Chemical fractionation of organic matter and organic phosphorus extractions from freshwater lake sediment.

Lake sediment organic matter (OM) is composed of a variety of organic compounds differing in their biolability and origin. Sources of sediment OM can include terrestrial input from the watershed and algal/microbial metabolic byproducts residing in the water column or sediment. Dissolved organic phosphorus (DOP) is a critical component of OM in freshwater eutrophic lakes, often acting as a source for bioavailable phosphorus that fuels harmful algal and/or cyanobacterial blooms. Parallel extractions of lake sediment collected from Missisquoi Bay, a eutrophic bay in Lake Champlain, were conducted with the goal of identifying OM and organic P sediment constituents using ultrahigh-resolution mass spectrometry from various extractants. Extractants converged into two groups based on the characteristics of their extracted OM; "stronger extractants" were composed of highly acidic and alkali media, while "milder extractants" represented weaker acids and bases. Sediment treated with the strong extractants afforded highly oxygenated and unsaturated OM thought to be stable with mostly lower heteroatomic content. In contrast, milder extractants yielded highly aliphatic and saturated compounds with lower masses and greater heteroatom functionally, sharing characteristics with labile molecules. Extracted organic P molecules mirrored the bulk OM in terms of lability, mass, and oxygenation within their corresponding extractants. Milder extractants resulted in greater organic P formulae assignments than the stronger extractants, with NaHCO3 resulting in the most aliphatic organic P formulae. We recommend the use of acetic acid to probe lake sediment for overall molecular characterization, spanning the greatest ranges of O/C and H/C ratios and representing both labile and mineral-associated OM. Other extractants should be implemented for a more targeted analysis. For instance, the use of NaHCO3 for organic P characterization, while using NaOH when interested in sediment geochemistry; both of which are critical for understanding the factors contributing to internal P loading.

Quantitative analysis of O2 and Fe2+ profiles in gradient tubes for cultivation of microaerophilic Iron(II)-oxidizing bacteria.

The classical approach for the cultivation of neutrophilic microaerophilic Fe(II)-oxidizing bacteria is agar-based gradient tubes where these bacteria find optimal growth conditions in opposing gradients of oxygen (O2) and dissolved Fe(II) (Fe2+). The goals of this study were to quantify the temporal development of O2 and Fe2+ concentrations over time, to compare abiotic and microbially inoculated tubes and to test the suitability of different Fe(II)-sources for the cultivation of freshwater and marine microaerophilic Fe(II)-oxidizers. O2 and Fe2+ gradients were monitored on a high spatial resolution as a function of time applying amperometric and voltammetric microsensors. Fe(II)-oxidizers could be cultivated well with FeS and zero-valent iron powder as Fe(II)-source, but FeCO3 and FeCl2 are extremely sensitive for this application. Fe(III) minerals accumulated in inoculated tubes within the first days in regions with an O2 concentration of 20-40 µM and were confirmed to be related to bacterial growth. Microbial Fe(II) oxidation could compete only for the first days with the abiotic reaction after which heterogeneous Fe(II) oxidation, catalyzed by Fe(III) minerals, dominated. Our results imply that transfer of cultures to fresh tubes within 48-72 h is crucial to provide optimal growth conditions for microaerophilic Fe(II)-oxidizers, particularly for the isolation of new strains.

Transformation of galena to pyromorphite produces bioavailable sulfur for neutrophilic chemoautotrophy.

The aqueous concentration of lead [Pb(II)] in geochemical environments is controlled by the solubility of Pb-bearing minerals and their weathering products. In contaminated soils, a common method for in situ stabilization of Pb(II) is the addition of phosphate to convert more redox sensitive sulfide minerals into sparingly soluble pyromorphite [Pb5 (PO4 )3 X]. In this study, we conducted experimental studies to investigate the fate of reduced sulfur during the conversion of galena [PbS] to chloropyromorphite [Pb5 (PO4 )3 Cl]. Powder X-ray diffraction analysis indicated that the reaction of phosphate with galena under oxic conditions resulted in the oxidation of sulfide and formation of elemental sulfur [S8 ]. Under oxic abiotic conditions, the S8 was retained in the solid phase, and negligible concentrations of sulfur as sulfide and thiosulfate were detected in the aqueous phase and only a small amount of sulfate. When PbS reacted in the presence of the chemoautotrophic organism Bosea sp. WAO, the S8 in the secondary mineral was oxidized to sulfate. Strain WAO produced significantly more sulfate from the secondary S8 than from the primary galena. Microscopic analysis of mineral-microbe aggregates on mineral-embedded slide cultures showed that the organism was colocalized and increased in biomass over time on the secondary mineral surface supporting a microbial role. The results of this study indicate that stimulation of sulfur-oxidizing activity may be a direct consequence of phosphate amendments to Pb(II)-contaminated soils.

Spatial variability in photosynthetic and heterotrophic activity drives localized δ13C org fluctuations and carbonate precipitation in hypersaline microbial mats.

Modern laminated photosynthetic microbial mats are ideal environments to study how microbial activity creates and modifies carbon and sulfur isotopic signatures prior to lithification. Laminated microbial mats from a hypersaline lagoon (Guerrero Negro, Baja California, Mexico) maintained in a flume in a greenhouse at NASA Ames Research Center were sampled for δ(13) C of organic material and carbonate to assess the impact of carbon fixation (e.g., photosynthesis) and decomposition (e.g., bacterial respiration) on δ(13) C signatures. In the photic zone, the δ(13) C org signature records a complex relationship between the activities of cyanobacteria under variable conditions of CO2 limitation with a significant contribution from green sulfur bacteria using the reductive TCA cycle for carbon fixation. Carbonate is present in some layers of the mat, associated with high concentrations of bacteriochlorophyll e (characteristic of green sulfur bacteria) and exhibits δ(13) C signatures similar to DIC in the overlying water column (-2.0‰), with small but variable decreases consistent with localized heterotrophic activity from sulfate-reducing bacteria (SRB). Model results indicate respiration rates in the upper 12 mm of the mat alter in situ pH and HCO3- concentrations to create both phototrophic CO2 limitation and carbonate supersaturation, leading to local precipitation of carbonate minerals. The measured activity of SRB with depth suggests they variably contribute to decomposition in the mat dependent on organic substrate concentrations. Millimeter-scale variability in the δ(13) C org signature beneath the photic zone in the mat is a result of shifting dominance between cyanobacteria and green sulfur bacteria with the aggregate signature overprinted by heterotrophic reworking by SRB and methanogens. These observations highlight the impact of sedimentary microbial processes on δ(13) C org signatures; these processes need to be considered when attempting to relate observed isotopic signatures in ancient sedimentary strata to conditions in the overlying water column at the time of deposition and associated inferences about carbon cycling.

Isotopic biosignatures in carbonate-rich, cyanobacteria-dominated microbial mats of the Cariboo Plateau, B.C.

Photosynthetic activity in carbonate-rich benthic microbial mats located in saline, alkaline lakes on the Cariboo Plateau, B.C. resulted in pCO2 below equilibrium and δ(13) CDIC values up to +6.0‰ above predicted carbon dioxide (CO2 ) equilibrium values, representing a biosignature of photosynthesis. Mat-associated δ(13) Ccarb values ranged from ~4 to 8‰ within any individual lake, with observations of both enrichments (up to 3.8‰) and depletions (up to 11.6‰) relative to the concurrent dissolved inorganic carbon (DIC). Seasonal and annual variations in δ(13) C values reflected the balance between photosynthetic (13) C-enrichment and heterotrophic inputs of (13) C-depleted DIC. Mat microelectrode profiles identified oxic zones where δ(13) Ccarb was within 0.2‰ of surface DIC overlying anoxic zones associated with sulphate reduction where δ(13) Ccarb was depleted by up to 5‰ relative to surface DIC reflecting inputs of (13) C-depleted DIC. δ(13) C values of sulphate reducing bacteria biomarker phospholipid fatty acids (PLFA) were depleted relative to the bulk organic matter by ~4‰, consistent with heterotrophic synthesis, while the majority of PLFA had larger offsets consistent with autotrophy. Mean δ(13) Corg values ranged from -18.7 ± 0.1 to -25.3 ± 1.0‰ with mean Δ(13) Cinorg-org values ranging from 21.1 to 24.2‰, consistent with non-CO2 -limited photosynthesis, suggesting that Precambrian δ(13) Corg values of ~-26‰ do not necessitate higher atmospheric CO2 concentrations. Rather, it is likely that the high DIC and carbonate content of these systems provide a non-limiting carbon source allowing for expression of large photosynthetic offsets, in contrast to the smaller offsets observed in saline, organic-rich and hot spring microbial mats.

Rapid arsenite oxidation by Thermus aquaticus and Thermus thermophilus: field and laboratory investigations.

Thermus aquaticus and Thermus thermophilus, common inhabitants of terrestrial hot springs and thermally polluted domestic and industrial waters, have been found to rapidly oxidize arsenite to arsenate. Field investigations at a hot spring in Yellowstone National Park revealed conserved total arsenic transport and rapid arsenite oxidation occurring within the drainage channel. This environment was heavily colonized by Thermus aquaticus. In laboratory experiments, arsenite oxidation by cultures of Thermus aquaticus YT1 (previously isolated from Yellowstone National Park) and Thermus thermophilus HB8 was accelerated by a factor of over 100 relative to a biotic controls. Thermus aquaticus and Thermus thermophilus may therefore play a large and previously unrecognized role in determining arsenic speciation and bioavailability in thermal environments.

Formation of sphalerite (ZnS) deposits in natural biofilms of sulfate-reducing bacteria.

Abundant, micrometer-scale, spherical aggregates of 2- to 5-nanometer-diameter sphalerite (ZnS) particles formed within natural biofilms dominated by relatively aerotolerant sulfate-reducing bacteria of the family Desulfobacteriaceae. The biofilm zinc concentration is about 10(6) times that of associated groundwater (0.09 to 1.1 parts per million zinc). Sphalerite also concentrates arsenic (0.01 weight %) and selenium (0.004 weight %). The almost monomineralic product results from buffering of sulfide concentrations at low values by sphalerite precipitation. These results show how microbes control metal concentrations in groundwater- and wetland-based remediation systems and suggest biological routes for formation of some low-temperature ZnS deposits.

Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems.

This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of approximately 0.5 to approximately 1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. "Ferroplasma" spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength. Leptospirillum spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured Leptospirillum sp. dominated. Sulfobacillus spp. were detected as a prominent inhabitant in warmer ( approximately 43 degrees C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.