Kangiella shandongensis sp. nov., a novel species isolated from saltern in Yantai, China.

A Gram-stain-negative, wheat, rod-shaped, non-motile, non-spore forming, and facultatively anaerobic bacterium strain, designated as PIT, was isolated from saline silt samples collected in saltern in Yantai, Shandong, China. Growth was observed within the ranges 4-45 °C (optimally at 33 °C), pH 6.0-9.0 (optimally at pH 7.0) and 1.0-11.0% NaCl (optimally at 3.0%, w/v). Strain PIT showed highest 16S rRNA gene sequence similarity to Kangiella sediminilitoris BB-Mw22T (98.3%) and Kangiella taiwanensis KT1T (98.3%). The major cellular fatty acids (> 10% of the total fatty acids) were iso-C15:0 (52.7%) and summed featured 9 (iso-C17:1ω9c/C16:0 10-methyl, 11.8%). The major polar lipids identified were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylglycerol. The major respiratory isoprenoid quinone was Q-8. The G + C content of the genomic DNA was 45.8%. Average Nucleotide Identity values between whole genome sequences of strain PIT and next related type strains supported the novel species status. Based on physiological, biochemical, chemotaxonomic characteristics and genomic analysis, strain PIT is considered to represent a novel species within the genus Kangiella, for which the name Kangiella shandongensis sp. nov. is proposed. The type strain is PIT (= KCTC 82509 T = MCCC 1K04352T).

Pseudaestuariivita rosea sp. nov., isolated from Acmaea sp., a marine mollusk.

A Gram-stain-negative, pink-pigmented, aerobic, non-motile and rod-shaped bacterium, designated as strain H15T, was isolated from Acmaea sp., collected from Weihai, Shandong Province, China. The novel isolate was able to grow at 4-37 °C (optimum 33 °C), pH 5.5-9.0 (optimum 7.0) and with 0.0-7.0% NaCl (optimum 4%, w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the strain belonged to the family Rhodobacteraceae and was associated to the type strain of Pseudaestuariivita atlantica (96.7%). Genome analysis showed that the genome size was 3,893,398 bp and the DNA G + C content obtained from the draft genome sequence was 56.7%. The secondary metabolites predicated that the strain H15T contained one cluster of lasso peptide, one cluster of bacteriocin, two clusters of terpene production, two clusters of homoserine lactone and one cluster of beta lactone. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between genome sequences of strain H15T and all the related strains compared were lower than 63.1, 72.0 and 19.7%, respectively. Based on the analysis of chemical components, the predominant cellular fatty acids were summed featured 8 (C18:1ω7c/ω6c, 46.1%), C20:1 ω7c (17.1%), the major polar lipids contained phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid and the predominant menaquinone was Q10. Therefore, the combined chemotaxonomic, phenotypic and phylogenetic data indicated that the strain was considered to represent a novel species of the genus Pseudaestuariivita and the name Pseudaestuariivita rosea sp. nov. was proposed for strain H15T (MCCC 1K04420T = KCTC 82505T).

Structure Characteristics, Biochemical Properties, and Pharmaceutical Applications of Alginate Lyases.

Alginate, the most abundant polysaccharides of brown algae, consists of various proportions of uronic acid epimers α-L-guluronic acid (G) and ß-D-mannuronic acid (M). Alginate oligosaccharides (AOs), the degradation products of alginates, exhibit excellent bioactivities and a great potential for broad applications in pharmaceutical fields. Alginate lyases can degrade alginate to functional AOs with unsaturated bonds or monosaccharides, which can facilitate the biorefinery of brown algae. On account of the increasing applications of AOs and biorefinery of brown algae, there is a scientific need to explore the important aspects of alginate lyase, such as catalytic mechanism, structure, and property. This review covers fundamental aspects and recent developments in basic information, structural characteristics, the structure-substrate specificity or catalytic efficiency relationship, property, molecular modification, and applications. To meet the needs of biorefinery systems of a broad array of biochemical products, alginate lyases with special properties, such as salt-activated, wide pH adaptation range, and cold adaptation are outlined. Withal, various challenges in alginate lyase research are traced out, and future directions, specifically on the molecular biology part of alginate lyases, are delineated to further widen the horizon of these exceptional alginate lyases.

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.

Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted.