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Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.

A taxonomic study was carried out of strain K7T, which was isolated from deep-sea water collected from the Indian Ocean. The bacterium was Gram-stain-negative, aerobic, oxidase-negative, catalase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0.5–10 % (optimum, 3 %), at a pH range of pH 6.0–10.0 (optimum, pH 7.0) and at temperatures of 10–40 °C (optimum, 28 °C). Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain K7T belonged to the family Flavobacteriaceae , with the high sequence similarities to the genera Mesonia (92.2 %–94.4 %), Salinimicrobium (91.9 %–93.2 %), Salegentibacter (92.1 %–92.6 %), Leeuwenhoekiella (92.1 %–92.3 %), Gramella (91.9 %–92.1 %) and Zunongwangia (91.8 %–92.1 %). The principal fatty acids were iso-C15 : 0 (28.4 %), iso-C15 : 1G (14.2 %), summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl; 11.6 %), iso-C17 : 0 3-OH (10.0 %) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 9.6 %). The G+C content of the chromosomal DNA was 35.8 mol%. The respiratory quinone was determined to be MK-6 (100 %). Phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipid and four unidentified lipids were detected. The combined genotypic and phenotypic data show that strain K7T represents a novel species of a novel genus, for which the name Paramesonia marina gen. nov., sp. nov. is proposed, with the type strain K7T (=MCCC 1A01093T=KCTC 52325T).

Four Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria (R-46770, R-48165T, R-50232 and R-50233) were isolated from intertidal sediment and water of the Westerschelde estuary between 2006 and 2012. Analysis of their 16S rRNA gene sequences revealed that the four strains form a separate cluster between validly described type strains of the genus Leeuwenhoekiella . DNA–DNA reassociation values of two representative strains (i.e. R-48165T and R-50232) of the new group with type strains of Leeuwenhoekiella species ranged from 18.7 to 56.6 %. A comparative genome analysis of the two strains and the type strains confirmed average nucleotide identity values from 75.6 to 94.4 %. The G+C contents of the genomic DNA of strains R-48165T and R-50232 were 37.80 and 37.83 mol%, respectively. The predominant cellular fatty acids of the four novel strains were summed feature 3 (i.e. C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The four new Leeuwenhoekiella -like strains grew with 0.5–12 % (w/v) NaCl, at pH 5.5–9.0 and displayed optimum growth between 20 and 30 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the four new strains represent a novel species of the genus Leeuwenhoekiella for which the name Leeuwenhoekiella aestuarii sp. nov. is proposed. The type strain is LMG 30908T (=R-48165T=CECT 9775T=DSM 107866T). Genome analysis of type strains of the genus Leeuwenhoekiella revealed a large number of glycosyl hydrolases, peptidases and carboxyl esterases per Mb, whereas the number of transporters per Mb was low compared to other bacteria. This confirmed the environmental role of Leeuwenhoekiella species as (bio)polymer degraders, with a specialization on degrading proteins and high molecular weight compounds. Additionally, the presence of a large number of genes involved in gliding motility and surface adhesion, and large numbers of glycosyl transferases per Mb confirmed the importance of these features for Leeuwenhoekiella species.

Polynyas are a key ecosystem for carbon cycling in the Antarctic Ocean due to the intensive primary production. Most of the knowledge regarding the bacterioplankton community in the Antarctic Ocean that is responsible for re-mineralization of fixed carbon comes from metagenomic analyses. Here, the extinction-dilution method was used to obtain representative heterotrophs from a polynya in the Amundsen Sea, Antarctica, and their biochemical potential for carbon re-mineralization were assessed. All 23 strains have close relatives belonging to type strains within the following genera (number of strains; % 16S rRNA gene sequence similarity): Bizionia (4; >97.8%), Leeuwenhoekiella (1; 96.2%), Pseudoalteromonas (14; >98.5%), Pseudomonas (1; 99.4%) and Sulfitobacter (3; 100%), which were also observed in 454 pyrosequencing-based analysis of 16S rRNA gene sequences of the polynya. Although sequence reads related to Polaribacter were the most common, Polaribacter strains could only be obtained from colonies cultured on agar plates. The strain of Leeuwenhoekiella showed a prominent ability in hydrolyzing diverse esters, amides, and glycosides while the strains of Pseudoalteromonas, Polaribacter, and Bizionia showed extracellular enzyme activities only on a narrow range of amides. The strains of Leeuwenhoekiella, Pseudoalteromonas, and Sulfitobacter utilized various labile carbon sources: carbohydrates, organic acids, amino acids, and peptides. The most frequent isolates, strains of Pseudoaltermonas, showed marked differences in terms of their potential to utilize different types of labile carbon sources, which may reflect high genomic diversity. The strains of Bizionia and Pseudomonas did not utilize carbohydrates. Unique biochemical properties associated with extracellular hydrolase activities and labile carbon utilization were revealed for dominant culturable heterotrophs which gives insights into their roles in active re-mineralization of fixed carbons in polynya.

A yellow-pigmented, Gram-staining-negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. The 16S rRNA gene sequence analysis demonstrated that it shared

The taxonomic status of a novel, heterotrophic, strictly aerobic, gliding and yellow-orange-pigmented bacterium (strain KMM 6264(T)), associated with the coral Palythoa, was determined. The 16S rRNA gene sequence analysis indicated that strain KMM 6264(T) clustered with the recognized species of the genus Leeuwenhoekiella of the family Flavobacteriaceae with 96.4-98.2 % sequence similarity. DNA-DNA reassociation levels between the isolate and the type strains of Leeuwenhoekiella species were 15-22 %. The DNA G+C content was 41.2 mol%. The phylogenetic evidence and the results of genomic and phenotypic analyses showed that the isolate should be classified as a member of a novel species of the genus Leeuwenhoekiella, for which the name Leeuwenhoekiella palythoae sp. nov. is proposed. The type strain is KMM 6264(T) (=KCTC 22020(T)=LMG 24856(T)).