scholarly journals Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway

2021 ◽  
Author(s):  
Jia-Wei Zhang ◽  
Hong-Po Dong ◽  
Li-Jun Hou ◽  
Yang Liu ◽  
Ya-Fei Ou ◽  
...  
Keyword(s):  
Nitrate Reduction ◽  
Coenzyme A ◽  
Organic Substrates ◽  
Mangrove Sediments ◽  
Sulfate Reducing ◽  
Sequence Read Archive ◽  
Wide Range ◽  
Genes Encoding ◽  
Sediment Carbon ◽  
Reducing Bacteria

AbstractAsgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

scholarly journals Novel Asgard archaea phylum Hermodarchaeota degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway

2020 ◽  
Author(s):  
Jia-Wei Zhang ◽  
Hong-Po Dong ◽  
Li-Jun Hou ◽  
Yang Liu ◽  
Ya-Fei Ou ◽  
...  
Keyword(s):  
16S Rrna ◽  
Carbon Cycling ◽  
Organic Compounds ◽  
Aromatic Compounds ◽  
Coenzyme A ◽  
Mangrove Sediments ◽  
Freshwater Sediments ◽  
Sulfate Reducing ◽  
Genes Encoding ◽  
Reducing Bacteria

AbstractAsgard superphylum is composed of a group of uncultivated archaea that are deemed the closest relatives of eukaryotes. These archaea are widely distributed in anaerobic environments and suggested to be important players in carbon cycling of sediments. Alkanes and aromatics are refractory organic compounds and abundant in sediments. However, little is known about degradation of these compounds by Asgard archaea to date. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered in metagenomes from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those found in alkanes-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes for alkyl-coenzyme A and benzoyl-coenzyme A oxidation, and the Wood–Ljungdahl pathway, as well as nitrate reductases. Furthermore, transcripts for these enzymes have been frequently detected in metatranscriptomes from mangrove sediments. This indicates that members of this phylum are able to anaerobically oxidize alkanes and aromatic compounds, coupling the reduction of nitrate. Genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in a range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Identification of the genes for hydrogenase and cytochrome c3 in Desulfovibrio

1987 ◽  
Vol 33 (11) ◽  
pp. 1006-1010 ◽  
Author(s):  
Gerrit Voordouw ◽  
Helen M. Kent ◽  
John R. Postgate
Keyword(s):  
Cytochrome C ◽  
Sequence Divergence ◽  
Desulfovibrio Vulgaris ◽  
Gene Probe ◽  
Cytochrome C3 ◽  
Sulfate Reducing ◽  
Genes Encoding ◽  
Reducing Bacteria ◽  
Cryptic Plasmids ◽  
Amino Acid Sequence Divergence

Cloned genes encoding cytochrome c3 and hydrogenase from Desulfovibrio vulgaris Hildenborough have been used to probe the genomes of 15 other desulfovibrios. The D. vulgaris strains Wandle and Brockhurst Hill cannot be distinguished from the Hildenborough strain by Southern hybridization using either probe, indicating similar genomes. Desulfovibrio vulgaris Groningen is completely different and lacks homologous cytochrome c3 and hydrogenase genes. The genomes of D. vulgaris ssp. oxamicus Monticello and D. desulfuricans strains El Agheila Z, Berre sol, and Canet 41 contain genes encoding a homologous but not identical periplasmic hydrogenase and cytochrome c3. Weak hybridization was observed with the cytochrome c3 gene probe for genomes of seven other sulfate-reducing bacteria, which reflects the known amino acid sequence divergence of cytochrome c3 in Desulfovibrio. The hydrogenase gene probe shows weak hybridization to the DNA from two strains of D. salexigens only, while the gene may be absent from D. vulgaris Groningen, two strains of D. africanus, D. thermophilus, D. gigas, and D. desulfuricans strains Norway and Teddington R. In desulfovibrios carrying cryptic plasmids the cytochrome c3 and hydrogenase genes are apparently chromosomal.

scholarly journals Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones

2019 ◽  
Vol 116 (20) ◽  
pp. 9925-9930 ◽  
Author(s):  
Jaclyn K. Saunders ◽  
Clara A. Fuchsman ◽  
Cedar McKay ◽  
Gabrielle Rocap
Keyword(s):  
Arsenate Reductase ◽  
Organic Matter Production ◽  
Sulfate Reducing ◽  
Matter Production ◽  
Reductase Gene ◽  
Water Columns ◽  
Large Particles ◽  
Genes Encoding ◽  
Marine Microbial Communities ◽  
Reducing Bacteria

Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (>30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.

scholarly journals Stable Carbon Isotope Fractionation by Sulfate-Reducing Bacteria

2003 ◽  
Vol 69 (5) ◽  
pp. 2942-2949 ◽  
Author(s):  
Kathleen L. Londry ◽  
David J. Des Marais
Keyword(s):  
Carbon Isotope ◽  
Isotope Fractionation ◽  
Carbon Isotope Discrimination ◽  
Stable Carbon Isotope ◽  
Reducing Power ◽  
Sulfate Reducing Bacteria ◽  
Organic Substrates ◽  
Isotope Discrimination ◽  
Sulfate Reducing ◽  
Reducing Bacteria

ABSTRACT Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record. Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB). For heterotrophic-growth experiments, substrate consumption was monitored to completion. Sealed vessels containing SRB cultures were harvested at different time intervals, and δ13C values were determined for gaseous CO2, organic substrates, and products such as biomass. For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO2, and the cell biomass were small, ranging from 0 to 2‰. However, for Desulfotomaculum acetoxidans, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9‰. SRB grown lithoautotrophically consumed less than 3% of the available CO2 and exhibited substantial discrimination (calculated as isotope fractionation factors [α]), as follows: for Desulfobacterium autotrophicum, α values ranged from 1.0100 to 1.0123; for Desulfobacter hydrogenophilus, the α value was 0.0138, and for Desulfotomaculum acetoxidans, the α value was 1.0310. Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO2 resulted in biomass with a δ13C composition intermediate to that of the substrates. The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase. To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H2), ecological forces can also influence carbon isotope discrimination by SRB.

scholarly journals Mercury Methylation Independent of the Acetyl-Coenzyme A Pathway in Sulfate-Reducing Bacteria

2003 ◽  
Vol 69 (9) ◽  
pp. 5414-5422 ◽  
Author(s):  
Eileen B. Ekstrom ◽  
François M. M. Morel ◽  
Janina M. Benoit
Keyword(s):  
Coenzyme A ◽  
Sulfate Reducing Bacteria ◽  
Mercury Methylation ◽  
Acetyl Coa ◽  
Acetyl Coenzyme A ◽  
Sulfate Reducing ◽  
Acetyl Coenzyme ◽  
Acetyl Coa Pathway ◽  
Reducing Bacteria ◽  
Methylmercury Production

ABSTRACT Sulfate-reducing bacteria (SRB) in anoxic waters and sediments are the major producers of methylmercury in aquatic systems. Although a considerable amount of work has addressed the environmental factors that control methylmercury formation and the conditions that control bioavailability of inorganic mercury to SRB, little work has been undertaken analyzing the biochemical mechanism of methylmercury production. The acetyl-coenzyme A (CoA) pathway has been implicated as being key to mercury methylation in one SRB strain, Desulfovibrio desulfuricans LS, but this result has not been extended to other SRB species. To probe whether the acetyl-CoA pathway is the controlling biochemical process for methylmercury production in SRB, five incomplete-oxidizing SRB strains and two Desulfobacter strains that do not use the acetyl-CoA pathway for major carbon metabolism were assayed for methylmercury formation and acetyl-CoA pathway enzyme activities. Three of the SRB strains were also incubated with chloroform to inhibit the acetyl-CoA pathway. So far, all species that have been found to have acetyl-CoA activity are complete oxidizers that require the acetyl-CoA pathway for basic metabolism, as well as methylate mercury. Chloroform inhibits Hg methylation in these species either by blocking the methylating enzyme or by indirect effects on metabolism and growth. However, we have identified four incomplete-oxidizing strains that clearly do not utilize the acetyl-CoA pathway either for metabolism or mercury methylation (as confirmed by the absence of chloroform inhibition). Hg methylation is thus independent of the acetyl-CoA pathway and may not require vitamin B12 in some and perhaps many incomplete-oxidizing SRB strains.

scholarly journals The oyster enigma variations: a hypothesis of microbial calcification

Paleobiology ◽  
10.1666/13002 ◽  
2014 ◽  
Vol 40 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Geerat J. Vermeij
Keyword(s):  
Sulfate Reducing Bacteria ◽  
Organic Substrates ◽  
Shell Layer ◽  
Shell Wall ◽  
Sulfate Reducing ◽  
Large Size ◽  
Thick Shells ◽  
Reducing Bacteria ◽  
Hard Substrata

Oysters, whose inner shell layer contains chambers, vesicles, and sometimes chalky deposits, often have extraordinarily thick shells of large size, prompting the idea that there is something unusual about the process of shell fPormation in these and similarly structured bivalves with the oyster syndrome. I propose the hypothesis that calcifying microbes, especially sulfate-reducing bacteria growing on organic substrates in fluid-filled shell-wall chambers, are responsible for shell calcification away from the shell-secreting mantle of the host bivalve. Other phenomena, including the formation of cameral deposits in fossil cephalopods, the cementation of molluscs and barnacles to hard substrata, the formation of a calcified intriticalx on the shell's exterior, and cementation of objects by gastropods on the shell for camouflage, may also involve calcifying bacteria. Several lines of inquiry are suggested to test these hypotheses.

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