A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere

Cragg, Barry A.; Bale, S. J.; Parkes, Ronald John

doi:10.1111/j.1472-765x.1992.tb00743.x

Cited by 34 publications

(21 citation statements)

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“…The deepest sediment obtained was sediment from 518 m below the seafloor. Whole round core samples were cut from intact cores under sterile anaerobic conditions (9) and were transported anaerobically (8) at 4°C back to a laboratory for analysis a few weeks later. Full details concerning the subsequent handling of the samples have been published elsewhere (9,31).…”

Section: Methodsmentioning

confidence: 99%

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea

Bale

Goodman

Rochelle

et al. 1997

International Journal of Systematic Bacteriology

205

125

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Several strains of a strictly anaerobic, vibrio-shaped or sigmoid, sulfate-reducing bacterium were isolated from deep marine sediments (depth, 80 and 500 m) obtained from the Japan Sea (Ocean Drilling Program Leg 128, site 798B). This bacterium was identified as a member of the genus Desulfovibrio on the basis of the presence of desulfoviridin and characteristic phospholipid fatty acids (is0 17:lw7 and is0 15:0), the small number of growth substrates utilized (lactate, pyruvate, and hydrogen), and 16s rRNA gene sequence analysis data. Based on data for 16s rRNA sequences (1,369 bp), all of the Japan Sea strains were identical to each other and were most closely related to Desulfovibrio salexigens and less closely related to Desulfuvibrio desulfuricans (levels of similarity, 91 and 89.6%, respectively). There were, however, considerable phenotypic differences (in temperatures, pressures, and salinities tolerated, growth substrates, and electron donors) between the Japan Sea isolates and the type strains of previously described desulfovibrios, as well as important differences among the Japan Sea isolates. The Japan Sea isolates were active (with sulfide production) over a wide temperature range (15 to 65°C) and a wide sodium chloride concentration range (0.2 to 10%) (moderate halophile), and they were barophiles that were active at pressures up to about 40 MPa (400 atm). The optimum pressures for activity corresponded to the calculated pressures at the depths from which the organisms were isolated (for isolates obtained at depths of 80 and 500 m the optimum activities occurred at 10 and 15 MPa, respectively [lo0 and 150 atm, respectively]). This confirms that the organisms came from deep sediments and indicates that they are well-adapted for deep sediment conditions, which is consistent with other characteristics (utilization of hydrogen, fermentation, and utilization of ferric iron and organic sulfonates as electron acceptors). We propose that Japan Sea isolate 500-1 is the type strain of a new species, Desulfovibrio profundus.Bacterial sulfate reduction is the dominant anaerobic terminal oxidation process in marine sediments, and in coastal sediments this process can be responsible for more than 50% of the organic matter degradation (21). The importance of sulfate reduction decreases in deeper-water sediments, where the diagenetic zones are greatly extended (16,22), and as a result sulfate can be present to a depth of several hundred meters in some pelagic sediments (4). Thus, there is the potential for active sulfate reduction to continue at great depth within marine sediments. Recently, this was demonstrated for Japan Sea sediments, where sulfate reduction was shown to be present to a depth of at least 425 m together with significant bacterial populations (30). Viable sulfate-reducing bacteria were also present to a depth of 80 m, and other viable bacterial types were present at even greater depths. These findings significantly extend the environment for sulfate-reducing bacteria and are consistent with report...

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Section: Methodsmentioning

confidence: 99%

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea

Bale

Goodman

Rochelle

et al. 1997

International Journal of Systematic Bacteriology

205

125

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“…The cut ends of the WRC were flamed and capped with sterile (gamma irradiated) core end caps while gassing with sterile oxygen-free-nitrogen (OFN). They were stored in gas-tight anaerobic bags (Cragg et al, 1992a) in the ships cold-room at 4°C for approximately two weeks and transported back to the laboratory in insulated trunks containing wet ice and ice-packs. During transportation the samples remained cold.…”

Section: Shipboard Sampling Handlingmentioning

confidence: 99%

The Impact of Fluid and Gas Venting on Bacterial Populations and Processes in Sediments from the Cascadia Margin Accretionary System (Sites 888892) and the Geochemical Consequences

Cragg¹,

Parkes²,

Fry³

et al. 1995

Proceedings of the Ocean Drilling Program, 146 Part 1 Scientific Results

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Bacterial populations and activity were quantified at four Ocean Drilling Program Leg 146 sites in the Cascadia Margin accretionary wedge, off the west Canadian/American coast. At two sites the sediments contained gas hydrates: Site 889/890 had a discrete hydrate zone for -10 m above the bottom-simulating reflector (BSR) at 225 m below the sea floor (mbsf), and Site 892 had disseminated hydrate in the top -20 mbsf and a BSR at 73 mbsf. Site 891 had fault zones and discrete zones of active fluid venting. The other site, 888, was a control site without gas hydrates or substantial fluid venting. Bacterial populations were present at all sites with deepest samples from Site 888 at 564 mbsf. The control Site 888 and the top -90 mbsf of Site 889/890 had bacterial distributions similar to previous sites studied in the Pacific Ocean. In the top -20 m of Site 892, however, bacterial populations were much lower than in the other two sites; they may have been inhibited by the high concentrations of hydrogen sulfide within the hydrate zone. Below this depth, bacterial populations increased to concentrations consistent with other sites, apart from local decreases in Hole 892A associated with thermally generated aromatic hydrocarbons, which might be toxic to a portion of the bacterial community. Near-surface bacterial populations at 891A were -4.5 times higher than expected, probably reflecting fluid venting near this site. Below about 50 mbsf at this site (Hole 891B), bacterial populations were also elevated and peaks corresponded to geochemical anomalies resulting from fluid venting.Bacterial processes generally decreased with increasing depth at the control site, which was dominated by sulfate reduction, and rates of methane oxidation in the top 90 m were low, ranging from 0.002 to 0.033 nmol/cm 3 /d. Fluid and gas venting have a marked effect on deep bacterial processes at Sites 891 and 889/890: in contrast to the control site, maximum bacterial activities occur and bacterial populations are elevated at depth (sub-200 mbsf), reflecting marked increases in methane oxidation. At Site 889/890, bacterial populations and activity were stimulated in the discrete hydrate zone. Methane oxidation rates increased in the middle of this zone to 134.5 nmol/cm 3 /d, and this resulted in a significant increase in the total bacterial population. The anaerobic process(es) responsible for methane oxidation remain unclear, but fluid flux into accretionary wedge sediments may be an important process in providing electron acceptors to maintain these high rates of methane oxidation. Variation in bacterial profiles between cores at the same site (891 and 892), only a few meters apart, closely reflect spatial heterogeneity in geochemistry and fluid expulsion in these accretionary sediments, demonstrating that bacterial processes are a sensitive index for the fluid and gas venting that may drive many of the geochemical changes.

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“…All details of the environmental conditions, sampling and sub-sampling procedures have been previously reported (Cragg et al, 1992a, b;Parkes et al, 1995;Moore et al, 2001;Toffin et al, 2004a).…”

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confidence: 99%

Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough

Toffin

Zink

Kato

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20 T ) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0-120 g l, with the optimum at 10-20 g l "1 . The temperature range for growth at pH 7?0 was 4-50 6C, with the optimum at 37-40 6C. The optimum pH for growth was 7?0-8?0. The optimum pressure for growth was 0?1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2 T (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA-DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20 T (=DSM 16108

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A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere

Cited by 34 publications

References 4 publications

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea

The Impact of Fluid and Gas Venting on Bacterial Populations and Processes in Sediments from the Cascadia Margin Accretionary System (Sites 888892) and the Geochemical Consequences

Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough

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A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere

Cited by 34 publications

References 4 publications

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea

The Impact of Fluid and Gas Venting on Bacterial Populations and Processes in Sediments from the Cascadia Margin Accretionary System (Sites 888892) and the Geochemical Consequences

Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough

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The Impact of Fluid and Gas Venting on Bacterial Populations and Processes in Sediments from the Cascadia Margin Accretionary System (Sites 888892) and the Geochemical Consequences