eThe 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 (ϳ7.5%) 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 HZ22T are worth further research. Members of the phylum Bacteroidetes, formerly also known as the Cytophaga-Flavobacteria-Bacteroides cluster, constitute one of the major groups of marine heterotrophic bacterioplankton (1, 2). They have been found in various marine habitats, including coastal sediments (3), coastal waters (4, 5), hydrothermal vents (6, 7), and open ocean waters (8-10). In previous studies, marine Bacteroidetes have been reported as important contributors to the utilization of biopolymers such as polysaccharides and proteins (2,(11)(12)(13)(14). As a result, marine Bacteroidetes are assumed to play an important role in the degradation of algae. Marine phytoplankton have been estimated to be responsible for about 50% of global net primary production (15). Polysaccharides constitute a substantial fraction of the primary production from marine phytoplankton. Algae can be an important source of polysaccharides. Brown seaweeds, a traditional and plentiful mariculture product in East Asia, make up a large proportion of the total biomass of algae and synthesize a wide variety of compounds, such as alginate, fucoidan, laminarin, and mannitol (16). Among these compounds, alginate has been assumed to be a potential source for bioethanol production (17-19).The genus Algibacter belongs...
A novel mesophilic, strictly anaerobic bacterium, strain BMT, was isolated from food industry wastewater. The cells were motile, non-spore-forming rods and stained Gram-negative. Growth of strain BMT was observed at 16–44 °C (optimum 37 °C) and pH 6.0–9.0 (optimum pH 7.5). The NaCl concentration range for growth was 0–8 % (optimum 1.5 %, w/v). Strain BMT was chemo-organotrophic, using a few sugars and amino acids as sole carbon and energy sources. The fermentation products from peptone-yeast extract broth were propionate, formate, acetate, ethanol and isovalerate. Indole, NH3 and H2S were produced from peptone. No respiratory quinones could be detected. The major fatty acids were iso-C15 : 0 (39.3 %), iso-C15 : 0 dimethyl acetal (10.1 %), anteiso-C15 : 0 (7.6 %), C14 : 0 (6.1 %) and C16 : 0 (5.6 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a number of unidentified aminoglycolipids, glycolipids and phospholipids. The DNA G+C content was 28.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain BMT was related to various genera of the family Clostridiaceae , and its closest relatives were Sporosalibacterium faouarense SOL3f37T (94.3 % 16S rRNA gene sequence similarity), Proteiniborus ethanoligenes GWT (92.1 %) and Clostridiisalibacter paucivorans 37HS60T (92.0 %). In recognition of its distinct phenotypic and genotypic characteristics, isolate BMT is proposed to represent a novel species of a new genus, Brassicibacter mesophilus gen. nov., sp. nov. The type strain of Brassicibacter mesophilus is BMT ( = JCM 16868T = DSM 24659T).
Two aerobic, Gram-negative, non-motile, non-sporulating, yellow-pigmented bacteria, strains TH92 T and TH91, were isolated from a hot spring located in Laibin, Guangxi, in the south-eastern geothermal area of China. The isolates grew at 40-77 6C (optimally at 70 6C) and at pH 6.0-9.5 (optimally at pH 7.5-8.0). Phylogenetic analysis of 16S rRNA gene sequences and levels of DNA-DNA relatedness together indicated that the new isolates represented a novel species of the genus Thermus with closest affinity to Thermus aquaticus, Thermus igniterrae and Thermus thermophilus. Compared with their closest relatives, strains TH92 T and TH91 were able to assimilate a wider range of carbohydrates, amino acids and organic acids as sole carbon sources for growth, such as lactose and melibiose. The new isolates had lower combined levels of C 16 : 0 and iso-C 16 : 0 compared with their closest relatives. On the basis of polyphasic taxonomic characterization, strains TH92 T and TH91 are considered to represent a single novel species of the genus Thermus, for which the name Thermus arciformis sp. nov. is proposed. The type strain is TH92 T (5CGMCC 1.6992 T 5JCM 15153 T ).
A bacterial strain, designated NS31-3 T , was isolated from the wastewater of a paper mill. Cells of the isolate were obligately anaerobic, non-pigmented, non-motile, Gram-negative, short rods (0.7-1.0¾1.4-2.5 mm).
A new agarase, AgaA CN41 , cloned from Vibrio sp. strain CN41, consists of 990 amino acids, with only 49% amino acid sequence identity with known -agarases. AgaA CN41 belongs to the GH50 (glycoside hydrolase 50) family but yields neoagarotetraose as the end product. AgaA CN41 was expressed and characterized.Agarase is a key enzyme that allows certain bacteria to degrade agar and is also an important enzyme for a variety of applications, e.g., in food and cosmetics (6, 9). According to their cleavage pattern, agarases are classified into ␣-and -agarases, which hydrolyze ␣-1,3 and -1,4 linkages of agarose, respectively (3). Agarases are also grouped into glycoside hydrolase (GH) families based on their amino acid sequence identities (8), e.g., GH16, GH50, and GH86 families are identified as -agarases and the GH96 family is identified as ␣-agarases. Agarases from different families have various catalytic domains and cleavage modes for agarose and, hence, different end products. The known GH50 agarases produce generally DP2 (neoagarobiose) or DP2 and DP4 (neoagarotetraose). Typically, the GH16 agarases yield DP4 as the main end product, while the GH86 agarases produce DP8 (neoagarooctaose) and DP6 (neoagarohexaose) (4).Currently, approximately 40 agarases have been characterized and deposited in the CAZy database (4). The majority are GH16 agarases, while a few are GH50 and GH86 agarases. Almost all agarase genes were previously cloned by constructing genomic libraries (see, e.g., references 5, 10, 11, and 14) or sequencing purified proteins followed by genomic DNA library screening or degenerate PCR (see, e.g., reference 2). Our goal was to find new agarases for industrial application by using simpler approaches. Here, we report the cloning of a novel GH50 agarase from Vibrio sp. strain CN41 by using homologybased cloning followed by SiteFinding PCR (17), a chromosome walking method to amplify the flanking sequences.A Vibrio strain, CN41, which formed depressions on agar plate surfaces, was isolated from Zhejiang coastal sediments at the East China Sea. The 16S rRNA gene amplified from genomic DNA of Vibrio sp. strain CN41 by using primers 27F and 1492R (1) had 99% identity with Vibrio azureus strain LC2-005T . The amino acid sequences of agarases from the CAZy database were aligned using the program ClustalW (18) to find conserved sequences for homology cloning. A phylogenetic tree (not shown) was constructed by MEGA 4.0, using the maximum-parsimony algorithm (16). Agarases clustered into distinct families revealed by the phylogenetic tree. Block Maker (7) was used to find conserved protein blocks in the GH16, GH50, and GH86 families. Degenerate primers for conserved protein blocks were then designed for each family by using the program COnsensus-DEgenerate
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