Catenovulum maritimus sp. nov., a novel agarolytic gammaproteobacterium isolated from the marine alga Porphyra yezoensis Ueda (AST58-103), and emended description of the genus Catenovulum

Saccharobesus litoralis gen. nov., sp. nov., a novel alginate-degrading bacterium isolated from the surface of intertidal algal turf

A novel rod-shaped, Gram-stain-negative, strictly aerobic and alginate-degrading marine bacterium, designated CCB-QB4^T, was isolated from a surface of algal turf collected from a coastal area of Penang, Malaysia. The cells showed motility by a lateral flagellum. The rod-shaped cells formed long chains end-to-end. Phylogenetic analysis based on the 16S rRNA gene sequence of strain CCB-QB4^T showed 94.07, 92.69, 91.52 and 90.90 % sequence similarity to Algibacillus agarilyticus RQJ05^T, Catenovulum maritimum Q1^T, Catenovulum agarivorans YM01^T and Catenovulum sediminis D2^T, respectively. Strain CCB-QB4^T formed a cluster with A. agarilyticus RQJ05^T. Strain CCB-QB4^T was catalase-negative, oxidase-positive, and degraded agar, alginate, and starch. Cell growth was observed at 15-40 °C, at pH 7.0-10.0 and in the presence of 1-6 % (w/v) NaCl and glucose. The major fatty acids were summed feature 3 (C_16 : 1 ω7c/iso-C_15 : 0 2-OH), C_16 : 0 and C_18 : 1 ω7c. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified glycolipids, an unidentified phospholipid and unidentified lipid. The major respiratory quinone was ubiquinone-8. The genomic DNA G+C content was 46.7 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain CCB-BQ4^T represents a novel species in a new genus, for which the name Saccharobesus litoralis gen. nov., sp. nov. is proposed. The type strain is CCB-QB4^T (=JCM 33513^T=CCB-MBL 5008^T).

Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24

Ulvan is an important marine polysaccharide. Bacterial ulvan lyases play important roles in ulvan degradation and marine carbon cycling. Until now, only a small number of ulvan lyases have been characterized. Here, a new ulvan lyase, Uly1, belonging to polysaccharide lyase family 24 (PL24) from the marine bacterium Catenovulum maritimum, is characterized. The optimal temperature and pH for Uly1 to degrade ulvan are 40°C and pH 9.0, respectively. Uly1 degrades ulvan polysaccharides in the endolytic manner, mainly producing ΔRha3S, consisting of an unsaturated 4-deoxy-l-threo-hex-4-enopyranosiduronic acid and a 3-O-sulfated α-l-rhamnose. The structure of Uly1 was resolved at a 2.10-Å resolution. Uly1 adopts a seven-bladed β-propeller architecture. Structural and site-directed mutagenesis analyses indicate that four highly conserved residues, H128, H149, Y223, and R239, are essential for catalysis. H128 functions as both the catalytic acid and base, H149 and R239 function as the neutralizers, and Y223 plays a supporting role in catalysis. Structural comparison and sequence alignment suggest that Uly1 and many other PL24 enzymes may directly bind the substrate near the catalytic residues for catalysis, different from the PL24 ulvan lyase LOR_107, which adopts a two-stage substrate binding process. This study provides new insights into ulvan lyases and ulvan degradation. IMPORTANCE Ulvan is a major cell wall component of green algae of the genus Ulva. Many marine heterotrophic bacteria can produce extracellular ulvan lyases to degrade ulvan for a carbon nutrient. In addition, ulvan has a range of physiological bioactivities based on its specific chemical structure. Ulvan lyase thus plays an important role in marine carbon cycling and has great potential in biotechnological applications. However, only a small number of ulvan lyases have been characterized over the past 10 years. Here, based on biochemical and structural analyses, a new ulvan lyase of polysaccharide lyase family 24 is characterized, and its substrate recognition and catalytic mechanisms are revealed. Moreover, a new substrate binding process adopted by PL24 ulvan lyases is proposed. This study offers a better understanding of bacterial ulvan lyases and is helpful for studying the application potentials of ulvan lyases.

Marinifaba aquimaris gen. nov., sp. nov., a novel chitin-degrading gammaproteobacterium in the family Alteromonadaceae isolated from seawater of the Mariana Trench

A novel Gram-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative bacterium, designated strain SM1970^T, was isolated from a seawater sample collected from the Mariana Trench. Strain SM1970^T grew at 15-37 ^oC and with 1-5% (w/v) NaCl. It hydrolyzed colloidal chitin, agar and casein but did not reduce nitrate to nitrite. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1970^T formed a distinct lineage close to the genus Catenovulum within the family Alteromonadaceae, sharing the highest sequence similarity (93.6%) with type strain of Catenovulum maritimum but < 93.0% sequence similarity with those of other known species in the class Gammaproteobacteria. The major fatty acids of strain SM1970^T were summed feature 3 (C_16: 1 ω7c and/or C_16: 1 ω6c), C_16: 0 and summed feature 8 (C_18: 1 ω7c and/or C_18: 1 ω6c). The major polar lipids of the strain included phosphatidylethanolamine and phosphatidylglycerol and its main respiratory quinone was ubiquinone 8. The draft genome of strain SM1970^T consisted of 77 scaffolds and was 4,172,146 bp in length, containing a complete set of genes for chitin degradation. The average amino acid identity (AAI) values between SM1970^T and type strains of known Catenovulum species were 56.6-57.1% while the percentage of conserved proteins (POCP) values between them were 28.5-31.5%. The genomic DNA G + C content of strain SM1970^T was 40.1 mol%. On the basis of the polyphasic analysis, strain SM1970^T is considered to represent a novel species in a novel genus of the family Alteromonadaceae, for which the name Marinifaba aquimaris is proposed with the type strain being SM1970^T (= MCCC 1K04323^T = KCTC 72844^T).

Algibacillus agarilyticus gen. nov., sp. nov., isolated from the surface of the red algae Gelidium amansii

A novel Gram-stain-negative, strictly aerobic, coccoid and agar-hydrolysing bacterium, designated RQJ05^T, was isolated from the marine red algae Gelidium amansii collected from the coastal area of Rizhao, PR China. Cells of strain RQJ05^T were approximately 0.8-1.0×1.3-3.0 µm in size and motile by means of a polar flagellum. Growth occurred at 4-33 °C (optimum, 25-30 °C), pH 7.0-8.5 (optimum, pH 7.5-8.0) and in the presence of 1.0-7.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Strain RQJ05^T showed oxidase-positive and catalase-negative activities. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RQJ05^T formed a phylogenetic lineage with members of the family Alteromonadaceae and exhibited 16S rRNA gene sequence similarities of 92.6, 91.3, 90.2 and 90.1 % to Catenovulum maritimum Q1^T, Catenovulum agarivorans YM01^T, Paraphotobacterium marinum NSCS20N07D^T and Algicola sagamiensis B-10-31^T, respectively. The major cellular fatty acids of strain RQJ05^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_16 : 0 and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The major polar lipids of strain RQJ05^T were phosphatidylethanolamine, phosphatidylglycerol and two aminophospholipids. Strain RQJ05^T contained Q-8 as the major respiratory quinone. The genomic DNA G+C content was 39.0 mol%. On the basis of genotypic, phenotypic and phylogenetic evidence, strain RQJ05^T is presented as a representative of a novel species in a new genus, for which the name Algibacillus agarilyticus gen. nov., sp. nov. is proposed. The type strain is RQJ05^T (=KCTC 62846^T=MCCC 1H00352^T).

Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation

Identifying the roles played by individual heterotrophic bacteria in the degradation of high molecular weight (HMW) substrates is critical to understanding the constraints on carbon cycling in the ocean. At five sites in the Atlantic Ocean, we investigated the processing of organic matter by tracking changes in microbial community composition as HMW polysaccharides were enzymatically hydrolysed over time. During this investigation, we discovered that a considerable fraction of heterotrophic bacteria uses a newly-identified ‘selfish’ mode of substrate processing. We therefore additionally examined the balance of individual substrate utilisation mechanisms at different locations by linking individual microorganisms to distinct substrate utilisation mechanisms. Through FISH and uptake of fluorescently-labelled polysaccharides, ‘selfish’ organisms were identified as belonging to the Bacteroidetes, Planctomycetes and Gammaproteobacteria. ‘Sharing’ (extracellular enzyme producing) and ‘scavenging’ (non-enzyme producing) organisms predominantly belonged to the Alteromonadaceae and SAR11 clades, respectively. The extent to which individual mechanisms prevail depended on the initial population structure of the bacterial community at a given location and time, as well as the growth rate of specific bacteria. Furthermore, the same substrate was processed in different ways by different members of a pelagic microbial community, pointing to significant follow-on effects for carbon cycling.

Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda

A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1^T, was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1^T in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1^T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1^T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculumagarivorans sp. nov. is proposed. The type strain is HZ1^T (=MCCC 1H00174^T=KCTC 52476^T).