In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device

Abstract

[1] The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge was used in the first long-term deployment of microbial enrichment flow cells using osmotically driven pumps in a subseafloor borehole. Three novel osmotically driven colonization systems with unidirectional flow were deployed in the borehole and incubated for 4 years to determine the microbial colonization preferences for 12 minerals and glasses present in igneous rocks. Following recovery of the colonization systems, we measured cell density on the minerals and glasses by fluorescent staining and direct counting and found some significant differences between mineral samples. We also determined the abundance of mesophilic and thermophilic culturable organotrophs grown on marine R2A medium and identified isolates by partial 16S or 18S rDNA sequencing. We found that nine distinct phylotypes of culturable mesophilic oligotrophs were present on the minerals and glasses and that eight of the nine can reduce nitrate and oxidize iron. Fe(II)-rich olivine minerals had the highest density of total countable cells and culturable organotrophic mesophiles, as well as the only culturable organotrophic thermophiles. These results suggest that olivine (a common igneous mineral) in seawater-recharged ocean crust is capable of supporting microbial communities, that iron oxidation and nitrate reduction may be important physiological characteristics of ocean crust microbes, and that heterogeneously distributed minerals in marine igneous rocks likely influence the distribution of microbial communities in the ocean crust.

Species Richness and Adaptation of Marine Fungi from Deep-Subseafloor Sediments

“…In our study, among the yeasts, Rhodotorula mucilaginosa was the most abundant species isolated from samples from depths ranging from 4 to 765 mbsf. The red yeast Rhodotorula mucilaginosa is widely distributed and has already been isolated from deep-sea sediments and basaltic crust (32)(33)(34). Bullera unica, isolated from 12 mbsf in our study, was the only isolate belonging to the Tremellomycetes.…”

Data report: cultivation of microorganisms from basaltic rock and sediment cores from the North Pond on the western flank of the Mid-Atlantic Ridge, IODP Expedition 336

“…Cultivation of seafloor basalts collected at low-and high-temperature fluid vent systems along the Mid-Atlantic Ridge detected diverse bacteria belonging to the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, and Bacilli, and some of the isolates that were assigned to the genus Bacillus were shown to grow on a medium specific for manganese oxidizers (Rathsack et al, 2009). In a study of an Integrated Ocean Drilling Program (IODP) site on the Juan de Fuca Ridge flank, in situ colonization systems deployed in the borehole for 4 years revealed the presence of active and cultivable Fe(II)-oxidizing bacteria belonging to eight genera, including gammaproteobacterial Alcanivorax, Marinobacter, and Halomonas as the predominant genera; however, all cultivated bacteria that utilized low-organic compounds for their growth were not proven to be facultative chemolithoautotrophs in that study (Smith et al, 2011). The existence of methanogens and sulfate reducers in the subseafloor basalt was indicated by a combination of molecular phylogenetic, isotopic, and cultivation analyses using cores collected at the Juan de Fuca Ridge flank during IODP Expedition 301 (Lever et al, 2013).…”

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

“…Microbial diversity surveys on the Juan de Fuca Ridge have focused at diffuse flow hydrothermal vents at Axial Seamount (e.g., Lynch, 2000; Alain et al, 2002;Pagé et al, 2004;Huber et al, 2006aHuber et al, , 2009Kaye et al, 2011;Meyer et al, 2013), high-temperature hydrothermal vents at Endeavor Segment (e.g., Wang et al, 2009aWang et al, , 2009bZhou et al, 2009;Anderson et al, 2013), a hydrothermal mound located at off-axis Cleft Segment (Davis et al, 2009), seafloor basalt (Mason et al, 2007(Mason et al, , 2009), sediment-buried basement fluid (Cowen et al, 2003;Huber et al, 2006b;Nakagawa et al, 2006;Jungbluth et al, 2013), and sediment-buried rock (Orcutt et al, 2011b;Smith et al, 2011;Lever et al, 2013). The limited number of microbiological studies focused on sediment of the Juan de Fuca Ridge have typically not incorporated phylogenetic marker-based surveys of community diversity such as small subunit ribosomal RNA (SSU rRNA) gene sequencing (e.g., Cragg et al, 2000;Mather and Parkes, 2000;Engelen et al, 2008); only studies focused on Cascadia margin methane hydrate-bearing sediment have incorporated such an approach (e.g., Bidle et al, 1999;Marchesi et al, 2001;Knittel et al, 2003;Inagaki et al, 2006;Nunoura et al, 2008;Briggs et al, 2012).…”