Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California.

Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders - and their metabolic capabilities - may be fundamental to the ecology of the SBC oil seep.

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel.

A new genus and species of Thyasiridae (Mollusca, Bivalvia) from deep-water, Beaufort Sea, northern Alaska.

Bivalve mollusk shells were collected in 2350 m depth in the Beaufort Sea, Arctic Ocean off northern Alaska. Initial identification suggested the specimens were a member of the bivalve family Thyasiridae, but no known eastern Pacific or Arctic living or fossil thyasirid resembled these deep-water specimens. Comparisons were made with the type of the genera Maorithyas Fleming, 1950, Spinaxinus Oliver & Holmes, 2006, Axinus Sowerby, 1821, and Parathyasira Iredale, 1930. We determined the Beaufort Sea species represents a new genus, herein described as Wallerconcha. These specimens also represent a new species, herein named Wallerconchasarae. These new taxa are compared with known modern and fossil genera and species of thyasirds.

Bacterial dominance in subseafloor sediments characterized by methane hydrates.

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (10(3)-10(5) cells cm(-3)). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.

Induction of lupus autoantibodies by adjuvants.

Exposure to the hydrocarbon oil pristane induces lupus specific autoantibodies in non-autoimmune mice. We investigated whether the capacity to induce lupus-like autoimmunity is a unique property of pristane or is shared by other adjuvant oils. Seven groups of 3-month-old female BALB/cJ mice received a single intraperitoneal injection of pristane, squalene (used in the adjuvant MF59), incomplete Freund's adjuvant (IFA), three different medicinal mineral oils, or saline, respectively. Serum autoantibodies and peritoneal cytokine production were measured. In addition to pristane, the mineral oil Bayol F (IFA) and the endogenous hydrocarbon squalene both induced anti-nRNP/Sm and -Su autoantibodies (20% and 25% of mice, respectively). All of these hydrocarbons had prolonged effects on cytokine production by peritoneal APCs. However, high levels of IL-6, IL-12, and TNFalpha production 2-3 months after intraperitoneal injection appeared to be associated with the ability to induce lupus autoantibodies. The ability to induce lupus autoantibodies is shared by several hydrocarbons and is not unique to pristane. It correlates with stimulation of the production of IL-12 and other cytokines, suggesting a relationship with a hydrocarbon's adjuvanticity. The potential to induce autoimmunity may complicate the use of oil adjuvants in human and veterinary vaccines.

Temporal and spatial distributions of contaminants in sediments of Santa Monica Bay, California.

Contaminant inputs from wastewater discharge, a major source of contamination to Santa Monica Bay (SMB), have declined drastically during the last three decades as a result of improved treatment processes and better source control. To assess the concomitant temporal changes in the SMB sediments, a study was initiated in June 1997, in which 25 box cores were collected using a stratified random sampling design. Five sediment strata corresponding to the time intervals of 1890-1920, 1932-1963, 1965-1979, 1979-1989, and 1989-1997 were identified using (210)Pb dating techniques. Samples from each stratum were analyzed for metals, 1,1,1-Trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) and its metabolites (DDTs), polychlorinated biphenyls (PCBs), and total organic carbon (TOC). Samples from the 1965-1979, 1979-1989, and 1989-1997 strata were also analyzed for polycyclic aromatic hydrocarbons (PAHs) and linear alkylbenzenes (LABs). Sediment metal concentrations increased from 1890-1979 and were similar during the time intervals of 1965-1979, 1979-1989, and 1989-1997, although the mass emissions of trace metals from sewage inputs declined substantially during the same time period. Trace organic contamination in SMB was generally highest in sediments corresponding to deposition during the years of 1965-1979 or 1979-1989 and showed a decline in concentration in the 1989-1997 stratum. Temporal trends of contamination were greatest in sediments collected from areas near the Hyperion Treatment Plant (HTP) outfall system and on the slope of Redondo Canyon. The highest contaminant concentrations were present in sediments near the HTP 7-mile outfall in the 1965-1979 stratum. Elevated trace metal and organic concentrations were still present in the 1989-1997 stratum of most stations, suggesting that sediment contaminants have moved vertically in the sediment column since sludge discharges from the 7-mile outfall (a dominant source of contamination to the bay) ceased in 1987. The widespread distributions of DDTs and PCBs in SMB and highly confined distribution of LABs around the HTP outfall system were indicative of a dispersal mechanism remobilizing historically deposited contaminants to areas relatively remote from the point of discharge.