Arsenic-rich Environments Research Articles

A large colonial choanoflagellate from Mono Lake harbors live bacteria.

The diversity of organisms that live in the extreme environment of Mono Lake (California, USA) is limited. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist in Mono Lake, a hypersaline, alkaline, arsenic-rich environment. We repeatedly isolated members of a new species of choanoflagellate, which we have named Barroeca monosierra. Characterization of B. monosierra revealed that it forms large spherical colonies containing diverse co-isolated bacteria, providing an opportunity to investigate mechanisms underlying physical associations between eukaryotes and bacteria.

The developmental and structural uniqueness of the embryo of the extremophile viviparous nematode, Tokorhabditis tufae.

Viviparity, a reproductive form that supplies nutrients to the embryo during gestation, has repeatedly and independently occurred in multiple lineages of animals. During the convergent evolution of viviparity, various modifications of development, structure, and physiology emerged. A new species of nematode, Tokorhabditis tufae, was discovered in the alkaline, hypersaline, and arsenic-rich environment of Mono lake. Its reproductive form is viviparity because it is obligately live-bearing and the embryo increases in size during development. However, the magnitude of the increase in size and nutrient provisioning are unclear. We measured egg and embryo sizes at three developmental stages in T. tufae. Eggs and embryos of T. tufae at the threefold stage were respectively 2.6- and 3.6-fold larger than at the single-cell stage. We then obtained T. tufae embryos at the single-cell, lima bean, and threefold developmental stages and investigated the egg hatching frequency at three different concentrations of egg salt buffer. Removal of embryos from the uterus halted embryonic development at the single-cell and lima bean stages in T. tufae irrespective of the solution used for incubation, indicating the provision of nutrients within the uterus. Ultrastructural and permeability evaluation showed that the permeability barrier did not form during embryonic development, resulting in increased molecular permeability. This high permeability caused by the absence of the permeability barrier likely enables supply of nutrients from the mother. The structural and physiological modifications in T. tufae are like those in other viviparous animals. We conclude that T. tufae is a viviparous rather than an ovoviviparous nematode. T. tufae will facilitate investigation of the evolution of viviparity in animals.

An Insight into Efflux-Mediated Arsenic Resistance and Biotransformation Potential of Enterobacter Cloacae RSC3 from Arsenic Polluted Area.

Indiscriminate discharge of heavy metals/metalloids from different sources into the sustainable agro-ecosystem is a major global concern for food security and human health. Arsenic (As), categorized as group one human carcinogen is a quintessential toxic metalloid that alters the microbial compositions and functions, induce physiological and metabolic changes in plants and contaminate surface/ground water. The management of arsenic toxicity, therefore, becomes imminent. Acknowledging the arsenic threat, the study was aimed at identifying arsenic resistant bacteria and evaluating its arsenic removal/detoxification potential. Of the total 118 bacterial isolates recovered from arsenic rich environment, the bacterial strain RSC3 demonstrating highest As tolerance was identified as Enterobacter cloacae by 16S rRNA gene sequence analysis. Enterobacter cloacae tolerated high concentration (6000ppm) of As and exhibited 0.55h-1 of specific growth rate as calculated from growth kinetics data. Strain RSC3 also displayed varying level of resistance to other heavy metals and many antibacterial drugs in plate bioassay. The bacterial strain RSC3 possessed gene (arsC) which causes transformation of arsenate to arsenite. The arsenate uptake and efflux of the bacterial cells was revealed by high throughput techniques such as AAS, SEM/TEM and EDX. The simultaneous As reducing ability, and multi metal/multi-antibiotics resistance potentials of E. cloacae provides a promising option in the microbes based remediation of As contaminated environments.

Human biological variation and the "normal".

Anatomically modern human being is a relatively young species (~300 000 years old) with small amounts of genetic variation contained within them. The vast majority of its existence was spent in Eastern Africa, migration out of the region began around 100 000 YBP. Sub-Saharan African populations have the greatest amount of human genetic variation. However, migration allowed populations to accumulate genomic variation associated with living in the arctic, higher altitudes, disease resistance, living on high fat or starchy foods, surviving toxic arsenic-rich environments, lactase persistence, changing skin pigmentation, gaining thicker hair, and changing height and body mass index. Understanding these aspects of human evolution forces us to reconsider our notion of the "normal." Thus, normal for our species includes having dark melanic skin, brown eyes, and brown tightly curled hair. Derived features include lighter skin (~10000 YBP), blue eyes (~6000 YBP), and blond straight hair (~6000 YBP). Yet in reality, "normal" has no meaning for a species that inhabits such a broad geographic range. Natural selection and genetic drift have genetically differentiated human populations in ways that impact our morphological and physiological traits. The genomic differentiation is small and does not allow any unambiguous classification of human populations into biological races. Despite these now well-established facts of human variation, significant confusion associated with Eurocentric notions of the normal still persist in both the lay public and various professions such as biomedical research and clinical practice.

Genetics and proteomics analyses reveal the roles of PhoB1 and PhoB2 regulators in bacterial responses to arsenite and phosphate

In bacteria, phosphate (Pi) stress response is governed by the two-component regulatory system, sensor kinase PhoR and its cognate response regulatory protein PhoB. The arsenite [As(III)]-oxidizing bacterium Agrobacterium tumefaciens GW4 contains two phoB genes, phoB1 and phoB2. phoB1 is adjacent to As(III)-oxidizing genes, however, the functions of PhoB1 and PhoB2 remain unclear. Here, phoB1 and phoB2 were each deleted in-frame, and proteomics, qRT-PCR and protein-DNA interaction were performed. We found that (1) phoB1 and phoB2 were both upregulated under low Pi conditions and phoB1 was induced by As(III), but phoB2 was not; (2) deletion of phoB1 reduced As(III)-oxidizing efficiency and protein-DNA interaction analysis showed PhoB1 could interact with aioXSR promoter to regulate As(III) oxidation; (3) deletions of phoB1 or phoB2 both reduced exopolysaccharides (EPS) synthesis; and (4) PhoB1 influenced Pi uptake, As(III) oxidation, EPS synthesis, TCA cycle, energy production and stress response with As(III), and PhoB2 was associated with Pi uptake and EPS synthesis in low Pi conditions. These results showed PhoB1 and PhoB2 were both involved in Pi acquisition, PhoB1 was more important with As(III) and PhoB2 played a major role without As(III). Strain GW4 uses these two regulators to survive under low Pi and arsenic-rich environments.

Origin, distribution, and geochemistry of arsenic in the Altiplano-Puna plateau of Argentina, Bolivia, Chile, and Perú

Elevated concentrations of arsenic in water supplies represent a worldwide health concern. In at least 14 countries of South America, high levels have been detected relative to international standards and guidelines. Within these countries, the high plateau referred to as the “Altiplano-Puna”, encompassing areas of Argentina, Bolivia, Chile, and Perú, exhibits high arsenic concentrations that could be affecting 3 million inhabitants.The origins of arsenic in the Altiplano-Puna plateau are diverse and are mainly natural in origin. Of the natural sources, the most important correspond to mineral deposits, brines, hot springs, and volcanic rocks, whereas anthropogenic sources are related to mining activities and the release of acid mine drainage (AMD). Arsenic is found in all water types of the Altiplano-Puna plateau over a wide range of concentrations (0.01 mg·L−1 < As in water > 10 mg·L−1) which in decreasing order correspond to: AMD, brines, saline waters, hot springs, rivers affected by AMD, rivers and lakes, and groundwater. Despite the few studies which report As speciation, this metalloid appears mostly in its oxidized form (As[V]) and its mobility is highly susceptible to the influence of dry and wet seasons. Once arsenic is released from its natural sources, it also precipitates in secondary minerals where it is generally stable in the form of saline precipitates and Fe oxides. In relation to human health, arsenic adaptation has been detected in some aboriginal communities of the Puna together with an efficient metabolism of this metalloid. Also, the inefficient methylation of inorganic As in women of the Altiplano might lead to adverse health effects such as cancer. Despite the health risks of living in this arsenic-rich environment with limited water resources, not all of the Altiplano-Puna is properly characterized and there exists a lack of information regarding the basic geochemistry of arsenic in the region.

Signature Arsenic Detoxification Pathways in Halomonas sp. Strain GFAJ-1.

ABSTRACTSince the original report that Halomonas sp. strain GFAJ-1 was capable of using arsenic instead of phosphorus to sustain growth, additional studies have been conducted, and GFAJ-1 is now considered a highly arsenic-resistant but phosphorus-dependent bacterium. However, the mechanisms supporting the extreme arsenic resistance of the GFAJ-1 strain remain unknown. In this study, we show that GFAJ-1 has multiple distinct arsenic resistance mechanisms. It lacks the genes to reduce arsenate, which is the essential step in the well-characterized resistance mechanism of arsenate reduction coupled to arsenite extrusion. Instead, GFAJ-1 has two arsenic resistance operons, arsH1-acr3-2-arsH2 and mfs1-mfs2-gapdh, enabling tolerance to high levels of arsenate. mfs2 and gapdh encode proteins homologous to Pseudomonas aeruginosa ArsJ and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), respectively, which constitute the equivalent of an As(V) efflux system to catalyze the transformation of inorganic arsenate to pentavalent organoarsenical 1-arseno-3-phosphoglycerate and its subsequent extrusion. Surprisingly, the arsH1-acr3-2-arsH2 operon seems to consist of typical arsenite resistance genes, but this operon is sufficient to confer both arsenite and arsenate resistance on Escherichia coli AW3110 even in the absence of arsenate reductase, suggesting a novel pathway of arsenic detoxification. The simultaneous occurrence of these two unusual detoxification mechanisms enables the adaptation of strain GFAJ-1 to the particularly arsenic-rich environment of Mono Lake.

Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic

The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic. To elucidate the history of arsenic adaptation across the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-adenosylmethionine (SAM) methyltransferase. Our results suggest that life successfully moved into arsenic-rich environments in the late Archean Eon and Proterozoic Eon, respectively, by the spread of arsM genes. The arsM genes of bacterial origin have been transferred to other kingdoms of life on at least six occasions, and the resulting domesticated arsM genes promoted adaptation to environmental arsenic. These results allow us to peer into the history of arsenic adaptation of life on our planet and imply that dissemination of genes encoding diverse adaptive functions to toxic chemicals permit adaptation to changes in concentrations of environmental toxins over evolutionary history.

The Arsenic Detoxification System in Corynebacteria: Basis and Application for Bioremediation and Redox Control.

Arsenic (As) is widespread in the environment and highly toxic. It has been released by volcanic and anthropogenic activitiesand causes serious health problems worldwide. To survive arsenic-rich environments, soil and saprophytic microorganisms have developed molecular detoxification mechanisms to survive arsenic-rich environments, mainly by the enzymatic conversion of inorganic arsenate (AsV) to arsenite (AsIII) by arsenate reductases, which is then extruded by arsenite permeases. One of these Gram-positive bacteria, Corynebacterium glutamicum, the workhorse of biotechnological research, is also resistant to arsenic. To sanitize contaminated soils and waters, C.glutamicum strains were modified to work as arsenic "biocontainers." Two chromosomally encoded ars operons (ars1 and ars2) are responsible for As resistance. The genes within these operons encode for metalloregulatory proteins (ArsR1/R2), arsenite permeases (Acr3-1/-2), and arsenate reductases (ArsC1/C2/C1'). ArsC1/C2 arsenate reductases are coupled to the low molecular weight thiol mycothiol (MSH) and to the recently discovered mycoredoxin-1 (Mrx-1) present in most Actinobacteria. This MSH/Mrx-1 redox system protects cells against different forms of stress, including reactive oxygen species (ROS), metals, and antibiotics. ROS can modify functional sulfur cysteines by oxidizing the thiol (-SH) to a sulfenic acid (-SOH). These oxidation-sensitive protein cysteine thiols are redox regulated by the MSH/Mrx-1 couple in Corynebacterium and Mycobacterium. In summary, the molecular mechanisms involved in arsenic resistance system in C. glutamicum have paved the way for understanding the cellular response against oxidative stress in Actinobacteria.

Human adaptation to arsenic-rich environments.

Adaptation drives genomic changes; however, evidence of specific adaptations in humans remains limited. We found that inhabitants of the northern Argentinean Andes, an arid region where elevated arsenic concentrations in available drinking water is common, have unique arsenic metabolism, with efficient methylation and excretion of the major metabolite dimethylated arsenic and a less excretion of the highly toxic monomethylated metabolite. We genotyped women from this population for 4,301,332 single nucleotide polymorphisms (SNPs) and found a strong association between the AS3MT (arsenic [+3 oxidation state] methyltransferase) gene and mono- and dimethylated arsenic in urine, suggesting that AS3MT functions as the major gene for arsenic metabolism in humans. We found strong genetic differentiation around AS3MT in the Argentinean Andes population, compared with a highly related Peruvian population (FST = 0.014) from a region with much less environmental arsenic. Also, 13 of the 100 SNPs with the highest genome-wide Locus-Specific Branch Length occurred near AS3MT. In addition, our examination of extended haplotype homozygosity indicated a selective sweep of the Argentinean Andes population, in contrast to Peruvian and Colombian populations. Our data show that adaptation to tolerate the environmental stressor arsenic has likely driven an increase in the frequencies of protective variants of AS3MT, providing the first evidence of human adaptation to a toxic chemical.

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in Burkholderiales

So far, numerous genes have been found to associate with various strategies to resist and transform the toxic metalloid arsenic (here, we denote these genes as “arsenic-related genes”). However, our knowledge of the distribution, redundancies and organization of these genes in bacteria is still limited. In this study, we analyzed the 188 Burkholderiales genomes and found that 95% genomes harbored arsenic-related genes, with an average of 6.6 genes per genome. The results indicated: a) compared to a low frequency of distribution for aio (arsenite oxidase) (12 strains), arr (arsenate respiratory reductase) (1 strain) and arsM (arsenite methytransferase)-like genes (4 strains), the ars (arsenic resistance system)-like genes were identified in 174 strains including 1,051 genes; b) 2/3 ars-like genes were clustered as ars operon and displayed a high diversity of gene organizations (68 forms) which may suggest the rapid movement and evolution for ars-like genes in bacterial genomes; c) the arsenite efflux system was dominant with ACR3 form rather than ArsB in Burkholderiales; d) only a few numbers of arsM and arrAB are found indicating neither As III biomethylation nor AsV respiration is the primary mechanism in Burkholderiales members; (e) the aio-like gene is mostly flanked with ars-like genes and phosphate transport system, implying the close functional relatedness between arsenic and phosphorus metabolisms. On average, the number of arsenic-related genes per genome of strains isolated from arsenic-rich environments is more than four times higher than the strains from other environments. Compared with human, plant and animal pathogens, the environmental strains possess a larger average number of arsenic-related genes, which indicates that habitat is likely a key driver for bacterial arsenic resistance.

ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases

Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifically arsenate respiratory reductase, ArrA, and arsenite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, represented by the haloalkaliphilic bacterium Alkalilimnicola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorhodospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arxA was strongly induced with arsenite. Microbial ecology investigation led to the identification of additional arxA-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely distributed in the environment presenting an opportunity for further investigations of the contribution of Arx-dependent arsenotrophy to the arsenic biogeochemical cycle.

Nested PCR and New Primers for Analysis of Sulfate-Reducing Bacteria in Low-Cell-Biomass Environments

New primers were designed for the amplification of dsrAB genes by nested PCR to investigate the diversity of sulfate-reducing prokaryotes (SRP) in environments with low bacterial cell density. The success of the nested PCR for the determination of SRP diversity was estimated by terminal-restriction fragment length polymorphism analysis in the Reigous, a small creek at an inactive mine (Carnoulès, France), which constitutes an extreme acidic arsenic-rich environment. Nested PCR limits were evaluated in dsrAB-rich sediments, and this technique was compared to direct PCR using either known primers (DSR1F/DSR4R) or new primers (dsr619AF/dsr1905BR). The comparison of clone libraries revealed that, even if the levels of diversity observed were not identical, nested PCR did not reduce the diversity compared to that of direct DSR1F/DSR4R PCR. Clone sequences were affiliated mainly with the Desulfobacteraceae and Desulfohalobiaceae families. Many sequences (approximately 30%) were related to a deeply branching lineage unaffiliated with any cultured SRP. Although this dsrAB cluster was found in all libraries, the new primers better amplified this lineage, providing more information on this unknown bacterial group. Thanks to these new primers in nested PCR, the SRP community from Carnoulès could be characterized. Specific SRP populations were obtained according to environmental characteristics. Desulfomicrobiaceae-related sequences were recovered in samples with low pH, low levels of dissolved oxygen, and high As content, while sequences belonging to the deeply branching group were found in a less extreme sample. Furthermore, for the first time, dsrAB sequences related to the latter group were recovered from freshwater.

A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.

A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments

A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments

The microbial arsenic cycle in Mono Lake, California

Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO 2 into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less “extreme” environments, such as drinking water aquifers.

Arsenic resistance in the archaeon "Ferroplasma acidarmanus": new insights into the structure and evolution of the ars genes.

Arsenic resistance in the acidophilic iron-oxidizing archaeon " Ferroplasma acidarmanus" was investigated. F. acidarmanus is native to arsenic-rich environments, and culturing experiments confirm a high level of resistance to both arsenite and arsenate. Analyses of the complete genome revealed protein-encoding regions related to known arsenic-resistance genes. Genes encoding for ArsR (arsenite-sensitive regulator) and ArsB (arsenite-efflux pump) homologues were found located on a single operon. A gene encoding for an ArsA relative (anion-translocating ATPase) located apart from the arsRB operon was also identified. Arsenate-resistance genes encoding for proteins homologous to the arsenate reductase ArsC and the phosphate-specific transporter Pst were not found, indicating that additional unknown arsenic-resistance genes exist for arsenate tolerance. Phylogenetic analyses of ArsA-related proteins suggest separate evolutionary lines for these proteins and offer new insights into the formation of the arsA gene. The ArsB-homologous protein of F. acidarmanus had a high degree of similarity to known ArsB proteins. An evolutionary analysis of ArsB homologues across a number of species indicated a clear relationship in close agreement with 16S rRNA evolutionary lines. These results support a hypothesis of arsenic resistance developing early in the evolution of life.

Arsenic and old plants

○ Pteris vittata was the first identified arsenic (As) hyperaccumulator. Our aim was to test whether As hyperaccumulation occurs in other fern species, and whether P. vittata collected from both contaminated and uncontaminated environments accumulates As similarly. ○ Three accessions of P. vittata, two cultivars of Pteris cretica, Pteris longifolia and Pteris umbrosa were grown with 0-500 mg As kg -1 added to the substrate. A second experiment compared As uptake by five common ferns obtained from commercial suppliers. ○ The results show that, in addition to P. vittata, P. cretica, P. longifolia and P. umbrosa also hyperaccumulate As to a similar extent. There was little difference between different Pteris species, or between different accessions of P. vittata. By contrast, Asplenium nidus, Davallia canarensis, Polypodium aureum, Polystichum tsussimense do not hyperaccumulate As. ○ This study identified three new species of As hyperaccumulators in the Pteris genus and suggests that As hyperaccumulation is a constitutive property in P. vittata.