Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction

Zaarur, Shikma; Wang, David T.; Ono, Shuhei; Bosak, Tanja

doi:10.3389/fmicb.2017.00890

Cited by 14 publications

(7 citation statements)

References 101 publications

(192 reference statements)

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“…Bioisotopic models have the potential to reveal details of the elusive mechanisms that control such isotopic fingerprints. Such models have been successfully applied to microbial sulfate reduction by demonstrating how the sulfur isotope fractionations of individual steps in the pathway combine to control the net fractionation (Wing & Halevy, 2014;Zaarur et al, 2017;Wenk et al, 2017).…”

Section: Isotopic Composition Of Methanementioning

confidence: 99%

Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Gropp

Iron

Halevy

2021

Geochimica et Cosmochimica Acta

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Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (13 C/ 12 C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., 13 C-D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed 13 β and 2 β values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in 13 C and D. Using the computed β values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 • C. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during

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Section: Isotopic Composition Of Methanementioning

confidence: 99%

Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Gropp

Iron

Halevy

2021

Geochimica et Cosmochimica Acta

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“…Right axis (green squares): Distribution of csSRR in laboratory cultures where also sulfur isotope fractionation factors were determined. Rates compiled for marine sediment are taken from D’Hondt et al (2002); Leloup et al (2009), and Beulig et al (2018), while pure culture data are a non-exhaustive compilation from Kaplan and Rittenberg (1964), Chambers et al (1975), Detmers et al (2001), Habicht et al (2005), Hoek et al (2006), Johnston et al (2007), Davidson et al (2009), Eckert et al (2011), Sim et al (2011a,b, 2012), Leavitt et al (2013), Pellerin et al (2015a), Antler et al (2017), Zaarur et al (2017) and Pellerin et al (2018b).…”

Section: Stable Sulfur Isotopesmentioning

confidence: 99%

The Biogeochemical Sulfur Cycle of Marine Sediments

2019

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Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.

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“…Walvis Bay , D. inopinatus DSM 10,711 and Desulfobacca acetoxidans DSM 11109, which have been isolated from a narrow diversity of environments. While the first three strains were isolated from marine sediments off the coast of Svalbard (Norway), Walvis Bay (South Africa), and Venice (Italy), respectively, D. acetoxidans DSM 11,109 was isolated from a UASB sludge reactor [ 58 , 59 , 60 , 61 ]. In contrast to cluster 1, three out of the four poly-lysogens of the cluster 2 are classified as slow growing bacteria.…”

Section: Resultsmentioning

confidence: 99%

Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes

et al. 2021

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Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.

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Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction

Cited by 14 publications

References 101 publications

Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane

The Biogeochemical Sulfur Cycle of Marine Sediments

Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes

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