Identification and quantification of arsC genes in environmental samples by using real-time PCR

Arsenic uptake by rice is influenced by microbe-mediated arsenic redox changes in the rhizosphere

Arsenic (As) uptake by rice is largely determined by As speciation, which is strongly influenced by microbial activities. However, little is known about interactions between root and rhizosphere microbes, particularly on arsenic oxidation and reduction. In this study, two rice cultivars with different radial oxygen loss (ROL) ability were used to investigate the impact of microbially mediated As redox changes in the rhizosphere on As uptake. Results showed that the cultivar with higher ROL (Yangdao) had lower As uptake than that with lower ROL (Nongken). The enhancement of the rhizospheric effect on the abundance of the arsenite (As(III)) oxidase gene (aroA-like) was greater than on the arsenate (As(V)) reductase gene (arsC), and As(V) respiratory reductase gene (arrA), resulting in As oxidation and sequestration in the rhizosphere, particularly for cultivar Yangdao. The community of As(III)-oxidizing bacteria in the rhizosphere was dominated by α-Proteobacteria and β-Proteobacteria and was influenced by rhizospheric effects, rice straw application, growth stage, and cultivar. Application of rice straw into the soil increased As release and accumulation into rice plants. These results highlighted that uptake of As by rice is influenced by microbial processes, especially As oxidation in the rhizosphere, and these processes are influenced by root ROL and organic matter application.

Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations

The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.

Microbial transformations of arsenic: perspectives for biological removal of arsenic from water

Arsenic is present in many environments and is released by various natural processes and anthropogenic actions. Although arsenic is recognized to cause a wide range of adverse health effects in humans, diverse bacteria can metabolize it by detoxification and energy conservation reactions. This review highlights the current understanding of the ecology, biochemistry and genomics of these bacteria, and their potential application in the treatment of arsenic-polluted water.

Characterization of arsenic resistant bacteria from arsenic rich groundwater of West Bengal, India

Sixty-four arsenic (As) resistant bacteria isolated from an arsenic rich groundwater sample of West Bengal were characterized to investigate their potential role in subsurface arsenic mobilization. Among the isolated strains predominance of genera Agrobacterium/Rhizobium, Ochrobactrum and Achromobacter which could grow chemolitrophically and utilize arsenic as electron donor were detected. Higher tolerance to As(3+) [maximum tolerable concentration (MTC): ≥10 mM], As(5+) (MTC: ≥100 mM) and other heavy metals like Cu(2+), Cr(2+), Ni(2+) etc. (MTC: ≥10 mM), presence of arsenate reductase and siderophore was frequently observed among the isolates. Ability to produce arsenite oxidase and phosphatase enzyme was detected in 50 and 34 % of the isolates, respectively. Although no direct correlation among taxonomic identity of bacterial strains and their metabolic abilities as mentioned above was apparent, several isolates affiliated to genera Ochrobactrum, Achromobacter and unclassified Rhizobiaceae members were found to be highly resistant to As(3+) and As(5+) and positive for all the test properties. Arsenate reductase activity was found to be conferred by arsC gene, which in many strains was coupled with arsenite efflux gene arsB as well. Phylogenetic incongruence between the 16S rRNA and ars genes lineages indicated possible incidence of horizontal gene transfer for ars genes. Based on the results we propose that under the prevailing low nutrient condition inhabitant bacteria capable of using inorganic electron donors play a synergistic role wherein siderophores and phosphatase activities facilitate the release of sediment bound As(5+), which is subsequently reduced by arsenate reductase resulting into the mobilization of As(3+) in groundwater.

Carbon, metals, and grain size correlate with bacterial community structure in sediments of a high arsenic aquifer

Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges–Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

Arsenite-oxidizing and arsenate-reducing bacteria associated with arsenic-rich groundwater in Taiwan

Drinking highly arsenic-contaminated groundwater is a likely cause of blackfoot disease in Taiwan, but microorganisms that potentially control arsenic mobility in the subsurface remain unstudied. The objective of this study was to investigate the relevant arsenite-oxidizing and arsenate-reducing microbial community that exists in highly arsenic-contaminated groundwater in Taiwan. We cultured and identified arsenic-transforming bacteria, analyzed arsenic resistance and transformation, and determined the presence of genetic markers for arsenic transformation. In total, 11 arsenic-transforming bacterial strains with different colony morphologies and varying arsenic transformation abilities were isolated, including 10 facultative anaerobic arsenate-reducing bacteria and one strictly aerobic arsenite-oxidizing bacterium. All of the isolates exhibited high levels of arsenic resistance with minimum inhibitory concentrations of arsenic ranging from 2 to 200 mM. Strain AR-11 was able to rapidly oxidize arsenite to arsenate at concentrations relevant to environmental groundwater samples without the addition of any electron donors or acceptors. We provide evidence that arsenic-reduction activity may be conferred by the ars operon(s) that were not amplified by the designed primers currently in use. The 16S rRNA sequence analysis grouped the isolates into the following genera: Pseudomonas, Bacillus, Psychrobacter, Vibrio, Citrobacter, Enterobacter, and Bosea. Among these genera, we present the first report of the genus Psychrobacter being involved in arsenic reduction. Our results further support the hypothesis that bacteria capable of either oxidizing arsenite or reducing arsenate coexist and are ubiquitous in arsenic-contaminated groundwater.

Hydrogen formation by an arsenate-reducing Pseudomonas putida, isolated from arsenic-contaminated groundwater in West Bengal, India

Anaerobic growth of a newly isolated Pseudomonas putida strain WB from an arsenic-contaminated soil in West Bengal, India on glucose, L: -lactate, and acetate required the presence of arsenate, which was reduced to arsenite. During aerobic growth in the presence of arsenite arsenate was formed. Anaerobic growth of P. putida WB on glucose was made possible presumably by the non-energy-conserving arsenate reductase ArsC with energy derived only from substrate level phosphorylation. Two moles of acetate were generated intermediarily and the reducing equivalents of glycolysis and pyruvate decarboxylation served for arsenate reduction or were released as H(2). Anaerobic growth on acetate and lactate was apparently made possible by arsenate reductase ArrA coupled to respiratory electron chain energy conservation. In the presence of arsenate, both substrates were totally oxidized to CO(2) and H(2) with part of the H(2) serving for respiratory arsenate reduction to deliver energy for growth. The growth yield for anaerobic glucose degradation to acetate was Y (Glucose) = 20 g/mol, leading to an energy coefficient of Y (ATP) = 10 g/mol adenosine-5'-triphosphate (ATP), if the Emden-Meyerhof-Parnas pathway with generation of 2 mol ATP/mol glucose was used. During growth on lactate and acetate no substrate chain phosphorylation was possible. The energy gain by reduction of arsenate was Y (Arsenate) = 6.9 g/mol, which would be little less than one ATP/mol of arsenate.

Population structure and abundance of arsenite-oxidizing bacteria along an arsenic pollution gradient in waters of the upper isle River Basin, France

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional aoxB genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the aoxB-carrying bacterial population, composed of members of the Alpha-, Beta- and Gammaproteobacteria, depending on arsenic (As) and E(h) levels in Upper Isle River Basin waters. The highest aoxB gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers seem to play a key role in As mobility in As-impacted waters.

Detection and quantification of functional genes of cellulose- degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea

Cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. Compared to the study of 16S rRNA genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. However, no methods are available for the broad quantification of these genes from uncultured microbes characteristic of complex environments. In this study, consensus degenerate hybrid oligonucleotide primers were designed and validated to amplify both sequenced and unsequenced glycoside hydrolase genes of cellulose-degrading bacteria, hydA genes of fermentative bacteria, dsrA genes of sulfate-reducing bacteria, and mcrA genes of methanogenic archaea. Specificity was verified in silico and by cloning and sequencing of PCR products obtained from an environmental sample characterized by the target functions. The primer pairs were further adapted to quantitative PCR (Q-PCR), and the method was demonstrated on samples obtained from two sulfate-reducing bioreactors treating mine drainage, one lignocellulose based and the other ethanol fed. As expected, the Q-PCR analysis revealed that the lignocellulose-based bioreactor contained higher numbers of cellulose degraders, fermenters, and methanogens, while the ethanol-fed bioreactor was enriched in sulfate reducers. The suite of primers developed represents a significant advance over prior work, which, for the most part, has targeted only pure cultures or has suffered from low specificity. Furthermore, ensuring the suitability of the primers for Q-PCR provided broad quantitative access to genes that drive critical anaerobic catalytic processes.

Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer

Bacterial enzymes capable of nitrile hydrolysis have significant industrial potential. Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270 and AJ300 were isolated from the same location in England and harbour identical nitrile hydratase/amidase gene clusters. Strain AJ270 has been well studied due to its nitrile hydratase and amidase activity. R. erythropolis ITCBP was isolated from Denmark and carries a very similar nitrile hydratase/amidase gene cluster. In this study, an identical nitrilase gene (nit1) was isolated from the four strains, and the nitrilase from strain AJ270 cloned and expressed in Escherichia coli. Analysis of the recombinant nitrilase has shown it to be functional with activity demonstrated towards phenylacetonitrile. A real-time PCR TaqMan assay was developed that allowed nit1 detection directly from soil enrichment cultures without DNA extraction, with nit1 detected in all samples tested. Real-time PCR screening of isolates from these soils resulted in the isolation of nit1 and also very similar nitrilase gene nit2 from a number of Burkholderia sp. The genes nit1 and nit2 have also been detected in many bacteria of different genera but are unstable in these isolates. It is likely that the genes were acquired by horizontal gene transfer and may be wide-spread in the environment.

Rapid detection and quantification of bisulfite reductase genes in oil field samples using real-time PCR

Sulfate-reducing bacteria (SRB) pose a serious problem to offshore oil industries by producing sulfide, which is highly reactive, corrosive and toxic. The dissimilatory sulfite reductase (dsr) gene encodes for enzyme dissimilatory sulfite reductase and catalyzes the conversion of sulfite to sulfide. Because this gene is required by all sulfate reducers, it is a potential candidate as a functional marker. Denaturing gradient gel electrophoresis fingerprints revealed the presence of considerable genetic diversity in the DNA extracts achieved from production water collected from various oil fields. A quantitative PCR (qPCR) assay was developed for rapid and accurate detection of dsrB in oil field samples. A standard curve was prepared based on a plasmid containing the appropriate dsrB fragment from Desulfomicrobium norvegicum. The quantification range of this assay was six orders of magnitude, from 4.5 x 10(7) to 4.5 x 10(2) copies per reaction. The assay was not influenced by the presence of foreign DNA. This assay was tested against several DNA samples isolated from formation water samples collected from geographically diverse locations of India. The results indicate that this qPCR approach can provide valuable information related to the abundance of the bisulfite reductase gene in harsh environmental samples.

Bacteria, hypertolerant to arsenic in the rocks of an ancient gold mine, and their potential role in dissemination of arsenic pollution

The aim of the present study was to find out if bacteria present in ancient gold mine could transform immobilized arsenic into its mobile form and increase its dissemination in the environment. Twenty-two arsenic-hypertolerant cultivable bacterial strains were isolated. No chemolithoautotrophs, which could use arsenite as an electron donor as well as arsenate as an electron acceptor, were identified. Five isolates exhibited hypertolerance to arsenic: up to 500mM of arsenate. A correlation between the presence of siderophores and high resistance to arsenic was found. The results of this study show that detoxification processes based on arsenate reductase activity might be significant in dissemination of arsenic pollution. It was concluded that the activity of the described heterotrophic bacteria contributes to the mobilization of arsenic in the more toxic As(III) form and a new mechanism of arsenic mobilization from a scorodite was proposed.

Advances in monitoring of catabolic genes during bioremediation

Biodegradation of xenobiotic compounds by microbes is exploited in the clean up of contaminated environments by bioremediation. Catabolic (or functional) genes encode for specific enzymes in catabolic pathways such as key enzymes in xenobiotic degradation pathways. By assessing the abundance or the expression of key genes in environmental samples one can get a potential measure of the degradation activity. One way of assessing the abundance and expression of specific catabolic genes is by analyzing the metagenomic DNA and RNA from environmental samples. Three major challenges in the detection and quantification of catabolic genes in bioremediation studies are 1) the accurate and sensitive quantification from environmental samples 2) the coverage of the enzymatic potential by the targeted genes 3) the validation of the correlation with actual observed degradation activities in field cases. New advances in realtime PCR, functional gene arrays and meta-transcriptomics have improved the applicability of catabolic gene assessment during bioremediation.

The use of molecular techniques to characterize the microbial communities in contaminated soil and water

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

Evaluation of quantitative polymerase chain reaction to assess nosZ gene prevalence in mixed microbial communities

The usefulness of quantitative polymerase chain reaction (QPCR) to measure nosZ gene prevalence in a multi-template reaction was assessed by comparing 19 nosZ template DNA samples and 91 model communities. Efficiencies of the QPCR varied but were not significantly different among nosZ genotypes and were not linked to genetic distance from Ralstonia eutropha. nosZ genotype QPCR efficiencies obtained from isolated denitrifiers were higher (84.8%) than those obtained from excised denaturing gradient gel electrophoresis bands or clones of PCR products from total community DNA (ca. 60%). Analysis of the model communities indicated that QPCR accurately predicts gene prevalence in communities composed of up to six templates.

Quantification of Salmonella spp. in composted biosolids using a TaqMan qPCR assay

Composting is increasingly used to transform biosolids, obtained following wastewater treatment, into a more stable organic product that can be released in the environment. The process must however be closely monitored to assure that the end product meets the regulations set by environmental agencies with regards to the amount of pathogenic microorganisms present. In this study, a TaqMan qPCR approach targeting the invA gene was developed to monitor the presence of Salmonella spp. in composted biosolids. A validation step was first performed to evaluate the effect of compost age on the quantification of various concentrations of seeded Salmonella typhimurium. Secondly, qPCR was used to investigate the effect of composting time, varying from 1 month to 24 months, on the presence of Salmonella spp. naturally present in biosolids samples. Culture media were used in parallel to corroborate the results obtained by qPCR. The detection limit of the invA gene obtained experimentally from composts seeded with S. typhimurium was 5.8 copies or the equivalent of 5.8 CFU per qPCR reaction. Although the results indicated that compost age had a marginal effect on the detection of seeded S. typhimurium, the TaqMan qPCR approach was efficient at detecting and quantifying the amount of Salmonella spp. present in naturally contaminated composted biosolids of different ages. Results showed that there was a significant decrease in the amount of Salmonella DNA present in composted biosolids over time, which was also corroborated by the CFU counts obtained on the BSA culture medium. However, qPCR was more specific, robust and rapid to execute than performing counts on culture media. qPCR shows promise for routine examination of composted biosolids to ascertain that pathogenic microorganisms, including Salmonella spp., are decreased below acceptable limits before their application in the environment.

Quantification of changing Pseudomonas aeruginosa sodA, htpX and mt gene abundance in response to trace metal toxicity: a potential in situ biomarker of environmental health

Sediment-dwelling prokaryotes play a vital role in determining the fate and speciation of metals, yet are also susceptible to the biological effects of trace metals. In this article, optimized DNA extraction and purification techniques and species-specific primers are used to assess the genetic incidence and abundance of metal detoxification and general stress genes of Pseudomonas aeruginosa to complement chemical analysis in inferring the severity of metal-contaminated sites along the Clark Fork River, Montana. Results show the highest incidence of candidate genes related to bacterial stress at the most polluted site, while multiple regression analysis demonstrated significant correlations (P<0.05, r(2)=0.9) between in situ metal concentrations (As, Cu and Zn), total gene incidence, and the incidence of metal detoxification genes. Furthermore, principal components plotting the incidence of genes related to metal resistance show clear separation of sites giving clear clusters on the basis of contamination. Quantification of three genes (sodA, htpX and mt) from surveyed sites found significantly higher (anova, P<0.05) copy numbers at the more contaminated sites compared with reference sites. The development of rapid microbial biomarker tools represents a significant advance in the field of environmental biomonitoring and the prediction of metal bioavailability.

Diversity of arsenite transporter genes from arsenic-resistant soil bacteria

A PCR approach was developed to assess the occurrence and diversity of arsenite transporters in arsenic-resistant bacteria. For this purpose, three sets of degenerate primers were designed for the specific amplification of approximately 750bp fragments from arsB and two subsets of ACR3 (designated ACR3(1) and ACR3(2)) arsenite carrier gene families. These primers were used to screen a collection of 41 arsenic-resistant strains isolated from two soil samples with contrasting amounts of arsenic. PCR results showed that 70.7% of the isolates contained a gene related to arsB or ACR3, with three of them carrying both arsB and ACR3-like genes. Phylogenetic analysis of the protein sequences deduced from the amplicons indicated a prevalence of arsB in Firmicutes and Gammaproteobacteria, while ACR3(1) and ACR3(2) were mostly present in Actinobacteria and Alphaproteobacteria, respectively. In addition to validating the use of degenerate primers for the identification of arsenite transporter genes in a taxonomically wide range of bacteria, the study describes a novel collection of strains displaying interesting features of resistance to arsenate, arsenite and antimonite, and the ability to oxidize arsenite.

Molecular analysis of arsenate-reducing bacteria within Cambodian sediments following amendment with acetate

The health of millions is threatened by the use of groundwater contaminated with sediment-derived arsenic for drinking water and irrigation purposes in Southeast Asia. The microbial reduction of sorbed As(V) to the potentially more mobile As(III) has been implicated in release of arsenic into groundwater, but to date there have been few studies of the microorganisms that can mediate this transformation in aquifers. With the use of stable isotope probing of nucleic acids, we present evidence that the introduction of a proxy for organic matter ((13)C-labeled acetate) stimulated As(V) reduction in sediments collected from a Cambodian aquifer that hosts arsenic-rich groundwater. This was accompanied by an increase in the proportion of prokaryotes closely related to the dissimilatory As(V)-reducing bacteria Sulfurospirillum strain NP-4 and Desulfotomaculum auripigmentum. As(V) respiratory reductase genes (arrA) closely associated with those found in Sulfurospirillum barnesii and Geobacter uraniumreducens were also detected in active bacterial communities utilizing (13)C-labeled acetate in microcosms. This study suggests a direct link between inputs of organic matter and the increased prevalence and activity of organisms which transform As(V) to the potentially more mobile and thus hazardous As(III) via dissimilatory As(V) reduction.

A targeted real-time PCR assay for studying naphthalene degradation in the environment

A quantitative real-time polymerase chain reaction (PCR) assay was developed for monitoring naphthalene degradation during bioremediation processes. The phylogenetic affiliations of known naphthalene-hydroxylating dioxygenase genes were determined to target functionally related bacteria, and degenerate primers were designed on the basis of the close relationships among dioxygenase genes identified from naphthalene-degrading Proteobacteria. Evaluation of the amplification specificity demonstrated that the developed real-time PCR assay represents a rapid, precise means for the group-specific enumeration of naphthalene-degrading bacteria. According to validation with bacterial pure cultures, the assay discriminated between the targeted group of naphthalene dioxygenase sequences and genes in other naphthalene or aromatic hydrocarbon-degrading bacterial strains. Specific amplification of gene fragments sharing a high sequence similarity with the genes included in the assay design was also observed in soil samples recovered from large-scale remediation processes. The target genes could be quantified reproducibly at over five orders of magnitude down to 3 x 10(2) gene copies. To investigate the suitability of the assay in monitoring naphthalene biodegradation, the assay was applied in enumerating the naphthalene dioxygenase genes in a soil slurry microcosm. The results were in good agreement with contaminant mineralization and dot blot quantification of nahAc gene copies. Furthermore, the real-time PCR assay was found to be more sensitive than hybridization-based analysis.

NHR-40, a Caenorhabditis elegans supplementary nuclear receptor, regulates embryonic and early larval development

Nuclear hormone receptors (NHRs) are important regulators of development and metabolism in animal species. They are characterized by the ability to regulate gene expression in response to the binding of small hydrophobic molecules, hormones, metabolites, and xenobiotics. The Caenorhabditis elegans genome contains 284 sequences that share homology to vertebrate and insect NHRs, a surprisingly large number compared with other species. The majority of C. elegans NHRs are nematode-specific and are referred to as supplementary nuclear receptors (supnrs) that are thought to have originated by duplications of an ancient homolog of vertebrate HNF4. Here, we report on the function of NHR-40, a member of a subgroup of 18 Caenorhabditis elegans supnrs that share DNA-binding domain sequence CNGCKT. NHR-40 is expressed from at least two promoters, generates at least three transcripts, and is detectable in pharyngeal, body wall, and sex muscles as well as in a subset of neurons. The downregulation of nhr-40 by RNAi, or a mutant with an intronic region deletion, results in late embryonic and early larval arrest with defects in elongation and morphogenesis. The nhr-40 loss of function phenotype includes irregular development of body wall muscle cells and impaired movement and coordination resembling neuromuscular affection. NHR-40 joins the list of C. elegans NHRs that regulate development and suggests that members of extensive nematode supnr family have acquired varied and novel functions during evolution.