The familyErythrobacteraceae, belonging to the orderSphingomonadales, classAlphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera:Altererythrobacter,Croceibacterium,Croceicoccus,Erythrobacter,Erythromicrobium,PorphyrobacterandQipengyuania. As more species are identified, the taxonomic status of the familyErythrobacteraceaeshould be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the namesAlteraurantiacibacter,Altericroceibacterium,Alteriqipengyuania,Alteripontixanthobacter,Aurantiacibacter,Paraurantiacibacter,Parerythrobacter,Parapontixanthobacter,Pelagerythrobacter,TsuneonellaandPontixanthobacterare proposed. We reclassified all species ofErythromicrobiumandPorphyrobacteras species ofErythrobacter. This study is the first genomic-based study of the familyErythrobacteraceae, and will contribute to further insights into the evolution of this family.

The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes , and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed ( Laminaria japonica ). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria . Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22 ^T can completely degrade alginate. This work reveals that strain HZ22 ^T has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22 ^T are worth further research.

Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine Streptomyces is a valuable resource of bacterial secondary metabolites. In this study, 87 marine Streptomyces genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine Streptomyces were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine Streptomyces ranged from 16 to 84. Statistical analysis pointed out that phylotypes and ecotypes were both associated with SMBGCs distribution patterns. The Clade I and marine sediment-derived Streptomyces harbored more specific SMBGCs, which consisted of several common ones; whereas the Clade II and marine invertebrate-derived Streptomyces have more SMBGCs, acting as more plentiful resources for mining secondary metabolites. This study is beneficial for broadening our knowledge about SMBGC distribution patterns in marine Streptomyces and developing their secondary metabolites in the future.

Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12^T and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12^T and Za6a-17 were approximately 1.5–2.0 µm×0.5–0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5–3.0 % (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12^T and Za6a-17 was ubiquinone-8 (>97 %), and the major fatty acids were C_14 : 0, C_16 : 1ω7c and/or iso-C_15 : 0 2-OH, C_16 : 0 and C_17 : 1ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722^T (95.9 %). Strains Za6a-12^T and Za6a-17 could be differentiated from T. loyana CBMAI 722^T according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12^T and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12^T ( = CGMCC 1.12115^T = JCM 18482^T) is the type strain of this novel species.

A Gram-staining-negative, aerobic, non-spore-forming, coccoid to rod shaped bacteria with prosthecate and flagellum, designated as HSF6T, was isolated from deep seawater samples collected from the South China Sea at depth of 2.5 km and subjected to a polyphasic taxonomic investigation. Colonies of strain HSF6T were 1–2 mm in diameter, smooth, circular, convex and yellow. Strain HSF6T was found to grow at 15–37 °C (optimum, 25–35 °C), pH 5.0–9.5 (optimum, pH 7.0–7.5) and with 0–8 % (w/v) NaCl (optimum, 2 %). Chemotaxonomic analysis showed the predominant respiratory quinone of strains HSF6T were ubiquinone-10, and the major fatty acids were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The polar lipids were monoglycosyldiglyceride (MGDG), sulfo-quinovosyl diacylglycerol (SQDG), three unknown glycolipids (GL1–3) and five unknown lipids (L1–5). The DNA G+C content of strain HSF6T was determined to be 51.0 mol% with HPLC. The comparison of 16S rRNA gene sequence similarities show that strain HSF6T was related most closely to genus Parvularcula with similarity ranging from 91.0 to 91.8 %. The phylogenetic trees, using the 16S rRNA gene sequence, reconstructed with neighbour-joining, maximum-parsimony and maximum-likelihood methods showed that strain HSF6T constituted a separated branch in the family ‘ Parvularculaceae ’. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain HSF6T is clearly distinct from validly published genera. On the basis of these features, we propose strain HSF6T (=MCCC 1K03223T=KCTC 52486T) represents a novel species of a novel genus with the name Hyphococcus flavus gen. nov., sp. nov.

DNA-segment copy number variations (DSCNVs), such as deletions and duplications, are important sources of genomic structural variation. However, the types and sizes of DSCNVs, as well as their genome-wide distribution and potential functions, are poorly understood in wheat. Here, we identified 198 985 DSCNVs by investigating 491 genomes of common wheat and found that they account for 20% of the entire genome. Interestingly, approximately 38% of genes are linked to DSCNVs. The number of DSCNVs within each accession ranges from 47 366 to 96 342, and their total sizes vary from 421.3 to 1267.9 Mb. We found that 957 and 1304 DSCNVs have been favored by breeders in China and the United States, respectively. By conducting DSCNV-based genome-wide association studies for the principal components of plant developmental and yield-component traits, we identified 34 loci as directly or indirectly involved in controlling the formation of multiple traits. Notably, a newly discovered DSCNV covering TaFT-D1 is significantly associated with flowering time and other agronomic traits. Overall, our findings highlight the potential of DSCNVs to drive fundamental discoveries in plant science. The comprehensive DSCNV map and the DSCNV-associated genes will also facilitate future research efforts to improve wheat yield, quality, and adaptation.