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Wind-driven redistribution of snow on sea ice alters its topography and microstructure, yet the impact of these processes on radar signatures is poorly understood. Here, we examine the effects of snow redistribution over Arctic sea ice on radar waveforms and backscatter signatures obtained from a surface-based, fully polarimetric Ka- and Ku-band radar at incidence angles between 0∘ (nadir) and 50∘. Two wind events in November 2019 during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition are evaluated. During both events, changes in Ka- and Ku-band radar waveforms and backscatter coefficients at nadir are observed, coincident with surface topography changes measured by a terrestrial laser scanner. At both frequencies, redistribution caused snow densification at the surface and the uppermost layers, increasing the scattering at the air–snow interface at nadir and its prevalence as the dominant radar scattering surface. The waveform data also detected the presence of previous air–snow interfaces, buried beneath newly deposited snow. The additional scattering from previous air–snow interfaces could therefore affect the range retrieved from Ka- and Ku-band satellite altimeters. With increasing incidence angles, the relative scattering contribution of the air–snow interface decreases, and the snow–sea ice interface scattering increases. Relative to pre-wind event conditions, azimuthally averaged backscatter at nadir during the wind events increases by up to 8 dB (Ka-band) and 5 dB (Ku-band). Results show substantial backscatter variability within the scan area at all incidence angles and polarizations, in response to increasing wind speed and changes in wind direction. Our results show that snow redistribution and wind compaction need to be accounted for to interpret airborne and satellite radar measurements of snow-covered sea ice.

13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/, Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4, The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes, This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle

© 2018 Beukes, Palmer, Manyaka, Chan, Avontuur, van Zyl, Huntemann, Clum, Pillay, Palaniappan, Varghese, Mikhailova, Stamatis, Reddy, Daum, Shapiro, Markowitz, Ivanova, Kyrpides, Woyke, Blom, Whitman, Venter and Steenkamp. A corrigendum on Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato by Beukes, C. W., Palmer, M., Manyaka, P., Chan, W. Y., Avontuur, J. R., van Zyl, E., et al. (2017) Front. Microbiol. 8:1154. doi: 10.3389/fmicb.2017.01154. In the original article, there was a spelling mistake in a species name contained in Table 3 as published. As the information in this table is required for validation of the novel species combinations, this mistake has been corrected from "Caballeronia ptereocthonis comb. nov." to "Caballeronia ptereochthonis comb. nov." and "Burkholderia ptereocthonis" to "Burkholderia ptereochthonis". The corrected Table 3 appears below. TABLE 3: Table 3. Summary of the novel combinations proposed for 13 species of Caballeronia. Also, an additional section titled "Description of New Species Combinations" was added to the original article. The section contains a short protologue for each proposed novel combination to conform to the rules of the Bacterial Code of Nomenclature. The protologues appear below. The authors apologize for this error. The original article has been updated. Description of New Species Combinations. Description of Caballeronia arvi comb. nov. Caballeronia arvi (ar'vi. L. gen. n. arvi of a field). Basonym: Burkholderia arvi Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Analysis of 106 conserved protein-coding sequences have shown that this species is placed in the genus Caballeronia with very high support. The type strain is LMG 29317T (= CCUG 68412T = MAN34T). Description of Caballeronia arationis comb. nov. Caballeronia arationis (a.ra.ti.o'nis. L. gen. n. arationis from a field). Basonym: Burkholderia arationis Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Phylogenetic analysis of 106 conserved protein-coding loci clearly showed that there is high support for the placement of this species in Caballeronia. The type strain is LMG 29324T (=CCUG 68405T). Description of Caballeronia calidae comb. nov. Caballeronia calidae (ca'li.dae. L. gen. n. calidae from warm water, because this strain was isolated from pond water in a tropical garden). Basonym: Burkholderia calidae Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Phylogenetic analysis of 106 conserved protein-coding loci showed (with a high degree of certainty) that this species belongs in the genus Caballeronia. The type strain is LMG 29321T (=CCUG 68408T). Description of Caballeronia catudaia comb. nov. Caballeronia catudaia (ca.tu.da'ia. Gr. adj. catudaios subterraneous; N. L. fem. adj. catudaia, earth-born). Basonym: Burkholderia catudaia Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Our analyses of 106 conserved protein-coding loci clearly indicate that this species has high support for being included in Caballeronia. The type strain is LMG 29318T (=CCUG 68411T). Description of Caballeronia concitans comb. nov. Caballeronia concitans (con.ci'tans. L. fem. part. pres. concitans disturbing, upsetting; because the isolation of this bacterium from human sources, including blood, further disturbs the image of this lineage of Burkholderia species as benign bacteria). Basonym: Burkholderia concitans Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Analysis of 106 conserved protein-coding loci showed that this species has high support for belonging to the genus Caballeronia. The type strain is LMG 29315T (=CCUG 68414T = AU12121T). Description of Caballeronia fortuita comb. nov. Caballeronia fortuita (for.tu.i'ta. L. fem. adj. fortuita accidental, unpremeditated; referring to its fortuitous isolation when searching for Burkholderia caledonica endophytes). Basonym: Burkholderia fortuita Peeters et al., 2016. The description is as described in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci clearly show this species is included in the genus Caballeronia. The type strain is LMG 29320T (=CCUG 68409T). Description of Caballeronia glebae comb. nov. Caballeronia glebae (gle'bae. L. gen. n. glebae from a lump or clod of earth, soil). Basonym: Burkholderia glebae Peeters et al., 2016. The description appears in Peeters et al. (2016). Analysis of 106 conserved protein-coding loci shows high support for the placement of this species in the genus Caballeronia. The type strain is LMG 29325T (=CCUG 68404T). Description of Caballeronia hypogeia comb. nov. Caballeronia hypogeia (hy.po.ge'ia. Gr. adj. hypogeios subterraneous; N. L. fem. adj. hypogeia, subterraneous, earth-born). Basonym: Burkholderia hypogeia Peeters et al., 2016. The description appears in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci supports the inclusion of this species into the genus Caballeronia. The type strain is LMG 29322T (=CCUG 68407T). Description of Caballeronia pedi comb. nov. Caballeronia pedi (pe'di. Gr. n. pedon soil, earth; N. L. gen. n. pedi, from soil). Basonym: Burkholderia pedi Peeters et al. 2016. The description is listed in Peeters et al. (2016). The analysis of 106 conserved protein-coding loci, showed that this species is placed in Caballeronia. The type strain is LMG 29323T (=CCUG 68406T). Description of Caballeronia peredens comb. nov. Caballeronia peredens (per.e'dens. L. fem. part. pres. peredens consuming, devouring; referring to the capacity of this bacterium to degrade fenitrothion). Basonym: Burkholderia peredens Peeters et al., 2016. The description is as discussed in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci clearly shows that this species should be included in the genus Caballeronia. The type strain is LMG 29314T (=CCUG 68415T = NF100T). Description of Caballeronia ptereochthonis comb. nov. Caballeronia ptereochthonis (pte.re.o.chtho'nis Gr. n. pteris fern; Gr. n. chthon soil; N. L. gen. n. ptereochthonis, from fern soil). Basonym: Burkholderia ptereochthonis Peeters et al., 2016. The description appears in Peeters et al. (2016). The analysis of 106 conserved protein-coding loci clearly shows that this species should be included in Caballeronia. The type strain is LMG 29326T (=CCUG 68403T). Description of Caballeronia temeraria comb. nov. Caballeronia temeraria (te.me.ra'ri.a. L. fem. adj. temeraria accidental, inconsiderate; referring to its accidental isolation when searching for Burkholderia caledonica endophytes). Basonym: Burkholderia temeraria Peeters et al., 2016. The description of this species appears in Peeters et al. (2016). The analysis of 106 conserved protein-coding loci here, shows that this species is included in Caballeronia with high support. The type strain is LMG 29319T (=CCUG 68410T). Description of Caballeronia turbans comb. nov. Caballeronia turbans (tur'bans. L. fem. part. pres. turbans disturbing, agitating, because the isolation of this bacterium from human pleural fluid further disturbs the image of this lineage of Burkholderia species as benign bacteria). Basonym: Burkholderia turbans Peeters et al., 2016. The original species description appears in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci shows that this species forms part of Caballeronia. The type strain is LMG 29316T (=CCUG 68413T = HI4065T). Conflict of Interest Statement. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

© 2018 Hahnke, Meier-Kolthoff, García-López, Mukherjee, Huntemann, Ivanova, Woyke, Kyrpides, Klenk and Göker. In the Taxonomic Consequences section of the Discussion chapter of the original article the type of the newly proposed class Saprospiria was incorrectly indicated (and in conflict with the etymology paragraph) within the description of the class. A correction has accordingly been made to Discussion, Taxonomic Consequences, Description of Saprospiria, class. nov.: Description of Saprospiria, class. nov. Sa.pros.pi'ri.a (N.L. fem. n. Saprospira, type genus of the type order of the class, -ia ending to denote a class; N.L. fem. pl. n. Saprospiria, the class of the order Saprospirales). The description is the same as for the order Saprospirales. This class is described on the basis of 16S rRNA gene and whole-genome phylogenetic analysis. The type and currently sole order of the class is Saprospirales. The authors apologize for this error and state that this does not change the scientific conclusions of the original article in any way. The original article has been updated.

© 2018 Pold et al. Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous forest in central Massachusetts. Here, we present the complete genome sequence of this phylogenetically novel organism, which consists of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and 3,273 predicted open reading frames.

© 2017 The Author(s). Paraburkholderiacaballeronis is a plant-associated bacterium. Strain TNe-841Twas isolated from the rhizosphere of tomato (Solanum lycopersicum L. var. lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was found to effectively nodulate Phaseolus vulgarisL. However, from an analysis of the genome of strain TNe-841Tand 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.

© 2017 Yassin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The permanent draft genome sequence of Actinotignum schaalii DSM 15541Tis presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogen-sis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.

© 2017 The Author(s). The genus Marinobacterium belongs to the family Alteromonadaceae within the class Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium contains 16 species. Marinobacterium rhizophilum CL-YJ9Twas isolated from sediment associated with the roots of a plant growing in a tidal flat of Youngjong Island, Korea. The genome of the strain CL-YJ9Twas sequenced through the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report the main features of the draft genome of the strain. The 5,364,574 bp long draft genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based on the genomic analyses, the strain seems to adapt to osmotic changes by intracellular production as well as extracellular uptake of compatible solutes, such as ectoine and betaine. In addition, the strain has a number of genes to defense against oxygen stresses such as reactive oxygen species and hypoxia.

© 2017 The Author(s). 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.

© 2017 The Author(s). Anaerobium acetethylicum strain GluBS11Tbelongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated from biogas slurry that was originally enriched with gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol 65:3289-3296, 2015). Here we describe the draft genome sequence of strain GluBS11Tand provide a detailed insight into its physiological and metabolic features. The draft genome sequence generated 4,609,043 bp, distributed among 105 scaffolds assembled using the SPAdes genome assembler method. It comprises in total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124 RNA genes and 867 pseudogenes. The content was 43.51 mol %. The annotated genome of strain GluBS11Tcontains putative genes coding for the pentose phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff pathway and the tricarboxylic acid cycle. The genome revealed the presence of most of the necessary genes required for the fermentation of glucose and gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for production of formate was not identified.

© 2017 The Author(s). Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.

© 2017 The Author(s). Thiobacillus thioparus DSM 505Tis 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 3,201,518 bp. 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.

© 2017 Miroshnikov et al. Methylocapsa palsarum NE2Tis an aerobic, mildly acidophilic, obligate methanotroph. Similar to other Methylocapsa species, it possesses only a particulate methane monooxygenase and is capable of atmospheric nitrogen fixation. The genome sequence of this typical inhabitant of subarctic wetlands and soils also contains genes indicative of aerobic anoxygenic photosynthesis.

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006. [KEYWORDS: Nitrosomonas Ammonia-oxidizing bacteria Ammonia oxidation nitrification nitrogen cycle freshwater oligotrophic DIFFERENT SENSITIVITIES KDP-ATPASE RNA GENES NOV-SP EUROPAEA NICHE MODEL PROTEOBACTERIA MULTIFORMIS EXPRESSION]

© 2016 The Author(s). The errors and associated corrections described in this document concerning the original manuscript were accountable to the production department handling this manuscript, and thus are no fault of the authors of this paper. Additionally, the online manuscript has now been updated with these corrections accordingly. In the original publication of this article [1], the title was displayed incorrectly as "Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia". The genus name "Thermithiobacillus" was misspelt as "Thermithiobaclillus". This has now been corrected in the original article.

© 2016 The Author(s). Thermithiobacillus tepidarius DSM 3134Twas 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.

© 2016 The Author(s). Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1Tis a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1T. The genome comprised 2,748,608 bp with a G+C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.

© 2016 The Author(s). Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004Tand Pseudomonas cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.

© 2016 The Author(s). Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5T (DSM 17707T) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5T is part of the Genomic Encyclopedia of Bacteria and Archaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5T. Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5T feeds rather on proteins than saccharides and lipids.

© 2016 The Author(s). Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050T(DSM 19838T) and Gramella portivictoriae UST040801-001T(DSM 23547T) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838Tand DSM 23547T. Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838T, whereas strain DSM 23547Thydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.

© 2016 Zhou et al. Thermus amyloliquefaciens type strain YIM 77409Tis 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 77409Ttogether with its genome sequence and annotation. The genome is 2,160,855 bp 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.

© 2016 Aizenberg-Gershtein et al. Phaseolibacter flectens strain ATCC 12775T(Halpern et al., Int J Syst Evol Microbiol 63:268-273, 2013) is a Gram-negative, rod shaped, motile, aerobic, chemoorganotroph bacterium. Ph. flectens is as a plant-pathogenic bacterium on pods of French bean and was first identified by Johnson (1956) as Pseudomonas flectens. After its phylogenetic position was reexamined, Pseudomonas flectens was transferred to the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA GC content is 44.34 mol%. The chromosome length is 2,748,442 bp. It encodes 2,437 proteins and 89 RNA genes. Ph. flectens genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.

© 2016 Ganji et al. The draft genome of Thermocrinis jamiesonii GBS1Tis 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.

© 2015 Choi et al. Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535T, was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535Twas sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. The strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535Tdid not form spore.

© 2014 Scheuner et al.; licensee BioMed Central Ltd. Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.