Brevibacillus marinus sp. nov., a thermophilic bacterium isolated from deep sea sediment in the South China Sea.

A novel thermophilic bacterium, designated SCSIO 07484T, was isolated from marine sediment sampled in the South China Sea. Growth occurred at 30-60 °C, pH 6.0-8.0 and in the presence of 0-3 % (w/v) NaCl. Cells of strain SCSIO 07484T were rod-shaped and flagellum-forming. No soluble pigment was observed. The phylogenetic analysis of the 16S rRNA gene sequences indicated that SCSIO 07484T belonged to the family Paenibacillaceae and clustered with members of the genus Brevibacillus in the phylogenetic trees with less than 96.2 % similarities. The cell wall contained meso-diaminopimelic acid. Whole-cell hydrolysates contained arabinose, glucose and ribose. The predominant menaquinone was MK-7. Major fatty acids were iso-C16 : 0, iso-C15 : 0, C16 : 0 and iso-C14 : 0. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine were its diagnostic polar lipids. The whole genome size of strain SCSIO 07484T was 4 079 826 bp with a DNA G+C content of 56.2 mol%, including one circular chromosome of 3 978392 bp and one plasmid of 101434 bp. Based on the polyphasic analysis of strain SCSIO 07484T, it is considered to represent a novel species of the genus Brevibacillus, for which the name Brevibacillus marinus sp. nov. is proposed with the type strain SCSIO 07484T (=DSM 106769T=CGMCC 1.15814T).

Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea.

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909T and SCSIO 52915T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909T and SCSIO 52915T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909T (=KCTC 49412T=CGMCC 1.13853T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915T (=KCTC 49411T=CGMCC 1.13852T), are proposed.

Autophagy Dually Induced by AMP Surplus and Oxidative Stress Enhances Hemocyte Survival and Bactericidal Capacity via AMPK Pathway in Crassostrea hongkongensis.

Crassostrea hongkongensis (Hong Kong oyster) is an ecologically and economically valuable shellfish endemic to South/Southeast Asia. Due to ocean acidification and warming waters, they have become increasingly vulnerable to invading microbes including Vibrio parahaemolyticus, a significant foodborne human pathogen. In recent years, outbreaks of V. parahaemolyticus have emerged as a perennial phenomenon in parts of the world, necessitating to better understand the biology of host-pathogen interactions in this under-examined marine invertebrate. Although an immunologically relevant autophagy apparatus has been identified in Crassostrea gigas, an evolutionarily close mollusk cousin, the precise mechanistic details of C. hongkongensis autophagy during V. parahaemolyticus infection are still wanting. Here, we compellingly demonstrated that in vivo V. parahaemolyticus challenge robustly triggered autophagic signaling in C. hongkongensis hemocytes peaking at 6 h post-infection, which subsequently promoted bacterial clearance and dampened premature apoptosis. Simultaneously, a large surplus of adenosine monophosphate (AMP) and elevations in reactive oxygen species (ROS, specifically mitochondrial O2 - and cellular H2O2) formation were observed post-infection. Extrinsically applied AMP and ROS could synergistically induce AMP-activated protein kinase (AMPK) phosphorylation to stimulate downstream autophagic events. V. parahaemolyticus infection-induced autophagy was pharmacologically shown to be AMPK-dependent in vivo. Overall, our results establish autophagy as a crucial arm of host defense against Vibrio infections in mollusks, and provide new insights into the underappreciated roles of ROS and AMP as co-regulators of autophagy.

Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments.

A novel marine actinobacterium, strain SCSIO 58843T, was isolated from the sediment sample collected from the South China Sea. Strain SCSIO 58843T was Gram-stain-positive, aerobic and rod shaped. The whole-cell hydrolysis of amino acids contained dd-DAP, alanine, glutamic acid, glycine and aspartic acid. The main menaquinone was MK-9(H8). The major fatty acids were C17 : 1 ω8c and C17 : 0. The major phospholipids were diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phospatidylcholine (PC) and phosphatidylinositolmannoside (PIM). The G+C content of the genomic DNA was 72.5 %. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 58843T formed a new lineage in the family Iamiaceae and had the highest similarity of 93.8 % with Iamia majanohamensis DSM 19957T. Strain SCSIO 58843T can be distinguished from these known genera in the family Iamiaceae by polyphasic data analyses, and represents a novel genus and novel species, for which Actinomarinicola tropica gen. nov., sp. nov is proposed with the type strain SCSIO 58843T(=KCTC 49408T=CGMCC 1.17503T).

Longirhabdus pacifica gen. nov., sp. nov., isolated from a deep-sea hydrothermal sediment in the West Pacific Ocean.

A novel Gram-stain-negative bacterium, designated as SCSIO 06110T, was isolated from a deep-sea sediment of the West Pacific Ocean. Cells were 0.5-0.8 µm in width and 3.0-4.0 µm in length, spore-forming, rod-shaped with peritrichous flagella. Positive for catalase and urease, negative for oxidase and nitrate reduction. Growth occurred at 15-37 °C, pH 6-9 and 1-5 % (w/v) NaCl, with optimum growth at 28 °C, pH 7 and 3 % (w/v) NaCl. MK-7 was the only menaquinone. The strain possessed diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids. Iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 were the major fatty acids. The novel isolate clustered with genera in the family Paenibacillaceae, but formed a separated branch with the closest relative Chengkuizengella sediminis J15A17T (91.1 % sequence similarity) when compared in a phylogenetic analysis of 16S rRNA gene sequences. The DNA G+C content of strain SCSIO 06110T was 38.5 mol%. Based on the polyphasic data presented, a new genus, Longirhabdus gen. nov., is proposed in the family Paenibacillaceae with the type species Longirhabdus pacifica sp. nov. and the type strain SCSIO 06110T (=DSM 105158T=CGMCC 1.16550T).

Staphylospora marina gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae, isolated from a deep-sea hydrothermal vent in the Pacific Ocean.

A novel bacterium, designated SCSIO 07575T, was isolated from a deep-sea hydrothermal sediment sample collected from the western Pacific Ocean. Growth at 65 °C was observed, but not at 70 °C or below 37 °C. The optimum conditions for growth were at 55-65 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Strain SCSIO 07575T showed filamentous growth. Unstable formation of white aerial mycelia was observed, which disappeared after several times' subculture. Abundant substrate mycelia were observed with grape-like spores. No soluble pigment was observed. Phylogenetic analysis of 16S rRNA gene sequences showed that SCSIO 07575T belonged to the family Thermoactinomycetaceae and formed a distinct clade in the phylogenetic tree. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose, xylose, glucose and galactose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and two unidentified phospholipids. The predominant menaquinone was MK-7. Major fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C16 : 0. Based on the whole genome sequence analysis, the genome size was 2 751 094 bp with a DNA G+C value of 57.2 mol%, including one circular chromosome and one plasmid. On the basis of polyphasic data, strain SCSIO 07575T represented a novel species of a new genus within the family Thermoactinomycetaceae, for which the name Staphylospora gen. nov. is proposed with the type species Staphylospora marina sp. nov. and the type strain SCSIO 07575T (=DSM 106793T=CGMCC 1.15879T).

Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment.

A novel mesophilic marine actinobacterial strain, designated as SCSIO 08198T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-positive, rod-shaped and salmon pink in colour. Good growth occurred on marine agar with 1-5 % (w/v) NaCl and incubation at 28 °C for more than a fortnight. Sensitive to short ultraviolet radiation. Analysis of 16S rRNA gene sequences revealed that strain SCSIO 08198T had the highest similarity of 97.2 % to Rubrobacter radiotolerans DSM 5868T, and loosely related (<94.2 %) to all other species in the genus Rubrobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the novel isolate shared a lineage with members of the genus Rubrobacter. The total cellular fatty acid profile was dominated by C16 : 0 12-methyl. MK-8 was the main menaquinone. The peptidoglycan type was A3α (l-Lys-l-Ala). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. Based on the whole genome sequence analysis, the genome size is 3 078 689 bp with DNA G+C value of 63.8 mol%, including one circular chromosome and two plasmids. Based on these polyphasic data, a new species, Rubrobacterindicoceani sp. nov., is proposed, with the type strain SCSIO 08198T (=DSM 105148T=CGMCC 1.16398T).

Effects of several amendments on rice growth and uptake of copper and cadmium from a contaminated soil.

Heavy metals in variable charge soil are highly bioavailable and easy to transfer into plants. Since it is impossible to completely eliminate rice planting on contaminated soils, some remediation and mitigation techniques are necessary to reduce metal bioavailability and uptake by rice. This pot experiment investigated the effects of seven amendments on the growth of rice and uptake of heavy metals from a paddy soil that was contaminated by copper and cadmium. The best results were from the application of limestone that increased grain yield by 12.5-16.5 fold, and decreased Cu and Cd concentrations in grain by 23.0%-50.4%. Application of calcium magnesium phosphate, calcium silicate, pig manure, and peat also increased the grain yield by 0.3-15.3 fold, and effectively decreased the Cu and Cd concentrations in grain. Cd concentration in grain was slightly reduced in the treatments of Chinese milk vetch and zinc sulfate. Concentrations of Cu and Cd in grain and straw were dependent on the available Cu and Cd in the soils, and soil available Cu and Cd were significantly affected by the soil pH.

[Effects of soil water status on gas exchange of peanut and early rice leaves].

The gas exchange characteristics of peanut and early rice leaves were investigated in experimental plots under different soil water conditions over a long growth period. The results showed that at the branching stage of peanut, the stomatal conductance (Gs) and transpiration rate (Tr) decreased slightly under mild and moderate soil water stress, while the net photosynthetic rate (Pn) and leaf water use efficiency (WUE) increased. The Gs/Tr ratio also increased under mild water stress, but decreased under moderate water stress. At podding stage, the Gs, Tr, Gs/Tr ratio and Pn decreased, while WUE increased significantly under mild and moderate water stress. The peanut was suffered from water stress at its pod setting stage. At the grain filling stage of early rice, the Gs, Tr and Gs/Tr ratio fluctuated insignificantly under mild and moderate water stress, while Pn and WUE increased significantly, with an increase in grain yield under mild water stress. It's suggested that the combination of Gs and Gs/Tr ratio could be a reference index for crop water stress, namely, crops could be hazarded by water stress when Gs and Gs/Tr decreased synchronously.