Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high‐pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG)

Abstract

Deep subseafloor sediments may contain depressurization-sensitive, anaerobic, piezophilic prokaryotes. To test this we developed the DeepIsoBUG system, which when coupled with the HYACINTH pressure-retaining drilling and core storage system and the PRESS core cutting and processing system, enables deep sediments to be handled without depressurization (up to 25 MPa) and anaerobic prokaryotic enrichments and isolation to be conducted up to 100 MPa. Here, we describe the system and its first use with subsurface gas hydrate sediments from the Indian Continental Shelf, Cascadia Margin and Gulf of Mexico. Generally, highest cell concentrations in enrichments occurred close to in situ pressures (14 MPa) in a variety of media, although growth continued up to at least 80 MPa. Predominant sequences in enrichments were Carnobacterium, Clostridium, Marinilactibacillus and Pseudomonas, plus Acetobacterium and Bacteroidetes in Indian samples, largely independent of media and pressures. Related 16S rRNA gene sequences for all of these Bacteria have been detected in deep, subsurface environments, although isolated strains were piezotolerant, being able to grow at atmospheric pressure. Only the Clostridium and Acetobacterium were obligate anaerobes. No Archaea were enriched. It may be that these sediment samples were not deep enough (total depth 1126–1527 m) to obtain obligate piezophiles.

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

“…The collection of bacterial strains isolated from the Gulf of Lion was represented by mesophilic or psychrophilic aerobic heterotrophs belonging to the Gamma-and the Alphaproteobacteria. These results are consistent with in situ temperatures, estimated to be between 13-14 • C. The cultivation of aerobic or facultative anaerobic strains from deep sediment layers has already been reported in the literature from samples collected between 77 and 420 m b.s.f (Batzke et al, 2007;Parkes et al, 2009). In this study, the isolation of bacterial strains under aerobic conditions from anoxic sediments may be explained by the fact that some of these strains are facultative anaerobes (e.g.…”

“…Three physiographic provinces characterize the Gulf of Lion margin: a wide shelf (with a slope of 0.1°), 70 km wide at the most; a continental slope (1.5°); and a rise (0.9°) (Baztan et al, 2005). In contrast, the morphology of the coastal plain of Nice, in the Ligurian Sea, is characterized by a very narrow continental shelf, 2-3 km wide on average, and a steep continental slope (3.4 to 6.3°) leading to water depths of 2000 m at a distance of less than 20 km from the coast (Pautot, 1981). Within the Ligurian Sea, the Var turbiditic system extends for 300 km, from the river mouth to the distal area at the base of the northern continental slope of Corsica (Migeon et al, 2006).…”

Sunxiuqinia faeciviva sp. nov., a facultatively anaerobic organoheterotroph of the Bacteroidetes isolated from deep subseafloor sediment

“…Its 16S rRNA gene sequence was most closely related with sequences of anaerobic Bacteroidetes strains isolated from different subseafloor sedimentary environments, such as the Indian Continental Shelf (strain G13a-B) (Parkes et al, 2009) and the mineral deposits associated with the deep crustal fluids in the Juan de Fuca Ridge flank (strain Kimo37) . Thus, this group within the Bacteroidetes may represent one of the significant organoheterotrophic microbial components living in global subseafloor sediments, particularly in the relatively organic-compounds-rich continental margins.…”

“…In particular, a certain phylogenetic group of organoheterotrophic Bacteroidetes strains have been isolated from geographically distinct subseafloor sedimentary habitats in north-east Japan (Kobayashi et al, 2008) and the Indian Continental Shelf (Parkes et al, 2009), and even from mineral deposits associated with the deep crustal fluids in the Juan de Fuca Ridge flank . Within the Bacteroidetes, only Meniscus glaucopis (Irgens, 1977) and Prolixibacter bellariivorans (Holmes et al, 2007), both facultatively anaerobic mesophilic organoheterotrophs, are related to the phylotypes of subseafloor isolates.…”

Hydro-bio-geomechanical properties of hydrate-bearing sediments from Nankai Trough

“…Nankai Trough data from other studies are included (Kormas et al, 2003;Li et al, 1999;Mills et al, 2012;Newberry et al, 2004;Reed et al, 2002). The shaded region represents results from other locations compiled in Parkes et al (1994Parkes et al ( , 2009. Cell counts in this study were taken from a BIO specimen with S S ¼ 19.4 m 2 /g, but the cell counts include only live, culturable aerobes, so a reduced cell count is expected relative to theoretical estimates (dashed curves) and compiled data (symbols and shaded region), which all include living and dead organisms.…”