Identification and characterization of arsenite methyltransferase from an archaeon, Methanosarcina acetivorans C2A

Occurrence and spatiotemporal distribution of arsenic biotransformation genes in urban dust

Microbially-mediated arsenic biotransformation plays a pivotal role in the biogeochemical cycling of arsenic; however, the presence of arsenic biotransformation genes (ABGs) in urban dust remains unclear. To investigate the occurrence and spatiotemporal distributions of ABGs, a total of one hundred and eighteen urban dust samples were collected from different districts of Xiamen city, China in summer and winter. Although inorganic arsenic species, including arsenate [As(V)] and arsenite [As(III)], were found to be predominant, the methylated arsenicals, particularly trimethylarsine oxide [TMAs(V)O] and dimethylarsenate [DMAs(V)], were detected in urban dust. Abundant ABGs were identified in urban dust via AsChip analysis (a high-throughput qPCR chip for ABGs), of which As(III) S-adenosylmethionine methyltransferase genes (arsM), As(V) reductase genes (arsC), As(III) oxidase genes (aioA), As(III) transporter genes (arsB), and arsenic-sensing regulator genes (arsR) were the most prevalent, collectively constituting more than 90 % of ABGs in urban dust. Microbes involved in arsenic methylation were assigned to bacteria (e.g., Actinomycetes and Alphaproteobacteria), archaea (e.g., Halobacteria), and eukaryotes (e.g., Chlamydomonadaceae) in urban dust via the arsM amplicon sequencing. Temperature, a season-dependent environmental factor, profoundly affected the abundance of ABGs and the composition of microbes involved in arsenic methylation. This study provides new insights into the presence of ARGs within the urban dust.

Controlling exposure to As and Cd from rice via irrigation management

Irrigation management controls biogeochemical cycles in rice production. Under flooded paddy conditions, arsenic becomes plant-available as iron-reducing conditions ensue, while oxic conditions lead to increased plant availability of Cd in acidic soils. Because Cd enters rice through Mn transporters, we hypothesized that irrigation resulting in intermediate redox could simultaneously limit both As and Cd in rice grain due to As retention in soil and Mn competition for Cd uptake. In a 2 year field study, we used 6 irrigation managements that varied in extent and frequency of inundation, and we observed strong effects of irrigation management on porewater chemistry, soil redox potentials, plant As and Cd concentrations, plant nutrient concentrations, and methane emissions. Plant As decreased with drier irrigation management, but in the grain this effect was stronger for organic As than for inorganic As. Grain organic As, but not inorganic As, was strongly and positively correlated with cumulative methane emissions. Conversely, plant Cd increased under more aerobic irrigation management and grain Cd was negatively correlated with porewater Mn. A hazard index approach showed that in the tested soil with low levels of As and Cd (5.4 and 0.072 mg/kg, respectively), irrigation management could not simultaneously decrease grain As and Cd. Many soil properties, such as reducible As, available Cd, soil pH, available S, and soil organic matter should be considered when attempting to optimize irrigation management when the goal is decreasing the risk of As and Cd in rice grain.

Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil

Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.

Changes in arsenic mobility and speciation across a 2000-year-old paddy soil chronosequence

Rice accumulates arsenic (As) when cultivated under flooded conditions in paddy soils threatening rice yield or its safety for human consumption, depending on As speciation. During long-term paddy use, repeated redox cycles systematically alter soil biogeochemistry and microbiology. In the present study, incubation experiments from a 2000-year-old paddy soil chronosequence revealed that As mobilization and speciation also change with paddy soil age. Younger paddies (≤100 years) showed the highest total As mobilization, with speciation dominated by carcinogenic inorganic oxyarsenic species and highly mobile inorganic thioarsenates. Inorganic thioarsenates formed by a high availability of reduced sulfur (S) due to low concentrations of reducible iron (Fe) and soil organic carbon (SOC). Long-term paddy use (>100 years) resulted in higher microbial activity and SOC, increasing the share of phytotoxic methylated As. Methylated oxyarsenic species are precursors for cytotoxic methylated thioarsenates. Methylated thioarsenates formed in soils of all ages being limited either by the availability of methylated As in young soils or that of reduced-S in older ones. The present study shows that via a linkage of As to the biogeochemistry of Fe, S, and C, paddy soil age can influence the kind and the extent of threat that As poses for rice cultivation.

Arsenite Methyltransferase Diversity and Optimization of Methylation Efficiency

Arsenic is methylated by arsenite (As(III)) S-adenosylmethionine (SAM) methyltransferases (ArsMs). ArsM crystal structures show three domains (an N-terminal SAM binding domain (A domain), a central arsenic binding domain (B domain), and a C-terminal domain of unknown function (C domain)). In this study, we performed a comparative analysis of ArsMs and found a broad diversity in structural domains. The differences in the ArsM structure enable ArsMs to have a range of methylation efficiencies and substrate selectivities. Many small ArsMs with 240-300 amino acid residues have only A and B domains, represented by RpArsM from Rhodopseudomonas palustris. These small ArsMs have higher methylation activity than larger ArsMs with 320-400 residues such as Chlamydomonas reinhardtii CrArsM, which has A, B, and C domains. To examine the role of the C domain, the last 102 residues in CrArsM were deleted. This CrArsM truncation exhibited higher As(III) methylation activity than the wild-type enzyme, suggesting that the C-terminal domain has a role in modulating the rate of catalysis. In addition, the relationship of arsenite efflux systems and methylation was examined. Lower rates of efflux led to higher rates of methylation. Thus, the rate of methylation can be modulated in multiple ways.

Methanogens-Driven Arsenic Methylation Preceding Formation of Methylated Thioarsenates in Sulfide-Rich Hot Springs

Hot springs represent a major source of arsenic release into the environment. Speciation is typically reported to be dominated by arsenite, arsenate, and inorganic thiolated arsenates. Much less is known about the relevance and formation of methylated thioarsenates, a group with species of high mobility and toxicity. In hot spring samples taken from the Tengchong volcanic region in China, methylated thioarsenates contributed up to 13% to total arsenic. Enrichment cultures were obtained from the corresponding sediment samples and incubated to assess their capability to convert arsenite into methylated thioarsenates over time and in the presence of different microbial inhibitors. In contrast to observations in other environmental systems (e.g., paddy soils), there was no solid evidence, supporting that the sulfate-reducing bacteria contributed to the arsenic methylation. Methanosarcina, the sole genus of methanogens detected in the enrichment cultures, as well as Methanosarcina thermophila TM-1, a pure strain within the genus, did methylate arsenic. We propose that methylated thioarsenates in a typical sulfide-rich hot spring environment like Tengchong form via a combination of biotic arsenic methylation driven by thermophilic methanogens and arsenic thiolation with either geogenic sulfide or sulfide produced by sulfate-reducing bacteria.

Microbial remediation and plant-microbe interaction under arsenic pollution

Arsenic contamination in aquatic and terrestrial ecosystem is a serious environmental issue. Both natural and anthropogenic processes can introduce it into the environment. The speciation of the As determine the level of its toxicity. Among the four oxidation states of As (-3, 0, +3, and + 5), As(III) and As(V) are the common species found in the environment, As(III) being the more toxic with adverse impact on the plants and animals including human health. Therefore, it is very necessary to remediate arsenic from the polluted water and soil. Different physicochemical as well as biological strategies can be used for the amelioration of arsenic polluted soil. Among the microbial approaches, oxidation of arsenite, methylation of arsenic, biosorption, bioprecipitation and bioaccumulation are the promising transformation activities in arsenic remediation. The purpose of this review is to discuss the significance of the microorganisms in As toxicity amelioration in soil, factors affecting the microbial remediation, interaction of the plants with As resistant bacteria, and the effect of microorganisms on plant arsenic tolerance mechanism. In addition, the exploration of genetic engineering of the bacteria has a huge importance in bioremediation strategies, as the engineered microbes are more potent in terms of remediation activity along with quick adaptively in As polluted sites.

Synchronous response of arsenic methylation and methanogenesis in paddy soils with rice straw amendment

Rice straw (RS) amendment promotes arsenic (As) methylation and methane (CH₄) emissions from paddy soils, which can cause straighthead disease and climate warming. Although methanogens have been identified as critical regulators of methylated As concentrations in flooded soils, the mechanism of these microbial groups on As methylation in paddy soils with RS amendment remains unknown. In this study, paddy soil was incubated to test the response in As methylation and methanogenesis in flooded soil with RS amendment. Our results showed that RS amendment increased the accumulation of monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) whether methanogenesis was inhibited or not. The methanogens in the genera of Methanocella probably played critical role in promoting As methylation in flooded soil with RS amendment. With the RS amendment, inhibition of methanogenesis led to the accumulation MMA and DMA by suppressing DMA demethylation. The demethylation of DMA was driven by methanogens possibly belonging to the genera of Methanobacterium. This study revealed a wealth of methanogens that dominate As methylation with RS amendment. It will provide guidance to RS amendment in As contaminated paddy soil and has important implications for rice quality and global climate change.

Localized intensification of arsenic methylation within landfill leachate-saturated zone

Leachate-saturated zone (LSZ) of landfills is a complicated biogeochemical hotspot due to the continuous input of electron donors and acceptors from the top refuse layer with leachate migration. In this study, the methylation behavior of the arsenic (As) was investigated. The results indicate that As-methylation processes are influenced by temperature fields in LSZ. The dimethylarsinic acid biotransformation capability can be enhanced with an increase in temperature. Microbial diversity, quantification of functional gene (arsM), and co-occurrence network analysis further characterized the drivers of As methylation in LSZ. As-biogeochemical cycle pathways, as well as As-functional gene distribution among different temperature fields, were modeled on the basis of KEGG annotation. Binning analysis was further employed to assemble As-methylated metagenomes, enabling the identification of novel species for As methylation in landfills. Then, 87 high-quality draft metagenome-assembled genomes (MAGs) were reconstructed from LSZ refuse samples; nearly 15 % (13 of 87) belonged to putative As-methylates functional MAGs. Combined with the model of the As-biogeochemical cycle, nine putative functional species could complete methylation processes alone. The findings of this study highlighted the temperature influence on the As-methylation behavior in LSZ and could facilitate the management of As contamination in landfills.

Methylation of arsenic differs with substrates in Arcticibacter tournemirensis R1 from an As-contaminated paddy soil

Arsenic can be methylated by arsenite (As(III)) S-adenosylmethionine methyltransferases (ArsMs) among various kingdoms of life. The intermediate product methylarsenite (MAs(III)) is highly toxic and can be utilized as an antibiotic by some microbes. ArsM gene is widely distributed in the members of every kingdom from bacteria to humans and displays a high diversity of sequence. Based on arsenic methylating capacity, ArsM proteins can be divided into two phylogenetically distinct clades (Groups 1 and 2). In this study, we show that Arcticibacter tournemirensis R1 isolated from arsenic contaminated paddy soil is resistant to both As(III) and MAs(III), but exhibits different methylation activities for As(III) and MAs(III). The A. tournemirensis R1 shows low As(III) methylation activity and produces an unknown arsenic compound. In contrast, it shows high methylation activity with MAs(III), with the main product of dimethylarsenate (DMAs(V)). An AtarsM gene is found in ars operon of A. tournemirensis R1 genome and is regulated by an atypical transcriptional repressor ArsR. Expressed in Escherichia coli AtArsM confers resistance to As(III) and MAs(III). Both in vivo and in vitro assays show that AtArsM methylates As(III) and MAs(III) to dimethyl- and trimethyl‑arsenicals. AtArsM has four conserved cysteine residues, which are present in most ArsMs and can be classified into phylogenetic group 2 family, producing trimethylated arsenic metabolites. The high arsenic methylation and volatilization activity of AtArsM provides a potential strategy for arsenic bioremediation. The methylation activity differs with As(III) and MAs(III) in A. tournemirensis R1 indicates that there may have different detoxification mechanisms for As(III) and MAs(III), which are worth investigating in the future.

Arsenic Mobilization and Transformation by Ammonium-Generating Bacteria Isolated from High Arsenic Groundwater in Hetao Plain, China

Arsenic (As) mobilization in groundwater involves biogeochemical cycles of carbon, iron, and sulfur. However, few studies have focused on the role of nitrogen-metabolizing bacteria in As mobilization, as well as in the transformation between inorganic and organic As in groundwater. In this study, the nitrogen and As metabolisms of Citrobacter sp. G-C1 and Paraclostridium sp. G-11, isolated from high As groundwater in Hetao Plain, China, were characterized by culture experiments and genome sequencing. The results showed Citrobacter sp. G-C1 was a dissimilatory nitrate-reducing bacterium. The dissimilatory nitrate reduction to ammonia (DNRA) and As-detoxifying pathways identified in the genome enabled Citrobacter sp. G-C1 to simultaneously reduce As(V) during DNRA. Paraclostridium sp. G-11 was a nitrogen-fixing bacterium and its nitrogen-fixing activity was constrained by As. Nitrogen fixation and the As-detoxifying pathways identified in its genome conferred the capability of As(V) reduction during nitrogen fixation. Under anaerobic conditions, Citrobacter sp. G-C1 was able to demethylate organic As and Paraclostridium sp. G-11 performed As(III) methylation with the arsM gene. Collectively, these results not only evidenced that ammonium-generating bacteria with the ars operon were able to transform As(V) to more mobile As(III) during nitrogen-metabolizing processes, but also involved the transformation between inorganic and organic As in groundwater.

Microbiomes in the Challenger Deep slope and bottom-axis sediments

Hadal trenches are the deepest and most remote regions of the ocean. The 11-kilometer deep Challenger Deep is the least explored due to the technical challenges of sampling hadal depths. It receives organic matter and heavy metals from the overlying water column that accumulate differently across its V-shaped topography. Here, we collected sediments across the slope and bottom-axis of the Challenger Deep that enable insights into its in situ microbial communities. Analyses of 586 metagenome-assembled genomes retrieved from 37 metagenomes show distinct diversity and metabolic capacities between bottom-axis and slope sites. 26% of prokaryotic 16S rDNA reads in metagenomes were novel, with novelty increasing with water and sediment depths. These predominantly heterotrophic microbes can recycle macromolecules and utilize simple and complex hydrocarbons as carbon sources. Metagenome and metatranscriptome data support reduction and biotransformation of arsenate for energy gain in sediments that present a two-fold greater accumulation of arsenic compared to non-hadal sites. Complete pathways for anaerobic ammonia oxidation are predominantly identified in genomes recovered from bottom-axis sediments compared to slope sites. Our results expand knowledge of microbially-mediated elemental cycling in hadal sediments, and reveal differences in distribution of processes involved in nitrogen loss across the trench.

Glutathione is involved in the reduction of methylarsenate to generate antibiotic methylarsenite in Enterobacter sp. CZ-1

Methylarsenate (MAs(V)) is a product of microbial arsenic (As) biomethylation and has also been widely used as an herbicide. Some microbes are able to reduce nontoxic MAs(V) to highly toxic methylarsenite (MAs(III)) possibly as an antibiotic. The mechanism of MAs(V) reduction in microbes has not been elucidated. Here, we found that the bacterium Enterobacter sp. CZ-1 isolated from an As-contaminated paddy soil has a strong ability to reduce MAs(V) to MAs(III). Using a MAs(III)-responsive biosensor to detect MAs(V) reduction in E. coli Trans5α transformants of a genomic library of Enterobacter sp. CZ-1, we identified gshA, encoding a glutamate-cysteine ligase, as a key gene involved in MAs(V) reduction. Heterologous expression of gshA increased the biosynthesis of glutathione (GSH) and MAs(V) reduction in E. coli Trans5α. Deletion of gshA in Enterobacter sp. CZ-1 abolished its ability to synthesize GSH and decreased its MAs(V) reduction ability markedly, which could be restored by supplementation of exogenous GSH. In the presence of MAs(V), Enterobacter sp. CZ-1 was able to inhibit the growth of Bacillus subtilis 168; this ability was lost in the gshA-deleted mutant. In addition, deletion of gshA greatly decreased the reduction of arsenate to arsenite. These results indicate that GSH plays an important role in MAs(V) reduction to generate MAs(III) as an antibiotic. IMPORTANCE Arsenic is a ubiquitous environmental toxin. Some microbes detoxify inorganic arsenic through biomethylation, generating relatively nontoxic pentavalent methylated arsenicals, such as methylarsenate. Methylarsenate has also been widely used as an herbicide. Surprisingly, some microbes reduce methylarsenate to highly toxic methylarsenite possibly to use the latter as an antibiotic. How microbes reduce methylarsenate to methylarsenite is unknown. Here, we show that gshA encoding a glutamate-cysteine ligase in the glutathione biosynthesis pathway is involved in methylarsenate reduction in Enterobacter sp. CZ-1. Our study provides new insights into the crucial role of glutathione in the transformation of a common arsenic compound to a natural antibiotic.

Arsenic Accumulation and Biotransformation Affected by Nutrients (N and P) in Common Blooming-Forming Microcystis wesenbergii (Komárek) Komárek ex Komárek (Cyanobacteria)

Arsenic accumulation and biotransformation in algae was mostly carried out in a medium that contained far higher nutrient concentrations than that in natural freshwaters. The obtained results might have limited environmental validity and result in a failure to describe authentic arsenic biogeochemical cycles in natural freshwater systems. To validate the assumption, arsenic accumulation, and biotransformation in common bloom forming Microcystis wesenbergii was performed under a high nutrient concentration in BG11 medium (N = 250 mg/L, P = 7.13 mg/L), and adjusted low nutrients that mimicked values in natural freshwaters (N = 1.5 mg/L, P = 0.3 mg/L). The growth rate and maximum M. wesenbergii cell density were much lower in the high nutrient set, but more inhibition was shown with increasing ambient iAs(V) concentrations both in the high and low nutrient sets. The proportion of intracellular contents in total arsenicals decreased with increasing iAs(V) concentrations in both high and low nutrient sets but increased with incubation time. Intracellular iAs(III) was not found in the high nutrient set, while it formed high concentrations that could be comparable to that of an extracellular level in the low nutrient set. M. wesenbergii could methylate arsenic, and a higher proportion of organoarsenicals was formed in the low nutrient set. Lower intracellular MMA(V) and DMA(V) concentrations were found in the high nutrient set; contrarily, they presented a higher concentration that could be comparable to the extracellular ones in the low nutrient set. The results demonstrated that different nutrient regimes could affect arsenic accumulation and biotransformation in M. wesenbergii, and low nutrient concentrations could inhibit the excretion of iAs(III), MMA(V) and DMA(V) out of cells. Further investigations should be based on natural freshwater systems to obtain an authentic arsenic accumulation and biotransformation in cyanobacteria.

A Hyperthermoactive-Cas9 Editing Tool Reveals the Role of a Unique Arsenite Methyltransferase in the Arsenic Resistance System of Thermus thermophilus HB27

Arsenic detoxification systems can be found in a wide range of organisms, from bacteria to humans. In a previous study, we discovered an arsenic-responsive transcriptional regulator in the thermophilic bacterium Thermus thermophilus HB27 (TtSmtB). Here, we characterize the arsenic resistance system of T. thermophilus in more detail. We employed TtSmtB-based pulldown assays with protein extracts from cultures treated with arsenate and arsenite to obtain an S-adenosyl-l-methionine (SAM)-dependent arsenite methyltransferase (TtArsM). In vivo and in vitro analyses were performed to shed light on this new component of the arsenic resistance network and its peculiar catalytic mechanism. Heterologous expression of TtarsM in Escherichia coli resulted in arsenite detoxification at mesophilic temperatures. Although TtArsM does not contain a canonical arsenite binding site, the purified protein does catalyze SAM-dependent arsenite methylation with formation of monomethylarsenites (MMAs) and dimethylarsenites (DMAs). In addition, in vitro analyses confirmed the unique interaction between TtArsM and TtSmtB. Next, a highly efficient ThermoCas9-based genome-editing tool was developed to delete the TtArsM-encoding gene on the T. thermophilus genome and to confirm its involvement in the arsenite detoxification system. Finally, the TtarsX efflux pump gene in the T. thermophilus ΔTtarsM genome was substituted by a gene encoding a stabilized yellow fluorescent protein (sYFP) to create a sensitive genome-based bioreporter system for the detection of arsenic ions.

Demethylation of the Antibiotic Methylarsenite is Coupled to Denitrification in Anoxic Paddy Soil

Arsenic (As) biomethylation is an important component of the As biogeochemical cycle, which produces methylarsenite [MAs(III)] as an intermediate product. Its high toxicity is used by some microbes as an antibiotic to kill off other microbes and gain a competitive advantage. Some aerobic microbes have evolved a detoxification mechanism to demethylate MAs(III) via the dioxygenase C-As lyase ArsI. How MAs(III) is demethylated under anoxic conditions is unclear. We found that nitrate addition to a flooded paddy soil enhanced MAs(III) demethylation. A facultative anaerobe Bacillus sp. CZDM1 isolated from the soil was able to demethylate MAs(III) under anoxic nitrate-reducing conditions. A putative C-As lyase gene (BcarsI) was identified in the genome of strain CZDM1. The expression of BcarsI in the As-sensitive Escherichia coli AW3110 conferred the bacterium the ability to demethylate MAs(III) under anoxic nitrate-reducing condition and enhanced its resistance to MAs(III). Both Bacillus sp. CZDM1 and E. coli AW3110 harboring BcarsI could not demethylate MAs(III) under fermentative conditions. Five conserved amino acid resides of cysteine, histidine, and glutamic acid are essential for MAs(III) demethylation under anoxic nitrate-reducing conditions. Putative arsI genes are widely present in denitrifying bacteria, with 75% of the sequenced genomes containing arsI, also possessing dissimilatory nitrate reductase genes narG or napA. These results reveal a novel mechanism in which MAs(III) is demethylated via ArsI by coupling to denitrification, and such a mechanism is likely to be common in an anoxic environment such as paddy soils and wetlands.

Increase in arsenic methylation and volatilization during manure composting with biochar amendment in an aeration bioreactor

Biochar is widely used as an amendment to optimize the composting process. In this study, we firstly investigated the effects of biochar amendment on methylation and volatilization of arsenic (As), and the microbial communities during manure composting. Biochar amendment was found to increase the concentrations of monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) during mesophilic (days 0-10) and early thermophilic (days 11-15) phases, and promote As volatilization during the maturing phase (days 60-80) of composting. In addition, the abundances of As(V) reductase (arsC) and As(III) S-adenosyl-L-methionine methyltransferase (arsM) genes were higher in the biochar treatment than that in the control. Moreover, biochar amendment influenced the microbial communities by promoting As methylation and volatilization via Ensifer and Sphingobium carrying arsC genes, and Rhodopseudomonas and Pseudomonas carrying arsM genes. This study emphasized the considerable role of biochar on methylation and volatilization of As during manure composting and provided an overall characterization of the community compositions of arsC and arsM genes during manure composting. It will broaden our insights in As biogeochemical cycle during manure composting with biochar amendment, which will facilitate the regulation of As during manure composting and its application in agricultural soil.

Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms

Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As. Amongst those, only the aerobic species were efficient methylators. The anaerobic microorganisms presented high resistance to As exposure, presumably through their efficient As(III) efflux, but methylated As poorly. The only exception were methanogens, for which efficient As methylation was seemingly an artifact of membrane disruption. Deletion of an efflux pump gene (acr3) in one of the anaerobes, Clostridium pasteurianum, rendered the strain sensitive to As and capable of more efficiently methylating As. Our results led to the following conclusions: (i) encoding a functional ArsM enzyme does not guarantee that a microorganism will actively drive As methylation in the presence of the metalloid and (ii) there is an inverse relationship between efficient microbial As efflux and its methylation, because the former prevents the intracellular accumulation of As.

The characterization of arsenic biotransformation microbes in paddy soil after straw biochar and straw amendments

Straw biochar and straw application to paddy soil dramatically altered arsenic (As) biogeochemical cycling in soil-rice system, but it remains unknown how As biotransformation microbes (ABMs) contribute to these processes. In this study, rice pot experiments combining terminal restriction fragment length polymorphism (T-RFLP) analysis and clone library were performed to characterize ABMs. Through linear discriminant analysis (LDA) effect size (LEfSe) and correlation analysis, results revealed that arrA-harbouring iron-reducing bacteria (e.g., Geobacter and Shewanella) and arsC-harbouring Gammaproteobacteria (e.g., fermentative hydrogen-producing and lignin-degrading microorganisms) potentially mediated arsenate [As(V)] reduction under biochar and straw amendments, respectively. Methanogens and sulfate-reducing bacteria (SRB) carrying arsM gene might regulate methylated As concentration in soil-rice system. Network analysis demonstrated that the association among ABMs in rhizosphere was significantly stronger than that in bulk soil. Arsenite [As(III)] methylators carrying arsM gene exhibited much stronger co-occurrence pattern with arsC-harbouring As(V) reducers than with arrA-harbouring As(V) reducers. This study would broaden our insights for the dramatic variation of As biogeochemical cycling in soil-rice system after straw biochar and straw amendments through the activities of ABMs, which could contribute to the safe rice production and high rice yield in As-contaminated fields.

Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil

The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.

Microbiomes inhabiting rice roots and rhizosphere

Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.

Arsenic and the gastrointestinal tract microbiome

Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.

ArsM-mediated arsenite volatilization is limited by efflux catalyzed by As efflux transporters

Arsenic (As) methylation is regarded as an efficient strategy for As contamination remediation by As volatilization. However, most microorganisms display low As volatilization efficiency, which is possibly linked to As efflux transporters competing for cytoplasmic As(III) as a substrate. Here, we developed two types of As biosensors in Escherichia coli to compare the As efflux rate of three efflux transporters and to further investigate the correlation between As efflux rates and As volatilization. The engineered As-sensitive E. coli AW3110 expressing arsB_RP, acr3_RP or arsB_EC displayed a higher As resistance compared to the control. The fluorescence intensity was in a linear correlation in the range of 0-2.0 μmol/L of As(III). The intracellular As(III) concentration was negatively related to As efflux activity of As efflux transporter, which was consistent with the As resistance assays. Moreover, arsM derived from R. palustris CGA009 was subsequently introduced to construct an E. coli AW3110 co-expressing arsB/acr3 and arsM, which exhibited higher As(III) resistance, lower fluorescence intensity and intracellular As concentration compared to the engineered E. coli AW3110 expressing only arsB/acr3. The As volatilization efficiency was negatively related to As efflux activity of efflux transporters, the recombinants without arsB/acr3 displayed the highest rate of As volatilization. This study provided new insights into parameters affecting As volatilization with As efflux being the main limiting factor for As methylation and subsequent volatilization in many microorganisms.

Unique diversity and functions of the arsenic-methylating microorganisms from the tailings of Shimen Realgar Mine

Microbial arsenic (As) methylation plays important roles in the As biogeochemical cycle. However, little is known about the diversity and functions of As-methylating microorganisms from the tailings of a Realgar Mine, which is characterized as containing extremely high concentrations of As. To address this issue, we collected five samples (T1-T5) from the tailings of Shimen Realgar Mine. Microcosm assays without addition of exogenous As and carbon indicated that all the five samples possess significant As-methylating activities, producing 0.8-5.7 μg/L DMAs^V, and 1.1-10.7 μg/L MMAs^V with an exception of T3, from which MMAs^V was not detectable after 14.0 days of incubation. In comparison, addition of 20.0 mM lactate to the microcosms significantly enhanced the activities of these samples; the produced DMAs^V and MMAs^V are 8.0-39.7 μg/L and 5.8-38.3 μg/L, respectively. The biogenic DMAs^V shows significant positive correlations with the Fe concentrations and negative correlations with the total nitrogen concentrations in the environment. A total of 63 different arsM genes were identified from the five samples, which code for new or new-type ArsM proteins, suggesting that a unique diversity of As-methylating microbes are present in the environment. The microbial community structures of the samples were significantly shaped by the environmental total organic carbon, total As contents and NO₃^- contents. These data help to better understand the microorganisms-catalyzed As methylation occurred in the environment with extremely high contents of As.

Distribution of arsenic and its biotransformation genes in sediments from the East China Sea

Microbial transformation of arsenic (As) plays a key role in As biogeochemical cycling and affects the mobility, bioavailability, and toxicity of As. This study aims to investigate the accumulation of As in marine sediments at different water depths in the East China Sea and reveal the abundance and diversity of the aioA, arrA, arsC, and arsM genes through quantitative real-time polymerase chain reaction (qPCR) and high-throughput sequencing. Results showed that the As content in sediments ranged from 5.53 mg kg^-1 to 17.70 mg kg^-1, which decreased with water depth. Abundant As biotransformation genes with low diversity were identified in these sediments, of which arsM and arrA were the most abundant. Significant positive correlation exists between the arsM and arrA gene abundance and between arsC and aioA, indicating the co-occurrence of the As biotransformation genes in microbes in marine sediments. Metagenomics analysis revealed that arsM gene was mainly distributed in Alphaproteobacteria, Solibacteres, Deltaproteobacteria, Clostridia, and Bacilli in these sediments. Among the sediment properties, total N, total S, C/N, and TOC were important factors that shaped the abundance profile of the genes involved in As transformation. This study provides a picture of As biotransformation genes in marine sediments from the East China Sea, which may affect As transformation and the ultimate fate of As in a marine environment.

Inhibition of Microbial Methylation via arsM in the Rhizosphere: Arsenic Speciation in the Soil to Plant Continuum

The interplay between rice roots and manuring with respect to arsenic speciation, subsequent assimilation into roots, and translocation to shoots in paddy soil was investigated, alongside bacterial diversity characterization. Planting increased soil Eh and decreased soil solution arsenic species: inorganic arsenic, monomethylarsonic acid, trimethylarsenic oxide, and dimethylarsinic acid. Presence of plant roots increased the copy number of Clostridium and Tumebacillus 16S rRNA as well as Streptomyces arsenic methylating gene ( arsM), but decreased Acidobacteria_GP1 16S rRNA and Rhodopseudomonas. palustris BisB5 arsM. Sum of arsenic species decreased under root influence due to the interplay of inorganic arsenic mobilization in bulk soil under anaerobic and immobilization under oxygenated rhizospheric conditions. Manuring increased all soil solution arsenic species (>90%), shoot total arsenic (60%), copy number of Geobacter 16S rRNA, and R. palustris TIE-1 arsM, indicative of a shift towards microbes with iron reduction and oxidation as well as arsenic methylation capabilities.

Identification of Steps in the Pathway of Arsenosugar Biosynthesis

Arsenosugars are arsenic-containing ribosides that play a substantial role in arsenic biogeochemical cycles. Arsenosugars were identified more than 30 years ago, and yet their mechanism of biosynthesis remains unknown. In this study we report identification of the arsS gene from the cyanobacterium Synechocystis sp. PCC 6803 and show that it is involved in arsenosugar biosynthesis. In the Synechocystis sp. PCC 6803 ars operon, arsS is adjacent to the arsM gene that encodes an As(III) S-adenosylmethionine (SAM) methyltransferase. The gene product, ArsS, contains a characteristic CX3CX2C motif which is typical for the radical SAM superfamily. The function of ArsS was identified from a combination of arsS disruption in Synechocystis sp. PCC 6803 and heterologous expression of arsM and arsS in Escherichia coli. Both genes are necessary, indicating a multistep pathway of arsenosugar biosynthesis. In addition, we demonstrate that ArsS orthologs from three other freshwater cyanobacteria and one picocyanobacterium are involved in arsenosugar biosynthesis in those microbes. This study represents the identification of the first two steps in the pathway of arsenosugar biosynthesis. Our discovery expands the catalytic repertoire of the diverse radical SAM enzyme superfamily and provides a basis for studying the biogeochemistry of complex organoarsenicals.

A methyltransferase gene from arbuscular mycorrhizal fungi involved in arsenic methylation and volatilization

Arbuscular mycorrhizal fungi (AMF), ubiquitous symbiotic fungi associated with the majority of terrestrial plants, were demonstrated to play important roles in arsenic (As) translocation and transformation in the plant-soil continuum, and substantially influence plant As tolerance. However, the direct involvement of AMF in As methylation and volatilization and their molecular mechanisms remain unsolved. Here, an arsenite methyltransferase gene RiMT-11 was identified and characterized from AM fungus Rhizophagus irregularis. Heterologous expression of RiMT-11 enhanced arsenite resistance of E. coli (Δars) through methylating As into monomethylarsonic acid (MMA), dimethylarsinic acid (DMA) and ultimately volatile trimethyl arsine (TMAs). In a two-compartment in vitro monoxenic cultivation system, methylated and volatile As were also detected from AM symbioses with arsenate addition, accompanied by strong up-regulation of RiMT-11 expression in extraradical hyphae. The present study provided direct evidence and illustrated an underlying mechanism of As methylation and volatilization by AMF, leading to a deeper insight into the role of AMF in As biogeochemical cycling.

Microbe mediated arsenic release from iron minerals and arsenic methylation in rhizosphere controls arsenic fate in soil-rice system after straw incorporation

Arsenic (As) contamination is a global problem. Straw incorporation is widely performed in As contaminated paddy fields. To understand how straw and straw biochar incorporation affect As transformation and translocation in the soil-microbe-rice system, a pot experiment was carried out with different dosages of rice straw and straw biochar application. Results showed that both straw biochar and straw application significantly increased As mobility. Straw biochar mobilized As mainly through increasing soil pH and DOM content. Straw incorporation mainly through enhancing As release from iron (Fe) minerals and arsenate (As(V)) reduction to arsenite (As(III)). Straw biochar didn't significantly affect As methylation, while straw incorporation significantly enhanced As methylation, elevated dimethylarsenate (DMA) concentration in soil porewater and increased As volatilization. Straw biochar didn't significantly change total As accumulation in rice grains, but decreased As(III) accumulation by silicon (Si) inhibition. Straw incorporation significantly increased DMA, but decreased As(III) concentration in rice grains. After biochar application, dissolved As was significantly positively correlated with the abundance of Bacillus, indicating that Bacillus might be involved in As release, and As(III) concentration in polished grains was negatively correlated with Si concentration. The significant positive correlation between dissolved As with Fe and the abundance of iron-reducing bacteria suggested the coupling of As and Fe reduction mediated by iron-reducing bacteria. The significant positive correlation between DMA in rice grains and the abundance of methanogenic bacteria indicated that methanogenic bacteria could be involved in As methylation after straw application. The results of this study would advance the understanding how rice straw incorporation affects As fate in soil-microbe-rice system, and provide some guidance to straw incorporation in As contaminated paddy soil. This study also revealed a wealth of microorganisms in the soil environment that dominate As mobility and transformation after straw incorporation.

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO₂ reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.

Arsenic methylation by a novel ArsM As(III) S-adenosylmethionine methyltransferase that requires only two conserved cysteine residues

Arsenic (As) biomethylation is an important component of the As biogeochemical cycle that can influence As toxicity and mobility in the environment. Biomethylation of As is catalyzed by the enzyme arsenite (As[III]) S-adenosylmethionine methyltransferase (ArsM). To date, all identified ArsM orthologs with As(III) methylation activities have four conserved cysteine residues, which are thought to be essential for As(III) methylation. Here, we isolated an As(III)-methylating bacterium, Bacillus sp. CX-1, and identified a gene encoding a S-adenosylmethionine methyltranserase termed BlArsM with low sequence similarities (≤ 39%) to other ArsMs. BlArsM has six cysteine residues (Cys10, Cys11, Cys145, Cys193, Cys195 and Cys268), three of which (Cys10, Cys145 and Cys195) align with conserved cysteine residues found in most ArsMs. BlarsM is constitutively expressed in Bacillus sp. CX-1. Heterologous expression of BlarsM conferred As(III) resistance. Purified BlArsM methylated both As(III) and methylarsenite (MAs[III]), with a final product of dimethylarsenate (DMAs[V]). When all six cysteines were individually altered to serine residues, only C145S and C195S derivatives lost the ability to methylate As(III) and MAs(III). The derivative C10S/C11S/C193S/C268S was still active. These results suggest that BlArsM is a novel As(III) S-adenosylmethionine methyltransferase requiring only two conserved cysteine residues. A model of As(III) methylation by BlArsM is proposed.

Microbial Processes Mediating the Evolution of Methylarsine Gases from Dimethylarsenate in Paddy Soils

Arsenic (As) biovolatilization is an important component of the global As biogeochemical cycle. Soils can emit various methylarsine gases, but the underlying microbial processes remain unclear. Here, we show that the addition of molybdate (Mo), an inhibitor of sulfate-reducing bacteria, greatly enhanced dimethylarsine evolution from dimethylarsenate [DMAs(V)] added to two paddy soils. Molybdate addition significantly affected the microbial community structure. The aerobic enrichment cultures from both soils volatilized substantial amounts of dimethylarsine from DMAs(V) in the presence of Mo, whereas the anaerobic enrichment cultures did not. A Bacillus strain (CZ-2) capable of reducing DMAs(V) to dimethylarsine was isolated from the aerobic enrichment culture, and its volatilization ability was enhanced by Mo. RNA-seq analysis identified 10 reductase genes upregulated by Mo. Addition of the reducing agent NADH increased dimethylarsine volatilization by strain CZ-2, suggesting that DMAs(V) reductase is an NADH-dependent enzyme. The strain could not methylate arsenite or convert monomethylarsenate and DMAs(V) to trimethylarsine. Our results show that dimethylarsine evolution from DMAs(V) is independent of the As methylation pathway and that Mo enhances dimethylarsine evolution from paddy soils by shifting the microbial community structure and enhancing the reduction of DMAs(V) to dimethylarsine, possibly through upregulating the expression of DMAs(V) reductase gene(s).

Arsenic Methylation Dynamics in a Rice Paddy Soil Anaerobic Enrichment Culture

Methylated arsenic (As) species represent a significant fraction of the As accumulating in rice grains, and there are geographic patterns in the abundance of methylated arsenic in rice that are not understood. The microorganisms driving As biomethylation in paddy environments, and thus the soil conditions conducive to the accumulation of methylated arsenic, are unknown. We tested the hypothesis that sulfate-reducing bacteria (SRB) are key drivers of arsenic methylation in metabolically versatile mixed anaerobic enrichments from a Mekong Delta paddy soil. We used molybdate and monofluorophosphate as inhibitors of sulfate reduction to evaluate the contribution of SRB to arsenic biomethylation, and developed degenerate primers for the amplification of arsM genes to identify methylating organisms. Enrichment cultures converted 63% of arsenite into methylated products, with dimethylarsinic acid as the major product. While molybdate inhibited As biomethylation, this effect was unrelated to its inhibition of sulfate reduction and instead inhibited the methylation pathway. Based on arsM sequences and the physiological response of cultures to media conditions, we propose that amino acid fermenting organisms are potential drivers of As methylation in the enrichments. The lack of a demethylating capacity may have contributed to the robust methylation efficiencies in this mixed culture.

Arsenic biotransformation by a cyanobacterium Nostoc sp. PCC 7120

Nostoc sp. PCC 7120 (Nostoc), a typical filamentous cyanobacterium ubiquitous in aquatic system, is recognized as a model organism to study prokaryotic cell differentiation and nitrogen fixation. In this study, Nostoc cells incubated with arsenite (As(III)) for two weeks were extracted with dichloromethane/methanol (DCM/MeOH) and the extract was partitioned between water and DCM. Arsenic species in aqueous and DCM layers were determined using high performance liquid chromatography - inductively coupled plasma mass spectrometer/electrospray tandem mass spectrometry (HPLC-ICPMS/ESIMSMS). In addition to inorganic arsenic (iAs), the aqueous layer also contained monomethylarsonate (MAs(V)), dimethylarsinate (DMAs(V)), and the two arsenosugars, namely a glycerol arsenosugar (Oxo-Gly) and a phosphate arsenosugar (Oxo-PO4). Two major arsenosugar phospholipids (AsSugPL982 and AsSugPL984) were detected in DCM fraction. Arsenic in the growth medium was also investigated by HPLC/ICPMS and shown to be present mainly as the inorganic forms As(III) and As(V) accounting for 29%-38% and 29%-57% of the total arsenic respectively. The total arsenic of methylated arsenic, arsenosugars, and arsenosugar phospholipids in Nostoc cells with increasing As(III) exposure were not markedly different, indicating that the transformation to organoarsenic in Nostoc was not dependent on As(III) concentration in the medium. Our results provide new insights into the role of cyanobacteria in the biogeochemical cycling of arsenic.

Evaluation of bioaugmentation and biostimulation on arsenic remediation in soil through biovolatilization

Arsenic (As) removal through microbially driven biovolatilization can be explored as a potential method for As bioremediation. However, its effectiveness needs to be improved. Biostimulation with organic matter amendment and bioaugmentation with the inoculation of genetic engineered bacteria could be potential strategies for As removal and site remediation. Here, the experiments were conducted to evaluate the impacts of rice straw and biochar amendment, inoculation of genetic engineered Pseudomonas putida KT2440 (GE P. putida) with high As volatilization activity, on microbial mediated As volatilization and removal from three different arseniferous soils. In general, the addition of rice straw (5%) significantly enhanced As methylation and volatilization in comparison with corresponding non-amended soils. Biochar amendments and inoculation of the GE P. putida increased As methylation and volatilization, respectively, but less than that of rice straw addition. The effectiveness of As volatilizations are quite different in the various paddy soils. The combined amendments of rice straw and GE P. putida exhibited the highest As removal efficiency (483.2 μg/kg/year) in Dayu soil, with 1.2% volatilization of the total As annually. The highest water-soluble As concentration (0.73 mg/kg) in this soil could be responsible for highest As volatilization besides the rice straw and bacteria in this soil.

Arsenic methylation by a genetically engineered Rhizobium-legume symbiont

BACKGROUND AND AIMS

Arsenic (As) is one of the most widespread environmental contaminants. The aim of our study was to test a novel bioremediation system based on the symbiosis between leguminous plant and genetically engineered rhizobia.

METHODS

The arsenite [As(III)] S-adenosylmethionine methyltransferase gene (CrarsM) from the alga Chlamydomonas reinhardtii was inserted into the chromosome of Rhizobium leguminosarum bv. trifolii strain R3. The As methylation ability of the recombinant Rhizobium was tested under free living conditions and in symbiosis with red clover plants. Arsenic speciation was determined using high-performance liquid chromatography-inductively coupled plasma mass spectrometry.

RESULTS

Under free-living conditions, CrarsM-recombinant R. leguminosarum gained the ability to methylate As(III) to methylated arsenicals, including methylarsenate [MAs(V)], dimethylarsenate [DMAs(V)] and trimethylarsine oxide [TMAs(V)O]. Red clover plants were inoculated with either control (non-recombinant) or CrarsM-recombinant R. leguminosarum and exposed to 5 or 10 μM arsenite. No methylated As species were detected in red clover plants inoculated with control R. leguminosarum. In contrast, all three methylated species were detected in both the nodules and the shoots when the recombinant Rhizobium established symbiosis with red clover, accounting for 74.7-75.1% and 29.1-42.4% of the total As in the two plant tissues, respectively. The recombinant symbiont also volatilized small amounts of As.

CONCLUSIONS

The present study demonstrates that engineered rhizobia expressing an algal arsM gene can methylate and volatilize As, providing a proof of concept for potential future use of legume-rhizobia symbionts for As bioremediation.

Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion

High concentrations of residual arsanilic acid occur in pig manure due to its use in feed to promote growth and control diseases. This study compared the effects of arsanilic acid at three concentrations (0, 325, and 650mg/kg dry pig manure) on the abundance of antibiotic resistance genes (ARGs) and the microbial community during anaerobic digestion. Addition of 650mg/kg arsanilic acid enhanced the absolute abundances of tetC, sul2, ermB, and gyrA more than twofold in the digestion product. Redundancy analysis indicated that the change in the microbial community structure was the main driver of variation in the ARGs profile. The As resistance gene arsC co-occurred with four ARGs and intI1, possibly causing the increase in ARGs under pressure by arsanilic acid. High arsanilic acid concentrations can increase the risk of ARGs occurring in anaerobic digestion products. The amount of arsanilic acid used as a feed additive should be controlled.

Heavy metal concentrations and arsenic speciation in animal manure composts in China

A nationwide survey of animal manure-based composts was carried out in China. Two hundred and twelve samples were collected and analyzed for the concentrations of 9 heavy metals or metalloids and arsenic (As) speciation. The concentrations of heavy metals vary widely (Zn 11.8-3692, Cu 3.6-916, Cr 0.7-6603, Ni 0.7-73, Pb 0.05-189, As 0.4-72, Co 0.1-94, Cd 0.01-8.7 and Hg 0.01-1.9mgkg^-1 dry weight). Compared with the maximum permissible values of the Chinese standard for organic fertilizers, 13.7% and 2.4% of the composts exceeded the limits for As (15mgkg^-1) and Cd (3mgkg^-1), respectively. Some samples contained very high concentrations of Zn and Cu, although no limits have been set for these two metals in China. Further analysis showed that As was present mainly as arsenate (As^Ⅴ), with dimethylarsenate (DMA) and monomethylarsenate (MMA) as the minor species in composts. There were significant correlations between the concentrations of Zn, Cu and As, suggesting co-contamination of these elements in some composts. Monte Carlo simulations based on the distributions of metal concentrations and application rate showed that repeated applications of compost likely increase the concentrations of Zn, Cu, Cd and Hg in soil significantly compared with the soil background levels. This study highlights a need to minimize the concentrations of Zn, Cu, Cd, Hg and As in animal manures to ensure their safe recycling to agricultural soils.

Land scale biogeography of arsenic biotransformation genes in estuarine wetland

As an analogue of phosphorus, arsenic (As) has a biogeochemical cycle coupled closely with other key elements on the Earth, such as iron, sulfate and phosphate. It has been documented that microbial genes associated with As biotransformation are widely present in As-rich environments. Nonetheless, their presence in natural environment with low As levels remains unclear. To address this issue, we investigated the abundance levels and diversities of aioA, arrA, arsC and arsM genes in estuarine sediments at low As levels across Southeastern China to uncover biogeographic patterns at a large spatial scale. Unexpectedly, genes involved in As biotransformation were characterized by high abundance and diversity. The functional microbial communities showed a significant decrease in similarity along the geographic distance, with higher turnover rates than taxonomic microbial communities based on the similarities of 16S rRNA genes. Further investigation with niche-based models showed that deterministic processes played primary roles in shaping both functional and taxonomic microbial communities. Temperature, pH, total nitrogen concentration, carbon/nitrogen ratio and ferric iron concentration rather than As content in these sediments were significantly linked to functional microbial communities, while sediment temperature and pH were linked to taxonomic microbial communities. We proposed several possible mechanisms to explain these results.

Conserved cysteine residues determine substrate specificity in a novel As(III) S-adenosylmethionine methyltransferase from Aspergillus fumigatus

Methylation of inorganic arsenic is a central process in the organoarsenical biogeochemical cycle. Members of every kingdom have ArsM As(III) S-adenosylmethionine (SAM) methyltransferases that methylates inorganic As(III) into mono- (MAs(III)), di- (DMAs(III)) and tri- (TMAs(III)) methylarsenicals. Every characterized ArsM to date has four conserved cysteine residues. All four cysteines are required for methylation of As(III) to MAs(III), but methylation of MAs(III) to DMAs(III) requires only the two cysteines closest to the C-terminus. Fungi produce volatile and toxic arsines, but the physiological roles of arsenic methylation and the biochemical basis is unknown. Here they demonstrate that most fungal species have ArsM orthologs with only three conserved cysteine residues. The genome of Aspergillus fumigatus has four arsM genes encoding ArsMs with only the second, third and fourth conserved cysteine residues. AfArsM1 methylates MAs(III) but not As(III). Heterologous expression of AfarsM1 in an Escherichia coli conferred resistance to MAs(III) but not As(III). The existence of ArsMs with only three conserved cysteine residues suggest that the ability to methylate MAs(III) may be an evolutionary step toward enzymes capable of methylating As(III), the result of a loss of function mutation in organisms with infrequent exposure to inorganic As(III) or as a resistance mechanism for MAs(III).

Biomethylation and Volatilization of Arsenic by Model Protozoan Tetrahymena pyriformis under Different Phosphate Regimes

Tetrahymena pyriformis, a freshwater protozoan, is common in aquatic systems. Arsenic detoxification through biotransformation by T. pyriformis is important but poorly understood. Arsenic metabolic pathways (including cellular accumulation, effluxion, biomethylation, and volatilization) of T. pyriformis were investigated at various phosphate concentrations. The total intracellular As concentration increased markedly as the external phosphate concentration decreased. The highest concentration was 168.8 mg·kg-1 dry weight, after exposure to As(V) for 20 h. Inorganic As was dominant at low phosphate concentrations (3, 6, and 15 mg·L-1), but the concentration was much lower at 30 mg·L-1 phosphate, and As(V) contributed only ~7% of total cellular As. Methylated As contributed 84% of total As at 30 mg·L-1 phosphate, and dimethylarsenate (DMAs(V)) was dominant, contributing up to 48% of total As. Cellular As effluxion was detected, including inorganic As(III), methylarsenate (MAs(V)) and DMAs(V). Volatile As was determined at various phosphate concentrations in the medium. All methylated As concentrations (intracellular, extracellular, and volatilized) had significant linear positive relationships with the initial phosphate concentration. To the best of our knowledge, this is the first study of As biotransformation by protozoa at different phosphate concentrations.

Arsenic methylation by an arsenite S-adenosylmethionine methyltransferase from Spirulina platensis

Arsenic-contaminated water is a serious hazard for human health. Plankton plays a critical role in the fate and toxicity of arsenic in water by accumulation and biotransformation. Spirulina platensis (S. platensis), a typical plankton, is often used as a supplement or feed for pharmacy and aquiculture, and may introduce arsenic into the food chain, resulting in a risk to human health. However, there are few studies about how S. platensis biotransforms arsenic. In this study, we investigated arsenic biotransformation by S. platensis. When exposed to arsenite (As(III)), S. platensis accumulated arsenic up to 4.1mg/kg dry weight. After exposure to As(III), arsenate (As(V)) was the predominant species making up 64% to 86% of the total arsenic. Monomethylarsenate (MMA(V)) and dimethylarsenate (DMA(V)) were also detected. An arsenite S-adenosylmethionine methyltransferase from S. platensis (SpArsM) was identified and characterized. SpArsM showed low identity with other reported ArsM enzymes. The Escherichia coli AW3110 bearing SparsM gene resulted in As(III) methylation and conferring resistance to As(III). The in vitro assay showed that SpArsM exhibited As(III) methylation activity. DMA(V) and a small amount of MMA(V) were detected in the reaction system within 0.5hr. A truncated SpArsM derivative lacking the last 34 residues still had the ability to methylate As(III). The three single mutants of SpArsM (C59S, C186S, and C238S) abolished the capability of As(III) methylation, suggesting the three cysteine residues are involved in catalysis. We propose that SpArsM is responsible for As methylation and detoxification of As(III) and may contribute to As biogeochemistry.

Anaerobic Disposal of Arsenic-Bearing Wastes Results in Low Microbially Mediated Arsenic Volatilization

The removal of arsenic from drinking water sources produces arsenic-bearing wastes, which are disposed of in a variety of ways. Several disposal options involve anaerobic environments, including mixing arsenic waste with cow dung, landfills, anaerobic digesters, and pond sediments. Though poorly understood, the production of gaseous arsenic species in these environments can be a primary goal (cow dung mixing) or an unintended consequence (anaerobic digesters). Once formed, these gaseous arsenic species are readily diluted in the atmosphere. Arsenic volatilization can be mediated by the enzyme arsenite S-adenosylmethionine methyltransferase (ArsM) or through the enzymes involved in methanogenesis. In this study, methanogenic mesocosms with arsenic-bearing ferric iron waste from an electrocoagulation drinking water treatment system were used to evaluate the role of methanogenesis in arsenic volatilization using methanogen inhibitors. Arsenic volatilization was highest in methanogenic mesocosms, but represented <0.02% of the total arsenic added. 16S rRNA cDNA sequencing, qPCR of mcrA transcripts, and functional gene array-based analysis of arsM expression, revealed that arsenic volatilization correlated with methanogenic activity. Aqueous arsenic concentrations increased in all mesocosms, indicating that unintended contamination may result from disposal in anaerobic environments. This highlights that more research is needed before recommending anaerobic disposal intended to promote arsenic volatilization.

Efficient Arsenic Methylation and Volatilization Mediated by a Novel Bacterium from an Arsenic-Contaminated Paddy Soil

Microbial arsenic (As) methylation and volatilization are important processes controlling the As biogeochemical cycle in paddy soils. To further understand these processes, we isolated a novel bacterial strain, SM-1, from an As-contaminated paddy soil. SM-1 showed strong As methylation and volatilization abilities, converting almost all arsenite (10 μM) to dimethylarsenate and trimethylarsenic oxide in the medium and trimethylarsine gas into the headspace within 24 h, with trimethylarsine accounting for nearly half of the total As. On the basis of the 16S rRNA sequence, strain SM-1 represents a new species in a new genus within the family Cytophagaceae. Strain SM-1 is abundant in the paddy soil and inoculation of SM-1 greatly enhanced As methylation and volatilization in the soil. An arsenite methyltransferase gene (ArarsM) was cloned from SM-1. When expressed in Escherichia coli, ArArsM conferred the As methylation and volatilization abilities to E. coli and increased its resistance to arsenite. The high As methylation and volatilization abilities of SM-1 are likely attributed to an efficient ArArsM enzyme coupled with low arsenite efflux. These results suggest that strain SM-1 plays an important role in As methylation and volatilization in the paddy soil and has a great potential for As bioremediation.

Arsenic Demethylation by a C·As Lyase in Cyanobacterium Nostoc sp. PCC 7120

Arsenic, a ubiquitous toxic substance, exists mainly as inorganic forms in the environment. It is perceived that organoarsenicals can be demethylated and degraded into inorganic arsenic by microorganisms. Few studies have focused on the mechanism of arsenic demethylation in bacteria. Here, we investigated arsenic demethylation in a typical freshwater cyanobacterium Nostoc sp. PCC 7120. This bacterium was able to demethylate monomethylarsenite [MAs(III)] rapidly to arsenite [As(III)] and also had the ability to demethylate monomethylarsenate [MAs(V)] to As(III). The NsarsI encoding a C·As lyase responsible for MAs(III) demethylation was cloned from Nostoc sp. PCC 7120 and heterologously expressed in an As-hypersensitive strain Escherichia coli AW3110 (ΔarsRBC). Expression of NsarsI was shown to confer MAs(III) resistance through arsenic demethylation. The purified NsArsI was further identified and functionally characterized in vitro. NsArsI existed mainly as the trimeric state, and the kinetic data were well-fit to the Hill equation with K0.5 = 7.55 ± 0.33 μM for MAs(III), Vmax = 0.79 ± 0.02 μM min(-1), and h = 2.7. Both of the NsArsI truncated derivatives lacking the C-terminal 10 residues (ArsI10) or 23 residues (ArsI23) had a reduced ability of MAs(III) demethylation. These results provide new insights for understanding the important role of cyanobacteria in arsenic biogeochemical cycling in the environment.

Adaptation of a methanogenic consortium to arsenite inhibition

Arsenic (As) is a ubiquitous metalloid known for its adverse effects to human health. Microorganisms are also impacted by As toxicity, including methanogenic archaea, which can affect the performance of process in which biological activity is required (i.e. stabilization of activated sludge in wastewater treatment plants). The novel ability of a mixed methanogenic granular sludge consortium to adapt to the inhibitory effect of arsenic (As) was investigated by exposing the culture to approximately 0.92 mM of AsIII for 160 d in an arsenate (AsV) reducing bioreactor using ethanol as the electron donor. The results of shaken batch bioassays indicated that the original, unexposed sludge was severely inhibited by arsenite (AsIII) as evidenced by the low 50% inhibition concentrations (IC50) determined, i.e., 19 and 90 μM for acetoclastic- and hydrogenotrophic methanogenesis, respectively. The tolerance of the acetoclastic and hydrogenotrophic methanogens in the sludge to AsIII increased 47-fold (IC50 = 910 μM) and 12-fold (IC50= 1100 μM), respectively, upon long-term exposure to As. In conclusion, the methanogenic community in the granular sludge demonstrated a considerable ability to adapt to the severe inhibitory effects of As after a prolonged exposure period.

Genetically Engineering Bacillus subtilis with a Heat-Resistant Arsenite Methyltransferase for Bioremediation of Arsenic-Contaminated Organic Waste

Organic manures may contain high levels of arsenic (As) due to the use of As-containing growth-promoting substances in animal feed. To develop a bioremediation strategy to remove As from organic waste, Bacillus subtilis 168, a bacterial strain which can grow at high temperature but is unable to methylate and volatilize As, was genetically engineered to express the arsenite S-adenosylmethionine methyltransferase gene (CmarsM) from the thermophilic alga Cyanidioschyzon merolae. The genetically engineered B. subtilis 168 converted most of the inorganic As in the medium into dimethylarsenate and trimethylarsine oxide within 48 h and volatized substantial amounts of dimethylarsine and trimethylarsine. The rate of As methylation and volatilization increased with temperature from 37 to 50°C. When inoculated into an As-contaminated organic manure composted at 50°C, the modified strain significantly enhanced As volatilization. This study provides a proof of concept of using genetically engineered microorganisms for bioremediation of As-contaminated organic waste during composting.