their production of acetate, hydrogen, and even smaller compounds, facilitate the specific activity of microbes involved in the terminal steps in organic matter degradation. The entire assembly line must cooperate and function in order for organic material to be recycled and, thus the critical first step that affects the entire ecosystem is the breakdown of organic compounds by heterotrophic bacteria. Most organic material in nature consists of large molecules that cannot directly enter cells. Before these compounds can be incorporated into bacterial cells, for instance, these substances must undergo initial degradation by a variety of enzymes. We are currently investigating the degradation of organic carbon in sediments under whale falls via measures of extracellular enzyme activity and 16S rRNA surveys of the bacterial population.

Goffredi, S.K. and V.J. Orphan (2010) Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea. Environ. Microbiol. 12: 344-363