Microbial mats are synergistic microbial consortia through which major elements, including sulfur, are cycled due to microbial and geological processes. Depth profiles of pH, O2, sulfide, exopolymeric substances (EPS), and the rate of sulfate reduction were determined in a Microcoleus -dominated marine microbial mat at the Great Sippewissett salt marsh, Massachusetts. In addition, measurements in spirochete enrichments and Spirochaetae litoralis cultures showed sulfide consumption during which polysulfides, thiosulfate, and presumably sulfate formed. These data suggest that spirochetes can play a role in the cycling of sulfur in these mats. The obligate to facultative anaerobic spirochetes consume sulfide to remove oxygen. Furthermore, spirochetes may enhance preservation of microbial mats within the rock record by degrading EPS and producing low molecular weight organic compounds (LMWOC). Both sulfide oxidation (i.e. oxygen removal) and EPS degradation (i.e. production of LMW organic compounds) stimulate the activity of sulfate-reducing bacteria (SRB), which are responsible for the precipitation of calcium carbonate in most lithifying mats.

Acid mine drainage (AMD) is an acidic, iron-rich leachate that causes the dissolution of metals. It constitutes a worldwide problem of environmental contamination detrimental to aquatic life and water quality. AMD, however, is naturally attenuated at Davis Mine in Rowe, Massachusetts. We hypothesize that sulfate-reducing bacteria (SRB) are attenuating AMD. To elucidate the mechanisms by which SRB attenuate AMD, three research projects were conducted using a suite of molecular and geochemical techniques. First we established biological influence on the attenuation of AMD by comparing the microbial community and geochemical trends of microcosms of two contrasting areas within the site: AMD attenuating (AZ) and AMD generating (GZ) zones. The differences in geochemical trends between these zones were related to differences in microbial community membership. SRB were only detected in microcosms of the AZ, while iron oxidizers were only detected in the GZ. This study indicates that biological activity contributes to the attenuation of AMD and that SRB may have a role. To further describe the role of SRB, we determined the rates of sulfate reduction, the abundance, and membership of SRB in the second project. The sulfate reduction rate was weakly correlated with the abundance of SRB. This indicates that the SRB population may be utilizing another electron acceptor. One such electron acceptor would be iron, which was investigated in the third project. When SRB are inhibited, neither accumulation of reduced iron nor the formation of reduced iron sulfide precipitates occurred. Higher concentration of sulfide produced an increase in reduced iron and pH. Therefore, iron reduction mediated by reaction with biogenic sulfide contributes to the attenuation of AMD. This is the first report of the biological enhancement of iron reduction by acidotolerant SRB. The interdisciplinary research described in this dissertation provides evidence that SRB attenuate AMD through sulfate and iron reduction and a greater understanding of SRB in acidic environments. It also demonstrates how the biogeochemical cycling of sulfur is coupled to the iron cycle. Overall, the ubiquity and metabolic versatility of SRB offers boundless potential and exciting opportunities of study in the fields of bioremediation, geomicrobiology, and microbial ecology.

The reduction of Fe(III) is one of the most significant reactions that takes place as anaerobic conditions develop in soils and sediments. The mechanisms by which Fe(III) is reduced in sediment and by pure cultures was examined in the research. Other than by direct contact between Fe(III) reducing microorganisms and Fe(III) oxide minerals, there are two ways Fe(III) oxide can be reduced. Fe(III) oxide reduction can occur without contact via electron shuttling by an environmental or microbially produced molecule or by chelation of Fe(III) by an environmental or microbially produced molecule. Both the environment and cultures were examined for these phenomena. Humics and humic analogs were found to serve as electron shuttles between Fe(III) oxides and Fe(III) reducing microorganisms in aquifer sediments while, other compounds found to serve as electron shuttles in culture did not function as electron shuttles in soils and sediments. Environments where humus materials are capable of serving as electron shuttles were located. Environments also existed where there were appreciable amounts of soluble Fe(III), indicating that chelators are present in these environments. The Fe(III) reducing microorganism Geobacter metallireducens was found to reduce Fe(III) oxides only via direct contact. The method used previously to assay for reduction of Fe(III) minerals without contact, dialysis tubing, was shown to be invalid. Another method was developed, by which Fe(III) oxides were entrapped in alginate beads. This method together with, cell suspensions, thin layer chromatography and soft agar plates were used to assay for the electron shuttling capacity. Both Geothrix ferrnentans and Shewanella alga strain BrY where found to produce both electron shuttles and Fe(III) chelators, thus eliminating the need for contact between Fe(III) mineral and these Fe(III) reducing microorganisms thus exhibiting methods of Fe(III) reduction different from Geobacter metallireducens.

Sustainability is one of the biggest goals of humankind in the new millennium. An increasing global demand on agricultural products stimulates agricultural expansion in Brazil, especially in the Southwestern Amazon, namely in the Cerrado and Amazon biomes. A better understanding of biogeochemical cycles and their influence on natural and agricultural systems is key to achieve environmental sustainability and improve agricultural efficiency. These biogeochemical cycles are driven by microbes, and the aim of this thesis was to correlate microbial functional group abundances with differences in carbon, nitrogen, and greenhouse gas cycles in response to land use changes in Southwestern Amazon soils. This work was performed at the University of São Paulo, Brazil, and at the University of Massachusetts Amherst, USA, while the candidate was enrolled in Ph.D. programs at both universities. The thesis is composed of five studies. The first study shows that land use change from Cerrado and forest to agriculture (soybean, Glycine max (L. Merrill), in succession with other crops) or pasture (Brachiaria brizantha (Hochst. ex A. Rich.) did not reduce soil microbial diversity but changed microbial structure. The second study, a physico-chemical background for this land use conversion, describes the alteration of C and N stocks, soil chemical parameters, and microbiological parameters such as biomass, biological C stocks, and changes in the abundance of prokaryotes and fungi. In the third and fourth studies microcosm experiments depict how the agricultural change to soybean and Brachiaria alter the original microbial structure found in forest or cerrado. These studies focused on abundances of key biogeochemical genes (amoA, nirK, nirS, norB, nosZ, mcrA, and pmoA) and correlated gene copy abundances with C, N, and GHG measurements. In the fifth study, in situ soil surveys and GHG samplings were used to characterize the changes from forest to pasture (B. brizantha , 25 years) or soybean crop system (for 2 years or 25 years in succession). We found correlations between genes and processes, indicating that gene abundances provide important microbial information for the understanding of the targeted biogeochemical cycles. Land use, rather than plant species, promotes alterations in microbial gene abundances and processes. During the survey period, forest exhibited higher microbial activity, resulting in higher nitrate availability and N2O emissions. These processes were correlated with higher abundances of process related genes. Nitrate and N2O emissions were lower in agricultural and pasture soils. CO2 emission was higher in the two-year-old soybean plot. The forest and two-year-old soybean plots acted as a sink for CH4, while the pasture plots represented a source of it. The results validated the use of gene abundance determination as a valuable tool to better understand C, N, and GHG processes. The genes nirK, nosZ, and 16S rRNA presented the best correlations with the processes. A larger temporal and spatial analysis is needed to infer statements on the processes' dynamics due to land use change. For the first time gene abundance measurements were used to integrate the C, N and GHG cycles, giving insights into land use changes in Southwestern Amazon.

From the time of their discovery in the early 1980's, hyperthermophilic microorganisms have been at the center of intense research to describe their diversity as well as the extreme geologic environments they inhabit. Although much has been learned about the metabolism of a select few pure culture isolates, very little is known about the great diversity of their metabolic potential, particularly in situ. Recent models for the fate of short-chain organic acids, and presumably aromatics and long-chain fatty acids, indicated that they must diffuse out of hydrothermal environments before being metabolized because no hyperthermophilic microorganisms in pure culture or in actual sediment or rock were known to utilize these substrates. In this study, the metabolism of the key fermentation product, acetate, as well as aromatic compounds was investigated in the hyperthermophilic microorganisms, Ferroglobus placidus and Geoglobus ahangari. In addition, the fate of 14C-radiolabeld organic compounds was evaluated in hydrothermal sediments collected from a shallow marine vent on Vulcano, Italy. F. placidus and G. ahangari grew at 85°C in anaerobic medium with acetate as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. Additionally, F. placidus was capable of using a variety of aromatic compounds as the sole electron donor for the reduction of Fe(III). In hydrothermal sediments from Vulcano, Italy, the radiolabeled acetate, palmitate, and glucose were completely oxidized to carbon dioxide coupled to sulfate reduction. Radiolabeled L-glutamate and benzoate were primarily oxidized to carbon dioxide, although incompletely. These results are the first indication that complex organic matter can be oxidized to carbon dioxide by hyperthermophilic microorganisms, and thus a complete carbon cycle may be modeled for hydrothermal systems.

<p> For over 3.5Ga microbial activities have profoundly altered planetary geochemistry. In particular, sulfur-cycling hydrothermal vent communities have been important players in shaping biogeochemistry and the habitability of Earth. However, the remote nature of deep-sea vents makes investigations challenging. Using the White Point (WP) shallow-sea hydrothermal vent field as a proxy, I employed molecular sequencing, fluorescent in situ hybridization (FISH) and ³⁵S-radiotracer assays to investigate the diversity and function of chemoautotrophic microbial mats. This study revealed a highly active and diverse sulfur-cycling microbial community. Potential epibiotic associations between sulfur-oxidizing (SOxB) and sulfate/sulfur-reducing bacteria (SRB) were identified using FISH. Comparative analyses of 16S rRNA sequences revealed the WP sulfur vent microbial mat community to be similar to deep-sea microbial communities from hydrothermal vents in a range of biotopes and lithologic settings and supported the relevancy of the WP hydrothermal sulfur-vent microbial mats as an excellent model for studying "thiobiotic" vent communities.</p>

Thesis (Ph.D.)--Indiana University, Dept. of Geological Sciences, 2004. / Title from PDF t.p. (viewed Dec. 1, 2008). Source: Dissertation Abstracts International, Volume: 66-01, Section: B, page: 0161. Chair: Lisa M. Pratt.

<p>Limestone dissolution in karst environments is likely due to geochemistry of the water, the actions of microbial communities, and the effect of water flow. We explored the rate of limestone dissolution and will examine here the microbial communities associated with the limestone. A conduit within the brackish cave, Double Keyhole Spring, on the coast of central west Florida was the site of the experiment. PVC pipes (5cm x 16cm) were filled with crushed limestone that was screened to a 1.9cm ? 2.54cm size range. There were three treatments (5 replicates each): Control - sealed autoclaved controls with limestone and conduit water; Low Flow ? sealed at one end, with a screen on the other so water contacts the limestone but cannot flow through; High Flow ? screen mesh at both ends to allow the flow of conduit water over the limestone in the tube. After 9 months, the samples were retrieved. The Controls showed a loss of 0.33% ? 0.10, Low Flow samples showed a loss of 1.63% ? 0.71, and High Flow samples lost 2.28% ?0.29. Other studies in freshwater conditions found an average mass loss of 2.25% over the same time period under conditions similar to the High Flow sample in this experiment. Q-PCR and LH-PCR were used to estimate microbial density and species richness. The microbial community growing on the limestone samples were found to be significantly different from sediment or water column samples in both diversity and richness. The conclusion of this study is that the archaeal community growing on the limestone is the main biological driver of limestone dissolution in Double Keyhole Spring.

The potential for in situ anaerobic benzene degradation in petroleum-contaminated aquifers was investigated. Sediments collected from a contaminated aquifer near Bemidji, MN in which Fe(III)-reduction was the dominant microbial process readily mineralized benzene when incubated with [U-14C]benzene while sediments from other aquifers did not. Benzene mineralization was localized within a narrow zone at the downgradient edge of the Fe(III) reduction zone. Analysis of MPN cultures and sediment by a variety of 16S rRNA-based techniques indicated a selective enrichment of Geobacteraceae in benzene degrading, Fe(III)-reducing sediments. Members of the Geobacteraceae are known to couple the oxidation of aromatic compounds to the reduction of Fe(III) and could be responsible for the observed benzene degradation at this site. Bemidji sediments also mineralized other aromatic compounds commonly found in hydrocarbon-contaminated groundwaters. Benzene-degrading sediments readily mineralized toluene and naphthalene indicating that these compounds were also being oxidized in situ. The unusual aromatic degradation activity at the Bemidji site could not be attributed to the presence of Fe(III)-chelators and/or electron shuttling compounds in the groundwater. Uncontaminated sediments could be adapted to benzene suggesting that Bemidji sediments naturally contain a microbial population capable of anaerobic benzene degradation. Results obtained from the Bemidji aquifer encouraged the investigation of anaerobic treatment alternatives for contaminated aquifers. Anaerobic bioremediation of benzene was evaluated at a petroleum-contaminated aquifer in Oklahoma. The injection of sulfate into the subsurface stimulated benzene degradation within a treatment zone located downgradient from an injection gallery. Benzene concentrations in the groundwater decreased by an average of 90% (100% in one well) during the study period. Sulfate concentrations, relative to a bromide tracer, decreased with distance from the injection gallery suggesting that benzene removal was coupled to the removal of sulfate from the groundwater. [U-14C]Benzene mineralization and [2-14C]acetate analysis of sediments confirmed that benzene degradation was indeed coupled to sulfate reduction within treatment zone sediments. Mass balance calculations suggested that as much as 42% of the removed sulfate within the treatment zone could be attributed to the anaerobic oxidation of benzene. The results demonstrate that stimulation of anaerobic processes can be an effective treatment alternative for heavily contaminated aquifers.

We present research aimed at determining the role of soil structure in the organization of microbial communities in soil. We have focused on the microbial communities involved in functional roles within the nitrogen cycle, particularly nitrogen fixation. We have studied how different aggregate structures of varying size and stability provide different environments for these communities. Initially, we compared the nitrogen-fixing communities between aggregate structures obtained from soils from arctic, temperate and tropical environments. We also compared the communities involved in nitrogen fixation, nitrate reduction and ammonia oxidation from adjacent agricultural plots under different tillage regimes. We continued to monitor the community composition of nitrogen fixers at the aggregate scale through the following year and season after a tillage disturbance. We further narrowed down our scale by comparing the total diversity and functional diversity of an individual microaggregate and compared it with others. We then looked that the effect of disturbance at larger time scales in forest soil plots of old and secondary forest growth over one hundred years after recovery. We have determined that very different functional community structure can be found across all aggregate fractions in soils from all over the world, as well as from adjacent plots. Tillage has a major effect on the community composition of communities involved in the nitrogen cycle evidenced at all aggregate scales. This disturbance also affects the overall activity of nitrogen fixers measured in soil. However, the community recovers a year after the tillage disturbance, both in terms of community composition and activity of nitrogen fixers. Individual microaggregates are different from each other in terms of overall community structure, but the functional community composition seems to be homogeneous and representative of the composition observed in a pooled microaggregate fraction. Prolonged agricultural activities significantly altered the communities obtained from secondary growth forests when compared to adjacent old forest soils. Different aggregate structures provide environments for very different microbial communities involved in the nitrogen cycle. However, even the most stable of these structures is affected by tillage at the level of community composition and activity. This work describes not only the extent of this community and niche disturbance and their ability to recover, but also the extent of functional diversity at the micro-scale of the most complex of natural environments.