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Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Antonie Van Leeuwenhoek 2023; 116:1447-1455. [PMID: 37899393 DOI: 10.1007/s10482-023-01888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).
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Short-chain fatty acids (SCFAs) as potential resuscitation factors that promote the isolation and culture of uncultured bacteria in marine sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:400-414. [PMID: 37637259 PMCID: PMC10449756 DOI: 10.1007/s42995-023-00187-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/20/2023] [Indexed: 08/29/2023]
Abstract
Many marine bacteria are difficult to culture because they are dormant, rare or found in low-abundances. Enrichment culturing has been widely tested as an important strategy to isolate rare or dormant microbes. However, many more mechanisms remain uncertain. Here, based on 16S rRNA gene high-throughput sequencing and metabolomics technology, it was found that the short-chain fatty acids (SCFAs) in metabolites were significantly correlated with uncultured bacterial groups during enrichment cultures. A pure culture analysis showed that the addition of SCFAs to media also resulted in high efficiency for the isolation of uncultured strains from marine sediments. As a result, 238 strains belonging to 10 phyla, 26 families and 82 species were successfully isolated. Some uncultured rare taxa within Chlorobi and Kiritimatiellaeota were successfully cultured. Amongst the newly isolated uncultured microbes, most genomes, e.g. bacteria, possess SCFA oxidative degradation genes, and these features might aid these microbes in better adapting to the culture media. A further resuscitation analysis of a viable but non-culturable (VBNC) Marinilabiliales strain verified that the addition of SCFAs could break the dormancy of Marinilabiliales in 5 days, and the growth curve test showed that the SCFAs could shorten the lag phase and increase the growth rate. Overall, this study provides new insights into SCFAs, which were first studied as resuscitation factors in uncultured marine bacteria. Thus, this study can help improve the utilisation and excavation of marine microbial resources, especially for the most-wanted or key players. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00187-w.
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Leader peptide removal in lasso peptide biosynthesis based on penultimate isoleucine residue. Front Microbiol 2023; 14:1181125. [PMID: 37497541 PMCID: PMC10368454 DOI: 10.3389/fmicb.2023.1181125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
Lasso peptides are ribosomally synthesized peptides that undergo post-translational modifications including leader peptide removal by B (or the segregated B1 and B2) proteins and core peptide macrolactamization by C proteins to form a unique lariat topology. A conserved threonine residue at the penultimate position of leader peptide is hitherto found in lasso peptide precursors and shown to be a critical recognition element for effective enzymatic processing. We identified a lasso peptide biosynthetic gene cluster (bsf) from Bradymonas sediminis FA350, a Gram-negative and facultatively prey-dependent bacterium that belongs to a novel bacterial order Bradymonadales in the class Deltaproteobacteria. The kinase BsfK specifically catalyzes the phosphorylation of the precursor peptide BsfA on the Ser3 residue. BsfB1 performs dual functions to accelerate the post-translational phosphorylation and assist BsfB2 in leader peptide removal. Most importantly, the penultimate residue of leader peptide is an isoleucine rather than the conserved threonine and this isoleucine has a marked impact on the phosphorylation of Ser3 as well as leader peptide removal, implying that BsfB1 and BsfB2 exhibit a new substrate selectivity for leader peptide binding and excision. This is the first experimentally validated penultimate isoleucine residue in a lasso peptide precursor to our knowledge. In silico analysis reveals that the leader peptide Ile/Val(-2) residue is rare but not uncommon in phosphorylated lasso peptides, as this residue is also discovered in Acidobacteriaceae and Sphingomonadales in addition to Bradymonadales.
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Gaoshiqia sediminis gen. nov., sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37133916 DOI: 10.1099/ijsem.0.005855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
A Gram-stain-negative, facultative anaerobic, motile, rod-shaped and orange bacterium, designated A06T, was obtained off the coast of Weihai, PR China. Cells were 0.4-0.5×0.6-1.0 µm in size. Strain A06T grew at 20-40 °C (optimum, 33 °C), at pH 6.0-8.0 (optimum, pH 6.5-7.0) and in the presence of 0-8 % NaCl (w/v) (optimum, 2 %). Cells were oxidase and catalase positive. Menaquinone-7 was detected as the major respiratory quinone. The dominant cellular fatty acids were identified as C15:0 2-OH, iso-C15:0, anteiso-C15:0 and iso-C15:1 ω6c. The DNA G+C content of strain A06T was 46.1 mol%. The polar lipids were phosphatidylethanolamine, one aminolipid, one glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A06T is a member of the family Prolixibacteraceae and exhibited the highest sequence similarity to Mangrovibacterium diazotrophicum DSM 27148T (94.3 %). Based on its phylogenetic and phenotypic characteristics, strain A06T is considered to represent a novel genus in the family Prolixibacteraceae, for which the name Gaoshiqia gen. nov. is proposed. The type species is Gaoshiqia sediminis sp. nov., with type strain A06T (=KCTC 92029T=MCCC 1H00491T). The identification and acquisition of microbial species and genes in sediments will help broaden the understanding of microbial resources and lay a foundation for its application in biotechnology. Strain A06T uses an enrichment method, so the isolation of strain A06T is of great significance to the enrichment of marine microbial resources.
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Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments. mBio 2023; 14:e0353522. [PMID: 36988509 PMCID: PMC10128000 DOI: 10.1128/mbio.03535-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.
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Aequorivita vitellina sp. nov. and Aequorivita xiaoshiensis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 36961878 DOI: 10.1099/ijsem.0.005801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Two Gram-stain-negative, strictly aerobic, chemoheterotrophic, short-rod-shaped and non-motile strains, forming yellow colonies and designated F47161T and F64183T, were isolated from marine sediment of Xiaoshi Island, Wei Hai, PR China. Strain F47161T grew at 15-37 °C (optimally at 30 °C) and pH 6.0-9.0 (optimally at pH 7.5) and in the presence of 1-9 % (w/v) NaCl (optimally at 3 %). Strain F64183T grew at 10-37 °C (optimally at 30 °C) and pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-8 % (w/v) NaCl (optimally at 3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that F47161T and F64183T were related to members of the genus Aequorivita. The strains shared 97.4 % 16S rRNA gene sequence similarity to each other. F47161T and F64183T shared highest 16S rRNA gene sequence similarity to Aequorivita sinensis JCM 19789T, and the values were 97.5 % and 98.4 %, respectively. The predominant cellular fatty acids of both F64183T and F47161T were iso-C15 : 0 and iso-C17 : 0 3-OH, but the predominant fatty acids of F47161T also included anteiso-C15 : 0. The sole respiratory quinone of F47161T and F64183T was menaquinone 6 (MK-6), consistent with that observed for all related strains. Between F47161T and F64183T, the average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values were 75.8 % and 20.5 %, respectively, and between the novel isolates (F47161T and F64183T) and A. sinensis JCM 19789T they were 76.0 % and 94.2 % and 20.6 % and 57.1 %, respectively. The genomic DNA G+C contents of F47161T and F64183T was 37.3 % and 34.5 %, respectively. The polar lipid profiles of F47161T and F64183T contained phosphatidylethanolamine, two aminolipids, one glycolipid, one phosphoglycolipid and two unidentified polar lipids. Differential phenotypic and genotypic characteristics of the two strains indicated that the two strains should be classified as representing two novel species of the genus Aequorivita, for which the names Aequorivita vitellina sp. nov. and Aequorivita xiaoshiensis sp. nov. are proposed. The type strains are F47161T (=MCCC 1H00509T=KCTC 92017T) and F64183T (=MCCC 1H00507T=KCTC 92016T), respectively.
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Description of Lujinxingia vulgaris sp. nov., isolated from coastal sediment via prey-traps. Antonie van Leeuwenhoek 2021; 114:1805-1818. [PMID: 34426860 DOI: 10.1007/s10482-021-01640-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/06/2021] [Indexed: 11/29/2022]
Abstract
Two Gram-stain negative, facultative anaerobic, oxidase-negative, catalase-positive bacilli, designated as strains TMQ4T and TMQ2, were isolated from Xiaoshi Island, China, using prey-traps. Growth was observed within the ranges 25-45 °C (optimally at 37 °C), pH 6.5-9.0 (optimally at pH 7.5-8.0) and 1-8% NaCl (optimally at 3-4%, w/v). The draft genome sequences of strains TMQ4T and TMQ2 contained 184 contigs of 5,609,735 bp with a G+C content of 64.4% and 148 contigs of 5,589,985 bp with a G+C content of 65.0%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Lujinxingia with the similarity of 98.9%. The phylogenetic and phylogenomic topologies and analyses demonstrated that both strains clustered together and differentiated from the closest neighbour, Lujinxingia sediminis SEH01T. Genomic analyses showed that two strains lost the biosynthesis pathway of several chemical compounds. Iso-C15:0 was contained in the predominant cellular fatty acids in both strains. The major polar lipids of both strains consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified lipids; and the respiratory quinone was menaquinone MK-7 for both strains. Both strains predated other bacteria, including Owenweeksia hongkongensis JCM 12287T and Paraliobacillus ryukyuensis DSM 15140T, and were lured with one prey Acinetobacter baumannii ATCC 19606T in prey-trap. Combining genomic analyses, two strains had the predatory indices of 2, similar to representative typical bacterial predators. The physiological, biochemical, and phylogenetic properties suggest that the two strains represent a novel species within the genus Lujinxingia. The name Lujinxingia vulgaris sp. nov. is proposed, with strain TMQ4T (= KCTC 62851T = MCCC 1H00392T) as type strain and strain TMQ2 (= KCTC 72,079 = MCCC 1H00381) as reference strain.
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What do we mean by viability in terms of 'viable but non-culturable' cells? ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:248-252. [PMID: 33900036 DOI: 10.1111/1758-2229.12953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
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Strategies for culturing active/dormant marine microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:121-131. [PMID: 37073338 PMCID: PMC10077298 DOI: 10.1007/s42995-020-00053-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/18/2020] [Indexed: 05/03/2023]
Abstract
Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.
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Inducible expression of agar-degrading genes in a marine bacterium Catenovulum maritimus Q1T and characterization of a β-agarase. Appl Microbiol Biotechnol 2020; 104:10541-10553. [DOI: 10.1007/s00253-020-10969-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/09/2020] [Accepted: 10/18/2020] [Indexed: 12/01/2022]
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Abstract
A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31T, was isolated from sediment of Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4-45 °C (optimum, 37 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 0-1 % (w/v) NaCl (optimum, 0 %). C18 : 1 ω7c/C18 : 1 ω6c and C16 : 0 were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31T shared 96.8 % similarity with Roseomonas wooponensis JCM 19527T and 95.9 % with R. terricola EM0302T. Digital DNA-DNA hybridization values between strain CQN31T and Roseomonas stagni DSM 19981T, R. rosea DSM 14916T and R. mucosa NCTC 13291T were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31T and R. stagni DSM 19981T, R. rosea DSM 14916T and R. mucosa NCTC 13291T were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas bella sp. nov. is proposed. The type strain is CQN31T (=KCTC 62447T=MCCC 1H00309T).
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Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. MICROBIOME 2020; 8:126. [PMID: 32867860 PMCID: PMC7460792 DOI: 10.1186/s40168-020-00902-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. RESULTS Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. CONCLUSIONS Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.
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Tichowtungia aerotolerans gen. nov., sp. nov., a novel representative of the phylum Kiritimatiellaeota and proposal of Tichowtungiaceae fam. nov., Tichowtungiales ord. nov. and Tichowtungiia class. nov. Int J Syst Evol Microbiol 2020; 70:5001-5011. [PMID: 32783807 DOI: 10.1099/ijsem.0.004370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kiritimatiellaeota is widespread and ecologically important in various anoxic environments. However, the portion of culturable bacteria within this phylum is quite low and, in fact, there is only one currently described species. In this study, a novel anaerobic, non-motile, coccoid, Gram-stain-negative bacterial strain, designated S-5007T, was isolated from surface marine sediment. The 16S rRNA gene sequence was found to have very low 16S rRNA gene sequence similarity to the nearest known type strain, Kiritimatiella glycovorans L21-Fru-ABT (84.9 %). The taxonomic position of the novel isolate was investigated using a polyphasic approach and comparative genomic analysis. Phylogenetic analyses based on 16S rRNA genes and genomes indicated that strain S-5007T branched within the radiation of the phylum Kiritimatiellaeota. Different from the type strain, strain S-5007T can grow under microaerobic conditions, and the genomes of strain S-5007T and the other strains in its branch have many more antioxidant-related genes. Meanwhile, other different metabolic features deduced from genome analysis supported the separate evolution of the proposed class (strain S-5007T branch) and K. glycovorans L21-Fru-ABT. Based on phylogenetic and phenotypic characterization studies, Tichowtungia aerotolerans gen. nov., sp. nov. is proposed with S-5007T (=MCCC 1H00402T=KCTC 15876T) as the type strain, as the first representative of novel taxa, Tichowtungiales ord. nov., Tichowtungiaceae fam. nov. in Tichowtungiia class. nov.
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Maribacter algarum sp. nov., a new member of the family Flavobacteriaceae isolated from the red alga Gelidium amansii. Int J Syst Evol Microbiol 2020; 70:3679-3685. [DOI: 10.1099/ijsem.0.004220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped (0.2–0.3×1.0-2.4 µm), catalase-positive, oxidase-negative and non-motile bacterium, designated strain RZ26T, was isolated from the marine red algae collected from the coast of Weihai, PR China. Growth of strain RZ26T occurred at 15–33 °C (optimum, 25–28 °C), pH 6.0–9.5 (optimum, pH 7.0–7.5) and 0.5–5.0 % (w/v) NaCl (optimum, 2.0–3.0 %). Resuls of phylogenetic analysis based on 16S rRNA gene sequences showed that strain RZ26T was most closely related to
Maribacter spongiicola
DSM 25233T (96.2 % sequence similarity), followed by
Maribacter forsetii
DSM 18668T (96.1 %) and
Maribacter vaceletii
DSM 25230T (95.4 %). The average nucleotide identity and the average amino acid identity values between strain RZ26T and
M. sedimenticola
KCTC 12966T,
M. spongiicola
DSM 25233T,
M. vaceletii
DSM 25230T and
M. forsetii
DSM 18668T were 75.6, 76.2, 76.0, 76.7, 64.3, 63.9, 68.6 and 68.0 %, respectively. The digital DNA–DNAhybridization values based on the draft genomes between strain RZ26T and
M. sedimenticola
KCTC 12966T,
M. spongiicola
DSM 25233T and
M. vaceletii
DSM 25230T were 38.0, 35.1 and 37.1 %, respectively. The major fatty acids in strain RZ26T were iso-C17 : 0 3-OH, iso-C15 : 0 and C16 : 1
ω7c/C16 : 1
ω6c. The major respiratory quinone was MK-6. The dominant polar lipid was phosphatidylethanolamine. The DNA G+C content was 38.0 mol%. Phylogenetic analysis shows strain RZ26T fell within a clade comprising species of the genus
Maribacter
. Polyphasic taxonomy indicates that the isolate represents a novel species of the genus
Maribacter
, for which the name Maribacter algarum sp. nov. is proposed, with type strain RZ26T (=KCTC 62992T=MCCC 1H00362T).
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Mesohalobacter halotolerans gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2020; 70:3588-3596. [PMID: 32453683 DOI: 10.1099/ijsem.0.004143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, fine rod or short filament shaped, jacinth pigmented bacterium, designated strain WDS2C27T, was isolated from a marine solar saltern in Wendeng, Weihai, PR China (37°31'5″ N, 122°1'47″ E). Growth of WDS2C27T occurred at 20-42 °C (optimum 37 °C) and pH 6.5-8.5 (optimal pH 7.0-8.0). Optimal growth occurred in modified marine broth containing 6 % (w/v) NaCl. The major polar lipids in WDS2C27T were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The major respiratory quinone of WDS2C27T was MK-6. The dominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 35.0 mol%. The nucleotide sequence of the 16S rRNA gene indicated that the most closely related strain was Psychroflexus planctonicus X15M-8T (92.0 % over 1452 bp). WDS2C27T showed 60.7 % average amino acid identity, 55.6 % percentage of conserved proteins, 75.0 % average nucleotide identity and 13.1 % digital DNA-DNA hybridization identity with the type species of the genus Psychroflexus, Psychroflexus torquis ATCC 700755T. The phenotypic and genotypic properties and phylogenetic inference indicated that WDS2C27T could be assigned to a novel species within a novel genus, for which the name Mesohalobacter halotolerans gen. nov., sp. nov. is proposed. Strain WDS2C27T (=MCCC 1H00133T=KCTC 52044T) is the type strain.
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Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:1617-1622. [PMID: 32228747 DOI: 10.1099/ijsem.0.003949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain SH27T, which was isolated from seawater collected around Xiaoshi Island, PR China. Cells of strain SH27T were Gram-stain-negative, non-motile, rod-shaped, orange-pigmented and grew at 15-37 °C (optimum, 28 °C), at pH 6.0-8.0 (pH 7.0) and in 1.0-7.0 % (w/v) NaCl (2.0-3.0 %). The isolate was positive for catalase, but negative for nitrate reduction, oxidase, indole production and urease. Carotenoid pigment was produced. Phylogenetic analysis based on the 16S rRNA gene placed strain SH27T in the genus Dokdonia with the closest relative being Dokdonia donghaensis KCTC 12391T, exhibiting 96.7 % 16S rRNA gene pairwise similarity. The results of genomic comparisons, including average nucleotide identity and digital DNA-DNA hybridization, showed 72.9 and 19.2 % identity to D. donghaensis KCTC 12391T, respectively. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Menaquinone-6 was the only respiratory quinone. The G+C content of the genomic DNA was 32.9 mol%. On the basis of the phenotypic and phylogenetic data, strain SH27T represents a novel species of the genus Dokdonia, for which the name Dokdonia sinensis sp. nov. is proposed, with the type strain SH27T (MCCC 1H00358T=CCTCC AB 2018323T=KCTC 62962T).
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Algoriphagus lacus sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:193-198. [DOI: 10.1099/ijsem.0.003734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Marinomonas agarivorans sp. nov., an agar-degrading marine bacterium isolated from red algae. Int J Syst Evol Microbiol 2020; 70:100-104. [DOI: 10.1099/ijsem.0.003723] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Marinospirillum perlucidum sp. nov., a novel helical bacterium isolated from a sea cucumber culture pond. Int J Syst Evol Microbiol 2019; 70:576-581. [PMID: 31613746 DOI: 10.1099/ijsem.0.003794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain F3212T, Gram-stain-negative, aerobic, helical and motile bacterium, was isolated from the marine sediment collected in a sea cucumber culture pond located in Rongcheng, China. Strain F3212T grew optimally at pH 8.5, at 30 °C and in the presence of 3.0 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain F3212T belongs to the genus Marinospirillum, clustering with M. celere, M. alkaliphilum, M. minutulum, M. megaterium and M. insulare (with 96.4, 94.6, 93.1, 92.4 and 92.1 % 16S rRNA gene sequence similarities, respectively). The chemotaxonomic properties of strain F3212T were similar to those of members of the genus Marinospirillum. Q-8 was the sole respiratory ubiquinone and the genomic DNA G+C content was 53.3 mol%. The major fatty acids were C18 : 1 ω9c, C16 : 0 and C18 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentifed lipid and an unidentified aminophospholipid. The average nucleotide identity scores for strains M. celere DSM 18438T and M. minutulum DSM 6287T were 74.5 and 69.4 %, respectively. The DNA-DNA homologies with M. celere DSM 18438T and M. minutulum DSM 6287T were less than 20 %. It's concluded that strain F3212T represents a new species of the genus Marinospirillum, for which the name Marinospirillum perlucidum sp. nov. is proposed. The type strain is F3212T (=KCTC 52892T=MCCC 1H00198T).
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Ferruginivarius sediminum gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2019; 69:3056-3061. [PMID: 31310196 DOI: 10.1099/ijsem.0.003589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic, oxidase-negative, catalase-positive bacillus, designated WD2A32T, was isolated from a marine solar saltern in the coast of Weihai, Shandong Province, PR China. Strain WD2A32T grew optimally at 37-40 °C (range, 20-45 °C) and pH 7.0-7.5 (range, 6.5-8.0) and was tolerant to 6-8 % (w/v) NaCl (range, 2-12 %). The 16S rDNA of strain WD2A32T was most similar (93.5 %) to that of Rhodovibrio salinarumDSM 9154T (the type species of the genus Rhodovibrio), followed by Limimonas halophilaDSM 25584T (92.4 %; the type species of the genus Limimonas). The similarities to the type strains of the genera Pelagibiusand Limibacilluswere less than 91.0 %. The draft genome sequence of strain WD2A32T contained 72 contigs (>507 bp) of 4 237 996 bp with a DNA G+C content of 65.5 mol%. The major polar lipids of strain WD2A32T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and unidentified aminolipids; major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C19 : 0 cyclo ω8c; the major respiratory quinone was Q-10. On the basis of the results from chemotaxonomic, physiological and biochemical analyses, strain WD2A32T represents a novel species of a novel genus in the family Rhodospirillaceae, for which the name Ferruginivarius sediminum gen. nov., sp. nov. has been proposed. The type strain is WD2A32T (=KCTC 52888T=MCCC 1H00201T).
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Abstract
In the present paper, we describe a new species of the genus Flavobacterium, designated as strain 1E403T, which was isolated from a soil sample collected from the Arctic. Strain 1E403T was Gram-stain-negative, yellow-pigmented, rod-shaped, gliding and aerobic. Growth occurred at 4-37 °C (optimum, 28 °C), pH 6.0-9.0 (pH 7.0) and with 0-2 % (w/v) NaCl (0 %) on modified marine agar 2216. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain 1E403T was affiliated with the genus Flavobacterium and was more closely related to Flavobacterium subsaxonicum DSM 21790T (96.6 %) than to other species. In silico genomic comparisons, including average nucleotide identity and the digital DNA-DNA hybridization values, showed 73.9 % and 18.8 % identity to the closest relative Flavobacterium subsaxonicum DSM 21790T, respectively. The average amino acid identity value between strain 1E403T and Flavobacterium aquatile DSM 1132T was 63.8 %. The DNA G+C content of the strain was 36.8 %, while the sole respiratory quinone was menaquinone-6. Iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major fatty acids (>10 %) of strain 1E403T. The polar lipid profile of strain 1E403T contained phosphatidylethanolamine, four unidentified aminolipids and two unidentified phospholipids. Based on the phenotypic characteristics, chemotaxonomic characteristics and phylogenetic inference, strain 1E403T represents a novel species of the genus Flavobacterium, and we propose the name Flavobacterium cerinum sp. nov. The type strain of Flavobacterium cerinum sp. nov. is 1E403T (=KCTC 62960T=MCCC 1H00356T).
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Functions of a Glucan Synthase Gene GFGLS in Mycelial Growth and Polysaccharide Production of Grifola frondosa. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8875-8883. [PMID: 31347830 DOI: 10.1021/acs.jafc.9b03569] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Glucan synthase (GLS) gene is known to be involved in the fungal biosynthesis of cell wall, differentiation, and growth. In the present study, a glucan synthase gene (GFGLS) in the edible mushroom Grifola frondosa with a full sequence of 5927 bp encoding a total of 1781 amino acids was cloned and characterized for the first time. GFGLSp is a membrane protein containing two large transmembrane domains connected with a hydrophilic cytoplasmic domain. With a constructed dual promoter RNA silencing vector pAN7-gfgls-dual, a GFGLS-silencing transformant iGFGLS-3 had the lowest GFGLS transcriptional expression level (26.1%) with a shorter length and thinner appearance of the mycelia, as well as decreased mycelial biomass and exo-polysaccharide production of 5.02 and 0.38 g/L, respectively. Further analysis indicated that GFGLS silence influenced slightly the monosaccharide compositions and ratios of mycelial and exo-polysaccharide. These findings suggest that GFGLS could affect mycelial growth and polysaccharide production by downregulating the glucan synthesis.
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Maribellus luteus gen. nov., sp. nov., a marine bacterium in the family Prolixibacteraceae isolated from coastal seawater. Int J Syst Evol Microbiol 2019; 69:2388-2394. [DOI: 10.1099/ijsem.0.003495] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Jannaschia formosa sp. nov., isolated from marine saltern sediment. Int J Syst Evol Microbiol 2019; 69:2037-2042. [DOI: 10.1099/ijsem.0.003424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Lujinxingia litoralis gen. nov., sp. nov. and Lujinxingia sediminis sp. nov., two new representatives in the order Bradymonadales. Int J Syst Evol Microbiol 2019; 69:2767-2774. [PMID: 31237538 DOI: 10.1099/ijsem.0.003556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, two bacterial strains designated B210T and SEH01T, isolated from coastal sediment sampled in Weihai, PR China, were characterized using a polyphasic approach. Strains were Gram-stain-negative, facultative anaerobic, rod-shaped and motile. According to the results of phylogenetic analyses based on their 16S rRNA genes, these two strains should be classified under the order Bradymonadales and they both show <90 % sequence similarities with Bradymonas sediminis FA350T. Moreover, strain B210T showed 98.6 % sequence similarity to strain SEH01T. Genomic characteristics including average nucleotide identity and in silico DNA-DNA hybridization values clearly separated strain B210T from strain SEH01T. The sole quinone of these two strains was menaquinone MK-7, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. Iso-C15 : 0 was the major fatty acid in both strains B210T and SEH01T, and iso-C14 : 0 3-OH was also a major fatty acid for strain SEH01T. Based on the polyphasic analysis, these two strains represent two novel species of a new genus within the family Bradymonadaceae. Consequently, the novel genus Lujinxingia gen. nov. is proposed, containing two new species Lujinxingia litoralis gen. nov. sp. nov. and Lujinxingia sediminis sp. nov., with strain B210T (=KCTC 42951T=CGMCC 1.16770T) and strain SEH01T (=KCTC 42950T=DSM 101859T) as the type strains, respectively.
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Abstract
A Gram-stain negative, spherical, obligately aerobic bacterium, designated strain WN38T, was isolated from a marine solar saltern on the coast of Weihai, China. Optimal growth occurred at 33 °C, pH 7.0-7.5 and in the presence of 3-4 % (w/v) NaCl. The genome of strain WN38T was found to contain the genes necessary for arsenate reductase and related proteins, indicating that it may have potential in bioremediation of heavy metal polluted environments. Comparative 16S rRNA gene sequence analysis showed that strain WN38T represented a member of the genus Coraliomargarita, and was related most closely to Coraliomargarita akajimensis KCTC 12865T (95.7 %). Pairwise sequence similarities to all other type strains of species were below 90 %. Genome-based calculations (average nucleotide identity, genome-to-genome distance and DNA G+C percentage) and results of pairwise amino acid identity (AAI >60 %) and percentage of conserved proteins (POCP >50 %) also indicated clearly that strain WN38T represents a novel species within this genus. Different phenotypic analyses, such as the detection of a quinone system composed of the sole respiratory quinone was menaquinone-7 (MK-7) and a fatty acid profile with iso-C14 : 0, C18 : 0 and C18 : 1ω9c as major components, supported this finding at the same time as contributing to a comprehensive characterization of strain WN38T. On the basis of its phenotypic and genotypic properties, strain WN38T represents a novel species of the genus Coraliomargarita, for which the name Coraliomargaritasinensis sp. nov. is proposed. The type strain is WN38T (=KCTC 62602T=MCCC 1H00313T).
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Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. MICROBIOME 2018; 6:230. [PMID: 30587241 PMCID: PMC6307301 DOI: 10.1186/s40168-018-0613-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be "culturable" may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. RESULTS We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the "uncultured" not only through enriching the abundance of "uncultured," but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. CONCLUSIONS Considering that cultivation techniques must evolve further-from axenic to mixed cultures-for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.
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Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda. Int J Syst Evol Microbiol 2017; 67:5139-5143. [PMID: 29043952 DOI: 10.1099/ijsem.0.002432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1T, was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1T in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculumagarivorans sp. nov. is proposed. The type strain is HZ1T (=MCCC 1H00174T=KCTC 52476T).
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Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Bioinformatic Identification of Potential MicroRNAs and Their Targets in the Lingzhi or Reishi Medicinal Mushroom Ganoderma lucidum (Higher Basidiomycetes). Int J Med Mushrooms 2015; 17:783-97. [PMID: 26559864 DOI: 10.1615/intjmedmushrooms.v17.i8.80] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MicroRNAs (miRNAs) are a class of small, endogenous, noncoding RNA molecules that negatively regulate gene expression at the transcriptional or the post-transcriptional level. Although a large number of miRNAs have been identified in many species, especially model plants and animals, miRNAs in fungi remain largely unknown. In this study, based on a database of expressed sequence tags in Ganoderma lucidum, 89 potential miRNAs were identified using computational methods. Real-time polymerase chain reaction analysis of miRNA-like samples prepared from G. lucidum at different development stages revealed that miRNA-like RNAs were differentially expressed in different stages. Furthermore, a total of 28 potential targets were found based on near-perfect or perfect complementarity between the randomly selected 9 miRNA-like RNAs and the target sequences, and potential targets for G. lucidum miRNA-like RNAs were predicted. Finally, we studied the expression pattern of 4 target genes in 3 different development stages of G. lucidum to further understand the mechanism of interaction between miRNA-like RNAs and their target genes. Our analysis paves the way toward identifying fungal miRNA-like RNAs that might be involved in various physiological and cellular differentiation processes.
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The cloning, characterization, and functional analysis of a gene encoding an isopentenyl diphosphate isomerase involved in triterpene biosynthesis in the Lingzhi or reishi medicinal mushroom Ganoderma lucidum (higher Basidiomycetes). Int J Med Mushrooms 2013; 15:223-32. [PMID: 23662611 DOI: 10.1615/intjmedmushr.v15.i3.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
An isopentenyl diphosphate isomerase (IDI) gene, GlIDI, was isolated from Ganoderma lucidum, which produces triterpenes through the mevalonate pathway. The open reading frame of GlIDI encodes a 252 amino acid polypeptide with a theoretical molecular mass of 28.71 kDa and a theoretical isoelectric point of 5.36. GlIDI is highly homologous to other fungal IDIs and contains conserved active residues and nudix motifs shared by the IDI protein family. The color complementation assay indicated that GlIDI can accelerate the accumulation of β-carotene and confirmed that the cloned complementary DNA encoded a functional GlIDI protein. Gene expression analysis showed that the GlIDI transcription level was relatively low in the mycelia and reached a relatively high level in the mushroom primordia. In addition, its expression level could be up-regulated by 254 µM methyl jasmonate. Our results suggest that this enzyme may play an important role in triterpene biosynthesis.
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Profiling and quantifying differential gene transcription provide insights into ganoderic acid biosynthesis in Ganoderma lucidum in response to methyl jasmonate. PLoS One 2013; 8:e65027. [PMID: 23762280 PMCID: PMC3676390 DOI: 10.1371/journal.pone.0065027] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/21/2013] [Indexed: 01/09/2023] Open
Abstract
Ganoderma lucidum is a mushroom with traditional medicinal properties that has been widely used in China and other countries in Eastern Asia. Ganoderic acids (GA) produced by G. lucidum exhibit important pharmacological activities. Previous studies have demonstrated that methyl jasmonate (MeJA) is a potent inducer of GA biosynthesis and the expression of genes involved in the GA biosynthesis pathway in G. lucidum. To further explore the mechanism of GA biosynthesis, cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) was used to identify genes that are differentially expressed in response to MeJA. Using 64 primer combinations, over 3910 transcriptionally derived fragments (TDFs) were obtained. Reliable sequence data were obtained for 390 of 458 selected TDFs. Ninety of these TDFs were annotated with known functions through BLASTX searching the GenBank database, and 12 annotated TDFs were assigned into secondary metabolic pathways by searching the KEGGPATHWAY database. Twenty-five TDFs were selected for qRT-PCR analysis to confirm the expression patterns observed with cDNA-AFLP. The qRT-PCR results were consistent with the altered patterns of gene expression revealed by the cDNA-AFLP technique. Additionally, the transcript levels of 10 genes were measured at the mycelium, primordia, and fruiting body developmental stages of G. lucidum. The greatest expression levels were reached during primordia for all of the genes except cytochrome b2 reached its highest expression level in the mycelium stage. This study not only identifies new candidate genes involved in the regulation of GA biosynthesis but also provides further insight into MeJA-induced gene expression and secondary metabolic response in G. lucidum.
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