Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes

Complete genome analysis of copper resistant bacteria Pseudoalteromonas sp. CuT4-3 isolated from a deep-sea hydrothermal vent

Pseudoalteromonas sp. CuT4-3, a copper resistant bacterium, was isolated from deep-sea hydrothermal sulfides on the Southwest Indian Ridge (SWIR), is an aerobic, mesophilic and rod-shaped bacterium belonging to the family Pseudoalteromonadaceae (class Gammaproteobacteria, order Alteromonadales). In this study, we present the complete genome sequence of strain CuT4-3, which consists of a single circular chromosome comprising 3,660,538 nucleotides with 41.05% G + C content and two circular plasmids comprising 792,064 nucleotides with 40.36% G + C content and 65,436 nucleotides with 41.50% G + C content. In total, 4078 protein coding genes, 105 tRNA genes, and 25 rRNA genes were obtained. Genomic analysis of strain CuT4-3 identified numerous genes related to heavy metal resistance (especially copper) and EPS production. The genome of strain CuT4-3 will be helpful for further understanding of its adaptive strategies, particularly its ability to resist heavy metal, in the deep-sea hydrothermal vent environment.

Metagenomic and genomic analysis of heavy metal-tolerant and -resistant bacteria in resource islands in a semi-arid zone of the Colombian Caribbean

Bacteria from resource islands can adapt to different extreme conditions in semi-arid regions. We aimed to determine the potential resistance and tolerance to heavy metals from the bacterial community under the canopy of three resource islands in a semi-arid zone of the Colombian Caribbean. Total DNA was extracted from soil and through a metagenomics approach, we identified genes related to heavy metal tolerance and resistance under the influence of drought and humidity conditions, as well as the presence or absence of vegetation. We characterized the genomes of bacterial isolates cultivated in the presence of four heavy metals. The abundances of genes related to heavy metal resistance and tolerance were favored by soil moisture and the presence of vegetation. We observed a high abundance of resistance genes (60.4%) for Cu, Zn, and Ni, while 39.6% represented tolerance. These genes positively correlated with clay and silt content, and negatively correlated with sand content. Resistance and tolerance were associated with detoxification mechanisms involving oxidoreductase enzymes, metalloproteases, and hydrolases, as well as transmembrane proteins involved in metal transport such as efflux pumps and ion transmembrane transporters. The Bacillus velezensis C3-3 and Cytobacillus gottheilii T106 isolates showed resistance to 5 mM of Cd, Co, Mn, and Ni through detoxification genes associated with ABC pumps, metal transport proteins, ion antiporter proteins, and import systems, among others. Overall, these findings highlight the potential of bacteria from resource islands in bioremediation processes of soils contaminated with heavy metals.

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.

Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8

Our current knowledge on bacterial cadmium (Cd) resistance is mainly based on the functional exploration of specific Cd-resistance genes. In this study, we carried out a genomic study on Cd resistance of a newly isolated Cellulomonas strain with a MIC of 5 mM Cd. Full genome of the strain, with a genome size of 4.47 M bp and GC-content of 75.35%, was obtained through high-quality sequencing. Genome-wide annotations identified 54 heavy metal-related genes. Four potential Cd-resistance genes, namely zntAY8, copAY8, HMTY8, and czcDY8, were subjected to functional exploration. Quantitative PCR determination of in vivo expression showed that zntAY8, copAY8, and HMTY8 were strongly Cd-inducible. Expression of the three inducible genes against time and Cd concentrations were further quantified. It is found that zntAY8 responded more strongly to higher Cd concentrations, while expression of copAY8 and HMTY8 increased over time at lower Cd concentrations. Heterologous expression of the four genes in Cd-sensitive Escherichia coli led to different impacts on hosts’ Cd sorption, with an 87% reduction by zntAY8 and a 3.7-fold increase by HMTY8. In conclusion, a Cd-resistant Cellulomonas sp. strain was isolated, whose genome harbors a diverse panel of metal-resistance genes. Cd resistance in the strain is not controlled by a dedicated gene alone, but by several gene systems collectively whose roles are probably time- and dose-dependent. The plasmid-free, high-GC strain Y8 may provide a platform for exploring heavy metal genomics of the Cellulomonas genus.

Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

BACKGROUND

Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants' survival.

RESULTS

In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion.

CONCLUSIONS

Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

Bacterial and fungal diversity in the lorandite (TlAsS2) mine 'Allchar' in the Republic of North Macedonia

The Allchar mineral mine is one of the oldest arsenic-antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.

Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus

Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5^T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.

Impacts of Cu and Zn on the performance, microbial community dynamics and resistance genes variations during mesophilic and thermophilic anaerobic digestion of swine manure

In this work, fate of antibiotic resistance genes (ARGs), heavy metal resistance genes (MRGs) and intI1 were investigated during mesophilic (mAD) and thermophilic anaerobic digestion (tAD) of swine manure with presence of Cu and Zn. Results showed that metal reduced the lag phase time. Cu showed stronger inhibition than Zn on archaea community and metals inhibited the growth of acetoclastic methanogens during mAD. Although total concentration of metals increased after AD, they were transformed into stable state. The abundance of qnrS, sul1, sul2 and drfA7 increased 1.2-5.7 times after mAD, while reduced after tAD, showed that tAD was effective in ARGs removal. Structural equation model analysis suggested that intI1 had the most standardized direct effects on ARGs variation in mAD (R = 0.85, p < 0.01), while the co-occurrence of MRGs with ARGs showed significantly positive influences on ARGs variation in tAD (R = 0.82, p < 0.01).

Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance

Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.

Functional metagenomic exploration identifies novel prokaryotic copper resistance genes from the soil microbiome

Functional metagenomics is a premise-free approach for exploring metal resistance genes, enabling more profound effects on the development of bioremediation tools than pure culture based selection. Six soil metagenomic libraries were screened for copper (Cu) resistance genes in the current study through conventional functional genomics. Clones from the six metagenomic libraries were randomly selected from solid medium supplied with Cu, resulting in 411 Cu resistance clones. Thirty-five clones with the strongest Cu resistance were sequenced and 12 unique sequences harboring 25 putative open reading frames were obtained. It is inferred by bioinformatic analysis that putative genes carried by these recombinant plasmids probably function in the pathways of responding to Cu stress, including energy metabolism, integral components of membrane, ion transport/chelation, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, signal transduction and DNA binding. The sequenced clones were re-transformed into Escherichia coli strain DH5α, and the host's biomass and the metal sorption under Cu stress were subsequently determined. The results showed that the biomass of eight of the clones was significantly increased, whereas four of them were significantly reduced. A negative correlation (R = 0.86) was found between the biomass and Cu sorption capacity. The 12 positive clones were further transferred into a Cu-sensitive E. coli strain (ΔCopA), among which nine restored the host's Cu resistance substantially. The Cu resistant genes explored in this study by functional metagenomics possess a potential capacity for developing novel bioremediation strategies, and the findings imply a vast diversity of microbial Cu resistance genetic factors in soil yet to be discovered.

Functional Genomic Identification of Cadmium Resistance Genes from a High GC Clone Library by Coupling the Sanger and PacBio Sequencing Strategies

Functional (meta) genomics allows the high-throughput identification of functional genes in a premise-free way. However, it is still difficult to perform Sanger sequencing for high GC DNA templates, which hinders the functional genomic exploration of a high GC genomic library. Here, we developed a procedure to resolve this problem by coupling the Sanger and PacBio sequencing strategies. Identification of cadmium (Cd) resistance genes from a small-insert high GC genomic library was performed to test the procedure. The library was generated from a high GC (75.35%) bacterial genome. Nineteen clones that conferred Cd resistance to Escherichia coli subject to Sanger sequencing directly. The positive clones were in parallel subject to in vivo amplification in host cells, from which recombinant plasmids were extracted and linearized by selected restriction endonucleases. PacBio sequencing was performed to obtain the full-length sequences. As the identities, partial sequences from Sanger sequencing were aligned to the full-length sequences from PacBio sequencing, which led to the identification of seven unique full-length sequences. The unique sequences were further aligned to the full genome sequence of the source strain. Functional screening showed that the identified positive clones were all able to improve Cd resistance of the host cells. The functional genomic procedure developed here couples the Sanger and PacBio sequencing methods and overcomes the difficulties in PCR approaches for high GC DNA. The procedure can be a promising option for the high-throughput sequencing of functional genomic libraries, and realize a cost-effective and time-efficient identification of the positive clones, particularly for high GC genetic materials.

Nonferrous metal (loid) s mediate bacterial diversity in an abandoned mine tailing impoundment

Migration and transformation of toxic metal (loid) s in tailing sites inevitably lead to ecological disturbances and serious threats to the surroundings. However, the horizontal and vertical distribution of bacterial diversity has not been determined in nonferrous metal (loid) tailing ponds, especially in Guangxi China, where the world's largest and potentially most toxic sources of metal (loid) s are located. Distribution of bacterial communities was stable at horizontal levels. At the surface (0-10 cm), the stability was most attributed to Bacillus and Enterococcus, while bacterial communities at the subsurface (50 cm) were mainly contributed by Nitrospira and Sulfuricella. Variable vertical distribution of bacterial communities has led to the occurrence of specific genera and specific predicted functions (such as transcription regulation factors). Sulfurifustis (a S-oxidizing and inorganic carbon fixing bacteria) genera were specific at the surface, whereas Streptococcus-related genera were found at the surface and subsurface, but were more abundant in the latter depth. Physical-chemical parameters, such as pH, TN, and metal (loid) (As, Cd, Pb, Cu, and Zn) concentrations were the main drivers of bacterial community abundance, diversity, composition, and metabolic functions. These results increase our understanding of the physical-chemical effects on the spatial distribution of bacterial communities and provide useful insight for the bioremediation and site management of nonferrous metal (loid) tailings.

Metagenomic insights into the microbial diversity in manganese-contaminated mine tailings and their role in biogeochemical cycling of manganese

To extend the knowledge on the microbial diversity of manganese rich environments, we performed a clone library based study using metagenomic approach. Pyrosequencing based analysis of 16S rRNA genes were carried out on an Illumina platform to gain insights into the bacterial community inhabiting in a manganese mining site and the taxonomic profiles were correlated with the inherent capacities of these strains to solubilise manganese. The application of shot gun sequencing in this study yielded results which revealed the highest prevalence of Proteobacteria (42.47%), followed by Actinobacteria (23.99%) in the area of study. Cluster of orthologous group (COG) functional category has 85,066 predicted functions. Out of which 11% are involved in metabolism of amino acid, 9% are involved in production and conversion of energy while Keto Encyclopedia of Gene and Genomes (KEGG) functional category has 107,388 predicted functions, out of which 55% are involved in cellular metabolism, 15% are environmental and information processing and 12% are genetic information processing in nature. The isolated microbial consortia demonstrated visible growth in presence of high concentrations of Mn. Solubilisation studies resulted in 86% of manganese recovery after 20 days. The result presented in this study has important implications in understanding the microbial diversity in manganese contaminated mine tailings and their role in natural geochemical cycling of Mn.

The effects of bio-available copper on macrolide antibiotic resistance genes and mobile elements during tylosin fermentation dregs co-composting

In this study, aerobic co-composting of tylosin fermentation dregs (TFDs) and sewage sludge with different adding concentrations of copper (Cu) was investigated to inspect the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Results showed that two concentrations of Cu did affect not only the abiotic factors but the relative abundances of resistance genes. High concentration of Cu inhibited the metabolic capacity of microbial community and the nitrogen-fixing process while had little effect on the degradation of TYL and TOC. The abundance of ermT, mefA, mphA increased partly attributed to the toxic effects and co-selective pressure from heavy metal reflected by MRGs. There was significant correlation among some environmental factors like pH, bio-Cu, organic matters and ARGs.

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647^T (here referred to as Leptospirillum ferriphilum ^T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum ^T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS₂). Adaptations of Leptospirillum ferriphilum ^T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum ^T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum ^T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.

Real-time PCR based analysis of metal resistance genes in metal resistant Pseudomonas aeruginosa strain J007

A uranium (U)-resistant and -accumulating Pseudomonas aeruginosa strain was characterized to assess the response of toxic metals toward its growth and expression of metal resistance determinants. The bacterium showed MIC (minimum inhibitory concentration) values of 6, 3, and 2 mM for Zn, Cu, and Cd, respectively; with resistance phenotype conferred by periplasmic Cu sequestering copA and RND type heavy metal efflux czcA genes. Real-time PCR-based expression analysis revealed significant upregulation of both these genes upon exposure to low concentrations of metals for short duration, whereas the global stress response gene sodA encoding superoxide dismutase enzyme was upregulated only at higher metal concentrations or longer exposure time. It could also be inferred that copA and czcA are involved in providing resistance only at low metal concentrations, whereas involvement of "global stress response" phenomenon (expression of sodA) at higher metal concentration or increased exposure was evident. This study provides significant understanding of the adaptive response of bacteria surviving in metal and radionuclide contaminated environments along with the development of real-time PCR-based quantification method of using metal resistance genes as biomarker for monitoring relevant bacteria in such habitats.