Sylvan
Jason B.
Sylvan
Jason B.
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ArticleDynamic accretion beneath a slow-spreading ridge segment: IODP hole 1473A and the Atlantis Bank oceanic core complex(American Geophysical Union, 2019-11-07) Dick, Henry J. B. ; MacLeod, Christopher J. ; Blum, Peter ; Abe, Natsue ; Blackman, Donna K. ; Bowles, Julie A. ; Cheadle, Michael J. ; Cho, K. ; Ciazela, Jakub ; Deans, Jeremy ; Edgcomb, Virginia P. ; Ferrando, Carlotta ; France, Lydéric ; Ghosh, Biswajit ; Ildefonse, Benoit ; John, Barbara E. ; Kendrick, Mark A. ; Koepke, Juergen ; Leong, James ; Liu, Chuanzhou ; Ma, Qiang ; Morishita, Tomoaki ; Morris, Antony ; Natland, James H. ; Nozaka, Toshio ; Pluemper, Oliver ; Sanfilippo, Alessio ; Sylvan, Jason B. ; Tivey, Maurice A. ; Tribuzio, Riccardo ; Viegas, G.809 deep IODP Hole U1473A at Atlantis Bank, SWIR, is 2.2 km from 1,508‐m Hole 735B and 1.4 from 158‐m Hole 1105A. With mapping, it provides the first 3‐D view of the upper levels of a 660‐km2 lower crustal batholith. It is laterally and vertically zoned, representing a complex interplay of cyclic intrusion, and ongoing deformation, with kilometer‐scale upward and lateral migration of interstial melt. Transform wall dives over the gabbro‐peridotite contact found only evolved gabbro intruded directly into the mantle near the transform. There was no high‐level melt lens, rather the gabbros crystallized at depth, and then emplaced into the zone of diking by diapiric rise of a crystal mush followed by crystal‐plastic deformation and faulting. The residues to mass balance the crust to a parent melt composition lie at depth below the center of the massif—likely near the crust‐mantle boundary. Thus, basalts erupted to the seafloor from >1,550 mbsf. By contrast, the Mid‐Atlantic Ridge lower crust drilled at 23°N and at Atlantis Massif experienced little high‐temperature deformation and limited late‐stage melt transport. They contain primitive cumulates and represent direct intrusion, storage, and crystallization of parental MORB in thinner crust below the dike‐gabbro transition. The strong asymmetric spreading of the SWIR to the south was due to fault capture, with the northern rift valley wall faults cutoff by a detachment fault that extended across most of the zone of intrusion. This caused rapid migration of the plate boundary to the north, while the large majority of the lower crust to spread south unroofing Atlantis Bank and uplifting it into the rift mountains.
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ArticleIdentification and removal of contaminant sequences from ribosomal gene databases : lessons from the Census of Deep Life(Frontiers Media, 2018-04-30) Sheik, Cody S. ; Kiel Reese, Brandi ; Twing, Katrina I. ; Sylvan, Jason B. ; Grim, Sharon L. ; Schrenk, Matthew O. ; Sogin, Mitchell L. ; Colwell, Frederick S.Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
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ArticleMicrobial activity in the marine deep biosphere : progress and prospects(Frontiers Media, 2013-07-11) Orcutt, Beth N. ; LaRowe, Douglas E. ; Biddle, Jennifer F. ; Colwell, Frederick S. ; Glazer, Brian T. ; Kiel Reese, Brandi ; Kirkpatrick, John B. ; Lapham, Laura L. ; Mills, Heath J. ; Sylvan, Jason B. ; Wankel, Scott D. ; Wheat, C. GeoffreyThe vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
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PreprintTime-series analysis of two hydrothermal plumes at 9°50′N East Pacific Rise reveals distinct, heterogeneous bacterial populations( 2011-12-05) Sylvan, Jason B. ; Pyenson, Benjamin C. ; Rouxel, Olivier J. ; German, Christopher R. ; Edwards, Katrina J.We deployed sediment traps adjacent to two active hydrothermal vents at 9°50’N on the East Pacific Rise (EPR) to assess variability in bacterial community structure associated with plume particles on the time scale of weeks to months, to determine if an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (>1 mm) Fe/(Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (<1 mm) Fe/(Fe+Mn+Al), Fe, Ca and Co are reflected in shifts in microbial populations. 16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift towards the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exists on the plume environment that physically and chemically connects them. By employing sediment traps for a time series approach to sampling, we show that bacterial community composition on plume particles changes on time scales much shorter than previously known.
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PreprintEvidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii( 2016-10-24) Sylvan, Jason B. ; Wankel, Scott D. ; LaRowe, Douglas E. ; Charoenpong, Chawalit N. ; Huber, Julie A. ; Moyer, Craig L. ; Edwards, Katrina J.The role of nitrogen cycling in submarine hydrothermal systems is far less studied than that of other biologically reactive elements such as sulfur and iron. In order to address this knowledge gap, we investigated nitrogen redox processes at Loihi Seamount, Hawaii, using a combination of biogeochemical and isotopic measurements, bioenergetic calculations and analysis of the prokaryotic community composition in venting fluids sampled during four cruises in 2006, 2008, 2009 and 2013. Concentrations of NH4+ were positively correlated to dissolved Si and negatively correlated to NO3-+NO2-, while NO2- was not correlated to NO3-+NO2-, dissolved Si or NH4+. This is indicative of hydrothermal input of NH4+ and biological mediation influencing NO2- concentrations. The stable isotope ratios of NO3- (d15N and d18O) was elevated with respect to background seawater, with d18O values exhibiting larger changes than corresponding d15N values, reflecting the occurrence of both production and reduction of NO3- by an active microbial community. d15N-NH4+ values ranged from 0‰ to +16.7‰, suggesting fractionation during consumption and potentially N-fixation as well. Bioenergetic calculations reveal that several catabolic strategies involving the reduction of NO3- and NO2- coupled to sulfide and iron oxidation could provide energy to microbes in Loihi fluids, while 16S rRNA gene sequencing of Archaea and Bacteria in the fluids reveals groups known to participate in denitrification and N-fixation. Taken together, our data support the hypothesis that microbes are mediating N-based redox processes in venting hydrothermal fluids at Loihi Seamount.