Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment

Arsenic biogeochemical cycling association with basin-scale dynamics of microbial functionality and organic matter molecular composition

Geogenic arsenic (As)-contaminated groundwater is a sustaining global health concern that is tightly constrained by multiple interrelated biogeochemical processes. However, a complete spectrum of the biogeochemical network of high-As groundwater remains to be established, concurrently neglecting systematic zonation of groundwater biogeochemistry on the regional scale. We uncovered the geomicrobial interaction network governing As biogeochemical pathways by merging in-field hydrogeochemical monitoring, metagenomic analyses, and ultrahigh resolution mass spectrometry (FT-ICR MS) characterization of dissolved organic matter. In oxidizing to weakly reducing environments, the nitrate-reduction and sulfate-reduction encoding genes (narGHI, sat) inhibited the dissolution of As-bearing iron minerals, leading to lower As levels in groundwater. In settings from weakly to moderately reducing, high abundances of sulfate-reduction and iron-transport encoding genes boosted iron mineral dissolution and consequent As release. As it evolved to strongly reducing stage, elevated abundance of methane cycle-related genes (fae, fwd, fmd) further enhanced As mobilization in part by triggering the formation of gaseous methylarsenic. During redox cycling of N, S, Fe, C and As in groundwater, As migration to groundwater and immobilization in mineral particles are geochemically constrained by basin-scale dynamics of microbial functionality and DOM molecular composition. The study constructs a theoretical model to summarize new perspectives on the biogeochemical network of As cycling.

Transformation of phenylarsenic chemical warfare agents and their effect on bacterial communities in Baltic Sea sediment

During the World Wars large quantities of phenylarsenic chemical warfare agents (CWAs) were dumped in the Baltic Sea. Many transformation products of these chemicals have been identified, but the pathways that produce the found chemicals has not been investigated. Here we studied the biotic and abiotic transformation of phenylarsenic CWAs under oxic and anoxic conditions and investigated how the sediment bacterial communities are affected by CWA exposure. By chemical analysis we were able to identify seventeen CWA-related phenylarsenicals, four of which (methylphenylarsinic acid (MPAA), phenylthioarsinic acid (PTAA), phenyldithioarsinic acid (PDTAA) and diphenyldithioarsinic acid (DPDTAA)) have not been reported for marine sediments before. For the first time PTAA was verified from environmental samples. We also observed equilibrium reactions between the found transformation products, which may explain the occurrence of the chemicals. 16S rRNA-analysis showed that bacterial communities in sediments are affected by exposure to phenylarsenic CWAs. We observed increases in the amounts of arsenic-resistant and sulphur-metabolising bacteria. Different transformation products were found in biotic and abiotic samples, which suggests that bacteria participate in the transformation of phenylarsenic CWAs. We propose that methylated phenylarsenicals are produced in microbial metabolism and that chemical reactions with microbially produced sulphur species form sulphur-containing transformation products.

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.

Risk assessment of toxic and hazardous metals in paddy agroecosystem by biochar-for bio-membrane applications

Toxic and carcinogenic metal (loid)s, such arsenic (As) and cadmium (Cd), found in contaminated paddy soils pose a serious danger to environmental sustainability. Their geochemical activities are complex, making it difficult to manage their contamination. Rice grown in Cd and As-polluted soils ends up in people's bellies, where it can cause cancer, anemia, and the deadly itai sickness. Solving this issue calls for research into eco-friendly and cost-effective remediation technology to lower rice's As and Cd levels. This research delves deeply into the origins of As and Cd in paddy soils, as well as their mobility, bioavailability, and uptake mechanisms by rice plants. It also examines the current methods and reactors used to lower As and Cd contamination in rice. Iron-modified biochar (Fe-BC) is a promising technology for reducing As and Cd toxicity in rice, improving soil health, and boosting rice's nutritional value. Biochar's physiochemical characteristics are enhanced by the addition of iron, making it a potent adsorbent for As and Cd ions. In conclusion, Fe-BC's biomembrane properties make them an attractive option for remediating As- and Cd-contaminated paddy soils. More efficient mitigation measures, including the use of biomembrane technology, can be developed when sustainable agriculture practices are combined with these technologies.

Regulating sludge composting with percarbonate facilitated the methylation and detoxification of arsenic mediated via reactive oxygen species

This study purposed to demonstrate the impact of reactive oxygen species (ROS) on arsenic detoxification mechanism in sludge composting with percarbonate. In this study, sodium percarbonate was used as an additive. Adding sodium percarbonate increased the content of H2O2 and OH, which the experimental group (SPC) was higher than the control group (CK). In addition, it decreased the bioavailability of arsenic by 19.10%. Metagenomic analysis found that Firmicutes and Pseudomonas took an active part in the overall compost as the dominant bacteria of arsenic methylation. ROS positively correlated with arsenic oxidation and methylation genes (arsC, arsM), with the gene copy number of arsC and arsM increasing to 7.74 × 1012, 5.24 × 1012 in SPC. In summary, the passivation of arsenic could be achieved by adding percarbonate, which promoted the methylation of arsenic, reduced the toxicity of arsenic, and provided a new idea for the harmless management of sludge.

Insight into the plant-associated bacterial interactions: Role for plant arsenic extraction and carbon fixation

This study investigated the interactions between rhizosphere and endosphere bacteria during phytoextraction and how the interactions affect arsenic (As) extraction and carbon (C) fixation of plants. Pot experiments, high-throughput sequencing, metabonomics, and network analysis were integrated. Results showed that positive correlations dominated the interconnections within modules (>95 %), among modules (100 %), and among keystone taxa (>72 %) in the bacterial networks of plant rhizosphere, root endosphere, and shoot endosphere. This confirmed that cooperative interactions occurred between bacteria in the rhizosphere and endosphere during phytoextraction. Modules and keystone taxa positively correlating with plant As extraction and C fixation were identified, indicating that modules and keystone taxa promoted plant As extraction and C fixation simultaneously. This is mainly because modules and keystone taxa in plant rhizosphere, root endosphere, and shoot endosphere carried arsenate reduction and C fixation genes. Meanwhile, they up-regulated the significant metabolites related to plant As tolerance. Additionally, shoot C fixation increased peroxidase activity and biomass thereby facilitating plant As extraction was confirmed. This study revealed the mechanisms of plant-associated bacterial interactions contributing to plant As extraction and C fixation. More importantly, this study provided a new angle of view that phytoextraction can be applied to achieve multiple environmental goals, such as simultaneous soil remediation and C neutrality.

Rapid arsenite oxidation by Paenarthrobacter nicotinovorans strain SSBW5: unravelling the role of GlpF, aioAB and aioE genes

A novel arsenite resistant bacterial strain SSBW5 was isolated from the battery waste site of Corlim, Goa, India. This strain interestingly exhibited rapid arsenite oxidation with an accumulation of 5 mM arsenate within 24 h and a minimum inhibitory concentration (MIC) of 18 mM. The strain SSBW5 was identified as Paenarthrobacter nicotinovorans using 16S rDNA sequence analysis. Fourier-transformed infrared (FTIR) spectroscopy of arsenite-exposed cells revealed the interaction of arsenite with several important functional groups present on the cell surface, possibly involved in the resistance mechanism. Interestingly, the whole genome sequence analysis also clearly elucidated the presence of genes, such as GlpF, aioAB and aioE encoding transporter, arsenite oxidase and oxidoreductase enzyme, respectively, conferring their role in arsenite resistance. Furthermore, this strain also revealed the presence of several other genes conferring resistance to various metals, drugs, antibiotics and disinfectants. Further suggesting the probable direct or indirect involvement of these genes in the detoxification of arsenite thereby increasing its tolerance limit. In addition, clumping of bacterial cells was observed through microscopic analysis which could also be a strategy to reduce arsenite toxicity thus indicating the existence of multiple resistance mechanisms in strain SSBW5. In the present communication, we are reporting for the first time the potential of P. nicotinovorans strain SSBW5 to be used in the bioremediation of arsenite via arsenite oxidation along with other toxic metals and metalloids.

Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater

BACKGROUND

Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.

RESULTS

Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.

CONCLUSIONS

Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.

Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize

Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.

Ecological risk assessment and identification of the distinct microbial groups in heavy metal-polluted river sediments

To assess the health of river ecosystems, it is essential to quantify the ecological risk of heavy metals in river sediments and the structure of microbial communities. As important tributaries of the Tuo River in the upper reaches of the Yangtze River, the Mianyuan River and the Shiting River, are closely related to the economic development and human daily life in the region. This study assessed the ecological risks of heavy-metal-polluted river sediments, the heavy-metal-driven bacterial communities were revealed, and the relationships between the ecological risks and the identical bacterial communities were discussed. The Cd content was significantly greater than the environmental background value, leading to a serious pollution and very high ecological risk at the confluence of the two rivers and the upper reaches of the Mianyuan River. Microbial community analysis showed that Rhodobacter, Nocardioides, Sphingomonas, and Pseudarthrobacter were the dominant bacterial genera in the sediments of the Shiting River. However, the dominant bacterial genera in the Mianyuan River were Kouleothrix, Dechloromonas, Gaiella, Pedomicrobium, and Hyphomicrobium. Mantel test results showed (r = 0.5977, P = 0.005) that the Cd, As, Zn, Pb, Cr, and Cu were important factors that influenced differences in the distribution of sediment bacterial communities Mianyuan and Shiting rivers. A correlation heatmap showed that heavy metals were negatively correlated for most bacterial communities, but some bacterial communities were tolerant and showed a positive correlation. Overall, the microbial structure of the river sediments showed a diverse spatial distribution due to the influence of heavy metals. The results will improve the understanding of rivers contaminated by heavy metals and provide theoretical support for conservation and in situ ecological restoration of river ecosystems.

Negative Impacts of Arsenic on Plants and Mitigation Strategies

Arsenic (As) is a metalloid prevalent mainly in soil and water. The presence of As above permissible levels becomes toxic and detrimental to living organisms, therefore, making it a significant global concern. Humans can absorb As through drinking polluted water and consuming As-contaminated food material grown in soil having As problems. Since human beings are mobile organisms, they can use clean uncontaminated water and food found through various channels or switch from an As-contaminated area to a clean area; but plants are sessile and obtain As along with essential minerals and water through roots that make them more susceptible to arsenic poisoning and consequent stress. Arsenic and phosphorus have many similarities in terms of their physical and chemical characteristics, and they commonly compete to cause physiological anomalies in biological systems that contribute to further stress. Initial indicators of arsenic's propensity to induce toxicity in plants are a decrease in yield and a loss in plant biomass. This is accompanied by considerable physiological alterations; including instant oxidative surge; followed by essential biomolecule oxidation. These variables ultimately result in cell permeability and an electrolyte imbalance. In addition, arsenic disturbs the nucleic acids, the transcription process, and the essential enzymes engaged with the plant system's primary metabolic pathways. To lessen As absorption by plants, a variety of mitigation strategies have been proposed which include agronomic practices, plant breeding, genetic manipulation, computer-aided modeling, biochemical techniques, and the altering of human approaches regarding consumption and pollution, and in these ways, increased awareness may be generated. These mitigation strategies will further help in ensuring good health, food security, and environmental sustainability. This article summarises the nature of the impact of arsenic on plants, the physio-biochemical mechanisms evolved to cope with As stress, and the mitigation measures that can be employed to eliminate the negative effects of As.

Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments

The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (C_org/N_org and δ¹³C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.

Environmental sporobiota: Occurrence, dissemination, and risks

Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.

The key role of biogenic arsenic sulfides in the removal of soluble arsenic and propagation of arsenic mineralizing communities

Biogeochemical processes govern the transport and availability of arsenic in sediments. However, little is known about the transition from indigenous communities to cultivable consortia when exposed to high arsenic concentrations. Such cultivable communities could be exploited for arsenic bioremediation of waste streams and polluted sites. Thus, it is crucial to understand the dynamics and selective pressures that shape the communities during the development of customized bacterial consortia. First, from the arsenic partitioning of two sediments with high arsenic concentrations, we found that up to 55% of arsenic was bioavailable because it was associated with the soluble, carbonate, and ionically exchangeable fractions. Next, we prepared sediment enrichment cultures under arsenate- and sulfate-reducing conditions to precipitate arsenic sulfide biominerals and analyze the communities. The produced biominerals were used as the inoculum to develop bacterial consortia via successive transfers. Tracking of the 16S rRNA gene in the fresh sediments, sediment enrichments, biogenic minerals, and bacterial consortia revealed differences in the bacterial communities. Removing the sediment caused a substantial decrease in diversity and shifts toward the dominance of the Firmicutes phylum to the detriment of Proteobacteria. In agreement with the 16S rRNA gene results, the sequencing of the arrA gene confirmed the presence of phylotypes closely related to Desulfosporosinus sp. Y5 (100% similarity), highlighting the pivotal role of this genus in the removal of soluble arsenic. Here, we demonstrated for the first time that besides being important as arsenic sinks, the biogenic arsenic sulfide minerals are reservoirs of arsenic resistant/respiring bacteria and can be used to culture them.

Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential

The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.

Characterization and whole-genome sequencing of an extreme arsenic-tolerant Citrobacter freundii SRS1 strain isolated from Savar area in Bangladesh

Citrobacter freundii SRS1, gram-negative bacteria, were isolated from Savar, Bangladesh. The strain could tolerate up to 80 mmol L^-1 sodium arsenite, 400 mmol L^-1 sodium arsenate, 5 mmol L^-1 manganese sulfate, 3 mmol L^-1 lead nitrate, 2.5 mmol L^-1 cobalt chloride, 2.5  mmol L^-1 cadmium acetate, and 2.5 mmol L^-1 chromium chloride. The whole-genome sequencing revealed that the genome size of C. freundii SRS1 is estimated to be 5.4 Mb long, and the G + C content is 51.7%. The genome of C. freundii SRS1 contains arsA, arsB, arsC, arsD, arsH, arsR, and acr3 genes for arsenic resistance; czcA, czcD, cbiN, and cbiM genes for cobalt resistance; chrA and chrB genes for chromium resistance; mntH, sitA, sitB, sitC, and sitD genes for manganese resistance; and zntA gene for lead and cadmium resistance. This novel acr3 gene has never previously been reported in any C. freundii strain except SRS1. A set of 130 completely sequenced strains of C. freundii was selected for phylogenomic analysis. The phylogenetic tree showed that the SRS1 strain is closely related to the C. freundii 62 strain. Further analyses of the genes involved in metal and metalloid resistance might facilitate identifying the mechanisms and pathways involved in high metal resistance in the C. freundii SRS1 strain.

Arsenate decreases production of methylmercury across increasing sulfate concentration amendments in freshwater lake sediments

Arsenic (As) and sulfate pollution are often found co-occurring as a result of smelting metal ores. Previous studies showed that sulfate reducing microbes (SRMs) can use As(V) as a terminal electron acceptor, while others reported that SRMs are the main mercury (Hg) methylators in freshwater systems. However, we have yet to fully explore how As(V) can affect methylmercury (MeHg) production. In this study, we examined whether additions of As(V) and sulfate in freshwater sediments collected near a major gold mine with a history of S and As emissions affect Hg methylation. First, we show that Hg methylation in lake sediments was primarily limited by carbon substrate availability rather than by that of sulfate as terminal electron acceptors. Then, under conditions where carbon is not limiting, sulfate addition to the system significantly increased Hg methylation rate constants. Finally, we show that MeHg production rates in sediments significantly decreased with increasing As(V) concentrations, regardless of the sulfate concentration amended to sediments. This work underscores the apparent antagonistic effects of As(V) on the one hand, and carbon and sulfate on the other hand on the kinetics of Hg methylation. Arsenic controls on Hg methylation are complex and a combination of direct impact on the methylators' fitness, the formation of As-bearing mineral phases affecting Hg bioavailability, or changes in the microbial community structures over increasing As concentrations should be the focus of additional investigations.

Arsenic as hazardous pollutant: Perspectives on engineering remediation tools

Arsenic (As) is highly toxic metal (loid) that impairs plant growth and proves fatal towards human population. It disrupts physiological, biochemical and molecular attributes of plants associated with water/nutrient uptake, redox homeostasis, photosynthetic machineries, cell/membrane damage, and ATP synthesis. Numerous transcription factors are responsive towards As through regulating stress signaling, toxicity and resistance. Additionally, characterization of specific genes encoding uptake, translocation, detoxification and sequestration has also explained their underlying mechanisms. Arsenic within soil enters the food chain and cause As-poisoning. Plethora of conventional methods has been used since decades to plummet As-toxicity, but the success rate is quite low due to environmental hazards. Henceforth, exploration of effective and eco-friendly methods is aimed for As-remediation. With the technological advancements, we have enumerated novel strategies to address this concern for practicing such techniques on global scale. Novel strategies such as bioremediation, phytoremediation, mycorrhizae-mediated remediation, biochar, algal-remediation etc. possess extraordinary results. Moreover, nitric oxide (NO), a signaling molecule has also been explored in relieving As-stress through reducing oxidative damages and triggering antioxidative responses. Other strategies such as role of plant hormones (salicylic acid, indole-3-acetic acid, jasmonic acid) and micro-nutrients such as selenium have also been elucidated in As-remediation from soil. This has been observed through stimulated antioxidant activities, gene expression of transporters, defense genes, cell-wall modifications along with the synthesis of chelating agents such as phytochelatins and metallothioneins. This review encompasses the updated information about As toxicity and its remediation through novel techniques that serve to be the hallmarks for stress revival. We have summarised the genetic engineering protocols, biotechnological as well as nanotechnological applications in plants to combat As-toxicity.

Microbial mediated reaction of dimethylarsinic acid in wetland water and sediments

The biogeochemical reactions of dimethylarsinic acid (DMAs(V)) were investigated using simulated wetland systems in a laboratory. DMAs(V) was injected into the wetland water, and the As concentrations in the water, plants, and sediments were monitored. Aqueous and solid-phase As speciation was evaluated, and the results revealed that the DMAs(V) was completely transported to the sediments and plants. X-ray absorption spectroscopic measurement of the As in the sediment revealed that approximately 85-95% of As existed as inorganic As species, demonstrating the important role of microorganisms in the biogeochemical reaction of DMAs(V). The influences of microbes were further investigated in smaller batches under aerobic and anaerobic conditions. The microbial batch results showed that DMAs(V) demethylation reduced the total aqueous As concentration, demonstrating that As(V) has higher affinity to wetland sediment than DMAs(V). The redox conditions were also revealed as an important controlling factor of the As reaction and, under anaerobic conditions, we observed the presence of the most toxic form of inorganic As(III) in the aqueous phase. Although this study reports one example from a specific wetland, the important roles of the redox conditions and microbial influences were identified from the comprehensive analysis of As speciation and mass balance.

Arsenic biotransformation in industrial wastewater treatment residue: Effect of co-existing Shewanella sp. ANA-3 and MR-1

Shewanella sp. ANA-3 with the respiratory arsenate reductase (ArrAB) and MR-1 with ferric reduction ability always coexist in the presence of high arsenic (As)-containing waste residue. However, their synergistic impacts on As transformation and mobility remain unclear. To identify which bacterium, ANA-3 or MR-1, dominates As mobility in the coexisting environment, we explored the As biotransformation in the industrial waste residue in the presence of Shewanella sp. ANA-3 and MR-1. The incubation results show that As(III) was the main soluble species, and strain ANA-3 dominated As mobilization. The impact of ANA-3 was weakened by MR-1, probably due to the survival competition between these two bacteria. The results of micro X-ray fluorescence and X-ray photoelectron spectroscopy analyses further reveal the pathway for ANA-3 to enhance As mobility. Strain ANA-3 almost reduced 100% surface-bound Fe(III), and consequently led to As(V) release. The dissolved As(V) was then reduced to As(III) by ANA-3. The results of this study help to understand the fate of arsenic in the subsurface and highlight the importance of the safe disposal of high As-containing industrial waste.

Effects of heavy metals pollution on the co-selection of metal and antibiotic resistance in urban rivers in UK and India

Heavy metal pollution and the potential for co-selection of resistance to antibiotics in the environment is growing concern. However, clear associations between heavy metals and antibiotic resistance in river systems have not been developed. Here we investigated relationships between total and bioavailable heavy metals concentrations; metal resistance gene (MRG) and antibiotic resistance gene (ARG) abundances; mobile genetic elements; and the composition of local bacterial communities in low and high metal polluted rivers in UK and India. The results indicated that MRGs conferring resistance to cobalt (Co) and nickel (Ni) (rcnA), and Co, zinc (Zn), and cadmium (Cd) (czcA), and ARGs conferring resistance to carbapenem and erythromycin were the dominating resistant genes across the samples. The relative MRGs, ARGs, and integrons abundances tended to increase at high metal polluted environments, suggesting high metals concentrations have a strong potential to promote metal and antibiotic resistance by horizontal gene transmission and affecting bacterial communities, leading to the development of multi-metal and multi-antibiotic resistance. Network analysis demonstrated the positive and significant relationships between MRGs and ARGs as well as the potential for integrons playing a role in the co-transmission of MRGs and ARGs (r > 0.80, p < 0.05). Additionally, the major host bacteria of various MRGs and ARGs that could be accountable for greater MRGs and ARGs levels at high metal polluted environments were also identified by network analysis. Spearman's rank-order correlations and RDA analysis further confirm relationships between total and bioavailable heavy metals concentrations and the relative MRG, ARG, and integron abundances, as well as the composition of related bacterial communities (r > 0.80 (or < -0.80), p < 0.05). These findings are critical for assessing the possible human health concerns associated with metal-driven antibiotic resistance and highlight the need of considering metal pollution for developing appropriate measures to control ARG transmission.

Recycled concrete aggregates are an economic form of urban riparian erosion management with limited impacts on freshwater chemistry and microbial diversity

Urban streams are at high risk of riparian erosion which impacts adjacent infrastructure stability. Methods to prevent stream erosion have been proposed including using recycled concrete (RC) materials to help stabilize the streambed; however, little is known about the environmental and biological impacts of using RC in urban streams. RC, new concrete (NC), and river rock controls were evaluated for their impact on water chemistry, water quality, and microbial community composition over 6.5 months in controlled laboratory mesocosms. Concentrations of 19 metals, nutrients, and pH of mesocosms containing RC were not significantly different from the river rock mesocosm throughout the experiment; however, NC mesocosms contained significantly higher (p < 0.05) concentrations of Co, As, Al, and V in mesocosm water samples compared to both RC and the river rock control. Microbial community diversity was not significantly impacted by mesocosm treatment. Microbial sequences mapping to taxa including Rhodoferax, Acidovorax, Nitrosomonas, and Novosphingobium were significantly more abundant (p < 0.01) in RC and NC mesocosm samples; however, the overall microbial community structure was similar across treatment types. Results from this study suggest that RC does not significantly alter the stream environment including microbial community diversity and is a viable option for use in stream restoration projects.

Rhizospheric plant-microbe synergistic interactions achieve efficient arsenic phytoextraction by Pteris vittata

Phytoextraction is a cost-effective and eco-friendly technology to remove arsenic (As) from contaminated soil using plants and associated microorganisms. Pteris vittata is the most studied As hyperaccumulator, which effectively takes up inorganic arsenate via roots. Arsenic solubilization and speciation occur prior to plant absorption in the rhizosphere, which play a key role in As phytoextraction by P. vittata. This study investigated the metabolomic correlation of P. vittata and associated rhizospheric microorganisms during As phytoextraction. Three-month pot cultivation of P. vittata in As polluted soil was conducted. In rhizosphere, an increase of water-soluble As concentration and a decrease of pH was observed in the second month, suggesting acidic metabolites as a possible cause of As solubilization. A correlation network was built to elucidate the interactions among metabolites, bacteria and fungi in the rhizosphere of P. vittata. Our results demonstrate that the plant is the major driving force of rhizospheric microbiota generation, and both microbial community and metabolites in rhizosphere of P. vittata correlate to increased bioavailable As. Multi-omics analysis revealed that pterosins enrich microbes that potentially promote As phytoextraction. This study extends the current view of rhizospheric plant-microbes synergistic effects of hyperaccumulators on phytoextraction, which provides clues for developing efficient As phytoremediation approaches.

Gut microbiota of Anabas testudineus (Bloch, 1792) in the e-waste dismantling region: In situ status and relationship with internal metal burden

Due to the production of large quantities of electronic waste (e-waste), unsafe dismantling has caused serious pollution as well as toxicological impacts on both wildlife and humans. As an important aspect of physiology and health, the wildlife's gut microbiota and its changes induced by pollution have been recruiting increasing concerns. To reveal the gut microbiota-related ecotoxicology induced by e-waste dismantling, this study resolves the gut microbiota profile of Anabas testudineus, a native highly adapted nonmodel fish under the in situ exposure, and reveals whether and how the microbiota was altered. The comparisons are made by collecting samples from different e-waste polluted sites in Guiyu (a town in South China) and a nearby reference (nonpolluted) site. The overall gut microbiota landscape of A. testudineus is similar to that of other reported fishes, with an average of ∼300 OTUs, and constituted by Firmicutes (34.51%), Fusobacteria (29.16%) as the major phyla. Obviously different liver metal burdens/fingerprints were observed between the e-waste and reference sites. Accordingly, although the alpha-diversity (ACE, Simpson, and Shannon) of the gut microbiota did not significantly vary, a detailed exploration of the microbiota constitution indicated significant differences at various taxonomic levels, including a series of significantly different species and biomarkers, and showing site-specific beta-diversity clustering patterns. Interestingly, a few bacteria with greater abundance in the fish gut of e-waste polluted sites were also reported to present in other contaminated environments, have a role in wastewater treatment, be capable to transform metal, etc. Redundancy analysis (RDA) and Pearson association analyses indicated significant associations between Mn and Cetobacterium somerae (Pearson r = 0.3612, p = 0.0008) and between Pb and Clostridium colicanis (Pearson r = 0.5151, p < 0.0001). In summary, pollution from e-waste dismantling may have a role in altering the fish gut microbiota, and this research provides insights for better understanding e-waste ecotoxicology and improving future conservation.

Microbial compositions, ecological networks, and metabolomics in sediments of black-odour water in Dongguan, China

Black-odour water with organic compounds and heavy metals caused by domestic and industrial activities has aroused people's attention in recent years, yet little is known about the ecological effects on aquatic organisms, especially microorganisms in sediments. To explore the response of microbial communities to environmental factors, the community and metabolites of nine river sediments with different pollution in Dongguan city, China were investigated using 16S rRNA gene sequencing and liquid chromatography tandem-mass. The results revealed that the composition and structure of sedimentary microbial communities significantly changed in rivers with varying pollution levels. Cyanobacteria were the most abundant organisms in the sediment of black-odorous rivers, while the relative abundance of Thaumarchaeota was gradually increased with the river quality gets better. The relative abundance of organic acids (including amino acids), alcohols, esters, and ketones associated with microbial metabolism in sediments of polluted rivers was increased. The 16S rRNA gene sequencing-based molecular ecological network analysis indicated that the interactions amongst bacteria were enhanced in severely contaminated communities. Sphingomonadaceae and Cyanobacteria have important roles in bacterial community structures of polluted rivers and those with ongoing treatment. The correlation analysis showed significant metal resistance and/or tolerance of the following bacteria species Thalassiosira weissflogii, Aminicenantes bacterium clone OPB95, 'Candidatus Halomonas phosphatis', and archaeal species Methanolinea and unidentified Thermoplasmata. These results indicated that sedimentary microbial communities may shift in composition and structure, as well as their interaction network, to adapt and resist environmental contamination and promote restoration.

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.

Hydrous ferric oxides (HFO's) precipitated from contaminated waters at several abandoned Sb deposits - Interdisciplinary assessment

The presented paper represents a comprehensive analysis of ochre sediments precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 7 g·kg^-1 to 130 g·kg^-1 and content of antimony ranging from 0.25 g·kg^-1 up to 12 g·kg^-1. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2%) were mainly Proteobacteria (68.8%) and Bacteroidetes (10.2%) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. In this As and Sb rich, circumneutral microenvironment, rich in iron, sulfates and carbonates, methylotrophic bacteria (Methylobacter, Methylotenera), metal/reducing bacteria (Geobacter, Rhodoferax), metal-oxidizing and denitrifying bacteria (Gallionella, Azospira, Sphingopyxis, Leptothrix and Dechloromonas), sulfur-oxidizing bacteria (Sulfuricurvum, Desulphobulbaceae) and nitrifying bacteria (Nitrospira, Nitrosospira) accounted for the most dominant ecological groups and their impact over Fe, As, Sb, sulfur and nitrogen geocycles is discussed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.

Influence of tetracycline on arsenic mobilization and biotransformation in flooded soils

This study examined the effect of tetracycline addition on arsenic (As) mobilization and biotransformation in two contrasting soils (upland soil and paddy soil) under flooded conditions. The soils with added tetracycline (0-50 mg kg^-1) were incubated for 30 days, and soil properties and microbial functional genes over time were quantified. Tetracycline significantly promoted As reduction and As release into porewater in both soils. The enhancement had resulted from an increase in the concentration of dissolved organic carbon and a decrease in soil redox potential. Tetracycline also increased the abundances of As-reducing genes (arsC and arrA) and the relative abundances of As-reducing bacteria Streptomyces, Bacillus, Burkholderia, Clostridium and Rhodococcus, all of which have been found resistant to tetracycline. These genera play a key part in stimulating As reduction in the presence of tetracycline. The study indicated the significance of tetracycline in the biochemical behavior of As in flooded soils and provided new insights into the potential effects of tetracycline on the quality and safety of agricultural products in the future.

Adaptation mechanisms of arsenic metabolism genes and their host microorganisms in soils with different arsenic contamination levels around abandoned gold tailings

Soil around the gold tailing due to the smelting process of wastewater and solid waste can lead to metal (loids) contamination, especially arsenic (As). Soil microorganisms have gradually evolved adaptive mechanisms in the process of long-term adaptation to As contamination. However, comprehensive investigations on As metabolism genes and their host microbial communities in soil profiles with different levels under long-term As contamination are lacking. There are selected three typical soil profiles (0-100 cm) with different metal (loids) contamination levels (L-low, M-moderate and H-high) around tailings in this research. It uses a Metagenomic approach to explore the adaptation mechanisms of arsenic metabolism genes and arsenic metabolism gene host microorganisms in both horizontal and vertical dimensions. The results showed that four categories of As metabolism genes were prevalent in soil profiles at different As contamination, with As reduction genes being the most abundant, followed by As oxidation genes, then respiration genes and methylation genes. The As metabolism genes arsBCR, aioE, arsPH, arrAB increased with the increase of metal (loid) contaminants concentration. Longitudinal arsA, arrA, aioA, arsM and acr3 increased in abundance in deep soil. Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi were the dominant phylum of As metabolism gene host microorganisms. Different concentrations of metal (loid) contamination significantly affected the distribution of host As metabolism genes. Random forest prediction identified As as the most critical driver of As metabolism genes and their host microorganisms. Overall, this study provides a reference for a comprehensive investigation of the detoxification mechanisms of As metabolism microorganisms in soil profiles with different As contamination conditions, and is important for the development of As metabolism gene host microbial strains and engineering applications of microbial technologies to manage As contamination.

Connections between endoplasmic reticulum stress-associated unfolded protein response, mitochondria, and autophagy in arsenic-induced carcinogenesis

Arsenic exposure in contaminated drinking water is a global health issue, as more than 200 million people are affected globally. Arsenic has been known to cause skin, liver, lung, bladder and prostate cancers. Accordingly, it has been categorized as a group I human carcinogen by the International Agency for Research on Cancer (IARC). Various natural and anthropogenic activities lead to the release of arsenic in the environment, contaminating air, water and food sources. Traditionally, genetic mutations have been the center of cancer research. However, emerging studies have now focused on the importance of epigenetics, metabolism and endoplasmic reticulum (ER) stress in cancer. Arsenic is highly capable of inducing stress in the cells via the generation of free radicals causing oxidative stress, epigenetic and genetic alterations, mitochondrial dysfunction, activation of intracellular signaling pathways, and impairment of autophagy and DNA repair systems. The cancer cells are able to utilize the unfolded protein response (UPR) to overcome these internal stresses in various stages of arsenic-induced carcinogenesis, from cancer growth to immune responses. The UPR is an evolutionarily conserved stress response that has both survival and apoptotic outcomes. PERK, IRE1α and ATF6α are the three ER stress sensors that are activated to maintain cellular proteostasis, which can also promote apoptosis on prolonged ER stress. The dual nature of UPR in different cancer types and stages is a challenge for researchers. We must investigate the role and the connections among ER stress-associated UPR, mitochondrial dysfunction and autophagy in arsenic malignancies to identify key targets for cancer prevention and therapeutics.

Culture-dependent study of arsenic-reducing bacteria in deep aquatic sediments of Bengal Delta

Biogeochemical release of soil-bound arsenic (As) governs mobilization of the toxic metalloid into the groundwater. The present study has examined As^V-reduction ability of bacteria from anoxic aquatic sediments that might contribute to arsenic mobilization in the Bengal Delta. Arsenic-reducing bacteria from deep layers of pond sediment were enriched and isolated in anaerobic environments and As^V reduction was assessed in culture medium. The pond sediment enrichments harboured As^V-reducing bacteria belonging to the phyla Firmicutes and Proteobacteria with dominance of Paraclostridium benzoelyticum and P. bifermentans. Among total 17 isolates, the respiratory reductase genes were not detected by the most common primers and only 3 strains had arsenic reductase ArsC gene suggesting involvement of resistance and some unknown mechanisms in As^V reduction. Presence of high levels of organic matter, As, and As-reducing bacteria might make deep aquatic sediments a hot spot of As mobilization and aquifer contamination.

Arsenic behavior in soil-plant system and its detoxification mechanisms in plants: A review

Arsenic (As) is one of the most toxic and cancer-causing metals which is generally entered the food chain via intake of As contaminated water or food and harmed the life of living things especially human beings. Therefore, the reduction of As content in the food could be of great importance for healthy life. To reduce As contamination in the soil and food, the evaluation of plant-based As uptake and transportation mechanisms is critically needed. Different soil factors such as physical and chemical properties of soil, soil pH, As speciation, microbial abundance, soil phosphates, mineral nutrients, iron plaques and roots exudates effectively regulate the uptake and accumulation of As in different parts of plants. The detoxification mechanisms of As in plants depend upon aquaporins, membrane channels and different transporters that actively control the influx and efflux of As inside and outside of plant cells, respectively. The xylem loading is responsible for long-distance translocation of As and phloem loading involves in the partitioning of As into the grains. However, As detoxification mechanism based on the clear understandings of how As uptake, accumulations and translocation occur inside the plants and which factors participate to regulate these processes. Thus, in this review we emphasized the different soil factors and plant cell transporters that are critically responsible for As uptake, accumulation, translocation to different organs of plants to clearly understand the toxicity reasons in plants. This study could be helpful for further research to develop such strategies that may restrict As entry into plant cells and lead to high crop yield and safe food production.

Bioaugmentation with As-transforming bacteria improves arsenic availability and uptake by the hyperaccumulator plant Pteris vittata (L)

Inorganic arsenic (As) is a toxic and carcinogenic pollutant that has long-term impacts on environmental quality and human health. Pteris vittata plants hyperaccumulate As from soils. Soil bacteria are critical for As-uptake by P. vittata. We examined the use of taxonomically diverse soil bacteria to modulate As speciation in soil and their effect on As-uptake by P. vittata. Aqueous media inoculated with Pseudomonas putida MK800041, P. monteilii MK344656, P. plecoglossicida MK345459, Ochrobactrum intermedium MK346993 or Agrobacterium tumefaciens MK346997 resulted in the oxidation of 5-30% As(III) and a 49-79% reduction of As(V). Soil inoculated with P. monteilii increased extractable As(III) and As(V) from 0.5 and 0.09 in controls to 0.9 and 0.39 mg As kg^-1 soil dry weight, respectively. Moreover, and P. vittata plants inoculated with P. monteilii, P. plecoglossicida, O. intermedium strains, and A. tumefaciens strains MK344655, MK346994, MK346997, significantly increased As-uptake by 43, 32, 12, 18, 16, and 14%, respectively, compared to controls. The greatest As-accumulation (1.9 ± 0.04 g kg^-1 frond Dwt) and bioconcentration factor (16.3 ± 0.35) was achieved in plants inoculated with P. monteilii. Our findings indicate that the tested bacterial strains can increase As-availability in soils, thus enhancing As-accumulation by P. vittata. Novelty statement Pteris vittata, a well-known As-hyperaccumulator, has the remarkable ability to accumulate higher levels of As in their above-ground biomass. The As-tolerant bacteria-plant interactions play a significant role in bioremediation by mediating As-redox and controlling As-availability and uptake by P. vittata. Our studies indicated that most of the tested bacterial strains isolated from As-impacted soil significantly enhanced As-uptake by P. vittata. P. monteilii oxidized 20% of As(III) and reduced 50% of As(V), increased As-extraction from soils, and increased As-uptake by 43% greater compared with control. Therefore, these strains associated with P. vittata can be used in large-scale field applications to remediate As-contaminated soil.

Genome Sequence of Brevundimonas sp., an Arsenic Resistant Soil Bacterium

Brevundimonas sp. is a bacteria able to grow in metal(loid) contaminated soil from Puchuncaví Valley, central Chile. This study has isolated a bacterial strain capable of growth under high doses of arsenic (As) (6000 mg L−1), and a draft genome sequence was generated. Additionally, real-time PCR was performed to examine the effect of As on some genes related to As resistance. Results demonstrated a total of 3275 predicted annotated genes with several genes related to the ars operon, metal(loid) resistance-related genes, metal efflux pumps, and detoxifying enzymes. Real-time PCR showed that the arsB involved in the efflux of As was down-regulated, whereas arsR, arsH, and ACR3 did not show differences with the addition of As. Our study provides novel evidence of diverse As regulating systems in tolerant bacteria that will lead to a better understanding of how microorganisms overcome toxic elements and colonize As contaminated soils and to the possible use of their specific properties in bioremediation.

Variable response of arsenic contaminated groundwater microbial community to electron acceptor regime revealed by microcosm based high-throughput sequencing approach

Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. Acinetobacter, Deinococcus, Nocardioides, etc., and several unclassified bacteria (Ignavibacteria) and archaea (Bathyarchaeia, Micrarchaeia) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to Denitratisoma (NO₃-), Spirochaetaceae (Mn⁴⁺), Deinococcus (As⁵⁺), Ruminiclostridium (Fe³⁺), Macellibacteroides (SO₄²-), Holophagae-Subgroup 7 (HCO₃-), Dechloromonas and Geobacter (EA mixture) was noted. Alternatively, As³⁺ amendment as electron donor allowed predominance of Rhizobium. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO₃-, Fe³⁺, SO₄²-, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.

Evolutionary, genomic, and biogeographic characterization of two novel xenobiotics-degrading strains affiliated with Dechloromonas

Xenobiotics are generally known as man-made refractory organic pollutants widely distributed in various environments. For exploring the bioremediation possibility of xenobiotics, two novel xenobiotics-degrading strains affiliated with Azonexaceae were isolated. We report here the phylogenetics, genome, and geo-distribution of a novel and ubiquitous Azonexaceae species that primarily joins in the cometabolic process of some xenobiotics in natural communities. Strains s22 and t15 could be proposed as a novel species within Dechloromonas based on genomic and multi-phylogenetic analysis. Pan-genome analysis showed that the 63 core genes in Dechloromonas include genes for dozens of metabolisms such as nitrogen fixation protein (nifU), nitrogen regulatory protein (glnK), dCTP deaminase, C4-dicarboxylate transporter, and fructose-bisphosphate aldolase. Strains s22 and t15 have the ability to metabolize nitrogen, including nitrogen fixation, NirS-dependent denitrification, and dissimilatory nitrate reduction. Moreover, the novel species possesses the EnvZ-OmpR two-component system for controlling osmotic stress and QseC-QseB system for quorum sensing to rapidly sense environmental changes. It is intriguing that this new species has a series of genes for the biodegradation of some xenobiotics such as azathioprine, 6-Mercaptopurine, trinitrotoluene, chloroalkane, and chloroalkene. Specifically, glutathione S-transferase (GST) and 4-oxalocrotonate tautomerase (praC) in this novel species play important roles in the detoxification metabolism of some xenobiotics like dioxin, trichloroethene, chloroacetyl chloride, benzo[a]pyrene, and aflatoxin B1. Using data from GenBank, DDBJ and EMBL databases, we also demonstrated that members of this novel species were found globally in plants (e.g. rice), guts (e.g. insect), pristine and contaminated regions. Given these data, Dechloromonas sp. strains s22 and t15 take part in the biodegradation of some xenobiotics through key enzymes.

Citrobacter arsenatis sp. nov., an arsenate-reducing bacterium isolated from freshwater sediment

A novel arsenate-reducing bacterium, LY-1^T, was isolated from freshwater sediment in Huangshi, China. Morphological analysis indicated that the cells were shaped like rods and were gram-negative. The major fatty acids (> 10%) were C_16:0, summed feature 3 (C_16:1 ω7c, C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c, C_18:1 ω6c). An assessment of the phylogeny based on 16S rRNA gene sequences indicated that the strain LY-1^T belonged to the genus Citrobacter, while further analysis based on the recN gene indicated that LY-1^T occupies a distinct phylogenetic niche within the Citrobacter genus. Moreover, average nucleotide identity and digital DNA-DNA hybridization between the strain LY-1^T and the type strains of closely related species of the genus Citrobacter (C. europaeus, C. brakii, C. portucalensis, C. freundii, C. werkmanii, C. cronae, C. youngae, C. pasteurii, C. tructae, C. gillenii, and C. murliniae) were 85.8-93.8% and 31.2-56.9%, respectively. In addition, the LY-1^T strain's capacity to metabolize various compounds and its characteristic G + C content of 51.9% were also distinct from other species of the Citrobacter genus. These discriminatory features cumulatively indicate the LY-1^T strain as a new species within the Citrobacter genus. We propose the species name Citrobacter arsenatis for this new species, with LY-1^T (= CCTCC AB 2019169^T = KCTC 72440^T) as the type strain.

Engineering Biological Electron Transfer and Redox Pathways for Nanoparticle Synthesis

Many species of bacteria are naturally capable of types of electron transport not observed in eukaryotic cells. Some species live in environments containing heavy metals not typically encountered by cells of multicellular organisms, such as arsenic, cadmium, and mercury, leading to the evolution of enzymes to deal with these environmental toxins. Bacteria also inhabit a variety of extreme environments, and are capable of respiration even in the absence of oxygen as a terminal electron acceptor. Over the years, several of these exotic redox and electron transport pathways have been discovered and characterized in molecular-level detail, and more recently synthetic biology has begun to utilize these pathways to engineer cells capable of detecting and processing a variety of metals and semimetals. One such application is the biologically controlled synthesis of nanoparticles. This review will introduce the basic concepts of bacterial metal reduction, summarize recent work in engineering bacteria for nanoparticle production, and highlight the most cutting-edge work in the characterization and application of bacterial electron transport pathways.

The biotransformation of arsenic by spent mushroom compost - An effective bioremediation agent

Spent mushroom compost (SMC) is a lignocellulose-rich waste material commonly used in the passive treatment of heavy metal-contaminated environments. In this study, we investigated the bioremediation potential of SMC against an inorganic form of arsenic, examining the individual abiotic and biotic transformations carried out by SMC. We demonstrated, that key SMC physiological groups of bacteria (denitrifying, cellulolytic, sulfate-reducing, and heterotrophic) are resistant to arsenites and arsenates, while the microbial community in SMC is also able to oxidize As(III) and reduce As(V) in respiratory metabolisms, although the SMC did not contain any As. We showed, that cooperation between arsenate and sulfate-reducing bacteria led to the precipitation of As_xS_y. We also found evidence of the significant role organic acids may play in arsenic complexation, and we demonstrated the occurrence of As-binding proteins in the SMC. Furthermore, we confirmed, that biofilm produced by the microbial community in SMC was able to trap As(V) ions. We postulated, that the above-mentioned transformations are responsible for the sorption efficiency of As(V) (up to 25%) and As(III) (up to 16%), as well as the excellent buffering properties of SMC observed in the sorption experiments.

Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

BACKGROUND

Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations.

RESULTS

Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences.

CONCLUSION

These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.

Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic

Nanoscale Zero-Valent Iron (nZVI) is a cost-effective nanomaterial that is widely used to remove a broad range of metal(loid)s and organic contaminants from soil and groundwater. In some cases, this material alters the taxonomic and functional composition of the bacterial communities present in these matrices; however, there is no conclusive data that can be generalized to all scenarios. Here we studied the effect of nZVI application in situ on groundwater from the site of an abandoned fertilizer factory in Asturias, Spain, mainly polluted with arsenic (As). The geochemical characteristics of the water correspond to a microaerophilic and oligotrophic environment. Physico-chemical and microbiological (cultured and total bacterial diversity) parameters were monitored before and after nZVI application over six months. nZVI treatment led to a marked increase in Fe(II) concentration and a notable fall in the oxidation-reduction potential during the first month of treatment. A substantial decrease in the concentration of As during the first days of treatment was observed, although strong fluctuations were subsequently detected in most of the wells throughout the six-month experiment. The possible toxic effects of nZVI on groundwater bacteria could not be clearly determined from direct observation of those bacteria after staining with viability dyes. The number of cultured bacteria increased during the first two weeks of the treatment, although this was followed by a continuous decrease for the following two weeks, reaching levels moderately below the initial number at the end of sampling, and by changes in their taxonomic composition. Most bacteria were tolerant to high As(V) concentrations and showed the presence of diverse As resistance genes. A more complete study of the structure and diversity of the bacterial community in the groundwater using automated ribosomal intergenic spacer analysis (ARISA) and sequencing of the 16S rRNA amplicons by Illumina confirmed significant alterations in its composition, with a reduction in richness and diversity (the latter evidenced by Illumina data) after treatment with nZVI. The anaerobic conditions stimulated by treatment favored the development of sulfate-reducing bacteria, thereby opening up the possibility to achieve more efficient removal of As.

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia

Novel hyper-resistant bacteria were isolated from the Crven Dol mine (Allchar, North Macedonia), arsenic-rich extreme environment. Bacteria were recovered from a secondary mineral mixture, an alteration of hydrothermal realgar rich in arsenates (pharmacolite, hornesite, and talmessite). The sample was recovered from the dark part of the mine at 28 m depth. Three bacterial strains and a bacterial consortium were isolated for their capacity to survive exposure to 32 g/L (209 mM) of arsenite, and 176 g/L (564 mM) of arsenate. The 16S rRNA gene analysis identified bacterial isolates as Stenotrophomonas sp. and two Microbacterium spp. This analysis also revealed that bacterial consortium comprise two Bacteriodetes exhibiting similarity to Olivibacter ginsengisoli and to uncultured bacterium, and one γ-proteobacteria with similarity to Luteimonas sp. Among all isolates Stenotrophomonas sp. exhibited the highest tolerance to As compound as well as the capacity to accumulate As inside the cells. Analysis of genes involved in As-resistance showed that recovered isolates possess the genes encoding the ArsB, Acr3(1) and Acr3(2) proteins, indicating that at least a part of their resistance could be ascribed to As-efflux systems described in isolates obtained from human-polluted environments.

Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis

In nature, arsenic (As) and iron (Fe) biotransformation are interconnected, influencing local As mobility and toxicity. While As- or Fe-metabolizing microorganisms are widely documented, knowledge concerning their cycling genes, associated with geophysicochemical data and taxonomic distribution, remains scarce. We performed a meta-analysis to explore the distribution and environmental importance of As- and Fe-redox genes (AsRGs and FeRGs) and predict their significant correlations and hosts. The most abundant and ubiquitous AsRGs and FeRGs were arsC and ccoN, respectively. The ccoN gene had the highest frequency at pH ≥ 9.1, in which dissolved Fe(II) is scarce, possibly contributing to enhanced host survival. Fe(III) oxidation genes iro and ccoN appear to be associated with As(V) detoxification in mesophilic environments. No correlation was observed between Fe(III) reduction gene omcB and arsenate reductase genes. Cytochromes with putative roles in Fe-redox reactions were identified (including yceJ and fbcH) and were significantly correlated with As(V) reduction genes under diverse geophysicochemical conditions. The taxonomies of AsRGs and FeRGs-carrying contigs revealed great diversity, among which various, such as Chlamydea (arsC) and Firmicutes (omcB), were previously undescribed. Nearly all (98.9%) of the AsRGs and FeRGs were not carried by any plasmid sequences. This meta-analysis expands our understanding of the global environmental, taxonomic and functional microbiome involved in As- and Fe-redox transformations. Moreover, these findings should help guide studies on putative in vivo functional roles of cytochromes in Fe-redox pathways.

Arsenic uptake, speciation and physiological response of tree species (Acer pseudoplatanus, Betula pendula and Quercus robur) treated with dimethylarsinic acid

The aim of the study was to evaluate the effect of dimethylarsinic acid (DMA) on growth parameters and levels of stress-related metabolites in Acer pseudoplatanus, Betula pendula and Quercus robur. The increase of DMA concentration in the solution led to a notable growth retardation of trees. An intense As accumulation (mainly As(III) and As(V)) expressed as BCF and TF > 1 was recorded only for Q. robur. Generally a decrease in contents of cellulose, hemicellulose and holocellulose with a simultaneous increase in lignin content were recorded. Phenolic composition of leaf extracts was modified by DMA, while root and rhizosphere extracts were poor in phenolics. Toxicity of DMA leads to a significant drop in salicylic acid content in leaves observed at lower doses. Higher DMA levels caused a second, probably ROS-derived depletion of the metabolite accompanied with a severe growth retardation, most pronounced in the case of B. pendula. DMA caused the inhibition of LMWOA biosynthesis in roots of A. pseudoplatanus, B. pendula and their exudation into the rhizosphere, while in Q. robur roots and leaves a stimulation of their accumulation was observed. Disturbances in the activity of enzymatic antioxidants were observed for all the species following the increasing level of DMA.

Biologically mediated release of endogenous N2O and NO2 gases in a hydrothermal, hypoxic subterranean environment

The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO₂-rich fluids. Anomalous concentrations of N₂O and NO₂ were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO₂ and CH₄ during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O₂, temperature, and GHG concentration. Both the N₂O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N₂O and NO₂ emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH₂OH, NO, and NO₂^- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.

Assessing the Plant Growth Promoting and Arsenic Tolerance Potential of Bradyrhizobium japonicum CB1809

Accumulation of heavy metals in soil is of concern to the agricultural production sector, because of the potential threat to food quality and quantity. Inoculation with plant growth-promoting bacteria (PGPR) has previously been shown to alleviate heavy metal stress but the mechanisms are unclear. Potential mechanisms by which inoculation with Bradyrhizobium japonicum CB1809 affected the legume soybean (Glycine max cv. Zeus) and the non-legume sunflower (Helianthus annus cv. Hyoleic 41) were investigated in solution culture under 5 μM As stress. Adding As resulted in As tissue concentrations of up to 5 mg kg^-1 (shoots) and 250 mg kg^-1 (roots) in both species but did not reduce shoot or root biomass. Inoculation increased root biomass but only in the legume (soybean) and only with As. Inoculation resulted in large (up to 100%) increases in siderophore concentration but relatively small changes (±10-15%) in auxin concentration in the rhizosphere. However, the increase in siderophore concentration in the rhizosphere did not result in the expected increases in tissue N or Fe, especially in soybean, suggesting that their function was different. In conclusion, siderophores and auxins may be some of the mechanisms by which both soybean and sunflower maintained plant growth in As-contaminated media.

Influence of epiphytic bacteria on arsenic metabolism in Hydrilla verticillata

Microbial assemblages such as biofilms around aquatic plants play a major role in arsenic (As) cycling, which has often been overlooked in previous studies. In this study, arsenite (As(III))-oxidizing, arsenate (As(V))-reducing and As(III)-methylating bacteria were found to coexist in the phyllosphere of Hydrilla verticillata, and their relative activities were shown to determine As speciation, accumulation and efflux. When exposed to As(III), As(III) oxidation was not observed in treatment H(III)-B, whereas treatment H(III)+B showed a significant As(III) oxidation ability, thereby indicating that epiphytic bacteria displayed a substantial As(III) oxidation ability. When exposed to As(V), the medium only contained 5.89% As(III) after 48 h of treatment H(V)-B, while an As(III) content of 86.72% was observed after treatment H(V)+B, thereby indicating that the elevated As(III) in the medium probably originated from As(V) reduction by epiphytic bacteria. Our data also indicated that oxidizing bacteria decreased the As accumulation (by approximately 64.44% compared with that of treatment H(III)-B) in plants, while reducing bacteria played a critical role in increasing As accumulation (by approximately 3.31-fold compared with that of treatment H(V)-B) in plants. Regardless of whether As(III) or As(V) was supplied, As(III) was dominant in the plant tissue (over 75%). Furthermore, the presence of epiphytic bacteria enhanced As efflux by approximately 9-fold. Metagenomic analysis revealed highly diverse As metabolism genes in epiphytic bacterial community, particularly those related to energetic metabolism (aioAB), and As resistance (arsABCR, acr3, arsM). Phylogenetic analysis of As metabolism genes revealed evidence of both vertical inheritance and horizontal gene transfer, which might have contributed to the evolution of the As metabolism genes. Taken together, our research suggested that the diversity of As metabolism genes in epiphytic bacterial community is associated with aquatic submerged macrophytes which may play an important role in As biogeochemistry in aquatic environments.