Microbiology of vadose zone paleosols in south-central Washington State

Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability

Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.

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.

Modified Lipid Extraction Methods for Deep Subsurface Shale

Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures. Here, we test three different lipid extraction methods: modified Bligh and Dyer (mBD), Folch (FOL), and microwave assisted extraction (MAE), to examine their ability in the recovery and reproducibility of lipid biomarkers in deeply buried shales. The lipid biomarkers were analyzed as fatty acid methyl esters (FAMEs) with the GC-MS, and the average PL-FAME yield ranged from 67 to 400 pmol/g, while the average DG-FAME yield ranged from 600 to 3,000 pmol/g. The biomarker yields in the intact phospholipid Bligh and Dyer treatment (mBD + Phos + POPC), the Folch, the Bligh and Dyer citrate buffer (mBD-Cit), and the MAE treatments were all relatively higher and statistically similar compared to the other extraction treatments for both PLFAs and DGFAs. The biomarker yields were however highly variable within replicates for most extraction treatments, although the mBD + Phos + POPC treatment had relatively better reproducibility in the consistent fatty acid profiles. This variability across treatments which is associated with the highly complex nature of deeply buried shale matrix, further necessitates customized methodological developments for the improvement of lipid biomarker recovery.

Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China

Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.

Significance of Heavy-Ion Beam Irradiation-Induced Avermectin B1a Production by Engineered Streptomyces avermitilis

Heavy-ion irradiation technology has advantages over traditional methods of mutagenesis. Heavy-ion irradiation improves the mutation rate, broadens the mutation spectrum, and shortens the breeding cycle. However, few data are currently available regarding its effect on Streptomyces avermitilis morphology and productivity. In this study, the influence of heavy-ion irradiation on S. avermitilis when cultivated in approximately 10 L stirred-tank bioreactors was investigated. The specific productivity of the avermectin (AVM) B1a-producing mutant S. avermitilis 147-G₅8 increased notably, from 3885 to 5446 μg/mL, approximately 1.6-fold, compared to the original strain. The mycelial morphology of the mutant fermentation processes was microscopically examined. Additionally, protein and metabolite identification was performed by using SDS-PAGE, 2- and 3-dimensional electrophoresis (2DE and 3DE). The results showed that negative regulation gene deletion of mutants led to metabolic process upregulating expression of protein and improving the productivity of an avermectin B1a. The results showed that the heavy-ion beam irradiation dose that corresponded to optimal production was well over the standard dose, at approximately 80 Gy at 220 AMeV (depending on the strain). This study provides reliable data and a feasible method for increasing AVM productivity in industrial processes.

Disentangling interactions between microbial communities and roots in deep subsoil

Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown. We characterized fossil and living microbial communities based on molecular markers in a Central European Late Pleistocene loess-paleosol sequence containing recent and ancient roots with ages of several millenia. The molecular approach, comprising free and phospholipid fatty acids (FAs), core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs), as well as 16S rRNA genes from bacterial DNA, revealed the presence of living microorganisms along the sequence, with bacterial community composition comparable to that of modern topsoils. Up to 88% redundancy between bacterial genetic fingerprint and molecular signature of fossil microorganisms suggested a time-integrated signal of the molecular markers accumulated over a time span potentially lasting from sedimentation over one or more rooting phases until today. Free FAs, core GDGTs and DNA, considered as remains of fossil microorganisms, corresponded with ancient and recent root quantities, whereas phospholipid FAs and intact polar GDGTs, presumably derived from living microorganisms, correlated only with living roots. The biogeochemical and ecological disequilibrium induced by postsedimentary rooting may entail long-term microbial processes like OM mineralization, which may continue even millenia after the lifetime of the root. Deep roots and their fossil remains have been observed in various terrestrial settings, and roots as well as associated microorganisms cause both, OM incorporation and mineralization. Therefore, these findings are crucial for improved understanding of OM dynamics and carbon sequestration potential in deep subsoils.

In situ vadose zone bioremediation

Contamination of the vadose zone with various pollutants is a world-wide problem, and often technical or economic constraints impose remediation without excavation. In situ bioremediation in the vadose zone by bioventing has become a standard remediation technology for light spilled petroleum products. In this review, focus is given on new in situ bioremediation strategies in the vadose zone targeting a variety of other pollutants such as perchlorate, nitrate, uranium, chromium, halogenated solvents, explosives and pesticides. The techniques for biostimulation of either oxidative or reductive degradation pathways are presented, and biotransformations to immobile pollutants are discussed in cases of non-degradable pollutants. Furthermore, research on natural attenuation in the vadose zone is presented.

The Mojave vadose zone: a subsurface biosphere analogue for Mars

If life ever evolved on the surface of Mars, it is unlikely that it would still survive there today, but as Mars evolved from a wet planet to an arid one, the subsurface environment may have presented a refuge from increasingly hostile surface conditions. Since the last glacial maximum, the Mojave Desert has experienced a similar shift from a wet to a dry environment, giving us the opportunity to study here on Earth how subsurface ecosystems in an arid environment adapt to increasingly barren surface conditions. In this paper, we advocate studying the vadose zone ecosystem of the Mojave Desert as an analogue for possible subsurface biospheres on Mars. We also describe several examples of Mars-like terrain found in the Mojave region and discuss ecological insights that might be gained by a thorough examination of the vadose zone in these specific terrains. Examples described include distributary fans (deltas, alluvial fans, etc.), paleosols overlain by basaltic lava flows, and evaporite deposits.

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.

Spatiotemporal distribution of microbial communities in a coastal, sandy aquifer system (Doñana, SW Spain)

The aquifer system of Doñana (SW Spain) represents the most important freshwater source in the Doñana Natural Area. Its spatiotemporal dynamics favours the hydrological connection between surface and subsurface ecosystems, and promotes matter fluxes among the different terrestrial and aquatic systems present here. This aquifer has been intensively studied from a hydrogeological point of view but little is known from an ecological perspective. In order to understand the ecological roles played by microbial communities in this system, we conducted a long-term seasonal study of bacterial abundance, cell biomass, bacterial biomass and functional activities over a 2-year period. Bacterial abundance ranged between 2.11 +/- 1.79 x 10(5) and 8.58 +/- 6.99 x 10(7) bacteria mL(-1) groundwater, average cell biomass was estimated to be 77.01 +/- 31.56 fgC and bacterial biomass varied between 8.99 +/- 4.10 x 10(-2) and 5.65 +/- 0.70 microgC mL(-1). Iron-related bacteria showed the highest activities among the functional groups studied. Moreover, among the variables that usually control spatial distributions of microbial communities in aquifer systems, depth did not have a relevant effect on this aquifer, at least in the range of depths studied, but grain size, probably due to its direct effects on hydrogeological parameters, such as permeability or porosity, appeared to exert moderate control, principally in terms of bacterial abundance. Finally, significant seasonal differences in the means of these microbiological variables were also observed; temperature seems to be the main factor controlling the temporal distribution of microbial communities in this aquifer system.

Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), (137)Cs, and (99)Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to approximately 10(4) CFU g(-1), but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 microCi of (137)Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 microCi of (137)Cs g(-1)) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste.

An assessment of a mesocosm approach to the study of microbial respiration in a sandy unsaturated zone

Microbial respiration rates were determined through a 3.2 m thick, sandy unsaturated zone in a 2.4 m diameter x 4.6 m high mesocosm. The mesocosm was maintained under near constant temperature (18 degrees to 23 degrees C) and reached steady moisture content conditions after several hundred days. Soil-gas CO2 concentrations in the mesocosm ranged from 0.09% to 3.31% and increased with depth. Respiration rates within the mesocosm were quantified over a 342-day period using measured CO2 concentrations and a transient, one-dimensional finite-element model. Microbial respiration rates were 2 x 10(-1) micrograms C.g-1.d-1 throughout most of the system, but decreased to 10(-4) to 10(-3) micrograms C.g-1.d-1 within the capillary fringe. Microbial respiration rates were also determined in minicosms (500 g sample mass) over a range in temperatures (4 degrees to 30 degrees C) and volumetric moisture contents (0.044 to 0.37). The functional dependence of CO2 production on temperature and soil-moisture content was similar for the two scales of laboratory observation. Respiration rates in the minicosms, for temperatures and moisture contents in the mesocosm, were up to an order of magnitude greater than those determined for the mesocosm. The higher respiration rates in the minicosms, compared to the mesocosm, were attributed to greater disturbance of the samples and to shorter acclimation time in the minicosms. Extrapolating the laboratory respiration rates to field conditions yielded rates that were two to three orders of magnitude greater than rates previously determined in situ for C-horizon material. Results show that in situ microbial reaction rates determined using disturbed samples in minicosms and mesocosms yielded respiration rates that greatly exceeded field conditions. Mesocosms can, however, provide a useful environment for conducting process-related research in unsaturated environments.

Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps

Bispeptide nucleic acids (bis-PNAs; PNA clamps), PNA oligomers, and DNA oligonucleotides were evaluated as affinity purification reagents for subfemtomolar 16S ribosomal DNA (rDNA) and rRNA targets in soil, sediment, and industrial air filter nucleic acid extracts. Under low-salt hybridization conditions (10 mM NaPO(4), 5 mM disodium EDTA, and 0.025% sodium dodecyl sulfate [SDS]) a PNA clamp recovered significantly more target DNA than either PNA or DNA oligomers. The efficacy of PNA clamps and oligomers was generally enhanced in the presence of excess nontarget DNA and in a low-salt extraction-hybridization buffer. Under high-salt conditions (200 mM NaPO(4), 100 mM disodium EDTA, and 0.5% SDS), however, capture efficiencies with the DNA oligomer were significantly greater than with the PNA clamp and PNA oligomer. Recovery and detection efficiencies for target DNA concentrations of > or =100 pg were generally >20% but depended upon the specific probe, solution background, and salt condition. The DNA probe had a lower absolute detection limit of 100 fg of target (830 zM [1 zM = 10(-21) M]) in high-salt buffer. In the absence of exogenous DNA (e.g., soil background), neither the bis-PNA nor the PNA oligomer achieved the same absolute detection limit even under a more favorable low-salt hybridization condition. In the presence of a soil background, however, both PNA probes provided more sensitive absolute purification and detection (830 zM) than the DNA oligomer. In varied environmental samples, the rank order for capture probe performance in high-salt buffer was DNA > PNA > clamp. Recovery of 16S rRNA from environmental samples mirrored quantitative results for DNA target recovery, with the DNA oligomer generating more positive results than either the bis-PNA or PNA oligomer, but PNA probes provided a greater incidence of detection from environmental samples that also contained a higher concentration of nontarget DNA and RNA. Significant interactions between probe type and environmental sample indicate that the most efficacious capture system depends upon the particular sample type (and background nucleic acid concentration), target (DNA or RNA), and detection objective.

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.

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.

Survival and phospholipid Fatty Acid profiles of surface and subsurface bacteria in natural sediment microcosms

Although starvation survival has been characterized for many bacteria, few subsurface bacteria have been tested, and few if any have been tested in natural subsurface porous media. We hypothesized that subsurface bacteria may be uniquely adapted for long-term survival in situ. We further hypothesized that subsurface conditions (sediment type and moisture content) would influence microbial survival. We compared starvation survival capabilities of surface and subsurface strains of Pseudomonas fluorescens and a novel Arthrobacter sp. in microcosms composed of natural sediments. Bacteria were incubated for up to 64 weeks under saturated and unsaturated conditions in sterilized microcosms containing either a silty sand paleosol (buried soil) or a sandy silt nonpaleosol sediment. Direct counts, plate counts, and cell sizes were measured. Membrane phospholipid fatty acid (PLFA) profiles were quantified to determine temporal patterns of PLFA stress signatures and differences in PLFAs among strains and treatments. The Arthrobacter strains survived better than the P. fluorescens strains; however, differences in survival between surface and subsurface strains of each genus were not significant. Bacteria survived better in the paleosol than in the nonpaleosol and survived better under saturated conditions than under unsaturated conditions. Cell volumes of all strains decreased; however, sediment type and moisture did not influence rates of miniaturization. Both P. fluorescens strains showed PLFA stress signatures typical for gram-negative bacteria: increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl to monoenoic precursor fatty acids. The Arthrobacter strains showed few changes in PLFAs. Environmental conditions strongly influenced PLFA profiles.

Estimating biodegradative gene numbers at a JP-5 contaminated site using PCR

We have utilized a most-probable-number polymerase chain reaction (MPN-PCR) procedure to estimate gene numbers and biodegradative potential at a jet fuel (JP-5) contaminated site undergoing the first phase of bioremediation. Nucleic acid analysis was used to determine whether a lack of genetic potential for bioremediation was responsible for low levels of oxygen utilization at the site. Total community DNA was extracted and analyzed by PCR for genes (nahAc,alkB, and xylE) known to be involved in the degradation of certain JP-5 constituents. Results indicate that significant aromatic biodegradative potential exists at the site and outlying areas not subjected to engineered remediation, suggesting that physical and/or chemical factors are inhibiting oxygen delivery. xylE and nahAc were often present in significant portions of the microbial community, whereas alkB was rarely detected. This study illustrates the utility of molecular techniques in evaluating biodegradative potential in the field during active bioremediation.

Evaluation of media and techniques to enumerate heterotrophic microbes from karst and sand aquifer springs

Several media and techniques were compared for their efficiency to enumerate viable heterotrophs from both a karst and sand aquifer spring. A medium designed to enumerate bacteria from nutrient-poor waters (HCFU) as well as R2A medium proved superior to tryptic soy agar; however, the difference was always less than one order of magnitude. Membrane filtration resulted in lower counts of microbes than the spread plate, multitube turbidity, or drop plate methods from samples of both sand and karst springs. The drop plate technique yielded higher viable counts from the sand spring and basin of the karst spring, with a precision of 21% (coefficient of variation) and a maximum plating efficiency of 3.4% (viable count/direct count × 100). Subsequently, 63% of isolates from drop plates were recovered on HCFU. Microcolonies were visible by epifluorescence microscopy, acridine orange staining, and subsequent examination of excised agar sections containing drops.

Biodegradation of trichloroethylene and toluene by indigenous microbial populations in vadose sediments

The unsaturated subsurface (vadose zone) receives significant amounts of hazardous chemicals, yet little is known about its microbial communities and their capacity to biodegrade pollutants. Trichloroethylene (TCE) biodegradation occurs readily in surface soils; however, the process usually requires enzyme induction by aromatic compounds, methane, or other cosubstrates. The aerobic biodegradation of toluene and TCE by indigenous microbial populations was measured in samples collected from the vadose zone at unpolluted and gasoline-contaminated sites. Incubation at field moisture levels showed little activity on either TCE or toluene, so samples were tested in soil suspensions. No degradation occurred in samples suspended in water or phosphate buffer solution; however, both toluene and TCE were degraded in samples suspended in mineral salts medium. TCE degradation depended on toluene degradation, and little loss occurred under sterile conditions. Studies with specific nutrients showed that addition of ammonium sulfate was essential for degradation, and addition of other mineral nutrients further enhanced the rate. Additional studies with vadose sediments amended with nutrients showed similar trends to those observed in sediment suspensions. Initial rates of biodegradation in suspensions were faster in uncontaminated samples than in gasolinecontaminated samples, but the same percentages of chemicals were degraded. Biodegradation was slower and less extensive in shallower samples than deeper samples from the uncontaminated site. Two toluene-degrading organisms isolated from a gasoline-contaminated sample were identified as Corynebacterium variabilis SVB74 and Acinetobacter radioresistens SVB65. Inoculation with 10(6) cells of C. variabilis ml(-1) of soil solution did not enhance the rate of degradation above that of the indigenous population. These results indicate that mineral nutrients limited the rate of TCE and toluene degradation by indigenous populations and that no additional benefit was derived from inoculation with a toluene-degrading bacterial strain.

Aromatic-degrading Sphingomonas isolates from the deep subsurface

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds (J. K. Fredrickson, F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens, Appl. Environ. Microbiol. 57:796-803, 1991) was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1 omega 7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16S rRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequence analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [14C]toluene and [14C]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobilis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment.

Isolation and characterization of RNA from low-biomass deep-subsurface sediments

Three methods for the isolation of microbial RNA from low-biomass deep-subsurface sediments have been developed and evaluated. RNA was isolated from samples taken from depths ranging from 173 to 217 m, and samples represented a variety of lithologies, including lacustrine, fluvial sand, and paleosol sediments. Cell numbers in these samples were estimated to be between log 4.0 and log 5.1/g on the basis of phospholipid fatty acid analysis. The most efficient method examined is based on the direct lysis of microbial cells followed by the extraction of RNA with alkaline phosphate buffers and subsequent inactivation of nucleases by extraction with guanidinium isothiocyanate. Estimated recoveries of mRNA for this method are approximately 26%. The recovered RNA included both mRNA and rRNA, as evidenced by the detection of sequences homologous to transcripts from the toluene-4-monooxygenase gene of Pseudomonas mendocina KR1 and bacterial, archaeal, and eukaryotic rRNA. An unexpectedly high relative concentration of archaeal rRNA (22 to 40%) was observed for these samples.

Changes in Ester-Linked Phospholipid Fatty Acid Profiles of Subsurface Bacteria during Starvation and Desiccation in a Porous Medium

Ester-linked phospholipid fatty acid (PLFA) profiles of a Pseudomonas aureofaciens strain and an Arthrobacter protophormiae strain, each isolated from a subsurface sediment, were quantified in a starvation experiment in a silica sand porous medium under moist and dry conditions. Washed cells were added to sand microcosms and maintained under saturated conditions or subjected to desiccation by slow drying over a period of 16 days to final water potentials of approximately - 7.5 MPa for the P. aureofaciens and - 15 MPa for the A. protophormiae. In a third treatment, cells were added to saturated microcosms along with organic nutrients and maintained under saturated conditions. The numbers of culturable cells of both bacterial strains declined to below detection level within 16 days in both the moist and dried nutrient-deprived conditions, while direct counts and total PLFAs remained relatively constant. Both strains of bacteria maintained culturability in the nutrient-amended microcosms. The dried P. aureofaciens cells showed changes in PLFA profiles that are typically associated with stressed gram-negative cells, i.e., increased ratios of saturated to unsaturated fatty acids, increased ratios of trans - to cis -monoenoic fatty acids, and increased ratios of cyclopropyl fatty acids to their monoenoic precursors. P. aureofaciens starved under moist conditions showed few changes in PLFA profiles during the 16-day incubation, whereas cells incubated in the presence of nutrients showed decreases in the ratios of both saturated fatty acids to unsaturated fatty acids and cyclopropyl fatty acids to their monoenoic precursors. The PLFA profiles of A. protophormiae changed very little in response to either nutrient deprivation or desiccation. Diglyceride fatty acids, which have been proposed to be indicators of dead or lysed cells, remained relatively constant throughout the experiment. Only the A. protophormiae desiccated for 16 days showed an increase in the ratio of diglyceride fatty acids to PLFAs. The results of this laboratory experiment can be useful for interpreting PLFA profiles of subsurface communities of microorganisms for the purpose of determining their physiological status.

Changes in Bacteria Recoverable from Subsurface Volcanic Rock Samples during Storage at 4°C

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4°C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at both sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage.

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.