@article {Edgcomb2016,
	title = {{Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins}},
	journal = {ISME Journal},
	volume = {10},
	year = {2016},
	pages = {2643{\textendash}2657},
	abstract = {Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most polyextreme habitats on Earth. In comparison to microbial activities occurring within the haloclines and brines of these unusual water column habitats near the Mediterranean seafloor, relatively little is known about microbial metabolic activities in the underlying sediments. In addition, it is not known whether activities are shaped by the unique chemistries of the different DHAB brines and whether evidence exists for active microbial eukaryotes in those sediments. Metatranscriptome analysis was applied to sediment samples collected using ROV Jason from underneath the haloclines of Urania, Discovery and L{\textquoteright}Atalante DHABs and a control site. We report on expression of genes associated with sulfur and nitrogen cycling, putative osmolyte biosynthetic pathways and ion transporters, trace metal detoxification, selected eukaryotic activities (particularly of fungi), microbemicrobe interactions, and motility in sediments underlying the haloclines of three DHABs. Relative to our control sediment sample collected outside of Urania Basin, microbial communities (including eukaryotes) in the Urania and Discovery DHAB sediments showed upregulation of expressed genes associated with nitrogen transformations, osmolyte biosynthesis, heavy metals resistance and metabolism, eukaryotic organelle functions, and cell-cell interactions. Sediments underlying DHAB haloclines that have cumulative physico-chemical stressors within the limits of tolerance for microoorganisms can therefore be hotspots of activity in the deep Mediterranean Sea.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1038/ismej.2016.58},
	author = {Edgcomb, V P and Pachiadaki, M and Mara, P and Kormas, K and Leadbetter, E R and Bernhard, J M}
}
@article {Kormas2015,
	title = {{Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins}},
	journal = {Extremophiles},
	volume = {19},
	year = {2015},
	pages = {949{\textendash}960},
	abstract = {The sediment microbiota of the Mediterranean deep-sea anoxic hypersaline basins (DHABs) are understudied relative to communities in the brines and halocline waters. In this study, the active fraction of the prokaryotic community in the halocline sediments of L{\textquoteright} Atalante, Urania, and Discovery DHABs was investigated based on extracted total RNA and 454 pyrosequencing of the 16S rRNA gene. Bacterial and archaeal communities were different in the sediments underlying the halocline waters of the three habitats, reflecting the unique chemical settings of each basin. The relative abundance of unique operational taxonomic units (OTUs) was also different between deep-sea control sediments and sediments underlying DHAB haloclines, suggesting adaptation to the steep DHAB chemical gradients. Only a few OTUs were affiliated to known bacterial halophilic and/or anaerobic groups. Many OTUs, including some of the dominant ones, were related to aerobic taxa. Archaea were detected only in few halocline samples, with lower OTU richness relative to Bacteria, and were dominated by taxa associated with methane cycling. This study suggests that, while metabolically active prokaryotic communities appear to be present in sediments underlying the three DHABs investigated, their diversity and activity are likely to be more reduced in sediments underlying the brines.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	author = {Kormas, K and Pachiadaki, M and Karayanni, H and Leadbetter, E R and Bernhard, J M and Edgcomb, V P}
}
@article {Bernhard2014,
	title = {{Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments}},
	journal = {Frontiers in Microbiology},
	volume = {5},
	year = {2014},
	pages = {605},
	abstract = {Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth \~{}3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L{\textquoteright} Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	doi = {10.3389/fmicb.2014.00605},
	author = {Bernhard, J M and Kormas, K and Pachiadaki, M and Rocke, E and Beaudoin, D J and Morrison, C and Visscher, P T and Cobban, A and Starczak, V R and Edgcomb, V P}
}
@article {Gieskes2011,
	title = {{Cold seeps in Monterey Bay, California: Geochemistry of pore waters and relationship to benthic foraminiferal calcite}},
	journal = {Applied Geochemistry},
	volume = {26},
	number = {5},
	year = {2011},
	pages = {738{\textendash}746},
	abstract = {An extensive geochemical and biogeochemical examination of CH4 seeps in the Clam Flats area of Monterey Bay provides insight into the character of relationships between seep geochemistry and benthic foraminiferal geochemistry. The area is characterized by sulfide-rich fluids. Sulfide increases are associated with large increases in alkalinity, as well as small decreases in dissolved Ca and Mg. In addition, only small increases in NH4 are observed, but values of $δ$13C of dissolved inorganic C are as low as -60{\textperthousand} at shallow depths (C of dissolved inorganic C are as low as -60{\textperthousand} at shallow depths (4, which is transported upward by slow seepage of pore fluids. The geochemistry of the pore fluids should be relevant to the geochemistry of the carbonate tests of living and dead foraminifera. However, a profound disequilibrium of approximately an order of magnitude occurs between the $δ$13C values of stained (cytoplasm-containing) foraminiferal carbonate and the C isotope values of ambient pore water dissolved inorganic C. Reasons are unclear for this isotopic disequilibrium, but have important implications for interpretations of foraminiferal carbonate as a paleoenvironmental proxy. Much fine scale work is needed to fully understand the relationships between the biogeochemistry of benthic foraminifera and the geochemistry of the pore waters where they live.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {0883-2927},
	doi = {10.1016/j.apgeochem.2011.01.032},
	url = {http://dx.doi.org/10.1016/j.apgeochem.2011.01.032},
	author = {Gieskes, J M and Rathburn, A E and Martin, J B and Perez, M E and Mahn, C and Bernhard, J M and Day, S}
}
@article {Bernhard2010,
	title = {{Combined carbonate carbon isotopic and cellular ultrastructural studies of individual benthic foraminifera : 2. Toward an understanding of apparent disequilibrium in hydrocarbon seeps}},
	journal = {Paleoceanography},
	volume = {25},
	year = {2010},
	pages = {PA4206},
	abstract = {Numerous previous studies show disequilibrium between stable carbon isotope ratios of foraminiferal calcite and pore water dissolved inorganic carbon in hydrocarbon seeps, calling into question the utility of this widely used paleoceanographic tracer as a proxy. We use a recently developed method to compare stable carbon isotope ratios of foraminiferal carbonate with cell ultrastructural observations from individual benthic foraminifera from seep (under chemosynthetic bivalves) and nonseep habitats in Monterey Bay, California, to better understand control(s) of benthic foraminiferal carbon isotope ratios. Two attributes previously proposed to cause the isotopic offsets are diet and symbionts. Ultrastructural analysis shows that positive staining with Rose Bengal indicates presence of foraminiferal cytoplasm, bacterial biomass, or a combination of both and, thus, is not an unequivocal indicator of viability. We also show for the first time that some living seep foraminifera have endobionts. Results from our unique, yet limited, data set are consistent with suggestions that, in our sites, several foraminiferal species collected from seep clam beds may not survive there, diet and symbiont presence do not appear to be major contributors to disequilibrium, little calcification of seep-tolerant foraminiferal species occurs while seep conditions prevail, and microscale variability in habitats could influence $δ$13C of benthic foraminiferal carbonate. Results further suggest that our knowledge of benthic foraminiferal ecology and biomineralization, especially in extreme habitats such as seeps, must be bolstered before we fully understand the fidelity of paleoenvironmental records derived from benthic foraminiferal test $δ$13C data.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {0883-8305},
	doi = {10.1029/2010PA001930},
	url = {http://dx.doi.org/10.1029/2010PA001930},
	author = {Bernhard, J M and Martin, J B and Rathburn, A E}
}
@article {Martin2010,
	title = {{Combined carbonate carbon isotopic and cellular ultrastructural studies of individual benthic foraminifera: Method description}},
	journal = {Paleoceanography},
	volume = {25},
	year = {2010},
	pages = {PA2211},
	abstract = {Carbon isotopes of foraminiferal tests provide a widely used proxy for past oceanographic environmental conditions. This proxy can be calibrated using live specimens, which are reliably identified with observations of cell ultrastructure. Observations of ultrastructures can also be used for studies of biological characteristics such as diet and presence of symbionts. Combining biological and isotopic studies on individual foraminifera could provide novel information, but standard isotopic methods destroy ultrastructures by desiccating specimens and observations of ultrastructure require removal of carbonate tests, preventing isotope measurements. The approach described here preserves cellular ultrastructure during isotopic analyses by keeping the foraminifera in an aqueous buffer (Phosphate Buffered Saline (PBS)). The technique was developed and standardized with 36 aliquots of NBS-19 standard of similar weight to foraminiferal tests (5 to 123 $μ$g). Standard errors ranged from {\textpm} 0.06 to {\textpm} 0.85{\textperthousand} and were caused by CO2 contaminants dissolved in the PBS. The technique was used to measure $δ$13C values of 96 foraminifera, 10 of which do not precipitate carbonate tests. Calcareous foraminiferal tests had corrected carbon isotope ratios of -8.5 to +3.2{\textperthousand}. This new technique allows comparisons of isotopic compositions of tests made by foraminifera known to be alive at the time of collection with their biological characteristics such as prey composition and presence or absence of putative symbionts. The approach may be applied to additional biomineralizing organisms such as planktonic foraminifera, pteropods, corals, and coccolithophores to elucidate certain biological controls on their paleoceanographic proxy signatures.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {0883-8305},
	doi = {10.1029/2009PA001846},
	url = {http://dx.doi.org/10.1029/2009PA001846},
	author = {Martin, J B and Bernhard, J M and Curtis, J and Rathburn, A E}
}
@article {Rona2009,
	title = {{Paleodictyon nodosum: a living fossil on the deep sea floor}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {56},
	number = {19-20},
	year = {2009},
	pages = {1700{\textendash}1712},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2009.05.015},
	url = {http://dx.doi.org/10.1016/j.dsr2.2009.05.015},
	author = {Rona, P A and Seilacher, A and de Vargas, C and Gooday, A J and Bernhard, J M and Bowser, S and Vetriani, C and Wirsen, C O and Mullineaux, L and Sherrell, R and Grassle, J F and Low, S and Lutz, R A}
}
@article {Robinson2004,
	title = {{Surficial hydrocarbon seep infauna from the Blake Ridge (Atlantic Ocean, 2150 m) and the Gulf of Mexico (690{\textendash}2240 m)}},
	journal = {Marine Ecology},
	volume = {25},
	number = {4},
	year = {2004},
	pages = {313{\textendash}336},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0173-9565},
	doi = {10.1111/j.1439-0485.2004.00034.x},
	url = {http://dx.doi.org/10.1111/j.1439-0485.2004.00034.x},
	author = {Robinson, C A and Bernhard, J M and Levin, L A and Mendoza, G F and Blanks, J K}
}
@article {VanDover2003a,
	title = {{Blake Ridge methane seeps: Characterization of a soft-sediment, chemosynthetically based ecosystem}},
	journal = {Deep-Sea Research. Part I: Oceanographic Research Papers},
	volume = {50},
	number = {2},
	year = {2003},
	pages = {281{\textendash}300},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0967-0637},
	doi = {10.1016/S0967-0637(02)00162-0},
	url = {http://dx.doi.org/10.1016/S0967-0637(02)00162-0},
	author = {Van Dover, C L and Aharon, P and Bernhard, J M and Caylor, E and Doerries, M B and Flickinger, W and Gilhooly, W and Goffredi, S K and Knick, K E and Macko, S A and Rapoport, S and Raulfs, E C and Ruppel, C and Salerno, J L and Seitz, R D and Sen Gupta, B K and Shank, T M and Turnipseed, M and Vrijenhoek, R C}
}
