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Chemical investigation on the aqueous extract of Dendrobium aphyllum led to the isolation of thirty-one constituents with structures identified by analysis of the extensive spectroscopic data (1D/2D NMR, MS, UV, and ECD), including previously undescribed two bibenzyls, one furfural, and one phenolic acid, namely trigonopol D (1), trigonopol C (2), dendrofunan A (10), and 6-(4-hydroxy-3-methoxyphenyl)-3,6-dioxohexyl acetate (30), respectively, as well as twenty-seven known ones. Among them, there were one new natural product (11), seven compounds (6-7, 9, 12, 20, 28, 31) described from the genus Dendrobium for the first time, and fifteen compounds (8, 13-17, 19, 21-27, 29) isolated from D. aphyllum for the first time. Further, the antioxidant and anti-inflammatory potentials of fifteen compounds (4-5, 8, 11-12, 14-19, 22, 24, 26, and 29) with significant scavenging capacities against DPPH and hydroxyl radicals, and virtual docking activities inhibiting COX-2 and 5-LOX, respectively. Our study may draw the attention of medicinal plant taxonomists and supply potential quality markers for discrimination of D. aphyllum from other species in Dendrobium genus., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Alginate oligosaccharides (AOS), products of alginate degradation by endotype alginate lyases, possess favorable biological activities and have broad applications. Although many have been reported, alginate lyases with homogeneous AOS products and secretory production by an engineered host are scarce. Herein, the alginate lyase AlyC7 from Vibrio sp. C42 was characterized as a trisaccharide-producing lyase exhibiting high activity and broad substrate specificity. With PelB as the signal peptide and 500 mM glycine as the additive, the extracellular production of AlyC7 in Escherichia coli reached 1122.8 U/mL after 27 h cultivation in Luria-Bertani medium. The yield of trisaccharides from sodium alginate degradation by the produced AlyC7 reached 758.6 mg/g, with a purity of 85.1%. The prepared AOS at 20 μg/mL increased the root length of lettuce, tomato, wheat, and maize by 27.5%, 25.7%, 9.7%, and 11.1%, respectively. This study establishes a robust foundation for the industrial and agricultural applications of AlyC7.

The human central nervous system (CNS) has a limited capacity for regeneration and repair, as many other organs do. Partly as a result, neurological diseases are the leading cause of medical burden globally. Most neurological disorders cannot be cured, and primary treatments focus on managing their symptoms and slowing down their progression. Cell therapy for neurological disorders offers several therapeutic potentials and provides hope for many patients. Here we provide a general overview of cell therapy in neurological disorders such as Parkinson's disease (PD), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), Wilson's disease (WD), stroke and traumatic brain injury (TBI), involving many forms of stem cells, including embryonic stem cells and induced pluripotent stem cells. We also address the current concerns and perspectives for the future. Most studies for cell therapy in neurological diseases are in the pre-clinical stage, and there is still a great need for further research to translate neural replacement and regenerative therapies into clinical settings.

Importance: Although Xanthomonas oryzae pv. oryzae ( Xoo ) has been found to be a bacterial pathogen causing bacterial leaf blight in rice for many years, the molecular mechanisms of the rice- Xoo interaction has not been fully understood. In this study, we found that XanFur of Xoo is a novel ferric uptake regulator (Fur) protein conserved among major pathogenic Xanthomonas species. XanFur is required for the virulence of Xoo in rice, and likely involved in regulating the virulence determinants of Xoo . The expression of xanfur is induced by H 2 O 2 , and positively regulated by the global transcriptional regulator Clp. Our results reveal the function and regulation of the novel virulence-related Fur protein XanFur in Xoo, providing new insights into the interaction mechanisms of rice- Xoo ., Competing Interests: The authors declare no conflict of interest.

A new tetrahydroimidazopyridine named butyl (5 R ,6 R ,7 S ,8 S )-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2- a ]pyridine-2-carboxylate( 1 ), together with eight known compounds ( 2 - 9 ), were isolated from the fermentation broth of a marine-derived fungus Paraconiothyrium sp. YK-03. Their chemical structures were elucidated by extensive analysis of one-dimensional and two-dimensional NMR spectroscopy, HR-ESIMS and optical rotation. Among these compounds, compound 1 represented a rare tetrahydroimidazopyridine, and compounds 2 - 7 were isolated from the Paraconiothyrium species for the first time. A plausible biosynthetic pathway for compound 1 was proposed.

Three undescribed santalane-type sesquiterpenoids (parasantalenoic acids A-C) and two undescribed epimeric isobenzofuranones (paraphthalides A and B) were isolated from cultures of the marine mud-associated fungus Paraconiothyrium sporulosum YK-03. Their structures were elucidated by analysis of the extensive spectroscopic and crystal X-ray diffraction data, combined with ECD calculations and comparison. Santalane-type sesquiterpenoids have been firstly found in the Paraconiothyrium species. Parasantalenoic acids A-C represent three rare polyhydroxylated santalane-type sesquiterpenoid carboxylic acids, and parasantalenoic acid A represents the first example of 2-chlorinated santalane-type sesquiterpenoid. A plausible biosynthetic pathway for parasantalenoic acids A-C was proposed. Additionally, the anti-neuroinflammatory activities of parasantalenoic acids A-C were investigated by evaluating their inhibitory effects on nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated BV-2 microglia cells. Among them, parasantalenoic acid C showed significant anti-neuroinflammatory activity with an inhibition of 86.45 ± 2.45% at 10 μM., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

A Gram-stain-negative, aerobic, flagellated, and long rod-shaped bacterium, designated strain SM1973 T , was isolated from an intertidal sediment sample collected from the coast of Qingdao, PR China. Strain SM1973 T grew at 15-37 °C and with 0-5.5 % NaCl. It reduced nitrate to nitrite and hydrolysed aesculin but did not hydrolyse casein and gelatin. The strain showed the highest 16S rRNA gene sequence similarity (98.2 %) to the type strain of Spartinivicinus ruber . The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM1973 T clustered with S. ruber , forming a separate lineage within the family Zooshikellaceae . The major cellular fatty acids were summed feature 3 (C 16 : 1 ω 7 с and/or C 16 : 1 ω 6 с ) and C 16 : 0 . The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The main respiratory quinone was ubiquinone-9. The genomic DNA G+C content of strain SM1973 T was 40.4 mol%. Based on the polyphasic evidence presented in this paper, strain SM1973 T is considered to represent a novel species within the genus Spartinivicinus , for which the name Spartinivicinus marinus sp. nov. is proposed. The type strain is SM1973 T (=MCCC 1K04833 T =KCTC 72846 T ).

Buckwheat is an important crop which originated in China and spread widely across Eurasia. However, exactly where in China domestication took place remains controversial. Archaeological and palynological records suggest a longer cultivation history of buckwheat in northern China than in southwestern China, but this conflicts with phylogenetic evidence implicating southwestern China as the centre of origin and diversity of buckwheat. We investigate alternative methodologies for inferring the occurrence of buckwheat cultivation and suggest that relative abundance could provide a reliable measure for distinguishing between wild and cultivated buckwheat in both present-day and fossil samples. Approximately 12 800-yr palaeoecological record shows that Fagopyrum pollen occurred only infrequently before the early Holocene. As southwestern China entered the early agricultural period, c. 8000-7000 yr ago, a slight increase in abundance of Fagopyrum pollen was observed. Approximately 4000 yr ago, concurrent with the Pu minority beginning to develop dry-land agriculture, the abundance of Fagopyrum pollen increased significantly, suggesting the cultivation of this crop. Fagopyrum pollen rose to a maximum value c. 1270 yr ago, suggesting an intensification of agricultural activity. These findings fill a gap in the Fagopyrum pollen record in southwestern China and provide new indications that early cultivation may have occurred in this region., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)

Diaminopimelic acid (DAP) is a unique component of the cell wall of Gram-negative bacteria. It is also an important component of organic matter and is widely utilized by microbes in the world's oceans. However, neither DAP concentrations nor marine DAP-utilizing microbes have been investigated. Here, DAP concentrations in seawater were measured and the diversity of marine DAP-utilizing bacteria and the mechanisms for their DAP metabolism were investigated. Free DAP concentrations in seawater, from surface to a 5,000 m depth, were found to be between 0.61 μM and 0.96 μM in the western Pacific Ocean. DAP-utilizing bacteria from 20 families in 4 phyla were recovered from the western Pacific seawater and 14 strains were further isolated, in which Pseudomonadota bacteria were dominant. Based on genomic and transcriptomic analyses combined with gene deletion and in vitro activity detection, DAP decarboxylase (LysA), which catalyzes the decarboxylation of DAP to form lysine, was found to be a key and specific enzyme involved in DAP metabolism in the isolated Pseudomonadota strains. Interrogation of the Tara Oceans database found that most LysA-like sequences (92%) are from Pseudomonadota , which are widely distributed in multiple habitats. This study provides an insight into DAP metabolism by marine bacteria in the ocean and contributes to our understanding of the mineralization and recycling of DAP by marine bacteria. IMPORTANCE DAP is a unique component of peptidoglycan in Gram-negative bacterial cell walls. Due to the large number of marine Gram-negative bacteria, DAP is an important component of marine organic matter. However, it remains unclear how DAP is metabolized by marine microbes. This study investigated marine DAP-utilizing bacteria by cultivation and bioinformational analysis and examined the mechanism of DAP metabolism used by marine bacteria. The results demonstrate that Pseudomonadota bacteria are likely to be an important DAP-utilizing group in the ocean and that DAP decarboxylase is a key enzyme involved in DAP metabolism. This study also sheds light on the mineralization and recycling of DAP driven by bacteria.

Bacterial leaf blight caused by Gram-negative pathogen Xanthomonas oryzae pv. oryzae ( Xoo ) is one of the most destructive bacterial diseases on rice. Due to the resistance, toxicity and environmental issues of chemical bactericides, new biological strategies are still in need. Although peptaibols produced by Trichoderma spp. can inhibit the growth of several Gram-positive bacteria and plant fungal pathogens, it still remains unclear whether peptaibols have anti- Xoo activity to control bacterial leaf blight on rice. In this study, we evaluated the antibacterial effects of Trichokonins A (TKA), peptaibols produced by Trichoderma longibrachiatum SMF2, against Xoo . The in vitro antibacterial activity analysis showed that the growth of Xoo was significantly inhibited by TKA, with a minimum inhibitory concentration of 54 μg/mL and that the three TKs in TKA all had remarkable anti- Xoo activity. Further inhibitory mechanism analyses revealed that TKA treatments resulted in the damage of Xoo cell morphology and the release of intracellular substances, such as proteins and nucleic acids, from Xoo cells, suggesting the damage of the permeability of Xoo cell membrane by TKA. Pathogenicity analyses showed that the lesion length on rice leaf was significantly reduced by 82.2% when treated with 27 μg/mL TKA. This study represents the first report of the antibacterial activity of peptaibols against a Gram-negative bacterium. Thus, TKA can be of a promising agent in controlling bacterial leaf blight on rice., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Zhang, Sun, Su, Li, Kun-Liu, Zhang, Chen, Cao and Song.)

Oxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)-2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH 3 via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria., (© 2022. The Author(s).)

A Gram-stain-negative, aerobic, flagellated and rod-shaped bacterium, designated strain SM2107 T , was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM2107 T grew at 4-40 °C and with 0-10.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed casein, gelatin, chitin and DNA. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM2107 T , together with Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense , formed a separate clade, having the highest similarity to the type strain of Rheinheimera tuosuensis (98.3%). The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and the major cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ), C 16 : 0 , C 17 : 1 ω 8 с and summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ). The only respiratory quinone was Q-8. The genomic DNA G+C content of strain SM2107 T was 48.8 %. The digital DNA-DNA hybridization values between strain SM2107 T and type strains of Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense were 41.16, 37.70 and 31.80 %, while the average amino acid identity values between them were 87.59, 86.76 and 83.64 %, respectively. Based on the polyphasic evidence presented in this study, strain SM2107 T was considered to represent a novel species within the genus Arsukibacterium , for which the name Arsukibacterium indicum was proposed. The type strain is SM2107 T (=MCCC M24986 T =KCTC 82921 T ). Moreover, the transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. (type strain TS-T4 T =CGMCC 1.12461 T =JCM 19264 T ) and Arsukibacterium perlucidum comb. nov. (type strain BA131 T =LMG 23581 T =CIP 109200 T ) is also proposed.

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated strain SM 2104 T , was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM 2104 T grew at 10-37 °C (optimum at 25 °C), and with 1.0-9.0% (w/v, optimum with 2-4%) NaCl. It hydrolyzed starch, tween 80 and gelatin but did not reduced nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM 2104 T was affiliated with the genus Alteromonas, sharing the highest 16S rRNA gene sequence similarities with type strains of Alteromonas flava (97.5%) and Alteromonas facilis (97.4%) and forming a distinct clade together with the two Alteromonas species. The digital DNA-DNA hybridization and average nucleotide identity values between strain SM 2104  T and type strains of Alteromonas flava and Alteromonas facilis were below 14.5%, and 71.0%, respectively. The major fatty acids of strain SM 2104 T were summed feature 3 (C 16:1 ω6c/C 16:1 ω7c), C 16:0 and summed feature 8 (C 18:1 ω7c/C 18:1 ω6c). The major polar lipids of strain SM 2104 T were phosphatidylethanolamine and phosphatidylglycerol and the only respiratory quinone of strain SM 2104 T was ubiquinone-8. The genomic DNA G + C content of strain SM 2104 T was 48.0%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic analyses presented in this study, strain SM 2104 T is considered to represent a novel species within the genus Alteromonas, for which the name Alteromonas oceansediminis sp. nov. is proposed. The type strain is SM 2104 T (= CCTCC AB 2021121 T  = KCTC 82867 T )., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Introduction: To analyze the clinicopathological characteristics, immunohistochemistry, genotyping and prognosis of patients in the multicenter GIST data in Inner Mongolia, China., Methods: Retrospective analysis was performed on GIST data from January 2013 to January 2018 in Inner Mongolia. Descriptive statistics were used to analyze the clinical characteristics of GIST patients. The Chi-square test was performed on the modified NIH criteria by age distribution, and Kaplan-Merie method was used for survival analysis., Results: A total of 804 patients were included in the GIST database in Inner Mongolia, with a male to female ratio of 1.1102:1. The most common location was the gastric (465). Mitotic count ≤5/50HPFs was found in 67.3 % patients. There were 276 patients with tumor diameter of 2-5 cm and 354 patients with tumor diameter of 5.1-10 cm.The modified NIH criteria was mainly of intermediate risk (210) and high risk (342). The recurrence and metastasis of patients were related to the tumor location, mitotic index, tumor size, and modified NIH criteria. All patients were followed up for 1-10 years, in which 63.1 % of them were followed up for at least three years. The 3-year survival rates of patients with modified NIH criteria of very low risk, low risk, intermediate risk, and high risk were 100 %, 100 %, 100 %, and 96.3 %, respectively., Conclusions: The incidence of GIST in middle-aged and elder people in Inner Mongolia is high, and the long-term prognosis of patients after surgical treatment is good, which can objectively reflect the incidence, diagnosis and treatment of GIST in Inner Mongolia., Competing Interests: Declaration of competing interest A conflict of interest occurs when an individual's objectivity is potentially compromised by a desire for financial gain, prominence, professional advancement or a successful outcome. ASJSUR Editors strive to ensure that what is published in the Journal is as balanced, objective and evidence-based as possible. Since it can be difficult to distinguish between an actual conflict of interest and a perceived conflict of interest, the Journal requires authors to disclose all and any potential conflicts of interest., (Copyright © 2021. Published by Elsevier Taiwan LLC.)

Bovine bone is rich in collagen and is a good material for collagen peptide preparation. Although thermolysin-like proteases (TLPs) have been applied in different fields, the potential of TLPs in preparing bioactive collagen peptides has rarely been evaluated. Here, we characterized a thermophilic TLP, A69, from a hydrothermal bacterium Anoxybacillus caldiproteolyticus 1A02591, and evaluated its potential in preparing bioactive collagen peptides. A69 showed the highest activity at 60 °C and pH 7.0. We optimized the conditions for bovine bone collagen hydrolysis and set up a process with high hydrolysis efficiency (99.4%) to prepare bovine bone collagen peptides, in which bovine bone collagen was hydrolyzed at 60 °C for 2 h with an enzyme-substrate ratio of 25 U/g. The hydrolysate contained 96.5% peptides that have a broad molecular weight distribution below 10000 Da. The hydrolysate showed good moisture-retention ability and a high hydroxyl radical (•OH) scavenging ratio of 73.2%, suggesting that the prepared collagen peptides have good antioxidative activity. Altogether, these results indicate that the thermophilic TLP A69 has promising potential in the preparation of bioactive collagen peptides, which may have potentials in cosmetics, food and pharmaceutical industries. This study lays a foundation for the high-valued utilization of bovine bone collagen.

Bacterial polar flagella, comprised of flagellin, are essential for bacterial motility. Pseudoalteromonas sp. strain SM9913 is a bacterium isolated from deep-sea sediments. Unlike other Pseudoalteromonas strains that have a long polar flagellum, strain SM9913 has an abnormally short polar flagellum. Here, we investigated the underlying reason for the short flagellum and found that a single-base mutation was responsible for the altered flagellar assembly. This mutation leads to the fragmentation of the flagellin gene into two genes, PSM_A2281 , encoding the core segment and the C-terminal segment, and PSM_A2282 , encoding the N-terminal segment, and only gene PSM_A2281 is involved in the production of the short polar flagellum. When a chimeric gene of PSM_A2281 and PSM_A2282 encoding an intact flagellin, A2281::82, was expressed, a long polar flagellum was produced, indicating that the N-terminal segment of flagellin contributes to the production of a polar flagellum of a normal length. Analyses of the simulated structures of A2281 and A2281::82 and that of the flagellar filament assembled with A2281::82 indicate that due to the lack of two α-helices, the core of the flagellar filament assembled with A2281 is incomplete and is likely too weak to support the stability and movement of a long flagellum. This mutation in strain SM9913 had little effect on its growth and only a small effect on its swimming motility, implying that strain SM9913 can live well with this mutation in natural sedimentary environments. This study provides a better understanding of the assembly and production of bacterial flagella. IMPORTANCE Polar flagella, which are essential organelles for bacterial motility, are comprised of multiple flagellin subunits. A flagellin molecule contains an N-terminal segment, a core segment, and a C-terminal segment. The results of this investigation of the deep-sea sedimentary bacterium Pseudoalteromonas sp. strain SM9913 demonstrate that a single-base mutation in the flagellin gene leads to the production of an incomplete flagellin without the N-terminal segment and that the loss of the N-terminal segment of the flagellin protein results in the production of a shortened polar flagellar filament. Our results shed light on the important function of the N-terminal segment of flagellin in the assembly and stability of bacterial flagellar filament.

Pelagovum pacificum SM1903 T , belonging to a novel genus of the family Rhodobacteraceae, was isolated from the surface seawater of the Mariana Trench. Here, we report the first complete genome sequence of the novel genus Pelagovum. The genome of strain SM1903 T consists of a circular chromosome of 4,040,866 bp and two plasmids of 41,363 bp and 9705 bp, respectively. Gene annotation and metabolic pathway analyses showed that strain SM1903 T possesses a series of genes related to adaptation to marine oligotrophic environments, which are involved in utilization of aromatic compounds, allantoin, and alkylphosphonate, and second messenger signaling in response to the oligotrophic stress. This strain also contains a variety of genes involved in coping with other stresses including osmotic stress, oxidative stress, cold shock, and heat shock. These features would assist this strain to survive under the natural nutrient limitation and other stresses from the environment. The genome of strain SM1903 T of the novel genus Pelagovum would deepen our knowledge on marine bacterioplankton and their adaption strategies to marine oligotrophic environments., (Copyright © 2021. Published by Elsevier B.V.)

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 o C 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 ).

Protease-producing bacteria play key roles in the degradation of marine organic nitrogen. Although some deep-sea bacteria are found to produce proteases, there has been no report on protease-secreting Anoxybacillus from marine hydrothermal vent regions. Here, we analyzed the diversity and functions of the proteases, especially the extracellular proteases, of Anoxybacillus caldiproteolyticus 1A02591, a protease-secreting strain isolated from a deep-sea hydrothermal vent sediment of the East Pacific Ocean. Strain 1A02591 is a thermophilic bacterium with a strong protease-secreting ability, which displayed the maximum growth rate (0.139 h -1 ) and extracellular protease production (307.99 U/mL) at 55°C. Strain 1A02591 contains 75 putative proteases, including 65 intracellular proteases and 10 extracellular proteases according to signal peptide prediction. When strain 1A02591 was cultured with casein, 12 proteases were identified in the secretome, in which metalloproteases (6/12) and serine proteases (4/12) accounted for the majority, and a thermolysin-like protease of the M4 family was the most abundant, suggesting that strain 1A02591 mainly secreted a thermophilic metalloprotease. Correspondingly, the secreted proteases of strain 1A02591 showed the highest activity at the temperature as high as 70°C, and was inhibited 70% by metalloprotease inhibitor o -phenanthroline and 50% by serine protease inhibitor phenylmethylsulfonyl fluoride. The secreted proteases could degrade different proteins, suggesting the role of strain 1A02591 in organic nitrogen degradation in deep-sea hydrothermal ecosystem. These results provide the first insight into the proteases of an Anoxybacillus strain from deep-sea hydrothermal ecosystem, which is helpful in understanding the function of Anoxybacillus in the marine biogeochemical cycle., Competing Interests: XZ was employed by the company Qingdao Vland Biotech Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Cheng, Wang, Zhang, Sun, Zhang, Song, Zhang, Zhang and Chen.)

Collagens from marine animals are an important component of marine organic nitrogen. Collagenase-producing bacteria and their collagenases play important roles in collagen degradation and organic nitrogen recycling in the ocean. However, only a few collagenase-producing marine bacteria have been so far discovered. Here, we reported the isolation and characterization of a collagenase-secreting bacterium, designated strain SM1988 T , isolated from a green alga Codium fragile sample. Strain SM1988 T is a Gram-negative, aerobic, oxidase-, and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988 T formed a distinct phylogenetic lineage along with known genera within the family Pseudoalteromonadaceae , with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988 T was considered to represent a novel species in a novel genus in the family Pseudoalteromonadaceae , for which the name Flocculibacter collagenilyticus gen. nov., sp. nov. is proposed, with the type strain being SM1988 T (= MCCC 1K04279 T = KCTC 72761 T ). Strain SM1988 T showed a high production of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genome and secretome analyses indicated that the collagenases secreted by strain SM1988 T are serine proteases from the MEROPS S8 family. These data suggest that strain SM1988 T acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Li, Cheng, Teng, Sun, He, Wang, Shi, Song, Chen, Zhang, Tian and Zhang.)

A Gram-stain-negative, aerobic, ovoid-rod-shaped bacterium, designated strain SM1903 T , was isolated from surface seawater of the Mariana Trench. The strain grew at 15-37 °C (optimum, 35 °C) and with 1-15 % (optimum, 4 %) NaCl. It hydrolysed aesculin but did not reduce nitrate to nitrite and hydrolyse Tween 80. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1903 T formed a separate lineage within the family Rhodobacteraceae , sharing the highest 16S rRNA gene sequence similarity with type strains of Pseudooceanicola antarcticus (95.7 %) and Roseisalinus antarcticus (95.7 %). In phylogenetic trees based on single-copy OCs and whole proteins sequences, strain SM1903 T fell within a sub-cluster encompassed by Oceanicola granulosus , Roseisalinus antarcticus and Histidinibacterium lentulum and formed a branch adjacent to Oceanicola granulosus . The major cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ), C 16 : 0 and 11-methyl-C 18 : 1  ω 7 c . The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903 T was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903 T , it is considered to represent a novel species of a novel genus in the family Rhodobacteraceae , for which the name Pelagovum pacificum gen. nov., sp. nov. is proposed. The type strain is SM1903 T (=MCCC 1K03608 T =KCTC 72046 T ).

A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6 T , was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.0 (optimum, pH 7.0) and with 0.5-14.0  % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6 T was affiliated with the genus Marinomonas , sharing 93.1-97.0  % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C 16 : 1 ω 6 c /C 16 : 1 ω 7 c ), summed feature 8 (C 18 : 1 ω 7 c /C 18 : 1 ω 6 c ), C 16 : 0 , C 10 : 0 3-OH and C 18 : 0 . The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6 T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6 T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6 T was considered to represent a novel species within the genus Marinomonas , for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6 T (=KCTC 72501 T =MCCC 1K03890 T ).

A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and rod-shaped bacterium, designated strain SM1977 T , was isolated from the surface of coralline algae collected from the intertidal zone at Qingdao, PR China. The strain grew at 10-35 °C, pH 4.5-8.5 and with 1-8.5% (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20 and DNA. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1977 T was affiliated with the genus Vibrio , having the highest sequence similarity (97.6 %) to the type strain of Vibrio casei , followed by those of another five species (95.6-97.6 %) in the Rumoiensis clade of the genus Vibrio . However, the in silico DNA-DNA hybridization (75.3-75.9 %) and average nucleotide identity (21.6-22.8 %) values of SM1977 T against these close relatives were all below the corresponding thresholds to discriminate bacterial species. The major fatty acids were summed feature 3 (C 16:1  ω 7 c and/or C 16:1  ω 6 c ), C 16:0 and summed feature 8 (C 18:1  ω 6 c and /or C 18:1  ω 7 c ). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The sole respiratory quinone was Q-8. The genomic DNA G+C content of strain SM1977 T , determined from the obtained whole genomic sequence, was 42.3 mol%. On the basis of the polyphasic results obtained in this study, strain SM1977 T is considered to represent a novel species within the genus Vibrio , for which the name Vibrio algicola sp. nov. is proposed. The type strain is SM1977 T (=MCCC 1K04351 T =KCTC 72847 T ).

Recently, an increasing number of studies have focused on the biogeographic distribution of marine microorganisms. However, the extent to which geographic distance can affect marine microbial communities is still unclear, especially for the microbial communities in well-connected surface seawaters. In this study, the bacterial community compositions of 21 surface seawater samples, that were distributed over a distance of 7800 km, were surveyed to investigate how bacterial community similarity changes with increasing geographical distance. Proteobacteria and Bacteroidetes were the dominant bacterial phyla, with Proteobacteria accounting for 52.6-92.5% and Bacteroidetes comprising 3.5-46.9% of the bacterial communities. A significant bacterial distance-decay relationship was observed in the well-connected Southern Ocean surface seawater. The number of pairwise shared operational taxonomic units (OTUs), and community similarities tended to decrease with increasing geographic distance. Calculation of the similarity indices with all, abundant or rare OTUs did not affect the observed distance-decay relationship. Spatial distance can largely explain the observed bacterial community variation. This study shows that even in well-connected surface waters, bacterial distance-decay patterns can be found as long as the geographical distance is great enough. The biogeographic patterns should then be present for marine microorganisms considering the large size and complexity of the marine ecosystem.

The biocontrol fungus Trichoderma longibrachiatum SMF2 secretes a large quantity of peptaibols that have been shown to have a range of biological activities and therefore great application values. However, the mechanism of the regulatory expression of peptaibols is still unclear. The putative methyltransferase LaeA/LAE1 is a global regulator involved in the biosynthesis of some secondary metabolites in filamentous fungi. In this study, we demonstrated that the ortholog of LaeA/LAE1 in the biocontrol fungus T. longibrachiatum SMF2, Tl LAE1, plays an important role in the regulation of peptaibols production. Deletion of Tllae1 resulted in a slight negative impact on mycelial growth, and a significant defect in conidial production. Deletion of Tllae1 also compromised the production of peptaibols to a large degree. Further analyses indicated that this defect occurred at the transcriptional level of the two synthetases-encoding genes, tlx1 and tlx2 , which are responsible for peptaibols production. By contrast, constitutive expression of Tllae1 in T. longibrachiatum SMF2 led to 2-fold increased peptaibols production, suggesting that this is a strategy to improve peptaibols production in Trichoderma fungi. These results demonstrate the important role of LAE1 in the regulation of peptaibols production in T. longibrachiatum SMF2., (Copyright © 2020 Shi, Shi, Zhou, Chen, Zhang, Zhang, Zhang and Song.)

Although microbial exopolysaccharides (EPSs) are applied in different fields, no EPS has been used to protect human skin cells against UV-induced oxidative stress. The EPS produced by the Arctic bacterium Polaribacter sp. SM1127 has high moisture-retention ability and antioxidant activity, suggesting its good industrial potentials. In this study, we improved the EPS production of SM1127 and evaluated its protective effect on human dermal fibroblasts (HDFs) against UV-induced oxidative stress. With glucose as carbon source, the EPS yield was increased from 2.11 to 6.12 g/L by optimizing the fermentation conditions using response surface methodology. To lower the fermentation cost and decrease corrosive speed in stainless steel tanks, whole sugar, whose price is only 8% of that of glucose, was used to replace glucose and NaCl concentration was reduced to 4 g/L in the medium. With the optimized conditions, fed-batch fermentation in a 5-L bioreactor was conducted, and the EPS production reached 19.25 g/L, which represents the highest one reported for a polar microorganism. Moreover, SM1127 EPS could maintain the cell viability and integrity of HDFs under UV-B radiation, probably via decreasing intracellular reactive oxygen species level and increasing intracellular glutathione content and superoxide dismutase activity. Therefore, SM1127 EPS has significant protective effect on HDFs against UV-induced oxidative stress, suggesting its potential to be used in preventing photoaging and photocarcinogenesis. Altogether, this study lays a good foundation for the industrialization of SM1127 EPS, which has promising potential to be used in cosmetics and medical fields.

A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41 T , was isolated from Antarctic intertidal sediment. The isolate grew at 0-37 °C and with 0.5-10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41 T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria , Phaeobacter , Pseudopuniceibacterium , Sulfitobacter , Puniceibacterium and Poseidonocella with 98.6-95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C 16 : 0 , summed feature 8 (C 18 : 1   ω7 c and/or C 18 : 1   ω6 c ) and C 18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41 T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41 T is considered to represent a novel species in a new genus within the family Rhodobacteraceae , for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41 T (=MCCC 1K03508 T =KCTC 62793 T ). Moreover, the transfer of Ruegeria lutea Kim et al . 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1 T =JCM 30927 T =KCTC 72105 T ) is also proposed.

In this study, two types of cooling methods (vacuum cooling and air cooling) were used to cool cooked macro-porous sausage. Alterations in the microbiological conditions, pH, instrumental color ( L *, a * , and b *), total volatile nitrogenous bases (TVB-N), lipid oxidation (TBARS), water activity (aW), moisture content, and texture indicators were evaluated to determine sausages' quality changes during storage under refrigeration for up to 10 days. In general, the shelf life of sausages chilled by vacuum cooling (8 days) was similar to that of sausages cooled by air cooling (9 days). For pH, no significant difference ( p  > .05) was obtained between two cooling methods. However, vacuum-cooled sausages have lower L * value ( p  < .05), lower moisture content, and water activity compared with the air-cooled sausages. However, sausages cooled by vacuum cooling showed a sharp increase in TBARS and TVB-N values but maintained texture characteristics for a longer time compared with air-cooled sausages. Although the results indicated that the quality of sausages treated by those two methods remarkably decreased after 7 days, characteristics of sausages cooled by vacuum cooling are better within accepted standards compared with air-cooled sausages. In conclusion, vacuum cooling can be a feasible cooling method with great potential to be used in cooked macro-porous sausages to maintain the quality and may provide reference experiences for the food with similar structure., Competing Interests: No conflict of interest was declared by the authors., (© 2020 The Authors. Food Science & Nutrition published by Wiley Periodicals, Inc.)

A Gram-stain negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1810 T , was isolated from deep-sea sediment collected from the Southwest Indian Ocean. Strain SM1810 T grows at 15-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0) and with 0-8% (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1810 T is affiliated with the genus Pedobacter, sharing high sequence similarity (95.8%) with the type strain of Pedobacter bauzanensis. The major fatty acids of strain SM1810 T are iso-C 15:0 , summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) and iso-C 17:0 3OH. The predominant respiratory quinone is MK-7. The polar lipids are phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified phospholipid and eight unidentified lipids. The genomic DNA G + C content of strain SM1810 T was determined to be 40.8 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1810 T is concluded to represent a novel species of the genus Pedobacter, for which the name Pedobacter indicus sp. nov. is proposed. The type strain is SM1810 T (KCTC 62798 T  = CCTCC AB 2018198 T ).

A Gram-stain-negative, facultatively anaerobic, flagellated and rod-shaped bacterium, designated strain SM1901 T , was isolated from a brown algal sample collected from Kings Bay, Svalbard, Arctic. Strain SM1901 T grew at -4‒30 °C and with 0-7.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed DNA and Tween 80. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SM1901 T was affiliated with the genus Shewanella , showing the highest sequence similarity to the type strain of Shewanella litoralis (97.5%), followed by those of Shewanella vesiculosa , Shewanella livingstonensis and Shewanella saliphila (97.3 % for all three). The major cellular fatty acids were summed feature 3 (C 16 : 1 ω 7 с and/or C 16 : 1 ω 6 с ), C 16 : 0 , C 18 : 0 , iso-C 15 : 0 and C 17 : 1 ω 8 с and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The respiratory quinones were ubiquinones Q-7, Q-8, menaquinones MK-7(H) and MK-8. The genome of strain SM1901 T was 4648537 nucleotides long and encoded a variety of cold adaptation related genes, providing clues for better understanding the ecological adaptation mechanisms of polar bacteria. The genomic DNA G+C content of strain SM1901 T was 40.5 mol%. Based on the polyphasic evidence presented in this paper, strain SM1901 T was considered to represent a novel species, constituting a novel psychrotolerant lineage out of the known SF clade encompassed by polar Shewanella species, within the genus Shewanella , for which the name Shewanella polaris sp. nov. is proposed. The type strain is SM1901 T (=KCTC 72047 T =MCCC 1K03585 T ).

Monoacylglycerol lipases (MGLs) are present in all domains of life. However, reports on bacterial MGLs are still limited. Until now, reported bacterial MGLs are all thermophilic/mesophilic enzymes from warm terrestrial environments or deep-sea hydrothermal vent, and none of them originates from marine environments vastly subject to low temperature, high salts, and oligotrophy. Here, we characterized a novel MGL, GnMgl, from the marine cold-adapted and halophilic bacterium Glaciecola nitratireducens FR1064 T . GnMgl shares quite low sequence similarities with characterized MGLs (lower than 31%). GnMgl and most of its bacterial homologs harbor a catalytic Ser residue located in the conserved C(A/S)HSMG motif rather than in the typical GxSxG motif reported on other MGLs, suggesting that GnMgl-like enzymes might be different from reported MGLs in catalysis. Phylogenetic analysis suggested that GnMgl and its bacterial homologs are clustered as a separate group in the monoglyceridelipase&#95;lysophospholipase family of the Hydrolase&#95;4 superfamily. Recombinant GnMgl has no lysophospholipase activity but could hydrolyze saturated (C12:0-C16:0) and unsaturated (C18:1 and C18:2) MGs and short-chain triacylglycerols, displaying distinct substrate selectivity from those of reported bacterial MGLs. The substrate preference of GnMgl, predicted to be a membrane protein, correlates to the most abundant fatty acids within the strain FR1064 T , suggesting the role of GnMgl in the lipid catabolism in this marine bacterium. In addition, different from known bacterial MGLs that are all thermostable enzymes, GnMgl is a cold-adapted enzyme, with the maximum activity at 30°C and retaining 30% activity at 0°C. GnMgl is also a halotolerant enzyme with full activity in 3.5M NaCl. The cold-adapted and salt-tolerant characteristics of GnMgl may help its source strain FR1064 T adapt to the cold and saline marine environment. Moreover, homologs to GnMgl are found to be abundant in various marine bacteria, implying their important physiological role in these marine bacteria. Our results on GnMgl shed light on marine MGLs., (Copyright © 2020 Li, Zhang, Zhang, Jiang, Wang, Zhang, Sun, Li, Zhang, Shi, Song, Zhao and Chen.)

Many marine microorganisms synthesize exopolysaccharides (EPSs), and some of these EPSs have been reported to have potential in different fields. However, the pharmaceutical potentials of marine EPSs are rarely reported. The EPS secreted by the Artic marine bacterium Polaribacter sp. SM1127 has good antioxidant activity, outstanding moisture-retention ability, and considerable protective property on human dermal fibroblasts (HDFs) at low temperature. Here, the effects of SM1127 EPS on skin wound healing and frostbite injury prevention were studied. Scratch wound assay showed that SM1127 EPS could stimulate the migration of HDFs. In the full-thickness cutaneous wound experiment of Sprague-Dawley (SD) rats, SM1127 EPS increased the wound healing rate and stimulated tissue repair detected by macroscopic observation and histologic examination, showing the ability of SM1127 EPS to promote skin wound healing. In the skin frostbite experiment of SD rats, pretreatment of rat skin with SM1127 EPS increased the rate of frostbite wound healing and promoted the repair of the injured skin significantly, indicating the good effect of SM1127 EPS on frostbite injury prevention. These results suggest the promising potential of SM1127 EPS in the pharmaceutical area to promote skin wound healing and prevent frostbite injury.

D-amino acids (DAAs) are an important component of the refractory dissolved organic matter pool in the ocean. Microbes play a vital role in promoting the recycling of DAAs in the ocean. However, the diversity of marine DAA-utilizing bacteria and how they metabolize DAAs are seldom studied. Here, by enrichment culture with DAAs as the sole nitrogen source, bacteria of 12 families from three phyla were recovered from surface seawater and sediment from Kongsfjorden, Arctic, and seven DAA-utilizing bacterial strains were isolated. These strains have different DAA-utilizing abilities. Of the seven DAAs used, Halomonas titanicae SM1922 and Pseudoalteromonas neustonica SM1927 were able to utilize seven and five of them, respectively, while the other strains were able to utilize only one or two. Based on genomic, transcriptional and biochemical analyses, the key genes involved in DAA metabolism in each strain were identified and the metabolic pathways for the seven DAAs in these marine bacteria were identified. Conversion of DAAs into α-keto acids is generally the main pathway in marine DAA-utilizing bacteria, which is performed by several key enzymes, including DAA oxidoreductases/dehydrogenases, D-serine ammonia-lyases, D-serine ammonia-lyase DSD1s and DAA transaminases. In addition, conversion of DAAs into LAAs is another pathway, which is performed by amino acid racemases. Among the identified key enzymes, D-serine ammonia-lyase DSD1 and Asp racemase are first found to be employed by bacteria for DAA utilization. These results shed light on marine DAA-utilizing bacteria and the involved DAA metabolism pathways, offering a better understanding of the DAA recycling in the ocean., (Copyright © 2020 Yu, Yang, Zheng, Sheng, Li, Wang, Zhang, McMinn, Zhang, Song and Chen.)

A Gram-negative, aerobic, non-flagellated and ovoid- or rod-shaped bacterium, designated strain SM1902 T , was isolated from the sediment sampled at the Jia River estuary, Yantai, PR China. The strain grew at 10-37 °C (optimum, 25-30 °C), pH 6.0-10.0 (pH 7.0) and with 0.5-13.0 % (w/v) NaCl (2.5%). It reduced nitrate to nitrite, but did not produce bacteriochlorophyll a . The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1902 T constituted a separated lineage within the family Rhodobacteraceae and was closely related to Meridianimarinicoccus roseus TG-679 T and Phycocomes zhengii LMIT002 T with 96.1 and 94.3 % 16S rRNA gene sequence similarities, respectively. The predominant cellular fatty acid was summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid. The sole respiratory quinone was ubiquinone-10. The in silico DNA-DNA hybridization values between strain SM1902 T and Meridianimarinicoccus roseus TG-679 T and Phycocomes zhengii LMIT002 T were 19.6 and 19.5 %, respectively; and the average nucleotide identity values between them were 76.1 and 74.2 %, respectively. The genomic DNA G+C content of strain SM1902 T was 58.2 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1902 T is considered to represent a novel species in a new genus within the family Rhodobacteraceae , for which the name Fluviibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is SM1902 T (=KCTC 72045 T =MCCC 1K03596 T =CCTCC AB 2018346 T ).

Trichoderma spp. are main producers of peptide antibiotics known as peptaibols. While peptaibols have been shown to possess a range of biological activities, molecular understanding of the regulation of their production is largely unclear, which hampers the production improvement through genetic engineering. Here, we demonstrated that the orthologue of glucose sensors in the outstanding biocontrol fungus Trichoderma longibrachiatum SMF2, TlSTP1, participates in the regulation of peptaibols production. Deletion of Tlstp1 markedly impaired hyphal growth and conidiation, but significantly increased peptaibols yield by 5-fold for Trichokonins A and 2.6-fold for Trichokonins B. Quantitative real-time polymerase chain reaction analyses showed that the increased peptaibols production occurs at the transcriptional levels of the two nonribosomal peptide synthetase encoding genes, tlx1 and tlx2. Transcriptome analyses of the wild type and the Tlstp1 mutant strains indicated that TlSTP1 exerts a regulatory effect on a set of genes that are involved in a number of metabolic and cellular processes, including synthesis of several other secondary metabolites. These results suggest an important role of TlSTP1 in the regulation of vegetative growth and peptaibols production in T. longibrachiatum SMF2 and provide insights into construction of peptaibol-hyperproducing strains through genetic engineering., (© 2019 Wiley Periodicals, Inc.)

Bacterial endochitinases play important roles in environmental chitin degradation and have good applications. Although the structures of some endochitinases, most belonging to the glycoside hydrolase (GH) family 18 and thermostable, have been reported, the structural basis of these enzymes for chitin degradation still remain unclear due to the lack of functional confirmation, and the molecular mechanism for their thermostability is also unknown. Here, we characterized a GH18 endochitinase, Chi23, from marine bacterium Pseudoalteromonas aurantia DSM6057, and solved its structure. Chi23 is a thermostable enzyme that can non-processively hydrolyze crystalline and colloidal chitin. Chi23 contains only a catalytic domain that adopts a classical (β/α) 8 TIM-barrel fold. Compared to other GH18 bacterial endochitinases, Chi23 lacks the chitin-binding domain and the β-hairpin subdomain, indicating that Chi23 has a novel structure. Based on structural analysis of Chi23 docked with (GlcNAc) 5 and mutational analysis, the key catalytic residue (Glu117) and seven substrate-binding residues (Asn9, Gln157, Tyr189, Asn190, Asp229, Trp260, and Gln261) are revealed. Among these identified residues, Asn9, Asp229 and Gln261 are unique to Chi23, and their cumulative roles contribute to the activity of Chi23 against both crystalline and soluble chitin. Five substrate-binding residues (Tyr189, Asn190, Asp229, Trp260, and Gln261) are found to play important roles in maintaining the thermostability of Chi23. In particular, hydrogen bond networks involving Asp229 and Gln261 are formed to stabilize the protein structure of Chi23. Phylogenetic analysis indicated that Chi23 and its homologs represent a new group of GH18 endochitinases, which are widely distributed in bacteria. This study sheds light on the molecular mechanism of a GH18 endochitinase for chitin degradation., (Copyright © 2019 Wang, Jiang, Zhang, Cao, Zhang, Chen, Li, Wang, Zhang, Song and Li.)

Extracellular enzymes, initiating the degradation of organic macromolecules, are important functional components of marine ecosystems. Measuring in situ seawater extracellular enzyme activity (EEA) can provide fundamental information for understanding the biogeochemical cycling of organic matter in the ocean. Here we investigate the patterns of EEA and the major factors affecting the seawater EEA of Chinese marginal seas. The geographic distribution of EEA along a latitudinal transect was examined and found to be associated with dissolved organic carbon. Compared with offshore waters, inshore waters had higher enzyme activity. All the tested substrates were hydrolyzed at different rates and phosphatase, β-glucosidase and protease contributed greatly to summed hydrolysis rates. For any particular enzyme activity, the contribution of dissolved to total EEA was strongly heterogenous between stations. Comparisons of hydrolysis rates of the polymers and their corresponding oligomers suggest that molecule size does not necessarily limit the turnover of marine organic matter. In addition, several typical enzyme-producing clades, such as Bacteroidetes, Planctomycetes, Chloroflexi, Roseobacter , Alteromonas , and Pseudoalteromonas , were detected in the in situ environments. These enzyme-producing clades may be responsible for the production of different enzymes. Overall, each enzyme was found to flexibly respond to environmental conditions and were linked to microbial community composition. It is likely that this activity will profoundly affect organic matter cycling in the Chinese marginal seas., (Copyright © 2019 Li, Sun, Sun, Cha, Li, Zhao, Song, Wang, McMinn, Chen, Zhang and Qin.)

A Gram-reaction-negative, aerobic, flagellated and coccoid-shaped bacterial strain, designated SM1702 T , was isolated from Antarctic intertidal sediment collected off Ardely Island, West Antarctica. The strain grew at 0-30 °C and with 0.5-5.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and single-copy orthologous clusters both showed that strain SM1702 T , together with Poseidonibacter lekithochrous , occupied an independent phylogenetic branch, sharing the highest 16S rRNA gene sequence similarity with type strain of the latter (95.6 %). The major fatty acids were summed feature 3 (C 16 : 1 ω 7 c and/or C 16 : 1 ω 6 c ), summed feature 8 (C 18 : 1 ω 7 c and/or C 18 : 1 ω 6 c ), C 16 : 0 , and summed feature 2 (C 14 : 0 3-OH and/or iso-C 16 : 1 I). Polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of strain SM1702 T was 27.1 mol%. Based on the results of the polyphasic characterisation for strain SM1702 T , it is identified as the representative of a novel species of Poseidonibacter , for which the name Poseidonibacter antarcticus sp. nov. is proposed. The type strain of Poseidonibacter antarcticus is SM1702 T (=MCCC 1K03471 T =KCTC 62796 T ).

Coat color genetics successfully adapted and applied to different animal species, which provides a good demonstration of the concept of comparative genetics. In this study, we sequenced 945 bp fragments of melanocortin 1 receptor ( MC1R ) gene, 421 bp fragments of exon 1 of tyrosinase ( TYR ) gene and 266 bp fragments of exon 3 of agouti signaling protein ( ASIP ) gene for 250 individuals with five plumage color patterns. We detected a total of three SNPs (T398A, T637C, and G920C) in MC1R and built six haplotypes (H1-H6) based on the three SNPs. H5 and H6 haplotypes were mainly concentrated in white and grey chicken. And diplotypes H2H3 occurred in white feather and black-speckle feather with the same frequency. Moreover, a total of three SNPs (C47G, T120C, and T172C) in TYR were found and built six haplotypes (P1-P6) based on the three SNPs. Among them, haplotype P2, P3 and P6 were not occurred in black chicken, the diplotypes P1P6 and P4P6 were only distributed in white, gray and black-speckled feather. We only detected one SNP (T168C) in ASIP gene and found that genotype TT was advantage genotype in the different plumage color groups of chickens. Collectively, our study suggested an association between plumage color and genetic variation of MC1R , TYR and ASIP in chicken., Competing Interests: All authors have no declared conflict of interest.All procedures carried out in this experiment were reviewed and approved by the Institutional Animal Care and Use Committee of Sichuan Agricultural University, China.

Long non-coding RNA (lnc)TCF7 has been reported to promote the self‑renewal of human cancer stem cells, and enhance the aggressiveness of human non‑small cell lung cancer and hepatocellular carcinoma cells. However, the effect of lncTCF7 on colorectal cancer (CRC) tumorigenesis and progression is currently unclear. In the present study, reverse transcription‑quantitative polymerase chain reaction results demonstrated that lncTCF7 expression was higher in CRC tissues compared with adjacent normal tissues and was significantly associated with tumor size, differentiation degree, tumor‑node‑metastasis grade, lymph node metastasis and invasion depth. In addition, lncTCF7 demonstrated a high sensitivity and specificity for diagnosing CRC, as determined by receiver operating characteristic curve analysis. Furthermore, lncTCF7 silencing in SW‑620 and HT29 CRC cell lines inhibited the proliferation, cell cycle, migration and invasion of cells, as determined by Cell Counting Kit‑8 assays, propidium iodide (PI) staining and flow cytometry, wound healing assays and Transwell invasion assays, respectively; however, Annexin V/PI double staining and flow cytometry indicated that lncTCF7 silencing did not significantly affect the apoptosis of CRC cells. These results indicate that lncTCF7 may predict the progression, and promote the growth and metastasis, of CRC, and may therefore be a novel diagnostic marker and therapeutic target for CRC treatment.

Strain DSM9414, the type strain of Pseudoalteromonas espejiana, is a Gram-negative, and amino-acid-requiring stain isolated from seawater off the coast of Northern California. In this study, we report the complete genome sequence of Pseudoalteromonas espejiana DSM9414 T . The genome (4,500,451bp; 40.3% G+C) is composed of two circular chromosomes: chromosome I is 3,720,756bp with 40.4% G+C content and chromosome II is 779,695bp with 39.8% G+C content. Genomic analysis showed that chromosome I encodes a complete set of ABC transporters responsible for branched-chain amino acids, whose homologous proteins were not discovered in other Pseudoalteromonas genomes released. This result indicated the tight dependence of extracellular amino acids for strain DSM9414 T , which is consistent with its phenotype. The complete genome sequence of P. espejiana provides further genetic insights into the diversity of dependence on extracellular amino acids for Pseudoalteromonas species., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Although several serine collagenolytic proteases from bacteria were reported, none has been used to prepare bioactive collagen peptides. MCP-01 is the most abundant extracellular protease of deep-sea Pseudoalteromonas sp. SM9913 and is a serine collagenolytic protease with high efficiency on fish collagen hydrolysis. Here, we set up a pilot scale process to ferment SM9913 for extracellular protease production. With SM9913 extracellular protease as a tool, a process to prepare collagen oligopeptide-rich hydrolysate from codfish skin was set up, which was further scaled up to pilot (100 L) and plant (2000 L) levels with yields >66%. The hydrolysates from laboratory-, pilot- and plant-scales had quite similar quality, containing ~95% peptides with molecular weights lower than 3000 Da and approximately 60% lower than 1000 Da, in which collagen oilgopeptides account for approximately 95%. Bioactivity analyses showed that the hydrolysate had moisture-retention ability, antioxidant activity, and promoting effect on cell viability of human dermal fibroblasts. Safety evaluation showed that the hydrolysate was nontoxic and nonirritating to skin. Therefore, SM9913 extracellular protease is a good enzyme to prepare bioactive oligopeptides from fish skin. The results also suggest that the collagen oligopeptides-rich hydrolysate may have potentials in biomedical, functional food, pharmaceutical and cosmetic industries.

Nitrogen is one of the most important nutrients needed for plants and algae to survive, and the photosynthetic ability of algae is related to nitrogen abundance. Red algae are unique photosynthetic eukaryotic organisms in the evolution of algae, as they contain phycobilisomes (PBSs) on their thylakoid membranes. In this report, the in vivo chlorophyll (Chl) a fluorescence kinetics of nitrogen-starved Porphyridium cruentum were analyzed to determine the effects of nitrogen deficiency on photosynthetic performance using a multi-color pulse amplitude modulation (PAM) chlorophyll fluorometer. Due to nitrogen starvation, the photochemical efficiency of PSII and the activity of PSII reaction centers (RCs) decreased, and photoinhibition of PSII occurred. The water-splitting system on the donor side of PSII was seriously impacted by nitrogen deficiency, leading to the inactivation of the oxygen-evolving complex (OEC) and decreased light energy conversion efficiency. In nitrogen-starved cells, a higher proportion of energy was used for photochemical reactions, and thermal dissipation was reduced, as shown by qP and qN. The ability of nitrogen-starved cells to tolerate and resist high photon flux densities was weakened. Our results showed that the photosynthetic performance of P. cruentum was severely impacted by nitrogen deficiency.

A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped and yellow-pigmented bacterium, designated strain SM1502T, was isolated from Arctic seawater. The isolate grew at 10-40 °C and with 0-8.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was affiliated with the genus Flavobacterium, with the highest sequence similarity (96.0 %) found with Flavobacterium suzhouense XIN-1T. The major fatty acids of strain SM1502T were iso-C15 : 0, iso-C17 : 1ω9c, iso-C15 : 1 G, C15 : 0, iso-C17 : 0 3-OH and unknown ECL 13.565. The major respiratory quinone of strain SM1502T was menaquinone-6 (MK-6). Polar lipids of strain SM1502T included phosphatidylethanolamine and one unidentified aminolipid and lipid. The genomic DNA G+C content of strain SM1502T was 37.0 mol%. Based on the polyphasic data obtained in this study, strain SM1502T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium arcticum sp. nov. is proposed. The type strain is SM1502T (=KCTC 42668T=CCTCC AB 2015346T).

Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin-containing monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half-reaction and an oxidative half-reaction. In the reductive half-reaction, FAD is reduced and a C4a-hydroperoxyflavin intermediate forms. In the oxidative half-reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP + bends and interacts with D317, shutting off the entrance to create a protected micro-environment for catalysis and exposing C4a-hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP + undergoes a conformational change in the oxidative half-reaction of FMOs., (© 2016 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.)

The Hengduan Mountains, with a distinct altitudinal differentiation and strong vertical vegetation zonation, occupy an important position in southwestern China as a global hotspot of biodiversity. Pollen analysis of lake sediments sampled along an altitudinal gradient in this region helps us to understand how this vegetation zonation arose and how it has responded to climate change and human impacts through time. Here we present a ~30-ka pollen record and interpret it in terms of vegetational and climatic change from a 310 cm-long core from Shudu Lake, located in the Hengduan Mountains region. Our results suggest that from 30 to 22 cal. ka BP, the vegetation was dominated by steppe/grassland (comprising mainly Artemisia, Poaceae and Polygonaceae) and broad-leaved forest (primarily Quercus, Betula and Castanopsis) in the lake catchment, reflecting a relatively warm, wet climate early in this phase and slightly warmer, drier conditions late in the phase. The period between 22 and 13.9 cal. ka BP was marked by a large expansion of needle- and broad-leaved mixed forest (Pinus, Abies and Quercus) and a decline in the extent of steppe/grassland, indicating warming, drying climatic conditions followed by a cold, wet period. Between 13.9 and 3 cal. ka BP, steppe/grassland expanded and the area covered by needle- and broad-leaved mixed forest reduced, implying a fluctuating climate dominated by warm and humid conditions. After 3 cal. ka BP, the vegetation was characterized by an increase in needle-leaved forest and reduction in steppe/grassland, suggesting warming and drying climate. A synthesis of palynological investigations from this and other sites suggests that the vegetation succession patterns seen along an altitudinal gradient in northwestern Yunnan since the Late Pleistocene are comparable, but that each site has its own characteristics probably due to the influences of altitude, topography, microclimate and human impact., Competing Interests: The authors have declared that no competing interests exist.

Bacterial extracellular proteases are important for bacterial nutrition and marine sedimentary organic nitrogen degradation. However, only a few proteases from marine sedimentary bacteria have been characterized. Some subtilases have a protease-associated (PA) domain inserted in the catalytic domain. Although structural analysis and deletion mutation suggests that the PA domain in subtilases is involved in substrate binding, direct evidence to support this function is still absent. Here, a protease, P57, secreted by Photobacterium sp. A5-7 isolated from marine sediment was characterized. P57 could hydrolyze casein, gelatin and collagen. It showed the highest activity at 40°C and pH 8.0. P57 is a new subtilase, with 63% sequence identity to the closest characterized protease. Mature P57 contains a catalytic domain and an inserted PA domain. The recombinant PA domain from P57 was shown to have collagen-binding ability, and Phe349 and Tyr432 were revealed to be key residues for collagen binding in the PA domain. This study first shows direct evidence that the PA domain of a subtilase can bind substrate, which provides a better understanding of the function of the PA domain of subtilases and bacterial extracellular proteases from marine sediment.

An intermittently aerated sequencing batch reactor (IASBR) and a traditional sequencing batch reactor (SBR) were respectively used for treating digested piggery wastewater, and the pollutant removal performance was studied at different ratios of chemical oxygen demand (COD) to total nitrogen (TN) in the influent and different loading rates. The results showed that the pollutant removal rates in the IASBR were much higher than those in the SBR. Under influent COD/TN of about 2.2 and NH 4 + -N loading of (0.12±0.04) kg·(m 3 ·d) -1 , the removal rates of NH 4 + -N, TN and TOC in the IASBR were 97.2%±4.4%, 81.5%±7.5% and 88.5%±2.4%, respectively, higher than the corresponding rates of 78.3%±19.6%, 79.8%±4.9% and 86.6%±3.2% in the SBR. As the NH 4 + -N loading was increased to (0.18±0.02) kg·(m 3 ·d) -1 , the removal rates of NH 4 + -N, TN and TOC in the IASBR were slightly decreased to 92.4%±7.3%, 77.5%±5.3% and 86.4%±2.2%, but still higher than the corresponding values of 78.1%±15.4%, 61.8%±11.2% and 81.8%±5.6% in the SBR. As the NH 4 + -N loading was remained at (0.20±0.01) kg·(m 3 ·d) -1 , but the influent COD/TN ratio was increased to about 3.0, the pollutant removal rates in both IASBR and SBR were increased, compared to those at influent COD/TN ratio of 2.2.The removal rates of NH 4 + -N, TN and TOC in the IASBR were 99.6%±0.2%, 91.5%±2.9% and 92.0%±0.9%, respectively, higher than the corresponding rates of 90.2%±1.4%, 83.0%±1.9% and 90.2%±0.5% in the SBR. Based on the above, the IASBR was more efficient in TN and ammonium removal and more shocking load resistant, and therefore was more feasible than SBR for treating low COD/TN ratio wastewaters such as the digested piggery wastewater.

Stability of short-cut nitrification nitrogen removal performance was studied in a step-feeding, intermittently aerated sequencing batch reactor (IASBR) at 30°C to treat digested piggery wastewater. Results showed that the nitrogen removal was greatly influenced by the ratio of chemical oxygen demand (COD) to total nitrogen (TN) in the influent. Nitrite nitrogen kept accumulating up to 800 mg · L⁻1 when the influent COD/TN ratio was 0.8 ± 0.2, and the removal rates of TN, ammonium nitrogen and total organic carbon (TOC) were only 18.3% ± 12.2%, 84.2% ± 10.3% and 60.7% ± 10.7%, respectively. By contrast, as the influent COD/ TN ratio was increased to 2.4 ± 0.5, the accumulated concentration of nitrite nitrogen sharply decreased from 800 mg · L⁻¹ to below 10 mg-L⁻¹, and the removal rates of TN, ammonium nitrogen and TOC were increased to over 90%, 95% and 85%, respectively. Gradually shortened hydraulic retention time ( HRT) reveales that the ammonia load is a restricting factor for nitrogen removal. The ammonia load should be controlled at no more than 0.30 kg · (m³ · d) ⁻¹, or else, the removal rates of TN, ammonium and TOC would be greatly decreased. The nitrite accumulation rate over the whole run was 74.6%-97.8% and the TN removal rate in the stable phase was over 90%. With efficient and stable short-cut nitrification-denitrification in a low COD/TN, moreover, and unnecessary for addition of alkaline, IASBR shows great advantage for treating wastewater with high concentration of ammonia while low COD/TN ratio.

Trichoderma spp. are well known biocontrol agents that produce a variety of antibiotics. Peptaibols are a class of linear peptide antibiotics mainly produced by Trichoderma Alamethicin, the most studied peptaibol, is reported as toxic to plants at certain concentrations, while the mechanisms involved are unclear. We illustrated the toxic mechanisms of peptaibols by studying the growth-inhibitory effect of Trichokonin VI (TK VI), a peptaibol from Trichoderma longibrachiatum SMF2, on Arabidopsis primary roots. TK VI inhibited root growth by suppressing cell division and cell elongation, and disrupting root stem cell niche maintenance. TK VI increased auxin content and disrupted auxin response gradients in root tips. Further, we screened the Arabidopsis TK VI-resistant mutant tkr1. tkr1 harbors a point mutation in GORK, which encodes gated outwardly rectifying K(+)channel proteins. This mutation alleviated TK VI-induced suppression of K(+)efflux in roots, thereby stabilizing the auxin gradient. The tkr1 mutant also resisted the phytotoxicity of alamethicin. Our results indicate that GORK channels play a key role in peptaibol-plant interaction and that there is an inter-relationship between GORK channels and maintenance of auxin homeostasis. The cellular and molecular insight into the peptaibol-induced inhibition of plant root growth advances our understanding of Trichoderma-plant interactions., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.)