- Extended genome report
- Open Access
Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey
Standards in Genomic Sciencesvolume 13, Article number: 6 (2018)
This genome report describes the draft genome and physiological characteristics of Bosea sp. WAO (=DSM 102914), a novel strain of the genus Bosea in the family Bradyrhizobiaceae. Bosea sp. WAO was isolated from pulverized pyritic shale containing elevated levels of arsenic. This aerobic, gram negative microorganism is capable of facultative chemolithoautotrophic growth under aerobic conditions by oxidizing the electron donors arsenite, elemental sulfur, thiosulfate, polysulfide, and amorphous sulfur. The draft genome is of a single circular chromosome 6,125,776 bp long consisting of 21 scaffolds with a G + C content of 66.84%. A total 5727 genes were predicted of which 5665 or 98.92% are protein-coding genes and 62 RNA genes. We identified the genes aioA and aioB, which encode the large and small subunits of the arsenic oxidase respectively. We also identified the genes for the complete sulfur oxidation pathway sox which is used to oxidize thiosulfate to sulfate.
Bosea sp. WAO (white arsenic oxidizer) was enriched from a pulverized sample of weathered black shale obtained from an outcropping near Trenton, NJ that contained high levels of arsenic . Bosea sp. WAO belongs to the class Alphaproteobacteria and family Bradyrhizobiaceae which currently consists of 12 genera: Bradyrhizobium , Afipia , Agromonas , Balneimonas , Blastobacter , Bosea , Nitrobacter , Oligotropha , Rhodoblastus , Rhodopseudomomonas, Salinarimonas , and Tardiphaga . This phenotypically diverse family is composed of microorganisms that are involved in nitrogen cycling, human diseases, phototropism in non-sulfur environments, plant commensalism, and chemolithoautotrophic growth . 16S rRNA gene analysis of the Bradyrhizobiaceae family indicates that the Bosea genus is most closely related to the genus Salinarimonas which currently consists of two species, Salinarimonas rosea and Salinarmonas ramus . The microorganisms belonging to the genus Bosea have been isolated from a variety of environments such as soils, sediments, hospital water systems, and digester sludge [3,4,5]. The type strain Bosea thiooxidans BI-42Tis capable of thiosulfate oxidation and the initial genus definition included this characteristic . In 2003 La Scola emended the genus description to remove thiosulfate oxidation as a key descriptor after isolation of several other Bosea spp. that were unable to oxidized thiosulfate . These organisms have a very diverse metabolism but their common characteristics include being Gram-negative, aerobic, rod shaped, motile, good growth between 25 to 35 °C, intolerant to salt concentrations above 6% NaCl and have been described to be heterotrophic [3,4,5]. Using selective enrichment and isolation techniques with arsenite [As(III)] as the sole electron donor Bosea sp. WAO was isolated under autotrophic conditions . Here we summarize the physiological features together with the draft genome sequence and data analysis of Bosea sp. WAO.
Classification and features
The genus Bosea has nine species with validly published names isolated from various environments: B. thiooxidans BI-42T (AF508803) from agricultural soil , B. eneae 34614T (AF288300), B. vestrisii 34635T (AF288306), and B. massiliensis 63287T (AF288309) from a hospital water system , B. minatitlanensis AMX51T (AF273081) from anaerobic digester sludge  B. lupini R-45681T (FR774992), B. lathyri R-46060T (FR774993), and B. robiniae R-46070T (FR774994) from the root nodules of legumes , and B. vaviloviae Vaf-18T(KJ848741) from the root nodules of Vavilovia formosa . Strain WAO’s previously published identity was confirmed using the EzTaxon server . The highest 16S rRNA pairwise similarities for strain WAO were found with the type strains B. vestrisii 34635T (99.72%), B. eneae 34614T (99.65%), B. lupini R-45681T (99.65%), B. thiooxidans BI-42T (99.24%), B. robiniae R-46070T (98.88%), B. massiliensis 63287T (98.81%), B. minatitlanensis AMX51T (98.48%) and B. lathyri R-46060T (98.18%). Phylogenetic analysis based on the 16S rRNA gene of Bosea spp. and phylogenetically related organisms placed Bosea sp. WAO closest to the type strain B. lupini DSM 26673T with B. vestrisii 34635T and B. eneae 34614T in the same cluster (Fig. 1, Table 1). An average nucleotide identity analysis (ANI) score between strain WAO and B. lupini DSM 26673T of 84.64% was computed using IMG/ER . This value is lower than the ANI species demarcation threshold range (95–96%) . To further identify Bosea sp. WAO to the species level phylogenic trees based on the housekeeping genes atpD, dnaK, recA, gyrB and rpoB were produced from available Bosea and related Bradyrhizobiaceae type strains using MEGA7 (Figs. 2, 3, 4, 5, 6 and 7). Strain WAO did not consistently group with any of the type strains for all five genes further suggesting that it is a separate species. The ability of B. lupini to oxidize thiosulfate has not been determined ; however, B. vestrisii , B. eneae , and B. massiliensis have been determined to not oxidize thiosulfate to sulfate . These results suggest that strain WAO represents a distinct species in the genus Bosea .
Extended feature descriptions
Bosea sp. WAO cells are Gram-negative, aerobic, motile, and rod shaped. Colonies on trypticase soy agar are smooth, mucoid, round, convex, and beige with a diameter as large as 10 mm after 2 weeks at 30 °C. Colonies on minimal salts medium supplemented with 5 mM sodium thiosulfate are smooth, round, white and only grow to a diameter of 2 mm after 2 weeks at 30 °C. Optimal growth occurs at a temperature range from + 25 to 30 °C and pH 6 to 9 with an optimum at pH 8 (Table 1). Growth did not occur at salinity > 3.5% w/v of NaCl. Cells will grow freely floating or attached to a mineral surface as shown in Fig. 8.
Strain WAO is a strict aerobe that can grow heterotrophically on acetate, glucose, and lactate in addition to autotrophically on carbon dioxide with the electron donors arsenite, thiosulfate, polysulfide, and elemental sulfur. The organism is also able to grow on the mineral arsenopyrite (FeAsS) by oxidizing both the arsenic and sulfur to produce sulfate and arsenate. No growth was observed under aerobic conditions with the aromatic compounds phenol, benzoate or ferulic acid or with the electron donors sulfite, ammonium, nitrite, selenite, or chromium(III). This organism was enriched from pulverized black shale that contained high levels of arsenic. The initial enrichment cultures using the shale material were amended with 5 mM arsenite and then serially diluted until purity was obtained .
Genome sequencing information
Genome project history
Bosea sp. WAO was selected for sequencing based on the organism’s ability to grow both heterotrophically and chemolithoautotrophically with arsenite and reduced sulfur compounds. Sequencing and assembly was completed at the Rutgers School of Environmental and Biological Sciences Genome Cooperative. A paired-end library was constructed using an Illumina Nextera Kit and sequenced using an Illumina Genome Analyzer IIX (Illumina Inc., San Diego, CA). The sequence assembly was performed using a CLC Genomics Workbench 5.1 (CLC Bio, Cambridge, MA). The draft genome was submitted to NCBI Whole Genome Shotgun (WGS) and to the JGI Integrated Microbial Genomes/ Expert Review (IMG/ER). A summary of the project is shown in Table 2.
Growth conditions and genomic DNA preparation
A culture of Bosea sp. WAO (GeneBank: DQ986321.1, DSM 102914) was grown in a dilute (50% normal strength) trypticase soy broth amended with 5 mM sodium arsenite and 5 mM sodium thiosulfate then incubated at 30 °C on an orbital shaker for maximum oxygen exchange. Once turbid genomic DNA was extracted using the MoBio Powersoil Kit following manufacturer’s directions with the modification that DNA was eluted into 100 uL water instead of buffer.
Genome sequencing and assembly
A paired-end library was constructed using an Illumina Nextera Kit and sequenced using an Illumina Genome Analyzer IIX (Illumina Inc., San Diego, CA). The sequence assembly was performed using the CLC Genomics Workbench 5.1 (CLC Bio, Cambridge, MA). An average coverage of 240× and a mean read length of 106 bp was obtained. The genome was assembled into 42 contigs with no additional gap closures.
Genes were identified using the standard operating procedures of the DOE-JGI Microbial Genome Annotation pipeline  and The RAST Server: Rapid Annotation using subsystem technology [11, 12]. JGI-IMG/ER was used to obtain COG identities and overall statistics of the genome. RAST was used to identify functional genes of interest involved in sulfur and arsenic metabolism.
The draft genome is 6,125,776 bp with 66.84% G + C content. There are 62 RNA genes, 1 each of 5S rRNA, 16S rRNA, and 23S rRNA, and 46 tRNA, plus 13 unclassified RNA (Table 3). Of the predicted 5727 genes, 5665 or 98.92% are protein-coding genes, with 82.77% identified with protein function. The draft genome contains no identified pseudo genes. Of the protein-coding genes 4193 were sorted into COG functional categories. The COG categories are broken down in Table 4. COG analysis assigned a large number of genes to amino acid transport and metabolism (13.76%), transcription (8.13%), inorganic ion transport and metabolism (8.06%), and energy production and conservation (6.97%). Bosea sp. WAO has 53 genes encoding for cytochromes alone. RAST subsystem analysis placed 44% of the protein coding genes into subsystem categories with the largest percentage assigned to amino acids and derivatives. The genome sequence was deposited in GenBank ID JXTJ00000000.
Ten other genome sequences of Bosea spp. are publicly available of which four are validly named and characterized to the species level: B. thiooxidans CGMCC 9174 V5_1, B. lathyri DSM 26656T, B. lupini DSM 26673T, B. vaviloviae strain SD260 and six uncharacterized: Bosea sp. 117, Bosea sp. UNC402CLCol, Bosea sp. LC85, Bosea sp. OK403, Bosea sp. AAP35, and Bosea sp. AAP25. Only B. thiooxidans CGMCC 9174 V5_1 and B. vaviloviae strain SD260 are complete genomes. Table 5 details the basic characteristics of the ten genomes. The genomes range in size from 4.4 Mb to 6.6 Mb and G + C content between 64 to 68%, a predicated gene number range from 3984 to 6267. Bosea sp. WAO’s genome size (6.1 Mb), number of predicted genes (5727), number genes with function (4570), and number placed in COGs (4193) are all higher than the average for the draft genomes. However, both the percentage values for genes with functional predication (79.8%) and percentage in COGs (73.2%) are similar to the average values for the draft genomes. B. thiooxidans CGMCC 9174 V5_1, B. vaviloviae strain SD260, Bosea sp. 117 and Bosea sp. UNC402CLCol contain pseudo genes. None of the IMG database genomes have been finished with scaffold numbers ranging between 16 and 72.
Bosea sp. WAO is able to grow under chemolithoautotrophic conditions with arsenite in addition to growing under heterotrophic conditions. Metabolic studies indicated that the organism was able to stoichiometically oxidize the electron donors As(III) to As(V). Aerobic arsenite oxidation occurs using the aio genes renamed to reduce confusion from aso, aro and aox, which were formerly used to identify these genes in different organisms . aioA encodes for a large molybdopterin containing subunit with a guanosine dinucleotide at the active site and aioB encodes for a small Rieske subunit [13,14,15]. This pathway has a two component regulatory system that includes a sensor histidine kinase encoded by aioS (aoxS, aroS) and a transcriptional regulator encoded by aioR (aoxR, aroR) [13,14,15]. For the initial publication of Bosea sp. WAO, only the large subunit gene for the arsenite oxidation pathway aioA (EF015463) was amplified by traditional PCR [1, 16]. Analysis of the genome herein revealed that the arsenite oxidation pathway was complete with Bosea sp. WAO possessing both the small subunit aioB and reconfirming the large subunit aioA in addition to the remaining genes in the pathway. Of the available genomes only Bosea sp. WAO, and Bosea sp. 117 genomes contain both the large and small arsenite subunits with an amino acid similarity of 78% for AioA and 73% for AioB. The genes within the arsenite oxidation operon are in the same order (Fig. 9). The operon begins with a sensor histidine kinase, aioS, followed by a transcriptional response regulator, aioR, and then aioB, followed by aioA.
Reduced sulfur compound oxidation
Bosea sp. WAO is also able to grow under chemolithoautotrophic conditions with thiosulfate, polysulfide, and elemental sulfur. Metabolic studies indicated that the organism is able to stoichiometically oxidize the electron donor S2O3 to SO42−. The sox gene cluster is a pathway consisting of seven essential genes, soxXYZABCD, that code for proteins required for direct oxidation from sulfide to sulfate in vivo . The genome analysis indicated that strain WAO possesses all the genes necessary for the sulfur oxidation pathway. KEGG analysis indicated genes are all present to code for the enzymes SoxB, SoxX, SoxY, SoxA, SoxC, and SoxD to allow for complete oxidation of S2O3 to SO42−. Bosea sp. WAO, in addition to B. thiooxidans CGMCC 9174 V5_1, Bosea sp. 117, Bosea sp. LC85, and B. lupini contain the complete sox system. For the four genomes available in IMG the overall gene order in the operons are the same for all organisms; however, Bosea sp. WAO and B. lupini have soxA and soxX on the plus strand and soxY, soxZ, soxB, soxC, soxD on the minus strand (Fig. 10). While Bosea sp. 117 and Bosea sp. LC85 have the genes on the reverse strands with soxY, soxZ, soxB, soxC, soxD on the plus and soxA and soxX on the minus strand (Fig. 10). Comparison of the translated nucleotide sequence of soxB from Bosea sp. WAO to the translated soxB of the other five organisms showed that the protein sequence is 90% similar to Bosea sp. LC85, 88% similar to B. lupini and B. thiooxidans CGMCC 9174 V5_1, and 70% similar to Bosea sp. 117. The presence of all the genes in the same order suggests other strains in addition to the experimentally confirmed Bosea thiooxidans BI-42T, may be able to perform thiosulfate oxidation.
Additional metabolic pathways
The Calvin Cycle consists of 13 enzymatic reactions with the enzyme ribulose-1,5 bisphosphate carboxylase/oxygenase (RuBisCO) responsible for the carbon fixation step . For the initial publication of Bosea sp. WAO the type II ribulose-1,5’bisphosphate carboxylase/oxygenase (RuBisCO) was amplified by traditional PCR [1, 16]. Analysis for the remaining genes of the Calvin-Benson-Bassham Cycle for carbon fixation indicated that all the other required genes were present for carbon fixation to occur. Nine of the available genomes have a match for strain WAO’s ribulose 1,5-bisphosphate carboxylase amino acid sequence: B. thiooxidans CGMCC 9174 V5_1, (85%), B. lathyri DSM 26656T, (86%), B. lupini DSM 26673T, (82%), B. vaviloviae strain SD260, (85%), Bosea sp. 117, (72%), Bosea sp. UNC402CLCol, (85%), Bosea sp. LC85, (84%), Bosea sp. OK403, (87%), and Bosea sp. AAP35, (84%). Since RuBisCO is considered a biomarker for the Calvin Cycle this suggests carbon fixation maybe be widespread in this genus despite the limited experimental evidences.
Additional KEGG analysis indicated incomplete pathways for nitrogen reduction. Bosea sp. WAO possesses some genes for each of the reductive pathways but each is incomplete supporting the observation that no growth occurred when nitrate was provided as an electron acceptor. No genes involved in ammonia oxidation were identified again supporting the absence of growth when cultivated under those conditions . Using IMG/ER Pipeline analysis Bosea sp. WAO was determined to be prototrophic for L-aspartate, L-glutamate, and glycine; auxotrophic for L-lysine, L-alanine, L-phenylalanine, L-tyrosine, L-tryptophan, L-histine, L-arginine, L-isoleucine, L-leucine, and L-valine; and not able to synthesize selenocycteine synthesizer or biotin based on the draft of the genome . Using the SEED viewer Bosea sp. WAO has complete pathways for the: tricarboxylic acid cycle, pentose phosphate pathway, acetyl-coA acetogenesis pathway, methylglyoxal metabolism, dihydroxyacetone kinases, catechol branch of beta-ketoadipate pathway, glycerol and clycerol-3-phosphate uptake and utilization, D-ribose utilization, deoxyribose and deoxynucleoside catabolism, and lactate utilization.
Bosea sp. WAO is able to grow chemolithoautotrophically on both arsenite and reduced sulfur compounds. It was originally enriched from pyritic shale obtained from a rock outcropping containing arsenic in the Lockatong geological formation in the Newark Basin near Trenton, New Jersey . The draft genome is 6.1 Mbps and a G + C content of 66.84%. COG analysis for Bosea sp. WAO assigned a large number of genes to amino acid transport and metabolism (13.76%), transcription (8.13%), inorganic ion transport and metabolism (8.06%), and energy production and conservation (6.97%). Bosea sp. WAO has 53 genes encoding for cytochromes alone. Strain WAO is able to engage in the oxidative part of biogeochemical cycling and grow autotrophically when nutrient conditions are low. When conditions favor heterotrophic growth, however, the organism is able to rapidly increase in biomass and maintain its population under the varying conditions that expected to prevail at an oxic mineral surface.
Rhine ED, Onesios KM, Serfes ME, Reinfelder JR, Young LY. Arsenic transformation and mobilization from minerals by the arsenite oxidizing strain WAO. Environ Sci Technol. 2008;42:1423–9.
de Souza JAM, Carrareto Alves LM, de Mello Varani A, de Macedo Lemos E. The family Bradyrhizobiaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The prokaryotes. Berlin Heidelberg: Springer; 2014. p. 135–54.
Das SK, Mishra AK, Tindall B, Rainey FA. Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans. (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing. Int J Syst Bacteriol. 1996;46:981–7.
La Scola B, Mallet M, Grimont PAD, Raoult D. Bosea eneae sp. nov., Bosea massiliensis sp. nov. and Bosea vestrisii sp. nov., isolated from hospital water supplies, and emendation of the genus Bosea (Das et al. 1996). Int J Syst Evol Microbiol. 2003;53:15–20.
Ouattara AS, Assih EA, Thierry S, Cayol J, Labat M, Monroy O, et al. Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester. Int J Syst Evol Microbiol. 2003;53:1247–51.
De Meyer SE, Willems A. Multilocus sequence analysis of Bosea species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes. Int J Syst Evol Microbiol. 2012;62:2505–10.
Safronova VI, Kuznetsova IG, Sazanova AL, Kimeklis AK, Belimov AA, Andronov EE, et al. Bosea vaviloviae sp. nov., a new species of slow-growing rhizobia isolated from nodules of the relict species Vavilovia formosa (Stev.) Fed. Antonie Van Leeuwenhoek J Microb. 2015;107:911–20.
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012;62:716–21.
Markowitz VM, Chen IA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–22.
Kim M, Oh H, Park S, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–51.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H, Cohoon M, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33:5691–702.
Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Lett M, Muller D, Lièvremont D, Silver S, Santini J. Unified nomenclature for genes involved in prokaryotic aerobic arsenite oxidation. J Bacteriol. 2012;194:207–8.
Silver S, Phung LT. Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl Environ Microbiol. 2005;71:599–608.
Amend JP, Saltikov C, Lu G, Hernandez J. Microbial arsenic metabolism and reaction energetics. Rev Mineral Geochem. 2014;79:391–433.
Rhine ED, Ní Chadhain SM, Zylstra GJ, Young LY. The arsenite oxidase genes (aroAB) in novel chemoautotrophic arsenite oxidizers. Biochem Biophys Res Commun. 2007;354:662–7.
Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J. Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl Environ Microbiol. 2001;67:2873–82.
Shively JM, van Keulen G, Meijer WG. Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu Rev Microbiol. 1998;52:191–230.
Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10:512–26.
Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. 2016.
Meyer B, Imhoff JF, Kuever J. Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria - evolution of the sox sulfur oxidation enzyme system. Environ Microbiol. 2007;9:2957–77.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci. 1990;87:4576–9.
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Garrity GM, Bell J, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Bergey’s manual of systematic bacteriology, vol. Part B; 2005. p. 1.
Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In: Garrity G, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s manual® of systematic bacteriology. US: Springer; 2005. p. 1–574.
List Editor. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published, vol. 56; 2006. p. 1–6.
Kuykendall LD. Order Vi. Rhizobiales ord. nov. In: Garrity G, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s manual® of systematic bacteriology. US: Springer; 2005. p. 324.
Garrity GM, Bell JA, Lilburn T. Family VII. Bradyrhizobiaceae fam. nov. In: Garrity G, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s manual® of systematic bacteriology. US: Springer; 2005. p. 438.
Das SK. Genus V. Bosea Das, Mishra, TIndall, Rainey and Stackebrandt 1996, 985 VP. In: Garrity G, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s manual® of systematic bacteriology. US: Springer; 2005. p. 459–461.
Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32:D258–61.
Gan HY, Gan HM, Tarasco AM, Busairi NI, Barton HA, Hudson AO, et al. Whole-genome sequences of five oligotrophic bacteria isolated from deep within Lechuguilla Cave, New Mexico. Genome Announc. 2014;2 https://doi.org/10.1128/genomeA.01133-14.
Technical support was provided by the Rutgers School of Environmental and Biological Sciences Genome Cooperative.
This work was supported in part by the New Jersey Water Resources Research Institute at Rutgers University.
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
- Neutrophilic sulfur oxidizer
- Arsenite oxidase gene
- Microbe-mineral interactions, carbon fixation RuBisCO