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Cold seep

Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding, Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored "differential coverage binning" method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed "Gsub") may represent a new deep-sea SOB group...
March 2017: MSystems
Petra Pop Ristova, Christina Bienhold, Frank Wenzhöfer, Pamela E Rossel, Antje Boetius
Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas...
2017: PloS One
Xinzheng Li
This paper reviews the taxonomic and biodiversity studies of the deep-sea invertebrates in the South China Sea based on the samples collected by the Chinese manned deep-sea submersible Jiaolong. To date, six new species were described, including the sponges Lophophysema eversa Gong, Li & Qiu, 2014, Saccocalyx microhexactin Gong, Li & Qiu, 2015, and Semperella jiaolongae Gong, Li & Qiu, 2015 as well as the crustaceans Uroptychus jiaolongae Dong & Li, 2015, Uroptychus spinulosus Dong & Li, 2015 and Globospongicola jiaolongi Jiang, Kou & Li, 2015, and some newly recorded species from the South China Sea were reported...
January 5, 2017: Integrative Zoology
Weipeng Zhang, Wei Ding, Bo Yang, Renmao Tian, Shuo Gu, Haiwei Luo, Pei-Yuan Qian
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation...
2016: Frontiers in Microbiology
Rokas Kubilius, Geir Pedersen
There is an increased need to detect, identify, and monitor natural and manmade seabed gas leaks. Fisheries echosounders are well suited to monitor large volumes of water and acoustic frequency response [normalized acoustic backscatter, when a measure at one selected frequency is used as a denominator, r(f)] is commonly used to identify echoes from fish and zooplankton species. Information on gas plume r(f) would be valuable for automatic detection of subsea leaks and for separating bubble plumes from natural targets such as swimbladder-bearing fish...
October 2016: Journal of the Acoustical Society of America
Damianos Chatzievangelou, Carolina Doya, Laurenz Thomsen, Autun Purser, Jacopo Aguzzi
Three benthic megafaunal species (i.e. sablefish Anoplopoma fimbria; pacific hagfish Eptatretus stoutii and a group of juvenile crabs) were tested for diel behavioral patterns at the methane hydrates site of Barkley Canyon (890 m depth), off Vancouver Island (BC, Canada). Fluctuations of animal counts in linear video-transects conducted with the Internet Operated Deep-Sea Crawler "Wally" in June, July and December of 2013, were used as proxy of population activity rhythms. Count time series and environmental parameters were analyzed under the hypothesis that the environmental conditioning of activity rhythms depends on the life habits of particular species (i...
2016: PloS One
James B Bell, Alfred Aquilina, Clare Woulds, Adrian G Glover, Crispin T S Little, William D K Reid, Laura E Hepburn, Jason Newton, Rachel A Mills
Despite a number of studies in areas of focused methane seepage, the extent of transitional sediments of more diffuse methane seepage, and their influence upon biological communities is poorly understood. We investigated an area of reducing sediments with elevated levels of methane on the South Georgia margin around 250 m depth and report data from a series of geochemical and biological analyses. Here, the geochemical signatures were consistent with weak methane seepage and the role of sub-surface methane consumption was clearly very important, preventing gas emissions into bottom waters...
September 2016: Royal Society Open Science
Marie Portail, Karine Olu, Stanislas F Dubois, Elva Escobar-Briones, Yves Gelinas, Lénaick Menot, Jozée Sarrazin
In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB) cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA) cycles...
2016: PloS One
Chunya Huang, Stephen W Schaeffer, Charles R Fisher, Dominique A Cowart
BACKGROUND: Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp...
2016: PeerJ
Andrea M Quattrini, Amanda W J Demopoulos
A complete understanding of how parasites influence marine ecosystem functioning requires characterizing a broad range of parasite-host interactions while determining the effects of parasitism in a variety of habitats. In deep-sea fishes, the prevalence of parasitism remains poorly understood. Knowledge of ectoparasitism, in particular, is limited because collection methods often cause dislodgment of ectoparasites from their hosts. High-definition video collected during 43 remotely operated vehicle surveys (2013-2014) provided the opportunity to examine ectoparasitism on fishes across habitats (open slope, canyon, seamount, cold seep) and depths (494-4689 m) off the northeastern U...
December 2016: International Journal for Parasitology. Parasites and Wildlife
Michael G Reuscher, Dieter Fiege
The new ampharetid species Eclysippe yonaguniensis sp. nov. and Glyphanostomum bilabiatum sp. nov. from the Yonaguni Knoll IV hydrothermal field off the coast of Taiwan and Pavelius makranensis sp. nov. from the cold seeps in the Makran accretionary prism off the coast of Pakistan are described. Amage cf. ehlersi Reuscher, Fiege & Imajima, 2015 and Anobothrus dayi Imajima, Reuscher & Fiege, 2013 are newly recorded from the Yonaguni Knoll IV hydrothermal field.
July 20, 2016: Zootaxa
S J Loyd, J Sample, R E Tripati, W F Defliese, K Brooks, M Hovland, M Torres, J Marlow, L G Hancock, R Martin, T Lyons, A E Tripati
Methane cold seep systems typically exhibit extensive buildups of authigenic carbonate minerals, resulting from local increases in alkalinity driven by methane oxidation. Here, we demonstrate that modern seep authigenic carbonates exhibit anomalously low clumped isotope values (Δ47), as much as ∼0.2‰ lower than expected values. In modern seeps, this range of disequilibrium translates into apparent temperatures that are always warmer than ambient temperatures, by up to 50 °C. We examine various mechanisms that may induce disequilibrium behaviour in modern seep carbonates, and suggest that the observed values result from several factors including kinetic isotopic effects during methane oxidation, mixing of inorganic carbon pools, pH effects and rapid precipitation...
2016: Nature Communications
Adrien Assié, Christian Borowski, Karina van der Heijden, Luciana Raggi, Benedikt Geier, Nikolaus Leisch, Mario P Schimak, Nicole Dubilier, Jillian M Petersen
Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfide-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world...
July 18, 2016: Environmental Microbiology Reports
Teng-Wei Wang, Shane T Ahyong, Tin-Yam Chan
Lithodid crabs (Lithodidae Samouelle, 1819), commonly known as king crabs, are frequent targets of commercial fishing worldwide with most of them living in deep water (Sakai 1971; Ahyong et al. 2010). Lithodes Latreille, 1806, is the second largest genus of lithodid crabs, currently including 29 species worldwide (Ahyong 2010). In Taiwanese waters, however, only two species, L. turritus Ortmann, 1892, and L. formosae Ahyong & Chan, 2010, have been reported (Wu et al. 1998; Ahyong & Chan 2010; Ahyong et al. 2010)...
January 14, 2016: Zootaxa
Erik C L Trampe, Jens E N Larsen, Mikkel A Glaring, Peter Stougaard, Michael Kühl
The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns...
2016: Frontiers in Microbiology
Igor Y Oshkin, Svetlana E Belova, Olga V Danilova, Kirill K Miroshnikov, W Irene C Rijpstra, Jaap S Sinninghe Damsté, Werner Liesack, Svetlana N Dedysh
Two isolates of aerobic methanotrophic bacteria, strains Sph1T and Sph2, were obtained from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia. Another morphologically and phenotypically similar methanotroph, strain OZ2, was isolated from a sediment of a subarctic freshwater lake, Archangelsk region, northern Russia. Cells of these three strains were Gram-stain-negative, light-pink-pigmented, non-motile, encapsulated, large cocci that contained an intracytoplasmic membrane system typical of type I methanotrophs...
June 2016: International Journal of Systematic and Evolutionary Microbiology
Dimitri Kalenitchenko, Marlène Dupraz, Nadine Le Bris, Carole Petetin, Christophe Rose, Nyree J West, Pierre E Galand
Chemosynthetic mats involved in cycling sulfur compounds are often found in hydrothermal vents, cold seeps and whale falls. However, there are only few records of wood fall mats, even though the presence of hydrogen sulfide at the wood surface should create a perfect niche for sulfide-oxidizing bacteria. Here we report the growth of microbial mats on wood incubated under conditions that simulate the Mediterranean deep-sea temperature and darkness. We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features...
September 2016: ISME Journal
Frederick Dowell, Zena Cardman, Srishti Dasarathy, Matthias Y Kellermann, Julius S Lipp, S Emil Ruff, Jennifer F Biddle, Luke J McKay, Barbara J MacGregor, Karen G Lloyd, Daniel B Albert, Howard Mendlovitz, Kai-Uwe Hinrichs, Andreas Teske
The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed "Mat Mound") were characterized by porewater geochemistry of methane, C2-C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing...
2016: Frontiers in Microbiology
Greg W Rouse, Nerida G Wilson, Jose I Carvajal, Robert C Vrijenhoek
The discovery of four new Xenoturbella species from deep waters of the eastern Pacific Ocean is reported here. The genus and two nominal species were described from the west coast of Sweden, but their taxonomic placement remains unstable. Limited evidence placed Xenoturbella with molluscs, but the tissues can be contaminated with prey. They were then considered deuterostomes. Further taxon sampling and analysis have grouped Xenoturbella with acoelomorphs (=Xenacoelomorpha) as sister to all other Bilateria (=Nephrozoa), or placed Xenacoelomorpha inside Deuterostomia with Ambulacraria (Hemichordata + Echinodermata)...
February 4, 2016: Nature
Ajit Kumar Patra, Yong Min Kwon, Sung Gyun Kang, Yoshihiro Fujiwara, Sang-Jin Kim
The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83...
April 2016: Marine Genomics
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