Indicators of Microbial Sulfate Reduction in Acidic Sulfide-Rich Mine Tailings

Sulfate-reducing bacteria (SRB) are thought to be actively involved in the cycling of sulfur in acidic mine tailings. However, most studies have used circumstantial evidence to assess microbial sulfate activity in such environments. In order to fully ascertain the role of sulfate-reducing bacteria (SRB) in sulfur cycling in acidic mine tailings, we measured sulfate reduction rates, sulfur isotopic composition of reduced sulfide fractions, porewaters and solid-phase geochemistry and SRB populations in four different Cu-Zn tailings located in Timmins, Ontario, Canada. The tailings were sampled in the summer and in the spring, shortly after snowmelt. The results first indicate that all four sites showed very high sulfate reduction rates in the summer (～100–1000 nmol cm^{? 3}d^?1), which corresponded to the presence of sulfide in the porewaters and to high SRB populations. In some of the sites, zones of microbial sulfate reduction also corresponded to a decline of organic carbon and to an apparent pyrite (with slightly negative δ³⁴S values) enrichment around the same depth. Microbial sulfate reduction was also important in permanently acidic (pH 2–3) mine tailings sites, suggesting that SRB can be active under very acidic conditions. Secondly, the results showed that microbial sulfate reduction was greatly reduced in the spring, suggesting that temperature might be a key factor in the activity of SRB. However, a closer look at the results indicated that temperature was not the sole factor and that acidic conditions and limited substrate availability in the spring appeared to be important as well in limiting microbial sulfate par reduction in sulfidic mine tailings. Finally, the results indicate that sulfur undergoes rapid cycling throughout the year and that microbial sulfate reduction and metal sulfide precipitation do not appear to be a permanent sink for metals.     

Competition and coexistence of sulfate-reducing bacteria,acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio

The microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. The population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. At the influent lactate to sulfate molar ratio of 0.35 mol mol⁻¹, i.e., electron donor limitation, lactate oxidation was mainly carried out by incompletely oxidizing sulfate-reducing bacteria, which formed 80–85% of the total bacterial population. Desulfomicrobium- and Desulfovibrio-like species were the most abundant sulfate-reducing bacteria. Acetogens and methanogenic Archaea were mostly outcompeted, although less than 2% of an acetogenic population could still be observed at this limiting concentration of lactate. In the near absence of sulfate (i.e., at very high lactate/sulfate ratio), acetogens and methanogenic Archaea were the dominant microbial communities. Acetogenic bacteria represented by Dendrosporobacter quercicolus-like species formed more than 70% of the population, while methanogenic bacteria related to uncultured Archaea comprising about 10–15% of the microbial community. At an influent lactate to sulfate molar ratio of 2 mol mol⁻¹, i.e., under sulfate-limiting conditions, a different metabolic route was followed by the mixed anaerobic community. Apparently, lactate was fermented to acetate and propionate, while the majority of sulfidogenesis and methanogenesis were dependent on these fermentation products. This was consistent with the presence of significant levels (40–45% of total bacteria) of D. quercicolus-like heteroacetogens and a corresponding increase of propionate-oxidizing Desulfobulbus-like sulfate-reducing bacteria (20% of the total bacteria). Methanogenic Archaea accounted for 10% of the total microbial community.     

Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H2S production

Nitrate injection into oil fields is an alternative to biocide addition for controlling sulfide production (‘souring’) caused by sulfate-reducing bacteria (SRB). This study examined the suitability of several cultivation-dependent and cultivation-independent methods to assess potential microbial activities (sulfidogenesis and nitrate reduction) and the impact of nitrate amendment on oil field microbiota. Microcosms containing produced waters from two Western Canadian oil fields exhibited sulfidogenesis that was inhibited by nitrate amendment. Most probable number (MPN) and fluorescent in situ hybridization (FISH) analyses of uncultivated produced waters showed low cell numbers (≤10³ MPN/ml) dominated by SRB (>95% relative abundance). MPN analysis also detected nitrate-reducing sulfide-oxidizing bacteria (NRSOB) and heterotrophic nitrate-reducing bacteria (HNRB) at numbers too low to be detected by FISH or denaturing gradient gel electrophoresis (DGGE). In microcosms containing produced water fortified with sulfate, near-stoichiometric concentrations of sulfide were produced. FISH analyses of the microcosms after 55 days of incubation revealed that Gammaproteobacteria increased from undetectable levels to 5–20% abundance, resulting in a decreased proportion of Deltaproteobacteria (50–60% abundance). DGGE analysis confirmed the presence of Delta- and Gammaproteobacteria and also detected Bacteroidetes. When sulfate-fortified produced waters were amended with nitrate, sulfidogenesis was inhibited and Deltaproteobacteria decreased to levels undetectable by FISH, with a concomitant increase in Gammaproteobacteria from below detection to 50–60% abundance. DGGE analysis of these microcosms yielded sequences of Gamma- and Epsilonproteobacteria related to presumptive HNRB and NRSOB (Halomonas, Marinobacterium, Marinobacter, Pseudomonas and Arcobacter), thus supporting chemical data indicating that nitrate-reducing bacteria out-compete SRB when nitrate is added.     

Pyrite formation in marshes during early diagenesis

Pyrite was removed from peat cores by draining the sediments and allowing the pyrite to oxidize. Then the peat cores were placed back into intertidal salt marsh sediments to incubate. Pyrite accumulated rapidly in peat incubated in situ. A greater accumulation of pyrite was observed in peat that contained living grass than peat in which the grass had been killed.

Resin‐imbedded samples of peat from nearby sediments showed that small single crystals of pyrite were abundant, supporting the idea that pyrite in marshes forms rapidly through direct precipitation. Pyrite was also observed filling vascular channels in roots. It had been proposed that pyrite fills root channels in freshwater environments where the primary sulfur source used by sulfate‐reducing bacteria is organic sulfur rather than sulfate. The widespread occurrence of pyrite filling vascular channels in salt marsh peat makes it unlikely that pyrite morphology can be used to infer the salinity of the overlying water.

Marsh sediments are characterized by higher carbon/sulfur ratios and pyritization (Fe‐pyritel(Fe‐pyrite + Fe‐HCl)) indices than marine subtidal sediments. Within wide ranges these indices do not seem to be very sensitive to salinity of flooding water or carbon concentrations in sediments. Oxidation and iron availability appear to be the major controls on pyrite accumulation in marshes. While pyrite concentrations in submerged sediments can be used as indicators of relative rates of sulfate reduction, sulfur storage in intertidal marsh sediments is not as tightly linked to this microbial process.     

Sulfidogenesis in Low pH (3.8–4.2) Media by a Mixed Population of Acidophilic Bacteria

A defined mixed bacterial culture was established which catalyzed dissimilatory sulfate reduction, using glycerol as electron donor, at pH 3.8–4.2. The bacterial consortium comprised a endospore-forming sulfate reducing bacterium (isolate M1) that had been isolated from acidic sediment in a geothermal area of Montserrat (West Indies) and which had 94% sequence identity (of its 16S rRNA gene) to the Gram-positive neutrophile Desulfosporosinus orientis, and a Gram-negative (non sulfate-reducing) acidophile (isolate PFBC) that shared 99% gene identity with Acidocella aromatica. Whilst M1 was an obligate anaerobe, isolate PFBC, as other Acidocella spp., only grew in pure culture in aerobic media. Analysis of microbial communities, using a combination of total bacterial counts and fluorescent in situ hybridization, confirmed that concurrent growth of both bacteria occurred during sulfidogenesis under strictly anoxic conditions in a pH-controlled fermenter. In pure culture, M1 oxidized glycerol incompletely, producing stoichiometric amounts of acetic acid. In mixed culture with PFBC, however, acetic acid was present only in small concentrations and its occurrence was transient. Since M1 did not oxidize acetic acid, it was inferred that this metabolite was catabolized by Acidocella PFBC which, unlike glycerol, was shown to support the growth of this acidophile under aerobic conditions. In fermenter cultures maintained at pH 3.8–4.2, sulfidogenesis resulted in the removal of soluble zinc (as solid phase ZnS) whilst ferrous iron remained in solution. Potential syntrophic interactions, involving hydrogen transfer between M1 and PFBC, are discussed, as is the potential of sulfidogenesis in acidic liquors for the selective recovery of heavy metals from wastewaters.     

Establishment of a Vegetation Cover on Tundra Kimberlite Mine Tailings: 1. A Greenhouse Study

High erosion potential of dewatered kimberlite mine tailings after diamond extraction has prompted research at the Ekati Diamond Mine in the Canadian subarctic heath tundra ecosystem. Coarse texture, no organic component, lack of available macronutrients, and a serpentine chemistry are the principal limitations of these kimberlite tailings to plant colonization. Structure‐improving (peat moss, lake sediment, sewage sludge, Agri‐Boost, and composted papermill sludge) and nutrient‐providing (fertilizer, calcium carbonate, gypsum, and rock phosphate) amendments were tested in the greenhouse to ameliorate these limitations, thereby facilitating the field establishment of a permanent vegetation cover, which would stabilize the surface materials and promote natural colonization by the surrounding tundra vegetation. Seven native grass species (Arctagrostis latifolia, Calamagrostis canadensis, Poa glauca, Poa alpina, Deschampsia beringensis, Deschampsia caespitosa, and Festuca rubra) were used to measure amendment success. With the addition of structure‐improving and nutrient‐providing amendments, plant growth on kimberlite tailings was significantly enhanced. Tailings properties, including cation exchange capacity, percentage of organic carbon, and macronutrient availability, were also improved by amendment addition.     

Spatiotemporal variations in the abundances of the prokaryotic rRNA genes, <Emphasis Type="Italic">pmoA</Emphasis>, and <Emphasis Type="Italic">mcrA</Emphasis> in the deep layers of a peat bog in Sarobetsu-genya wetland,Japan

Spatiotemporal variations in microbial gene abundances were investigated to identify potential zones of methanotroph and methanogen biomass in a peat bog in Sarobetsu-genya wetland. The abundances of the bacterial and archaeal 16S rRNA genes, pmoA, and mcrA were 10⁷–10⁹, 10⁷–10⁸, 10⁴–10⁶, and 10⁴–10⁷ copies g⁻¹ dry peat, respectively. Correlation analysis based on microbial gene abundances and environmental factors showed that the spatiotemporal distributions of the abundances of the four microbial genes in peat layers were similar. The mcrA abundance showed a significant negative correlation with the dissolved organic carbon content and a significant positive correlation with the peat temperature. The pmoA abundance was not detectable during the spring thaw when the lowest peat temperature at a depth of 50 cm was recorded. At a depth of 200 cm, the peat temperature exceeded 6°C throughout the year, and the mcrA abundance exceeded 10⁴ copies g⁻¹ dry peat. These results indicate that the seasonal microbial activity related to methane should be evaluated in not only the shallow but also the deep peat layers in order to elucidate the methane dynamics in boreal wetlands.     

Abundance and Activity of 16S rRNA,AmoA and NifH Bacterial Genes During Assisted Phytostabilization of Mine Tailings

Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings.     

Aerobic Organic Carbon Mineralization by Sulfate-Reducing Bacteria in the Oxygen-Saturated Photic Zone of a Hypersaline Microbial Mat

The sulfate-reducing bacterium strain SRB D2 isolated from the photic zone of a hypersaline microbial mat, from Lake Chiprana, NE Spain, respired pyruvate, alanine, and α-ketoglutarate but not formate, lactate, malate, succinate, and serine at significant rates under fully oxic conditions. Dehydrogenase enzymes of only the former substrates are likely oxygen-tolerant as all substrates supported anaerobic sulfate reduction. No indications were found, however, that aerobic respiration supported growth. Although strain SRB D2 appeared phylogenetically closely related to the oxygen-tolerant sulfate-reducing bacterium Desulfovibrio oxyclinae, substrate spectra were markedly different. Most-probable-number (MPN) estimates of sulfate-reducing bacteria and aerobic heterotrophic bacteria indicated that the latter were numerically dominant in both the photic and aphotic zones of the mat. Moreover, substrate spectra of representative isolates showed that the aerobic heterotrophic bacteria are metabolically more diverse. These findings indicate that sulfate-reducing bacteria in the fully oxic photic zone of mats have to compete with aerobic heterotrophic bacteria for organic substrates. Porewater analysis revealed that total carbohydrates and low-molecular-weight carbon compounds (LMWC) made up substantial fractions of the total dissolved organic carbon (DOC) pool and that nighttime degradation of the former was concomitant with increased concentration of the latter. Our findings indicate that aerobic respiration by sulfate-reducing bacteria contributes to organic carbon mineralization in the oxic zone of microbial mats as daytime porewater LMWC concentrations are above typical half-saturation constants.     

施磷对干旱胁迫下箭竹根际土壤养分及微生物群落的影响

以箭竹及其根际土壤作为研究对象,采用两因素随机区组实验,设置2种水分处理（正常浇水和干旱胁迫）和2种施磷量处理（施磷和不施磷）,探究施磷对干旱胁迫下箭竹根际土壤养分及微生物群落结构和多样性的影响。结果表明：（1）干旱胁迫显著降低了箭竹根际土壤中微生物量碳、可溶性有机氮和有效磷的含量,虽对箭竹根际土壤微生物群落的多样性无显著影响,但显著降低了箭竹根际土壤中总PLFA（phospholipid fatty acid contents）的含量和真菌、细菌、革兰氏阳性菌与革兰氏阴性菌的PLFA含量以及革兰氏阳性菌/革兰氏阴性菌的PLFA比值,显著改变了箭竹根际土壤微生物群落结构,结果显著降低了箭竹的生物量。（2）施磷显著增加了受旱箭竹根际土壤中微生物量碳和有效磷的含量,虽大体上对受旱箭竹根际土壤微生物群落的多样性无显著影响,但显著增加了受旱箭竹根际土壤中总PLFA和真菌PLFA的含量,并在一定程度上增加了细菌、革兰氏阳性菌、革兰氏阴性菌和放线菌的PLFA含量以及革兰氏阳性菌/革兰氏阴性菌和真菌/细菌的PLFA比值,也在一定程度上改善了受旱箭竹根际土壤微生物群落结构,从而改善受旱箭竹的生长。（3）主成分分析表明,干旱对箭竹根际土壤微生物群落结构的影响显著,而施磷的影响不明显。（4）相关分析发现,箭竹根际土壤微生物群落结构与箭竹根际土壤微生物量碳、可溶性有机氮及箭竹生物量呈显著正相关。综上,干旱降低了箭竹根际土壤养分含量和微生物生物量,改变了箭竹根际土壤微生物群落结构,抑制了箭竹的生长;施磷能增加受旱箭竹根际土壤养分含量和微生物生物量,改善受旱箭竹根际土壤微生物群落结构,进而改善受旱箭竹的生长。     

Evaluation of small organic acids present in fast pyrolysis bio‐oil from lignocellulose as feedstocks for bacterial bioconversion

Small organic acids derived from fast pyrolysis of lignocellulosic biomass represent a significant proportion of microbially accessible carbon in bio‐oil. However, using bio‐oil for microbial cultivation is a highly challenging task due to its strong adverse effects on microbial growth as well as its complex composition. In this study, the main small organic acids present in bio‐oil as acetate, formate and propionate were evaluated with respect to their suitability as feedstocks for bacterial growth. For this purpose, the growth behavior of four biotechnological production hosts—Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Corynebacterium glutamicum—was quantified and compared. The bacteria were cultivated on single acids and mixtures of acids in different concentrations and evaluated using common biotechnological efficiency parameters. In addition, cultivation experiments on pretreated fast pyrolysis‐derived bio‐oil fractions were performed with respect to the suitability of the bacterial strains to tolerate inhibitory substances. Results suggest that both P. putida and C. glutamicum metabolize acetate—the major small organic acid generated during fast pyrolysis of lignocellulosic biomass—as sole carbon source over a wide concentration range, are able to grow on mixtures of small organic acids present in bio‐oil and can, to a limited extent, tolerate the highly toxic inhibitory substances within bio‐oil. This work provides an important step in search of suitable bacterial strains for bioconversion of lignocellulosic‐based feedstocks and thus contributes to establishing efficient bioprocesses within a future bioeconomy.     

Leaf litter decomposition in a tropical peat swamp forest in Peninsular Malaysia

It has long been assumed that the peat underlying tropical peat swamp forests accumulates because the extreme conditions (water logged, nutrient poor, anaerobic and acidic—pH 2.9–3.5) impede microbial activity. Litterbag studies in a tropical Malaysian peat swamp (North Selangor peat swamp forest) showed that although the sclerophyllous, toxic leaves of endemic peat forest plants (Macaranga pruinosa, Campnosperma coriaceum, Pandanus atrocarpus, Stenochlaena palustris) were barely decomposed by bacteria and fungi (decay rates of only 0.0006–0.0016 k day⁻¹), leaves of M. tanarius, a secondary forest species were almost completely decomposed (decay rates of 0.0047–0.005 k day⁻¹) after 1 year. Thus it is intrinsic properties of the leaves (that are adaptations to deter herbivory in the nutrient poor environment) that impede microbial breakdown. The water of the peat swamp was very high in dissolved organic carbon (70–84 mg l⁻¹ DOC). Laboratory studies revealed initial rapid leaching of DOC from leaves (up to 1,720 mg l⁻¹ from 4 g of leaves in 7 days), but the DOC levels then fell rapidly. The leaching of DOC resulted in weight loss but the physical structure of the leaves remained intact. It is suggested that the DOC is used as a substrate for microbial growth hence lowering the concentration of DOC in the water and transferring energy from the leaves to other trophic levels. This would explain how nutrient poor tropical peatswamps support diverse, abundant flora and fauna despite low nutrient levels and lack of rapid litter cycling such as occurs in other types of tropical rainforests.     

Injection of hydrogen gas stimulates acid mine drainage treatment in laboratory‐scale hydroponic root mats

The environmentally benign disposal of acid mine drainage (AMD) is still a technical challenge. In the present study, artificial AMD was treated in a laboratory‐scale floating hydroponic root mat of soft rush, Juncus effusus. This ecotechnological system was operated with hydrogen injection and water recirculation but without an external carbon supply. It achieved a mean increase of ΔpH = 3.3 up to pH ≈ 8.2, high sulfate removal of up to 87%, and efficient removal of iron (100%), aluminum (99.8%), manganese (97.4%), and zinc (99.6%). Sulfide was not detected in the outflow. Treatment performance correlated with the amount of hydrogen loading. Daily oscillations of the redox potential up to amplitudes of ΔE_h ≈ 450 mV in a mean range of E_h ≈ ?150 to +300 mV indicated a correlation of plant physiology and removal processes. Apparently, sulfate and metal removal were the result of chemolithotrophic microbial sulfate reduction supported by the externally provided H₂ and chemoorganotrophic sulfate reduction driven by rhizodeposits. Bicarbonate generated in the microbial transformation of such plant‐derived organic carbon contributed to pH neutralization. The effluent's pH increase was governed further by recirculation of the treated AMD. The flow regime and the injection of hydrogen at the ground of the root mat caused concentration gradients where the most efficient removal occurred in the deepest zone of the root mat. Further investigations should target long‐term stability, plant growth dynamics, load variations, balances of carbon and sulfur, the removal of H₂S and metal precipitates from the system as well as efficient hydrogen supply.     

Factors Affecting Methylmercury Levels in Surficial Tailings from Historical Nova Scotia Gold Mines

Large quantities of Hg remain in tailings dumps from historical Nova Scotian gold mines. Depth profiles of total Hg (Hg_T) and methylmercury (MeHg) were compared with geochemical and microbiological variables, to identify factors influencing MeHg levels in tailings. Hg_T and MeHg were highly variable in tailings (0.2–73.5 μ mol kg^{? 1} and < dl-56.4 nmol kg^{? 1}, respectively), and were influenced by a complex set of in situ factors. Elevated MeHg was linked with > 5 μ mol kg^?1 Hg_T, organic matter, hydrology, abundance and activity of sulfate reducing bacteria, and demethylation processes. Methylmercury levels in tailings from a wet, bog-like site appeared to undergo seasonal fluctuations, with higher concentrations measured in September and October, and lower concentrations in May. Evaluations of amalgamation tailings should examine MeHg and Hg_T transport out of low-lying, saturated tailings dumps after snowmelt and major rainfall events, and should take into account the possibility of seasonal variation in MeHg levels in northern regions.     

A Novel Community of Acidophiles in an Acid Mine Drainage Sediment

A sediment sample (pH 2.5) was collected at an acid mine drainage site in Anhui, China. The present acidophilic microbial community in the sediment was studied with a 16S rRNA gene clone library. Small-subunit rRNA genes were PCR amplified, cloned and screened by amplified rDNA restriction analysis (ARDRA). Subsequently, 10 different clones were identified and they were affiliated with Acidobacteria, β/γ-Proteobacteria, δ-Proteobacteria, Nitrospira, Candidate division TM7, and Low G + C Gram-positives. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity of acidophiles in the sediment that were mostly novel. Unexpectedly, 16S rRNA gene sequences affiliated with δ-Proteobacteria were found to constitute more than 60% of clone library. To our knowledge, this is the first occasion that bacteria of δ-Proteobacteria have been found dominant in the acidic habitat. Anaerobic sulfate- or metal reduction is the predominant physiological trait of bacteria of this subdivision. The high sulfate, ferric iron and the presence of bioavailable carbon in the anaerobic microenvironment may result in the dominance of bacteria of δ-Proteobacteria.     

Arbuscular Mycorrhizal Fungi (AMF) and Biosolids Enhance the Growth of a Native Australian Grass on Sulphidic Gold Mine Tailings

We tested the effect of the addition of biosolids combined with a native mycorrhizal inoculum (Arbuscular Mycorrhizal Fungi [AMF]) on growth of a native Australian grass, and on trace element stabilization of sulphidic gold mine tailings. A glasshouse trial was established on four substrates: tailings (T); tailings with a layer of 5 cm topsoil (TS); tailings amended with 100 dry t ha^?1 biosolids (LB), and tailings amended with 500 dry t ha^?1 biosolids (HB). Pots of 1.2 L of capacity were established; some were inoculated with a mixture of Glomus sp. (WUM51–9227), Scutelospora aurigloba (WUM51–53), and Acaulospora levis (WUM46) culture mix, and others were uninoculated controls. Seeds of the native Australian grass, Bothriochloa macra were sown in the pots. Root infection, plant biomass production, nutrients and trace element concentrations in shoots were investigated. Addition of biosolids significantly increased AMF infection of roots compared to unamended substrates. No clear qualitative differences in colonization were detected. Addition of biosolids and AMF together clearly improved the establishment and growth of the native grass. Similar trends in nutritional status were shown for biosolids and inoculation with AMF treatments. Mycorrhizal inoculation increased plant biomass production and the effectiveness of nutrient uptake. The combined use of biosolids and mycorrhizal inoculation could be a reliable method for phytostabilization purposes in polluted substrates.     

Insights into the Phylogeny and Metabolic Potential of a Primary Tropical Peat Swamp Forest Microbial Community by Metagenomic Analysis

A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.     

Concepts of sulfur,carbon, and nitrogen transformations in soil: evaluation by simulation modeling

The dynamics of sulfur immobilization and mineralization in soil were simulated to test hypotheses about their regulation by the availability of carbon and nitrogen. The concept of chemical bond classes was incorporated into the model to account for variation in composition of carbon, nitrogen, and sulfur compounds. Microbial biomass was differentiated into bacteria and fungi, and the element ratios of both groups were assumed to vary. Organic residues were divided between dead microbes plus microbial products, and the more labile fraction of stabilized soil organic matter. Concepts and hypotheses in the model were tested by applying it to data on microbial biomass, sulfate, nitrate, and CO₂ evolution obtained in laboratory incubations of two soils amended with sulfate and cellulose. An important mechanism of regulation tested in the model was the stimulation of sulfohydrolase enzyme production depending on sulfur stress in microbial biomass. The hypothesis that excess sulfate is stored as ester sulfate was supported by model dynamics.     

Accelerated microbial organic matter mineralization following salt-water intrusion into tidal freshwater marsh soils

The impact of salt-water intrusion on microbial organic carbon (C) mineralization in tidal freshwater marsh (TFM) soils was investigated in a year-long laboratory experiment in which intact soils were exposed to a simulated tidal cycle of freshwater or dilute salt-water. Gas fluxes [carbon dioxide (CO₂) and methane (CH₄)], rates of microbial processes (sulfate reduction and methanogenesis), and porewater and solid phase biogeochemistry were measured throughout the experiment. Flux rates of CO₂ and, surprisingly, CH₄ increased significantly following salt-water intrusion, and remained elevated relative to freshwater cores for 6 and 5 months, respectively. Following salt-water intrusion, rates of sulfate reduction increased significantly and remained higher than rates in the freshwater controls throughout the experiment. Rates of acetoclastic methanogenesis were higher than rates of hydrogenotrophic methanogenesis, but the rates did not differ by salinity treatment. Soil organic C content decreased significantly in soils experiencing salt-water intrusion. Estimates of total organic C mineralized in freshwater and salt-water amended soils over the 1-year experiment using gas flux measurements (18.2 and 24.9 mol C m^?2, respectively) were similar to estimates obtained from microbial rates (37.8 and 56.2 mol C m^?2, respectively), and to losses in soil organic C content (0 and 44.1 mol C m^?2, respectively). These findings indicate that salt-water intrusion stimulates microbial decomposition, accelerates the loss of organic C from TFM soils, and may put TFMs at risk of permanent inundation.