Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium

Sb/As immobilization and soil function improvement under the combined remediation strategy of modified biochar and Sb-oxidizing bacteria at a smelting site

Antimony (Sb) and arsenic (As) lead to soil pollution and structural degradation at Sb smelting sites. However, most sites focus solely on Sb/As immobilization, neglecting the restoration of soil functionality. Here, we investigated the effectiveness of Fe/H2O2 modified biochar (Fe@H2O2-BC) and Sb-oxidizing bacteria (Bacillus sp. S3) in immobilizing Sb/As and enhancing soil functional resilience at an Sb smelting site. Over a twelve-month period, the leaching toxicity of As and Sb was reduced to 0.05 and 0.005 mg L-1 (GB3838-2002) respectively, with 1% (w/w) Fe@H2O2-BC and 2% (v/v) Bacillus sp. S3 solution. Compared to CK, the combination of Fe@H2O2-BC and Bacillus sp. S3 significantly reduced the bioavailable As/Sb by 98.00%/93.52%, whilst increasing residual As and reducible Sb fractions by 210.31% and 96.51%, respectively. The combined application generally improved soil aggregate structure, pore characteristics, and water-holding capacity. Fe@H2O2-BC served as a pH buffer and long-term reservoir of organic carbon, changing the availability of carbon substrates to bacteria. The inoculation of Bacillus sp. S3 facilitated the transformation of Sb(III)/As(III) to Sb(V)/As(V) and differentiated the composition and functional roles of bacterial communities in soils. The combination increased the abundance of soil saprotrophs by 164.20%, whilst improving the relative abundance of N- and S-cycling bacteria according to FUNGuild and FAPROTAX analysis. These results revealed that the integrated application was instrumental in As/Sb detoxification/immobilization and soil function restoration, which demonstrating a promising microbially-driven ecological restoration strategy at Sb smelting sites.

The role of an Sb-oxidizing bacterium in modulating antimony speciation and iron plaque formation to reduce the accumulation and toxicity of Sb in rice (Oryza sativa L.)

Microbial antimony (Sb) oxidation in the root rhizosphere and the formation of iron plaque (IP) on the root surface are considered as two separate strategies to mitigate Sb(III) phytotoxicity. Here, the effect of an Sb-oxidizing bacterium Bacillus sp. S3 on IP characteristics of rice exposed to Sb(III) and its alleviating effects on plant growth were investigated. The results revealed that Fe(II) supply promoted IP formation under Sb(III) stress. However, the formed IP facilitated rather than hindered the uptake of Sb by rice roots. In contrast, the combined application of Fe(II) and Bacillus sp. S3 effectively alleviated Sb(III) toxicity in rice, resulting in improved rice growth and photosynthesis, reduced oxidative stress levels, enhanced antioxidant systems, and restricted Sb uptake and translocation. Despite the ability of Bacillus sp. S3 to oxidize Fe(II), bacterial inoculation inhibited the formation of IP, resulting in a reduction in Sb absorption on IP and uptake into the roots. Additionally, the bacterial inoculum enhanced the transformation of Sb(III) to less toxic Sb(V) in the culture solution, further influencing the adsorption of Sb onto IP. These findings highlight the potential of combining microbial Sb oxidation and IP as an effective strategy for minimizing Sb toxicity in sustainable rice production systems.

Selenium bio-nanocomposite based on extracellular polymeric substances (EPS): Synthesis, characterization and application in alleviating cadmium toxicity in rice (Oryza sativa L.)

Selenium nanoparticles (SeNPs) have gained significant attention owing to their favorable bioavailability and low toxicity, making them widely applications in the fields of medicine, food and agriculture. In this study, bacterial extracellular polymeric substances (EPS) were used as a novel stabilizer and capping agent to prepare dispersed SeNPs. Results show that EPS-SeNPs presented negative potential (-38 mV), spherical morphologies with average particle size about 100-200 nm and kept stable at room temperature for a long time. X-ray diffraction (XRD) analysis demonstrated that the synthesized nanoparticles were pure amorphous nanoparticles, and X-ray photoelectron spectroscopy (XPS) spectrum showed a spike at 55.6 eV, indicating the presence of zero-valent nano‑selenium. Fourier-transform infrared spectroscopy (FTIR) and three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy analysis confirmed proteins and polysaccharides in EPS played a crucial role in the synthesis of EPS-SeNPs. Compared to EPS or sodium selenite (Na2SeO3), EPS-SeNPs showed a relatively moderate result in terms of scavenging free radicals in vitro. In contrast, EPS-SeNPs demonstrated lower toxicity to rice seeds than Na2SeO3. Notably, the exogenous application of EPS-SeNPs effectively alleviated the growth inhibition and oxidative damaged caused by cadmium (Cd), and significantly reduced Cd accumulation in rice plants.

Characterization of a Novel Bacillus glycinifermentans Strain MGMM1 Based on Full Genome Analysis and Phenotypic Properties for Biotechnological Applications

Bacillus species have gained much attention based on their phenotypic characteristics and their genetic architecture as biological control agents and plant growth-promotor with bioremediation potential. In this study, we analyzed the whole genome of a novel strain, Bacillus glycinifermentans MGMM1, isolated from the rhizosphere of a weed plant (Senna occidentalis) and assayed its phenotypic characteristics, as well as antifungal and biocontrol ability. The whole genome analysis of MGMM1 identified 4259 putative coding sequences, with an encoding density of 95.75% attributed to biological functions, including genes involved in stimulating plant growth, such as acetolactate synthase, alsS, and genes involved in the resistance to heavy metal antimony (arsB and arsC). AntiSMASH revealed the presence of biosynthetic gene clusters plipastatin, fengycin, laterocidine, geobacillin II, lichenysin, butirosin A and schizokinen. Tests in vitro confirmed that MGMM1 exhibited antifungal activity against Fusarium oxysporum f.sp. radicis-lycopersici (Forl) ZUM2407, Alternaria alternata, F. graminearum and F. spp. and produce protease, lipase amylase and cellulase. Bacillus glycinifermentans MGMM1 demonstrated proteolytic (4.82 ± 1.04 U/mL), amylolytic (0.84 ± 0.05 U/mL) and cellulosic (0.35 ± 0.02 U/mL) enzymatic activities, as well as indole-3-acetic acid production (48.96 ± 1.43 μg/mL). Moreover, the probiotic strain MGMM1 demonstrated a high biocontrol potential of inhibiting (up to 51.45 ± 8.08%) the development of tomato disease caused by Forl ZUM2407. These results suggest that B. glycinifermentans MGMM1 has significant potential as a biocontrol, plant growth-promoting agent in agriculture.

Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine

The Burkholderia cepacia complex (BCC) is a Gram-negative bacterial, including Burkholderia contaminans species. Although the plain Burkholderia is pervasive from taxonomic and genetic perspectives, a common characteristic is that they may use the quorum-sensing (QS) system. In our previous study, we generated the complete genome sequence of Burkholderia contaminans SK875 isolated from the respiratory tract. To our knowledge, this is the first study to report functional genomic features of B. contaminans SK875 for understanding the pathogenic characteristics. In addition, comparative genomic analysis for five B. contaminans genomes was performed to provide comprehensive information on the disease potential of B. contaminans species. Analysis of average nucleotide identity (ANI) showed that the genome has high similarity (> 96%) with other B. contaminans strains. Five B. contaminans genomes yielded a pangenome of 8832 coding genes, a core genome of 5452 genes, the accessory genome of 2128 genes, and a unique genome of 1252 genes. The 186 genes were specific to B. contaminans SK875, including toxin higB-2, oxygen-dependent choline dehydrogenase, and hypothetical proteins. Genotypic analysis of the antimicrobial resistance of B. contaminans SK875 verified resistance to tetracycline, fluoroquinolone, and aminoglycoside. Compared with the virulence factor database, we identified 79 promising virulence genes such as adhesion system, invasions, antiphagocytic, and secretion systems. Moreover, 45 genes of 57 QS-related genes that were identified in B. contaminans SK875 indicated high sequence homology with other B. contaminans strains. Our results will help to gain insight into virulence, antibiotic resistance, and quorum sensing for B. contaminans species.

Antimony oxidation and whole genome sequencing of Phytobacter sp. X4 isolated from contaminated soil near a flotation site

The conversion of the more toxic Sb(III) into less toxic Sb(V) is an effective strategy for the treatment of antimony-contaminated sites. In this study, a strain, Phytobacter sp. X4, which can tolerate high concentrations of antimony and can use nitrate as an electron acceptor for Sb(III) oxidation under anaerobic conditions, was isolated from the deep soil of an antimony mine flotation tailing. Unlike other antimony oxidizing bacteria, X4 oxidized better under high Sb(III) concentration, and the oxidation efficiency of 10 mM Sb(III) reached the maximum at 110 h with 61.8 %. Kinetic study showed X4 yielded a V_max of 1.093 μM∙min^-1 and a K_m of 718.2 μM. The genome of Phytobacter sp. X4 consists of a complete circular chromosome and two plasmids. In addition, X4 had more metal(loid)s resistance genes and highly expressed genes than other Phytobacter spp., reflecting its stronger adaptive advantage in harsh survival environments. We also analyzed the origin and evolution of arsB, arsC, and arsH, which may have been transferred horizontally from other species. iscR and arsH may have an important contribution to Sb(III) oxidation. Thus, Phytobacter sp. X4 has a good ability to remediate high antimony-contaminated sites and can be applied to an anaerobic environment.

Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2

Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.

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.