Innovative techniques for collection of saturated and unsaturated subsurface basalts and sediments for microbiological characterization

Clay-associated microbial communities and their relevance for a nuclear waste repository in the Opalinus Clay rock formation

Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron-reducing bacteria were predominant in comparison to methanogenic archaea and sulfate-reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site-specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low-active mineral-associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.

Dyadobacter bucti sp. nov., isolated from subsurface sediment

A Gram-reaction-negative, yellow-pigmented, rod-shaped, aerobic, non-motile, non-spore-forming bacterium, designated strain QTA69^T, was isolated from a subsurface sediment sample collected at the Qiangtang basin, Qinghai-Tibetan Plateau, PR China. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain QTA69^T was a member of the genus Dyadobacter and was closely related to Dyadobacter sediminis, Dyadobacter ginsengisoli and Dyadobacter psychrophilus with sequence similarities from 97.90 % to 96.85 %. Strain QTA69^T grew at 4-35 °C, and the optimum temperature was 25-28 °C. It grew at the pH range of 6.0-9.0 (optimum, pH 7.0-8.0) and its NaCl tolerance was 0-2.0 % (optimum, 0-1.0 %). The major cellular fatty acids were summed feature 3 (iso-C_15 : 0 2-OH and C _16:1ω6c/C_16 : 1ω7c), iso-C_15 : 0 and C_16 : 1ω5c. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. Genome sequencing revealed a genome size of 8.41 Mbp and a G+C content of 46.87 mol%. Based on whole genome average nucleotide identity values, phenotypic data, phylogenetic data and genotypic data, strain QTA69^T represents a novel species of genus Dyadobacter, for which the name Dyadobacter bucti sp. nov is proposed. The type strain is QTA69^T (=CGMCC 1.13688^T=KCTC 72024^T).

Microbial lipid biomarkers detected in deep subsurface black shales

Evidence for microbes has been detected in extreme subsurface environments as deep as 2.5 km with temperatures as high as 90 °C, demonstrating that microbes can adapt and survive extreme environmental conditions. Deep subsurface shales are increasingly exploited for their energy applications, thus characterizing the prevalence and role of microbes in these ecosystems essential for understanding biogeochemical cycles and maximizing production from hydrocarbon-bearing formations. Here, we describe the distribution of bacterial ester-linked phospholipid fatty acids (PLFA) and diglyceride fatty acids (DGFA) in sidewall cores retrieved from three distinct geologic horizons collected to 2275 m below ground surface in a Marcellus Shale well, West Virginia, USA. We examined the abundance and variety of PLFA and DGFA prior to energy development within and above the Marcellus Shale Formation into the overlying Mahantango Formation of the Appalachian Basin. Lipid biomarkers in the cores suggest the presence of microbial communities comprising Gram (+), Gram (-) as well as stress indicative biomarkers. Microbial PLFA and DGFA degradation in the subsurface can be influenced by stressful environmental conditions associated with the subsurface. The PLFA concentration and variety were higher in the transition zone between the extremely low permeability Marcellus Shale Formation and the more permeable Mahantango Formation. In contrast to this distribution, more abundant and diverse DGFA membrane profiles were associated with the Mahantango Formation. The stress indicative biomarkers like the trans-membrane fatty acids, oxiranes, keto-, and dimethyl lipid fatty acids were present in all cores, potentially indicating that the bacterial communities had experienced physiological stress or nutrient deprivation during or after deposition. The DGFA profiles expressed more stress indicative biomarkers as opposed to the PLFA membrane profiles. These findings suggest the probable presence of indigenous microbial communities in the deep subsurface shale and also improves our understanding of microbial survival mechanisms in ancient deep subsurface environments.

Sphingomonas floccifaciens sp. nov., isolated from subterranean sediment

A Gram-stain-negative, non-motile, non-sporulating, rod-shaped, orange-pigmented bacterium, designated strain FQM01^T, was isolated from a subterranean sediment sample in the Mohe permafrost area, China. Strain FQM01^T grew optimally at 25 °C, pH 7.0 and NaCl concentration of 0 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FQM01^T belonged to the genus Sphingomonas. The closest phylogenetic relative was Sphingomonas spermidinifaciens GDMCC 1.657^T (97.6 %), followed by Sphingomonas mucosissima DSM 17494^T (97.2 %). The DNA G+C content of the isolate was 66.9 mol%. Strain FQM01^T contained Q-10 as the predominant ubiquinone, and C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C16 : 0, C14 : 0 2-OH and C18 : 1ω7c 11 methyl as the major fatty acids. Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified glycolipid. Only sym-homospermidine was detected as the polyamine. On the basis of phylogenetic and phenotypic data, strain FQM01^T is considered to represent a novel species of Sphingomonas for which the name Sphingomonasfloccifaciens sp. nov. is proposed. The type strain is FQM01^T (=CGMCC 1.15797^T=KCTC 52630^T).

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

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.

Contamination Control for Scientific Drilling Operations

Drilling is an integral part of subsurface exploration. Because almost all drilling operations require the use of a drill fluid, contamination by infiltration of drill fluid into the recovered core material cannot be avoided. Because it is impossible to maintain sterile conditions during drilling the drill fluid will contain surface microbes and other contaminants. As contamination cannot be avoided, it has to be tracked to identify those parts of the drill core that were not infiltrated by the drill fluid. This is done by the addition of tracer compounds. A great variety of tracers is available, and the choice depends on many factors. This review will first explain the basic principles of drilling before presenting the most common tracers and discussing their strengths and weaknesses. The final part of this review presents a number of key questions that have to be addressed in order to find the right tracer for a particular drilling operation.

Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes

Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from the surface biosphere, underground drilling was conducted for 300 m deep granitic rocks at the Mizunami underground research laboratory (URL), Japan. Slightly alkaline groundwater was characterized by low concentrations of dissolved organic matter and sulfate and the presence of > 100 nM H2 . The initial biomass was the highest (∼10(5)  cells ml(-1) ) with the dominance of Hydrogenophaga spp., whereas the phylum Nitrospirae became predominant after 3 years with decreasing biomass (∼10(4)  cells ml(-1) ). One week incubation of groundwater microbes after 3 years with (13) C-labelled bicarbonate and 1% H2 and subsequent single-cell imaging with nanometer-scale secondary ion mass spectrometry demonstrated that microbial cells were metabolically active. Pyrosequencing of microbial communities in groundwater retrieved at 3-4 years after drilling at the Mizunami URL and at 14 and 25 years after the drilling at the Grimsel Test Site, Switzerland, revealed the occurrence of common Nitrospirae lineages at the geographically distinct sites. As the close relatives of the Nitrospirae lineages were exclusively detected from deep groundwaters and terrestrial hot springs, it suggests that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.

Altererythrobacter buctense sp. nov., isolated from mudstone core

A yellow-pigmented, Gram-negative, non-flagellated, rod-shaped bacterial strain, designated M0322(T), was isolated from a mudstone core sample of the Mohe Basin, China. Growth of strain M0322(T) was observed at 15-40 °C (optimum, 30 °C), at pH 5.0-10.0, (optimum, pH 6.0-7.0) and in the presence 0-4 % NaCl (optimum, 0 %). Phylogenetic analyses of 16S rRNA gene sequences revealed that strain M0322(T) formed a distinct phyletic lineage with the members of the genus Altererythrobacter and is closely related to Altererythrobacter aestuarii JCM 16339(T) (96.1 %) and Altererythrobacter namhicola JCM 16345(T) (95.7 %). The only isoprenoid quinone was identified as ubiquinone 10 (Q-10), major polar lipids were determined to be phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and three unidentified phospholipids, while major cellular fatty acids were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) and 11-Methyl C18:1 ω7c. The DNA G+C content of strain M0322(T) was determined to be 64.6 mol%. Based on the results of the polyphasic taxonomic study, strain M0322(T) is considered to represent a novel species of the genus Altererythrobacter, for which the name Altererythrobacter buctense sp. nov. is proposed. The type strain is M0322(T) (=CGMCC 1.12871(T) = JCM 30112(T)).

Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment

A Gram-reaction-negative bacterial strain, designated fig4T, was isolated from a subsurface sediment core of Qiangtang Basin permafrost in China. Cells were catalase- and oxidase-positive and rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain fig4T was a member of the family Hyphomicrobiaceae and was most closely related to members of the genera Pelagibacterium, Vasilyevaea and Devosia with 93.8–96.2 % sequence similarities. The major cellular fatty acids were C16 : 0, C18 : 0, 11-methyl C18 : 1ω7c, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major respiratory quinone was Q-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The DNA G+C content was 60.7 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain fig4T is considered to represent a novel species of a new genus in the family Hyphomicrobiaceae, for which the name Youhaiella tibetensis gen. nov., sp. nov. is proposed. The type strain is fig4T ( = CGMCC 1.12719T = JCM 19854T).

Moheibacter sediminis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from sediment, and emended descriptions of Empedobacter brevis, Wautersiella falsenii and Weeksella virosa

A Gram-reaction-negative, yellow-pigmented, strictly aerobic bacterium, designated M0116T, was isolated from the sediment of the Mohe Basin in north-east China. Flexirubin-type pigments were produced. Cells were catalase- and oxidase-positive and non-gliding rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M0116T was a member of the family Flavobacteriaceae and was most closely related to members of the genera Empedobacter , Wautersiella and Weeksella with 90.5–91.0 % sequence similarities. The major cellular fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The major respiratory quinone was MK-6 and the major polar lipid was phosphatidylethanolamine. The DNA G+C content was 38.2 mol%. Based on phenotypic, phylogenetic and genotypic data, strain M0116T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Moheibacter sediminis gen. nov., sp. nov. is proposed. The type strain is M0116T ( = CGMCC 1.12708T = JCM 19634T). Emended descriptions of Empedobacter brevis , Wautersiella falsenii and Weeksella virosa are also proposed.

Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter

A red-pink, Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain DK6-37 was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter, with low sequence similarities (<97 %) to recognized Hymenobacter species. Optimum growth was observed at 28 °C, pH 7.0 and 0 % NaCl. The strain was found to contain MK-7 as the predominant menaquinone. The polar lipids were identified as phosphatidylethanolanmine, two unknown aminophospholipids, one unknown aminolipid and three unknown polar lipids. The major fatty acids were identified as summed feature 3 (C16:1 ω7c/C16:1 ω6c as defined by MIDI), summed feature 4 (anteiso-C17:1 B/iso-C17:1 I), C16:1 ω5c, iso-C17:0 3-OH, iso-C15:0 and C18:0. The DNA G + C content was determined to be 67.4 mol %. On the basis of the polyphasic evidence presented, it is proposed that strain DK6-37 represents a novel species of the genus Hymenobacter, for which the name Hymenobacter qilianensis sp. nov. is proposed. The type strain is DK6-37(T) (= CGMCC 1.12720(T) = JCM 19763(T)).

Novel microbial populations in deep granitic groundwater from Grimsel Test Site, Switzerland

Freshwater aquifers in granitic rocks are widespread microbial habitats in the terrestrial subsurface. Microbial populations in deep granitic groundwater from two recently drilled (1 and 2 years) and two old boreholes (14 and 25 years) were compared. The 16S rRNA gene sequences related to "Candidatus Magnetobacterium bavaricum", Thermodesulfovibrio spp. of Nitrospirae (90.5-93.1 % similarity) and a novel candidate division with <90 % similarity to known cultivated species were dominant in all boreholes. Most of the environmental clones closely related to the novel lineages in Nitrospirae, which have been detected exclusively in deep groundwater samples. In contrast, betaproteobacterial sequences related to the family Rhodocyclaceae were obtained only from the recently drilled boreholes, which had higher total cell numbers. Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis supported the result from clone library analysis; betaproteobacterial cells were dominantly detected in recently drilled boreholes. These results suggest that while indigenous microbial populations represented by the novel phylotypes persisted in the boreholes for 25 years, betaproteobacterial species disappeared after 2 years owing to the change of substrate availability.

Challenges for coring deep permafrost on Earth and Mars

A scientific drilling expedition to the High Lake region of Nunavut, Canada, was recently completed with the goals of collecting samples and delineating gradients in salinity, gas composition, pH, pe, and microbial abundance in a 400 m thick permafrost zone and accessing the underlying pristine subpermafrost brine. With a triple-barrel wireline tool and the use of stringent quality assurance and quality control (QA/QC) protocols, 200 m of frozen, Archean, mafic volcanic rock was collected from the lower boundary that separates the permafrost layer and subpermafrost saline water. Hot water was used to remove cuttings and prevent the drill rods from freezing in place. No cryopegs were detected during penetration through the permafrost. Coring stopped at the 535 m depth, and the drill water was bailed from the hole while saline water replaced it. Within 24 hours, the borehole iced closed at 125 m depth due to vapor condensation from atmospheric moisture and, initially, warm water leaking through the casing, which blocked further access. Preliminary data suggest that the recovered cores contain viable anaerobic microorganisms that are not contaminants even though isotopic analyses of the saline borehole water suggests that it is a residue of the drilling brine used to remove the ice from the upper, older portion of the borehole. Any proposed coring mission to Mars that seeks to access subpermafrost brine will not only require borehole stability but also a means by which to generate substantial heating along the borehole string to prevent closure of the borehole from condensation of water vapor generated by drilling.

Utilization of fluorescent microspheres and a green fluorescent protein-marked strain for assessment of microbiological contamination of permafrost and ground ice core samples from the Canadian High Arctic

Fluorescent microspheres were applied in a novel fashion during subsurface drilling of permafrost and ground ice in the Canadian High Arctic to monitor the exogenous microbiological contamination of core samples obtained during the drilling process. Prior to each drill run, a concentrated fluorescent microsphere (0.5-microm diameter) solution was applied to the interior surfaces of the drill bit, core catcher, and core tube and allowed to dry. Macroscopic examination in the field demonstrated reliable transfer of the microspheres to core samples, while detailed microscopic examination revealed penetration levels of less than 1 cm from the core exterior. To monitor for microbial contamination during downstream processing of the permafrost and ground ice cores, a Pseudomonas strain expressing the green fluorescent protein (GFP) was painted on the core exterior prior to processing. Contamination of the processed core interiors with the GFP-expressing strain was not detected by culturing the samples or by PCR to detect the gfp marker gene. These methodologies were quick, were easy to apply, and should help to monitor the exogenous microbiological contamination of pristine permafrost and ground ice samples for downstream culture-dependent and culture-independent microbial analyses.

Indigenous and contaminant microbes in ultradeep mines

Rock, air and service water samples were collected for microbial analyses from 3.2 kilometres depth in a working Au mine in the Witwatersrand basin, South Africa. The approximately metre-wide mined zone was comprised of a carbonaceous, quartz, sulphide, uraninite and Au bearing layer, called the Carbon Leader, sandwiched by quartzite and conglomerate. The microbial community in the service water was dominated by mesophilic aerobic and anaerobic, alpha-, beta- and gamma-Proteobacteria with a total biomass concentration approximately 10(4) cells ml(-1), whereas, that of the mine air was dominated by members of the Chlorobi and Bacteroidetes groups and a fungal component. The microorganisms in the Carbon Leader were predominantly mesophilic, aerobic heterotrophic, nitrate reducing and methylotrophic, beta- and gamma-Proteobacteria that were more closely related to service water microorganisms than to air microbes. Rhodamine WT dye and fluorescent microspheres employed as contaminant tracers, however, indicated that service water contamination of most of the rock samples was < 0.01% during acquisition. The microbial contaminants most likely originated from the service water, infiltrated the low permeability rock through and accumulated within mining-induced fractures where they survived for several days before being mined. Combined PLFA and terminal restriction fragment length profile (T-RFLP) analyses suggest that the maximum concentration of indigenous microorganisms in the Carbon Leader was < 10(2) cells g(-1). PLFA, 35S autoradiography and enrichments suggest that the adjacent quartzite was less contaminated and contained approximately 10(3) cells gram(-1) of thermophilic, sulphate reducing bacteria, SRB, some of which are delta-Proteobacteria. Pore water and rock geochemical analyses suggest that these SRB's may have been sustained by sulphate diffusing from the adjacent U-rich, Carbon Leader where it was formed by radiolysis of sulphide.

The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects

The majority of the Earth's petroleum resource is partly biodegraded. This is of considerable practical significance and can limit economic exploitation of petroleum reserves and lead to problems during petroleum production. Knowledge of the microorganisms present in petroleum reservoirs, their physiological properties and the biochemical potential for hydrocarbon degradation benefits successful petroleum exploration. Anaerobic conditions prevail in petroleum reservoirs and biological hydrocarbon degradation is apparently inhibited at temperatures above 80-90 degrees C. We summarise available knowledge and conjecture on the dominant biological processes active during subsurface petroleum biodegradation.

Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer

The bacteria colonizing geologic core sections (attached) were contrasted with those found suspended in the groundwater (unattached) by examining the microbiology of 16 depth-paired core and groundwater samples using a suite of culture-independent and culture-dependent analyses. One hundred twenty-two meters was continuously cored from a buried chalcopyrite ore hosted in a biotite-quartz-monzonite porphyry at the Mineral Park Mine near Kingman, Ariz. Every fourth 1.5-m core was acquired using microbiologically defensible methods, and these core sections were aseptically processed for characterization of the attached bacteria. Groundwater samples containing unattached bacteria were collected from the uncased corehole at depth intervals corresponding to the individual cores using an inflatable straddle packer sampler. The groundwater was acidic (pH 2.8 to 5.0), with low levels of dissolved oxygen and high concentrations of sulfate and metals, including ferrous iron. Total numbers of attached cells were less than 10(5) cells g of core material(-1) while unattached cells numbered about 10(5) cells ml of groundwater(-1). Attached and unattached acidophilic heterotrophs were observed throughout the depth profile. In contrast, acidophilic chemolithotrophs were not found attached to the rock but were commonly observed in the groundwater. Attached communities were composed of low numbers (<40 CFU g(-1)) of neutrophilic heterotrophs that exhibited a high degree of morphologic diversity, while unattached communities contained higher numbers (ca. 10(3) CFU ml(-1)) of neutrophilic heterotrophs of limited diversity. Sulfate-reducing bacteria were restricted to the deepest samples of both core and groundwater. 16S ribosomal DNA sequence analysis of attached, acidophilic isolates indicated that organisms closely related to heterotrophic, acidophilic mesophiles such as Acidiphilium organovorum and, surprisingly, to the moderately thermophilic Alicyclobacillus acidocaldarius were present. The results indicate that viable (but possibly inactive) microorganisms were present in the buried ore and that there was substantial distinction in biomass and physiological capabilities between attached and unattached populations.

Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments

Forty strains of Gram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy's Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 16S rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to Arthrobacter: The other two strains appeared to be most closely related to Kocuria. The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological, physiological and biochemical traits of the subsurface strains were consistent with those of Arthrobacter, Micrococcus and genera recently separated from Micrococcus, such as Kocuria. Some of the subsurface strains were phylogenetically closely related to certain species of Arthrobacter. (16S rDNA sequence similarities >99%). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 16S rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to Arthrobacter. also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of Arthrobacter.

In situ imaging of microorganisms in geologic material

In order to fully delineate the interactions of microorganisms with geological substrates, unequivocal identification of intact microbial cells within geologic samples is required without the disruption of either the rock texture or the relationship of the microorganisms to the mineral fabric. To achieve this objective we developed a protocol that enables the visualization of intact microbial cells in petrographic thin sections, avoids detaching the cells from their host mineral surfaces and avoids microbial contamination during the lapidary process. Propidium iodide and POPO-3, nucleic acid stains that specifically target double-stranded DNA and RNA were utilized for in situ visualization of cells in surface and subsurface basalts from northeastern Idaho. Additionally, examination of samples incubated with acetic acid-UL-14C via phosphor imagining facilitated the in situ visualization of 14C labeled biomass. Biomass observed was low (<10(7) cells/g). These observations indicate that the microbial distribution in these rocks exhibits a high degree of spatial heterogeneity at the sub-centimeter scale.

Phylogenetic characterization of bacteria in the subsurface microbial culture collection

The Subsurface Microbial Culture Collection (SMCC) was established by the U.S. Dept. of Energy (DOE) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. Selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. Among these isolates were members of six major phylogenetic groups of bacteria: the high-G+C and low-G+C Gram-positive bacteria; the alpha-, beta-, and gamma-subdivisions of the Proteobacteria; and the Flexibacter/Cytophaga/Bacteroides group. A small number of the SMCC strains may be members of new bacterial genera, but most of them could be placed with reasonable confidence into more than 35 previously described genera. The majority of the Gram-positive isolates were species of Arthrobacter, Bacillus, or Streptococcus, whereas Acinetobacter, Comamonas, Pseudomonas, Sphingomonas, and Variovorax were among the most frequently encountered Gram-negative genera. A high proportion of the strains were placed in fewer than 10 genera, implying that there is substantial duplication within the SMCC at the genus level. When groups of isolates assigned to Acinetobacter, Arthrobacter, or Sphingomonas were analyzed in more detail, however, it was found that each group consisted of subgroups of strains that probably differed at the species level. Restriction endonuclease analysis (applied to the strains from one sample site) indicated that additional diversity was present at the strain level. Most of the SMCC isolates assigned to some genera (e.g., Acinetobacter) were very closely related to previously described species in those genera, but most of the isolates assigned to other genera (e.g., Arthrobacter and Sphingomonas) appeared (or were shown) to be new species, thereby indicating that a reasonable amount of novelty is present within the SMCC at the species level.

Monitoring deep subsurface microbiota for assessment of safe long-term nuclear waste disposal

Microbes with their resistance to heat and radioactivity, if present and metabolically active, could have major effects on the safety of nuclear waste disposal by posing potential problems in long-term containment. This paper reviews the applicability of the signature lipid biomarker (SLB) analysis in the quantitative assessment of the viable biomass, community composition, and nutritional/physiological status of the subsurface microbiota as it exists in situ in subsurface samples. The samples described in this review are not unlike those expected to be recovered from proposed deep subsurface disposal sites. Assessment of the microbial community ecology using SLB analysis can be utilized to predict potential problems engendered by microbial metabolic activities of these communities in breaching containment by microbially facilitated corrosion and in the potential for subsequent facilitated transport of nuclides into the environment. SLB analysis of the in situ microbial ecology can be utilized to monitor the feasibility of containment options in modeling tests at the specific disposal sites.Key words: nuclear waste, deep subsurface, microbiota, microbial corrosion, safe long-term storage, signature lipid biomarkers.

Microbial abundance and activities in relation to water potential in the vadose zones of arid and semiarid sites

Numbers and activities of microorganisms were measured in the vadose zones of three arid and semiarid areas of the western United States, and the influence of water availability was determined. These low-moisture environments have vadose zones that are commonly hundreds of meters thick. The specific sampling locations chosen were on or near U.S. Department of Energy facilities: the Nevada Test Site (NTS), the Idaho National Engineering Laboratory (INEL), and the Hanford Site (HS) in southcentral Washington State. Most of the sampling locations were uncontaminated, but geologically representative of nearby locations with storage and/or leakage of waste compounds in the vadose zone. Lithologies of samples included volcanic tuff, basalt, glaciofluvial and fluvial sediments, and paleosols (buried soils). Samples were collected aseptically, either by drilling bore-holes (INEL and HS), or by excavation within tunnels (NTS) and outcrop faces (paleosols near the HS). Total numbers of microorganisms were counted using direct microscopy, and numbers of culturable microorganisms were determined using plate-count methods. Desiccation-tolerant microorganisms were quantified by plate counts performed after 24 h desiccation of the samples. Mineralization of (14)C-labeled glucose and acetate was quantified in samples at their ambient moisture contents, in dried samples, and in moistened samples, to test the hypothesis that water limits microbial activities in vadose zones. Total numbers of microorganisms ranged from log 4.5 to 7.1 cells g(-1) dry wt. Culturable counts ranged from log <2 to 6.7 CFU g(-1) dry wt, with the highest densities occurring in paleosol (buried soil) samples. Culturable cells appeared to be desiccation-tolerant in nearly all samples that had detectable viable heterotrophs. Water limited mineralization in some, but not all samples, suggesting that an inorganic nutrient or other factor may limit microbial activities in some vadose zone environments.