@article {ISI:000328605200015,
	title = {{Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane}},
	journal = {ISME JOURNAL},
	volume = {8},
	number = {1},
	year = {2014},
	month = {jan},
	pages = {150{\textendash}163},
	type = {Article},
	abstract = {Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher N-15-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {1751-7362},
	doi = {10.1038/ismej.2013.147},
	author = {Green-Saxena, A and Dekas, A E and Dalleska, N F and Orphan, V J}
}
@article {Thurber2012,
	title = {{Archaea in metazoan diets: implications for food webs and biogeochemical cycling}},
	journal = {ISME Journal},
	volume = {6},
	number = {8},
	year = {2012},
	pages = {1602{\textendash}1612},
	publisher = {International Society for Microbial Ecology},
	abstract = {Although the importance of trophic linkages, including {\textquoteleft}top-down forcing{\textquoteright}, on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk $δ$13C=-92{\textpm}4{\textperthousand}; polar lipids -116{\textperthousand}) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as {\textquoteleft}archivory{\textquoteright}.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1751-7362},
	doi = {10.1038/ismej.2012.16},
	url = {http://www.nature.com/ismej/journal/v6/n8/suppinfo/ismej201216s1.html},
	author = {Thurber, A R and Levin, L A and Orphan, V J and Marlow, J J}
}
@booklet {Levin2012,
	title = {{A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems}},
	howpublished = {Proceedings of the Royal Society B: Biological Sciences},
	volume = {279},
	number = {1738},
	year = {2012},
	pages = {2580{\textendash}2588},
	abstract = {Upon their initial discovery, hydrothermal vents and methane seeps were considered to be related but distinct ecosystems, with different distributions, geomorphology, temperatures, geochemical properties and mostly different species. However, subsequently discovered vents and seep systems have blurred this distinction. Here, we report on a composite, hydrothermal seep ecosystem at a subducting seamount on the convergent Costa Rica margin that represents an intermediate between vent and seep ecosystems. Diffuse flow of shimmering, warm fluids with high methane concentrations supports a mixture of microbes, animal species, assemblages and trophic pathways with vent and seep affinities. Their coexistence reinforces the continuity of reducing environments and exemplifies a setting conducive to interactive evolution of vent and seep biota.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	doi = {10.1098/rspb.2012.0205},
	url = {http://rspb.royalsocietypublishing.org/content/279/1738/2580.abstract},
	author = {Levin, L A and Orphan, V J and Rouse, G W and Rathburn, A E and Ussler, W and Cook, G S and Goffredi, S K and Perez, Elena M and Waren, A and Grupe, B M and Chadwick, G and Strickrott, B}
}
@article {Bailey2011,
	title = {{Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria}},
	journal = {ISME Journal},
	volume = {5},
	number = {12},
	year = {2011},
	pages = {1926{\textendash}1935},
	publisher = {International Society for Microbial Ecology},
	abstract = {We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1751-7362},
	doi = {10.1038/ismej.2011.66},
	url = {http://www.nature.com/ismej/journal/v5/n12/suppinfo/ismej201166s1.html 10.1038/ismej.2011.66},
	author = {Bailey, J V and Salman, V and Rouse, G W and Schulz-Vogt, H and Levin, L A and Orphan, V J}
}
@article {Bailey2010,
	title = {{Pseudofossils in relict methane seep carbonates resemble endemic microbial consortia}},
	journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	volume = {285},
	number = {1-2},
	year = {2010},
	pages = {131{\textendash}142},
	abstract = {Pleistocene-age methane seep carbonates from the Eel River Basin, California contain aggregate-like structures composed of tightly-packed hollow spheres that morphologically resemble syntrophic archaeal{\textendash}bacterial consortia known to catalyze the anaerobic oxidation of methane (AOM). Tetragonal microstructures also present in the carbonates resemble seep-endemic Methanosarcinales cell clusters. Despite morphological similarities to the seep-endemic microbes that likely mediated the authigenesis of Eel River Basin carbonates and sulfides, detailed petrographic, SEM, and magnetic microscopic imaging, remanence rock magnetism, laser Raman, and energy dispersive X-ray spectroscopy, suggest that these microstructures are not microfossils, but rather mineral structures that result from the diagenetic alteration of euhedral Fe-sulfide framboids. Electron microscopy shows that during diagenesis, reaction rims composed of Fe oxide form around framboid microcrystalites. Subsequent dissolution of greigite or pyrite crystals leaves behind hollow cell-like casings (external molds) {\textemdash} a transformation that occurs on timescales of \~{}100 kyr or less. Despite their superficial resemblance to morphologically-distinctive extant microbes in local sediments, the presence of acellular precursor grains, as well as of partially-altered transitional forms, complicate the interpretation of these and other framboidal microstructures that have been reported from the rock record.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0031-0182},
	doi = {10.1016/j.palaeo.2009.11.002},
	url = {http://dx.doi.org/10.1016/j.palaeo.2009.11.002},
	author = {Bailey, J V and Raub, T D and Meckler, A N and Harrison, B K and Raub, T M D and Green, A M and Orphan, V J}
}
