Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine

Adaptation to metal(loid)s in strain Mucilaginibacter rubeus P2 involves novel arsenic resistance genes and mechanisms

Arsenic is a ubiquitous environmental toxi substance that affects human health. Compared to inorganic arsenicals, reduced organoarsenicals are more toxic, and some of them are recognized as antibiotics, such as methylarsenite [MAs(III)] and arsinothricin (2-amino-4-(hydroxymethylarsinoyl)butanoate, or AST). To date, organoarsenicals such as MAs(V) and roxarsone [Rox(V)] are still used in agriculture and animal husbandry. How bacteria deal with both inorganic and organoarsenic species is unclear. Recently, we identified an environmental isolate Mucilaginibacter rubeus P2 that has adapted to high arsenic and antinomy levels by triplicating an arsR-mrarsUBact-arsN-arsC-(arsRhp)-hp-acr3-mrme1Bact-mrme2Bactgene cluster. Heterologous expression of mrarsMBact, mrarsUBact, mrme1Bact and mrme2Bact, encoding putative arsenic resistance determinants, in the arsenic hypersensitive strain Escherichia coli AW3110 conferred resistance to As(III), As(V), MAs(III) or Rox(III). Our data suggest that metalloid exposure promotes plasticity in arsenic resistance systems, enhancing host organism adaptation to metalloid stress.

Complex interactions between diverse mobile genetic elements drive the evolution of metal-resistant bacterial genomes

In this study, we compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. We identified diverse and novel MGEs with evidence of multiple LGT events shaping their genomic structure and heavy metal resistance. Among the three metal-resistant strains, Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals including mercury, cadmium, copper, zinc and lead. Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing by Illumina and Oxford Nanopore technologies was undertaken to obtain comprehensive genomic data. The Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, whereas the Pseudoxanthomonas strain contained one circular chromosome. Consistent with their metal resistance profiles, the strains of Sphingobium and Sphingopyxis contained a higher quantity of diverse metal resistance genes across their chromosomes and plasmids compared to the single-metal resistant Pseudoxanthomonas SE1. In all three strains, metal resistance genes were principally associated with various novel MGEs including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements and group II introns, indicating their importance in facilitating metal resistance adaptation in a contaminated environment. In the Pseudoxanthomonas strain, metal resistance regions were largely situated on a GI. The chromosomes of the strains of Sphingobium and Sphingopyxis contained multiple metal resistance regions, which were likely acquired by several GIs, ICEs, numerous IS elements, several Tn3 family transposons and RIT elements. Two of the plasmids of Sphingobium were impacted by Tn3 family transposons and ISs likely integrating metal resistance genes. The two plasmids of Sphingopyxis harboured transposons, IS elements, an RIT element and a group II intron. This study provides a comprehensive annotation of complex genomic regions of metal resistance associated with novel MGEs. It highlights the critical importance of LGT in the evolution of metal resistance of bacteria in contaminated environments.

Complete genome sequence of Mucilaginibacter gossypii P3, a heavy metal(loid)-resistant bacterium, isolated from a gold and copper mine

Mucilaginibacter gossypii P3, which was isolated from the sub-surface soil of the Zijin Gold and Copper Mine, displayed extremely high resistance to multiple heavy metal(loid)s and contained two novel ars operons. Complete genome sequencing of P3 yielded a single, closed genome of 7,187,928 bp, with GC content of 42.79%.

Longitudinal physiological and transcriptomic analyses reveal the short term and long term response of Synechocystis sp. PCC6803 to cadmium stress

Due to the bioaccumulation and non-biodegradability of cadmium, Cd can pose a serious threat to ecosystem even at low concentration. Microalgae is widely distributed photosynthetic organisms in nature, which is a promising heavy metal remover and an effective industrial sewage cleaner. However, there are few detailed reports on the short-term and long-term molecular mechanisms of microalgae under Cd stress. In this study, the adsorption behavior (growth curve, Cd removal efficiency, scanning electron microscope, Fourier transform infrared spectroscopy, and dynamic change of extracellular polymeric substances), cytotoxicity (photosynthetic pigment, MDA, GSH, H₂O₂, O₂^-) and stress response mechanism of microalgae were discussed under EC50. RNA-seq detected 1413 DEGs in 4 treatment groups. These genes were related to ribosome, nitrogen metabolism, sulfur transporter, and photosynthesis, and which been proved to be Cd-responsive DEGs. WGCNA (weighted gene co-expression network analysis) revealed two main gene expression patterns, short-term stress (381 genes) and long-term stress (364 genes). The enrichment analysis of DEGs showed that the expression of genes involved in N metabolism, sulfur transporter, and aminoacyl-tRNA biosynthesis were significantly up-regulated. This provided raw material for the synthesis of the important component (cysteine) of metal chelate protein, resistant metalloprotein and transporter (ABC transporter) in the initial stage, which was also the short-term response mechanism. Cd adsorption of the first 15 min was primary dependent on membrane transporter and beforehand accumulated EPS. Simultaneously, the up-regulated glutathione S-transferase (GSTs) family proteins played a role in the initial resistance to exogenous Cd. The damaged photosynthetic system was repaired at the later stage, the expressions of glycolysis and gluconeogenesis were up-regulated, to meet the energy and substances of physiological metabolic activities. The study is the first to provide detailed short-term and long-term genomic information on microalgae responding to Cd stress. Meanwhile, the key genes in this study can be used as potential targets for algae-mediated genetic engineering.

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.

Interactive effects of biochar amendment and lead toxicity on soil microbial community

This study determined the interactive effects of biochar and lead toxicity on the soil microbial community in a phytoextraction experiment. Arranged with a completely randomized design in a greenhouse, banana liners were planted singly in a sandy soil spiked with Pb(NO3)2 at 0, 400 and 1200 mg kg-1 and amended with bamboo biochar (pyrolyzing at 600 °C) at 0, 1, 3%. Soil samples were taken from triplicated pots five months after planting and measured for (i) content of lead and organic carbon; (ii) lead speciation; and (iii) microbial community composition through 16S rRNA gene sequencing. DNA sequencing results showed that lead and biochar treatments had significant individual and interactive effects on soil microbial dissimilarities from taxonomic levels of phyla to genera. While some specific taxa were lead resistant, biochar addition apparently alleviated lead toxicity and increased their richness (e.g., Alkanibacter, Muciaginibacter, Burkholderiaceae, and Beggiatoaceae). Soil analysis data indicated that biochar not only helped retain more lead in the soil matrix but created a soil environment inducive for transformation of lead into highly insoluble pyromorphite. This study highlights the effectiveness of biochar for lead remediation and the sensitivity of soil microorganisms in sensing changes in soil environment and lead bioavailability.

Extrapolymeric substances (EPS) in Mucilaginibacter rubeus P2 displayed efficient metal(loid) bio-adsorption and production was induced by copper and zinc

Strains of the genus Mucilaginibacter, belonging to the phylum Bacteroidetes, have been noted for exhibiting high genome plasticity and for the vigorous production of extracellular polymeric substances (EPS). Here we analyzed the composition and properties of EPS generated by M. rubeus P2, isolated from a gold-copper mine and exhibiting extremely high resistance to multiple heavy metals. Production of EPS increased significantly upon exposure to elevated concentrations of Cu(II) and Zn(II), but not Au(III). In addition, the EPS produced by M. rubeus P2 displayed extremely high bio-adsorption of As(III), Cu(II) and Au(III), but not of Zn(II). Moreover, EPS production in Mucilaginibacter rubeus P2 exposed to 1 mM of Cu(II) was 8.5 times higher than EPS production in the same strain without metal (loid)-exposure. These findings constitute the basis for a future use of these EPS-overproducing bacteria in bioremediation of heavy metal contaminated environments. The functional groups, especially -SH, CO, and N-H/C-N in the fingerprint zone of glutathione (GSH) and polysaccharides-like components of EPS, were the main components of EPS involved in both Zn(II) and Cu(II) binding and removal. Around 31.22% and 5.74% of Cu(II)-treated EPS was shown to exist as (CO) structures and these structures were converted into C-OH and O-C-O upon exposure to Cu(II), respectively. In contrast, (C-OH/C-O-C/P-O-C) groups in EPS were observed to be positively correlated to increasing concentrations of Zn(II) in strain P2. Furthermore, the complete genome of M. rubeus P2 helped us to identify 350 genes involved in carbohydrate metabolism, some of which are predicted to be involved in EPS production and modification. This work describes the first detailed biochemical and biophysical analysis of EPS from any strain of Mucilaginibacter with unique heavy metal binding properties. The results will be useful for a better understanding of how microorganisms such as M. rubeus P2 adapt to heavy metal polluted environments and how this knowledge can potentially be harnessed in biotechnological applications such as industrial waste water purification, bioremediation of heavy metal contaminated soil and beneficial plant microbe interactions. The toolbox provided in this paper will provide a valuable basis for future studies.

Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam

In 2015 a mine dam with Mn-Fe-rich tailings collapsed releasing million tons of sediments over an estuary, in the Southwest of Brazil. The tailings have a high concentration of metals that contaminated soil until the present day. The high contaminant concentrations possibly caused a selection for microorganisms able to strive in such harsh conditions. Here, we isolated metal(loid) and anti-biotic resistance bacteria from the contaminated estuarine soil. After 16S rDNA sequencing to identify the strains, we selected the Mucilaginibacter sp. strain for a whole-genome sequence due to the bioprospective potential of the genus and the high resistance profile. We obtained a complete genome and a genome-guided characterization. Our finding suggests that the 21p strain is possibly a new species of the genus. The species presented genes for resistance for metals (i.e., As, Zn, Co, Cd, and Mn) beyond resistance and cross-resistance for antibiotics (i.e., quinolone, aminoglycoside, β-lactamase, sulphonamide, tetracycline). The Mucilaginibacter sp. 21p description as new species should be further explored, as their extracellular polymeric substances and the potential of this strain as bioremediation and as a growth promoter in high met-al(loid) contaminated soil.

Rehabilitation of mine soils by phytostabilization: Does soil inoculation with microbial consortia stimulate Agrostis growth and metal(loid) immobilization?

Metal(loid) soil pollution resulting from mining activities is an important issue that has negative effects on the environment (soil acidification, lack of vegetation, groundwater pollution) and human health (cancer, chronic diseases). In the context of a phytostabilization process for the bioremediation of a mine soil highly contaminated by arsenic (As) and lead (Pb), a pot experiment was set up to study the effect of plant sowing and microbial inoculation on soil properties, metal(loid) (im)mobilization in soil and accumulation in plant, and plant growth. For this, mine soil was sown with endemic metallicolous Agrostis seeds and/or inoculated with endogenous microbial consortia previously selected for their As and Pb tolerance. Agrostis was able to develop on the contaminated mine soil and immobilized metal(loid)s through metal(loid) accumulation in the roots. Its growth was improved by microbial consortium inoculation. Moreover, microbial consortium inoculation increased soil organic content and electrical conductivity, and led to an increase in soil microbial activities (linked to C and P cycles); however, it also induced a metal(loid) mobilization. In conclusion, microbial consortium inoculation stimulated the growth of endemic Agrostis plants and thus ameliorated the phytostabilization of a former mine soil highly polluted by As and Pb. This study is thus a good example of the benefits of coupling several approaches such as phytostabilization and bioaugmentation for the bioremediation of former mine contaminated sites.

Complete Genome Sequence of a Mucilaginibacter sp. Strain Isolated from Estuarine Soil Contaminated with Mine Tailings from the Samarco Disaster at Fundão Dam

We report the complete genome sequence of Mucilaginibacter strain 21P, which was isolated from estuarine soil contaminated with mine tailings from the Samarco disaster, which occurred in 2015 in Brazil. The genome sequence comprised 4,739,655 bp, with a G+C content of 43.2%, and harbors multiple antibiotic and metal resistance genes.

Improved grain yield and lowered arsenic accumulation in rice plants by inoculation with arsenite-oxidizing Achromobacter xylosoxidans GD03

Arsenite is the predominant arsenic species in flooded paddy soil, and arsenite bioaccumulation in rice grains has been identified as a major problem in many Asian countries. Lowering arsenite level in rice plants and grain via accelerating arsenite oxidation is a potential strategy to help populations, who depended on rice consumption, to reduce the internal exposure level of arsenic. We herein isolated a strain, Achromobacter xylosoxidans GD03, with the high arsenite-oxidizing ability and plant growth-promoting traits. We observed that arsenite exposure could promote A. xylosoxidans GD03 to excrete indole-3-acetic acid and thus promoted rice growth. The pot culture experiments of Indica rice cultivar Guang You Ming 118 (GYM118) demonstrated that A. xylosoxidans GD03 inoculation of paddy soil (4.5-180 × 10⁸ CFU GD03/kg soil) significantly accelerated arsenite oxidation in flooded soil. The daily arsenic oxidation rate with GD03 inoculation was 1.5-3.3 times as that without strain GD03 inoculation within the whole growth period of Indica GYM118 in the presence of the native microflora. It thus led to a 34-69%, 43-74%, 24-76% and 35-57% decrease in arsenite concentration of the stems, leaves, bran and grain of Indica GYM118 respectively and a 59-96% increase in rice grain yield. The paddy soil inoculated with 40.0 mL/kg of A. xylosoxidans GD03 resulted in a lowest As(III) concentrations in all rice organs of Indica GYM118, which equivalent to only 24-50% of the As(III) concentrations in the group without GD03 inoculation. The results highlight that a highly arsenite-oxidizing bacterium could accelerate arsenite oxidation of paddy soil when facing competition with the native microflora, thus decrease arsenic toxicity and bioavailable soil arsenic.

Recent advances in exploring the heavy metal(loid) resistant microbiome

Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.

Metal-Resistance in Bacteria: Why Care?

Heavy metal resistance is more than the tolerance one has towards a particular music genera [...].

Azolla filiculoides L. as a source of metal-tolerant microorganisms

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95–105 versus 36–44). In these treatments the share of subdominant Actinobacteria (0.4–0.8%), Firmicutes (0.5–0.9%) and Bacteroidetes (0.2–0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.