@article {Hansman2017,
	title = {{Methane fates in the benthos and water column at cold seep sites along the continental margin of Central and North America}},
	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	volume = {120},
	year = {2017},
	pages = {122{\textendash}131},
	abstract = {The potential influence of methane seeps on carbon cycling is a key question for global assessments, but the study of carbon cycling in surface sediments and the water column of cold seep environments is complicated by the high temporal and spatial variability of fluid and gas fluxes at these sites. In this study we directly examined carbon sources supporting benthic and planktonic food webs at venting methane seeps using isotopic and molecular approaches that integrate this variability. At four seep environments located along North and Central America, microorganisms from two size fractions were collected over several days from 2800 to 9050 l of seawater to provide a time-integrated measure of key microbial groups and the carbon sources supporting the overall planktonic microbial community. In addition to water column measurements, the extent of seafloor methane release was estimated at two of the sites by examining the stable carbon isotopic signature ($δ$13C) of benthic metazoan infauna. This signature reveals carbon sources fueling the base of the food chain and thus provides a metric that represents a time-integrated view of the dominant microbial processes within the sediment. The stable carbon isotopic composition of microbial DNA ($δ$13C-DNA), which had values between -17.0 and -19.5{\textperthousand}, indicated that bulk planktonic microbial production was not ultimately linked to methane or other 13C-depleted seep-derived carbon sources. Instead these data support the importance of organic carbon derived from either photo- or chemoautotrophic CO2 fixation to the planktonic food web. Results of qPCR of microbial DNA sequences coding for a subunit of the particulate methane monooxygenase gene (pmoA) showed that only a small percentage of the planktonic microbial community were potential methane oxidizers possessing pmoA ({\textless}5{\%} of 16S rRNA gene copies). There was an overall decrease of 13C-depleted carbon fueling the benthic metazoan community from 3 to 5 cm below the seafloor to the sediment surface, reflecting limited use of isotopically depleted carbon at the sediment surface. Rare methane emission as indicated by limited aerobic methane oxidation acts to corroborate our findings for the planktonic microbial community.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	doi = {10.1016/j.dsr.2016.12.016},
	author = {Hansman, R L and Thurber, A R and Levin, L A and Aluwihare, L I}
}
@article {Levin2013,
	title = {{Ecological release and niche partitioning under stress:lessons from dorvilleid polychaetes in sulfidic sediments at methane seeps}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {92},
	year = {2013},
	pages = {214{\textendash}233},
	abstract = {Organisms inhabiting methane seep sediments are exposed to stress in the form of high levels of hydrogen sulfide, which result mainly from sulfate reduction coupled to anaerobic methane oxidation. Dorvilleidae (Polychaeta) have successfully invaded this ecosystem, and multiple species in divergent genetic clades co-occur at high densities. At methane seeps in the NE Pacific off California and Oregon, the genera Ophryotrocha, Parougia and Exallopus are especially well represented. To test the hypothesis that dorvilleid coexistence is facilitated by niche partitioning through sulfide tolerance and trophic patterns, we examined dorvilleid species-specific patterns of occurrence and nutrition at methane seeps off Eel R. [ER] on the Californian continental slope and at Hydrate Ridge [HR] on the Oregon continental slope, and in two habitats (clam bed and microbial mat) characterized by lower and higher hydrogen sulfide levels, respectively. Microelectrode measurements of hydrogen sulfide enabled characterization of environmental sulfide levels for species sampled in background sediment cores and in colonization trays. Dorvilleids tolerated H2S levels from 10~$μ$M to over 2.6~mM, with the majority of species inhabiting sediments with similar environmental H2S concentrations (median 85{\textendash}100~$μ$M). Dorvilleid species richness was greater at HR than ER, but did not differ between clam bed and microbial mat habitats. Species distribution patterns reflected preferences for ER clam bed (lower sulfide levels), ER mat and HR clam bed (moderate sulfide levels), or HR mat (very high sulfide levels). Nutritional patterns, including trophic diversity and functional similarity, were examined using community stable isotope metrics based on $δ$15N and $δ$13C. Within each region, dorvilleid species exhibited multiple trophic strategies. Co-existing congeners typically exhibited distinct isotope signatures, suggesting trophic partitioning. Trophic diversity and $δ$15N range for whole assemblages (measured by Total Hull Area and Standard Elliptical Area using species averages) and functional redundancy or species packing (measured as distance to nearest neighbor) among species and individuals were generally higher at ER, where sulfide levels were lower than at HR. In contrast, average trophic diversity among individuals within a species was greater at HR than ER. In colonization experiments involving agar-based manipulations of sulfide in tray sediments that mimicked clam bed and mat conditions, dorvilleids comprised 68{\%} and 48{\%} of colonists at ER and HR, respectively. Dorvilleid species richness was higher in trays that were initially more sulfidic. However, habitat exerted stronger influence on the composition of colonizing dorvilleids than did sulfide additions. In the NE Pacific, regional, habitat and vertical (down-core) variation in hydrogen sulfide creates complex environmental heterogeneity at methane seeps, promoting high diversity of stress-tolerant taxa such as dorvilleid polychaetes.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2013.02.006},
	url = {http://www.sciencedirect.com/science/article/pii/S0967064513000635},
	author = {Levin, L A and Ziebis, W and Mendoza, G and Bertics, V J and Washington, T and Gonzalez, J and Thurber, A R and Ebbe, B and Lee, R W}
}
@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}
}
@article {Levin2010,
	title = {{Diversity of bathyal macrofauna on the northeastern Pacific margin: the influence of methane seeps and oxygen minimum zones}},
	journal = {Marine Ecology},
	volume = {31},
	number = {1},
	year = {2010},
	pages = {94{\textendash}110},
	publisher = {Blackwell Publishing Ltd},
	abstract = {The upper continental slope in the northeastern Pacific Ocean is intercepted by a deep oxygen minimum zone (OMZ; 650{\textendash}1100 m) and punctuated by conduits of methane seepage. We examined the effects of these two dominant sources of heterogeneity on the density, composition and diversity of heterotrophic macrofauna off Hydrate Ridge, Oregon (OR; 800 m water depth), where the seeps co-occur within an OMZ, and off the Eel River, Northern California (CA; 500 m), where seeps are overlain by better oxygenated waters. We hypothesized that seeps (containing clam beds and microbial mats) should contribute a suite of distinct species to the regional margin species pool but that OMZ-associated hypoxia would dampen seep-related heterogeneity. Macrofaunal densities were highest (23,000{\textendash}33,510 ind{\textperiodcentered}m-2) in the CA seep sediments and in the OR near-seep samples, intermediate in the OR seep, CA near seep and CA and OR 500-m margin sediments (10,054{\textendash}19,777 ind{\textperiodcentered}m-2), and lowest in the CA and OR OMZ habitats at 800 m (4269{\textendash}7847 ind{\textperiodcentered}m-2). Annelids constituted over 50{\%} of the taxa in all but the CA clam bed and OR microbial mat sediments, where mollusks were abundant. Approximately 50{\%} of seep species appeared to be habitat endemic; species present in microbial mats largely formed a subset of those present in the clam beds. Dorvilleid and ampharetid polychaetes were dominant in the seep sediments; non-seep margin sediments at 500 and 800 m were populated heavily by branchiate polychaetes including cossurids and paraonids. Alpha diversity (Es[20] calculated per core) was lowest and rank 1 dominance was highest in the CA and OR microbial mat habitats. Pooled analyses of Es[100] revealed highest species richness in the CA clam bed and near-seep habitats (30.3 and 29.6, respectively), and lowest species richness in the OR microbial mat and near-seep habitats (16.5 and 17.9, respectively). Non-seep sediments (500 and 800 m) off both CA and OR were more homogeneous (55{\textendash}57{\%} within-habitat similarity) than clam bed and microbial mat sediments (only 32{\textendash}37{\%} within-habitat similarity). CA sediment macrofauna generally exhibit higher alpha diversity, and as habitats are combined, a higher rate of increase in the slope of the species accumulation curves than do OR margin macrofauna. Methane seeps in the NE Pacific introduce significant heterogeneity that increases margin biodiversity at multiple spatial scales. However, our hypothesis that the OMZ would lessen the seep contributions to diversity was not supported. The better oxygenated CA seeps at 500 m shared more of the background margin fauna (at 500 m) than did the OR seeps at 800 m (with OMZ fauna at 800 m). Geographical differences in the fluxes of methane-rich fluids and the increased reliance on chemosynthetic food sources with increased depth could explain these results.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {1439-0485},
	doi = {10.1111/j.1439-0485.2009.00335.x},
	url = {http://dx.doi.org/10.1111/j.1439-0485.2009.00335.x},
	author = {Levin, L A and Mendoza, G F and Gonzalez, J P and Thurber, A R and Cordes, E E}
}
