Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains

Recent advance of microbial mercury methylation in the environment

Methylmercury formation is mainly driven by microbial-mediated process. The mechanism of microbial mercury methylation has become a crucial research topic for understanding methylation in the environment. Pioneering studies of microbial mercury methylation are focusing on functional strain isolation, microbial community composition characterization, and mechanism elucidation in various environments. Therefore, the functional genes of microbial mercury methylation, global isolations of Hg methylation strains, and their methylation potential were systematically analyzed, and methylators in typical environments were extensively reviewed. The main drivers (key physicochemical factors and microbiota) of microbial mercury methylation were summarized and discussed. Though significant progress on the mechanism of the Hg microbial methylation has been explored in recent decade, it is still limited in several aspects, including (1) molecular biology techniques for identifying methylators; (2) characterization methods for mercury methylation potential; and (3) complex environmental properties (environmental factors, complex communities, etc.). Accordingly, strategies for studying the Hg microbial methylation mechanism were proposed. These strategies include the following: (1) the development of new molecular biology methods to characterize methylation potential; (2) treating the environment as a micro-ecosystem and studying them from a holistic perspective to clearly understand mercury methylation; (3) a more reasonable and sensitive inhibition test needs to be considered. KEY POINTS: • Global Hg microbial methylation is phylogenetically and functionally discussed. • The main drivers of microbial methylation are compared in various condition. • Future study of Hg microbial methylation is proposed.

Simultaneous treatment of chromium-containing wastewater and electricity generation using a plant cathode-sediment microbial fuel cell: investigation of associated mechanism and influencing factors

A novel plant cathode-sediment microbial fuel cell (P-SMFC) was constructed to treat Cr-containing wastewater, and the effects of the plants used, initial concentrations of Cr(VI) employed, and the external resistance on the treatment of wastewater and generation of electricity were investigated. The results showed that the system achieved the best performance when Acorus calamus was the cathode plant, the external resistance was 2000 Ω, and the initial Cr (VI) concentration of the overlying water of is 230 mg/L. A maximum power density of 40.16 mW/m² was reached, and Cr (VI) and COD removal efficiencies in the overlying water were 99.94% and 98.21%, respectively. The closed-circuit installation promoted the attachment of many microorganisms to the cathode, anode and sediment, increased species abundance, and reduced species diversity. The P-SMFC is inexpensive to construct, it consumes no energy, and it can generate bioelectricity; it thus has great application development value as a chromium-containing wastewater treatment method.

Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater

The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.

Desulfuromonas sp. 'CSMB_57', isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals

One of the most abundant and ubiquitous taxa observed in eastern Australian coal seams is an uncultured Desulfuromonas species and part of the Coal Seam Microbiome dataset assigned as 'CSMB_57'. Despite this abundance and ubiquity, knowledge about this taxon is limited. The present study aimed to generate an enrichment culture of Desulfuromonas sp. 'CSMB_57' using culturing strategies that exploit its sulphur-reducing capabilities by utilizing a polysulfide solution in a liquid medium. Using dilution to extinction methods, a highly enriched culture was successfully generated. The full-length 16S rRNA sequence revealed that all closely related taxa were observed in subsurface environments suggesting that D. sp. 'CSMB_57' may be a subsurface specialist. Subsequently, the DNA from the enrichment culture was sequenced and the genome of D. sp. 'CSMB_57' was assembled. Genomic annotation revealed a high number of CRISPR arrays for viral defence, a large array of ABC transporters for amino acid and peptide uptake, as well as genes likely associated with syntrophy such as genes associated with type-IVa pilus, often used for direct interspecies electron transfer, and multiple hydrogenases capable of producing hydrogen. From the various genomic observations, a conceptual ecological model was developed that explores its possible syntrophic roles with hydrogenotrophic methanogens and acetogenic bacteria within coal-seam environments.

Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils

Five strictly anaerobic strains, designated RG2^T, RG3, RG10^T, RF4^T, and RG29, were isolated from paddy soils in China. Strains RG2^T, RF4^T, RG10^T, RG3, and RG29 grew at temperatures ranging 5–42°C and pH ranging 5.5–8.5. Strains RG2^T, RF4^T, RG3, and RG29 could tolerate NaCl up to 0–0.7% (w/v) while strain RG10^T could tolerate NaCl up to 0–0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of Geomonas terrae Red111^T and Geomonas paludis Red736^T. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus Geomonas. Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C_15:1 ω6c, C_16:0, iso-C_15:0, and Summed Feature 3. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cutoff value (ANI 95–96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2^T, RG10^T, and RF4^T could easily be differentiated with the members of the genus Geomonas. Additionally, all the isolated strains possessed nifHDK clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus Geomonas, for which the names Geomonas oryzisoli sp. nov., Geomonas subterranea sp. nov., and Geomonas nitrogeniifigens sp. nov. are proposed. The type strains are RG10^T (= GDMCC1.2537^T = KCTC 26318^T), RG2^T (= GDMCC1.2536^T = KCTC 25317^T), and RF4^T (= GDMCC 1.2547^T = KCTC 25316^T).

Draft Genome Sequences of the Ferric Iron-Reducing Geobacter sp. Strains AOG1 and AOG2, Isolated from Enrichment Cultures on Crystalline Iron(III) Oxides

Here, we report the draft genome sequences of two Geobacter sp. strains, AOG1 and AOG2, isolated from enrichment cultures using crystalline Fe(III) oxides as electron acceptors. Strains AOG1 and AOG2 possess numerous genes encoding multiheme c-type cytochromes and pilA-N genes encoding the pilin monomer of nanowires in their genomes.