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1.  Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075T 
Standards in Genomic Sciences  2013;9(2):294-303.
Mesorhizobium opportunistum strain WSM2075T was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075T is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075T contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
doi:10.4056/sigs.4538264
PMCID: PMC4062634  PMID: 24976886
root-nodule bacteria; nitrogen fixation; evolution; lateral gene transfer; integrative and conjugative elements; symbiosis; Alphaproteobacteria
2.  Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor 
Genome Announcements  2014;2(5):e00870-14.
Methanoregula formicica SMSPT is a mesophilic H2/formate-utilizing methanogenic archaeon and a representative of the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales. Here, we report a 2.8-Mb complete genome sequence of this methanogenic archaeon.
doi:10.1128/genomeA.00870-14
PMCID: PMC4155587  PMID: 25189582
3.  Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge 
Genome Announcements  2014;2(5):e00876-14.
Here, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1T, a methanogenic archaeon isolated from an anaerobic digested sludge. This is the first genome report of the genus Methanolinea isolate belonging to the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales.
doi:10.1128/genomeA.00876-14
PMCID: PMC4155590  PMID: 25189585
4.  The Expanded Diversity of Methylophilaceae from Lake Washington through Cultivation and Genomic Sequencing of Novel Ecotypes 
PLoS ONE  2014;9(7):e102458.
We describe five novel Methylophilaceae ecotypes from a single ecological niche in Lake Washington, USA, and compare them to three previously described ecotypes, in terms of their phenotype and genome sequence divergence. Two of the ecotypes appear to represent novel genera within the Methylophilaceae. Genome-based metabolic reconstruction highlights metabolic versatility of Methylophilaceae with respect to methylotrophy and nitrogen metabolism, different ecotypes possessing different combinations of primary substrate oxidation systems (MxaFI-type methanol dehydrogenase versus XoxF-type methanol dehydrogenase; methylamine dehydrogenase versus N-methylglutamate pathway) and different potentials for denitrification (assimilatory versus respiratory nitrate reduction). By comparing pairs of closely related genomes, we uncover that site-specific recombination is the main means of genomic evolution and strain divergence, including lateral transfers of genes from both closely- and distantly related taxa. The new ecotypes and the new genomes contribute significantly to our understanding of the extent of genomic and metabolic diversity among organisms of the same family inhabiting the same ecological niche. These organisms also provide novel experimental models for studying the complexity and the function of the microbial communities active in methylotrophy.
doi:10.1371/journal.pone.0102458
PMCID: PMC4109929  PMID: 25058595
5.  Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring 
Standards in Genomic Sciences  2014;9(3):1105-1117.
Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum ‘Thermotogae’. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.3016383
PMCID: PMC4148951  PMID: 25197486
anaerobic; motile; thermophilic; chemoorganotrophic; solfataric spring; outer sheath-like structure; Thermotogaceae; GEBA
6.  Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2 
Genome Announcements  2014;2(3):e00509-14.
Desulfovibrio aespoeensis Aspo-2, DSM 10631T, is a mesophilic, hydrogenotrophic sulfate-reducing bacterium sampled from a 600-m-deep subsurface aquifer in hard rock under the island of Äspö in southeastern Sweden. We report the genome sequence of this bacterium, which is a 3,629,109-bp chromosome; plasmids were not found.
doi:10.1128/genomeA.00509-14
PMCID: PMC4038888  PMID: 24874683
7.  Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium 
Standards in Genomic Sciences  2014;9(3):821-839.
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.
doi:10.4056/sigs.5209235
PMCID: PMC4148979  PMID: 25197466
spore-forming anaerobes; sulfate reduction; autotrophic; anaerobic degradation of aromatic compounds; complete oxidizer; Peptococcaceae; Clostridiales
8.  The complete genome sequence of Clostridium indolis DSM 755T 
Standards in Genomic Sciences  2014;9(3):1089-1104.
Clostridium indolis DSM 755T is a bacterium commonly found in soils and the feces of birds and mammals. Despite its prevalence, little is known about the ecology or physiology of this species. However, close relatives, C. saccharolyticum and C. hathewayi, have demonstrated interesting metabolic potentials related to plant degradation and human health. The genome of C. indolis DSM 755T reveals an abundance of genes in functional groups associated with the transport and utilization of carbohydrates, as well as citrate, lactate, and aromatics. Ecologically relevant gene clusters related to nitrogen fixation and a unique type of bacterial microcompartment, the CoAT BMC, are also detected. Our genome analysis suggests hypotheses to be tested in future culture based work to better understand the physiology of this poorly described species.
doi:10.4056/sigs.5281010
PMCID: PMC4149025  PMID: 25197485
Clostridium indolis; citrate; lactate; aromatic degradation; nitrogen fixation; bacterial microcompartments
9.  Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia 
Standards in Genomic Sciences  2014;9(3):1076-1088.
Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847T, turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pre-genome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and annotation of the type strain, M3T. The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.5138968
PMCID: PMC4149034  PMID: 25197484
anaerobic; motile; mesophilic; methanogen; swamp; improved-high-quality draft; Methanomicrobiaceae; GEBA
10.  Genome sequence of Microvirga lupini strain LUT6T, a novel Lupinus alphaproteobacterial microsymbiont from Texas 
Standards in Genomic Sciences  2014;9(3):1159-1167.
Microvirga lupini LUT6T is an aerobic, non-motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Lupinus texensis. LUT6T was isolated in 2006 from a nodule recovered from the roots of the annual L. texensis growing in Travis Co., Texas. LUT6T forms a highly specific nitrogen-fixing symbiosis with endemic L. texensis and no other Lupinus species can form an effective nitrogen-fixing symbiosis with this isolate. Here we describe the features of M. lupini LUT6T, together with genome sequence information and its annotation. The 9,633,614 bp improved high quality draft genome is arranged into 160 scaffolds of 1,366 contigs containing 10,864 protein-coding genes and 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of a DOE Joint Genome Institute 2010 Community Sequencing Project.
doi:10.4056/sigs.5249382
PMCID: PMC4149012  PMID: 25197490
root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria
11.  Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans 
Standards in Genomic Sciences  2014;9(3):655-675.
Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.
doi:10.4056/sigs.4718645
PMCID: PMC4149029  PMID: 25197452
Thermophilic spore-forming anaerobes; sulfate reduction; carboxydotrophic; Peptococcaceae; Clostridiales
12.  Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph 
Genome Announcements  2014;2(1):e01064-13.
Syntrophorhabdus aromaticivorans strain UI is a mesophilic bacterium capable of degrading aromatic substrates in syntrophic cooperation with a partner methanogen. The draft genome sequence is 3.7 Mb, with a G+C content of 52.0%.
doi:10.1128/genomeA.01064-13
PMCID: PMC3916484  PMID: 24503990
13.  Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment 
Standards in Genomic Sciences  2014;9(3):687-703.
Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
doi:10.4056/sigs.3828824
PMCID: PMC4148953  PMID: 25197454
Marine; motile; facultative anaerobe; methylated compounds; Rhodobacteraceae; Roseobacter clade
14.  Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128 
Standards in Genomic Sciences  2014;9(3):602-613.
Ensifer meliloti strain RRI128 is an aerobic, motile, Gram-negative, non-spore-forming rod. RRI128 was isolated from a nodule recovered from the roots of barrel medic (Medicago truncatula) grown in the greenhouse and inoculated with soil collected from Victoria, Australia. The strain is used in commercial inoculants in Australia. RRI128 nodulates and forms an effective symbiosis with a diverse range of lucerne cultivars (Medicago sativa) and several species of annual medic (M. truncatula, Medicago littoralis and Medicago tornata), but forms an ineffective symbiosis with Medicago polymorpha. Here we describe the features of E. meliloti strain RRI128, together with genome sequence information and annotation. The 6,900,273 bp draft genome is arranged into 156 scaffolds of 157 contigs, contains 6,683 protein-coding genes and 87 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
doi:10.4056/sigs.4929626
PMCID: PMC4149011  PMID: 25197447
root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria
15.  Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer 
Genome Announcements  2014;2(1):e00845-13.
Zymomonas mobilis subsp. mobilis is one of the most rigorous ethanol-producing organisms known to date, considered by many to be the prokaryotic alternative to yeast. The two most applied Z. mobilis subsp. mobilis strains, ZM4 and CP4, derive from Recife, Brazil, and have been isolated from sugarcane fermentations. Of these, ZM4 was the first Z. mobilis representative strain to be sequenced and analyzed. Here, we report the finishing of the genome sequence of strain CP4, which is highly similar but not identical to that of ZM4.
doi:10.1128/genomeA.00845-13
PMCID: PMC3886940  PMID: 24407627
16.  Complete genome sequence of Anabaena variabilis ATCC 29413 
Standards in Genomic Sciences  2014;9(3):562-573.
Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has served as a model organism, with an extensive literature extending over 40 years. The strain has three distinct nitrogenases that function under different environmental conditions and is capable of photoautotrophic growth in the light and true heterotrophic growth in the dark using fructose as both carbon and energy source. While this strain was first isolated in 1964 in Mississippi and named Anabaena flos-aquae MSU A-37, it clusters phylogenetically with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile, growing well at approximately 40° C. Here we provide some additional characteristics of the strain, and an analysis of the complete genome sequence.
doi:10.4056/sigs.3899418
PMCID: PMC4148955  PMID: 25197444
17.  Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 
In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.
doi:10.1186/1944-3277-9-19
PMCID: PMC4273726  PMID: 25566348
Anaerobic lignin degradation; Tropical forest soil isolate; Facultative anaerobe
18.  Genome sequence of Ensifer arboris strain LMG 14919T; a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan 
Standards in Genomic Sciences  2013;9(3):473-483.
Ensifer arboris LMG 14919T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of several species of legume trees. LMG 14919T was isolated in 1987 from a nodule recovered from the roots of the tree Prosopis chilensis growing in Kosti, Sudan. LMG 14919T is highly effective at fixing nitrogen with P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum acacia). LMG 14919T does not nodulate the tree Leucena leucocephala, nor the herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago sativa, Lotus corniculatus and Galega orientalis. Here we describe the features of E. arboris LMG 14919T, together with genome sequence information and its annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7 scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
doi:10.4056/sigs.4828625
PMCID: PMC4148966  PMID: 25197433
root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria
19.  Genome sequence of Burkholderia mimosarum strain LMG 23256T, a Mimosa pigra microsymbiont from Anso, Taiwan 
Standards in Genomic Sciences  2013;9(3):484-494.
Burkholderia mimosarum strain LMG 23256T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256T was isolated from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan. LMG 23256T is highly effective at fixing nitrogen with M. pigra. Here we describe the features of B. mimosarum strain LMG 23256T, together with genome sequence information and its annotation. The 8,410,967 bp high-quality-draft genome is arranged into 268 scaffolds of 270 contigs containing 7,800 protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
doi:10.4056/sigs.4848627
PMCID: PMC4148967  PMID: 25197434
root-nodule bacteria; nitrogen fixation; rhizobia; Betaproteobacteria
20.  Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece 
Standards in Genomic Sciences  2013;9(3):514-526.
Ensifer medicae strain WSM1115 forms effective nitrogen fixing symbioses with a range of annual Medicago species and is used in commercial inoculants in Australia. WSM1115 is an aerobic, motile, Gram-negative, non-spore-forming rod. It was isolated from a nodule recovered from the root of burr medic (Medicago polymorpha) collected on the Greek Island of Samothraki. WSM1115 has a broad host range for nodulation and N2 fixation capacity within the genus Medicago, although this does not extend to all medic species. WSM1115 is considered saprophytically competent in moderately acid soils (pH(CaCl2) 5.0), but it has failed to persist at field sites where soil salinity exceeded 10 ECe (dS/m). Here we describe the features of E. medicae strain WSM1115, together with genome sequence information and its annotation. The 6,861,065 bp high-quality-draft genome is arranged into 7 scaffolds of 28 contigs, contains 6,789 protein-coding genes and 83 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
doi:10.4056/sigs.4938652
PMCID: PMC4148968  PMID: 25197437
root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria
21.  Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T) 
Standards in Genomic Sciences  2013;9(3):462-472.
Mesorhizobium ciceri bv. biserrulae strain WSM1271T was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus – a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271T consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
doi:10.4056/sigs.4458283
PMCID: PMC4148989  PMID: 25197432
root-nodule bacteria; nitrogen fixation; evolution; lateral gene transfer; integrative and conjugative elements; symbiosis; Alphaproteobacteria
22.  Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia 
Standards in Genomic Sciences  2013;9(3):551-561.
Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
doi:10.4056/sigs.5008793
PMCID: PMC4148995  PMID: 25197440
root-nodule bacteria; nitrogen fixation; rhizobia; Betaproteobacteria
23.  Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum 
Standards in Genomic Sciences  2013;9(3):527-539.
Rhizobium leguminosarum bv. trifolii is a soil-inhabiting bacterium that has the capacity to be an effective N2-fixing microsymbiont of Trifolium (clover) species. R. leguminosarum bv. trifolii strain WSM1689 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Trifolium uniflorum collected on the edge of a valley 6 km from Eggares on the Greek Island of Naxos. Although WSM1689 is capable of highly effective N2-fixation with T. uniflorum, it is either unable to nodulate or unable to fix N2 with a wide range of both perennial and annual clovers originating from Europe, North America and Africa. WSM1689 therefore possesses a very narrow host range for effective N2 fixation and can thus play a valuable role in determining the geographic and phenological barriers to symbiotic performance in the genus Trifolium. Here we describe the features of R. leguminosarum bv. trifolii strain WSM1689, together with the complete genome sequence and its annotation. The 6,903,379 bp genome contains 6,709 protein-coding genes and 89 RNA-only encoding genes. This multipartite genome contains six distinct replicons; a chromosome of size 4,854,518 bp and five plasmids of size 667,306, 518,052, 341,391, 262,704 and 259,408 bp. This rhizobial genome is one of 20 sequenced as part of a DOE Joint Genome Institute 2010 Community Sequencing Program.
doi:10.4056/sigs.4988693
PMCID: PMC4149022  PMID: 25197438
root-nodule bacteria; nitrogen fixation; lupin-nodulating; rhizobia; Alphaproteobacteria
24.  Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557T 
Standards in Genomic Sciences  2013;9(3):540-550.
Microvirga lotononidis is a recently described species of root-nodule bacteria that is an effective nitrogen- (N2) fixing microsymbiont of the symbiotically specific African legume Listia angolensis (Welw. ex Bak.) B.-E. van Wyk & Boatwr. M. lotononidis possesses several properties that are unusual in root-nodule bacteria, including pigmentation and the ability to grow at temperatures of up to 45°C. Strain WSM3557T is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a L. angolensis root nodule collected in Chipata, Zambia in 1963. This is the first report of a complete genome sequence for the genus Microvirga. Here we describe the features of Microvirga lotononidis strain WSM3557T, together with genome sequence information and annotation. The 7,082,538 high-quality-draft genome is arranged in 18 scaffolds of 104 contigs, contains 6,956 protein-coding genes and 84 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
doi:10.4056/sigs.4548266
PMCID: PMC4149032  PMID: 25197439
root-nodule bacteria; nitrogen fixation; symbiotic specificity; Alphaproteobacteria
25.  Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos 
Standards in Genomic Sciences  2013;9(2):420-430.
Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
doi:10.4056/sigs.4838624
PMCID: PMC4062641  PMID: 24976897
root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria

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