Biology subjects

Amend, J. P.

Publications and source records attributed to Amend, J. P..

5 recordsLinked to original sources

bioRxiv2023

Isolation of a putative sulfur comproportionating microorganism

Sulfur comproportionation is a heretofore undiscovered microbial catabolism that was predicted based on thermodynamic calculations. Here, we report the isolation of an Acidithiobacillus thiooxidans strain from extremely low pH snottite biofilms in the karst at Frasassi, Italy. The strain grew to cell densities of >107 cells mL-1 in autotrophic sulfur comproportionation medium. Whole genome sequencing of the isolate revealed the presence of numerous genes involved in sulfur transformations that could be linked in a sulfur comproportionation pathway. We describe an experimental framework, including measurements of sulfate, sulfide, and S0 concentrations, electron microscopy, and stable and radioisotope incubations coupled with NanoSIMS, scintillation counting and isotope ratio mass spectrometry, for future searches of sulfur comproportionators. SignificanceThe prediction of and search for novel microbial catabolic reactions can be streamlined by using thermodynamics to identify energy-yielding redox reactions that may be catalyzed by microorganisms. This strategy has been used to successfully predict several previously overlooked microbial catabolic reactions, including anaerobic ammonia oxidation (anammox), anaerobic oxidation of methane (AOM), and complete ammonia oxidation (comammox). Sulfur comproportionation, or the coupled reduction of sulfate and oxidation of sulfide to form elemental sulfur, was predicted by thermodynamic calculations to exist as a microbial catabolism in low pH, low-temperature environments. In this study, we describe the isolation of the first putative sulfur comproportionating microorganism and provide a detailed experimental approach that can be applied to future investigations of this novel link in the biogeochemical sulfur cycle.

microbiology↗

bioRxiv2023

Sulfur disproportionating microbial communities in a dynamic, microoxic-sulfidic karst system

Biogeochemical sulfur cycling in sulfidic karst systems is largely driven by abiotic and biological sulfide oxidation, but the fate of elemental sulfur (S0) that accumulates in these systems is not well understood. The Frasassi Cave system (Italy) is intersected by a sulfidic aquifer that mixes with small quantities of oxygen-rich meteoric water, creating Proterozoic-like conditions and supporting a prolific ecosystem driven by sulfur-based chemolithoautotrophy. To better understand the cycling of S0 in this environment, we examined the geochemistry and microbiology of sediments underlying widespread sulfide-oxidizing mats dominated by Beggiatoa. Sediment populations were dominated by uncultivated relatives of sulfur cycling chemolithoautotrophs related to Sulfurovum, Halothiobacillus, Thiofaba, Thiovirga, Thiobacillus, and Desulfocapsa, as well as diverse uncultivated anaerobic heterotrophs affiliated with Bacteroidota, Anaerolineaceae, Lentimicrobiaceae, and Prolixibacteraceae. Desulfocapsa and Sulfurovum populations accounted for 12-26% of sediment 16S rRNA amplicon sequences and were closely related to isolates which carry out autotrophic S0 disproportionation in pure culture. Gibbs energy ({Delta}Gr) calculations revealed that S0 disproportionation under in situ conditions is energy yielding. Microsensor profiles through the mat-sediment interface showed that Beggiatoa mats consume dissolved sulfide and oxygen, but a net increase in acidity was only observed in the sediments below. Together, these findings suggest that disproportionation is an important sink for S0 generated by microbial sulfide oxidation in this oxygen-limited system and may contribute to the weathering of carbonate rocks and sediments in sulfur- rich environments.

microbiology↗

bioRxiv2022

Thiovibrio frasassiensis gen. nov., sp. nov., an autotrophic, elemental sulfur disproportionating bacterium isolated from sulfidic karst sediment, and proposal of Thiovibrionaceae fam. nov.

A novel, autotrophic, mesophilic bacterium, strain RS19-109T, was isolated from sulfidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulfur (S0) and thiosulfate, but not sulfite with bicarbonate/CO2 as a carbon source. Autotrophic growth was also observed with molecular hydrogen as an electron donor, and S0, sulfate, thiosulfate, nitrate, and ferric iron as electron acceptors. Oxygen was not used as an electron acceptor and sulfide was not used as an electron donor. Weak growth was observed with sulfate as an electron acceptor and organic carbon as electron donors and carbon sources. The strain also showed weak growth by fermentation of tryptone. Strain RS19-109T was found to be phylogenetically distinct based on 16S rRNA gene sequence similarity (89.2%) to its closest relative, Desulfurivibrio alkaliphilus AHT2T. The draft genome sequence for strain RS19-109T had average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values of 72.2%, 63.0%, and 18.3%, respectively, compared with the genome sequence of D. alkaliphilus AHT2T. On the basis of its physiological and genomic properties, strain RS19-109T is proposed as the type strain of a novel species of a novel genus, Thiovibrio frasassiensis gen. nov., sp. nov. A novel family, Thiovibrionaceae fam. nov., is proposed to accommodate Thiovibrio within the order Desulfobulbales.

microbiology↗

bioRxiv2019

Another chemolithotrophic metabolism missing in nature--sulfur comproportionation

Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation-reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy ({Delta}Gr) can identify whether a reaction is thermodynamically favorable, and the accompanying energy yield at the temperature, pressure, and chemical composition in the system of interest. Based on carefully calculated values of {Delta}Gr, we predict a novel microbial metabolism--sulfur comproportionation (3H2S + SO42- + 2H+ = 4S0 + 4H2O). We show that at elevated concentrations of sulfide and sulfate in acidic environments over a broad temperature range, this putative metabolism can be exergonic ({Delta}Gr<0), yielding [~]30-50 kJ/mol. We suggest that this may be sufficient energy to support a chemolithotrophic metabolism currently missing in nature. Other versions of this metabolism, to thiosulfate (H2S + SO42- = S2O32- + H2O) and to sulfite (H2S + 3SO42- = 4SO32- + 2H+), are only moderately exergonic or endergonic even at ideal geochemical conditions. Natural and impacted environments, including sulfidic karst systems, shallow-sea hydrothermal vents, sites of acid mine drainage, and acid-sulfate crater lakes, may be ideal hunting grounds for finding microbial sulfur comproportionators.

microbiology↗

bioRxiv2019

In Situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

The terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling, in situ studies, and isolating of the in situ microbes. Motivated by the ability of microbes to gain energy from redox reactions at mineral interfaces, we here present in situ electrochemical colonization (ISEC) as a method to directly study microbial electron transfer activity and to enable the capture and isolation of electrochemically active microbes. We installed a potentiostatically controlled ISEC reactor containing four working electrodes 1500 m below the surface at the Sanford Underground Research Facility. The working electrodes were poised at different redox potentials, spanning anodic to cathodic, to mimic energy-yielding mineral reducing and oxidizing reactions predicted to occur at this site. We present a 16S rRNA analysis of the in situ electrode-associated microbial communities, revealing the dominance of novel bacterial lineages under cathodic conditions. We also demonstrate that the in situ electrodes can be further used for downstream electrochemical laboratory enrichment and isolation of novel strains. Using this workflow, we isolated Bacillus, Anaerospora, Comamonas, Cupriavidus, and Azonexus strains from the electrode-attached biomass. Finally, the extracellular electron transfer activity of the electrode-oxidizing Comamonas strain (isolated at -0.19 V vs. SHE and designated WE1-1D1) and the electrode-reducing Bacillus strain (isolated at +0.53 V vs. SHE and designated WE4-1A1-BC) were confirmed in electrochemical reactors. Our study highlights the utility of in situ electrodes and electrochemical enrichment workflows to shed light on microbial activity in the deep terrestrial subsurface. SIGNIFICANCEA large section of microbial life resides in the deep subsurface, but an organized effort to explore this deep biosphere has only recently begun. A detailed characterization of the resident microbes remains scientifically and technologically challenging due to difficulty in access, sampling, and emulating the complex interactions and energetic landscapes of subsurface communities with standard laboratory techniques. Here we describe an in situ approach that exploits the ability of many microbes to perform extracellular electron transfer to/from solid surfaces such as mineral interfaces in the terrestrial subsurface. By deploying and controlling the potential of in situ electrodes 4850 ft below the surface at the Sanford Underground Research Facility (South Dakota, USA), we highlight the promise of electrochemical techniques for studying active terrestrial subsurface microbial communities and enabling the isolation of electrochemically active microbes.

microbiology↗