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Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology is from aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cultures. These data will support phylogenomic studies of evolutionary relationships and gene content among these unique algae and their aquatic relatives.

Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.

Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.

Draft genome sequences of 11 bacteria belonging to the family Microbacteriaceae were obtained using Illumina technology. The genomes of these strains have sizes from 3.14 to 4.30 Mb with their genomic DNA characterized as having high G+C contents (above 65%)., Draft genome sequences of 11 bacteria belonging to the family Microbacteriaceae were obtained using Illumina technology. The genomes of these strains have sizes from 3.14 to 4.30 Mb with their genomic DNA characterized as having high G+C contents (above 65%). These genomic data will be useful for natural taxonomy and comparative genomic studies of bacterial strains of the family Microbacteriaceae.

For their food source, Trachymyrmex septentrionalis ants raise symbiotic fungus gardens that contain bacteria whose functions are poorly understood. Here, we report the genome sequences of eight bacteria isolated from these fungus gardens to better describe the ecology of these strains and their potential to produce secondary metabolites in this niche.

Thermoanaerobacterium sp. strain RBIITD was isolated from contaminated rich growth medium at 55°C in an anaerobic chamber. It primarily produces butyrate as a fermentation product from plant biomass-derived sugars. The whole-genome sequence of the strain is 3.4 Mbp, with 3,444 genes and 32.48% GC content.

Author(s): Beukes, Chrizelle W; Palmer, Marike; Manyaka, Puseletso; Chan, Wai Y; Avontuur, Juanita R; van Zyl, Elritha; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, TBK; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Blom, Jochen; Whitman, William B; Venter, Stephanus N; Steenkamp, Emma T | Abstract: [This corrects the article on p. 1154 in vol. 8, PMID: 28694797.].

caballeronis is a plant-associated bacterium. Strain TNe-841T was isolated from the rhizosphere of tomato (Solanum lycopersicum L. var. lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was found to effectively nodulate L. However, from an analysis of the genome of strain TNe-841T and from repeat inoculation experiments, we found that this strain did not nodulate bean and also lacked nodulation genes, suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G + C content of 67.01%. The sequence includes 6251 protein-coding genes and 87 RNA genes.

The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage. Electronic supplementary material The online version of this article (doi:10.1186/s40793-017-0258-y) contains supplementary material, which is available to authorized users.

Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.

Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.

The draft genome of Thermocrinis jamiesonii GBS1 T is 1,315,625 bp in 10 contigs and encodes 1,463 predicted genes. The presence of sox genes and various glycoside hydrolases and the absence of uptake NiFe hydrogenases ( hyaB ) are consistent with a requirement for thiosulfate and suggest the ability to use carbohydrate polymers.

Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.

Cupriavidus alkaliphilus ASC-732 T was isolated from the rhizosphere of agave plant growing in alkaline soils in San Carlos, Tamaulipas, Mexico. The species is able to grow in the presence of arsenic, zinc, and copper. The genome sequence of strain ASC-732 T is 6,125,055 bp with 5,586 genes and an average G+C content of 67.81%.

The draft genomes of Thermus tengchongensis YIM 77401 and T. caliditerrae YIM 77777 are 2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes, respectively. Gene content and growth experiments demonstrate broad metabolic capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation, incomplete denitrification, and polysulfide reduction.

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.

Thermus amyloliquefaciens type strain YIM 77409(T) is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409(T) together with its genome sequence and annotation. The genome is 2,160,855bp long and consists of 6 scaffolds with 67.4% average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.

We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

© 2016 Huntemann et al. The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases.

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb 3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia – by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.