Sulfate-reducing microorganism

Sulfate-reducing microorganisms (SRM) or sulfate-reducing prokaryotes (SRP) are a group composed of sulfate-reducing bacteria (SRB) and sulfate-reducing archaea (SRA), both of which can perform anaerobic respiration utilizing sulfate (SO42-) as terminal electron acceptor, reducing it to hydrogen sulfide (H2S). Therefore, these sulfidogenic microorganisms "breathe" sulfate rather than molecular oxygen (O2), which is the terminal electron acceptor reduced to water (H2O) in aerobic respiration. Most sulfate-reducing microorganisms can also reduce some other oxidized inorganic sulfur compounds, such as sulfite (SO32-), dithionite (S2O42-), thiosulfate (S2O32-), trithionate (S3O62-), tetrathionate (S4O62-), elemental sulfur (S8), and polysulfides (Sn2-). Other than sulfate reduction, some sulfate-reducing microorganisms are also capable of other reactions like disproportionation of sulfur compounds. Depending on the context, "sulfate-reducing microorganisms" can be used in a

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Rizlan Bernier-Latmani, Nicolas Louis Maurice Jacquemin, Karin Lederballe Meibom, Jiangtao Qiao, Matthew Charles Reid, Karen Elda Viacava Romo

Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harboring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

2022

Growth and viability of microorganisms in bentonite and their potential activity in deep geological repository environments

Niels Burzan

Radioactive waste is among the most dangerous anthropogenic waste and its safe disposal is a challenging multi-generational task. Many nations have sought for the peaceful application of nuclear fission for the reliable production of electric energy to power their societies. The increasing volumes of radioactive waste generated are, however, proving an increasingly urgent problem to tackle. Deep geological disposal is deemed our best option for the safe long-term disposal of radioactive waste. Different host rocks are being considered for deep geological disposal, depending on the nation's geology. Switzerland favours the Opalinus Clay Formation due to its very low hydraulic conductivity and good radionuclide retention capabilities. Microorganisms in the deep subsurface are active and must be considered as their activity will influence a deep geological repository for radioactive waste. On one hand, the microorganism's activity represents a safety concern due to the possibility of enhanced corrosion, when considering the metallic waste canister encapsulating spent fuel from nuclear power plants. In other cases, however, they can contribute to the safety of a deep geological repository, when considering the gas balance of a Swiss low- and intermediate-level repository. Anoxic corrosion of metallic radioactive waste poses risks to the structural integrity of the host rock. Harnessing the activity of naturally occurring microorganisms at a safe distance from the waste itself can result in the net reduction of gases and thus their activity can be viewed as beneficial and worth exploring. In this thesis, both the positive and negative aspects of the microbial presence are explored. Wyoming bentonite is a back-fill material and an important engineered barrier system for spent nuclear fuel and high-level waste. Within the framework of an in-situ corrosion experiment, the presence and growth of microorganisms in Wyoming bentonite are investigated. The results show that the activity of corrosion enhancing sulfate-reducing bacteria in Wyoming bentonite is inhibited during the critical bentonite saturation phase but other microorganisms were able to grow. The second in-situ research project explores the potential implementation of a microbial gas sink, a natural biofilm composed of hydrogen-oxidizing sulfate-reducing bacteria and methanogenic archaea. Indeed, under the right conditions, a microbial gas sink can fulfil its intended design purposes and consume all hydrogen-gas evolving from the anoxic corrosion of the waste. This thesis contributes to our understanding of the near-field processes of a Swiss radioactive waste repository within the Opalinus Clay Formation through the contribution of experimental insight obtained under in-situ conditions.

EPFL2021

Chlorinated ethene plume evolution after source thermal remediation: Determination of degradation rates and mechanisms

Christof Holliger, Julien Maillard, Alexandra Marie Murray, Jérémy Zimmermann

The extent, mechanism(s), and rate of chlorinated ethene degradation in a large tetrachloroethene (PCE) plume were investigated in an extensive sampling campaign. Multiple lines of evidence for this degradation were explored, including compound-specific isotope analysis (CSIA), dual C-Cl isotope analysis, and quantitative realtime polymerase chain reaction (qPCR) analysis targeting the genera Dehalococcoides and Dehalogenimonas and the genes vcrA, bvcA, and cerA. A decade prior to this sampling campaign, the plume source was thermally remediated by steam injection. This released dissolved organic carbon (DOC) that stimulated microbial activity and created reduced conditions within the plume. Based on an inclusive analysis of minor and major sampling campaigns since the initial site characterization, it was estimated that reduced conditions peaked 4 years after the remediation event. At the time of this study, 11 years after the remediation event, the redox conditions in the aquifer are returning to their original state. However, the DOC released from the remediated source zone matches levels measured 3 years prior and plume conditions are still suitable for biotic reductive dechlorination. Dehalococcoides spp., Dehalogenimonas spp., and vcrA, bvcA, and cerA reductive dehalogenase genes were detected close to the source, and suggest that complete, biotic PCE degradation occurs here. Further downgradient, qPCR analysis and enriched delta C-13 values for cis-dichloroethene (cDCE) suggest that cDCE is biodegraded in a sulfate-reducing zone in the plume. In the most downgradient portion of the plume, lower levels of specific degraders supported by dual C-CI analysis indicate that the biodegradation occurs in combination with abiotic degradation. Additionally, 16S rRNA gene amplicon sequencing shows that organizational taxonomic units known to contain organohalide-respiring bacteria are relatively abundant throughout the plume. Hydraulic conductivity testing was also conducted, and local degradation rates for PCE and cDCE were determined at various locations throughout the plume. PCE degradation rates from sampling campaigns after the thermal remediation event range from 0.11 to 0.35 yr(-1). PCE and cDCE degradation rates from the second to the third sampling campaigns ranged from 0.08 to 0.10 yr(-1) and 0.01 to 0.07 yr(-1), respectively. This is consistent with cDCE as the dominant daughter product in the majority of the plume and cDCE degradation as the time-limiting step. The extensive temporal and spatial analysis allowed for tracking the evolution of the plume and the lasting impact of the source remediation and illustrates that the multiple lines of evidence approach is essential to elucidate the primary degradation mechanisms in a plume of such size and complexity.

ELSEVIER2019