Mechanism of arsenic resistance in endophytic bacteria isolated from endemic plant of mine tailings and their arsenophore production

Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan

The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).

Insight into the genome of an arsenic loving and plant growth-promoting strain of Micrococcus luteus isolated from arsenic contaminated groundwater

Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated water of Purbasthali, West Bengal, India, and through draft genome sequence; it was identified as a strain of Micrococcus luteus that comprised of 2.4 Mb genome with 73.1% GC content and 2256 protein coding genes. As the accessory genome, about 22 genomic islands (GIs) associated with many metal-resistant genes were identified. This strain was capable to tolerate more than 46,800 mg/L arsenate and 390 mg/L arsenite salts as well as found to be tolerable to multi-metals such as Fe, Pb, Mo, Mn, and Zn up to a certain limit of concentrations. Strain AKS4c was able to oxidize arsenite to less toxic arsenate, and its arsenic adsorption property was qualitatively confirmed through X-ray fluorescence (XRF) and Fourier transform infrared spectroscopy (FTIR) analysis. Quantitative estimation of plant growth-promoting attributes like Indole acetic acid (IAA), Gibberellic acid (GA), and proline production and enhancement of rice seedling growth in laboratory condition leads to its future applicability in arsenic bioremediation as a plant growth-promoting rhizobacteria (PGPR).

Arsenic pollution cycle, toxicity and sustainable remediation technologies: A comprehensive review and bibliometric analysis

Arsenic pollution and its allied impacts on health are widely reported and have gained global attention in the last few decades. Although the natural distribution of arsenic is limited, anthropogenic activities have increased its mobility to distant locations, thereby increasing the number of people affected by arsenic pollution. Arsenic has a complex biogeochemical cycle which has a significant role in pollution. Therefore, this review paper has comprehensively analysed the biogeochemical cycle of arsenic which can dictate the occurrence of arsenic pollution. Considering the toxicity and nature of arsenic, the present work has also analysed the current status of arsenic pollution around the world. It is noted that the south of Asia, West-central Africa, west of Europe and Latin America are major hot spots of arsenic pollution. Bibliometric analysis was performed by using scopus database with specific search for keywords such as arsenic pollution, health hazards to obtain the relevant data. Scopus database was searched for the period of 20 years from year 2003-2023 and total of 1839 articles were finally selected for further analysis using VOS viewer. Bibliometric analysis of arsenic pollution and its health hazards has revealed that arsenic pollution is primarily caused by anthropogenic sources and the key sources of arsenic exposure are drinking water, sea food and agricultural produces. Arsenic pollution was found to be associated with severe health hazards such as cancer and other health issues. Thus considering the severity of the issue, few sustainable remediation technologies such as adsorption using microbes, biological waste material, nanomaterial, constructed wetland, phytoremediation and microorganism bioremediation are proposed for treating arsenic pollution. These approaches are environmentally friendly and highly sustainable, thus making them suitable for the current scenario of environmental crisis.

Production, characterization and in vitro biological activities of crude pigment from endophytic Micrococcus luteus associated with Avicennia marina

Due to their non-toxic and non-carcinogenic nature, biopigments have a phenomenal benefit over synthetic pigments, making them a desirable source for human utilization and a potential alternative to traditional synthetic pigments that are hazardous to the environment and public health. Endosymbiotic interactions between mangrove plants and bacteria could provide an alternate source for the synthesis of unique compounds with potent biomedical applications. Pigmented endophytic bacteria were screened from the explants of Avicennia marina, a mangrove plant, and identified as Micrococcus luteus by molecular characterization. The intracellular pigment was successfully extracted using the sonication-assisted solvent extraction method, and screening factors impacting the pigmentation bioprocess were determined using a one-factor-at-a-time approach. The endophyte produced yellow pigment in the liquid medium, with the maximum growth and pigment production recorded in nutrient broth at 37 ℃ and pH 7 after 96 h of incubation, while the maximum accumulation of pigment was observed in the media supplemented with glucose and tryptone as carbon and nitrogen sources, respectively. The extracted crude pigment was further characterized by ultraviolet, followed by Fourier transform infrared spectroscopy and gas chromatography-mass spectrometry. The obtained crude pigment has been evaluated for its antioxidant and anticancer activity by various assays, such as DPPH radical scavenging activity, FRAP assay, superoxide anion and nitric oxide radical scavenging, metal chelating activity, phosphomolybdenum assay, and MTT assay, respectively, at varying concentrations. The results of our study revealed that the yellow pigment produced by the endophyte showed significant dose-dependent antioxidant and anticancer activity.

Arsenic and mercury tolerant rhizobacteria that can improve phytoremediation of heavy metal contaminated soils

Background

Mining deposits often contain high levels of toxic elements such as mercury (Hg) and arsenic (As) representing strong environmental hazards. The purpose of this study was the isolation for plant growth promoting bacteria (PGPBs) that can improve phytoremediation of such mine waste deposits.

Methods

We isolated native soil bacteria from the rhizosphere of plants of mine waste deposits and agricultural land that was previously mine tailings from Tlalpujahua Michoacán, Mexico, and were identified by their fatty acid profile according to the MIDI Sherlock system. Plant growth promoting traits of all bacterial isolates were examined including production of 3-indoleacetic acid (IAA), siderophores, biofilm formation, and phosphate solubilization. Finally, the response of selected bacteria to mercury and arsenic was examined an in-vitro assay.

Results

A total 99 bacterial strains were isolated and 48 identified, representing 34 species belonging to 23 genera. Sixty six percent of the isolates produced IAA of which Pseudomonas fluorescens TL97 produced the most. Herbaspirillum huttiense TL36 performed best in terms of phosphate solubilization and production of siderophores. In terms of biofilm formation, Bacillus atrophaeus TL76 was the best.

Discussion

Most of the bacteria isolates showed high level of tolerance to the arsenic (as HAsNa₂O₄ and AsNaO₂), whereas most isolates were susceptible to HgCl₂. Three of the selected bacteria with PGP traits Herbispirillum huttiense TL36, Klebsiella oxytoca TL49 and Rhizobium radiobacter TL52 were also tolerant to high concentrations of mercury chloride, this might could be used for restoring or phytoremediating the adverse environmental conditions present in mine waste deposits.

Biological effect of phosphate on the dissimilatory arsenate-respiring bacteria-catalyzed reductive mobilization of arsenic from contaminated soils

Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be the major drive of the reductive mobilization of arsenic from solid phases. However, it is not fully understood how phosphate, a structural analog of arsenate, affects the DARPs-mediated arsenic mobilization. This work aimed to address this issue. As-contaminated soils were collected from a Shimen Realgar Mine-affected area. We identified a unique diversity of DARPs from the soils, which possess high As(V)-respiring activities using one of multiple small organic acids as the electron donor. After elimination of the desorption effect of phosphate on the As mobilization, the supplement of additional 10 mM phosphate to the active slurries markedly increased the microbial community-mediated reductive mobilization of arsenic as revealed by microcosm tests; this observation was associated to the fact that phosphate significantly increased the As(V)-respiratory reductase (Arr) gene abundances in the slurries. To confirm this finding, we further obtained a new DARP strain, Priestia sp. F01, from the samples. We found that after elimination of the chemical effect of phosphate, the supplement of 10 mM phosphate to the active slurries resulted in an 82.2% increase of the released As(III) in the solutions, which could be contributed to that excessive phosphate greatly increased the Arr gene abundance, and enhanced the transcriptional level of arrA gene and the bacterial As(V)-respiring activity of F01 cells. Considering that phosphate commonly coexists with As in the environment, and is a frequently-used fertilizer, these findings are helpful for deeply understanding why As concentrations in contaminated groundwater are dynamically fluctuated, and also provided new knowledge on the interactions between the biogeochemical processes of P and As.

Heavy metals distribution and ecological risk assessment including arsenic resistant PGPR in tidal mangrove ecosystem

Heavy metals (HM) are the major proximate drivers of pollution in the mangrove ecosystem. Therefore, ecological risk (ER) due to HM distribution/concentration in core-sediment of Puzi mangrove region (Taiwan) was examined with tidal influence (TI) along with indigenous rhizospheric bacteria (IRB). The HM concentration was observed higher at active-tidal-sediment compared to partially-active-sediment. Geo-accumulation index (I_geo) and contamination factor (CF) indicated the tidal-sediment was highly contaminated with arsenic (As) and moderately contaminated with Lead (Pb) and Zinc (Zn). However, the pollution loading index (PLI) and degree of contamination (C_d) exhibited 'no pollution' and 'low-moderate degree of contamination', in the studied region respectively. The isolated IRB (Priestia megaterium, Bacillus safenis, Bacillus aerius, Bacillus subtilis, Bacillus velenzenesis, Bacillus lichenoformis, Kocuria palustris, Enterobacter hormaechei, Pseudomonus fulva, and Paenibacillus favisporus; accession number OM979069-OM979078) exhibited the arsenic resistant behavior with plant-growth-promoting characters (IAA, NH₃, and P-solubilization), which can be used in mangrove reforestation and bioremediation of HM.

Metallophores production by bacteria isolated from heavy metal-contaminated soil and sediment at Lerma-Chapala Basin

Environmental pollution as a result of heavy metals (HMs) is a worldwide problem and the implementation of eco-friendly remediation technologies is thus required. Metallophores, low molecular weight compounds, could have important biotechnological applications in the fields of agriculture, medicine, and bioremediation. This study aimed to isolate HM-resistant bacteria from soils and sediments of the Lerma-Chapala Basin and evaluated their abilities to produce metallophores and to promote plant growth. Bacteria from the Lerma-Chapala Basin produced metallophores for all the tested metal ions, presented a greater production of As³⁺ metallophores, and showed high HM resistance especially to Zn²⁺, As⁵⁺, and Ni²⁺. A total of 320 bacteria were isolated with 170 strains showing siderophores synthesis. Members of the Delftia and Pseudomonas genera showed above 92 percent siderophore units (psu) during siderophores production and hydroxamate proved to be the most common functional group among the analyzed siderophores. Our results provided evidence that Lerma-Chapala Basin bacteria and their metallophores could potentially be employed in bioremediation processes or may even have potential for applications in other biotechnological fields.

Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation

Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.

Characterization of Arsenic-Resistant Endophytic Bacteria From Alfalfa and Chickpea Plants

The present investigation was carried out to isolate arsenic (As)-resistant endophytic bacteria from the roots of alfalfa and chickpea plants grown in arsenic-contamination soil, characterize their As tolerance ability, plant growth-promoting characteristics, and their role to induce As resistance by the plant. A total of four root endophytic bacteria were isolated from plants grown in As-contaminated soil (160-260-mg As kg^-1 of soil). These isolates were studied for plant growth-promoting (PGP) characteristics through siderophore, phosphate solubilization, nitrogen fixation, protease, and lipase production, and the presence of the arsenate reductase (arsC) gene. Based on 16S rDNA sequence analysis, these isolates belong to the genera Acinetobacter, Pseudomonas, and Rahnella. All isolates were found As tolerant, of which one isolate, Pseudomonas sp. QNC1, showed the highest tolerance up to 350-mM concentration in the LB medium. All isolates exhibited phosphate solubilization activity. Siderophore production activity was shown by only Pseudomonas sp. QNC1, while nitrogen fixation activity was shown by only Rahnella sp. QNC2 isolate. Acinetobacter sp. QNA1, QNA2, and Rahnella sp. QNC2 exhibited lipase production, while only Pseudomonas sp. QNC1 was able to produce protease. The presence of the arsC gene was detected in all isolates. The effect of endophytic bacteria on biomass production of alfalfa and chickpea in five levels of arsenic concentrations (0-, 10-, 50-, 75-, and 100-mg kg^-1 soil) was evaluated. The fresh and dry weights of roots of alfalfa and chickpea plants were decreased as the arsenic concentration of the soil was increased. Results indicate that the fresh and dry root weights of alfalfa and chickpea plants were significantly higher in endophytic bacteria-treated plants compared with non-treated plants. Inoculation of chickpea plants with Pseudomonas sp. QNC1 and Rahnella sp. QNC2 induced lower NPR3 gene expression in chickpea roots grown in soil with the final concentration of 100-mg kg^-1 sodium arsenate compared with the non-endophyte-treated control. The same results were obtained in Acinetobacter sp. QNA2-treated alfalfa plants grown in the soil plus 50-mg kg^-1 sodium arsenate. These results demonstrated that arsenic-resistant endophytic bacteria are potential candidates to enhance plant-growth promotion in As contamination soils. Characterization of bacterial endophytes with plant growth potential can help us apply them to improve plant yield under stress conditions.

Heavy-metal resistance mechanisms developed by bacteria from Lerma-Chapala basin

Heavy-metal (HM) contamination is a huge environmental problem in many countries including Mexico. Currently, microorganisms with multiple heavy-metal resistance and/or plant-promoting characteristics have been widely used for bioremediation of HM-contaminated soils. The aim of the study was isolated bacteria with multiple heavy-metal resistance and to determinate the resistance mechanism developed by these organisms. A total of 138 aerobic bacteria were isolated from soil and sediments surrounding the Lerma-Chapala basin located in the boundary of the States of Michoacán and Jalisco states of Mexico. One hundred and eight strains showed at least 1 plant growth-promoting features. The Lerma-Chapala basin bacteria were also resistant to high concentrations of HMs including the metalloid arsenic. Sequence analysis of 16S RNA genes reveled that these bacteria were mainly affiliated to the phyla Proteobacteria (38%), Firmicutes (31%) and Actinobacteria (25%), covering 21 genera with Bacillus as the most abundant one. Among them, at least 27 putative novel species were detected in the genera Acinetobacter, Arthrobacter, Bacillus, Agrobacterium, Dyadobacter, Enterobacter, Exiguobacterium, Kluyvera, Micrococcus, Microbacterium and Psychrobacter. In addition, these bacteria developed various heavy-metal-resistance mechanisms, such as biosorption/bioaccumulation, immobilization and detoxification. Therefore, the bacteria isolated from soils and sediments of Lerma-Chapala basin could be used in bioremediation strategies.

Bioimmobilization of toxic metals by precipitation of carbonates using Sporosarcina luteola: An in vitro study and application to sulfide-bearing tailings

Metal release from mining wastes is a major environmental problem affecting ecosystems that requires effective, low-cost strategies for prevention and reclamation. The capacity of two strains (UB3 and UB5) of Sporosarcina luteola was investigated to induce the sequestration of metals by precipitation of carbonates in vitro and under microcosm conditions. These strains carry the ureC gene and have high urease activity. Also, they are highly resistant to metals and have the capacity for producing metallophores and arsenophores. SEM, EDX and XRD reveal that the two strains induced precipitation of calcite, vaterite and magnesian calcite as well as several (M²⁺)CO₃ such as hydromagnesite (Mg²⁺), rhodochrosite (Mn²⁺), cerussite (Pb²⁺), otavite (Cd²⁺), strontianite (Sr²⁺), witherite (Ba²⁺) and hydrozincite (Zn²⁺) in vitro. Inoculation of the mixed culture of UB3+UB5 in tailings increased the pH and induced the precipitation of vaterite, calcite and smithsonite enhancing biocementation and reducing pore size and permeability slowing down the oxidation of residual sulfides. Results further demonstrated that the strains of S. luteola immobilize bioavailable toxic elements through the precipitation and coprecipitation of thermodynamically stable (M²⁺)CO₃, Fe-Mn oxyhydroxides and organic chelates.

Study of As-resistant bacteria from Nadia, India and a survey of two As resistance-related proteins

The present investigation deals with the characterisation of three As-resistant bacteria, Bacillus aryabhattai strain VPS1, Bacillus licheniformis strain VPS6 and Sporosarcina thermotolerans strain VPS7 isolated from the rhizosphere of a contaminated paddy field in Chakdaha, Nadia, West Bengal, India. Two strains, VPS6 and VPS7 showed ureolytic activity, which can be used for microbial-induced calcite precipitation of As as a bioremediation option. However, As reduction and oxidation capacities were not reported in any of these bacteria. A phylogenetic tree of 16S ribosomal RNA gene sequences was constructed for all three bacterial isolates, including different species of As-resistant Bacillus and Sporosarcina. Furthermore, literature survey and genome mining were employed to explore the diversity of As resistance-related proteins, arsenite S-adenosylmethyltransferase (ArsM) and arsenical pump membrane protein (ArsB) among different bacteria, and the phylogenetic relatedness was studied to understand the distribution and evolution of their amino acid sequences. ArsB was predominantly present in a wide variety of bacteria (347 taxa); however, ArsM was reported in comparatively fewer isolates (109 taxa). There were a total of 60 similar taxa that contained both ArsM and ArsB. Both proteins were most abundantly present in phylum Proteobacteria. Overall, this investigation enumerates As-resistant bacteria to understand the As metabolism in the environment, and the phylogenetic analysis of As resistance-related proteins helps in understanding the functional relationship in different bacteria for their role in As mobility in the environment.

Heavy metal resistance in bacteria from animals

Resistance to metals and antimicrobials is a natural phenomenon that existed long before humans started to use these products for veterinary and human medicine. Bacteria carry diverse metal resistance genes, often harboured alongside antimicrobial resistance genes on plasmids or other mobile genetic elements. In this review we summarize the current knowledge about metal resistance genes in bacteria and we discuss their current use in the animal husbandry.