Showing papers in "Geomicrobiology Journal in 2003"
TL;DR: In this article, the diversity and distribution of sulfate-reducing bacteria in cold seeps were investigated. But the authors focused on the presence of methanotrophic archaea, which can be identified by specific biomarker lipids and 16S rDNA analysis.
Abstract: Cold seep environments such as sediments above outcropping hydrate at Hydrate
Ridge (Cascadia margin off Oregon) are characterized by methane venting, high sulfide fluxes caused by the anaerobic oxidation of methane, and the presence of chemosynthetic communities. Recent investigations showed that another characteristic feature of cold seeps is the occurrence of methanotrophic archaea, which can be identified by specific biomarker lipids and 16S rDNA analysis. This investigation deals with the diversity and distribution of sulfate-reducing bacteria, some of which are directly involved in the anaerobic oxidation of methane as syntrophic partners of the methanotrophic archaea. The composition and activity of the microbial communities at methane vented and nonvented sediments are compared by quantitative methods including total cell counts, fluorescence in situ hybridization (FISH), bacterial production, enzyme activity, and sulfate reduction rates. Bacteria involved in the degradation of particulate organic carbon (POC) are as active and diverse as at other productive margin sites of similar water depths. The availability of methane supports a two orders of magnitude higher microbial biomass (up to 9.6 2 10 10 cells cm m 3 ) and sulfate reduction rates (up to 8 w mol cm m 3 d m 1 ) in hydrate-bearing sediments, as well as a high bacterial diversity, especially in the group of i -proteobacteria including members of the branches Desulfosarcina/Desulfococcus , Desulforhopalus , Desulfobulbus , and Desulfocapsa . Most of the diversity of sulfate-reducing bacteria in hydrate-bearing sediments comprises seep-endemic clades, which share only low similarities with previously cultured bacteria.
286 citations
TL;DR: The link between similarity in amino acid sequence for ammonia monooxygenase (AMO) and isotopic discrimination for ammonia oxidation ( l AMO ) was investigated in g-subdivision ammonia-oxidizing bacteria.
Abstract: The link between similarity in amino acid sequence for ammonia monooxygenase (AMO) and isotopic discrimination for ammonia oxidation ( l AMO ) was investigated in g -subdivision ammonia-oxidizing bacteria. The isotope effects for ammonia oxidation in pure cultures of the nitrifying strains Nitrosomonas marina , Nitrosomonas C-113a, Nitrosospira tenuis , Nitrosomonas europaea , and Nitrosomonas eutropha ranged from 14.2 to 38.2. The differences in isotope effects could not be readily explained by differential rates of ammonia oxidation, transport of NH 4 + , or accumulation of NH 2 OH or N 2 O among the strains. The major similarities and differences observed in l AMO are, however, paralleled by similarities and differences in amino acid sequences for the f -subunit of AMO (AmoA). Robust differences in l AMO among nitrifying bacteria may be expected to influence the stable isotopic signatures of nitrous oxide (N 2 O) produced in various environments.
282 citations
TL;DR: In this article, the authors extracted membrane fatty acids from a sediment core above marine gas hydrates at Hydrate Ridge, NE Pacific, which are characterized by high sulfate reduction rates driven by the anaerobic oxidation of methane (AOM).
Abstract: Membrane fatty acids were extracted from a sediment core above marine gas hydrates at Hydrate Ridge, NE Pacific. Anaerobic sediments from this environment are characterized by high sulfate reduction rates driven by the anaerobic oxidation of methane (AOM). The assimilation of methane carbon into bacterial biomass is indicated by carbon isotope values of specific fatty acids as low as m 103. Specific fatty acids released from bacterial membranes include C 16:1 y 5c , C 17:1 y 6c , and cyC 17:0 y 5,6 , all of which have been fully characterized by mass spectrometry. These unusual fatty acids continuously display the lowest i 13 C values in all sediment horizons and two of them are detected in high abundance (i.e., C 16:1 y 5c and cyC 17:0 y 5,6 ). Combined with microscopic examination by fluorescence in situ hybridization specifically targeting sulfate-reducing bacteria (SRB) of the Desulfosarcina/Desulfococcus group, which are present in the aggregates of AOM consortia in extremely high numbers, these spe...
249 citations
TL;DR: High levels of diversity with similarity to known methanogenic families Methanosarcinaceae, Methanosaetaceae, methanobacteriaceae, and likely Methanomicrobiaceae as well as two additional lineages previously characterized as groups of yet uncultivated Euryarchaeota commonly occurring in flooded rice soils are indicated.
Abstract: Rates of methane (CH4) production vary considerably among northern peat-forming wetlands, and it is not clear whether variability is caused by environmental factors affecting CH4 production or differences in methanogen communities. We investigated CH4 production and emission dynamics concomitantly with 16S rRNA gene sequence-based community analysis of Archaea in two contrasting peat-forming northern wetlands, an ombrotrophic bog and a minerotrophic conifer swamp. Individual measurements of CH4 emissions to the atmosphere followed a lognormal distribution pattern in both sites, and mean rates were 30× greater in the bog site. Rates of CH4 production measured in vitro were initially 3× greater in the bog than in the conifer swamp; although, after 30 days of incubation, production rates were similar suggesting that in situ environmental conditions limited production in the conifer swamp. Amplified ribosomal DNA restriction analysis (ARDRA) and rarefaction techniques indicated that both sites had similar lev...
213 citations
TL;DR: Water- and EDTA-extractable EPS are conceived to be a major factor in the structuring and diagenesis of coastal sediments and essential for increasing the sediment erosion threshold, but this relationship is now questioned.
Abstract: Intertidal sediments are important areas that separate the land from the sea and form natural coastal defenses. They are known as highly productive ecosystems, fueling the coastal food web. It is also conceived that microphytobenthos contribute to the stability of intertidal sediments by increasing the erosion threshold and that they are major players in coastal morphodynamics. Depending on the sedimentary composition of intertidal flats, different types of microphytobenthos colonize the sediment surface. Fine sand sediment is often colonized by cyanobacteria, prokaryotic algae, which form dense and rigid microbial mats. Mudflats on the other hand are characterized by the development of thin biofilms of epipelic diatoms. Both groups of phototrophic microorganisms excrete extracellular polymeric substances (EPS), but they do so in different ways and for different reasons. Two operationally defined fractions, water- and EDTA-extractable EPS, have been obtained from intertidal diatom biofilms and from cultur...
169 citations
TL;DR: The role of calcifying bacteria in natural precipitation of carbonates is discussed in this article, where 31 calcifying bacterial strains were isolated from natural habitats: 64% were of the genus Bacillus, 16% of the genera Arthrobacter, and 2 of the remaining isolates were identified as Kingella and Xanthomonas.
Abstract: To study the role of calcifying bacteria in monument protection, 31 calcifying bacterial strains were isolated from natural habitats: 64% were of the genus Bacillus , 16% of the genus Arthrobacter , and 2 of the remaining isolates were identified as Kingella and Xanthomonas . The ability to form CaCO 3 crystals, the extent of the precipitation, and the type of crystals formed were determined at incubation temperatures of 4, 22, and 32°C. The highest of these temperatures favored CaCO 3 formation. Most of the bacteria precipitated CaCO 3 in the form of calcite. This activity was strictly controlled by the growth of microbial colonies on a solid substrate. The role of the calcifying bacteria in natural precipitation of carbonates is discussed. Further experiments are in progress in order to select the most suitable bacterial strains for a controlled production of calcareous crusts.
135 citations
TL;DR: It is demonstrated that some Roseobacter group isolates are able to carry out the major DMSP transformations that have been observed in natural bacterial communities from seawater, and may be one of the bacterial taxa linked to DMSP dynamics in the surface ocean.
Abstract: Evidence from culture-independent molecular studies indicate that members of the Roseobacter group are ubiquitous in marine environments, and bacteria in this taxon have now been isolated from and identified in systems as diverse as sea ice and coastal lagoons and as widespread as Antarctica and the Sargasso Sea. Because some members of this successful bacterial lineage are amenable to culturing, Roseobacter group isolates can be studied in the laboratory to reveal hints about potential ecological and biogeochemical roles. Initial studies of isolates suggested a widespread ability to degrade dimethylsulfoniopropionate (DMSP), an organic sulfur compound produced in abundance by marine algae. Further investigations revealed that some Roseobacter group isolates are able to carry out the major DMSP transformations that have been observed in natural bacterial communities from seawater. These include two competing pathways for DMSP degradation that may ultimately regulate the flux of organic sulfur (in the form...
134 citations
TL;DR: A selenite-respiring bacterium, Bacillus selenitireducens, produced significant levels of Se(-II) (as aqueous HSe−) when supplied with Se(0), while no such activity was noted in formalin-killed controls as mentioned in this paper.
Abstract: A selenite-respiring bacterium, Bacillus selenitireducens, produced significant levels of Se(-II) (as aqueous HSe−) when supplied with Se(0). B. selenitireducens was also able to reduce selenite [Se(IV)] through Se(0) to Se(-II). Reduction of Se(0) by B. selenitireducens was more rapid in cells grown on colloidal sulfur [S(0)] or Se(IV) as their electron acceptor than for cell lines grown on fumarate. In contrast, three cultures of selenate-respiring bacteria, Sulfurospirillum barnesii, B. arsenicoselenatis, and Selenihalanaerobacter shriftii either were unable to reduce Se(0) to Se(-II) or had only a very limited capacity to achieve this reduction. Biological reduction of Se(0) to Se(-II) was observed during incubation of estuarine sediment slurries, while no such activity was noted in formalin-killed controls. The majority of the Se(-II) produced was found in the sediments as a solid precipitate of FeSe, rather than in solution as HSe−. These results demonstrate that certain anaerobic bacteria have the ...
121 citations
TL;DR: In this paper, the potential of Desulfitobacterium frappieri strain G2 to participate in iron redox reactions was investigated, and the results suggest that strains of G2 may play an important role in iron cycling in sedimentary environments.
Abstract: The potential of Desulfitobacterium frappieri strain G2, which was isolated from subsurface smectite bedding, to participate in iron redox reactions was investigated. Strain G2 can use poorly crystalline Fe(III) oxide, soluble forms of Fe(III) and Fe(III) in the structure of phyllosilicate minerals as electron acceptors. It can also oxidize Fe(II)-NTA or Fe(II) in the structure of phyllosilicate minerals with nitrate as the electron acceptor. These results suggest for the first time that strains of Desulfitobacterium frappieri may play an important role in iron cycling in sedimentary environments.
119 citations
Princeton University1, Pacific Northwest National Laboratory2, Florida State University3, University of Tennessee4, Japan Agency for Marine-Earth Science and Technology5, Indiana University6, University of Toronto7, Oak Ridge National Laboratory8, University of Western Ontario9, Northern Arizona University10, University of Wisconsin-Madison11, University of Pennsylvania12
TL;DR: The persistence of Desulfotomaculum-like bacteria throughout suggests that these organisms adapted to changing geochemical conditions as the redox decreased and pH increased following the isolation of the borehole from the mine atmosphere.
Abstract: A borehole draining a water-bearing dyke fracture at 3.2-km depth in a South African Au mine was isolated from the open mine environment. Geochemical, stable isotopic, nucleic acid-based, and phospholipid fatty acid (PLFA) analyses were employed as culture-independent means for assessing shifts in the microbial community and habitat as the system equilibrated with the native rock-water environment. Over a two-month period, the pH increased from 5.5 to 7.4, concurrent with a drop in pe from −2 to −3. Whereas rDNAs related to Desulfotomaculum spp. represented the major clone type encountered throughout, lipid biomarker profiling along with 16S rDNA clone library and terminal restriction fragment length polymorphism (T-RFLP) analyses indicated the emergence of other Gram-positive and deeply-branching lineages in samples during the later stages of the equilibration period. A biofilm that formed on the mine wall below the borehole produced abundant rDNAs related to the α Proteobacteria. β- and γ −Proteobacteri...
107 citations
TL;DR: Natural biofilms seems to generate microenvironments favoring the formation and preservation of metastable CaCO 3 polymorphs, and shows a major role of microbes in processes of low-temperature alteration of different hypogean rock-substrates.
Abstract: Natural precipitates of metastable polymorphs of CaCO 3 , such as vaterite, are rarely found in nature however, they have been widely synthesized in laboratory under particular conditions (ie, supersaturated solutions, relative high temperatures, etc.). By SEM and XRD we recognize vaterite spherulites from culturable microbial colonies isolated from hypogean environments. Spherical bodies (∽10μin diameter), probably composed of vaterite, occur in submilimetric microbial mats and biofilms on volcanic substrates (Saint Callixtus Catacombs, Rome, Italy) and karstic caves (Altamira, Candamo, and Tito Bustillo caves, Spain, and Grotta dei Cervi, Italy) where cyanobacteria and actinomycetes are the major microbial components. These particles form beneath dense biofilms, where particular physicochemical conditions are developed by the microbial activity. Natural biofilms seems to generate microenvironments favoring the formation and preservation of metastable CaCO 3 polymorphs. This also shows a major role of mi...
TL;DR: In this article, the authors investigated the role of the bacteria in the formation of iron oxides from the caldera of Axial Volcano, a site of hydrothermal vent activity along the Juan de Fuca Ridge.
Abstract: Iron oxides from the caldera of Axial Volcano, a site of hydrothermal vent activity along the Juan de Fuca Ridge, are characterized by abundant bacterial structures that closely resemble the sheaths of Leptothrix ochracea , the stalks of Gallionella ferruginea , and the filaments of a novel iron oxidizing PV-1 strain. These bacteria are commonly associated with iron-oxide precipitates and are proposed to play two causal roles in the formation of iron oxides at Axial Volcano. First, by increasing the rate of Fe 2+ oxidation, and second, by lowering the concentration of Fe 3+ required for precipitation by providing a reactive surface for heterogeneous nucleation. Rapid rates of oxidation and precipitation caused by the bacteria likely contribute to the poorly ordered nature of the iron oxides, determined to be primarily 2-line ferrihydrite, and in one case, poorly ordered goethite. The iron-oxide precipitates consist dominantly of iron, silicon (mostly diatoms), and organic carbon with a suite of sorbed tra...
TL;DR: A Neighbor Joining distance tree generated from SSU rRNA sequences of major prokaryotic lineages is used to estimate the dates for significant events in the history of life on Earth and suggests that the Last Common Ancestor occurred at about 4.29 Ga.
Abstract: Previous calibrations of prokaryotic phylogenetic events were based on the vertebrate fossil record because a detailed microbial fossil record does not exist. Recently, compounds (2-methylhopanoids) that are found in cyanobacterial membranes were identified among compounds extracted from late Archean sedimentary rocks. These lipids establish a minimum time, 2.65 Ga (Billion Years Ago), in the geologic record for the existence of cyanobacteria. We have used this new information to calibrate a Neighbor Joining distance tree generated from SSU rRNA sequences of major prokaryotic lineages and to estimate the dates for significant events in the history of life on Earth. The results suggest that the Last Common Ancestor occurred at about 4.29 Ga and that the individual Bacterial and Archaeal Domains began radiating about 3.46 Ga.
TL;DR: Piloderma is a broad host range ectomycorrhizal fungal genus that may benefit conifer growth through increased soil nutrient availability via enhanced soil mineral weathering as mentioned in this paper.
Abstract: Piloderma is a broad host range ectomycorrhizal fungal genus that may benefit conifer growth through increased soil nutrient availability via enhanced soil mineral weathering. In an in vitro study, we investigated the ability of Piloderma to extract K and/or Mg from three soil minerals commonly found in soils of central British Columbia: biotite, microcline, and chlorite. The growth, hyphal morphology, and chemical composition were compared among Piloderma grown for 110 days in media optimized for fungal growth as well as in media where K and/or Mg were supplied from biotite, microcline, and chlorite. Piloderma grown in treatments with low K showed fibrillar growths, hyphal swellings, and hyphae devoid of ornamentation, possibly indicating nutrient deficiency. Differences were found in growth rates, morphologies, and Mg content in hyphae grown in chlorite and biotite treatments, suggesting that Mg was limiting to the normal growth of Piloderma . Energy dispersive X-ray analysis indicated that Piloderma ex...
TL;DR: In this paper, the degree of bacterial attachment of the main microorganisms involved in the bio-leaching of metal sulfides and their influence on the dissolution rate and final metal extractions were determined.
Abstract: In this study the degree of bacterial attachment of the main microorganisms involved in the bioleaching of metal sulfides and their influence on the dissolution rate and final metal extractions were determined. Three different mineral sulfides were bioleached: chalcopyrite (CuFeS 2 ), sphalerite (ZnS) and pyrite (FeS 2 ). A mixed culture of mesophilic bacteria ( Acidithiobacillus and Leptospirillum spp.) was tested at 35°C and thermophilic bacteria ( Sulfolobus spp.) were tested at 68°C. The results confirmed that a relationship exists between attachment and mineral dissolution rates. The bioleaching process can be divided into three stages. An initial stage with extensive bacterial attachment to the pyritic phase, which is of major importance in order to obtain high dissolution rates (since attached cells liberate Fe 2+ by contact bioleaching and oxidize Fe 2+ to Fe 3+ avoiding iron accumulation at the surface). In a second stage the bacterial attachment diminishes due to the saturation of the surface by...
TL;DR: The high similarity between microbial community structure and activity corresponding with the prevalent geochemical conditions observed in deep subsurface petroleum reservoirs suggests that the resident microflora have adapted to the subsurfaced physicochemical conditions and may actively influence the geochemical environment in situ.
Abstract: The diversity of thermophilic microbial assemblages detected within two neighboring high temperature petroleum formations was shown to closely parallel the different geochemical regimes existing in each. A high percentage of archaeal 16S rRNA gene sequences, related to thermophilic aceticlastic and hydrogenotrophic methanogens, were detected in the natural gas producing Rincon Formation. In contrast, rRNA gene libraries from the highly sulfidogenic Monterey Formation contained primarily sulfur-utilizing and fermentative archaea and bacteria. In addition to the variations in microbial community structure, microbial activities measured in microcosm experiments using high temperature production fluids from oil-bearing formations also demonstrated fundamental differences in the terminal respiratory and redox processes. Provided with the same suite of basic energy substrates, production fluids from the South Elwood Rincon Formation actively generated methane, while thermophilic microflora within the Monterey production fluids were dominated by hydrogen sulfide producing microorganisms. In both cases, molecular hydrogen appeared to play a central role in the stimulation of carbon and sulfur cycling in these systems. In methanogenic production fluids, the addition of sulfur compounds induced a rapid shift in the terminal electron accepting process, stimulating hydrogen sulfide formation and illustrating the metabolic versatility of the subsurface thermophilic assemblage. The high similarity between microbial community structure and activity corresponding with the prevalent geochemical conditions observed in deep subsurface petroleum reservoirs suggests that the resident microflora have adapted to the subsurface physicochemical conditions and may actively influence the geochemical environment in situ.
TL;DR: The metal binding constants determined with the bacteria mixtures in this study are similar to the binding constants that have previously been measured for B. subtilis, suggesting that adsorption constants can be estimated using thermodynamic parameters determined for a limited number of bacterial species.
Abstract: In this study, we measure Cd, Co, Sr, and Zn adsorption onto mixtures of Gram-positive and Gram-negative bacteria, containing the bacterial species Streptococcus faecalis , Staphyloccocs aureus , Sporosarcina ureae , Bacillus subtilis , Bacillus licheniformis , Escherichia coli , Pseudomonas aeruginosa , Enterobacter aerogenes , Proteus vulgaris , and Serratia marscecens . Metal adsorption experiments were conducted with mixtures of Gram-positive bacteria, Gram-negative bacteria, and mixtures consisting of both bacterial types. The objective is to compare the metal adsorption behavior of Gram-positive and Gram-negative bacteria, and determine if the surface complexation model can be applied to describe metal adsorption onto complex assemblages of different bacterial types. The experimental results indicate that the metal adsorption behaviors of Gram-positive mixtures, Gram-negative mixtures, and mixtures of both Gram-positive and Gram-negative bacteria are nearly identical. We describe the metal adsorptio...
TL;DR: This review summarizes the state of microscale in situ analyses of nitrification and potential, limitations, and future perspectives of such combined microsensor/FISH approaches for the study ofNitrification are discussed.
Abstract: This review summarizes the state of microscale in situ analyses of nitrification. Microsensors and fluorescence in situ hybridization (FISH) have both become important methods for microbial ecology. In combination, they have offered a variety of exciting insights into structure and activity of microbial communities, including nitrifying biofilms, aggregates, and sediments. Several levels of information can be obtained: (a) identification of microenvironments or environmental conditions (such as concentrations of oxygen, ammonium, nitrite) favored by particular microorganisms; (b) qualitative evidence of certain metabolic activities of particular microorganisms, e.g., nitrite oxidation by Nitrospira sp.; and (c) quantification of cell-specific reaction rates and estimation of the in situ kinetics of uncultivated microorganisms. Potential, limitations, and future perspectives of such combined microsensor/FISH approaches for the study of nitrification are discussed.
TL;DR: In this paper, the authors show that minerals are biologically transformed, and as a result, Fe-rich diagenetic minerals in the form of iron hydroxide nanocrystals and biogenic clays are deposited around chasmoendolithic hyphae and bacterial cells.
Abstract: The cold, dry ecosystems of Antarctica have been shown to harbor traces left behind by microbial activity within certain types of rocks, but only two indirect biomarkers of cryptoendolithic activity in the Antarctic cold desert zone have been described to date. These are the geophysical and geochemical bioweathering patterns macroscopically observed in sandstone rock. Here we show that in this extreme environment, minerals are biologically transformed, and as a result, Fe-rich diagenetic minerals in the form of iron hydroxide nanocrystals and biogenic clays are deposited around chasmoendolithic hyphae and bacterial cells. Thus, when microbial life decays, these characteristic neocrystalized minerals act as distinct biomarkers of previous endolithic activity. The ability to recognize these traces may have potential astrobiological implications because the Antarctic Ross Desert is considered a terrestrial analogue of a possible ecosystem on early Mars.
TL;DR: The greatest rate of Cu solubilization from chalcopyrite was achieved at high temperatures (up to 70°C) at redox potentials below +550 mV (Ag/AgCl), rather than from the rates at which individual acidophiles generated the mineral leaching reactants such as Fe 3+ .
Abstract: A systematic study of the bioleaching of chalcopyrite (CuFeS 2 ) was conducted using axenic cultures of 11 species of acidophilic Bacteria and Archaea to obtain a direct comparison of the microbial chalcopyrite leaching capabilities of the different cultures and to determine the factors that affect Cu release. The characteristics of chalcopyrite leaching by the moderate thermophile Sulfobacillus thermosulfidooxidans , the mesophile Acidithiobacillus ferrooxidans , and the thermophile Acidianus brierleyi were used to elucidate the leaching process. Moderately thermophilic cultures of Sulfobacillus acidophilus, Acidimicrobium ferrooxidans , and Acidithiobacillus caldus were used to study the effects of different metabolic capabilities and relate those to leaching efficiency. The greatest rate of Cu solubilization from chalcopyrite was achieved at high temperatures (up to 70°C) at redox potentials below +550 mV (Ag/AgCl). The enhanced Cu solubilization observed at high temperatures resulted from accelerated ...
TL;DR: The addition of glucose or some other organic electron donor could provide an in situ or ex situ bioremediation strategy to raise pH at AMD sites resulting in a lower amount of metal leaching into drainage water by promoting reducing conditions favorable to iron reduction.
Abstract: Addition of organic carbon substrate (glucose) profoundly affected the growth of cultures of acidophilic bacteria typical of acid mine drainage (AMD) sites: the iron-oxidizing autotrophic bacteria, Acidithiobacillus ferrooxidans , and a common heterotrophic strain, Acidiphilium acidophilum . Growth of A. ferrooxidans on soluble ferrous iron media was significantly inhibited in the presence of 1,000 mg/L glucose, regardless of the initial cell density, and in spite of favorable pH and aeration conditions. Interestingly, inhibition of A. ferrooxidans was reduced with addition of the heterotroph, apparently due to the consumption of glucose because the onset of iron oxidation coincided with reduction in glucose concentration in the medium. Another mechanism, local production of CO 2 by A. acidophilum provided inorganic carbon required by A. ferrooxidans cells, was investigated. Although no direct proof of interspecies CO 2 exchange was identified, iron oxidation was enhanced and glucose inhibition reduced wi...
TL;DR: The presence of these biomarkers does not prove that Gram-positive bacteria produce the coatings, but finding them is consistent with the hypothesis that they may play a role in desert varnish formation.
Abstract: There has long been a debate as to whether desert varnish deposits are microbially mediated or are deposited by inorganic processes. Several researchers have cultured bacteria from the surface of desert varnish suggesting that bacteria are intimately associated with varnish coatings and may play a role in their formation. To test this hypothesis, we have collected scrapings of desert varnish from the Sonoran Desert in Arizona and the Mojave Desert in California and analyzed them for amino acids. Thirteen amino acids were found in desert varnish indicating a biogenic component of these varnishes. Two protein amino acids that were not detected in any of the varnishes are cysteine and tryptophan. Two nonprotein amino acids,β-alanine andγ-amino butyric acid, were found. These are known to be formed by enzymatic decarboxylation, thereby indicating possible organismal activity in varnish. Some D -enantiomers of the amino acids were also found. In addition to small amounts of the D -enantiomer of aspartic acid, ...
TL;DR: It is demonstrated here that EDTA carbonate dissolution is superior because it preserves vertical stratification of the microbial communities lost using the pulverization method, thus allowing for spatially resolved community analyses.
Abstract: We evaluated and optimized three rapid methods for extraction of high-quality DNA from carbonate-encrusted microbial communities using modern calcifying oncolites built by cyanobacteria and diatoms in a high-calcium freshwater river. Pulverization, acid (HCl) dissolution, and chelator-mediated (EDTA) dissolution of the carbonate matrix were used and optimized to liberate microbial cells from their mineral encasing. This was followed by cell lysis and DNA extraction and isolation. HCl dissolution yielded no measurable DNA, probably due to hydrolysis, whereas pulverization and EDTA dissolution yielded averages of 3.5 and 7.8 μg per gram of sample, respectively, of high molecular weight DNA. These DNA isolates could be used successfully for PCR-amplification of 16S rRNA gene segments (alleles) and subsequent fingerprinting of the cyanobacterial (including diatoms) and total bacterial communities through denaturing gradient gel electrophoresis (DGGE) separation. Fingerprints showed no differences in microbial...
TL;DR: The relationships among sedimentological, geochemical, and microbiological parameters in the vadose zone of a barrier sediment from the eastern shore of Virginia were examined in this paper, where pairs of samples were taken 10 cm apart in the vertical direction and 2 cm apart along three transects with one sample from each depth being processed aerobically and the other being processed anaerobically.
Abstract: The relationships among sedimentological, geochemical, and microbiological parameters in the vadose zone of a barrier sediment from the eastern shore of Virginia were examined. Pairs of samples were taken 10 cm apart in the vertical direction and 2 cm apart in the horizontal direction along three transects with one sample from each depth being processed aerobically and the other being processed anaerobically. Little variation was observed in the sedimentological and microbiological parameters tested. The sediment of all samples was fine-to-coarse sand, and the grain sizes ranged from 0.19-1.16 mm. Sediment moisture was low for all samples, but increased near the top and bottom of each sampling transect. These were regions where bioavailable Fe(III) concentrations were high. Rates of H 2 uptake ranged from below detection limit to 0.064 w mol H 2 · day m 1 · g m 1 of sediment with a median rate of 0.01 w mol H 2 · day m 1 · g m 1 of sediment. The variation in bacterial numbers was slightly more than an ord...
TL;DR: The data show that bacterial strains with hydrogenase activity are not necessarily corrosive and that corrosion induction can be modified substantially by the metabolic background provided by the larger bacterial community, especially its ferric-reducing members.
Abstract: Fourteen thermotolerant and thermophilic bacterial isolates from a hot spring in Guanajuato State, Mexico, were tested for their ability to induce the corrosion of carbon steel in monocultures and, in selected cases, in mixed cultures and co-culture with a sulfate-reducing strain, SRB-M. Characterization by 16S rDNA showed that three of the thermophilic isolates (G9a, G9c, and G11) belong to the genus Bacillus , one (G2) showed homology with Bacillus as well as Geobacillus , and the SRB-M strain is closely related to Desulfotomaculum sp. Ten of the fourteen thermophilic and thermotolerant isolates promoted significantly more corrosion than the sterile controls. Under microaerobic batch-culture conditions at 55°C, SRB-M in monoculture did not show a corrosive effect measured as weight loss; in a mixed culture with G2, G9a, and G11, however, the final corrosion was enhanced 3.6 times when compared to sterile controls. Co-cultures of "G" isolates with SRB-M showed various effects on the final corrosion, rang...
TL;DR: In this paper, the impact of sulfate-reduction on the immobilization of metals in subsurface aquifers was investigated and several electron donors were tested and all but toluene accelerated soluble Co 2+ loss.
Abstract: We investigated the impact of sulfate-reduction on immobilization of metals in subsurface aquifers. Co 2+ was used as a model for heavy metals. Factors limiting sulfate-reduction dependent Co 2+ immobilization were tested on pure cultures of sulfate-reducing bacteria, and in sediment columns from a landfill leachate contaminated aquifer. In the presence of 1 mM Co 2+ , the growth of pure cultures of sulfate-reducing bacteria was not impacted. Cultures of Desulfovibrio desulfuricans, Desulfotomaculum gibsoniae , and Desulfomicrobium hypogeia removed greater than 99.99% of the soluble Co 2+ when CoCl 2 was used with no chelators. The above cultures and Desulfoarcula baarsi removed 98-99.94% of the soluble Co(II) when the metal was complexed with the model ligand nitrilotriacetate (Co-NTA). Factors controlling the rate of sulfate-reduction based Co 2+ precipitation were investigated in sediment-cobalt mixtures. Several electron donors were tested and all but toluene accelerated soluble Co 2+ loss. Ethanol an...
TL;DR: In this article, the survival of lithobiontic microbial communities in Antarctica's extreme cold, dry environment is conditioned by changes in external climatic conditions that can lead to the death of these microorganisms.
Abstract: The survival of lithobiontic microbial communities in Antarctica's extreme cold, dry environment is conditioned by changes in external climatic conditions that can lead to the death of these microorganisms. In the present study, granite samples from maritime Antarctica and sandstone from the Antarctic continental desert were collected with the aim of searching for biomarkers and microbial fossils at the microscopic level of observation. The results reveal the presence of inorganic biomarkers in the form of physicochemical bioweathering mineral patterns, and inorganic deposits such as calcium oxalates and silica. The presence of fossilised algae and other microorganisms within the sandstone rock was also confirmed. Identifying the internal cell structure within the fossilised cells is proposed as a new criterion for the biogenicity of biomorphs.
TL;DR: The data suggested that the inhibition in methanogenesis in saline soils rich in sulphate as in coastal saline soils could be due to competitive inhibition of methanogens, while in inland soils, Cl− content could be a deciding factor.
Abstract: In a laboratory incubation study, effects of amendment with sodium salts of SO4 2−, Cl− and HCO3 − either singly or as a mixture on CH4 production in a nonsaline alluvial soil under flooded condition were investigated. Methane production was considerable in the unamended alluvial soil, but was significantly inhibited following amendment with salts of different anions to raise the pore water EC to 8 dS·m−1. SO4 2− was the most inhibitory to CH4 production and the degree of inhibition followed the order SO4 2− > salt mixture > HCO3 − > Cl−. Salt amendment did not adversely affect soil microbial activities as expressed in terms of soil redox potential (Eh) and soil pH. However, readily mineralizable carbon content, an indicator of substrate availability for methanogenic bacteria, differed significantly among the treatments. Most probable number estimates indicated that acetotrophic methanogenic bacterial population was lowest in Cl−-amended soils followed by SO4 2−-amendment with little or no changes in HCO3...
TL;DR: In this paper, a 1-meter long model aquifer has been used to simulate the effects of pH on the fate and transport of bacteriophage MS2 in a shallow groundwater system.
Abstract: A 1-meter long model aquifer has been used to simulate the effects of pH on the fate and transport of bacteriophage MS2 in a shallow groundwater system. The results show that transport of MS2 is sensitive to the pH of groundwater and the isoelectric points of minerals in the groundwater medium. At a slightly alkaline groundwater pH, transport rates of the MS2 bacteriophage were greater than that of a conservative tracer, bromide. Greater transport rates were interpreted as a preferential pathway effect due to the larger size of MS2. Pore exclusion and straining may also have contributed to the faster transport of MS2. At a neutral pH similar transport rates for both MS2 and the conservative tracer were observed. At a slightly acidic pH, however, the MS2 breakthrough concentration was trailing the breakthrough of the conservative tracer that was attributed to the pronounced effect of reversible adsorption at lower pH values. Acidic conditions also increased greatly the effect of irreversible sorption. The ...
TL;DR: In this article, the authors used atomic force microscopy (AFM) to remove Bacillus sp. from silicate surfaces using four different detergents and CO 2 snow cleaning.
Abstract: In order to study biosignatures documenting the effects of microbiota on mineral surfaces, microbial matter must be removed without chemically or physically changing the surface. In previous work for analysis by scanning electron microscopy (SEM) we removed soil bacteria from silicate surfaces with lysozyme; however, when lysozyme-treated surfaces were analyzed at nanoscale by atomic force microscopy (AFM), residual matter was observed. Therefore, we tested removal of bacteria by each of five methods, including four different detergents and CO 2 snow cleaning. AFM observations revealed residue on glass surfaces that underwent CO 2 snow cleaning after 13 days of growth of Bacillus sp . (a soil microbe). In contrast, treatment with each of four detergents followed by acetone completely removed Bacillus sp . without altering the topography of the surfaces even after 77 days of growth. However, X-ray photoelectron spectroscopic (XPS) analyses of the upper 25 A of the glass surfaces revealed chemical alteratio...