Quantifying CaCO3 Microprecipitates Within Developing Surface Mats of Marine Stromatolites Using GIS and Digital Image Analysis

The unique geochemical coupling of organic molecules and mineral CaCO₃ provides a fluorescence signature detectable using conventional confocal scanning laser microscopy (CSLM). The surface microbial mats of open-water marine stromatolites (Bahamas) exist in a continuum of states ranging from a Type 1 (i.e., nonlithifying) to Type 2 (i.e., lithified micritic laminae present) to Type 3 (i.e., fused grain layer). An approach was developed here, that utilizes geographical information systems (GIS) and digital image analysis, coupled with CSLM to estimate concentrations of calcium carbonate precipitates in developing marine stromatolites. We propose that the area occupied by particles within each image can be used to estimate concentrations of precipitates. Fluorescent polymeric microbeads and bacteria were used to calibrate the approach. We used this approach to demonstrate that CaCO₃ precipitates in lithifying layers were quantifiable and significantly different (p < 0.0001) from those in nonlithifying layers. The approach provided a useful tool for the unambiguous assessment of relative changes in microbial precipitates occurring over small ( μ m to mm) spatial scales, and that characterize the formation of lithified layers (micritic laminae) in open-water marine stromatolites.     

The impact of flash floods on microbial distribution and biogeochemistry in the parafluvial zone of a desert stream

1. The impact of flash flooding on microbial distribution and biogeochemistry was investigated in the parafluvial zone (the part of the active channel lateral to the surface stream) of Sycamore Creek, a Sonoran Desert stream in central Arizona. 2. It was hypothesized that subsurface bacteria were dependent on the import of algal-derived organic matter from the surface stream, and it was therefore predicted that microbial numbers and rates of microbially mediated processes would be highest at locations of surface to subsurface hydrologic exchange and at times when algal biomass was high. 3. Prior to a flash flood on 19 July 1994, chlorophyll a was high (≈ 400 mg m^–2) in the surface stream and microbial numbers were highest at the stream–parafluvial interface and declined along parafluvial flowpaths, supporting the hypothesized algal–bacterial linkage. Immediately following the flash flood, chlorophyll a was low (≈ 7 mg m^–2), and microbial numbers were reduced at the stream–parafluvial interface. 4. Counter to expectations, parafluvial functioning (in terms of nitrate production and dissolved oxygen decline along flowpaths) re-established immediately after the flood receded. Therefore, material other than algal exudates supported parafluvial metabolism immediately postflood, and terrestrially derived dissolved organic matter is the likely source. 5. Algae in the surface stream recovered quickly following flooding, but recovery of parafluvial bacteria lagged somewhat behind. These results highlight the importance of surface–subsurface interaction to stream ecosystem functioning and show that the nature of these interactions changes substantially in successional time.     

Shift of Bacterial Community Structures in Sediments From the Changjiang (Yangtze River) Estuary to the East China Sea Linked to Environmental Gradients

Abstract

The Changjiang estuary and its adjacent East China Sea (ECS) have been considered as one of the most dynamic areas significantly contributing to elemental exchanges globally. The purpose of this study was to understand the alteration of microbial consortia at the interface of riverine and coastal environments in relation to environmental variations as well as their roles in biogeochemical cycling at this dynamic region. We sampled surface sediment samples at 4 stations from the estuary to coastal regions of the ECS. Along with collections of physicochemical parameters, we sequenced bacterial 16S rRNA genes of clones from each sample. Results showed a distinct transition of bacterial community from typical freshwater sediment phyla (e.g., Betaproteobacteria and Firmicutes) to those commonly inhabited in saline environments (e.g., Deltaproteobacteria and Gammaproteobacteria). The bacterial group at the transition zone characterized by high accumulation of organic matters and intense mixing of riverine and coastal waters was most diverse. Bacterial community structures at two ECS stations showed a similar pattern but contained different dominant taxa, shifting from Deltaproteobacteria-affiliated sulfate-reducing bacteria at the station closer to the shore to Gammaproteobacteria-affiliated nitrate-reducing bacteria further offshore. It suggested that the sedimentary bacterial community structure was related to salinity, sediment type, and substrate availability and composition.     

A critical stage in the formation of acid mine drainage: Colonization of pyrite by Acidithiobacillus ferrooxidans under pH-neutral conditions

A dominant Acidithiobacillus ferrooxidans ssp. was isolated from the supergene copper deposit in Morenci, Arizona, USA. Washed bacterial suspensions (10⁸ MPN per treatment), in pH‐neutral buffer, were inoculated onto pyrite cubes for 24 h. Heterogeneous bacterial absorption onto the pyrite removed approximately 90% of the viable bacteria from the inoculum. At T = 0, the bacteria were observed primarily in regions enriched in phosphorus. Over 30 days, the bacterial population on the pyrite cubes increased from 1.3 × 10⁷ to 2.9 × 10⁸ bacteria cm^?2. During this growth stage, low levels of thiobacilli (228 ± 167 MPN mL^?1) were also recovered from the fluid phase; however, this population decreased to zero within 30 days. Growth on pyrite occurred as micrometre‐scale planar microcolonies, a biofilm, coating the mineral surfaces. These microcolonies possessed viable thiobacilli, even after 4 months at ‘circumneutral pH’. Imaging the pyrite cubes using SEM‐EDS and scanning force microscopy demonstrated that the thiobacilli grew as iron oxy‐hydroxide‐cemented cells, leading to the formation of mineralized microcolonies. Removing the iron oxy‐hydroxides with oxalic acid did not dislodge the bacteria, demonstrating that the secondary minerals were not responsible for ‘gluing’ the bacteria to the pyrite surface. Removing organic material, i.e. the cells, by an oxygen plasma treatment revealed the presence of corrosion pits the size and shape of bacteria. Because of the inherent geochemical constraints on pyrite oxidation at neutral pH, the colonization of pyrite under circumneutral pH conditions must be facilitated by the development of an acidic nanoenvironment between the bacteria and the pyrite mineral surface.     

Distribution Characteristics of Anammox Bacteria in Ancient Canal (Guyun River) Riparian Sediment of Zhenjiang,China

Riparian sediment is an important active interface zone for nitrogen-biogeochemical cycles. However, the distribution characteristics of anammox bacteria are not adequately described in the riparian sediment of urban rivers. Therefore, the distribution characteristics of anammox bacteria of Guyun river riparian sediment, which is the representative urban river, were investigated in this study. Research results showed that anammox bacterial abundance showed a significant spatial variation at the study area. Abundance values ranged from 2.00?×?10⁵ to 1.92?×?10⁷ copies·g^?1?dry sediment. And the average value was 6.64×10⁶ copies·g^?1 dry sediment in six collected samples. Abundance of anammox bacteria was significantly related to TN, NH₄⁺-N, and pH. Slight spatial variations of richness and diversity in Guyun river riparian sediment were obtained and physicochemical parameters of sediment samples did not significantly influence the biodiversity index of anammox bacteria. Phylogenetic analysis indicated that all amplified sequences fell within the known anammox bacterial group, i.e., Brocadia, Anammoxoglobus/Jettenia, and Kuenenia, with proportions of 33.91%, 24.35%, and 41.74%, respectively. The relative abundance of anammox bacteria showed distinctive spatial heterogeneity in six different sample sites. This finding indicated a distinct spatial variation of anammox bacterial in Guyun river riparian sediment.     

Microbiological Comparison of Surface Soil and Unsaturated Subsurface Soil from a Semiarid High Desert

Thirty-two chemoheterotrophic bacteria were isolated from unsaturated subsurface soil samples obtained from ca. 70 m below land surface in a high desert in southeastern Idaho. Most isolates were gram positive (84%) and strict aerobes (79%). Acridine orange direct counts of microbes in one subsurface sample showed lower numbers than similar counts performed on surface soils from the same location (ca. 5 × 10⁵ versus 2 × 10⁶ cells per g [dry weight] of soil), but higher numbers than those from plate counts performed on the subsurface material. Another sample taken from the same depth at another location showed no evidence of colonies under identical conditions. Soil analyses indicated that subsurface sediments versus surface soils were slightly alkaline (pH 7.9 versus 7.4), had a higher water content (25.7 versus 6.3%), and had lower organic carbon concentrations (0.05 to 0.17 versus 0.25% of soil dry weight). Analyses of biologically relevant gases from the unsaturated subsurface indicated an aerobic environment. As in other unsaturated soil environments, either a high proportion of bacteria in these subsurface sediments are not viable or they are incapable of growth on conventional media under aerobic conditions. The presence and numbers of bacteria in these deep sediments may be influenced by colonization opportunities afforded by periodic percolation of surface water through fractures in overlying strata.     

Biogeochemical cycling of methylmercury at Barn Island Salt Marsh,Stonington, CT,USA

Monomethylmercury (MMHg) is toxic, and is the primary form of Hg thatbioaccumulates in the food web. An understanding of its distribution,production, and transport is needed. Prior investigations indicate thatmethylation is mediated by sulfate-reducing bacteria, yet limited in highsulfate environments. High rates of microbial respiration and strong oxygengradients are found in salt marshes. It is hypothesized that significant in situ methylation takes place in the redox transition zone of sulfate rich( 28 mM) salt marsh sediment. Results from a water column surveyof Barn Island Salt Marsh in October 1996 showed that ca. 61pmol m^-2 d^-1 of dissolved MMHg were discharged toadjacent coastal waters, while 16 pmol m^-2 d^-1 ofparticulate MMHg were entrained in the marsh, implying an in situsource. In-sediment MMHg production rates were determined by²⁰³Hg radiotracer studies. At the surface, methylation rates variedover both long (i.e., 100's m; 11–1120 pmol m^-2 d^-1) andshort (i.e., 10 cm; 11–108 pmol m^-2 d^-1) spatial scales. Methylation rate profiles from both low and high MMHg production sitesexhibited an exponential decrease below the redox transition zone. Porewater was collected with multi-chambered in situ dialysis (30 kDa)samplers [Peepers] and analyzed for MMHg. Temporal differences in porewater MMHg accumulation (i.e., May > September > November)were found. Results from May showed a significant gradient at thesediment water interface. The transport out of the sediments estimated byFick's Law (ca. 390 pmol MMHg m-2 d^-1) suggeststhat MMHg entered the marsh water by diffusion. This workdemonstrates the potential for elevated in situ Hg methylation in highsulfate environments.     

Sulfur in Ghanaian soils

Studies were carried out to examine factors which might influence the distribution of S in Ghanaian soils. Nine soil profiles developed over granitic rocks, three each representing the upper slope (US), middle slope (MS) and lower slope (LS) of catena in the evergreen high rain forest (ERF), semi-deciduous rain forest (SDF) and the interior savanna (ISAV) zone of Ghana were selected. The total S contents varied from 9 to 347 ppm; the average for all the surface and subsurface horizons was 141 ppm and for subsoils 105 ppm. The contents also varied according to: (1) the ecological zone as follows: ERF 0) SDF>ISAV and (2) the topographic position: US>MS>LS. The total S was closely correlated with organic C and total N in the surface and subsurface horizons (r=0.931^*** and 0.941^*** respectively). Inorganic sulfate was generally higher in the subsoils than in the surface and subsurface horizons of the ERF and SDF profiles whereas the opposite was the case in the ISAV profiles. Based on the critical value of 6 ppm in surface soils, all the savanna soils would be considered S deficient.The total organic S, which constituted from 56 to over 95% of the total S in the profiles, was significantly correlated with total N both in the surface and subsurface horizons (N:S ratio=9.1:1) and in the subsoils (N:S ratio=7.6:1). Fractionation of the organic S showed that HI-reducible S ranged from 14 to 117 ppm in the surface and subsurface horizons (average 55 ppm, equivalent to 47% of the total organic S) and from 2 to 169 ppm (average 55 ppm, equivalent to 60% of the total organic S) in the subsoils. The C-bonded S ranged from 6 to 223 ppm (average 73 ppm, equivalent to 57% of the total organic S) in the surface and subsurface horizons and from 1 to 83 ppm (average 29 ppm, equivalent to 32% of the total organic S) in the subsoils. HI-reducible S was significantly correlated with organic C (r=0.805^***) and total N (r=0.845^***) in the surface and subsurface horizons only whereas C-bonded S was significantly correlated with organic C and total N in both the surface and subsurface horizons and subsoils (r=0.870^*** and 0.624^*** respectively).The N:S ratios varied from 6.0 to 12.7 in the surface and subsurface horizons and from 0.5 to 27.3 in the subsoils. However the N:S ratio was less variable within the profile than the C:S ratio. The C:N:S ratios varied considerably within the profile and among the different soils but they fall within the range of values reported world-wide.     

Deep Subsurface Microbial Biomass and Community Structure in Witwatersrand Basin Mines

The extreme environments of South Africa mines were investigated to determine microbial community structure and biomass in the deep subsurface. These community parameters were determined using phospholipid fatty acid (PLFA) technique. Air, water and rock samples were collected from several levels and shafts in eight different mines. Biomass estimates ranged over nine orders of magnitude. Biofilm samples exhibited the highest biomass with quantities ranging from 10 ³ to 10 ⁷ pmol PLFA g ^?1 . Rock samples had biomass ranging from 10 ³ to 10 ⁶ pmol PLFA g ^?1 . Mine service waters and rock fracture waters had biomass estimates ranging from 10 ⁰ to 10 ⁶ pmol PLFA L ^?1 . Air samples biomass values ranged from 10 ^?2 to 10 ⁰ pmol PLFA L ^?1 . The biomass estimates were similar to those estimates for other deep subsurface sites. Redundancy analysis of the PLFA profiles distinguished between the sample types, where signature lipid biomarkers for aerobic and anaerobic prokaryotes, sulfate-and metal-reducing bacteria were associated with biofilms. Rock samples were enriched in 18:1 ω 9 c , 18:2 ω 6, br17:1s and br18:1s, which are indicative of microeukaryotes and metal- reducing bacteria. Air samples were enriched with 22:0, 17:1, 18:1, and a polyunsaturated fatty acid. Service waters had monounsaturated fatty acids. Fracture waters contained i17:0 and 10Me18:0 which indicated gram-positive and other anaerobic bacteria. When the fracture and service water sample PLFA responses to changes in environmental parameters of temperature, pH, and anion concentrations were analyzed, service waters correlated with higher nitrate and sulfate concentrations and the PLFAs 18:1 ω 7 c and 16:1 ω 7 c . Dreifontein shaft 5 samples correlated with chloride concentrations and terminally branched saturated fatty acids and branched monounsaturated fatty acids. Kloof, Tau Tona, and Merriespruit fracture waters aligned with temperature and pH vectors and 18:0, 20:0 and 22:6 ω 3. The redundancy analysis provided a robust method to understand the PLFA responses to changes in environmental parameters.     

An Experimental Investigation of the Effect of Bacillus megaterium on Apatite Dissolution

Field observations suggest that some mineral dissolution rates can be enhanced by microbial activity indirectly, without direct contact with the mineral surface. A series of apatite dissolution experiments was performed to better understand this rate enhancement process. Far-from equilibrium abiotic apatite dissolution rates, measured in mixed-flow reactors at 25°C were enhanced by increasing concentration of aqueous organic acids and decreasing aqueous phosphate activity, demonstrating the existence of indirect pathways for microbial rate enhancement. Further apatite dissolution experiments were performed in closed-system reactors in the presence of Bacillus megaterium , a common heterotrophic aerobe. Experiments were designed to allow the bacteria to be either in direct contact or indirect contact with the apatite; in the latter case, the microbes were physically separated from the apatite using dialysis bags. Apatite dissolution in indirect contact with Bacillus megaterium was 50 to 900% faster than abiotic controls. Bacterial rate enhancement was, however, 3 to over 10 times lower when Bacillus megaterium was in direct contract versus indirect contact with the apatite surfaces. These results show that (1) bacteria can accelerate rates without being in physical contact with the dissolving mineral, and (2) microbially mediated dissolution may be less effective when bacteria are in direct contact with mineral surfaces. Supression of mineral dissolution is interpreted to stem from the preferential colonization of reactive sites on the mineral surface.     

Microfracture Surface Geochemistry and Adherent Microbial Population Metabolism in TCE-Contaminated Competent Bedrock

A TCE-contaminated competent bedrock site in Portsmouth, NH was used to determine if a relation existed between microfracture surface geochemistry and the ecology and metabolic activity of attached microbes relative to terminal electron accepting processes (TEAPs) and TCE biodegradation. The bedrock is a metasandstone and metashale of the Silurian Kittery Formation. Eleven microfractures (MF 01-11) were extracted from cores of competent rock from 2 boreholes (BBC5 and BBC6) at depths > 21.3 m below ground. The host rock had 3 nominal pore width sizes (131.1, 1.136, and 0.109 μ m), a porosity of 0.8%, and a permeability of < 1 μ d. Microfracture surface precipitates were polycrystalline with grain sizes ranging from 10 to 100 μ m. Petrography and XRD revealed that carbonates and quartz were the dominant microfracture surface precipitates. Mineral distribution was heterogeneous at the 10 μ m scale. Oxidized and reduced iron species were identified with XPS on the microfracture precipitate surfaces. Carbon functional groups characteristic of NOM were also identified. SIMS mass fragment fingerprints suggested that TCE, PCE and/or VC were possibly adsorbed to NOM on the microfracture surfaces. Packer waters were alkaline (131–190 mg/L as CaCO₃, pH 8.8 to 9.6), mildly reducing (Eh of ?208 to 160 mV, DO of 0.4 to 2.5 mg/L), with low NPDOC values (0.8–1.7 mg/L), and measurable Fe (II) (0.1 mg/L) and Fe (III) (0.02 to 0.3 mg/L). Sulfate was the dominant anion in the packer sample water (110–120 mg/L). No sulfide was detected. H ₂ was present in a number of the BBC wells at the site (2.2–7.3 nM). Amplification with specific primer sets of seven microfractures from BBC5 showed the presence of bacteria, Archaea, anaerobic dehalorespirers (Dehalococcoides sp.), sulfate reducing bacteria, and iron reducing bacteria (Geobacteraceae). Redox zonation may exist relative to spatial distance from within the microfracture network to the open fracture system. The microfracture surface precipitates, frequently spatially complex and comprised of a variety of C-, Fe- and S-containing minerals, may be another region for redox zonation. Fe was the dominant microfracture surface element and active Fe cycling is suspected. However, the primer data suggest that the microfracture network may have been more reducing than the open fracture system. In this case, the microfracture network may constitute a zone where more reductive metabolic processes occur, making this system similar to biogeochemical redox zones found in other environments.     

Surface metabolites of the brown alga Taonia atomaria have the ability to regulate epibiosis

This study aimed to improve understanding of the strategies developed by the Mediterranean seaweed Taonia atomaria to chemically control bacterial epibiosis. An experimental protocol was optimized to specifically extract algal surface-associated metabolites by a technique involving dipping in organic solvents whilst the integrity of algal cell membranes was assessed by fluorescent microscopy. This methodology was validated using mass spectrometry-based profiles of algal extracts and analysis of their principal components, which led to the selection of methanol as the extraction solvent with a maximum exposure time of 15 s. Six compounds (A–F) were identified in the resulting surface extracts. Two of these surface-associated compounds (B and C) showed selective anti-adhesion properties against reference bacterial strains isolated from artificial surfaces while remaining inactive against epibiotic bacteria of T. atomaria. Such specificity was not observed for commercial antifouling biocides and other molecules identified in the surface or whole-cell extracts of T. atomaria.     

Distribution of marine viruses and their potential hosts in Prydz Bay and adjacent Southern Ocean,Antarctic

Viruses play a key role in all marine ecosystems, and yet little is known of their distribution in Antarctic waters, especially in bathypelagic waters (>1000 m). In this study, the abundance and distribution of viruses and their potential hosts from the surface to the bottom of Prydz Bay, Antarctic, was investigated using flow cytometry. Viruses and autotrophs were abundant in nearshore and continental shelf waters, while heterotrophic bacteria and picoeukaryotes were abundant in offshore waters. Virus and bacteria abundances generally decreased with increasing depth but increased slightly just above the seafloor. Within the water column, maximum virus numbers coincided with the maximum values of chlorophyll a (when greater than 0.1 μg l^?1), in the surface and subsurface (25 m). In the open ocean, however, virus abundance usually correlated with bacterial abundance at greater depths (50, 300 and 500 m) where the surface chlorophyll a concentration was lower than 0.1 μg l^?1. Viral abundance was correlated with the host cell abundance, and this was different in different pelagic zones (bacteria and autotrophs (i.e., chlorophyll a concentration) in the epipelagic waters, picoeukaryotes and bacteria in mesopelagic waters and bacteria in bathypelagic waters). Principle component analysis and Pearson correlation analysis indicated that there was a close relationship between virus abundance and chlorophyll a, bacteria and nutrients (NO₂ + NO₃, phosphate and silicate), and picoeukaryote abundance was mainly correlated with water depth and salinity.     

Sorption of Glyphosate on Soil Components: The Roles of Metal Oxides and Organic Materials

Predicting the behavior, fate, and transport potential of a herbicide in any soil involves understanding the sorption characteristics. The sorption characteristics of glyphosate (GPS) on soil and their main components were investigated, indicating that the mineral phase is more important than the organic carbon in adsorption of GPS. Sorption isotherms were determined from each component using the batch equilibrium method at various concentrations (5, 10, 15, 20, 25, and 30 mg L^?1) and sorption affinity of GPS was approximated by the Freundlich equation. The sorption strength K _f [mg kg^?1 (L mg^?1)^?n] across the various components ranged from 2.1–134.9 while the organic carbon-normalized Freundlich sorption capacity values, K _foc, ranged from 1.28–3.53 mg kg^?1-OC/(mg L^?1)ⁿ. Infrared Fourier transform spectroscopy (FTIR) of the components showed significant structural differences. The results suggest that the presence of the oxides and hydroxides iron, in particular in soil solutions, enhanced GPS adsorption. They also suggest that reduction in OC% due to various treatments may enhance the remobilization of GPS into the aqueous phase (i.e., groundwater), though at different rates. Comparatively, contribution of surface area to the adsorption of GPS on the various components proved more significant than contents of organic carbon.     

The response surface optimization of β-mannanase produced by Lactobacillus casei HDS-01 and its potential in juice clarification

Abstract

Lactic acid bacteria (LAB) is an ideal mannanase source due to the bio-safety guarantee. LAB can heterogeneously express β-mannanase or be directly used as β-mannanase-producing strains. This research originally optimized the fermentation condition for β-mannanase produced by Lactobacillus casei HDS-01. The applicable potential of the crude enzyme in juice clarification was investigated. Two-factorial design screened out three factors, i.e., fermentation time (p?=?0.0001), glucose (p?=?0.0013), and initial pH (p?=?0.0167), which significantly affected L. casei HDS-01 β-mannanase activity. Under the predicted conditions resulting from the central composite design (CCD), i.e., fermentation time 18.23?hr, glucose 12.65?g L^?1, initial pH 5.18, the model reached maximal β-mannanase activity of 81.40?U mL^?1. This model was validated by conducting six repeated experiments and subsequent t-test (p?=?0.6308). RSM optimization obtained a 1.33-fold increase in β-mannanase activity. This increase could also be qualitatively detected by larger clearance zone on konjac powder-MRS agar through Congo Red dyeing. The yield and clarity of crude β-mannanase-treated juices from orange, apple, and pear were significantly higher than controls without enzyme treatment. This study conferred a relatively high β-mannanase-producing LAB strain with a high bio-safety level and easy and economical use in juice clarification as well as other food-level fields.     

Hydrogeologic parameters affecting vadose‐zone microbial distributions

Abstract

The vadose zone and its contaminant‐attenuating processes are physically interposed between surface contamination and groundwater supplies. Given the potential role of microorganisms in mediating vadose‐zone chemical processes, it is vital to understand vadose microbial distributions and factors controlling those distributions. Vadose and shallow saturated zone sediments obtained from cores drilled to approximately 8 m below the surface at two hydrogeologically contrasting sites, named Dalmeny and Washington State University (WSU), were examined for culturable heterotrophic bacteria, total organic carbon (TOC), and sediment texture. Pore‐water elutions were analyzed for dissolved organic carbon, sulfate, and inorganic nitrogen species. Numbers of cultured bacteria (10³‐10⁷ g^?1) generally decreased with depth at both sites. The TOC decreased uniformly with depth at WSU where soil processes are the sole carbon source; at Dalmeny, where both soil and kerogen carbon are present, TOC was higher and relatively constant with depth. Numbers of distinct colony types at Dalmeny did not decline below the solum. Bacteria at Dalmeny were more numerous, exhibited greater numbers of colony types, and were metabolically more flexible than those at WSU. The smooth decline of numbers with depth at WSU paralleled and may be caused by the TOC decline with distance from a solum source. Sediment permeability and pore‐water flux did not control bulk populations as suggested in previous studies; this may be explained by bacterial residence on fracture surfaces in low‐permeability materials. Psychrotolerant organisms did not appear to be as abundant as mean ambient temperatures might suggest.     

Microbial Communities in Subpermafrost Saline Fracture Water at the Lupin Au Mine, Nunavut, Canada

We report the first investigation of a deep subpermafrost microbial ecosystem, a terrestrial analog for the Martian subsurface. Our multidisciplinary team analyzed fracture water collected at 890 and 1,130 m depths beneath a 540-m-thick permafrost layer at the Lupin Au mine (Nunavut, Canada). ¹⁴C, ³H, and noble gas isotope analyses suggest that the Na–Ca–Cl, suboxic, fracture water represents a mixture of geologically ancient brine, ~25-kyr-old, meteoric water and a minor modern talik-water component. Microbial planktonic concentrations were ~10³ cells mL^?1. Analysis of the 16S rRNA gene from extracted DNA and enrichment cultures revealed 42 unique operational taxonomic units in 11 genera with Desulfosporosinus, Halothiobacillus, and Pseudomonas representing the most prominent phylotypes and failed to detect Archaea. The abundance of terminally branched and midchain-branched saturated fatty acids (5 to 15 mol%) was consistent with the abundance of Gram-positive bacteria in the clone libraries. Geochemical data, the ubiquinone (UQ) abundance (3 to 11 mol%), and the presence of both aerobic and anaerobic bacteria indicated that the environment was suboxic, not anoxic. Stable sulfur isotope analyses of the fracture water detected the presence of microbial sulfate reduction, and analyses of the vein-filling pyrite indicated that it was in isotopic equilibrium with the dissolved sulfide. Free energy calculations revealed that sulfate reduction and sulfide oxidation via denitrification and not methanogenesis were the most thermodynamically viable consistent with the principal metabolisms inferred from the 16S rRNA community composition and with CH₄ isotopic compositions. The sulfate-reducing bacteria most likely colonized the subsurface during the Pleistocene or earlier, whereas aerobic bacteria may have entered the fracture water networks either during deglaciation prior to permafrost formation 9,000 years ago or from the nearby talik through the hydrologic gradient created during mine dewatering. Although the absence of methanogens from this subsurface ecosystem is somewhat surprising, it may be attributable to an energy bottleneck that restricts their migration from surface permafrost deposits where they are frequently reported. These results have implications for the biological origin of CH₄ on Mars.     

Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

Abstract

To develop a greater understanding of hyporheic zone microbial biogeochemistry, we sampled pore fluids from a piezometer array associated with the McCarran Ranch channel bar (MRCB); a partially submerged cobble island in the Truckee River, NV, USA. Flowing surface water and pumped pore fluids were characterized by prokaryotic community structure, metabolic potential, and aqueous physicochemistry. Concentrations of potential respiratory electron acceptors were highest in surface water and riverbed porewater and sequentially depleted in porewaters along the inferred flowpath (O₂, then NO₃^?, then SO₄^2?). Correspondingly, cultivable nitrate reducers/denitrifiers were most abundant in surface water and riverbed porewater, despite oxic conditions. Cultivable sulfate reducers were overall most abundant in surface water. Prokaryotic community reconstruction from 16S rRNA gene sequences indicates that the surface water community was less diverse than that of porewater and supports a shift in metabolic strategy, from aerobic heterotrophy in surface water (e.g., Comamonadaceae and Sporichthyaceae) to chemolithotrophy and anaerobic metabolisms (e.g., Hydrogenophaga spp., Ferribacterium spp., Methanobacterium spp.) along the hyporheic flow path. These data indicate that prokaryotic communities within the MRCB are phylogenetically and metabolically diverse and contribute to biogeochemical cycling in this common yet relatively understudied habitat.     

Characterization of endophytic and symbiotic bacteria within plants of the endemic association Centaureetum horridae Mol

Abstract

We investigated the internal association of bacteria with Astragalus terraccianoi and Centaurea horrida, two endemic plants of the Mediterranean islands, forming the phytosociological association Centaureetum horridae, typical of windswept cliffs on the rocky shores of Asinara (Sardinia, Italy) and other limited locations. Sampling occurred in the protected natural park of the Asinara island. Roots and stems of the two plants and the root nodules of A. terraccianoi were surface sterilized in order to remove external and rhizospheric microbiota and to subsequently isolate the culturable bacterial communities. Plate counts revealed densities of endophytes between 3.7 × 10² and 2.8 × 10⁴ colony forming units per gram of fresh weight. 16S rDNA sequencing revealed the occurrence of bacteria displaying high similarity with Actinobacterium sp., Paenibacillus sp., Rhizobium sp., Methylobacterium sp., Pedobacter panaciterrae, Aerococcus viridans, Stenotrophomonas rhizophila, Bacillus sporothermodurans, Bacillus pumilus, Bacillus simplex, Bacillus flexus, Streptomyces ciscaucasicus and Dyella sp. The putative nitrogen-fixing rhizobium symbiont of A. terraccianoi was identified for the first time. It turned out to belong to the slow-growing Bradyrhizobium genus and to share a 97% similarity with Bradyrhizobium canariense. It was found to be nonculturable and to coexist in nodules with a number of different endophytes.