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Many soil Actinobacteria are potent producers of extracellular enzymes decomposing lignocellulose. Four strains of Actinobacteria with a high potential to hydrolyse cellulose and hemicellulose were identified among environmental isolates. The strains were grown on raw lignocellulosic substrates (olive pomace, oat flakes, sawdust, and wheat straw) under submerged fermentation in a laboratory scale. Modified Melin Norkrans Medium amended with raw lignocellulosic substrates as carbon sources (0.5%) was used to enhance lignocellulosic biomass decomposition. Three strains belonged to the genus Streptomyces and one strain to the genus Mycobacterium. Annotation of genomes showed high proportion of genes encoding for carbohydrate-active enzymes in Streptomyces sp. GESEQ-4 (537, i.e. 6% of 8404 genes), Streptomyces sp. GESEQ-13 (351 (5%) of 6705 genes), Streptomyces sp. GESEQ-35 (608 (6%) of 9788 genes), and Mycolicibacterium fortuitum subsp. fortuitum GESEQ-9 (222 (3%) of 6405 genes). These included plant cell wall-degrading enzymes belonging to the families GH1, GH2, GH3, GH5, GH6, GH9, GH10, GH12, GH16, GH26, GH30, GH39, GH48, GH51, and GH74, of which GH1, GH2, GH3, GH5, GH6, and GH16 were found in all four genomes. Assays for cellulose and hemicellulose degrading extracellular enzymes confirmed the ability of the isolates to decompose cellulose and hemicellulose. The highest endo-cleaving enzyme activities were produced by the strain Steptomyces sp. GESEQ-4 DSM 106287. Our results provide new perspectives into the enzymatic array by which the Actinobacteria break down complex lignocellulosic biomass. It is crucial to assess the genome to determine enzyme function as well as the enzyme families responsible for the degradation process in Actinobacteria. The potential degradation functions for these actinobacterial strains were validated by testing their cellulolytic and hemicellulolytic activities with various lignocellulosic substrates.

Strain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

A novel actinobacterium, designated ASO4wetT, was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wetT is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413T (98.87 %), Streptomyces glycovorans YIM M 10366T (98.38 %), and Streptomyces abyssalis YIM M 10400T (97.53 %). Strain ASO4wetT contained MK-9(H8) as the predominant menaquinone and the major fatty acids are iso-C16:0, anteiso-C15:0, and iso-C15:0. Polyphasic taxonomy was carried out between strain ASO4wetT and its phylogenetically closely related Streptomyces strains, which further elucidated their relatedness and revealed that strain ASO4wetT could be distinguished from currently known Streptomyces species. Strain ASO4wetT clearly represents a novel species in genus Streptomyces. We propose the name Streptomyces bathyalis sp. nov., with the type strain ASO4wetT (= DSM 106605T = NCCB 100657T). Analysis of the whole-genome sequence of S. bathyalis revealed that genome size is 7,377,472 bp with 6332 coding sequences.

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. The work (proposal DOI[s]: https://doi.org/10.46936/10.25585/60001024; https://doi.org/10.46936/10.25585/60000886; https://doi.org/10.46936/10. 25585/60001401; https://doi.org/10.46936/10.25585/60001087; https:// doi.org/10.46936/10.25585/60001079; https://doi.org/10.46936/10.25585/ 60001044) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no. DE-AC02-05CH11231. Design and synthesis of peptide constructs were supported by the Biosystems Design program (DOE Office of Science contract DE-SC0018260) and the US Department of Energy Joint Genome Institute (DOE Office of Science contract DEAC02-05CH1123), respectively. Characterization of the peptide was supported by the Secured Biosystem Design project entitled ‘‘Rapid Design and Engineering of Smart and Secure Microbiological Systems’’ (DOE Office of Science contract DE-AC02-05CH1123). We thank the following researchers for their support of this study by providing free use of their public genome data: Kristen De-Angelis, Grace Pold, Mallory Choudoir, Camila Carlos-Shanley, Paul Carini, H. Corby C. Kistler, James Elkins, Javier A. Izquierdo, Dimitris Hatzinikolaou, Daniel Schachtman, Paul R. Jensen, Aindrila Mukhopadhyay, John Vogel, Carolin Frank, Paul M. D’Agostino, Ann M. Hirsch, Satoshi Yuzawa, Regina Lamendella, Bernhard Fuchs, Dale Pelletier, Laila P. Partida-Martinez, Cameron Currie, Seth De-Bolt, Jeff Dangl, David Mead, Susannah Tringe, David A. Baltrus, Seung Bum Kim, Linda Kinkel, Kelly Wrighton, William Mohn, Ludmila Christoserdova, Sarah Lebeis, Janet Janssen, Sandra Baena Garzon, and Nicholas Coleman. Special thanks to Marie Louise Ballon at the JGI Communications and Outreach office for all her help with the graphical abstract and many other details.

During a cultural diversity survey on hydrolytic bacteria in saline alkaline soils, a hydrolytic actinobacterium strain ACPA39T was enriched and isolated in pure culture from a soda solonchak soil in southwestern Siberia. It forms a substrate mycelium with rod-shaped sporangia containing 1–3 exospores. The isolate is obligately alkaliphilic, growing at pH 7.5–10.3 (optimum at 8.5–9.0) and moderately halophilic, tolerating up to 3 M total Na+ in the form of sodium carbonates. It is an obligately aerobic, organoheteroterophic, saccharolytic bacterium, utilizing various sugars and alpha/beta-glucans as growth substrates. According to the 16S rRNA gene-based phylogenetic analysis, strain ACPA39T forms a distinct branch within the family Micromonosporaceae, with the sequence identities below 94.5% with type strains of other genera. This is confirmed by phylogenomic analysis based on the 120 conserved single copy protein-based markers and genomic indexes (ANI, AAI). The cell-wall of ACPA39T contained meso-DAP, glycine, glutamic acid and alanine in a equimolar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars include galactose and xylose. The major menaquinone is MK-10(H4). The identified polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C17:0, iso-C16:0, iso-C17:0, 10 Me-C18:0 and C18:1ω9. Based on the distinct phylogeny, the chemotaxonomy features and unique phenotypic properties, strain ACPA39T (DSM 106523T = VKM 2772T) is classified into a new genus and species in the family Micromonosporaceae for which the name Natronosporangium hydrolitycum gen. nov., sp. nov. is proposed.

A haloalkaliphilic hydrolytic actinobacterium, strain ACPA22T, was enriched and isolated in pure culture from saline alkaline soil (soda solonchak) in northeastern Mongolia. The isolate was facultatively alkaliphilic, growing at pH 6.5–10.5 (optimum at 7.3–9.0) and highly salt-tolerant, tolerating up to 3 M total Na+ as carbonates. The hydrolytic nature of ACPA22T was confirmed by two different growth-dependent methods and by the presence of multiple glycosidase-encoding genes in the genome. The 16S rRNA gene-based phylogenetic analysis demonstrated that strain ACPA22T formed a deep-branching lineage within the family Glycomycetaceae, with the highest sequence similarity value to Glycomyces buryatensis 18T (92.1 %) and Salininema proteolyticum Miq-4T (91.8 %). The average amino acid identity values (56.1–61.5 %) between ACPA22T and other Glycomycetaceae members with available genomes did not exceed the threshold reported for different genera. The cell wall of ACPA22T contained meso-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars included mannose, galactose, arabinose, ribose and xylose. The major menaquinones were MK-10(Н4) and MK-11(Н4). The identified polar lipids were represented by phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. In addition, the strain had a few unidentified characteristic polar lipids, including an amine-containing phospholipid with chromatographic mobility similar to that of phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C17 : 0 and iso-C16 : 0. The genome included a chromosome of 3.94 Mbp (G+C content 61.5 mol%) encoding 3285 proteins and two plasmids of 59.8 and 14.8 kBp. Based on the data obtained in this study, a new genus and species, Natronoglycomyces albus gen. nov., sp. nov, is proposed with the type strain ACPA22T (=DSM 106290T=VKM Ac-2771T).

A novel Gram-stain-positive, aerobic, cocci-shaped actinobacterium, designated YIM 75000T, was isolated from a soil sample collected from a dry-hot river valley in Yunnan Province, P.R. China. Growth was observed at 10–45 °C (optimal 37 °C), 0–8% (w/v) NaCl (optimal at 0–3% NaCl) and pH 6.0–8.0 (optimal at pH 7.3). The peptidoglycan contained LL-diaminopimelic acid, glycine, glutamic acid as well as alanine and its type was A3γ with an LL-Dpm-Gly interpeptide bridge. The major cellular fatty acids (> 10%) were C16:0, Summed In Feature 3 (C16:1 ω6c/C16:1 ω7c) and C17:1 ω8c. The predominant menaquinone was MK-9(H4). The major whole-cell sugars contained rhamnose, ribose, arabinose and mannose. The DNA G+C content was 77.0 mol%. The 16S rRNA gene sequence similarities of strain YIM 75000T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain YIM 75000T together with the genus Motilibacter formed a distinct phylogenetic lineage within the phylum Actinobacteria, separating them from members of all orders. Strain YIM 75000T showed 73.4–73.7% average nucleotide identity and 19.5–19.7% digital DNA–DNA hybridization identity with the closely related genus Motilibacter. Based on the phenotypic, phylogenetic and chemotaxonomic data, it is proposed that the new isolate represents the nomenclature type of the novel species Vallicoccus soli gen. nov., sp. nov. (YIM 75000T = DSM 45377T = KCTC 49228T = CGMCC 1.13844T) which is the nomenclature type of the novel genus Vallicoccus gen. nov. within Vallicoccaceae fam. nov and Motilibacterales ord. nov in the phylum Actinobacteria. The family Vallicoccaceae fam. nov. and the order Motilibacterales (contains Vallicoccaceae fam. nov. and Motilibacteraceae Lee 2013) ord. nov. are formally proposed.

Strain KT0803T was isolated from coastal eutrophic surface waters of Helgoland Roads near the island of Helgoland, North Sea, Germany. The taxonomic position of the strain, previously known as ‘ Gramella forsetii ’ KT0803, was investigated by using a polyphasic approach. The strain was Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, oxidase- and catalase-positive, rod-shaped, motile by gliding and had orange–yellow carotenoid pigments, but was negative for flexirubin-type pigments. It grew optimally at 22–25 °C, at pH 7.5 and at a salinity between 2–3 %. Strain KT0803T hydrolysed the polysaccharides laminarin, alginate, pachyman and starch. The respiratory quinone was MK-6. Polar lipids comprised phosphatidylethanolamine, six unidentified lipids and two unidentified aminolipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and iso-C17 : 1ω7c, with smaller amounts of iso-C15 : 0 2-OH, C15 : 0, anteiso-C15 : 0 and C17 : 1ω6c. The G+C content of the genomic DNA was 36.6 mol%. The 16S rRNA gene sequence identities were 98.6 % with Gramella echinicola DSM 19838T, 98.3 % with Gramella gaetbulicola DSM 23082T, 98.1 % with Gramella aestuariivivens BG-MY13T and Gramella aquimixticola HJM-19T, 98.0 % with Gramella lutea YJ019T, 97.9 % with Gramella portivictoriae DSM 23547T and 96.9 % with Gramella marina KMM 6048T. The DNA–DNA relatedness values were 98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803T has been assigned to the genus Gramella , as Gramella forsetii sp. nov. The type strain is KT0803T (=DSM 17595T=CGMCC 1.15422T). An emended description of Gramella gaetbulicola Cho et al. 2011 is also proposed.

Gammaproteobacterial Reinekea spp. were detected during North Sea spring algae blooms in the years 2009-2012, with relative abundances of up to 16% in the bacterioplankton. Here, we explore the ecophysiology of 'R. forsetii' strain Hel1_31_D35 that was isolated during the 2010 spring bloom using (i) its manually annotated, high-quality closed genome, (ii) re-analysis of in situ data from the 2009-2012 blooms and (iii) physiological tests. High resolution analysis of 16S rRNA gene sequences suggested that 'R. forsetii' dominated Reinekea populations during these blooms. This was corroborated by retrieval of almost complete Hel1_31_D35 genomes from 2009 and 2010 bacterioplankton metagenomes. Strain Hel1_31_D35 can use numerous low-molecular weight substrates including diverse sugar monomers, and few but relevant algal polysaccharides such as mannan, α-glucans, and likely bacterial peptidoglycan. It oxidizes thiosulfate to sulfate, and ferments under anoxic conditions. The strain can attach to algae and thrives at low phosphate concentrations as they occur during blooms. Its genome encodes RTX toxin and secretion proteins, and in cultivation experiments Hel1_31_D35 crude cell extracts inhibited growth of a North Sea Polaribacter strain. Our data suggest that the combination of these traits make strain Hel1_31_D35 a versatile opportunist that is particularly competitive during spring phytoplankton blooms.

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Studying the physiology and genomics of cultured hydrolytic bacteria is a valuable approach to decipher the biogeochemical cycling of marine polysaccharides, major nutrients derived from phytoplankton and macroalgae. We herein describe the profound potential of Alteromonas sp. 76-1, isolated from alginate-enriched seawater at the Patagonian continental shelf, to degrade the algal polysaccharides alginate and ulvan. Phylogenetic analyses indicated that strain 76-1 might represent a novel species, distinguished from its closest relative (Alteromonas naphthalenivorans) by adaptations to their contrasting habitats (productive open ocean vs. coastal sediments). Ecological distinction of 76-1 was particularly manifested in the abundance of carbohydrate-active enzymes (CAZymes), consistent with its isolation from alginate-enriched seawater and elevated abundance of a related OTU in the original microcosm. Strain 76-1 encodes multiple alginate lyases from families PL6, PL7, PL17, and PL18 largely contained in two polysaccharide utilization loci (PUL), which may facilitate the utilization of different alginate structures in nature. Notably, ulvan degradation relates to a 126 Kb plasmid dedicated to polysaccharide utilization, encoding several PL24 and PL25 ulvan lyases and monomer-processing genes. This extensive and versatile CAZyme repertoire allowed substantial growth on polysaccharides, showing comparable doubling times with alginate (2 h) and ulvan (3 h) in relation to glucose (3 h). The finding of homologous ulvanolytic systems in distantly related Alteromonas spp. suggests CAZyme plasmids as effective vehicles for PUL transfer that mediate niche gain. Overall, the demonstrated CAZyme repertoire substantiates the role of Alteromonas in marine polysaccharide degradation and how PUL exchange influences the ecophysiology of this ubiquitous marine taxon.

To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.

Fungal strains are abundantly used throughout all areas of biotechnology and many of them are adapted to degrade complex biopolymers like chitin or lignocellulose. We therefore assembled a collection of 295 fungi from nine different habitats in Vietnam, known for its rich biodiversity, and investigated their cellulase, chitinase, xylanase and lipase activity. The collection consists of 70 isolates from wood, 55 from soil, 44 from rice straw, 3 found on fruits, 24 from oil environments (butchery), 12 from hot springs, 47 from insects as well as 27 from shrimp shells and 13 strains from crab shells. These strains were cultivated and selected by growth differences to enrich phenotypes, resulting in 211 visually different fungi. DNA isolation of 183 isolates and phylogenetic analysis was performed and 164 species were identified. All were subjected to enzyme activity assays, yielding high activities for every investigated enzyme set. In general, enzyme activity corresponded with the environment of which the strain was isolated from. Therefore, highest cellulase activity strains were isolated from wood substrates, rice straw and soil and similar substrate effects were observed for chitinase and lipase activity. Xylanase activity was similarly distributed as cellulase activity, but substantial activity was also found from fungi isolated from insects and shrimp shells. Seven strains displayed significant activities against three of the four tested substrates, while three degraded all four investigated carbon sources. The collection will be an important source for further studies. Therefore representative strains were made available to the scientific community and deposited in the public collection of the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig.

International audience; Polysaccharide degradation by heterotrophic microbes is a key process within Earth’s carbon cycle. Here, we use environmental proteomics and metagenomics in combination with cultivation experiments and biochemical characterizations to investigate the molecular details of in situ polysaccharide degradation mechanisms during microalgal blooms. For this, we use laminarin as a model polysaccharide. Laminarin is a ubiquitous marine storage polymer of marine microalgae and is particularly abundant during phytoplankton blooms. In this study, we show that highly specialized bacterial strains of the Bacteroidetes phylum repeatedly reached high abundances during North Sea algal blooms and dominated laminarin turnover. These genomically streamlined bacteria of the genus Formosa have an expanded set of laminarin hydrolases and transporters that belonged to the most abundant proteins in the environmental samples. In vitro experiments with cultured isolates allowed us to determine the functions of in situ expressed key enzymes and to confirm their role in laminarin utilization. It is shown that laminarin consumption of Formosa spp. is paralleled by enhanced uptake of diatom-derived peptides. This study reveals that genome reduction, enzyme fusions, transporters, and enzyme expansion as well as a tight coupling of carbon and nitrogen metabolism provide the tools, which make Formosa spp. so competitive during microalgal blooms.

Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many microorganisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named 'Streptomyces davawensis' JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species. As we also worked with another isolate of Streptomyces cinnabarinus JS 360, the producer of the cinnabaramides, we wanted to clarify the taxonomic position of the three isolates by using a polyphasic approach. After analysis of the 16S rRNA gene sequence, we found in total 23 species of the genus Streptomyces that showed a similarity higher than 98.5% to the three strains. We showed that 'S. davawensis' JCM 4913 and S. cinnabarinus DSM 40467 were very closely related but belong to two different species. Hence, we validate 'S. davawensis' as Streptomyces davaonensis sp. nov. with the type strain JCM 4913(T) (=DSM 101723(T)). In addition, the cinnabaramide producer can be clearly differentiated from S. davaonensis and this isolate is described as Streptomyces cinnabarigriseus sp. nov. with strain JS360(T) (=NCCB 100590(T) = DSM 101724(T)) as the type strain.

The roles of individual bacterioplankton species in the re-mineralization of algal biomass are poorly understood. Evidence from molecular data had indicated that a spring diatom bloom in the German Bight of the North Sea in 2009 was followed by a rapid succession of uncultivated bacterioplankton species, including members of the genera Ulvibacter, Formosa, Polaribacter (class Flavobacteria) and Reinekea (class Gammaproteobacteria). We isolated strains from the same site during the diatom bloom in spring 2010 using dilution cultivation in an artificial seawater medium with micromolar substrate and nutrient concentrations. Flow cytometry demonstrated growth from single cells to densities of 10(4) -10(6) cells ml(-1) and a culturability of 35%. Novel Formosa, Polaribacter and Reinekea strains were isolated and had 16S rRNA gene sequence identities of > 99.8% with bacterioplankton in spring or summer 2009. Genomes of selected isolates were draft sequenced and used for read recruitment of metagenomes from bacterioplankton in 2009. Metagenome reads covered 93% of a Formosa clade B, 91% of a Reinekea and 74% of a Formosa clade A genome, applying a ≥ 94.5% nucleotide identity threshold. These novel strains represent abundant bacterioplankton species thriving on coastal phytoplankton blooms in the North Sea.

Physical and chemical characteristics define oceanographic regions. The potential for a distinct biogeography of bacterial communities in these oceanic provinces was studied in epipelagic and upper mesopelagic water bodies of the North Atlantic Ocean by terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes and flow cytometry. Water samples from 67 degrees N to 34 degrees N along the 30 degrees W meridian contained epipelagic populations of Synechococcus in the north and Prochlorococcus in the south. Bacterial communities were generally more diverse in phototrophic layers above the pycnocline. Communities significantly differed in the epipelagic zone along the latitudinal transect through the different oceanic provinces and between the epipelagic and the upper mesopelagic zone. Differences in the T-RFLP patterns coincided well with differences in the physico-chemical conditions of the sampling sites. Changes in bacterial communities were traced to characteristic terminal restriction fragments (TRFs). In silico assignments of phylogenetic groups to TRFs, e.g. populations of high-light and low-light ecotypes of Prochlorococcus, supported our T-RFLP analysis of bacterial communities. Distinct bacterial communities in water bodies of the North Atlantic Ocean hosted different bacterial populations, which may serve as biological markers for oceanic provinces.

In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria , and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901 T ), an isolate from the green alga Acrosiphonia sonderi . F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.

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 G enomic E ncyclopedia of B acteria and A rchaea 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.

Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2T and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2T to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.

Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.

Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the GenomicEncyclopedia ofBacteria andArchaea project, we here describe the features of E. coli DSM 30083T together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083T in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli. Electronic supplementary material The online version of this article (doi:10.1186/1944-3277-9-2) contains supplementary material, which is available to authorized users.

The roles of individual bacterioplankton species in the re-mineralization of algal biomass are poorly understood. Evidence from molecular data had indicated that a spring diatom bloom in the German Bight of the North Sea in 2009 was followed by a rapid succession of uncultivated bacterioplankton species, including members of the genera Ulvibacter, Formosa, Polaribacter (class Flavobacteria) and Reinekea (class Gammaproteobacteria). We isolated strains from the same site during the diatom bloom in spring 2010 using dilution cultivation in an artificial seawater medium with micromolar substrate and nutrient concentrations. Flow cytometry demonstrated growth from single cells to densities of 10(4) -10(6) cells ml(-1) and a culturability of 35%. Novel Formosa, Polaribacter and Reinekea strains were isolated and had 16S rRNA gene sequence identities of99.8% with bacterioplankton in spring or summer 2009. Genomes of selected isolates were draft sequenced and used for read recruitment of metagenomes from bacterioplankton in 2009. Metagenome reads covered 93% of a Formosa clade B, 91% of a Reinekea and 74% of a Formosa clade A genome, applying a ≥ 94.5% nucleotide identity threshold. These novel strains represent abundant bacterioplankton species thriving on coastal phytoplankton blooms in the North Sea.

Flavobacteria are abundant in the North Sea, an epeiric sea on the continental shelf of Europe. However, this abundance has so far not been reflected by the number of strains in culture collections. In this study, Flavobacteria were isolated from pelagic and benthic samples, such as seawater, phytoplankton, sediment and its porewater, and from surfaces of animals and seaweeds on agar plates with a variety of carbon sources. Dilution cultivation with a new medium, incubation at low temperatures and with long incubation times, and colony screening by a Flavobacteria-Cytophagia-specific PCR detecting 16S rRNA gene sequences led to a collection of phylogenetically diverse strains. Two strains affiliated with Flam-meovirgaceae and seven strains affiliated with Cyclobacteriaceae, whereas within the Flavobacteriaceae 20 isolated strains presumably represented seven novel candidate genera and 355 strains affiliated with 26 of 80 validly described marine Flavobacteriaceae genera, based on a genus boundary of 95.0% 16S rRNA gene sequence identity. The majority of strains (276) affiliated with 37 known species in 16 genera (based on a boundary of 98.7% 16S rRNA gene sequence identity), whereas 79 strains likely represented 42 novel species in 22 established Flavobacteriaceae genera. Pigmentation, iridescence, gliding motility, agar lysis, and flexirubin as a chemical marker supported the taxonomy at the species level. This study demonstrated the culturability on solid medium of phylogenetically diverse Flavobacteria originating from the North Sea. (C) 2013 Elsevier GmbH. All rights reserved.