Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Transcriptome analysis of an arsenite-/antimonite-oxidizer, Bosea sp. AS-1 reveals the importance of the type 4 secretion system in antimony resistance

Bosea sp. AS-1 is an arsenite [As(III)] and antimonite [Sb(III)] oxidizer previously isolated by our group from the Xikuangshan Antimony (Sb) Mine area. Our previous study showed that Bosea sp. AS-1 had a preference for oxidizing As(III) or Sb(III) with different carbon sources, which suggested that different metabolic mechanisms may be utilized by the bacteria to survive in As(III)- or Sb(III)-contaminated environments. Here, we conducted whole-genome and transcriptome sequencing to reveal the molecular mechanisms utilized by Bosea sp. AS-1 to resist As(III) or Sb(III). We discovered that AS-1 acquired various As- and Sb-resistant genes in its genome and might resist As(III) or Sb(III) through the regulation of multiple pathways, such as As and Sb metabolism, the bacterial secretion system, oxidative phosphorylation, the TCA cycle and bacterial flagellar motility. Interestingly, we discovered that genes of the type IV secretion system (T4SS) were activated in response to Sb(III), and inhibiting T4SS activity in AS-1 dramatically reduced its oxidation efficiency and tolerance to Sb(III). To our knowledge, this is the first study showing the activation of T4SS genes by Sb and a direct involvement of T4SS in bacterial Sb resistance. Our findings establish the T4SS as an important Sb resistance factor in bacteria and may help us understand the spread of Sb resistance genes in the environment.

In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil

Background

Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized by using standard bioinformatics tools to investigate its phylogenetic relationships, three-dimensional structure and functional parameters.

Results

The phylogenetic relationship of all arsenite oxidase from unculturable microorganisms was revealed their closeness to bacterial order Rhizobiales. The higher aliphatic content showed that these enzymes are thermostable and could be used for in situ bioremediation. A representative protein from each phylogenetic cluster was analysed for secondary structure arrangements which indicated the presence of α-helices (~63%), β-sheets (57–60%) and turns (13–15%). The validated 3D models suggested that these proteins are hetero-dimeric with two chains whereas alpha chain is the main catalytic subunit which binds with arsenic oxides. Three representative protein models were deposited in Protein Model Database. The query enzymes were predicted with two conserved motifs, one is Rieske 3Fe-4S and the other is molybdopterin protein.

Conclusions

Computational analysis of protein interactome revealed the protein partners might be involved in the whole process of arsenic detoxification by Rhizobiales. The overall report is unique to the best of our knowledge, and the importance of this study is to understand the theoretical aspects of the structure and functions of arsenite oxidase in unculturable bacteria residing in arsenic-contaminated sites.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00146-x.

Enhanced reductive defluorination and inhibited infiltration of fluoroglucocorticoids in a river receiving reclaimed water amended by nano zero-valent iron-modified biochar: Performance and mechanisms

The main aim of this study was to investigate the effect of a nano zero-valent iron-modified biochar-amended composite riverbed (nZVI@BC-R) on inhibited infiltration and enhanced biodegradation of fluoroglucocorticoids (FGCs) in a river receiving reclaimed water. The results demonstrated that the removal efficiency of triamcinolone acetonide (TA), a representative FGC, increased from 38.40% and 77.91% to 91.60% in the nZVI@BC-R compared with that of a natural soil riverbed (S-R) and biochar-amended soil riverbed (BC-R). The main removal mechanismwas attributedto adsorption and biodegradation, of which the contribution rates were 32.2% and 59.4% in nZVI@BC-R, 18.9% and 19.5% in S-R, and 24.4% and 53.5% in BC-R, respectively. The removal process could be described by a two-compartment, first-order dynamic model with decay rate constants for adsorption and biodegradation of 4.02700, 22.44400, and 29.07300 d-1 and 0.00286, 0.01562, and 0.03484 d-1 in the S-R, BC-R and nZVI@BC-R, respectively. The mechanism of defluorination accounted for 42.2% of biodegradation in the nZVI@BC-R, which was accompanied by side-chain rupture, oxidation, and ringopening. Functional microbes with iron oxidizing ability and reductive dehalogenating genera, namely Pseudoxanthomonas, Pedobacter, and Bosea, contributed to the high removal rate of TA, particularly in the nZVI@BC-R. Overall, the nZVI@BC-R provided an effective method to inhibit glucocorticoids infiltration into groundwater.

Simultaneous decarburization, nitrification and denitrification (SDCND) in coking wastewater treatment using an integrated fluidized-bed reactor

There are two problems in biological treatment of coking wastewater (CWW): incapability of pre-anaerobic treatment to eliminate the toxicity in wastewater, and the lack of carbon source for subsequent denitrification in pre-aerobic treatment. To achieve simultaneous decarburization, nitrification and denitrification (SDCND) in CWW treatment, biological carrier materials was used to build an integrated fluidized-bed reactor (Reactor B, RB). A conventional fluidized-bed reactor (Reactor A, RA) was used as a control reactor under the same condition. The results showed that RB was more advantageous since its removal efficiencies of COD and TN were 90% and 87%, respectively, which were significantly higher than these in RA (82% and 45%), at a hydraulic retention time (HRT) of 60 h. Microelectrode measurement indicated that oxygen transfer was limited inside the carrier where the formation of a dissolved oxygen (DO) concentration gradient was observed. Microbial community analysis showed that the aerobic and anoxic microenvironments in RB promoted the co-existence of a wider variety of bacteria, thus achieving SDCND. These results indicated the integrated fluidized-bed reactor exhibited promising feasibility for simultaneous carbon and nitrogen removal in CWW treatment under the same aeration driven conditions. The SDCND process realized by fluidized-bed reactor provided a reference for the treatment of toxic industrial wastewater with high carbon to nitrogen ratio.