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

Abstract

Microorganisms inhabiting sediment in close proximity to recharging basement outcrops are of interest because of the enhanced advective fluid flow in these locations, which is expected to exert unique selective pressures on the resident microbial communities. Here, Integrated Ocean Drilling Program (IODP) boreholes were used to access sediment microbial communities near Grizzly Bare recharge seamount on the Juan de Fuca Ridge eastern flank. The two locations examined in this study, Holes U1363G and U1363B, are 50 and 177 m away from the center of the outcrop, respectively. In general, small subunit ribosomal RNA gene clones from all three domains of life were detected; these groups were predominantly related to microorganisms known to reside in marine sediment. A large fraction of environmental gene clones recovered from Hole U1363B and U1363G sediment were related to uncultivated, candidate phyla of Bacteria such as BHI80-139, BRC1, JS1, OPB41, and TA06. Hole U1363B and U1363G sediment clone libraries were generally dominated by the domain Bacteria and particularly the phylum Chloroflexi, which comprised approximately one-quarter of the total gene clones identified. However, borehole sediment also contained several archaeal lineages that were phylogenetically affiliated with the Miscellanenous Crenarchaeotal Group. Eukaryotic fungi were only detected within the interstitial water sample from Hole U1363B. Finally, a minor portion of clones recovered from sediment in this study were also recovered from basement fluid samples previously characterized from Baby Bare discharge seamount and Ocean Drilling Program and IODP borehole Circulation Obviation Retrofit Kit Observatories (CORKs) in Holes 1026B and U1301A, which are ~50 km to the north-northeast.

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

“…Nitrospirae are indicator taxa of altered crustal fluid in this environment ( Jungbluth et al, 2016 ). While they were not detected in previous studies of sediment from the Juan de Fuca Ridge flank ( Jungbluth et al, 2013 , 2016 ), the sequences in our dataset are quite divergent from the sequences identified in the crustal fluid (78% similarity). Similarly, Atribacteria (candidate division JS-1) OTUs were in high abundance in the shallower clay samples from Hole U1363F and U1363B (∼17% of all QC tags), although not in the deeper clays from Hole U1363D.…”

“…Planctomycetes had higher abundance in the clay-rich samples, and the majority of the sequences grouped mostly closely to Phycisphaerae clade MSBL9 observed in other deep sediment samples ( Inagaki et al, 2006 ; Durbin and Teske, 2011 ), where they can be associated with fermentation at the sulfate-methane transition zone ( Harrison et al, 2009 ). This same Planctomycetes group was also observed in an earlier clone library from Hole U1362B deep sediment ( Jungbluth et al, 2013 ). Two Nitrospirales order OTUs were present in all clay samples, but the function of Nitrospirae in marine sediment is unknown.…”

“…Similarly, Atribacteria (candidate division JS-1) OTUs were in high abundance in the shallower clay samples from Hole U1363F and U1363B (∼17% of all QC tags), although not in the deeper clays from Hole U1363D. This group was also observed in earlier clone libraries from Hole U1363B deep sediment ( Jungbluth et al, 2013 ) as well as recent re-sequencing of those DNA extracts ( Jungbluth et al, 2016 ). Atribacteria are common in anaerobic, organic-rich sediment, where they are thought to be involved in organotrophic processes including fermentation ( Dodsworth et al, 2013 ; Carr et al, 2015 ).…”

“…Phylogenetic analysis of all 136 Dehalococcoidia-related OTUs showed that all were highly similar to environmental sequences from other sediment environments and distinct from cultured isolates (Supplementary Figure 2 ). In an earlier clone library-based study from sediment squeeze cakes and resulting porewater from Hole U1363B deep sediment samples, Chloroflexi sequences were also detected, as well as in deeper re-sequencing of some of those samples ( Jungbluth et al, 2013 , 2016 ). Chloroflexi from the terrestrial subsurface are known to be involved in dehalogenation as a metabolic process, and may include sulfur cycling ( Wasmund et al, 2016 ), but the function of Chloroflexi in organic-rich deep sediment are not verified ( Kaster et al, 2014 ; Wasmund et al, 2014 ; Fullerton and Moyer, 2016 ).…”

“…Over the past decade, several studies have expanded our understanding of the composition and function of “deep biosphere” microbial communities in deep marine sediments in both organic-rich ( D’Hondt et al, 2004 ; Inagaki et al, 2006 ; Biddle et al, 2006 , 2008 ; Lever et al, 2010 ) and organic-poor environments ( D’Hondt et al, 2009 ; Kallmeyer et al, 2012 ; Røy et al, 2012 ). Studies of the form and function of microbial communities within or expelled from the deep oceanic crust are rarer and geographically more limited ( Cowen et al, 2003 ; Thorseth et al, 2003 ; Huber et al, 2006 ; Santelli et al, 2008 ; Orcutt et al, 2011a ; Lin et al, 2012 ; Jungbluth et al, 2013 ; Lever et al, 2013 ; Lee et al, 2015 ), even though this habitat type is spatially extensive and occupies a large volume of the crust ( Bach and Edwards, 2003 ; Orcutt et al, 2011b ). Recent studies have challenged traditional microbiological concepts of what it means for cells to be alive, active, or dormant ( Hoehler and Jørgensen, 2013 ).…”