Tibetan Plateau grasslands might increase sequestration of microbial necromass carbon under future warming.

Microbial necromass carbon (MNC) can reflect soil carbon (C) sequestration capacity. However, changes in the reserves of MNC in response to warming in alpine grasslands across the Tibetan Plateau are currently unclear. Based on large-scale sampling and published observations, we divided eco-clusters based on dominant phylotypes, calculated their relative abundance, and found that their averaged importance to MNC was higher than most other environmental variables. With a deep learning model based on stacked autoencoder, we proved that using eco-cluster relative abundance as the input variable of the model can accurately predict the overall distribution of MNC under current and warming conditions. It implied that warming could lead to an overall increase in the MNC in grassland topsoil across the Tibetan Plateau, with an average increase of 7.49 mg/g, a 68.3% increase. Collectively, this study concludes that alpine grassland has the tendency to increase soil C sequestration capacity on the Tibetan Plateau under future warming.

Vegetation restoration in an alpine meadow: Insights from soil microbial communities and resource limitation across soil depth.

Aboveground vegetation restoration shapes the soil microbial community structure and affects microbial resource acquisition. However, the changes in soil microbial resource limitation in subsoil during vegetation restoration are still unclear. In this study, the microbial community structure and resource limitation in an alpine meadow soil profile that had undergone natural restoration for short-term (4-year) and long-term (10-year) restoration in response to vegetation restoration were explored through high-throughput sequencing analysis and extracellular enzyme stoichiometry (EES). There was no significant difference in microbial composition and α diversity between short- and long-term restoration soils. Soil microorganisms in this alpine meadow were mainly limited by phosphorus. Carbon limitation of soil microorganisms was significantly decreased in each layer (0-15, 15-30, 30-45, 45-60, and 60-80 cm corresponding to L1, L2, L3, L4, and L5, respectively) of long-term restoration soils when compared to that of the short-term restoration soil layers, while phosphorus limitation of microorganisms in subsoil (60-80 cm) was significantly increased by 17.38%. Soil nutrients, pH, moisture content, and microbial composition are the main drivers of microbial resource limitation in restoration, and their effects on microbial resource limitation were different in short- and long-term restoration. Meanwhile, key microbial taxa have a significant impact on microbial resource limitation, especially in short-term restoration soils. This study suggested that vegetation restoration significantly affected soil microbial resource limitation, and could alleviate microbial resource limitations by adding nutrients, thus accelerating the process of vegetation restoration in alpine ecosystems.

Microbial Diversity in Actively Forming Iron Oxides from Weathered Banded Iron Formation Systems.

The surface crust that caps highly weathered banded iron formations (BIFs) supports a unique ecosystem that is a post-mining restoration priority in iron ore areas. Geochemical evidence indicates that biological processes drive the dissolution of iron oxide minerals and contribute to the ongoing evolution of this duricrust. However, limited information is available on present-day biogeochemical processes in these systems, particularly those that contribute to the precipitation of iron oxides and, thus, the cementation and stabilization of duricrusts. Freshly formed iron precipitates in water bodies perched on cangas in Karijini National Park, Western Australia, were sampled for microscopic and molecular analyses to understand currently active microbial contributions to iron precipitation in these areas. Microscopy revealed sheaths and stalks associated with iron-oxidizing bacteria. The iron-oxidizing lineages Sphaerotilus, Sideroxydans, and Pedomicrobium were identified in various samples and Leptothrix was common in four out of five samples. The iron-reducing bacteria Anaeromyxobacter dehalogens and Geobacter lovleyi were identified in the same four samples, with various heterotrophs and diverse cyanobacteria. Given this arid, deeply weathered environment, the driver of contemporary iron cycling in Karijini National Park appears to be iron-reducing bacteria, which may exist in anaerobic niches through associations with aerobic heterotrophs. Overall oxidizing conditions and Leptothrix iron-oxidizers contribute to net iron oxide precipitation in our sampes, rather than a closed biogeochemical cycle, which would result in net iron oxide dissolution as has been suggested for canga caves in Brazil. Enhancements in microbial iron oxide dissolution and subsequent reprecipitation have potential as a surface-crust-ecosystem remediation strategy at mine sites.

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments.

Comparison of Gastric versus Gastrointestinal PBET Extractions for Estimating Oral Bioaccessibility of Metals in House Dust.

Oral bioaccessibility estimates for six metals which are prevalent as contaminants in Canada (zinc, lead, cadmium, copper, nickel, and chromium) are investigated for house dust using the simple gastric phase versus the two-phase physiologically-based extraction technique (PBET). The purpose is to determine whether a complete gastrointestinal (GI) assay yields a more conservative (i.e., higher) estimate of metal bioaccessibility in house dust than the gastric phase alone (G-alone). The study samples include household vacuum dust collected from 33 homes in Montreal, Canada, plus four certified reference materials (NIST 2583, NIST 2584, NIST 2710 and NIST 2710a). Results indicate that percent bioaccessibilities obtained using G-alone are generally greater than or equivalent to those obtained using the complete GI simulation for the six studied metals in house dust. Median bioaccessibilities for G-alone/GI in household vacuum dust samples (n = 33) are 76.9%/19.5% for zinc, 50.4%/6.2% for lead, 70.0%/22.4% for cadmium, 33.9%/30.5% for copper and 28.5%/20.7% for nickel. Bioaccessible chromium is above the detection limit in only four out of 33 samples, for which G-alone results are not significantly different from GI results (p = 0.39). It is concluded that, for the six studied metals, a simple G-alone extraction provides a conservative and cost-effective approach for estimating oral bioaccessibility of metals in house dust.

Microscale characterization and trace element distribution in bacteriogenic ferromanganese coatings on sand grains from an intertidal zone of the East China Sea.

An ancient wood layer dated at about 5600 yr BP by accelerator mass spectrometry (AMS) 14C was discovered in an intertidal zone of the East China Sea. Extensive and horizontally stratified sediments with black color on the top and yellowish-red at the bottom, and some nodule-cemented concretions with brown surface and black inclusions occurred in this intertidal zone. Microscale analysis methods were employed to study the microscale characterization and trace element distribution in the stratified sediments and concretions. Light microscopy, scanning electron microscopy (SEM) and backscattered electron imaging (BSE) revealed the presence of different coatings on the sand grains. The main mineral compositions of the coatings were ferrihydrite and goethite in the yellowish-red parts, and birnessite in the black parts using X-ray powder diffraction (XRD). SEM observations showed that bacteriogenic products and bacterial remnants extensively occurred in the coatings, indicating that bacteria likely played an important role in the formation of ferromanganese coatings. Post-Archean Australian Shale (PAAS)-normalized middle rare earth element (MREE) enrichment patterns of the coatings indicated that they were caused by two sub-sequential processes: (1) preferentially release of Fe-Mn from the beach rocks by fermentation of ancient woods and colloidal flocculation in the mixing water zone and (2) preferential adsorption of MREE by Fe-Mn oxyhydroxides from the seawater. The chemical results indicated that the coatings were enriched with Sc, V, Cr, Co, Ni, Cu, Zn, Ba, especially with respect to Co, Ni. The findings of the present study provide an insight in the microscale features of ferromanganese coatings and the Fe-Mn biogeochemical cycling during the degradation of buried organic matter in intertidal zones or shallow coasts.

Fossilized iron bacteria reveal a pathway to the biological origin of banded iron formation.

Debates on the formation of banded iron formations in ancient ferruginous oceans are dominated by a dichotomy between abiotic and biotic iron cycling. This is fuelled by difficulties in unravelling the exact processes involved in their formation. Here we provide fossil environmental evidence for anoxygenic photoferrotrophic deposition of analogue banded iron rocks in shallow marine waters associated with an Early Quaternary hydrothermal vent field on Milos Island, Greece. Trace metal, major and rare earth elemental compositions suggest that the deposited rocks closely resemble banded iron formations of Precambrian origin. Well-preserved microbial fossils in combination with chemical data imply that band formation was linked to periodic massive encrustation of anoxygenic phototrophic biofilms by iron oxyhydroxide alternating with abiotic silica precipitation. The data implicate cyclic anoxygenic photoferrotrophy and their fossilization mechanisms in the construction of microskeletal fabrics that result in the formation of characteristic banded iron formation bands of varying silica and iron oxide ratios.

Enrichment of sulfate-reducing bacteria and resulting mineral formation in media mimicking pore water metal ion concentrations and pH conditions of acidic pit lakes.

Acid mine drainage sites are extreme environments with high acidity and metal ion concentrations. Under anoxic conditions, microbial sulfate reduction may trigger the formation of secondary minerals as a result of H2S production and pH increase. This process was studied in batch experiments with enrichment cultures from acidic sediments of a pit lake using growth media set at different pH values and containing elevated concentrations of Fe²âº and Al³âº. At initial pH values of 5 and 6, sulfate reduction occurred shortly after inoculation. Sulfate- reducing bacteria affiliated to the genus Desulfosporosinus predominated the microbial communities as shown by 16S rRNA gene analysis performed at the end of the incubation. At initial pH values of 3 and 4, sulfate reduction and cell growth occurred only after an extended lag phase, however, at a higher rate than in the less acidic assays. At the end of the growth phase, enrichments were dominated by Thermodesulfobium spp. suggesting that these sulfate reducers were better adapted to acidic conditions. Iron sulfides in the bulk phase were common in all assays, but specific aluminum precipitates formed in close association with cell surfaces and may function as a detoxification mechanism of dissolved Al species at low pH.

Prevalence of anaerobic ammonium-oxidizing bacteria in contaminated groundwater.

Anaerobic ammonium-oxidizing (anammox) bacteria perform an important step in the global nitrogen cycle: anaerobic oxidation of ammonium and reduction of nitrite to form dinitrogen gas (N(2)). Anammox organisms appear to be widely distributed in natural and artificial environments. However, their roles in groundwater ammonium attenuation remain unclear and only limited biomarker-based data confirmed their presence prior to this study. We used complementary molecular and isotope-based methods to assess anammox diversity and activity occurring at three ammonium-contaminated groundwater sites: quantitative PCR, denaturing gradient gel electrophoresis, sequencing of 16S rRNA genes, and (15)N-tracer incubations. Here we show that anammox performing organisms were abundant bacterial community members. Although all sites were dominated by Candidatus Brocadia-like sequences, the community at one site was particularly diverse, possessing four of five known genera of anammox bacteria. Isotope data showed that anammox produced up to 18 and 36% of N(2) at these sites. By combining molecular and isotopic results we have demonstrated the diversity, abundance, and activity of these autotrophic bacteria. Our results provide strong evidence for their important biogeochemical role in attenuating groundwater ammonium contamination.

Biogeochemical factors influencing net mercury methylation in contaminated freshwater sediments from the St. Lawrence River in Cornwall, Ontario, Canada.

The activity of various anaerobic microbes, including sulfate reducers (SRB), iron reducers (FeRP) and methanogens (MPA) has been linked to mercury methylation in aquatic systems, although the relative importance of each microbial group in the overall process is poorly understood in natural sediments. The present study focused on the biogeochemical factors (i.e. the relative importance of various groups of anaerobic microbes (FeRP, SRB, and MPA) that affect net monomethylmercury (MMHg) formation in contaminated sediments of the St. Lawrence River (SRL) near Cornwall (Zone 1), Ontario, Canada. Methylation and demethylation potentials were measured separately by using isotope-enriched mercury species ((200)Hg(2+) and MM(199)Hg(+)) in sediment microcosms treated with specific microbial inhibitors. Sediments were sampled and incubated in the dark at room temperature in an anaerobic chamber for 96h. The potential methylation rate constants (K(m)) and demethylation rates (K(d)) were found to differ significantly between microcosms. The MPA-inhibited microcosm had the highest potential methylation rate constant (0.016d(-1)), whereas the two SRB-inhibited microcosms had comparable potential methylation rate constants (0.003d(-1) and 0.002d(-1), respectively). The inhibition of methanogens stimulated net methylation by inhibiting demethylationand by stimulating methylation along with SRB activity. The inhibition of both methanogens and SRB was found to enhance the iron reduction rates but did not completely stop MMHg production. The strong positive correlation between K(m) and Sulfate Reduction Rates (SRR) and between K(d) and Methane Production Rates (MPR) supports the involvement of SRB in Hg methylation and MPA in MMHg demethylation in the sediments. In contrast, the strong negative correlation between K(d) and Iron Reduction Rates (FeRR) shows that the increase in FeRR corresponds to a decrease in demethylation, indicating that iron reduction may influence net methylation in the SLR sediments by decreasing demethylation rather than favouring methylation.

Simplified sample preparation procedure for measuring isotope-enriched methylmercury by gas chromatography and inductively coupled plasma mass spectrometry.

Many procedures have been developed to measure the concentration of monomethylmercury (MeHg) from different sample matrices, and the use of stable isotopes of mercury now provides opportunities to determine its formation and degradation rates. Here, a modified procedure for measuring mercury isotopes in sediment samples that uses acid leaching-ion exchange-thiosulfate extraction (TSE) to isolate and purify the methylated mercury from the matrix is proposed. The latter is followed by aqueous-phase ethylation, purge and trap on Tenax, gas chromatography separation of ethylated mercury compounds, and inductively coupled plasma mass spectrometry detection. The new TSE procedure bridges together two well-known methods, the acid-leaching and distillation-derivatization procedures, offering the advantages of artifact-free formation of the first, and low detection limits and the possibility of quantification of individual isotopes of mercury of the second. The modified procedure retains the derivatization, purge and trap, and gas chromatography and inductively coupled plasma mass spectrometry (GC-ICP-MS) detection steps from the distillation-derivatization procedure, and eliminates the distillation step, which is not only laborious but also expensive, due to the high cost of installation and time-consuming cleaning process. Major advantages of the TSE procedure proposed include the extraction and analysis of a large number of samples in a short time, excellent analyte recoveries, and the lack of artifact formation. Sediment certified reference materials (CRMs), BCR 580 and IAEA 405, were used to test the TSE procedure accuracy. Recoveries between 94 to 106% and 95 to 96% were obtained for CRMs and spiked samples (Milli-Q(R) water), respectively. Comparisons among thiosulfate extraction, distillation, and acid-leaching procedures have shown good agreement of methylmercury values.

Microbial diversity in endostromatolites (cf. Fissure Calcretes) and in the surrounding permafrost landscape, Haughton impact structure region, Devon Island, Canada.

In recent years, endostromatolites, which consist of finely laminated calcite columns that grow orthogonally within millimeter- to centimeter-thick fissures in limestone bedrock outcrops, have been discovered in dolomitic outcrops in the Haughton impact structure region, Devon Island, Canada. The growth mechanism of the endostromatolites is believed to be very slow and possibly intertwined with biotic and abiotic processes. Therefore, to discern how endostromatolites form in this polar desert environment, the composition of the microbial community of endostromatolites was determined by means of molecular phylogenetic analysis and compared to the microbial communities found in the surrounding soils. The microbial community present within endostromatolites can be inferred to be (given the predominant metabolic traits of related organisms) mostly aerobic and chemoheterotrophic, and belongs in large part to the phylum Actinobacteria and the subphylum Alphaproteobacteria. The identification of these bacteria suggests that the conditions within the fissure were mostly oxidizing during the growth of endostromatolite. The DNA sequences also indicate that a number of bacteria that closely resemble Rubrobacter radiotolerans are abundant in the endostromatolites as well as other Actinobacteria and Alphaproteobacteria. Some of these taxa have been associated with calcite precipitation, which suggests that the endostromatolites might in fact be microbially mediated. Bacterial communities from nearby permanently frozen soils were more diverse and harbored all the phyla found in the endostromatolites with additional taxa. This study on the microbial communities preserved in potentially microbially mediated secondary minerals in the Arctic could help in the search for evidence of life-forms near the edge of habitability on other planetary bodies.

Sorption of strontium onto bacteriogenic iron oxides.

Bacteriogenic iron oxides (BIOS) were obtained from a dilute, circumneutral groundwater seep, characterized with respect to mineralogy, and examined for their ability to sorb aqueous Sr2+. BIOS were composed of microbial sheaths encrusted in 2-line ferrihydrite. Sorption experiments indicated that Sr remained completely unbound at pH < 4.5, but sorption increased with increasing pH (maximum of 95% at pH > 7.6). EXAFS analysis of Sr-loaded BIOS failed to elucidate whether Sr sorption occurred on sites specific to the mineral or microbial fraction, but indicated that sorption likely occurred by outer-sphere complexation between BIOS and hydrated Sr2+. Sorption experiments showed that at low ionic strength (I = 0.001 M), sorption followed a Langmuir isotherm (S(max) = 3.41 mol Sr (g of Fe)(1-), K(ads) = 1.26). At higher ionic strength (I = 0.1 M), there was significant inhibition of Sr sorption (S(max) = 1.06 mol Sr (g of Fe)(1-), K(ads) = 1.23), suggesting that sorption to BIOS occurs by outer-sphere complexation. The results suggest that, under dilute circumneutral conditions, BIOS deposits should efficiently sorb dissolved Sr from groundwater flow systems where such deposits exist. This finding has particular relevance to sites impacted by radioactive 90Sr groundwater contamination.

Identification of sulfate-reducing bacteria in methylmercury-contaminated mine tailings by analysis of SSU rRNA genes.

Sulfate-reducing bacteria (SRB) are often used in bioremediation of acid mine drainage because microbial sulfate reduction increases pH and produces sulfide that binds with metals. Mercury methylation has also been linked with sulfate reduction. Previous geochemical analysis indicated the occurrence of sulfate reduction in mine tailings, but no molecular characterization of the mine tailings-associated microbial community has determined which SRB are present. This study characterizes the bacterial communities of two geochemically contrasting, high-methylmercury mine tailing environments, with emphasis on SRB, by analyzing small subunit (SSU) rRNA genes present in the tailings sediments and in enrichment cultures inoculated with tailings. Novel Deltaproteobacteria and Firmicutes-related sequences were detected in both the pH-neutral gold mine tailings and the acidic high-sulfide base-metal tailings. At the subphylum level, the SRB communities differed between sites, suggesting that the community structure was dependent on local geochemistry. Clones obtained from the gold tailings and enrichment cultures were more similar to previously cultured isolates whereas clones from acidic tailings were more closely related to uncultured lineages identified from other acidic sediments worldwide. This study provides new insights into the novelty and diversity of bacteria colonizing mine tailings, and identifies specific organisms that warrant further investigation with regard to their roles in mercury methylation and sulfur cycling in these environments.

Hg(II) adsorption by bacteria: a surface complexation model and its application to shallow acidic lakes and wetlands in Kejimkujik National Park, Nova Scotia, Canada.

The fate and environmental threat posed by mercury in aquatic systems is controlled, in part, bythe transport of Hg(II) from oxic to anoxic zones in lakes and its subsequent transformation to organic mercury. The transport of Hg(II) in aquatic systems can be affected by its partitioning between the dissolved and particulate phases. In this study, batch experiments were performed to quantify Hg(II) adsorption to Bacillus subtilis as bacteria-to-metal ratio, pH, chloride concentration, growth phase, and reaction time were independently varied. The laboratory data were well described by a surface complexation model (SCM) considering the adsorption of neutral Hg(II) hydroxide and chloride complexes by specific functional groups on the bacterial surface. To evaluate its applicability to complex aquatic systems, the SCM was used to predict the distributions of Hg(II) in 36 shallow acidic lakes and wetlands in Kejimkujik National Park, Nova Scotia, Canada. The lab-derived SCM provided a statistically accurate (r2 = 0.615, P < 0.01) fit to the field data when it was expanded to consider Hg(II) complexation by dissolved organic matter. Inclusion of Hg(II)-mineral adsorption reactions did not improve the fit of the model. The quality of fit provided by the expanded SCM suggested that the major assumptions implicit in applying a lab-derived model to the field were justifiable. Our study has demonstrated that SCMs are powerful tools for dynamic prediction of the sorption of environmental contaminants to biocolloids at the regional scale.