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

Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage

Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage.

IMPORTANCE

In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.

Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer

Biodegradation is responsible for most contaminant removal in plumes of organic compounds and is fastest at the plume fringe where microbial cell numbers and activity are highest. As the plume migrates from the source, groundwater containing the contaminants and planktonic microbial community encounters uncontaminated substrata on which an attached community subsequently develops. While attached microbial communities are important for biodegradation, the time needed for their establishment, their relationship with the planktonic community and the processes controlling their development are not well understood. We compare the dynamics of development of attached microbial communities on sterile substrata in the field and laboratory microcosms, sampled simultaneously at intervals over two years. We show that attached microbial cell numbers increased rapidly and stabilised after similar periods of incubation (∼100 days) in both field and microcosm experiments. These timescales were similar even though variation in the contaminant source evident in the field was absent in microcosm studies, implying that this period was an emergent property of the attached microbial community. 16S rRNA gene sequencing showed that attached and planktonic communities differed markedly, with many attached organisms strongly preferring attachment. Successional processes were evident, both in community diversity indices and from community network analysis. Community development was governed by both deterministic and stochastic processes and was related to the predilection of community members for different lifestyles and the geochemical environment.

Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin

Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 - 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15 : 0, C15 : 0, C16 : 0 and C14 : 0. The percentage of the straight-chain fatty acid C15 : 0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).

Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India

Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.

Low Energy Subsurface Environments as Extraterrestrial Analogs

Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.

Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems

Aromatic hydrocarbons belong to the most abundant contaminants in groundwater systems. They can serve as carbon and energy source for a multitude of indigenous microorganisms. Predictions of contaminant biodegradation and microbial growth in contaminated aquifers are often vague because the parameters of microbial activity in the mathematical models used for predictions are typically derived from batch experiments, which don’t represent conditions in the field. In order to improve our understanding of key drivers of natural attenuation and the accuracy of predictive models, we conducted comparative experiments in batch and sediment flow-through systems with varying concentrations of contaminant in the inflow and flow velocities applying the aerobic Pseudomonas putida strain F1 and the denitrifying Aromatoleum aromaticum strain EbN1. We followed toluene degradation and bacterial growth by measuring toluene and oxygen concentrations and by direct cell counts. In the sediment columns, the total amount of toluene degraded by P. putida F1 increased with increasing source concentration and flow velocity, while toluene removal efficiency gradually decreased. Results point at mass transfer limitation being an important process controlling toluene biodegradation that cannot be assessed with batch experiments. We also observed a decrease in the maximum specific growth rate with increasing source concentration and flow velocity. At low toluene concentrations, the efficiencies in carbon assimilation within the flow-through systems exceeded those in the batch systems. In all column experiments the number of attached cells plateaued after an initial growth phase indicating a specific “carrying capacity” depending on contaminant concentration and flow velocity. Moreover, in all cases, cells attached to the sediment dominated over those in suspension, and toluene degradation was performed practically by attached cells only. The observed effects of varying contaminant inflow concentration and flow velocity on biodegradation could be captured by a reactive-transport model. By monitoring both attached and suspended cells we could quantify the release of new-grown cells from the sediments to the mobile aqueous phase. Studying flow velocity and contaminant concentrations as key drivers of contaminant transformation in sediment flow-through microcosms improves our system understanding and eventually the prediction of microbial biodegradation at contaminated sites.

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils

In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds

Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12.7 and 48 m depth). Quantitative PCR and amplicon pyrosequencing of nirK and nirS genes encoding copper-containing or cytochrome cd1 heme-type nitrite reductase, respectively, and of bacterial 16S ribosomal RNA genes showed a numerical predominance of nirS-type denitrifiers in both attached and suspended groundwater communities and a dominance of nirS-type denitrifiers closely related to the autotrophic thiosulfate- and hydrogen-oxidizing Sulfuritalea hydrogenivorans and the iron- and sulfide-oxidizing Sideroxydans lithotrophicus ES-1. Potential rates of nitrate reduction in association with exposed crushed rock material were higher with an inorganic electron donor (thiosulfate) compared to an organic electron donor (fumarate/acetate) in the upper aquifer assemblage but similar in the lower, oxic aquifer. Our results have clearly demonstrated that groundwater from pristine limestone aquifers harbors diverse denitrifier communities which appear to selectively attach to rock surfaces and harbor a high potential for nitrate reduction. Our findings suggest that the availability of suitable inorganic versus organic electron donors rather than oxygen availability shapes denitrifier communities and their potential activity in these limestone aquifers.

In-situ sonication for enhanced recovery of aquifer microbial communities

Sampling methods for characterization of microbial communities in aquifers should target both suspended and attached microorganisms (biofilms). We investigated the effectiveness and reproducibility of low-frequency (200 Hz) sonication pulses on improving extraction efficiency and quality of microorganisms from a petroleum-contaminated aquifer in Studen (Switzerland). Sonication pulses at different power levels (0.65, 0.9, and 1.1 kW) were applied to three different groundwater monitoring wells. Groundwater samples extracted after each pulse were compared with background groundwater samples for cell and adenosine tri-phosphate concentration. Turbidity values were obtained to assess the release of sediment fines and associated microorganisms. The bacterial community in extracted groundwater samples was analyzed by terminal-restriction-fragment-length polymorphism and compared with communities obtained from background groundwater samples and from sediment cores. Sonication enhanced the extraction efficiency up to 13-fold, with most of the biomass being associated with the sediment fines extracted with groundwater. Consecutive pulses at constant power were decreasingly effective, while pulses with higher power yielded the best results both in terms of extraction efficiency and quality. Our results indicate that low-frequency sonication may be a viable and cost-effective tool to improve the extraction of microorganisms from aquifers, taking advantage of existing groundwater monitoring wells.

Variability in bacteria and virus-like particle abundances during purging of unconfined aquifers

Standard methodologies for sampling the physicochemical conditions of groundwater recommend purging a bore for three bore volumes to avoid sampling the stagnant water within a bore and instead gain samples representative of the aquifer. However, there are currently no methodological standards addressing the amount of purging required to gain representative biological samples to assess groundwater bacterial and viral abundances. The objective of this study was to examine how bacterial and viral abundances change during the purging of bore volumes. Six bores infiltrating into unconfined aquifers were pumped for five or six bore volumes each and bacteria and virus-like particles (VLPs) were enumerated from each bore volume using flow cytometry. In examination of the individual bores trends in bacterial abundances were observed to increase, decrease, or remain constant with each purged bore volume. Furthermore, triplicates taken at each bore volume indicated substantial variations in VLP and bacterial abundances that are often larger than the differences between bore volumes. This indicates a high level of small scale heterogeneity in microbial community abundance in groundwater samples, and we suggest that this may be an intrinsic feature of bore biology. The heterogeneity observed may be driven by bottom up processes (variability in the distribution of organic and inorganic nutrients), top-down processes (grazing and viral lysis), physical heterogeneities in the bore, or technical artifacts associated with the purging process. We suggest that a more detailed understanding of the ecology underpinning this variability is required to adequately describe the microbiological characteristics of groundwater ecosystems.

Using boreholes as windows into groundwater ecosystems

Groundwater ecosystems remain poorly understood yet may provide ecosystem services, make a unique contribution to biodiversity and contain useful bio-indicators of water quality. Little is known about ecosystem variability, the distribution of invertebrates within aquifers, or how representative boreholes are of aquifers. We addressed these issues using borehole imaging and single borehole dilution tests to identify three potential aquifer habitats (fractures, fissures or conduits) intercepted by two Chalk boreholes at different depths beneath the surface (34 to 98 m). These habitats were characterised by sampling the invertebrates, microbiology and hydrochemistry using a packer system to isolate them. Samples were taken with progressively increasing pumped volume to assess differences between borehole and aquifer communities. The study provides a new conceptual framework to infer the origin of water, invertebrates and microbes sampled from boreholes. It demonstrates that pumping 5 m³ at 0.4–1.8 l/sec was sufficient to entrain invertebrates from five to tens of metres into the aquifer during these packer tests. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. There was some variability in invertebrate abundance and bacterial community structure between habitats, indicating ecological heterogeneity within the aquifer. However, invertebrates were captured in all aquifer samples, and bacterial abundance, major ion chemistry and dissolved oxygen remained similar. Therefore the study demonstrates that in the Chalk, ecosystems comprising bacteria and invertebrates extend from around the water table to 70 m below it. Hydrogeological techniques provide excellent scope for tackling outstanding questions in groundwater ecology, provided an appropriate conceptual hydrogeological understanding is applied.

Dynamics of natural prokaryotes, viruses, and heterotrophic nanoflagellates in alpine karstic groundwater

Seasonal dynamics of naturally occurring prokaryotes, viruses, and heterotrophic nanoflagellates in two hydro-geologically contrasting alpine karst springs were monitored over three annual cycles. To our knowledge, this study is the first to shed light on the occurrence and possible interrelationships between these three groups in karstic groundwater. Hydrological and microbiological standard indicators were recovered simultaneously in order to estimate surface influence, especially during rainfall events. Data revealed a strong dependence of the microbial communities on the prevailing hydrological situation. Prokaryotic numbers averaged 5.1 × 10⁷ and 1.3 × 10⁷ cells L⁻¹, and heterotrophic nanoflagellate abundance averaged 1.1 × 10⁴ and 3 × 10³ cells L⁻¹ in the limestone spring type (LKAS2) and the dolomitic spring type (DKAS1), respectively. Viral abundance in LKAS2 and DKAS1 averaged 9.4 × 10⁸ and 1.1 × 10⁸ viruses L⁻¹. Unlike in DKAS1, the dynamic spring type LKAS2 revealed a clear difference between base flow and high discharge conditions. The virus-to-prokaryotes ratio was generally lower by a factor of 2–3, at higher average water residence times. Furthermore, the high prokaryotes-to-heterotrophic nanoflagellate ratios, namely about 4700 and 5400 for LKAS2 and DKAS1, respectively, pointed toward an uncoupling of these two groups in the planktonic fraction of alpine karstic aquifers.

Seasonal dynamics of naturally occurring prokaryotes, viruses and heterotrophic nanoflagellates in two hydro-geologically contrasting alpine karst springs were monitored over three annual cycles. Data revealed a strong dependence of the microbial communities on the prevailing hydrological situation.

Detection and quantification of microbial cells in subsurface sediments

Quantification of total cell abundance is one of the most fundamental parameters in the exploration of subsurface life. Despite all recent advances in molecular techniques, this parameter is usually determined by fluorescence microscopy. In order to obtain reliable and reproducible results, it is important not just to focus on the actual cell enumeration but also to consider the entire chain of processing. Starting with the retrieval of the sample, over subsampling and sample processing to the final step of fluorescence microscopy, there are many potential sources of contamination that have to be assessed and, if possible, avoided. Because some degree of sample contamination will always occur, it is necessary to employ some form of contamination control. Different tracers are available, each one with its specific advantages and drawbacks. In many cases, the problems arise not after the sample has arrived in a well-equipped laboratory with highly trained personnel, but much earlier at the drill site or in a field camp. In this review, I discuss the different aspects of cell enumeration in subsurface sediment, evaluating every step in the long process chain.

Deep, subsurface microflora after excavation respiration and biomass and its potential role in degradation of fossil organic matter

Three types of Miocene claystones (amorphous, lamellar, and transitional) were aseptically sampled from depths of 30 m and 150 m below the soil surface. Respiration of these sediments was measured under conditions that prevented inoculation by other microorganisms not indigenous to the claystones in situ. Microbial respiration was higher in lamellar than amorphous claystones and was not affected by sampling depth. During cultivation, microbial biomass (as indicated by PLFA) significantly increased. Microbial biomass after cultivation was significantly higher in sediments from 30 m than from 150 m depth. Both microbial respiration and biomass increased after glucose addition.

Diversity of Bacterial Communities in Contrasting Aquatic Environments: Lake Timsah, Egypt

Effect of pollution on diversity of attached and free-living bacteria in two contrasting stations, namely, Suez Canal and outlet of West Lagoon to Lake Timsah was investigated. Bacillus was the most abundant genus especially in West Lagoon station where higher organic agricultural and municipal loads was discharged. Bacterial species richness differed among water depths and was higher in subsurface samples. In Suez Canal more Gram negative populations were isolated. The possible influences of pollution in the West Lagoon station on the bacterial community composition were discussed.

Assessing the activity and diversity of fumarate-fed denitrifying bacteria by performing field single-well push-pull tests

In situ biological denitrification has been proposed as an important metabolic activity in the remediation of nitrate-contaminated groundwater. In this study, the effects of fumarate, an electron donor for biological denitrification, on the in situ denitrifying activity were determined by using three types of single-well push-pull tests; transport, biostimulation and activity tests. During the tests, changes in microbial community composition were also investigated using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes. Transport test demonstrated that non-reactive tracer and biologically reactive solutes behaved similarly. A biostimulation test was conducted to stimulate the denitrifying activities of native microorganisms, which were monitored by detecting the simultaneous production of CO(2) and drastic degradations of both nitrate and fumarate after the injection of fumarate as an electron donor and/or carbon source, with nitrate as an electron acceptor. A phylogenetic analysis suggested that the taxonomic affiliation of the dominant species before biostimulation was γ-Proteobacteria, including Acinetobacter species and Pseudomonas fluorescens, while the dominant species after biostimulation were affiliated with β-Proteobacteria, cytophaga-Flavobacterium-Bacteroides and high G+C gram-positive bacteria. These results suggest that the analyses of groundwater samples using a combination of single well push pull tests with DGGE can be applied to investigate the activity, diversity and composition shift of denitrifying bacteria in a nitrate-contaminated aquifer.

Fecal indicator bacteria variability in samples pumped from monitoring wells

The detection of microbiological contamination in drinking water from groundwater wells is often made with a limited number of samples that are collected using traditional geochemical sampling protocols. The objective of this study is to examine the variability of fecal indicator bacteria, as observed using discrete samples, due to pumping. Two wells were instrumented as multilevel piezometers in a bedrock aquifer, and bacterial enumeration was conducted on a total of 166 samples (for total coliform, fecal coliform, Escherichia coli, and fecal streptococci) using standard membrane filtration methods. Five tests were conducted using pumping rates ranging from 0.3 to 17 L/min in a variety of purging scenarios, which included constant and variable (incremental increase and decrease) flow. The results clearly show a rapid and reproducible, 1 to 2 log-unit decrease in fecal indicator bacteria at the onset of pumping to stabilized, low-level concentrations prior to the removal of three to five well volumes. The pumping rate was not found to be correlated with the magnitude of observed bacterial counts. Based on the results, we suggest sampling protocols for fecal indicator bacteria that include multiple collections during the course of pumping, including early-time samples, and consider other techniques such as microscopic enumeration when assessing the source of bacteria from the well-aquifer system.

Stimulation of microbial urea hydrolysis in groundwater to enhance calcite precipitation

Addition of molasses and urea was tested as a means of stimulating microbial urea hydrolysis in the Eastern Snake River Plain Aquifer in Idaho. Ureolysis is an integral component of a novel remediation approach for divalent trace metal and radionuclide contaminants in groundwater and associated geomedia, where the contaminants are immobilized by coprecipitation in calcite. Generation of carbonate alkalinity from ureolysis promotes calcite precipitation. In calcite-saturated aquifers, this represents a potential long-term contaminant sequestration mechanism. In a single-well experiment, dilute molasses was injected three times over two weeks to promote overall microbial growth, followed by one urea injection. With molasses addition, total cell numbers in the groundwater increased 1-2 orders of magnitude. Estimated ureolysis rates in recovered groundwater samples increased from < 0.1 to > 25 nmol L(-1) hr(-1). A quantitative PCR assay for the bacterial ureC gene indicated that urease gene numbers increased up to 170 times above pre-injection levels. Following urea injection, calcite precipitates were recovered. Estimated values for an in situ first order ureolysis rate constant ranged from 0.016 to 0.057 d(-1). Although collateral impacts such as reduced permeability were observed, overall results indicated the viability of manipulating biogeochemical processes to promote contaminant sequestration.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems.

Community analysis of a mercury hot spring supports occurrence of domain-specific forms of mercuric reductase

Mercury is a redox-active heavy metal that reacts with active thiols and depletes cellular antioxidants. Active resistance to the mercuric ion is a widely distributed trait among bacteria and results from the action of mercuric reductase (MerA). Protein phylogenetic analysis of MerA in bacteria indicated the occurrence of a second distinctive form of MerA among the archaea, which lacked an N-terminal metal recruitment domain and a C-terminal active tyrosine. To assess the distribution of the forms of MerA in an interacting community comprising members of both prokaryotic domains, studies were conducted at a naturally occurring mercury-rich geothermal environment. Geochemical analyses of Coso Hot Springs indicated that mercury ore (cinnabar) was present at concentrations of parts per thousand. Under high-temperature and acid conditions, cinnabar may be oxidized to the toxic form Hg2+, necessitating mercury resistance in resident prokaryotes. Culture-independent analysis combined with culture-based methods indicated the presence of thermophilic crenarchaeal and gram-positive bacterial taxa. Fluorescence in situ hybridization analysis provided quantitative data for community composition. DNA sequence analysis of archaeal and bacterial merA sequences derived from cultured pool isolates and from community DNA supported the hypothesis that both forms of MerA were present. Competition experiments were performed to assess the role of archaeal merA in biological fitness. An essential role for this protein was evident during growth in a mercury-contaminated environment. Despite environmental selection for mercury resistance and the proximity of community members, MerA retains the two distinct prokaryotic forms and avoids genetic homogenization.

Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site

The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.

A rationally assembled microbial community for growing Tagetes patula L. in a lunar greenhouse

Well-defined plant-associated bacteria were used for growing French marigolds (Tagetes patula L.) in anorthosite, a substrate of low bioavailability, analogous to a lunar rock. The consortium was composed mainly of plant growth-promoting rhizobacteria and biocontrol agents that were used for seed inoculation. Simultaneously, the sterile substrate was inoculated with the siliceous bacterium Paenibacillus sp. IMBG156. The plant benefited from bacterial activity which resulted in stimulation of seed germination, better plant development, and finally in flowering of inoculated tagetes. In contrast, control plants grew poorly in sterile anorthosite and never flowered. Analysis of bacterial community composition showed that both species colonized plant roots, and there were no shifts in the consortium structure in the rhizosphere of French marigolds within 6 weeks. Paenibacillus sp. IMBG156 was able to release some elements (Ca, Fe, Si) from substrate anorthosite. It was assumed that a rationally assembled consortium of bacterial strains supported growth and development of the model plant under growth-limiting conditions, at least by means of bioleaching and delivering of essential nutritional elements to the plants, and by promoting plant growth.

Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities

Spring water of two alpine karst aquifers differing in hydrogeology but of nearby catchments were investigated for their bacterial population dynamics. Dolomite karst aquifer spring 1 (DKAS 1) represents a dolomitic-limestone karst aquifer spring showing high average water residence time and relative constant flow. Limestone karst aquifer spring 2 (LKAS 2) constitutes a typical limestone karst aquifer spring with a dynamic hydrological regime and discharge. Dolomite karst aquifer spring 1 yielded constantly lower cell counts and biomasses (median of 15 x 10(6) cells l(-1) and 0.22 microg C l(-1)) as the LKAS 2 (median of 63 x 10(6) cells l(-1) and 1.1 microg C l(-1)) and distribution of morphotypes and mean cell volumes was also different between the considered systems, indicating the influence of hydrogeology on microbial spring water quality. Molecular bacterial V3 16S-rDNA profiles revealed remarkable constancy within each spring water throughout the investigation period. Time course analysis of a flood event in LKAS 2 further supported the trend of the temporal constancy of the microbial community. Except for one case, retrieval of partial and full length 16S rDNA gene sequences from the relative constant DKAS 1 revealed similarities to presently known sequences between 80% to 96%, supporting the discreteness of the microbial populations. The gathered results provide first evidence for the presence of autochthonous microbial endokarst communities (AMEC). Recovery of AMEC may be considered of relevance for the understanding of alpine karst aquifer biogeochemistry and ecology, which is of interest as many alpine and mountainous karst springs are important water resources throughout the world.

Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer

Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H(2) plus CO(2), or methanol to target different groups of methanogenic Archaea. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day(-1) for methanol, 0.38 mM day(-1) for acetate, 0.90 mM day(-1) for H(2), and 1.85 mM day(-1) for formate. Substrate consumption and CH(4) production during all tests suggested that at least three different physiologic types of methanogens were present: H(2) plus CO(2) or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H(2) and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI [4',6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO(2)-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.

Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes

The integrated biomass beneath the surface horizon in unsaturated soils is large and potentially important in nutrient and carbon cycling. Compared to surface soils, the ecology of these subsurface soils is weakly understood, particularly in terms of the composition of bacterial communities. We compared soil bacterial communities along two vertical transects by terminal restriction fragment length polymorphisms (TRFLPs) of PCR-amplified 16S rRNA genes to determine how surface and deep bacterial communities differ. DNA yield from soils collected from two Mediterranean grassland transects decreased exponentially from the surface to 4 m deep. Richness, as assessed by the number of peaks obtained after restriction with HhaI, MspI, RsaI, or HaeIII, and diversity, as assessed by the Shannon diversity indices, were lowest in the deepest sample. Lower diversity at depth is consistent with species-energy theory, which would predict relatively low diversity in the low organic matter horizons. Principal components analysis suggested that, in terms of HhaI and HaeIII generated TRFLPs, bacterial communities differed between depths. The most abundant amplicons cloned from the deepest sample contained sequences with restriction sites consistent with the largest peaks observed in TRFLPs generated from deep samples. These more abundant operational taxonomic units (OTUs) appeared related to Pseudomonas and Variovorax. Several OTUs were more related to each other than any previously described ribotypes. These OTUs showed similarity to bacteria from the divisions Actinobacteria and Firmicutes.

Determination of in situ bacterial growth rates in aquifers and aquifer sediments

Laboratory and field-scale studies with stained cells were performed to monitor cell growth in groundwater systems. During cell division, the fluorescence intensity of the protein stain 5-(and 6-)-carboxyfluorescein diacetate succinimidyl ester (CFDA/SE) for each cell is halved, and the intensity can be tracked with a flow cytometer. Two strains of bacteria, Comamonas sp. strain DA001 and Acidovorax sp. strain OY-107, both isolated from a shallow aquifer, were utilized in this study. The change in the average generation or the average fluorescence intensity of the CFDA/SE-stained cells could be used to obtain estimates of doubling times. In microcosm experiments, the CFDA/SE-based doubling times were similar to the values calculated by total cell counting and were independent of cell concentration. Intact and repacked sediment core experiments with the same bacteria indicated that changes in groundwater chemistry were just as important as growth rates in determining planktonic cell concentrations. The growth rates within the sediment cores were similar to those calculated in microcosm experiments, and preferential transport of the daughter cells was not observed. The experiments indicated that the growth rates could be determined in systems with cell losses due to other phenomena, such as attachment to sediment or predation. Application of this growth rate estimation method to data from a field-scale bacterial transport experiment indicated that the doubling time was approximately 15 days, which is the first known direct determination of an in situ growth rate for bacteria in an aquifer.

Comparison of extracellular enzyme activities and community composition of attached and free-living bacteria in porous medium columns

Free-living and surface-associated microbial communities in sand-packed columns perfused with groundwater were compared by examination of compositional and functional characteristics. The composition of the microbial communities was assessed by bulk DNA extraction, PCR amplification of 16S ribosomal DNA fragments, separation of these fragments by denaturing gradient gel electrophoresis, and sequence analysis. Community function was assessed by measurement of beta-glucosidase and aminopeptidase extracellular enzyme activities. Free-living populations in the aqueous phase exhibited a greater diversity of phylotypes than populations associated with the solid phase. The attached bacterial community displayed significantly greater beta-glucosidase and aminopeptidase enzyme activities per volume of porous medium than those of the free-living community. On a per-cell basis, the attached community had a significantly higher cell-specific aminopeptidase enzyme activity (1.07 x 10(-7) nmol cell(-1) h(-1)) than the free-living community (5.02 x 10(-8) nmol cell(-1) h(-1)). Conversely, the free-living community had a significantly higher cell-specific beta-glucosidase activity (1.92 x 10(-6) nmol cell(-1) h(-1)) than the surface-associated community (6.08 x 10(-7) nmol cell(-1) h(-1)). The compositional and functional differences observed between these two communities may reflect different roles for these distinct but interacting communities in the decomposition of natural organic matter or biodegradation of xenobiotics in aquifers.

Attached and unattached microbial communities in a simulated basalt aquifer 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 alpha, beta, and gamma 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 alpha- and beta-Proteobacteria subclasses in comparison to those in the corresponding groundwater. In the fractured columns, attached communities were enriched in gram-positive Bacteria and gamma-Proteobacteria and depleted of beta-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.