Microbiology of inorganic arsenic: From metabolism to bioremediation
9
REVIEW Microbiology of inorganic arsenic: From metabolism to bioremediation Shigeki Yamamura 1 and Seigo Amachi 2, * Center for Regional Environmental Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan 1 and Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan 2 Received 29 October 2013; accepted 11 December 2013 Available online xxx Arsenic (As) contamination of drinking water and soils poses a threat to a large number of people worldwide, especially in Southeast Asia. The predominant forms of As in soils and aquifers are inorganic arsenate [As(V)] and arsenite [As(III)], with the latter being more mobile and toxic. Thus, redox transformations of As are of great importance to predict its fate in the environment, as well as to achieve remediation of As-contaminated water and soils. Although As has been recognized as a toxic element, a wide variety of microorganisms, mainly bacteria, can use it as an electron donor for autotrophic growth or as an electron acceptor for anaerobic respiration. In addition, As detoxification systems in which As is oxidized to the less toxic form or reduced for subsequent excretion are distributed widely in microor- ganisms. This review describes current development of physiology, biochemistry, and genomics of arsenic-transforming bacteria. Potential application of such bacteria to removal of As from soils and water is also highlighted. Ó 2013, The Society for Biotechnology, Japan. All rights reserved. [Key words: Arsenate reduction; Arsenite oxidation; Arsenic contamination; Biogeochemical cycle of arsenic; Bioremediation] Although arsenic (As) is commonly known as a toxin, it is ubiquitous in the environment (1); however, its abundance in the earth’s crust is low (0.0001%) and its background concentrations in soils are generally less than 15 mg kg 1 (2,3). Nevertheless, local concentrations can vary depending on parent materials and geological history of the region. For example, Himalayan-derived sediment is the source of groundwater As contamination in large areas of south and southeast Asia (4). In Bangladesh and West Bengal, India, approximately 60e100 million people rely on drinking water that contains As in excess of the World Health Or- ganization standard (5). Direct consumption of rice irrigated with As-contaminated water is another significant route of human exposure (6). Accordingly, health problems associated with expo- sure to As are a worldwide concern. Although As has both toxic and therapeutic properties, chronic exposure to As has caused a wide variety of adverse health effects including dermatological condi- tions and skin and internal cancers (7). In addition, recent studies have indicated that gestational As exposure is associated with increased cancer incidence in adulthood (8). Anthropogenic discharges such as air emissions, soil amend- ments, mining operations, and wood preservation have also resulted in elevated As levels (9). Indeed, As has become a prevalent soil contaminant throughout the world (9,10). Accumulated As in contaminated soils has the potential to leach into ground and surface water, and direct exposure from ingestion, inhalation, and dermal routes can impact animal and human health. In Japan, the Soil Contamination Countermeasures Law was enacted in 2003 to address issues caused by harmful substances, including As. Although As can exist in four oxidation states (V, III, 0, eIII) with a variety of inorganic and organic forms, inorganic arsenate [As(V)] and arsenite [As(III)] predominate in aquatic and soil environments (11e 13). As(V) is present as negatively charged oxyanions ðH 2 AsO 4 =HAsO 2 4 Þ at moderate pH. These oxyanions are strongly adsorbed to the surface of common soil minerals such as Fe and Al (hydr)oxides. As(III) primarily exists as uncharged H 3 AsO 0 3 with a pKa of 9.2, and is therefore less adsorptive and more mobile than As(V) in most environments (12). In aerobic environments, As(V) is found to be the predominant species and immobilized in solid phase. In contrast, As(III) is more prevalent in anoxic environments, which leads to mobilization into the aqueous phase (14). Microorganisms can mediate redox transformations of As via As(V) reduction and As(III) oxidation (2). To date, a wide variety of As(V)-reducing and As(III)-oxidizing prokaryotes have been isolated from various As-contaminated environments (2,15), and a recent study suggested that they are also distributed in the natural envi- ronment containing background levels of As (16,17). Because both As(V) reduction and As(III) oxidation directly affect the mobility and bioavailability of As, microbial activities play a key role in biogeo- chemical As cycling. Such microbial processes have the potential to promote As removal from contaminated soils/waters when used as intended. This article outlines the latest physiology and phylogeny for microbial metabolism of inorganic As and highlights their ad- vances as bioremediation techniques. AS(III) OXIDATION Aerobic As(III) oxidizers The bacterial oxidation of As(III) was first reported in 1918, although the finding went largely un- noticed until 1949, when Turner isolated 15 strains of heterotrophic As(III)-oxidizing bacteria (18e20). Currently, physiologically * Corresponding author. Tel./fax: þ81 47 308 8867. E-mail address: [email protected] (S. Amachi). www.elsevier.com/locate/jbiosc Journal of Bioscience and Bioengineering VOL. xx No. xx, 1e9, 2013 1389-1723/$ e see front matter Ó 2013, The Society for Biotechnology, Japan. All rights reserved. http://dx.doi.org/10.1016/j.jbiosc.2013.12.011 Please cite this article in press as: Yamamura, S., and Amachi, S., Microbiology of inorganic arsenic: From metabolism to bioremediation, J. Biosci. Bioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
Transcript of Microbiology of inorganic arsenic: From metabolism to bioremediation
www.elsevier.com/locate/jbiosc
Journal of Bioscience and BioengineeringVOL. xx No. xx, 1e9, 2013
REVIEW
Microbiology of inorganic arsenic: From metabolism to bioremediation
Shigeki Yamamura1 and Seigo Amachi2,*
Center for Regional Environmental Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan1 andGraduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan2
Received 29 October 2013; accepted 11 December 2013Available online xxx
* CorrespondE-mail add
1389-1723/$http://dx.doi
Please citeBioeng., (20
Arsenic (As) contamination of drinking water and soils poses a threat to a large number of people worldwide,especially in Southeast Asia. The predominant forms of As in soils and aquifers are inorganic arsenate [As(V)] andarsenite [As(III)], with the latter being more mobile and toxic. Thus, redox transformations of As are of great importanceto predict its fate in the environment, as well as to achieve remediation of As-contaminated water and soils. Although Ashas been recognized as a toxic element, a wide variety of microorganisms, mainly bacteria, can use it as an electrondonor for autotrophic growth or as an electron acceptor for anaerobic respiration. In addition, As detoxification systemsin which As is oxidized to the less toxic form or reduced for subsequent excretion are distributed widely in microor-ganisms. This review describes current development of physiology, biochemistry, and genomics of arsenic-transformingbacteria. Potential application of such bacteria to removal of As from soils and water is also highlighted.
� 2013, The Society for Biotechnology, Japan. All rights reserved.
[Key words: Arsenate reduction; Arsenite oxidation; Arsenic contamination; Biogeochemical cycle of arsenic; Bioremediation]
Although arsenic (As) is commonly known as a toxin, it isubiquitous in the environment (1); however, its abundance in theearth’s crust is low (0.0001%) and its background concentrations insoils are generally less than 15 mg kg�1 (2,3). Nevertheless, localconcentrations can vary depending on parent materials andgeological history of the region. For example, Himalayan-derivedsediment is the source of groundwater As contamination in largeareas of south and southeast Asia (4). In Bangladesh and WestBengal, India, approximately 60e100 million people rely ondrinking water that contains As in excess of the World Health Or-ganization standard (5). Direct consumption of rice irrigated withAs-contaminated water is another significant route of humanexposure (6). Accordingly, health problems associated with expo-sure to As are a worldwide concern. Although As has both toxic andtherapeutic properties, chronic exposure to As has caused a widevariety of adverse health effects including dermatological condi-tions and skin and internal cancers (7). In addition, recent studieshave indicated that gestational As exposure is associated withincreased cancer incidence in adulthood (8).
Anthropogenic discharges such as air emissions, soil amend-ments, mining operations, and wood preservation have alsoresulted in elevated As levels (9). Indeed, As has become a prevalentsoil contaminant throughout the world (9,10). Accumulated As incontaminated soils has the potential to leach into ground andsurface water, and direct exposure from ingestion, inhalation, anddermal routes can impact animal and human health. In Japan, theSoil Contamination Countermeasures Law was enacted in 2003 toaddress issues caused by harmful substances, including As.
ing author. Tel./fax: þ81 47 308 8867.ress: [email protected] (S. Amachi).
e see front matter � 2013, The Society for Biotechnology, Japan..org/10.1016/j.jbiosc.2013.12.011
this article in press as: Yamamura, S., and Amachi, S., Microbiolo13), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
Although As can exist in four oxidation states (V, III, 0, eIII) witha variety of inorganic and organic forms, inorganic arsenate [As(V)]and arsenite [As(III)] predominate in aquatic and soil environments(11e13). As(V) is present as negatively charged oxyanionsðH2AsO
�4 =HAsO
2�4 Þ at moderate pH. These oxyanions are strongly
adsorbed to the surface of common soil minerals such as Fe and Al(hydr)oxides. As(III) primarily exists as uncharged H3AsO
03 with a
pKa of 9.2, and is therefore less adsorptive and more mobile thanAs(V) in most environments (12). In aerobic environments, As(V) isfound to be the predominant species and immobilized in solidphase. In contrast, As(III) is more prevalent in anoxic environments,which leads to mobilization into the aqueous phase (14).
Microorganisms can mediate redox transformations of As viaAs(V) reduction and As(III) oxidation (2). To date, a wide variety ofAs(V)-reducing and As(III)-oxidizing prokaryotes have been isolatedfrom various As-contaminated environments (2,15), and a recentstudy suggested that they are also distributed in the natural envi-ronment containing background levels of As (16,17). Because bothAs(V) reduction and As(III) oxidation directly affect the mobility andbioavailability of As, microbial activities play a key role in biogeo-chemical As cycling. Such microbial processes have the potential topromote As removal from contaminated soils/waters when used asintended. This article outlines the latest physiology and phylogenyfor microbial metabolism of inorganic As and highlights their ad-vances as bioremediation techniques.
AS(III) OXIDATION
Aerobic As(III) oxidizers The bacterial oxidation of As(III)was first reported in 1918, although the finding went largely un-noticed until 1949, when Turner isolated 15 strains of heterotrophicAs(III)-oxidizing bacteria (18e20). Currently, physiologically
All rights reserved.
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
2 YAMAMURA AND AMACHI J. BIOSCI. BIOENG.,
diverse As(III) oxidizers are found in various groups of Bacteria andArchaea and include both heterotrophic As(III) oxidizers (HAOs)and chemolithoautotrophic As(III) oxidizers (CAOs) (2,21,22).Heterotrophic As(III) oxidation is generally considered adetoxification mechanism that converts As(III) into less toxicAs(V), although it may be used as a supplemental energy source(23). In contrast, CAOs use As(III) as an electron donor duringfixation of CO2 coupled with reduction of oxygen (24). AnaerobicCAOs have also recently been isolated (see below). In addition,some researchers have reported curious facultative anaerobicHAOs capable of either aerobic As(III) oxidation or anaerobicAs(V) reduction (25,26). In recent studies, As(III) oxidizers wereisolated from As-rich environments (27,28), as well as metal-contaminated soil containing low levels of As anduncontaminated garden soil (29,30).
Arsenite oxidase, which was first isolated in 1992 (31), has beenidentified in both CAOs and HAOs (24,32). In both cases, theenzyme contains two subunits, a large subunit containing amolybdopterin center and a [3Fee4S] cluster and a small subunitcontaining a Rieske [2Fee2S] cluster (33,34). Although homologousgenes encoding these two subunits were formerly assigneddifferent names (aoxB-aoxA/aroA-aroB/asoA-asoB), nomenclaturefor genes involved in prokaryotic aerobic As(III) oxidation wasrecently unified and the name aio was newly assigned; therefore,the large and small subunit are denoted aioA and aioB, respectively(35). AioA is similar to the molybdenum-containing subunits in theDSMO reductase family and distantly related to the catalytic sub-unit of respiratory As(V) reductase (ArrA) (2,21,22).
Homologs of genes encoding AioA are found in phylogeneticallydiverse strains including members of a-, b-, g-Proteobacteria, Bac-teroidetes, Actinobacteria, Firmicutes, Aquificae, Deinococcus-Ther-mus, Chlorobi, Chloroflexi, Nitrospira, and Crenarchaeota (Fig. 1).These genes are found clustered in several groups in the AioA-based tree, with strains in the phyla including thermophiles basi-cally forming distinct phylogenetic branches from mesophiles. Themajor mesophile branches are divided into two groups, group I,which is mainly composed of a-Proteobacteria, and group II, whichis primarily composed of b- and g-Proteobacteria. This patternsuggests that these groups probably originated from respectiveproteobacterial divisions. However, there are considerable in-consistencies between the AioA-based phylogeny and 16S rRNA-based classification, suggesting that horizontal gene transfer plays arole in the propagation of aio genes in prokaryotes (36). In somecases, two identical copies of the aioA gene have been found insame strain. For example, the DGGE profile of Thiomonas arsen-ivorans DSM 16361 showed two bands corresponding to twodistinct aioA-related sequences (37), whereas two copies of aioA inAncylobacter sp. OL1 were clustered more closely (38).
aioA-like genes have been amplified from a variety of As-richenvironments including mine, arsenical pesticide- or smelter-impacted sites, and geothermal sites (36,37,39e43). Additionally,Engel et al. (44) recently detected Chloroflexi and Proteobacteria-related aioA sequences from the same microbial mat collected at ageyser. Taken together, these investigations suggest that the di-versity of aioA genes in prokaryotes is wider than previously sus-pected. Moreover, aioA-like genes have been obtained from soil orsediments containing background levels of As (16,45), indicatingthat diverse aerobic As(III) oxidizers reside in the environment,regardless of As contamination.
Anaerobic As(III) oxidizers In 2002, Oremland et al. (46)isolated an anaerobic As(III)-oxidizing bacterium, strain MLHE-1,from anoxic bottom water of Mono Lake, CA, USA, which is analkaline soda lake known for its high concentration of As(V)(200 mM). Strain MLHE-1, later proposed as Alkalilimnicola ehrlichiisp. nov. (47), is a chemolithoautotrophic bacterium that can
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
couple As(III) oxidation to nitrate reduction under anaerobicconditions. A purple sulfur bacterium, Ectothiorhodospira sp. PHS-1, was also isolated from red-pigmented biofilms in Mono Lake(48). This strain can use As(III) as the electron donor foranoxygenic photosynthesis and produces As(V) anaerobicallyunder light conditions. Interestingly, both of these bacteria appearto lack aioA genes and instead possess genes that are much moreclosely related to arrA (49,50) (Fig. 2). This gene, designated arxA,is required for chemoautotrophic growth on As(III) and nitrate bystrain MLHE-1. In addition, arxA is strongly induced by As(III) instrain PHS-1. Thus, it is possible that ArxA is a novel type of As(III)oxidase that forms a distinct phylogenetic clade within thedimethyl sulfoxide (DMSO) reductase family. arxA-like genes haverecently been found in a nearly complete genome sequence ofuncultured bacterium within the candidate division OP1 (51) andin a reconstructed complete genome of the dominant organism(RBG-1) in deep sediment of the Colorado River, CO, USA (52).As(III)-oxidizing denitrifying chemoautotrophs (strains DAO-1 andDAO-10 within the classes b- and a-Proteobacteria, respectively)have been isolated from As-contaminated soils, but it is stillunclear which genes are required for As(III) oxidation (53).
AS(V) REDUCTION
A wide variety of bacteria known as As(V)-resistant microbes(ARMs) can reduce As(V) via detoxification systems (15,54). As(V)usually enters bacterial cells through phosphate transporters (Pit orPst). Once inside, As(V) is reduced to As(III) by a cytoplasmic As(V)reductase (ArsC) with the aid of glutathione or ferredoxin as thereducing power. As(III) is finally excreted out of the cells via amembrane efflux pump, ArsB or Acr3 (55). In some cases, an ATPaseArsA is bound to ArsB to facilitate As(III) efflux, conferring anadvantage to organisms exposed to high levels of As. As(III), whichenters bacterial cells through aquaglyceroporin, may also beextruded by the same system.
In addition to the detoxifying As(V) reduction, certain bacteriacan reduce As(V) as the terminal electron acceptor for anaerobicrespiration. Such bacteria are defined as dissimilatory As(V)-reducing prokaryotes (DARPs). These bacteria are phylogeneticallydiverse, including members of Firmicutes, g-, d-, and ε-Proteobac-teria (Fig. 2) (15). The respiratory As(V) reductase (ARR) consists ofa larger catalytic subunit ArrA and a smaller subunit ArrB (56).ArrA is a member of the DMSO reductase family containing amolybdenum center and a [4Fee4S] cluster, while ArrB containsthree to four [4Fee4S] clusters. ARR of Alkaliphilus oremlandii andShewanella sp. ANA-3, which are both As(V)-respiring bacteria,was recently found to be biochemically reversible (57), showingboth As(III) oxidation and As(V) reduction activities upon in vitrogel assay. Richey et al. (57) suggested that the physiological role ofARR depends on the electron potentials of the molybdenum centerand [FeeS] clusters, additional subunits, or constitution of theelectron transfer chain.
As sorption onto metal oxide minerals, especially on iron (hydr)oxides, is an important process controlling the dissolved concen-tration of As in various environments. As(V) is strongly associatedwith iron and aluminum (hydr)oxides, whereas As(III) is moremobile than As(V) (58). Thus, reductive dissolution of As-bearingiron (hydr)oxides by dissimilatory iron-reducing bacteria can causeAs release (59,60). In addition, direct reduction of As(V) adsorbedonto soil minerals by DARPs may be another important mechanismof As mobilization (61,62). ARMs are generally not considered to beinvolved in As release because ArsC, the cytoplasmic As(V) reduc-tase, is not able to directly reduce As(V) adsorbed onto soil minerals(63). Therefore, ARR is believed to be responsible for As(V) reduc-tion in solid phase, although how periplasmic ARR transfers
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
Marinobacter santoriniensis NKSG1 (ACF09051)Pseudomonas sp. 72 (ABY19330)Pseudomonas sp. 89 (ABY19328)Thiomonas arsenivorans DSM16361_band2 (ADE33057)
Pseudomonas sp. 1 (ABY19326)Pseudomonas sp. 73 (ABY19327)
Pseudomonas stutzeri TS44 (ACB05943)Achromobacter sp. 40AGIII (AEL22195)Achromobacter sp. NT-10 (ABD72610)Alcaligenes sp. S46 (ADF47192)Alcaligenes sp. YI13H (ABY19322)Alcaligenes sp. T12RB (ABY19321)Achromobacter sp. WA20 (ABD72615)Ralstonia sp. 22 (ABY19329)Achromobacter arsenitoxydans SY8 (ABP63660)
Alcaligenes faecalis NCIB8687 (Q7SIF4)Burkholderia sp. YI019A (ABY19323)
Burkholderia sp. S31R (ADF47190)Burkholderia sp. S232 (ADF47189)Burkholderia sp. S32 (ADF47191)Burkholderia sp. S222 (ADF47188)Herminiimonas arsenicoxydans ULPAs1 (AAN05581)
Thiomonas sp. WJ68 (ABY19318)Thiomonas arsenivorans DSM16361 (ABY19316)Thiomonas arsenivorans DSM16361_band1 (ADE33058)
Micromonospora sp. X14 (CCD32987)Thiomonas sp. NO115 (ABY19317)
Acidovorax sp.75 (ABY19324)Hydrogenophaga sp NT-14 (ABD72609)Hydrogenophaga sp. WA13 (ABD72613)Acinetobacter sp. WA19 (ABD72614)
Limnobacter sp.83 (ABY19325)Polaromonas sp.GM1 (ABW84260)
Variovorax sp. MM-1 (AFN80467)Variovorax sp. RM1 (ABD35886)Variovorax sp.4-2 (ABY19319)Leptothrix sp.S1-1 (ABY19320)Flavobacterium sp.19AAV (AEL22198)Acinetobacter sp.18AAV (AEL22197)Acinetobacter sp.16AAV (AEL22196)Ralstonia sp. R229 (CCA82914)Ralstonia solanacearum PSI07 (YP_003749888)Ralstonia syzygii R24 (CCA86643)
Acinetobacter sp.33 (ABY19331)Pseudomonas sp.5AAV (AEL22194)
Pseudomonas sp.D2OHCJ (ABY19332)Rhodococcus sp.46AAIII (AEL22193)
Pseudomonas sp. 46 (ABY19333)Flavobacterium sp.16AGV (AEL22190)Flavobacterium sp.18AGV (AEL22191)Pseudomonas sp.15AGV (AEL22189)
Pseudomonas sp. 20AAIII (AEL22181)Achromobacter sp. 38AGIII (AEL22188)Pseudomonas sp. 25AAIII (AEL22184)Pseudomonas sp. 25AGIII (AEL22187)Pseudomonas sp. 24AGIII (AEL22186)Bacillus sp. 21AAIII (AEL22182)
Stenotrophomonas sp. MM-7 (AFN80468)Polymorphum gilvum (YP_004304060)
Bosea sp.43AGV (AEL22179)Agromyces sp. 44AGV (AEL22180)Bosea sp. S41RM2 (ADF47199)Bosea sp. S41RM1 (ADF47198)
Bosea sp. WAO (ABJ55855)Bosea sp. 7AGV (AEL22177)Bosea sp. 8AGV (AEL22178)
Thiobacillus sp. S1 (ABJ55851)Hydrogenophaga sp. CL3 (ABJ55854)Ancylobacter sp. OL1_2 (ABJ55853)Ancylobacter sp. OL1_1 (ABJ55852)
Ancylobacter dichloromethanicus As3-1b (CBY79896)Methylobacterium sp. S47 (ADF47200)Nitrobacter hamburgensis (YP_571843)
Methylocystis sp. SC2 (CCJ06851)Aminobacter sp. 86 (ABY19334)Sinorhizobium sp. DAO10 (ABJ55850)
Mesorhizobium sp. DM1 (ABD35887)Ensifer adhaerens (CBY79895)Sinorhizobium sp. IK-A2 (AGC82137)
Agrobacterium sp. Ben-5 (ABD72612)Rhizobium sp. NT-26 (AAR05656)Agrobacterium tumefaciens 5A (ABB51928)
Agrobacterium sp. TS45 (ACB05955)Ochrobactrum tritici (ACK38267)Sinorhizobium sp. NT-4 (ABD7261)
Candidatus Nitrospira defluvii (YP_003799308)Chloroflexus sp. Y-400-fl (YP_002569069)Chloroflexus aurantiacus J-10-fl (YP_001634827)
Thermus thermophilus (BAD71923)Thermus sp. HR13 (ABB17184)
Thermus scotoductus SA-01 (ADW22085)Chloroflexus aggregans DSM9485 (YP_002461759)
Chlorobium phaeobacteroides BS1 (YP_001960747)Chlorobium limicola DSM245 (YP_001942454)
Sulfurihydrogenibium sp. Y04ANG1 (ACN59445)Sulfurihydrogenibium yellowstonense SS-5 (ACN59446)Hydrogenobaculum sp. 3684 (ACJ04807)
Sulfolobus tokodaii str.7 (BAB67500)Pyrobaculum oguniense TE7 (AFA38559)
Aeropyrum pernix K1 (BAA81573)Aeropyrum camini SY1 (BAN91066)
Roseobacter litoralis Och149 (YP_004691143)Vibrio splendidus LGP32 (YP_002395243)
ArrA Chrysiogenes arsenatis (AAU11839)
0.2
Group I
Group II
α-Proteobacteria
β-Proteobacteria
γ-Proteobacteria
Actinobacteria
Firmicutes
Bacteroidetes
NitrospiraChloroflexi
Deinococcus-Thermus
Chlorobi
Aquificae
Crenarchaeota
FIG. 1. Neighbor-joining phylogenetic tree of AioA sequences found in isolated strains. The ArrA of Chrysiogenes arsenatis was used as the outgroup. Circles and triangles at thebranch nodes represent bootstrap percentages (1000 replicates): filled circles, 90e100%; open circles, 70e89%; open triangles, 50e69%. Values <50% are not shown. The scale barrepresents the estimated number of substitutions per site.
VOL. xx, 2013 MICROBIOLOGY OF INORGANIC ARSENIC 3
electrons to As(V) adsorbed onto mineral surface is still unclear.Below, we describe the physiological and biochemical aspects ofrepresentative DARPs, as well as the genomic organization of thegenes involved in respiratory As(V) reduction and As resistance.
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
Sulfurospirillum spp. The first DARP, strain MIT-13, was iso-lated in 1994 from As contaminated sediments of the AberjonaWatershed, MA, USA (64). This strain, which was later proposedas Sulfurospirillum arsenophilum (65), is a member of the
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
ArrA
ArxA
FIG. 2. Neighbor-joining phylogenetic tree of ArrA and ArxA sequences found in isolated strains. The AioA of Rhizobium sp. NT-26 was used as the outgroup. Circles and triangles atthe branch nodes represent bootstrap percentages (1000 replicates): filled circles, 90e100%; open circles, 70e89%; open triangles, 50e69%. Values <50% are not shown. The scalebar represents the estimated number of substitutions per site.
4 YAMAMURA AND AMACHI J. BIOSCI. BIOENG.,
ε-Proteobacteria that can use As(V) as the electron acceptor whenlactate is supplied as the electron donor and carbon source.Several other members of Sulfurospirillum spp., includingSulfurospirillum barnesii, S. multivorans, and S. halorespirans, arealso capable of dissimilatory As(V) reduction (66). Many strains ofSulfurospirillum spp. can use nitrate, nitrite, Fe(III), elementalsulfur, thiosulfate, and oxygen (microaerobic) as the electronacceptors in addition to As(V). S. barnesii has been found toreduce As(V) adsorbed on ferrihydrite as well as on aluminumhydroxide (62). S. arsenophilum also released As from sterilizedAberjona sediments (61).
Chrysiogenes arsenatis C. arsenatis, which is a phylogeneti-cally unique member of the phylum Chrysiogenetes, was isolatedfrom Australian gold mine wastewater as an acetate-usingdissimilatory As(V)-reducer that also uses nitrate and nitrite aselectron acceptors in the presence of acetate (67). ARR ofC. arsenatis has been purified and characterized (68). Specifically,it is a heterodimer (a1b1) consisting of two subunits (ArrA andArrB) that is located in the periplasmic space. The expression ofARR is induced in the presence of As(V).
Bacillus spp. To date, at least five Bacillaceae, Bacillus arsen-icoselenatis (69), B. selenitireducens (69), B. macyae (70),B. selenatarsenatis (71), and B. beveridgei (72), have been isolatedas dissimilatory As(V)-reducing bacteria. Among these,B. selenatarsenatis strain SF-1 is able to release As from iron andaluminum (hydr)oxides coprecipitated with As(V), as well as fromAs-contaminated soils (73). The membrane-bound ARR ofB. selenitireducens has been purified and characterized (74).
Desulfitobacterium spp. Niggemyer et al. (75) isolated adissimilatory As(V)-reducing bacterium, Desulfitobacterium sp.strain GBFH, from As-contaminated sediments. They alsodemonstrated that Desulfitobacterium hafniense DCB-2 andD. frappieri PCP-1, which are both known to be reductivelydechlorinating bacteria, can also respire As(V). TheseDesulfitobacterium strains are metabolically versatile and can usea wide variety of electron acceptors including Fe(III), Se(VI),
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
Mn(IV), fumarate, elemental sulfur, sulfite, and thiosulfate (75). Ina genome of D. hafniense DCB-2, arsenic-metabolizing genes areencoded on an arsenic island (Fig. 3). In addition to arrA and arrBgenes, genes encoding a NrfD-like membrane protein (ArrC), aTorD-like chaperone protein (ArrD), and putative regulatoryproteins involved in the two-component signal transductionsystem (ArrR, ArrS, and ArrT) are present. Furthermore, Asdetoxification genes encoding a putative transcriptional repressor(ArsR), an As(III) chaperone protein (ArsD), and an ATPase (ArsA)are present, but are encoded on the opposite strand.
Shewanella sp. ANA-3 Shewanella sp. ANA-3 was isolatedfrom an As-treated wooden pier located in a brackish estuary (76).This organism can also use nitrate, Fe(III), Mn(IV), thiosulfate,fumarate, and oxygen as electron acceptors. Because Shewanellaspp. are genetically tractable, comprehensive molecularcharacterization of dissimilatory As(V) reduction has beenperformed using this strain. ARR of Shewanella sp. ANA-3 is aperiplasmic enzyme that is expressed during the exponential andstationary phases (77). Interestingly, ARR is finally released fromthe cells into the surrounding environment (77). The expressiondynamics of arrA in strain ANA-3 were determined and comparedby Saltikov et al. (78), and the results revealed that it is onlyexpressed anaerobically, while it is repressed by other electronacceptors such as oxygen, nitrate, and fumarate. Conversely, arsCis expressed under both aerobic and anaerobic conditions. arrA isalso induced by 100 nM As(III), while 1000 times more As(III) isrequired for the induction of arsC. A gene encoding a membrane-associated tetraheme c-type cytochrome, cymA, is required forANA-3 to grow on As(V) (79). This cytochrome is alsoindispensable for growth on Fe(III), Mn(IV), and fumarate. Whenincubated with As(V)-adsorbed ferrihydrite, a Fe(III) reductiondeficient mutant of strain ANA-3 effectively reduced solid-phaseAs(V), while an As(V) reduction deficient mutant did not (80).These findings strongly suggest that the Fe(III) reduction pathwayis not required for ferrihydrite-adsorbed As(V) reduction. Theorganization of arrA and arrB genes in the genome of strain ANA-
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
arrBarrAarsDarsAarsBarsC
arrA arrB arrD arrEarrFarrT arrS arrRarsRacr3
arrBarrA arrDarsA arsDarsR
arrS arrCarrT arrR
arrFarsRacr3 arrA arrD arrEarrB
FIG. 3. Arsenic islands found in the genomes of Desulfitobacterium hafniense DCB-2 (110), Shewanella sp. ANA-3, Geobacter lovleyi SZ (111), and Geobacter uraniireducens Rf4. Geneorganizations surrounding respiratory As(V) reductase genes (arr) are shown. Note that D. hafniense DCB-2 and Shewanella sp. ANA-3 are dissimilatory As(V)-reducing bacteria(75,76), while the other two Geobacter strains are not able to grow using As(V) as the electron acceptor (86). The arr genes and putative functions of their products are describedaccording to Reyes et al. (112). arrA, respiratory As(V) reductase catalytic subunit; arrB, respiratory As(V) reductase small subunit; arrC, a NrfD-like membrane protein that mayfunction as an anchor for ArrAB; arrD, a TorD-like chaperone that may be involved in cofactor insertion into ArrA; arrE, a putative FeeS protein; arrF, a putative multiheme c-typecytochrome; arrR, arrS, and arrT, putative regulatory proteins involved in two-component signal transduction systems; arsA, an ATPase bound to ArsB; arsB and acr3, membrane-bound As(III) efflux proteins; arsC, a cytoplasmic As(V) reductase; arsD, a chaperone protein that transfers As(III) to the ArsAB pump; arsR, a putative transcriptional repressor. Anasterisk indicates that arrB of G. uraniireducens Rf4 contains a stop codon (86).
VOL. xx, 2013 MICROBIOLOGY OF INORGANIC ARSENIC 5
3 is shown in Fig. 3. Genes encoding ArsD, ArsA, ArsB (a membraneefflux pump), and ArsC are also present, which may confer strainANA-3 As resistance (76).
Geobacter spp. Geobacter spp., which are the most commonand ubiquitous iron-reducing bacteria, play a pivotal role indissimilatory iron reduction in terrestrial and freshwater environ-ments (81). Recent studies have demonstrated that Geobacter spp.also function as dissimilatory As(V)-reducing bacteria, and mayplay a role in As reduction and mobilization. Islam et al. (60)found that As release from West Bengal sediments occurredwhen they were incubated anaerobically with acetate as theelectron donor, and subsequent 16S rRNA gene clone libraryanalysis indicated that 70% of clones in the acetate-amendedsediments were affiliated with the family Geobacteraceae. Similarresults were observed upon microbial community analysis ofCambodian sediments (82). In addition, dissimilatory As(V)reductase genes (arrA) closely related to Geobacter spp. havefrequently been detected in As-contaminated sediments (83e86).Until recently, only two Geobacter species, Geobacteruraniireducens Rf4 and G. lovleyi SZ, had been known to possessputative arrA and arrB genes in their genomes. However, neitherof these strains are able to grow using As(V) as the electronacceptor, even though resting cells of G. lovleyi SZ reduce As(V) inthe presence of acetate (86). Various arr genes with an operon-like structure are present in the G. lovleyi SZ genome, but itappears to lack the arsA and arsD genes (Fig. 3). An arsenic islandfound in the genome of G. uraniireducens Rf4 also lacks the arsAand arsD genes. Considering that both of these As detoxifyinggenes are frequently found in other dissimilatory As(V)-reducingbacterial genomes, their incapacity to grow on As(V) might be inpart due to the absence of arsA and arsD genes.
In 2013, Ohtsuka et al. (87) isolated a new dissimilatory As(V)-reducing bacterium, Geobacter sp. OR-1, from As-contaminatedJapanese paddy soil. Strain OR-1 also used nitrate, Fe(III), andfumarate as electron acceptors and catalyzed the release of As fromAs(V)-adsorbed ferrihydrite or sterilized paddy soil. Furthermore,As K-edge X-ray absorption near-edge structure (XANES) analysissuggested that strain OR-1 reduced As(V) directly in the soil solidphase. Because strain OR-1 is the first Geobacter species with thecapacity to grow using As(V) as the sole electron acceptor, it may beuseful as a model microorganism influencing mobilization of As in
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
flooded soils and anoxic sediments (87). Preliminary draft genomeanalysis of strain OR-1 identified two arsenic islands containingmultiple arsA and arsD genes (Ehara and Amachi, unpublisheddata).
Anaeromyxobacter sp. PSR-1 Anaeromyxobacter dehalo-genans was isolated by Sanford et al. (88) as a reductivelydechlorinating d-Proteobacterium that grows using 2-chlorophenol as an electron acceptor. This organism has a glidingmotility, forms a spore-like structure, and can also use nitrate,Fe(III), U(VI), Se(IV), fumarate, and oxygen (microaerobic) aselectron acceptors (89e91). Kudo et al. (92) recently isolated adissimilatory As(V)-reducing bacterium, strain PSR-1, from As-contaminated soil and found that it had 99.7% 16S rRNA genesimilarity with A. dehalogenans. As release was observed whenstrain PSR-1 was incubated with As(V)-adsorbed ferrihydrite orsterile As-contaminated soil. Multiple attempts to amplify theputative arrA gene from genomic DNA of strain PSR-1 wereunsuccessful, indicating that strain PSR-1 may harbor an atypicalarrA gene that cannot be amplified using previously designeddegenerate primers (92). Although complete genome sequencesof several strains of Anaeromyxobacter spp. have been released,none possess putative genes for arrA and arrB.
APPLICATION TO BIOREMEDIATION
Removal from water As described above, As(III) is lessadsorptive than As(V); therefore, As(III) oxidation is an importantpretreatment process for adsorption and coprecipitation using Al/Fe(III) minerals. Because chemical oxidation of As(III) via oxygen isvery slow (93), application of aerobic As(III) oxidizers can be aneffective remediation strategy for removal of As fromcontaminated water. For example, Ike et al. (94) successfullyobtained an enrichment culture with a soil free from Ascontamination that showed high As(III)-oxidizing activity andgreatly enhanced As adsorption by activated alumina. Threeaerobic HAOs, presumably classified as Haemophilus spp.,Micrococcus spp., and Bacillus spp., were isolated from theirenrichment culture. Andrianisa et al. (95) demonstrated that anactivated sludge collected from a treatment plant receiving no As-contaminated wastewater rapidly oxidized As(III). Furthermore,they isolated an aerobic CAO through subculture of the sludge
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
6 YAMAMURA AND AMACHI J. BIOSCI. BIOENG.,
without an organic carbon source. They also found that biologicalAs(III) oxidation can occur in a full-scale plant based on fieldinvestigations of an oxidation ditch activated sludge processreceiving As-contaminated wastewater. In their investigation,oxidized As in the effluent was shown to be effectively removed bycoprecipitation with ferric hydroxide. In a recent study by thesame group, a continuous-flow bioreactor with immobilizedaerobic As(III)-oxidizing bacteria was performed as a pretreatmentstep for As removal from groundwater (96).
Anaerobic CAOs can be also used as an alternative process forpre-oxidation of As(III). Sun et al. (97) constructed two differentcontinuous bioreactors with a denitrifying granular sludge and amethanogenic granular sludge. The anoxic oxidation of As(III)linked to chemolithotrophic denitrification was continuouslyobserved in both bioreactors. They inoculated the As(III)-oxidizingdenitrifying granular biofilms into continuous flow columns packedwith activated alumina and found that nitrate-dependent oxidationof As(III) enhanced adsorption and immobilization of As ontoactivated alumina (98). In another study, simultaneous oxidation ofAs(III) and Fe(II) linked to denitrification was performed incontinuous flow sand columns inoculated with As(III)-oxidizingdenitrifying sludge (99). The oxidation of soluble Fe(II) led to for-mation of a mixture of Fe(III) oxides dominated by hematite,resulting in enhanced immobilization of As in the column. Theseinvestigations imply that anaerobic treatment has the potential forboth nitrate and As removal from water in a single system.
Under greater reducing conditions, the opposite approach,namely As(V) reduction, can be used to remove As from theaqueous phase because As(III) forms precipitates with sulfide (100).Formation of As sulfides or decreases in aqueous As resulting frommicrobial As(V) and sulfate reduction have been observed in severalbioreactors (101e103). Additionally, Upadhyaya et al. (102)demonstrated simultaneous removal of nitrate and As from asynthetic groundwater containing nitrate, sulfate, and As(V) using afixed-bet bioreactor system consisting of two consecutive columns.In their system, nitrate was primarily removed in the first column,while As was mainly immobilized in the subsequent columnthrough As sulfide precipitation and surface precipitation on ironsulfides. In a recent study, theymodified operation of the bioreactorsystem to minimize the formation of As-laden solids in the firstcolumn because it contained high biomass generating zones (dis-solved oxygen- and nitrate-reducing zones) and required frequentbackwashing to remove excess biomass (103).
Removal from soil Because As(V) is often detected as themajor species of As in contaminated soils (104e106), its reductionto less adsorptive As(III) can promote As removal from solid tothe aqueous phase; therefore, it might be applicable forremediation of soils. From this aspect, DARPs are desirable agentsbecause ARMs can only reduce aqueous As(V) that has enteredthe cell. Several studies have demonstrated reductive dissolutionof As from As-laden solids and As-rich soils/sediments by DARPs(60e62,73,87,92). However, the applicability of microbial Asmobilization to bioremediation is largely unknown because moststudies conducted to date have focused on biogeochemical aspects.
Yamamura et al. (107) investigated the removal of As from twotypes of industrially contaminated soils by microbial reductivedissolution. A DARP, B. selenatarsenatis SF-1, successfully mobilizedAs into the aqueous phase from both contaminated soils throughreduction of solid-phase As(V) and Fe(III). They also showed thatthe coexistence of an extracellular electron-shuttling quinone andthe DARP improved the efficiency of As removal from contaminatedsoils with concomitant release of Fe(II). Indeed, about 56% and 40%of As was removed from contaminated soils containing 250 and2400 mg/kg of As, respectively. Soda et al. (108) proposed appli-cation of a slurry bioreactor using the DARP for remediation of
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
As-contaminated soil and developed a mathematical model thatprovides a framework for understanding and predicting thedissolution of As from soil. Lee et al. (109) applied a combination ofmicrobial As mobilization and electrokinetic remediation to As-contaminated mine tailing soils. In both batch- and column-typebioleaching reactors, stimulation of indigenous bacteria by the in-jection of organic carbon sources led to the reductive dissolution ofAs. Subsequent electrokinetic treatment enhanced As removal ef-ficiency, and the combined process achieved about 67% removal ofAs from soil containing 4023mg/kg of As. Although similar removalefficiency was only obtained during electrokinetic treatment, thepreliminary microbial As mobilization reduced the duration ofelectrokinetics, with the combined process resulting in a 26.4% costreduction. Because the treatment methods available for As-contaminated soils are mainly soil replacement, containment, andsolidification/stabilization, these studies indicate a great potentialfor application of DARPs as a novel bioremediation strategy for Asremoval from soils.
In conclusion, the history of the interaction between As andprokaryotes considerably exceeds that of its interaction with hu-man beings. Although the microbiological study of As is a centuryold, we still have only a limited understanding of the ancient pro-cesses by which prokaryotes utilize or tolerate As. The more welearn about them, the more complex they appear to become.However, we believe that the development of research in this fieldcan provide the key to handling this toxic and ubiquitous metalloid.
ACKNOWLEDGMENTS
This work was partly supported by JSPS KAKENHI GrantNumbers 23681005 for S. Y. and 23580103 for S. A. In addition, S. A.is grateful to A. Ehara and M. Tonomura (Chiba University) forproviding technical assistance with informatics.
References
1. Cullen, W. R. and Reimer, K. J.: Arsenic speciation in the environment, Chem.Rev., 89, 713e764 (1989).
2. Oremland, R. S. and Stolz, J. F.: The ecology of arsenic, Science, 300, 939e944(2003).
3. Smith, E., Naidu, R., and Alston, A. M.: Arsenic in the soil environment: areview, Adv. Agron., 64, 149e195 (1998).
4. Fendorf, S., Michael, H. A., and van Geen, A.: Spatial and temporal variationsof ground water arsenic in south and southeast Asia, Science, 328, 1123e1127(2010).
5. Ng, J. C., Wang, J., and Shraim, A.: A global health problem caused by arsenicfrom natural sources, Chemosphere, 52, 1353e1359 (2003).
6. Williams, P. N., Islam, M. R., Adomako, E. E., Raab, A., Hossain, S. A.,Zhu, Y. G., Feldmann, J., and Meharg, A. A.: Increase in rice grain arsenic forregions of Bangladesh irrigating paddies with elevated arsenic in ground-waters, Environ. Sci. Technol., 40, 4903e4908 (2006).
7. Nriagu, J. O.: Arsenic poisoning through the ages, pp. 1e26, in:Frankenberger, W. T., Jr. (Ed.), Environmental chemistry of arsenic. MarcelDekker, New York (2002).
8. Nohara, K., Tateishi, Y., Suzuki, T., Okamura, K., Murai, H., Takumi, S.,Maekawa, F., Nishimura, N., Kobori, M., and Ito, T.: Late-onset increases inoxidative stress and other tumorigenic activities and tumor with a Ha-rasmutation in the liver of adult male C3H mice gestationally exposed to arsenic,Toxicol. Sci., 129, 293e304 (2012).
9. Belluck, D. A., Benjamin, S. L., Baveye, P., Sampson, J., and Johnson, B.:Widespread arsenic contamination of soils in residential areas and publicspace: an emerging regulatory or medical crisis? Int. J. Toxicol., 22, 109e128(2003).
10. Mandal, B. K. and Suzuki, K. T.: Arsenic round the world: a review, Talanta,58, 201e235 (2002).
11. Lièvremont, D., Bertin, P. N., and Lett, M.-C.: Arsenic in contaminated wa-ters: biogeochemical cycle, microbial metabolism and biotreatment processes,Biochimie, 91, 1229e1237 (2009).
12. Bhumbla, D. K. and Keefer, R. F.: Arsenic mobilization and bioavailability insoils, pp. 51e82, in: Nriagu, J. O. (Ed.), Arsenic in the environment part I:cycling and characterization. Wiley-Interscience, New York (1994).
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
VOL. xx, 2013 MICROBIOLOGY OF INORGANIC ARSENIC 7
13. Huang, Y.-C.: Arsenic distribution in soils, pp. 17e49, in: Nriagu, J. O. (Ed.),Arsenic in the environment part I: cycling and characterization. Wiley-Interscience, New York (1994).
14. Mok, M. W. and Wai, C. M.: Mobilization of arsenic in contaminated riverwaters, pp. 99e117, in: Nriagu, J. O. (Ed.), Arsenic in the environment part I:cycling and characterization. Wiley-Interscience, New York (1994).
15. Oremland, R. S. and Stolz, J. F.: Arsenic, microbes and contaminated aquifers,Trends Microbiol., 13, 45e49 (2005).
16. Yamamura, S., Watanabe, K., Suda, W., Tsuboi, S., and Watanabe, M.: Effectof antibiotics on redox transformations of arsenic and diversity of arsenite-oxidizing bacteria in sediment microbial communities, Environ. Sci. Technol.,48, 350e357 (2014).
17. Yamamura, S., Watanabe, M., Yamamoto, N., Sei, K., and Ike, M.: Potentialfor microbially mediated redox transformations and mobilization of arsenic inuncontaminated soils, Chemosphere, 77, 169e174 (2009).
18. Turner, A. W.: Bacterial oxidation of arsenic, Nature, 164, 76e77 (1949).19. Ehrlich, H. L.: Bacterial oxidation of As(III) compounds, pp. 313e327, in:
Frankenberger, W. T., Jr. (Ed.), Environmental chemistry of arsenic. MarcelDekker, New York (2002).
20. Santini, J. M., vanden Hoven, R. N., and Macy, J. M.: Characteristics of newlydiscovered arsenite-oxidizing bacteria, pp. 329e342, in:Frankenberger, W. T., Jr. (Ed.), Environmental chemistry of arsenic. MarcelDekker, New York (2002).
21. Silver, S. and Phung, L. T.: Genes and enzymes involved in bacterial oxidationand reduction of inorganic arsenic, Appl. Environ. Microbiol., 71, 599e608(2005).
22. Stolz, J. F., Basu, P., and Oremland, R. S.: Microbial arsenic metabolism: newtwists on an old poison, Microbe, 5, 53e59 (2010).
23. vanden Hoven, R. N. and Santini, J. M.: Arsenite oxidation by the heterotrophHydrogenophaga sp. str. NT-14: the arsenite oxidase and its physiologicalelectron acceptor, Biochim. Biophys. Acta, 1656, 148e155 (2004).
24. Santini, J. M., Sly, L. I., Wen, A., Comrie, D., Wulf-Durand, P., and Macy, J. M.:A new chemolithoautotrophic arsenite-oxidizing bacterium isolated from agold mine: phylogenetic, physiological, and preliminary biochemical studies,Appl. Environ. Microbiol., 66, 92e97 (2000).
25. Gihring, T. M. and Banfield, J. F.: Arsenite oxidation and arsenate respirationby a new Thermus isolate, FEMS Microbiol. Lett., 204, 335e340 (2001).
26. Handley, K. M., Héry, M., and Lloyd, J. R.: Redox cycling of arsenic by thehydrothermal marine bacterium Marinobacter santoriniensis, Environ. Micro-biol., 11, 1601e1611 (2009).
27. Andreoni, V., Zanchi, R., Cavalca, L., Corsini, A., Romagnoli, C., and Canzi, E.:Arsenite oxidation in Ancylobacter dichloromethanicus As3-1b strain: detec-tion of genes involved in arsenite oxidation and CO2 fixation, Curr. Microbiol.,65, 212e218 (2012).
28. Hamamura, N., Fukushima, K., and Itai, T.: Identification of antimony- andarsenite-oxidizing bacteria associated with antimony mine tailing, MicrobesEnviron., 28, 257e263 (2013).
29. Bachate, S. P., Khapare, R. M., and Kodam, K. M.: Oxidation of arsenite bytwo b-proteobacteria isolated from soil, Appl. Microbiol. Biotechnol., 93,2135e2145 (2012).
30. Bahar, M. M., Megharaj, M., and Naidu, R.: Arsenic bioremediation potentialof a new arsenite-oxidizing bacterium Stenotrophomonas sp. MM-7 isolatedfrom soil, Biodegradation, 23, 803e812 (2012).
31. Anderson, G. L., Williams, J., and Hille, R.: The purification and character-ization of arsenite oxidase from Alcaligenes faecalis, a molybdenum containinghydroxylase, J. Biol. Chem., 267, 23674e23682 (1992).
32. Muller, D., Lièvremont, D., Simeonova, D. D., Hubert, J. C., and Lett, M. C.:Arsenite oxidase aox genes from a metal-resistant betaproteobacterium,J. Bacteriol., 185, 135e141 (2003).
33. Ellis, P. J., Conrads, T., Hille, R., and Kuhn, P.: Crystal structure of the 100 kDaarsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and2.03 Å, Structure, 9, 125e132 (2001).
34. Santini, J. M. and vanden Hoven, R. N.: Molybdenum-containing arseniteoxidase of the chemolithoautotrophic arsenite oxidizer NT-26, J. Bacteriol.,186, 1614e1619 (2004).
35. Lett, M. C., Muller, D., Lièvremont, D., Silver, S., and Santini, J.: Unifiednomenclature for genes involved in prokaryotic aerobic arsenite oxidation,J. Bacteriol., 194, 207e208 (2012).
36. Heinrich-Salmeron, A., Cordi, A., Brochier-Armanet, C., Halter, D.,Pagnout, C., Abbaszadeh-fard, E., Montaut, D., Seby, F., Bertin, P. N.,Bauda, P., and Arsène-Ploetze, F.: Unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of aoxB gene inprokaryotes, Appl. Environ. Microbiol., 77, 4685e4692 (2011).
37. Quéméneur, M., Cébron, A., Billard, P., Battaglia-Brunet, F., Garrido, F.,Leyval, C., and Joulian, C.: Population structure and abundance of arsenite-oxidizing bacteria along an arsenic pollution gradient in waters of the UpperIsle River Basin, France, Appl. Environ. Microbiol., 76, 4566e4570 (2010).
38. Rhine, E. D., Ní Chadhain, S. M., Zylstra, G. J., and Young, L. Y.: The arseniteoxidase genes (aroAB) in novel chemoautotrophic arsenite oxidizers, Biochem.Biophys. Res. Commun., 354, 662e667 (2007).
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
39. Quéméneur, M., Heinrich-Salmeron, A., Muller, D., Lièvremont, D.,Jauzein, M., Bertin, P. N., Garrido, F., and Joulian, C.: Diversity surveys andevolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacte-ria, Appl. Environ. Microbiol., 74, 4567e4573 (2008).
40. Inskeep, W. P., Macur, R. E., Hamamura, N., Warelow, T. P., Ward, S. A., andSantini, J. M.: Detection, diversity and expression of aerobic bacterial arseniteoxidase genes, Environ. Microbiol., 9, 934e943 (2007).
41. Hamamura, N.,Macur, R. E., Korf, S., Ackerman, G., Taylor,W. P., Kozubal,M.,Reysenbach, A.-L., and Inskeep, W. P.: Linking microbial oxidation of arsenicwith detection and phylogenetic analysis of arsenite oxidase genes in diversegeothermal environments, Environ. Microbiol., 11, 421e431 (2009).
42. Cai, L., Liu, G., Rensing, C., and Wang, G.: Genes involved in arsenic trans-formation and resistance associated with different levels of arsenic-contam-inated soils, BMC Microbiol., 9, 4 (2009).
43. Sultana, M., Vogler, S., Zargar, K., Schmidt, A.-C., Saltikov, C., Seifert, J., andSchlömann, M.: New clusters of arsenite oxidase and unusual bacterialgroups in enrichments from arsenic-contaminated soil, Arch. Microbiol., 194,623e635 (2012).
44. Engel, A. S., Johnson, L. R., and Porter, M. L.: Arsenite oxidase gene diversityamong Chloroflexi and Proteobacteria from EI Tatio Geyser Field, Chile, FEMSMicrobiol. Ecol., 83, 745e756 (2013).
45. Lami, R., Jones, L. C., Cottrell, M. T., Lafferty, B. J., Ginder-Vogel, M.,Sparks, D. L., and Kirchman, D. L.: Arsenite modifies structure of soil mi-crobial communities and arsenite oxidation potential, FEMS Microbiol. Ecol.,84, 270e279 (2013).
46. Oremland, R. S., Hoeft, S. E., Santini, J. M., Bano, N., Hollibaugh, R. A., andHollibaugh, J. T.: Anaerobic oxidation of arsenite in Mono Lake water and by afacultative, arsenite-oxidizing chemoautotroph, strain MLHE-1, Appl. Environ.Microbiol., 68, 4795e4802 (2002).
47. Hoeft, S. E., Blum, J. S., Stolz, J. F., Tabita, F. R., Witte, B., King, G. M.,Santini, J. M., and Oremland, R. S.: Alkalilimnicola ehrlichii sp. nov., a novel,arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable ofchemoautotrophic or heterotrophic growth with nitrate or oxygen as theelectron acceptor, Int. J. Syst. Evol. Microbiol., 57, 504e512 (2007).
48. Kulp, T. R., Hoeft, S. E., Asao, M., Madigan, M. T., Hollibaugh, J. T.,Fisher, J. C., Stolz, J. F., Culbertson, C. W., Miller, L. G., and Oremland, R. S.:Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from MonoLake, California, Science, 321, 967e970 (2008).
49. Zarger, K., Hoeft, S., Oremland, R., and Saltikov, C. W.: Identification of anovel arsenite oxidase gene, arxA, in the haloalkaliphilic, arsenite-oxidizingbacterium Alkalilimnicola ehrlichii strain MLHE-1, J. Bacteriol., 192,3755e3762 (2010).
50. Zarger, K., Conrad, A., Bernick, D. L., Lowe, T. M., Stolc, V., Hoeft, S.,Oremland, R. S., Stolz, J., and Saltikov, C. W.: ArxA, a new clade of arseniteoxidase within the DMSO reductase family of molybdenum oxidoreductase,Environ. Microbiol., 14, 1635e1645 (2012).
51. Takami, H., Noguchi, H., Takaki, Y., Uchiyama, I., Toyoda, A., Nishi, S.,Chee, G.-J., Arai, W., Nunoura, T., Itoh, T., Hattori, M., and Takai, K.: A deeplybranching thermophilic bacterium with an ancient acetyl-CoA pathwaydominates a subsurface ecosystem, PLoS One, 7, e30559 (2012).
52. Castelle, C. J., Hug, L. A., Wrighton, K. C., Thomas, B. C., Williams, K. H.,Wu, D., Tringe, S. G., Singer, S. W., Eisen, J. A., and Banfield, J. F.: Extraor-dinary phylogenetic diversity and metabolic versatility in aquifer sediment,Nature. Commun., 4, 2120 (2013).
53. Rhine, E. D., Phelps, C. D., and Young, L. Y.: Anaerobic arsenite oxidation bynovel denitrifying isolates, Environ. Microbiol., 8, 899e908 (2006).
54. Rosen, B.: Biochemistry of arsenic detoxification, FEBS Lett., 529, 86e92(2002).
55. Rosen, B.: Families of arsenic transporters, Trends Microbiol., 7, 207e212(1999).
56. Saltikov, C. W. and Newman, D. K.: Genetic identification of a respiratoryarsenate reductase, Proc. Natl. Acad. Sci. USA, 100, 10983e10988 (2003).
57. Richey, C., Chovanec, P., Hoeft, S. E., Oremland, R. S., Basu, P., andStolz, J. F.: Respiratory arsenate reductase as a bidirectional enzyme, Bio-chem. Biophys. Res. Commun., 382, 298e302 (2009).
58. Dixit, S. and Hering, J. G.: Comparison of arsenic(V) and arsenic(III) sorptiononto iron oxide minerals: implications for arsenic mobility, Environ. Sci.Technol., 37, 4182e4189 (2003).
59. Cummings, D. E., Caccavo, F., Jr., Fendorf, S., and Rosenzweig, R. F.: Arsenicmobilization by the dissimilatory Fe(III)-reducing bacterium Shewanella algaBrY, Environ. Sci. Technol., 33, 723e729 (1999).
60. Islam, F. S., Gault, A. G., Boothman, C., Polya, D. A., Charnock, J. M.,Chatterjee, D., and Lloyd, J. R.: Role of metal-reducing bacteria in arsenicrelease from Bengal delta sediments, Nature, 430, 68e71 (2004).
61. Ahmann, D., Krumholz, L. R., Hemond, H. F., Lovley, D. R., andMorel, F. M. M.: Microbial mobilization of arsenic from sediments of theAberjona watershed, Environ. Sci. Technol., 31, 2923e2930 (1997).
62. Zobrist, J., Dowdle, P. R., Davis, J. A., and Oremland, R. S.: Mobilization ofarsenite by dissimilatory reduction of adsorbed arsenate, Environ. Sci. Tech-nol., 34, 4747e4753 (2000).
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
8 YAMAMURA AND AMACHI J. BIOSCI. BIOENG.,
63. Langner, H. W. and Inskeep, W. P.: Microbial reduction of arsenate in thepresence of ferrihydrite, Environ. Sci. Technol., 34, 3131e3136 (2000).
64. Ahmann, D., Roberts, A. L., Krumholz, L. R., and Morel, F. M. M.: Microbegrows by reducing arsenic, Nature, 371, 750 (1994).
65. Stolz, J. F., Ellis, D. J., Blum, J. S., Ahmann, D., Lovley, D. R., andOremland, R. S.: Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsen-ophilum sp. nov., new members of the Sulfurospirillum clade of the ε-Proteo-bacteria, Int. J. Syst. Bacteriol., 49, 1177e1180 (1999).
66. Luijten, M. L. G. C., de Weert, J., Smidt, H., Boschker, H. T. S., de Vos, W. M.,Schraa, G., and Stams, A. J. M.: Description of Sulfurospirillum halorespiranssp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer ofDehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillummultivorans comb. nov. Int. J. Syst. Evol. Microbiol., 53, 787e793 (2003).
67. Macy, J. M., Nunan, K., Hagen, K. D., Dixon, D. R., Harbour, P. L., Cahill, M.,and Sly, L. I.: Chrysiogenes arsenatis gen. nov., sp. nov., a new arsenate-respiring bacterium isolated from gold mine wastewater, Int. J. Syst. Bacteriol.,46, 1153e1157 (1996).
68. Krafft, T. and Macy, J. M.: Purification and characterization of the respiratoryarsenate reductase of Chrysiogenes arsenatis, Eur. J. Biochem., 255, 647e653(1998).
69. Blum, J. S., Bindi, A. B., Buzzelli, J., Stolz, J. F., and Oremland, R. S.: Bacillusarsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two hal-oalkaliphiles from Mono Lake, California that respire oxyanions of seleniumand arsenic, Arch. Microbiol., 171, 19e30 (1998).
70. Santini, J. M., Streimann, I. C. A., and vanden Hoven, R. N.: Bacillus macyaesp. nov., an arsenate-respiring bacterium isolated from an Australian goldmine, Int. J. Syst. Evol. Microbiol., 54, 2241e2244 (2004).
71. Yamamura, S., Yamashita, M., Fujimoto, N., Kuroda, M., Kashiwa, M.,Sei, K., Fujita, M., and Ike, M.: Bacillus selenatarsenatis sp. nov., a selenate-and arsenate-reducing bacterium isolated from the effluent drain of a glass-manufacturing plant, Int. J. Syst. Evol. Microbiol., 57, 1060e1064 (2007).
72. Baesman, S. M., Stolz, J. F., Kulp, T. R., and Oremland, R. S.: Enrichment andisolation of Bacillus beveridgei sp. nov., a facultative anaerobic haloalkaliphilefrom Mono Lake, California, that respires oxyanions of tellurium, selenium,and arsenic, Extremophiles, 13, 695e705 (2009).
73. Yamamura, S., Yamamoto, N., Ike, M., and Fujita, M.: Arsenic extractionfrom solid phase using a dissimilatory arsenate-reducing bacterium, J. Biosci.Bioeng., 100, 219e222 (2005).
74. Afkar, E., Lisak, J., Saltikov, C., Basu, P., Oremland, R. S., and Stolz, J. F.: Therespiratory arsenate reductase from Bacillus selenitireducens strain MLS10,FEMS Microbiol. Lett., 226, 107e112 (2003).
75. Niggemyer, A., Spring, S., Stackebrandt, E., and Rosenzweig, R. F.: Isolationand characterization of a new As(V)-reducing bacterium: implication forarsenic mobilization and the genus Desulfitobacterium, Appl. Environ. Micro-biol., 67, 5568e5580 (2001).
76. Saltikov, C. W., Cifuentes, A., Venkateswaran, K., and Newman, D. K.: Thears detoxification system is advantageous but not required for As(V) respi-ration by the genetically tractable Shewanella species strain ANA-3, Appl.Environ. Microbiol., 69, 2800e2809 (2003).
77. Malasarn, D., Keeffe, J. R., and Newman, D. K.: Characterization of thearsenate respiratory reductase from Shewanella sp. strain ANA-3, J. Bacteriol.,190, 135e142 (2008).
78. Saltikov, C. W., Wildman, R. A., Jr., and Newman, D. K.: Expression dynamicsof arsenic respiration and detoxification in Shewanella sp. strain ANA-3,J. Bacteriol., 187, 7390e7396 (2005).
79. Murphy, J. N. and Saltikov, C. W.: The cymA gene, encoding a tetraheme c-type cytochrome, is required for arsenate respiration in Shewanella species,J. Bacteriol., 189, 2283e2290 (2007).
80. Reyes, C., Murphy, J. N., and Saltikov, C. W.: Mutational and gene expressionanalysis of mtrDEF, omcA and mtrCAB during arsenate and iron reduction inShewanella sp. ANA-3, Environ. Microbiol., 12, 1878e1888 (2010).
81. Lovley, D. R., Ueki, T., Zhang, T., Malvankar, N. S., Shrestha, P. M.,Flanagan, K. A., Aklujkar, M., Butler, J. E., Giloteaux, L., Rotaru, A.-E., andother 5 authors: Geobacter: the microbe electric’s physiology, ecology, andpractical applications, Adv. Microb. Physiol, 59, 1e100 (2011).
82. Rowland, H. A. L., Pederick, R. L., Polya, D. A., Pancost, R. D., vanDongen, B. E., Gault, A. G., Vaughan, D. J., Bryant, C., Anderson, B., andLloyd, J. R.: The control of organic matter on microbially mediated ironreduction and arsenic release in shallow alluvial aquifers, Cambodia, Geo-biology, 5, 281e292 (2007).
83. Héry, M., Gault, A. G., Rowland, H. A. L., Lear, G., Polya, D. A., and Lloyd, J. R.:Molecular and cultivation-dependent analysis of metal-reducing bacteriaimplicated in arsenic mobilization in South-East Asian aquifers, Appl. Geo-chem., 23, 3215e3223 (2008).
84. Héry, M., van Dongen, B. E., Gill, F., Mondal, D., Vaughan, D. J., Pancost, R. R.,Polya, D. A., and Lloyd, J. R.: Arsenic release and attenuation in low organiccarbon aquifer sediments from West Bengal, Geobiology, 8, 155e168 (2010).
85. Lear, G., Song, B., Gault, A. G., Polya, D. A., and Lloyd, J. R.:Molecular analysisof arsenate-reducing bacteria within Cambodian sediments followingamendment with acetate, Appl. Environ. Microbiol., 73, 1041e1048 (2007).
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
86. Giloteaux, L., Holmes, D. E., Williams, K. H., Wrighton, K. C., Wilkins, M. L.,Montgomery, A. P., Smith, J. A., Orellana, R., Thompson, C. A., Roper, T. J.,Long, P. E., and Lovley, D. R.: Characterization and transcription of arsenicrespiration and resistance genes during in situ uranium bioremediation, IJME.J., 7, 370e383 (2013).
87. Ohtsuka, T., Yamaguchi, N., Makino, T., Sakurai, K., Kimura, K., Kudo, K.,Homma, E., Dong, D. T., and Amachi, S.: Arsenic dissolution from Japanesepaddy soil by a dissimilatory arsenate-reducing bacterium Geobacter sp. OR-1,Environ. Sci. Technol., 47, 6263e6271 (2013).
88. Sanford, R. A., Cole, J. R., and Tiedje, J. M.: Characterization and description ofAnaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiringfacultative anaerobic myxobacterium, Appl. Environ. Microbiol., 68, 893e900(2002).
89. He, Q. and Sanford, R. A.: Characterization of Fe(III) reduction by chlorores-piring Anaeromyxobacter dehalogenans, Appl. Environ. Microbiol., 69,2712e2718 (2003).
90. Wu, Q., Sanford, R. A., and Löffler, F. E.: Uranium(VI) reduction by Anaero-myxobacter dehalogenans strain 2CP-C, Appl. Environ. Microbiol., 72,3608e3614 (2006).
91. He, Q. and Yao, K.: Microbial reduction of selenium oxyanions by Anaero-myxobacter dehalogenans, Bioresour. Technol., 101, 3760e3764 (2010).
92. Kudo, K., Yamaguchi, N., Makino, T., Ohtsuka, T., Kimura, K., Dong, D. T.,and Amachi, S.: Release of arsenic from soil by a novel dissimilatory arsenate-reducing bacterium, Anaeromyxobacter sp. strain PSR-1, Appl. Environ.Microbiol., 79, 4635e4642 (2013).
93. Inskeep, W. P., McDermott, T. R., and Fendorf, S.: Arsenic (V)/(III) cycling insoils and natural waters: chemical and microbiological processes, pp.183e215, in: Frankenberger, W. T., Jr. (Ed.), Environmental chemistry ofarsenic. Marcel Dekker, New York (2002).
94. Ike, M., Miyazaki, T., Yamamoto, N., Sei, K., and Soda, S.: Removal of arsenicfrom groundwater by arsenite-oxidizing bacteria, Water Sci. Technol., 58,1095e1100 (2008).
95. Andrianisa, H. A., Ito, A., Sasaki, A., Aizawa, J., and Umita, T.: Biotransfor-mation of arsenic species by activated sludge and removal of bio-oxidizedarsenate from wastewater by coagulation with ferric chloride, Water Res., 42,4809e4817 (2008).
96. Ito, A., Miura, J., Ishikawa, N., and Umita, T.: Biological oxidation of arsenitein synthetic groundwater using immobilized bacteria, Water Res., 46,4825e4831 (2012).
97. Sun, W., Sierra-Alvarez, R., Hsu, I., Rowlette, P., and Field, J. A.: Anoxicoxidation of arsenite linked to chemolithotrophic denitrification in contin-uous bioreactors, Biotechnol. Bioeng., 105, 909e917 (2010).
98. Sun, W., Sierra-Alvarez, R., and Field, J. A.: The role of denitrification onarsenite oxidation and arsenic mobility in an anoxic sediment column modelwith activated alumina, Biotechnol. Bioeng., 107, 786e794 (2010).
99. Sun, W., Sierra-Alvarez, R., Milner, L., Oremland, R., and Field, J. A.: Arseniteand ferrous iron oxidation linked to chemolithotrophic denitrification for theimmobilization of arsenic in anoxic environments, Environ. Sci. Technol., 43,6585e6591 (2009).
100. Newman, D. K., Beveridge, T. J., and Morel, F. M. M.: Precipitation of arsenictrisulfide by Desulfotomaculum auripigmentum, Appl. Environ. Microbiol., 63,2022e2028 (1997).
101. Chung, J., Li, X., and Rittmann, B. E.: Bio-reduction of arsenate using ahydrogen-based membrane biofilm reactor, Chemosphere, 65, 24e34 (2006).
102. Upadhyaya, G., Jackson, J., Clancy, T. M., Hyun, S. P., Brown, J., Hayes, K. F.,and Raskin, L.: Simultaneous removal of nitrate and arsenic from drinkingwater sources utilizing a fixed-bed bioreactor system, Water Res., 44,4958e4969 (2010).
103. Upadhyaya, G., Clancy, T. M., Brown, J., Hayes, K. F., and Raskin, L.: Opti-mization of arsenic removal water treatment system through characterizationof terminal electron accepting processes, Environ. Sci. Technol., 46,11702e11709 (2012).
104. Bissen, M. and Frimmet, H. F.: Speciation of As(III), As(V), MMA and DMA incontaminated soil extracts by HPLC-ICP/MS, Fresenius, J. Anal. Chem., 367,51e55 (2000).
105. Garcia-Manyes, S., Jiménez, G., Padró, A., Rubio, R., and Rauret, G.: Arsenicspeciation in contaminated soils, Talanta, 58, 97e109 (2002).
106. Cancès, B., Juillot, F., Morin, G., Laperche, V., Alvarez, L., Proux, O.,Hzemann, J.-L., Brown, G. E., Jr., and Calas, G.: XAS evidence of As(V) asso-ciation with iron oxyhydroxides in a contaminated soil at a former arsenicalpesticide processing plant, Environ. Sci. Technol., 39, 9398e9405 (2005).
107. Yamamura, S., Watanabe, M., Kanzaki, M., Soda, S., and Ike, M.: Removal ofarsenic from contaminated soils by microbial reduction of arsenate andquinone, Environ. Sci. Technol., 42, 6154e6159 (2008).
108. Soda, S., Kanzaki,M., Yamamura, S., Kashiwa,M., Fujita,M., and Ike,M.: Slurrybioreactor modeling using a dissimilatory arsenate-reducing bacterium forremediationof arsenic-contaminatedsoil, J. Biosci. Bioeng.,107, 130e137 (2009).
109. Lee, K.-Y., Yoon, I.-H., Lee, B.-T., Kim, S.-O., and Kim, K.-W.: A novel com-bination of anaerobic bioleaching and electrokinetics for arsenic removalfrom mine tailing soil, Environ. Sci. Technol., 43, 9354e9360 (2009).
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
VOL. xx, 2013 MICROBIOLOGY OF INORGANIC ARSENIC 9
110. Kim, S.-H., Harzman, C., Davis, J. K., Hutcheson, R., Broderick, J. B.,Marsh, T. L., and Tiedje, J. M.: Genome sequence of Desulfitobacterium haf-niense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metalreduction, BMC Microbiol., 12, 21 (2012).
111. Wagner, D. D., Hug, L. A., Hatt, J. K., Spitzmiller, M. R., Padilla-Crespo, E.,Ritalahti, K. M., Edwards, E. A., Konstantinidis, K. T., and Löffler, F. E.:
Please cite this article in press as: Yamamura, S., and Amachi, S., MicrobioloBioeng., (2013), http://dx.doi.org/10.1016/j.jbiosc.2013.12.011
Genomic determinants of organohalide-respiration in Geobacter lovleyi, anunusual member of the Geobacateraceae, BMC Microbiol., 13, 200 (2012).
112. Reyes, C., Lloyd, J. R., and Saltikov, C. W.: Geomicrobiology of iron andarsenic in anoxic sediments, pp. 123e146, in: Ahuja, S. (Ed.), Arseniccontamination of groundwater: mechanism, analysis, and remediation. JohnWiley & Sons, New Jersey (2008).
gy of inorganic arsenic: Frommetabolism to bioremediation, J. Biosci.
