@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 {Beaudoin2016,
	title = {{Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {129},
	year = {2016},
	pages = {350{\textendash}359},
	abstract = {In spite of significant advancements towards understanding the dynamics of petroleum hydrocarbon degrading microbial consortia, the impacts (direct or indirect via grazing activities) of bacterivorous protists remain largely unknown. Microcosm experiments were used to examine whether protistan grazing affects the petroleum hydrocarbon degradation capacity of a deep-sea sediment microbial community from an active Gulf of Mexico cold seep. Differences in n-alkane content between native sediment microcosms and those treated with inhibitors of eukaryotes were assessed by comprehensive two-dimensional gas chromatography following 30{\textendash}90 day incubations and analysis of shifts in microbial community composition using small subunit ribosomal RNA gene clone libraries. More biodegradation was observed in microcosms supplemented with eukaryotic inhibitors. SSU rRNA gene clone libraries from oil-amended treatments revealed an increase in the number of proteobacterial clones (particularly $\gamma$-proteobacteria) after spiking sediments with diesel oil. Bacterial community composition shifted, and degradation rates increased, in treatments where protists were inhibited, suggesting protists affect the hydrocarbon degrading capacity of microbial communities in sediments collected at this Gulf of Mexico site.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2014.01.007},
	url = {http://www.sciencedirect.com/science/article/pii/S0967064514000216},
	author = {Beaudoin, D J and Carmichael, C A and Nelson, R K and Reddy, C M and Teske, A P and Edgcomb, V P}
}
@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 {Edgcomb2014,
	title = {{Ciliates along Oxyclines of Permanently Stratified Marine Water Columns}},
	journal = {Journal of Eukaryotic Microbiology},
	volume = {61},
	number = {4},
	year = {2014},
	pages = {434{\textendash}445},
	abstract = {Studies of microbial communities in areas of the world where permanent marine water column oxyclines exist suggest they are "hotspots" of microbial activity, and that these water features and the anoxic waters below them are inhabited by diverse protist taxa, including ciliates. These communities have minimal taxonomic overlap with those in overlying oxic water columns. Some ciliate taxa have been detected in multiple locations where these stable water column oxyclines exist; however, differences in such factors as hydrochemistry in the habitats that have been studied suggest local selection for distinct communities. We compare published data on ciliate communities from studies of deep marine water column oxyclines in Caricao Basin, Venezuela, and the Black Sea, with data from coastal, shallower oxycline waters in Framvaren and Mariager fjords, and from several deep-sea hypersaline anoxic basins in the Eastern Mediterranean Sea. Putative symbioses between Bacteria, Archaea, and ciliates observed along these oxyclines suggests a strategy of cooperative metabolism for survival that includes chemosynthetic autotrophy and exchanges of metabolic intermediates or end products between hosts and their prokaryotic partners.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1111/jeu.12122},
	author = {Edgcomb, V P and Pachiadaki, M}
}
