The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale

Włodarczyk, Agnieszka; Lirski, Maciej; Fogtman, Anna; Koblowska, Marta; Bidziński, Grzegorz; Matlakowska, Renata

doi:10.3389/fmicb.2018.00972

Cited by 16 publications

(22 citation statements)

References 45 publications

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“…The relatives of Sulfuricella and Sulfuritalea have also been detected based on detection of sequences related to other genes of these genera (Watanabe et al, 2013; Kojima et al, 2014; Herrmann et al, 2015, 2017; Lau et al, 2016; Kumar et al, 2017, 2018; Feng et al, 2018; Luo et al, 2018). This is also the case for the other genome-sequenced species of Sulfurifustis and Sulfuricaulis (Watanabe et al, 2016a; Herrmann et al, 2017; Kumar et al, 2018; Włodarczyk et al, 2018). Furthermore, detailed inspections of the genomes of Sulfuricella and Sulfuritalea revealed the presence of characteristic genes for arsenic metabolism, arxAB and arrAB (Watanabe et al, 2014, 2017).…”

Section: Introductionmentioning

confidence: 62%

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

et al. 2019

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Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria . Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘ Sulfuricellaceae ’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.

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Section: Introductionmentioning

confidence: 62%

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

et al. 2019

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“…Jiang et al 2015) or in culture-independent analyses (e.g. Włodarczyk et al 2018). Furthermore, most of these genera are well-known rock weathering organisms such as Arthrobacter (Frey et al 2010),…”

Section: Discussionmentioning

confidence: 99%

“…C, Fe and S) and soil formation (Uroz et al 2009;Brantley et al 2012). The role of microbes in the weathering of shale has been extensively studied in natural environments (Petsch et al 2001;Petsch et al 2005;Joeckel et al 2005;Cockell et al 2011;Yesavage et al 2012;Zhu and Reinfelder, 2012;Li et al 2014;Włodarczyk et al 2018).…”

Section: Introductionmentioning

confidence: 99%

pH Influences the Distribution of Microbial Rock-Weathering Phenotypes in Weathered Shale Environments

Samuels

Pybus²,

Wilkinson

et al. 2019

Geomicrobiology Journal

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Microbial rock weathering of shale forms an important part of global biogeochemical cycling and soil formation. Culture-independent analyses have revealed diverse microbial communities in weathered shale environments, yet few studies have attempted to discern the functional ecology of such communities in relatiFon to their rock weathering capabilities. In this study, phenotypic plate assays were used to determine the abundance of microbes with different rock weathering phenotypic traits in weathered shale environments. A physicochemical parameter (pH) is shown to influence the abundance of aerobic rock weathering microbes in weathered shale. Iron and manganese oxidizers were restricted to acidic environments, while siderophore producing and alkaline phosphatase producing microbes were largely confined to pH neutral environments. Furthermore, a clear separation in the spatial distribution of aerobic iron oxidizing and siderophore-producing microbes, as defined by a pH gradient across the sites sampled, was demonstrated. Phylogenetic analysis of isolates revealed that siderophore producing and alkaline phosphatase producing bacteria belonged to commonly identified rock weathering genera including Arthrobacter, Pseudomonas and Streptomyces. These results enhance our understanding how physicochemical parameters can define the composition and rock weathering potential of microbial communities.

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“…Previous research has shown that this shale rock contains nickel and vanadium porphyrins ( Tokarska, 1971 ; Sawłowicz, 1985 ; Szubert et al, 2006 ). So far, we have shown that the community of microorganisms inhabiting the shale rocks were responsible for the oxidation and dehydrogenation of kerogen and for the mobilization of fossil organic carbon in the oxidized form ( Stasiuk et al, 2017 ; Włodarczyk et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

“…The first sample (SR) was shale rock taken from a freshly exposed rock profile in which microorganisms were not detected ( Stasiuk et al, 2017 ). The second sample was a bacteria-inhabited shale rock (BISR) collected from the profile created 12 years ago ( Włodarczyk et al, 2018 ). In the second part of our study, SR was exposed to the bacterium Pseudomonas sp.…”

Section: Introductionmentioning

confidence: 99%

Postdiagenetic Bacterial Transformation of Nickel and Vanadyl Sedimentary Porphyrins of Organic-Rich Shale Rock (Fore-Sudetic Monocline, Poland)

Stasiuk

Matlakowska

2021

Front. Microbiol.

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Nickel and vanadyl porphyrins belong to the so-called fossil geo- or sedimentary porphyrins. They occur in different types of organic matter-rich sediments but mostly occur in crude oils and their source rocks, oil shales, coals, and oil sands. In this study, we aimed to understand the process of bacterial transformation of geoporphyrins occurring in the subsurface shale rock (Fore-Sudetic Monocline, SW Poland). We studied these transformations in rock samples directly obtained from the field; in rock samples treated with bacterial strain isolated from shale rock (strain LM27) in the laboratory; and using synthetic nickel and vanadyl porphyrins treated with LM27. Our results demonstrate the following: (i) cleavage and/or degradation of aliphatic and aromatic substituents of porphyrins; (ii) degradation of porphyrin (tetrapyrrole) ring; (iii) formation of organic compounds containing 1, 2, or 3 pyrrole rings; (iv) formation of nickel- or vanadium-containing organic compounds; and (v) mobilization of nickel and vanadium. Our results also showed that the described bacterial processes change the composition and content of geoporphyrins, composition of extractable organic matter, as well as nickel and vanadium content in shale rock.

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The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale

Cited by 16 publications

References 45 publications

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

pH Influences the Distribution of Microbial Rock-Weathering Phenotypes in Weathered Shale Environments

Postdiagenetic Bacterial Transformation of Nickel and Vanadyl Sedimentary Porphyrins of Organic-Rich Shale Rock (Fore-Sudetic Monocline, Poland)

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