Showing papers in "Geomicrobiology Journal in 2013"

Mn(II)-Oxidizing Bacteria Are Abundant And Environmentally Relevant Members Of Ferromanganese Deposits In Caves Of The Upper Tennessee River Basin

Abstract: The upper Tennessee River Basin contains the highest density of our nation's caves; yet, little is known regarding speleogenesis or Fe and Mn biomineralization in these predominantly epigenic systems. Mn:Fe ratios of Mn and Fe oxide-rich biofilms, coatings, and mineral crusts that were abundant in several different caves ranged from ca. 0.1 to 1.0 as measured using ICP-OES. At sites where the Mn:Fe ratio approached 1.0 this represented an order of magnitude increase above the bulk bedrock ratio, suggesting that biomineralization processes play an important role in the formation of these cave ferromanganese deposits. Estimates of total bacterial SSU rRNA genes in ferromanganese biofilms, coatings, and crusts measured approximately 7×107–9×109 cells/g wet weight sample. A SSU-rRNA based molecular survey of biofilm material revealed that 21% of the 34 recovered dominant (non-singleton) OTUs were closely related to known metal-oxidizing bacteria or clones isolated from oxidized metal deposits. Several differe...

Inhibition of DNA Polymerases Used in Q-PCR by Structurally Different Soil-Derived Humic Substances

Abstract: Real-time PCR for the quantitative assessment of microbial genes in DNA extracted from environmental samples is increasingly being used in microbial ecology studies. A significant problem with the quantitative aspect of the method is the possible inhibition of the PCR process by humic substances co-extracted with the DNA. A comparison of the inhibition exerted by five structurally different humic substances on six commercially available DNA polymerases revealed large differences in the resistance of the polymerases to inhibition. Depending on the DNA polymerases (or their formulation) the addition of Bovine Serum Albumin (BSA) to the mastermix reaction generally increased the resistance to the different humic substances and decreased differences between the polymerases. One of the tested polymerases was clearly hampered by the addition of BSA, indicating that BSA cannot be added to just any mastermix to improve enzyme performance. The structural differences in the tested humic acids suggest that the mecha...

Phototrophic Community in Gypsum Crust from the Atacama Desert Studied by Raman Spectroscopy and Microscopic Imaging

Abstract: The hyperarid core of the Atacama Desert represents one of the driest places on Earth with an exceptional occurrence of microbial life coping with extreme environmental stress factors. The gypsum crusts have already been found to harbor diverse communities in this area. Here, we present a Raman spectroscopic study, complemented by correlative microscopic imaging using SEM-BSE and fluorescence microscopy, of the endolithic microbial communities inside the Ca-sulphate crusts dominated by phototrophic microorganisms. Differences of pigment composition within different zones follow the cyanobacterial and algal colonization and also reveal the degradation of phycobiliproteins within the decayed biomass of cyanobacteria. Carotenoids of at least three different types were recognized, differing in dependence on the particular phylum of phototrophic microorganisms. Moreover, calcium oxalate monohydrate – whewellite – was found to be associated with the algae and hyphal associations living in the lower regions of t...

Actinobacteria—An Ancient Phylum Active in Volcanic Rock Weathering

Abstract: A molecular biological analysis of Icelandic volcanic rocks of different compositions and glassiness revealed the presence of Actinobacteria as an abundant phylum. In outcrops of basaltic glass they were the dominant bacterial phylum. A diversity of Actinobacteria were cultured from the rocks on rock-agar plates showing that they are capable of growing on rock-derived nutrient sources and that many of the taxa identified by molecular methods are viable, potentially active members of the community. Laboratory batch-culture experiments using a Streptomyces isolate showed that it was capable of enhancing the release of major elements from volcanic rocks, including weathered basaltic glass, crystalline basalt and komatiite, when provided with a carbon source. Actinobacteria of a variety of other sub-orders were also capable of enhancing volcanic rock weathering, measured as Si release. However, most strains did not significantly increase the weathering of the silica-rich rock, obsidian. These data show that A...

Mineralogy Drives Bacterial Biogeography of Hydrothermally Inactive Seafloor Sulfide Deposits

Abstract: Mid-ocean ridge hydrothermal venting creates sulfide deposits containing gradients in mineralogy, fluid chemistry, and temperature. Even when hydrothermal circulation ceases, sulfides are known to host microbial communities. The relationship between mineralogy and microbial community composition in low-temperature, rock-hosted systems has not been resolved at any spatial scale, local or global. To examine the hypothesis that geochemistry of seafloor deposits is a dominant parameter driving environmental pressure for bacterial communities at low-temperature, the shared community membership, richness, and structure was measured using 16S rRNA gene sequences. The focus of the study was on hydrothermally inactive seafloor deposits from multiple locations within one deposit (e.g., single extinct chimney), within one vent field (intra-vent field), and among globally distributed vent fields from three ocean basins (inter-vent field). Distinct mineral substrates, such as hydrothermally inactive sulfides versus ba...

Arsenite Oxidation Using Biogenic Manganese Oxides Produced by a Deep-Sea Manganese-Oxidizing Bacterium, Marinobacter sp. MnI7-9

Abstract: Marinobacter sp. MnI7-9, a deep-sea manganese [Mn(II)]-oxidizing bacterium isolated from the Indian Ocean, showed a high resistance to Mn(II) and other metals or metalloids and high Mn(II) oxidation/removal abilities. This strain was able to grow well when the Mn(II) concentration reached up to 10 mM, and at that concentration, 76.4% of the added Mn(II) was oxidized and 23.4% of the Mn(II) was adsorbed by the generated biogenic Mn oxides (total 99.9% Mn removal). Scanning electron microscope observation and X-ray diffraction analysis showed that the biogenic Mn oxides were in stick shapes, adhered to the cell surface, and contained two typical crystal structures of γ-MnOOH and δ-MnO2. In addition, the biogenic Mn oxides generated by strain MnI7-9 showed abilities to oxidize the highly toxic As(III) to the less toxic As(V), in both co-culture and after-collection systems. In the co-culture system containing 10 mM Mn(II) and 55 μM As(III), the maximum percentage of As(III) oxidation was 83.5%. In the after-...

Geomicrobial Kinetics: Extrapolating Laboratory Studies to Natural Environments

Abstract: Predicting metabolic rates and population sizes of microorganisms in natural environments is a central problem in geomicrobiology. Such predictions can be made on the basis of a thermodynamically consistent rate law that accounts for both kinetic and thermodynamic controls on microbial metabolism. Application of the rate law requires kinetic and growth parameters, the values of which have been determined for pure and mixed cultures growing in laboratory reactors. However, not all parameter values derived from laboratory studies can be validly applied to the environment. This article illustrates a best-choice approach for extrapolating experimentally-derived parameter values to natural environments, using microbial sulfate reduction coupled to acetate oxidation as an example. We compiled kinetic and growth parameters determined by previous laboratory studies and evaluated their applicability to natural environments. Our results suggest that some parameters, such as rate constants and maximum growth yields,...

Zinc Sorption During Bio-oxidation and Precipitation of Manganese Modifies the Layer Stacking of Biogenic Birnessite

Abstract: The formation and structural evolution of fungal mediate biogenic birnessite are dynamic processes. Although the associations of Zn with the pre-formed biogenic Mn oxides are relatively well understood, the reactivity of the intermediate precipitate at the initial stage of Mn bio-oxidation appears to differ from the final precipitate. In the present work, Zn sorption during precipitation of biogenic Mn oxides was investigated contrasting Zn sorption to pre-formed biogenic Mn oxides, using the Mn-oxidizing fungus Paraconiothyrium sp. WL-2. A substantially higher Zn uptake was found during precipitation of biogenic Mn oxides compared to Zn sorption to pre-formed biogenic Mn oxides. The presence of Zn during Mn oxidation resulted in a biogenic Mn oxide with reduced ordering in the c-axis. The precipitate was identified by X-ray diffraction (XRD) as a layer-type Mn oxide with structural properties similar to hexagonal birnessite. Extended X-ray absorption fine structure (EXAFS) spectroscopy showed that Zn for...

Reactive Transport Modeling of Induced Selective Plugging by Leuconostoc Mesenteroides in Carbonate Formations

Abstract: A process-based mechanistic reactive transport model was developed to understand how in-situ coupled processes and operational factors affect selective plugging of reactive carbonate formations by the fermenting bacteria Leuconostoc mesenteroides that produces a plugging polymer dextran. The growth and transport of L. mesenteroides and the associated (bio) geochemical reactions were simulated explicitly with enzyme activity at the field scale over spatial extents of hundreds of meters. Simulations were performed to explore controls on selective bioplugging of high permeability zones in a representative carbonate reservoir, a process that can be used to improve oil sweep efficiency through lower permeability layers. Simulation results indicate that dextran production and the effectiveness of plugging can be largely affected by sucrose and bacteria injection rates. Selective plugging of high permeability zones can only be achieved when the injection rates are high compared to the rates of dextran production...

Chromium Adsorption by Three Yeast Strains Isolated from Sediments in Morocco

Abstract: Biosorption is an effective method to remove heavy metals from wastewater. In this work, Biosorption of Cr(VI) has been investigated by live and dead cells of three yeasts species: Cyberlindnera fabianii, Wickerhamomyces anomalus and Candida tropicalis. Sorption experiments were conducted in aqueous solutions at various pH conditions. Cr(VI) adsorption was highly pH dependent and the results indicated that the most effective pH range was found to be between 2 and 4 for the three species. Adsorption isotherms were modeled with the Langmuir and Freundlich equations and isotherm constants were calculated. The adsorption capacity calculated from Langmuir isotherm was 18.9 mg, 28.14 mg and 29.1 mg Cr(VI) g−1 Cr(VI) g−1 for C. fabianii, W. anomalus and C. tropicalis, respectively. The results suggest that the three yeasts could be used as effective adsorbents for the removal of Cr(VI) ions from contaminated sites.

Processes Forming Daily Lamination in a Microbe-Rich Travertine Under Low Flow Condition at the Nagano-yu Hot Spring, Southwestern Japan

Abstract: A daily rhythm of microbial processes, in terms of sub-mm order lamination, was identified for a microbe-rich aragonite travertine formed at a low-flow site of the Nagano-yu Hot Spring in Southwestern Japan. Continuous observation and sampling clearly showed that the lamination consisted of diurnal microbe-rich layers (M-layers) and nocturnal crystalline layers (C-layers). The M-layers originated from biofilm formed by growth and upward migration of filamentous cyanobacteria related to Microcoleus sp., which can rapidly glide and secrete extracellular polymeric substances (EPS). During the daytime, cyanobacterial biofilm development inhibited aragonite precipitation on the travertine surface due to the calcium-binding ability of EPS. After sunset, aragonite precipitation started on the surface where aerobic heterotrophic bacteria decomposed EPS, which induced precipitation of micritic crystals. This early stage of C-layer formation was followed by abiotic precipitation of fan-shaped aragonite aggregates. ...

Serpentine Dissolution in the Presence of Bacteria Bacillus mucilaginosus

Abstract: Dissolution of serpentine in the presence of soil bacteria Bacillus mucilaginosus is examined through solution chemistry analysis, X-ray diffraction and 3D X-ray microscopy. Microbe-mineral interactions were carried out by incubating serpentine powder and the bacteria for 30 days. Measured Mg concentrations in the culture media were significantly higher than that in any of the control experiments at any time during the experiments. However, the behavior of the Mg/Si ratio was similar to what was known for inorganic dissolution of silicate minerals. XRD analysis revealed increased quantity of amorphous components in the reacted mineral samples, and tomography images showed a very porous and powdered appearance of the dissolved serpentine grains. These data suggest the dissolution probably proceeds through an incongruent route. Further, these observations imply that there is little genetic control by the microbes during the bacteria-mineral interaction; rather, the accelerated dissolution results primarily ...

The Effect of Dew and Fog on Lithic Lichens Along an Altitudinal Gradient in the Negev Desert

Abstract: The effect of dew upon lichen communities was studied in three sites along an altitudinal gradient in the Negev Desert. The sites [Nizzana, NIZ (250m a.s.l), Sede Boqer, SB (530m a.s.l.) and Har Harif, HH (990m a.s.l.)] have similar rain precipitation (∼100 mm) but different dew precipitation of 0.11, 0.21 and 0.32 mm, respectively. A clear gradient was found for the chlorophyll content with NIZ (38.6 mg m−2)

Microbial Diversity in High Arsenic Groundwater in Hetao Basin of Inner Mongolia, China

Abstract: The microbial diversity and community structure in twenty-one groundwater samples from high arsenic shallow aquifers of Hetao Basin, Inner Mongolia, China was investigated with an integrated approach including polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene phylogenetic analyses. A total of 25 bacterial and 32 archaeal DGGE bands were exercised for sequencing. Phylogenetic analyses showed that the bacterial DGGE bands were dominated by Proteobacteria, and the archaeal bands were dominated by Thaumarchaeota and Euryarchaeota. Based on arsenic concentrations, three samples (corresponding to low, medium, and high level of arsenic, respectively) were selected for construction of 16S rRNA gene clone libraries. A total of 912 (468 and 444 for bacteria and archaea, respectively) 16S rRNA gene clone sequences were obtained and subjected to phylogenetic analyses. The results showed that bacterial communities of these samples were dominated by Acinetobacter, Pseudomo...

Characterization of Rhizobium sp. Q32 Isolated from Weathered Rocks and its Role in Silicate Mineral Weathering

Abstract: One mineral-solubilizing strain was isolated from weathered potassic trachyte surfaces and identified as Rhizobium sp. Q32 based on the 16S rRNA gene sequence analysis. The mineral (feldspar and biotite) dissolution potential and the physiological characteristics of the bacterium were investigated. Laboratory mineral dissolution experiments indicated that inoculation with the live bacterium significantly increased feldspar and biotite dissolution by a factor of 1.2–4.7 for Si and 1.2–1.5 for K in comparison with the dead bacterium inoculated controls. In addition, extracellular polysaccharide production by the bacterium increased with time but the bacterium produced small pH changes (6.0–6.5) in the course of mineral dissolution experiment. The bacterium was found to produce siderophores and have the characteristics of acid or alkali and salt tolerance and temperature resistance. The result suggested that feldspar and biotite dissolution may be mainly caused by extracellular polysaccharide and/or sideroph...

Pyrosequencing Reveals Bacterial Diversity in the Rhizosphere of Three Phragmites australis Ecotypes

Abstract: Here we present the use of high-throughput DNA pyrosequencing to assess bacterial diversity in the rhizosphere of three Phragmites australis ecotypes from the Hexi Corridor, China. In total, 43404 sequences were obtained for the three ecotypes, representing 31 phyla and a small amount of unclassified bacteria. The predominant bacterial groups in the rhizosphere of P. australis were Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes. The bacterial community structure varied with the different degrees of wetland degradation, which were exhibited by the three P. australis ecotypes in the study area. At the phylum level, the Caldiserica, Chlamydiae, Deferribacteres, Lentisphaerae, and candidate division WS3 were only detected in the swamp reed (SR) sample. Then, δ-proteobacteria, Acidobacteria, Cyanobacteria and Fusobacteria decreased, the Actinobacteria increased with the degree of degradation from SR through salt meadow reed (SMR) to dune reed (DR). The functiona...

Salinity Impact on Bacterial Community Composition in Five High-Altitude Lakes from the Tibetan Plateau, Western China

Abstract: The influence of salinity and geographical distance on bacterial community composition (BCC) in five freshwater, oligosaline or polysaline lakes located at altitudes higher than 4400 m on the central and southern Tibetan Plateau were investigated using the 16S rRNA gene clone library approach together with multivariate analysis of environmental variables. A total of 10 clone libraries were constructed with two libraries in each lake, one in the epilimnion and the other in the hypolimnion. Geographical distance was not found to impact BCC significantly, but salinity, chl a and lake hydraulic retention time were significant factors influencing the BCC. Bacteria in lakes located on the central and southern Plateau owned the same community composition as that observed from the eastern Tibetan lakes. They were both predominated by Bacteroidetes and Cyanobacteria, had low taxon richness, and similar typical freshwater clusters and distributed characteristics. Supplemental materials are available for this articl...

Induction of Calcium Carbonate by Bacillus cereus

Abstract: The purpose of this research was to study how the bacteria Bacillus cereus (DCB1) utilizes calcium ions in a culture medium with carbon dioxide (CO2) to yield calcium carbonate (CaCO3). The bacteria strain DCB1 was a dominant strain isolated from dolomitic surfaces in areas of Karst topographies. The experimental method was as follows: a modified beef extract-peptone medium (beef extract 3.0 g, peptone 10 g, NaCl 5.0 g, CaCl2 2.0 g, glass powder 2.0 g, distilled water 1 L, and a pH between 6.5 and 7.5) was inoculated with B. cereus to attempt to induce the synthesis of CaCO3. The sample was then processed by centrifugation every 24 h during the 7-day cultivation period. The pH, carbonic anhydrase (CA) activity, and the concentrations of both HCO- 3 and Ca2+ in the supernatant fluid were measured. Subsequently, precipitation in the culture medium was analyzed to confirm, or otherwise, the presence and if present, the formation, of CaCO3. Methods used included X-ray diffraction (XRD), Scanning Electron Micr...

Carbonate Precipitation of Bacterial Strains Isolated from Sediments and Seawater: Formation Mechanisms

Abstract: This article presents a research study on carbonate formation in solid and liquid media by Thalassospira sp., Halomonas sp., Bacillus pumilus, and Pseudomonas grimontii, four bacterial strains isolated from sediments and deep seawater. As part of this study, we analyzed carbonic anhydrase activity, pH, adsorption of calcium and magnesium ions, and total organic and inorganic carbon. The geochemical program PHREEQC was also used to calculate the mineral saturation indexes in all the cultures. The minerals formed were studied with X-ray diffraction, X-ray dispersive energy microanalysis, and scanning electron microscopy. In addition, all four bacterial strains were found to induce carbonate precipitation and to have carbonic anhydrase activity. Sterile control experiments did not precipitate carbonate. In solid M1 and B4 media, all of the strains precipitated magnesium calcite, whereas in the liquid media, they precipitated different percentages of magnesium calcite, aragonite, and monohydrocalcite. In both...

Characterization of Microbial Mats from a Siliciclastic Tidal Flat (Bahía Blanca Estuary, Argentina)

Abstract: Biofilms and microbial mats cover the tidal flats of the central zone of the Bahia Blanca estuary (Argentina), creating extensive layers. The objective of this study was to characterize the microphytobenthic communities in these biofilms and mats from sediment cores taken in March, June, September and December 2010. Microorganisms were identified and enumerated by microscopy, and their biomass (chlorophyll a, biovolume) quantified at two different stations in the lower supratidal zone, located ∼210 m apart from each other (namely S1 and S2). Additionally, the colloidal carbohydrates produced by these microbial communities were quantified, together with physical parameters such as temperature, granulometry, moisture and organic matter content of the sediment layers that comprise a typical epibenthic mat. On the other hand, changes in biomass and colloidal carbohydrate content were studied through a half-tidal cycle (7 h). There were significant seasonal differences in microphytobenthic biovolume (P < 0.001...

Nanoscale Observations of Extracellular Polymeric Substances Deposition on Phyllosilicates by an Ectomycorrhizal Fungus

Abstract: Microorganisms colonizing surfaces can exude a wide range of substances, generally called Extracellular Polymeric Substances (EPS). While EPS has often been visualized as thick mature strata embedding microbes, the initial phases of EPS production, its structure at the micro- and nanoscale and the microbial wall areas involved in its exudation are less known. In this work we use Atomic Force Microscopy to image EPS produced by the fungus Paxillus involutus on phyllosilicate surfaces. Hyphal tips initially deposit EPS which assumes the shape of a “halo” surrounding hyphae. The fusion of adjacent EPS halos is likely responsible for the creation of EPS monolayers covering mineral surfaces. It is also proposed that a specific region of hyphae initiates the formation of mineral channels produced by fungi. The results presented here permit for the first time to propose a model for the initial stages of EPS accumulation in fungi and filamentous microorganisms in general.

Changes in Bacterial Community Structure and Abundance in Agricultural Soils under Varying Levels of Arsenic Contamination

Abstract: Arsenic contamination from groundwater used to irrigate crops is a major issue across several agriculturally important areas of Asia. Assessing bacterial community composition in highly contaminated sites could lead to the identification of novel bioremediation strategies. In this study, the bacterial community structure and abundance are assessed in agricultural soils with varying levels of arsenic contamination at Ambagarh Chauki block, Chhattisgarh, India, based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of the 16S rRNA gene and the most probable number-polymerase chain reaction (MPN-PCR). The results revealed that the bacterial communities of arsenic-contaminated soils are dominated by β-proteobacteria (36%), γ-proteobacteria (21%), δ-proteobacteria (11%), α-proteobacteria (11%), and Bacteroidetes (11%). The bacterial composition of high arsenic-contaminated soils differed significantly from that of low arsenic-contaminated soils. The Proteobacteria appeared to be ...

Magnetite Formation by the Novel Fe(III)-reducing Geothrix fermentans Strain HradG1 Isolated from a Hydrocarbon-Contaminated Sediment with Increased Magnetic Susceptibility

Abstract: Surface sediments at the former military base Hradcany, Czech Republic, heavily contaminated with hydrocarbons, were remediated over years by air-sparging. The sediments show a strong magnetic enhancement at the groundwater fluctuation zone. Here we describe the isolation of a new Fe(III)-reducing and magnetite-producing bacterial strain Geothrix fermentans HradG1from this magnetic and redox-dynamic layer. This isolation underlines that the genus Geothrix is a relevant group of bacteria in hydrocarbon-contaminated environments that undergo dynamic oxic-anoxic redox fluctuations. The Fe(III)-reducing metabolic activity of these organisms potentially leads to changing magnetic soil properties that can potentially be used to identify biogeochemical hotspots.

Solubilization of Magnesium-Bearing Silicate Minerals and the Subsequent Formation of Glushinskite by Aspergillus niger

Abstract: Microbes may play a substantial role in the weathering and alteration of minerals. However, not enough concerns have been realized about the complexity of microbe-mineral interactions. The present work reports the interactions between fungi and minerals with emphasis on the role of silicate minerals as the metal donor for the precipitation of secondary mineral. Herein, two magnesium-bearing silicate minerals with different structures, forsterite and talc, were added to the submerged cultures of Aspergillus niger (A. niger). It is shown that forsterite exhibits a better solubilization effect than talc, and the secondary mineral glushinskite only precipitates in the presence of forsterite substrates. Oxalic acid excreted by A. niger plays a key role in the biological leaching and mineralization processes. Moreover, the forsterite particles with certain size added to the cultures tend to inhibit the aggregation of fungal biomass, and therefore affect the morphology of A. niger aggregates in the submerged cul...

Citrobacter sp. strain GW-M Mediates the Coexistence of Carbonate Minerals with Various Morphologies

Abstract: To better understand the formation mechanism of carbonate minerals by microbes, culture experiments with a duration of 70 days were performed under the mediation of strain GW-M isolated from soil using modified Lagoa Vermelha (LV, a hypersaline coastal Lagoon, Rio de Janeiro, Brazil) medium with 6:1 Mg/Ca molar ratio. The results demonstrated that strain GW-M can mediate the formations of both high-Mg calcite and aragonite and that dumbbell-, cauliflower-, rhombohedra-shaped, and irregular minerals coexist in the modified LV medium. The amount of rhombohedra-shaped crystals increased significantly with culture time. A proposed mechanism for these formations is the following. Heterogeneous nucleation on the surface of the extracellular polymeric substances (EPS) always occurred, and carbonates with irregular shape existed in experimental products at any stages. The morphologies evolved from rod to dumbbell and finally to cauliflower. At the initial stage (till day 20), hydrogen ions and EPS secreted by the...

A Biogeochemical and Genetic Survey of Acetylene Fermentation by Environmental Samples and Bacterial Isolates

Abstract: Anoxic samples (sediment and groundwater) from 13 chemically diverse field sites were assayed for their ability to consume acetylene (C2H2). Over incubation periods ranging from ∼ 10 to 80 days, selected samples from 7 of the 13 tested sites displayed significant C2H2 removal. No significant formation of ethylene was noted in these incubations; therefore, C2H2 consumption could be attributed to acetylene hydratase (AH) rather than nitrogenase activity. This putative AH (PAH) activity was observed in only 21% of the total of assayed samples, while amplification of AH genes from extracted DNA using degenerate primers derived from Pelobacter acetylenicus occurred in even fewer (9.8%) samples. Acetylene-fermenting bacteria were isolated as a pure culture from the sediments of a tidal mudflat in San Francisco Bay (SFB93) and as an enrichment culture from freshwater Searsville Lake (SV7). Comparison of 16S rDNA clone libraries revealed that SFB93 was closely related to P. carbolinicus, while SV7 consisted of se...

Bacterial Community Structure in a Semi-Arid Haloalkaline Soil Using Culture Independent Method

Abstract: Bacterial community structures in two physicochemically different soils from the coastal region of Gujarat, India were investigated using PCR, 16S rRNA gene clone libraries and sequencing methods. The aim of the study was to determine the diversity of bacterial communities inhabiting haloalkaline soil from a semi-arid coastal region. The phylogenetic diversity of bacteria in a haloalkaline soil (EC 20 dS/m; pH 9.5) was compared with a normal soil (EC 0.93 dS/m; pH 7.2). Clones representing phyla Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Actinobacteria, Acidobacteria and Planctomycetes were found in both soils. Cyanobacteria, Verrucomicrobia, OP10 and Bacteria incertae sedis were detected in normal soil whereas Nitrospira was found only in haloalkaline soil. The dominant phylum in the haloalkaline soil was Bacteroidetes followed by Proteobacteria whereas normal soil was dominated by Proteobacteria and Actinobacteria. About 82% of the sequences from the haloalkaline library were related to tho...

Cellular ATP Changes in Acidithiobacillus ferrooxidans Cultures Oxidizing Ferrous Iron and Elemental Sulfur

Abstract: Cellular ATP content of Acidithiobacillus ferrooxidans cultures was determined with a bioluminescence assay in relation to batch growth and oxidation of ferrous iron and elemental sulfur. Inhibitory effects of inorganic substrates and products on luciferase were eliminated. Extracellular ATP levels were negligible. The ATP content of sulfur-grown cells decreased anomalously due to a culture pH increase at the stationary phase. Although the rates of growth and sulfur oxidation reached the original levels, the ATP content of the culture remained constant because of gradual decrease in the cellular ATP. The maximum ATP levels in A. ferrooxidans grown with Fe2+ and S0 were 1.16 and 0.33 amol per cell, respectively. The results defined conditions under which biomass growth could be monitored by the ATP assay to study biogeochemical activities of acidophilic iron- and sulfur-oxidizing bacteria.

Arsenic Resistance and Bioaccumulation of an Indigenous Bacterium Isolated from Aquifer Sediments of Datong Basin, Northern China

Abstract: To obtain bacteria with arsenic accumulation potential that can be used to remove arsenic from contaminated waters, experiments were made to investigate the tolerance and accumulation to arsenic of an indigenous bacterium XZM002 isolated from aquifer sediments of Datong Basin, northern China. The results showed that strain XZM002 belongs to the genus Bacillus and has evolved defense mechanisms to reduce arsenic injury: the change of cellular shape from initial rod to oval and then to round with increment of arsenic toxicity. The effect of arsenate or arsenite on the bacterial growth was also investigated. Results showed that growth of the strain was inhibited under As(III) and high concentration As(V) (over 1200 μg l−1) conditions in the first 2 days and promoted under low concentration As(V) (under 400 μg l−1) condition. Its arsenic bioaccumulation potential was surveyed by monitoring the concentration changes of total arsenic and arsenic speciation in the medium and in the cytoplasm, and those of total ...

Microbial Communities Involved in Fe Reduction and Mobility During Soil Organic Matter (SOM) Mineralization in Two Contrasted Paddy Soils

Abstract: Lowland rice fields of West Africa (Ivory Coast) and South Asia (Thailand) are affected by ferrous toxicity or salinity, respectively, and their soil waters contain large amounts of ferrous iron, depending on reducing irrigation condition and suggesting occurrence of bacterial reducing processes. To determine the involvement, dynamic and activities of bacterial communities in Fe(III) reduction and mobilization during anaerobic degradation and mineralization of soil organic matter (SOM), different experiments and analyses have been performed. Results demonstrated that the utilization of SOM as sole carbon, nutrient and energy sources favored the presence of large bacterial communities: facultative anaerobic and anaerobic bacteria, Fe(III)-reducing bacteria (FeRB) (fermentative and Fe respiring), sulfate reducing bacteria (SRB) which are involved in carbon, nitrogen, iron and sulfur cycling. The larger functional diversity is observed in the Ivory Coast paddy soils containing larger amounts of organic matte...