Prokaryotic sulfur oxidation

Friedrich, Cornelius G.; Bardischewsky, Frank; Röther, Dagmar; Quentmeier, Armin; Fischer, Jörg

doi:10.1016/j.mib.2005.04.005

Cited by 432 publications

(411 citation statements)

References 38 publications

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“…The presence of bacterial species with closest affiliation to Fe-oxidizer bacteria (Acidithiobacillus spp.) indicates that the microbial oxidation of Fe(II) is a significant biogeochemical process in the sediments of AML 2 as noted in previous studies (e.g., Friedrich et al 2005;Rohwerder and Sand 2007;Ghosh and Dam 2009;Schippers et al 2010;Dopson and Johnson 2012;Chen et al 2013). Insignificant variations in pH, along with observed changes in DO and Fe concentration throughout the water column until a depth of 6 m, also suggest co-occurrences of Fe(II) oxidation and precipitation of Fe(III) minerals buffering pH as reported in various AMLs with pH ranging from 2.59 to 3.79 (Kusel 2003;Peiffer et al 2013;Vithana et al 2015).…”

Section: Geochemical and Biogeochemical Processes In The Water Columnsupporting

confidence: 78%

Generation of Acid Mine Lakes Associated with Abandoned Coal Mines in Northwest Turkey

Yücel

Balcı

Baba

2016

Arch Environ Contam Toxicol

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A total of five acid mine lakes (AMLs) located in northwest Turkey were investigated using combined isotope, molecular, and geochemical techniques to identify geochemical processes controlling and promoting acid formation. All of the investigated lakes showed typical characteristics of an AML with low pH (2.59-3.79) and high electrical conductivity values (1040-6430 lS/cm), in addition to high sulfate (594-5370 mg/l) and metal (aluminum [Al], iron [Fe], manganese [Mn], nickel [Ni], and zinc [Zn]) concentrations. Geochemical and isotope results showed that the acid-generation mechanism and source of sulfate in the lakes can change and depends on the age of the lakes. In the relatively older lakes (AMLs 1 through 3), biogeochemical Fe cycles seem to be the dominant process controlling metal concentration and pH of the water unlike in the younger lakes (AMLs 4 and 5). Bacterial species determined in an older lake (AML 2) indicate that biological oxidation and reduction of Fe and S are the dominant processes in the lakes. Furthermore, O and S isotopes of sulfate indicate that sulfate in the older mine lakes may be a product of much more complex oxidation/dissolution reactions. However, the major source of sulfate in the younger mine lakes is in situ pyrite oxidation catalyzed by Fe(III) produced by way of oxidation of Fe(II). Consistent with this, insignificant fractionation between d 34 S SO 4 and d 34 S FeS 2 values indicated that the oxidation of pyrite, along with dissolution and precipitation reactions of Fe(III) minerals, is the main reason for acid formation in the region. Overall, the results showed that acid generation during early stage formation of an AML associated with pyrite-rich mine waste is primarily controlled by the oxidation of pyrite with Fe cycles becoming the dominant processes regulating pH and metal cycles in the later stages of mine lake development.Acidic and highly metal-loaded effluents (acid mine drainage [AMD]) resulting from the exposure of pyrite and other metal sulfide minerals to weathering conditions are the principal environmental problems faced by the mining industry today (Dold and Spangerberg 2005).The formation mechanisms of AMD (e.g., oxidation of pyrite and other sulfide minerals) has been extensively studied

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Section: Geochemical and Biogeochemical Processes In The Water Columnsupporting

confidence: 78%

Generation of Acid Mine Lakes Associated with Abandoned Coal Mines in Northwest Turkey

Yücel

Balcı

Baba

2016

Arch Environ Contam Toxicol

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“…When extrapolating these results to the full community composition per well, a range of putative chemolithoautotrophic communities are prevalent from saline wells, including Halothiobacillaceae (Chromatiales) that aerobically oxidize reduced sulfur compounds (Kelly and Wood, 2000), uncultured Epsilonproteobacteria and Hydrogenophilales (Thiobacillus spp.). Thiobacilli are perhaps the beststudied sulfur-oxidizing bacteria (Friedrich et al, 2005). In contrast, potential heterotrophic and chemoorganotrophic indicator taxa in freshwater wells correlated to dissolved oxygen and included the Caulobacterales, which are aerobic, oligotrophic aquatic bacteria with a high degree of metabolic versatility (Boone et al, 2001), Sphingomonadales, which have wide metabolic capabilities (Frederickson et al, 1995), and Rhizobiales, which are ecologically diverse, important in biofilm formation under oxic and anoxic conditions, and are even capable of oxidizing reduced sulfur (Masuda et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

Gray

Engel

2012

The ISME Journal

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Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

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“…The Dsr operon is used by sulfate/sulfitereducing microbes in anoxic environments, as well as sulfur-oxidizing bacteria in oxic and anoxic environments (Fig. 3A) 30,31 . DsrC, specifically, dictates sulfur metabolism rates, as it provides the sulfur substrate to DsrAB-sulfite reductase for processing 32 .…”

mentioning

confidence: 99%

“…Second, 4 soxYZ genes from the sox operon were identified on viral contigs (Extended Data Fig. 6) 30,31 . Like DsrC, SoxYZ is an important sulfur carrier protein harboring a sulfur interaction motif identified in GOV SoxYZ proteins (Fig.…”

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confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

641

885

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Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

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Prokaryotic sulfur oxidation

Cited by 432 publications

References 38 publications

Generation of Acid Mine Lakes Associated with Abandoned Coal Mines in Northwest Turkey

Generation of Acid Mine Lakes Associated with Abandoned Coal Mines in Northwest Turkey

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

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