High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T

Omics technology draws a comprehensive heavy metal resistance strategy in bacteria

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.

Forest management positively reshapes the phyllosphere bacterial community and improves community stability

Research has shown that forest management can improve the post-drought growth and resilience of Qinghai spruce in the eastern Qilian Mountains, located on the northeastern Tibetan Plateau. However, the impact of such management on the tree-associated phyllosphere microbiome is not yet fully understood. This study provides new evidence of positive forest management effects on the phyllosphere microbiome after extreme drought, from the perspectives of community diversity, structure, network inference, keystone species, and assembly processes. In managed Qinghai spruce forest, the α-diversity of the phyllosphere bacterial communities increased, whereas the β-diversity decreased. In addition, the phyllosphere bacterial community became more stable and resistant, yet less complex, following forest management. Keystone species inferred from a bacterial network also changed under forest management. Furthermore, forest management mediated changes in community assembly processes, intensifying the influence of determinacy, while diminishing that of stochasticity. These findings support the hypothesis that management can re-assemble the phyllosphere bacterial community, enhance community stability, and ultimately improve tree growth. Overall, the study highlights the importance of forest management on the phyllosphere microbiome and furnishes new insights into forest conservation from the perspective of managing microbial processes and effects.

Mucilaginibacter aquariorum sp. nov., Isolated from Fresh Water

A Gram-stain-negative, rod-shaped bacterial strain, JC4^T, was isolated from a freshwater sample and determined the taxonomic position. Initial identification based on 16S rRNA gene sequences revealed that strain JC4^T is affiliated to the genus Mucilaginibacter with a sequence similarity of 97.97% to Mucilaginibacter rigui WPCB133^T. The average nucleotide identity and digital DNA-DNA hybridization values between strain JC4^T and Mucilaginibacter species were estimated below 80.92% and 23.9%, respectively. Strain JC4^T contained summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and iso-C_15:0 as predominant cellular fatty acids. The dominant polar lipids were identified as phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was MK-7. The genomic DNA G+C content of strain JC4^T was determined to be 42.44%. The above polyphasic evidences support that strain JC4^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter aquariorum sp. nov. is proposed. The type strain is JC4^T (= KCTC 92230^T = LMG 32715^T).

Mucilaginibacter aurantiaciroseus sp. nov. and Mucilaginibacter flavidus sp. nov., isolated from Renlongba glacier on the Tibetan Plateau

Strains RB4R14^T and RT5R15^T, two Gram-stain-negative, aerobic, rod-shaped, non-motile bacteria, were isolated from ice and cryoconite of Renlongba glacier, respectively, on the Tibetan Plateau, PR China. The results of phylogenetic analysis based on 16S rRNA genes indicated that strains RB4R14^T and RT5R15^T belonged to the genus Mucilaginibacter with the highest similarities to Mucilaginibacter rigui WPCB133^T (98.78 %) and Mucilaginibacter xinganensis BJC16-A31^T (97.64 %), respectively. The genomic DNA G+C contents of strains RB4R14^T and RT5R15^T were 42.8 and 43.1 mol%, respectively. The digital DNA-DNA hybridization values between strains RB4R14^T, RT5R15^T and their close relatives were below 31.9 and 17.4 %, respectively. The average nucleotide identity values between the two novel strains and their close relatives were 79.5-82.0 and 77.9-79.3 % respectively, indicating the novelty of the two isolates at a species level. The two novel strains contained MK-7 as the major menaquinone, and summed feature 3 (comprising C_16 : 1  ω7c and/or C_16 : 1  ω6c), iso-C_15 : 0 and iso-C_17 : 0-3OH as the major fatty acids. The major polar lipid of the two novel strains were phosphatidylethanolamine. Based on phenotypic, chemotaxonomic and phylogenetic results, we propose two novel species, Mucilaginibacter aurantiaciroseus sp. nov. (RB4R14^T=CGMCC 1.11911^T=NBRC 114020^T) and Mucilaginibacter flavidus sp. nov. (RT5R15^T=CGMCC 1.23117^T=NBRC 113930^T).

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.

Nisaea sediminum sp. nov., a heavy metal resistant bacterium isolated from marine sediment in the East China Sea

A Gram-negative, rod-shaped, motile and strictly aerobic bacterium, designated NBU1469^T, was isolated from marine sediment sampled on Meishan Island located in the East China Sea. Strain NBU1469^T grew optimally at temperature of 40 °C, NaCl concentration of 2.0% (w/v) and pH 7.5. Catalase and oxidase activities, H₂S production, nitrate reduction and hydrolysis of Tween 20 were positive. Indole, methyl red reaction, urease, hydrolysis of gelatin, starch, casein, Tweens 40, 60 and 80 were negative. The major cellular fatty acids were C_16:0, C_19:0 cyclo ω8c and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The only respiratory quinone was ubiquinone-10 (Q-10). The major polar lipids were phosphatidylglycerol, two unidentified amino-phospholipids and two unidentified phospholipids. Comparative analysis of the 16S rRNA gene sequence showed highest similarities to the species with validated name Nisaea nitritireducens DR41_18^T (98.1%) and Nisaea denitrificans DR41_21^T (97.6%). Phylogenetic analyses indicated that strain NBU1469^T formed a distinct lineage with strains Nisaea nitritireducens DR41_18^T and Nisaea denitrificans DR41_21^T within the genus Nisaea. The average nucleotide identity and digital DNA-DNA hybridization values between strain NBU1469^T and related species of genus Nisaea were well below the threshold limit for prokaryotic species delineation. The DNA G + C content was 63.6%. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU1469^T is considered to be a representative of a novel species in the genus Nisaea, for which the name Nisaea sediminum sp. nov. is proposed. The type strain is NBU1469^T (=KCTC 82224 ^T =MCCC 1K04763^T).

Performance and mechanisms for V(v) bio-reduction by straw: key influencing factors

A high concentration of vanadium [V(v)] in groundwater is extremely harmful for humans. Weak movability and low toxicity after microbial V(v) reduction have attracted remarkable attention, especially for using solid carbon sources. However, the influencing factors remain unclear. In this study, the initial V(v) concentration, inocula amount and straw dosage were examined to ascertain the mechanisms behind them. Increasing the initial V(v) concentration led to the decrease of the V(v) removal efficiency, which was also positively correlated with the straw dosage within a certain range. The initial sludge amount was not a main factor affecting microbial V(v) removal in this study. With the initial amount of 10 mg L-1 V(v), 25 mL initial inocula and 5 g straw, 88.2% of V(v) was removed. According to the dissolved organic matter (DOM) analysis results, microbial activity prevailed in groups with higher V(v) removal efficiency, indicating that the V(v) bio-reduction was attributed to the microbial activity, which was considered a major factor. Functional species as unclassified_f_Enterobacteriaceae presumably contributed to the V(v) bioreduction, with upregulated ABC transporter genes and enzymes.

Mucilaginibacter hurinus sp. nov., isolated from briquette warehouse soil

A novel bacterial strain, designated ZR32^T, was isolated from briquette warehouse soil in Ulsan (Korea). The strain was aerobic, showing pink-colored colonies on R2A agar. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZR32^T was closely related to Mucilaginibacter soli R9-65^T (97.0%), Mucilaginibacter gynuensis YC7003^T (96.9%), and Mucilaginibacter lutimaris BR-3^T (96.8%). The values of DNA-DNA relatedness related two highest strains M. soli R9-65^T and M. gynuensis YC7003^T were 31.2 ± 6.9% and 19.7 ± 0.3%, respectively. Its genome size was 3.9 Mb, comprising 3402 predicted genes. The DNA G+C content of strain ZR32^T was 43.0 mol%. The major cellular fatty acids (> 5% of total) were summed feature 3 (C_16:1ω6c and/or C_16:1ω7c), C_16:0, C_16:1ω5c, iso-C_15:0, iso-C_17:0 3-OH, and C_17:1ω9c. The major respiratory quinine was menaquinone-7 (MK-7). The major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, one unidentified sphingolipid, and one unidentified polar lipid. Strain ZR32^T showed distinctive characteristics such as the temperature and pH for growth ranges, being positive for β-glucosidase, salicin production, negative for N-acetyl-glucosamine assimilation, being resistant to carbenicillin and piperacillin to related species. On the basis of phenotypic, chemotaxonomic, and phylogenetic data, strain ZR32^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter hurinus sp. nov. is proposed. The type strain is ZR32^T (= KCTC 62193 = CCTCC AB 2017285).