112 research outputs found
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Microbiological comparison of surface soil and unsaturated subsurface soil from a semiarid high desert
Thirty-two chemoheterotrophic bacteria were isolated from unsaturated subsurface soil samples obtained from ca. 70 m below land surface in a high desert in southeastern Idaho. Most isolates were gram positive (84%) and strict aerobes (79%). Acridine orange direct counts of microbes in one subsurface sample showed lower numbers than similar counts performed on surface soils from the same location (ca. 5 x 10┠versus 2 x 10ⶠcells per g [dry weight] of soil), but higher numbers than those from plate counts performed on the subsurface material. Another sample taken from the same depth at another location showed no evidence of colonies under identical conditions. Soil analyses indicated that subsurface sediments versus surface soils were slightly alkaline (pH 7.9 versus 7.4), had a higher water content (25.7 versus 6.3%), and had lower organic carbon concentrations (0.05 to 0.17 versus 0.25% of soil dry weight). Analyses of biologically relevant gases from the unsaturated subsurface indicated an aerobic environment. As in other unsaturated soil environments, either a high proportion of bacteria in these subsurface sediments are not viable or they are incapable of growth on conventional media under aerobic conditions. The presence and numbers of bacteria in these deep sediments may be influenced by colonization opportunities afforded by periodic percolation of surface water through fractures in overlying strata
Ancient metabolisms of a thermophilic subseafloor bacterium
© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Smith, A. R., Mueller, R., Fisk, M. R., & Colwell, F. S. Ancient metabolisms of a thermophilic subseafloor bacterium. Frontiers in Microbiology, 12, (2021): 764631, https://doi.org/10.3389/fmicb.2021.764631.The ancient origins of metabolism may be rooted deep in oceanic crust, and these early metabolisms may have persisted in the habitable thermal anoxic aquifer where conditions remain similar to those when they first appeared. The WoodâLjungdahl pathway for acetogenesis is a key early biosynthetic pathway with the potential to influence ocean chemistry and productivity, but its contemporary role in oceanic crust is not well established. Here, we describe the genome of a novel acetogen from a thermal suboceanic aquifer olivine biofilm in the basaltic crust of the Juan de Fuca Ridge (JdFR) whose genome suggests it may utilize an ancient chemosynthetic lifestyle. This organism encodes the genes for the complete canonical WoodâLjungdahl pathway, but is potentially unable to use sulfate and certain organic carbon sources such as lipids and carbohydrates to supplement its energy requirements, unlike other known acetogens. Instead, this organism may use peptides and amino acids for energy or as organic carbon sources. Additionally, genes involved in surface adhesion, the import of metallic cations found in Fe-bearing minerals, and use of molecular hydrogen, a product of serpentinization reactions between water and olivine, are prevalent within the genome. These adaptations are likely a reflection of local environmental micro-niches, where cells are adapted to life in biofilms using ancient chemosynthetic metabolisms dependent on H2 and iron minerals. Since this organism is phylogenetically distinct from a related acetogenic group of Clostridiales, we propose it as a new species, Candidatus Acetocimmeria pyornia.Metagenome sequencing was made possible by the Deep Carbon Observatory Census of Deep Life supported by the Alfred P. Sloan Foundation and was performed at the Marine Biological Laboratory (Woods Hole, MA, United States). This work was funded by NASA grant NNX08AO22G and a graduate fellowship from the NSF Center for Dark Energy Biosphere Investigations. The flow cells were funded under J0972A from the U.S. Science Support Program of Joint Oceanographic Institutions
Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea
The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin\u27s history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics
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Nature and Extent of the Deep Biosphere
In the last three decades we have learned a great deal about microbes in subsurface environments. Once, these habitats were rarely examined, perhaps because so much of the life that we are concerned with exists at the surface and seems to pace its metabolic and evolutionary rhythms with the overt planetary, solar, and lunar cycles that dictate our own lives. And it certainly remains easier to identify with living beings that are in our midst, most obviously struggling with us or against us for survival over time scales that are easiest to track using diurnal, monthly or annual periods. Yet, research efforts are drawn again and again to the subsurface to consider life there. No doubt this has been due to our parochial interests in the resources that exist there (the water, minerals, and energy) that our society continues to require and that in some cases are created or modified by microbes. However, we also continue to be intrigued by the scientific curiosities that might only be solved by going underground and examining life where it does and does not exist.
But really, is life underground just a peculiarity of most life on the planet and only a recently discovered figment of life? Or is it actually a more prominent and fundamental, if unseen, theme for life on our planet? Our primary purpose in this chapter is to provide an incremental assembly of knowledge of subsurface life with the aim of moving us towards a more complete conceptual model of deep life on the planet. We aim to merge the consideration of the subseafloor and the continental subsurface because it is only through such a unified treatment that we can reach a comprehensive view of this underground life. We also provide some thoughts on a way forward with what we consider to be interesting new research areas, along with the methods by which they might be addressed as we seek new knowledge about life in this Stygian realm.This is the publisherâs final pdf. The published article is copyrighted by Mineralogical Society of America and can be found at: http://www.minsocam.org/.Keywords: Subsurface sediments, Subseafloor sediments, Sea floor, Basalt aquifer, Terrestrial subsurface, Monitoring bacterial transport, In-situ hybridization, Push pull test, Lithoautotrophic microbial ecosystems, In-situ hybridization, Ocean crus
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Diffusion through a double-sided plate: Development of a method to study alga-bacterium interactions
Bacteria and algae isolated from a wastewater oxidation pond were inoculated onto opposing surfaces of double-layer agar plates (Lutri plates) to determine the usefulness of such plates for studying microbial interactions. The altered growth characteristics of various algae depending on the species of bacteria on the adjacent medium surface indicated that there was diffusion of extracellular products through the agar, suggesting that this simple assay can be used for screening potential interactions of actively growing organisms
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Metagenomic profiling : microarray analysis of an environmental genomic library
Genomic libraries derived from environmental DNA (metagenomic libraries) are useful for characterizing
uncultured microorganisms. However, conventional library-screening techniques permit characterization of
relatively few environmental clones. Here we describe a novel approach for characterization of a metagenomic
library by hybridizing the library with DNA from a set of groundwater isolates, reference strains, and communities.
A cosmid library derived from a microcosm of groundwater microorganisms was used to construct
a microarray (COSMO) containing ~1-kb PCR products amplified from the inserts of 672 cosmids plus a set
of 16S ribosomal DNA controls. COSMO was hybridized with Cy5-labeled genomic DNA from each bacterial
strain, and the results were compared with the results for a common Cy3-labeled reference DNA sample
consisting of a composite of genomic DNA from multiple species. The accuracy of the results was confirmed by
the preferential hybridization of each strain to its corresponding rDNA probe. Cosmid clones were identified
that hybridized specifically to each of 10 microcosm isolates, and other clones produced positive results with
multiple related species, which is indicative of conserved genes. Many clones did not hybridize to any
microcosm isolate; however, some of these clones hybridized to community genomic DNA, suggesting that they
were derived from microbes that we failed to isolate in pure culture. Based on identification of genes by end
sequencing of 17 such clones, DNA could be assigned to functions that have potential ecological importance,
including hydrogen oxidation, nitrate reduction, and transposition. Metagenomic profiling offers an effective
approach for rapidly characterizing many clones and identifying the clones corresponding to unidentified
species of microorganisms
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Attached and unattached microbial communities in a simulated basalt aquifier under fracture- and porous-flow conditions
Bench scale column studies were used to examine the partitioning of microorganisms between groundwater
and a geologic medium and to examine the effect of hydrogeology (i.e., porous- versus fracture-flow) on
organism partitioning. Replicated columns were constructed with intact basalt core segments that contained
natural fractures and with the same basalt crushed into particles. The columns were perfused with groundwater,
and upon reaching a steady state, the columns were sacrificed and the attached and unattached
communities were analyzed by multiple approaches. The analyses included the total number of cells, the
phylogenetic affiliation of the cells (i.e., the α, ÎČ, and Îł subclasses of the class Proteobacteria and gram positives
with high G + C DNA content) by fluorescent in situ hybridization (FISH), number and taxonomic affiliation
by fatty acid methyl ester profiles of culturable heterotrophs, most-probable-number estimates of methanotrophs
and phenol oxidizers, and whole-community sole carbon source utilization patterns from Biolog GN
microplates. In the packed columns, about 99% of the total biomass (per cubic centimeter of porous medium)
was attached to the geologic medium. Lack of equitable units precluded a comparison of attached and
unattached biomasses in the fractured columns where the attached biomass was expressed per unit of surface
area. Compositional differences in the attached and unattached communities were evidenced by (i) the recovery
of Pseudomonas stutzeri, an Enterococcus sp., and Bacillus psychrophilus from the groundwater and not from the
basalt, (ii) differences between community carbon source utilization patterns, and (iii) the relative abundances
of different phylogenetic groups estimated by FISH in both column types. In the packed columns, attached
communities were depleted of members of the α- and ÎČ-Proteobacteria subclasses in comparison to those in the
corresponding groundwater. In the fractured columns, attached communities were enriched in gram-positive
Bacteria and Îł-Proteobacteria and depleted of ÎČ-Proteobacteria, in comparison to those in the corresponding
groundwater. Segregation of populations and their activities, possibly modified by attachment to geologic
media, may influence contaminant fate and transport in the subsurface and impact other in situ applications
Distinct methane-dependent biogeochemical states in Arctic seafloor gas hydrate mounds
Archaea mediating anaerobic methane oxidation are key in preventing methane produced in marine sediments from reaching the hydrosphere; however, a complete understanding of how microbial communities in natural settings respond to changes in the flux of methane remains largely uncharacterized. We investigate microbial communities in gas hydrate-bearing seafloor mounds at Storfjordrenna, offshore Svalbard in the high Arctic, where we identify distinct methane concentration profiles that include steady-state, recently-increasing subsurface diffusive flux, and active gas seepage. Populations of anaerobic methanotrophs and sulfate-reducing bacteria were highest at the seep site, while decreased community diversity was associated with a recent increase in methane influx. Despite high methane fluxes and methanotroph doubling times estimated at 5â9 months, microbial community responses were largely synchronous with the advancement of methane into shallower sediment horizons. Together, these provide a framework for interpreting subseafloor microbial responses to methane escape in a warming Arctic Ocean
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Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia Margin
Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is
considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is
biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ
methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling
experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete
locations in the sediment column. When starved in a biomass recycle reactor, Methanoculleus submarinus
produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M
reductase subunit A gene (mcrA) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/
g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By
considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and
the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane
produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The
actual rates could vary depending on the real number of methanogens and various seafloor parameters that
influence microbial activity. However, our calculated rate is lower than rates previously reported for such
sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to
improve models that predict microbial gas generation in marine sediments and determine the potential
influence of this source of methane on the global carbon cycle
Microbial activity in the marine deep biosphere: progress and prospects
The 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 existsâall 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\u27s global biogeochemical cycles, and for understanding how microorganisms in these âextremeâ 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) âtheme teamâ on microbial activity (www.darkenergybiosphere.org)
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