scholarly journals Fungal Diversity in Intertidal Mudflats and Abandoned Solar Salterns as a Source for Biological Resources

Marine Drugs ◽  
2019 ◽  
Vol 17 (11) ◽  
pp. 601 ◽  
Author(s):  
Heo ◽  
Lee ◽  
Kim ◽  
Kwon ◽  
Park ◽  
...  
Keyword(s):  
Hot Spots ◽  
Fungal Diversity ◽  
Novel Species ◽  
Community Analysis ◽  
The Yellow Sea ◽  
Diversity Analysis ◽  
Tyrosinase Inhibition ◽  
Intertidal Zones ◽  
Cladosporium Sphaerospermum ◽  
Natural Restoration

Intertidal zones are unique environments that are known to be ecological hot spots. In this study, sediments were collected from mudflats and decommissioned salterns on three islands in the Yellow Sea of South Korea. The diversity analysis targeted both isolates and unculturable fungi via Illumina sequencing, and the natural recovery of the abandoned salterns was assessed. The phylogeny and bioactivities of the fungal isolates were investigated. The community analysis showed that the abandoned saltern in Yongyudo has not recovered to a mudflat, while the other salterns have almost recovered. The results suggested that a period of more than 35 years may be required to return abandoned salterns to mudflats via natural restoration. Gigasporales sp. and Umbelopsis sp. were selected as the indicators of mudflats. Among the 53 isolates, 18 appeared to be candidate novel species, and 28 exhibited bioactivity. Phoma sp., Cladosporium sphaerospermum, Penicillium sp. and Pseudeurotium bakeri, and Aspergillus urmiensis showed antioxidant, tyrosinase inhibition, antifungal, and quorum-sensing inhibition activities, respectively, which has not been reported previously. This study provides reliable fungal diversity information for mudflats and abandoned salterns and shows that they are highly valuable for bioprospecting not only for novel microorganisms but also for novel bioactive compounds.

scholarly journals Vibrio marisflavi sp. nov., isolated from seawater

2011 ◽  
Vol 61 (3) ◽  
pp. 568-573 ◽  
Author(s):  
Hong Wang ◽  
Jiwen Liu ◽  
Yan Wang ◽  
Xiao-Hua Zhang
Keyword(s):  
Gene Sequence ◽  
Water Mass ◽  
Cold Water ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Arginine Dihydrolase ◽  
Pr China ◽  
Curved Rods ◽  
Sequence Similarities

A Gram-reaction-negative, facultatively anaerobic bacterial strain, designated WH134T, was isolated from a seawater sample collected at a depth of 10 m near the Yellow Sea Cold Water Mass (YSCWM), 3 ° 59.970′ N 12 ° 0.157′ E, PR China. Cells of strain WH134T were slightly curved rods, motile by means of a polar flagellum and positive for poly-β-hydroxybutyrate (PHB) accumulation. The strain was able to grow in 1–6 % (w/v) NaCl, at pH 5–10 and 16–37 °C but not at 4 or 40 °C. The major cellular fatty acids were summed feature 3 C16  : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C18 : 1 ω7c, C18 : 0 and C14 : 0. The DNA G+C content was 42.5 mol%. Phylogenetic analyses based on 16S rRNA, gyrB, topA, recA, ftsZ, mreB, gapA and rpoA gene sequences revealed that strain WH134T belongs to the genus Vibrio and showed gene sequence similarities of 96.6, 75.7, 74.6, 83.6, 78.9, 82.9, 86.0 and 89.4 % , respectively, to Vibrio rumoiensis S-1T. The possession of a flagellum, activity of arginine dihydrolase and lysine decarboxylase and inability to utilize citrate, however, differentiated strain WH134T from V. rumoiensis DSM 19141T. On the basis of the phenotypic, chemotaxonomic and phylogenetic evidence, strain WH134T represents a novel species of the genus Vibrio, for which the name Vibrio marisflavi sp. nov. is proposed. The type strain is WH134T (=CGMCC 1.8994T =LMG 25284T =DSM 23086T).

scholarly journals Litoricola marina sp. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1303-1306 ◽  
Author(s):  
Ahyoung Choi ◽  
Kiyoung Lee ◽  
Hyun-Myung Oh ◽  
Jing Feng ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Marine Bacterium ◽  
Novel Species ◽  
Bacterial Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-negative, non-pigmented, non-motile, chemoheterotrophic marine bacterium, designated strain IMCC2782T, was isolated from a surface seawater sample of the Yellow Sea, Korea. On the basis of 16S rRNA gene sequence analysis and phenotypic and genotypic characterization, strain IMCC2782T is shown to represent a novel species of the genus Litoricola. Strain IMCC2782T grew at 15–37 °C and tolerated 7.5 % NaCl. Based on 16S rRNA gene sequences, strain IMCC2782T was related most closely to the type strain of Litoricola lipolytica (97.1 % similarity) but showed less than 90 % similarity to the type strains of other bacterial species. The predominant fatty acids were mono-unsaturated C18 : 1 and C16 : 1. The G+C content of the DNA of strain IMCC2782T was 59.6 mol%. A low level of DNA–DNA relatedness (28.1 %) together with several phenotypic characteristics, including enzyme activities, served to differentiate strain IMCC2782T from the type strain of L. lipolytica. Therefore, strain IMCC2782T is considered to represent a novel species of the genus Litoricola, for which the name Litoricola marina sp. nov. is proposed. The type strain is IMCC2782T (=KCTC 22683T =NBRC 105824T).

scholarly journals Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2007 ◽  
Vol 57 (4) ◽  
pp. 856-861 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh
Keyword(s):  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Novel Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Taxonomic Analysis ◽  
Bacterium Strain

A Gram-negative, motile and egg-shaped bacterium, strain TF-218T, was isolated from a tidal flat at Daepo Beach (Yellow Sea), Korea, and subjected to a polyphasic taxonomic analysis. Strain TF-218T grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and an aminolipid. The DNA G+C content was 64.9 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain TF-218T is phylogenetically closely related to the genera Phaeobacter, Leisingera and Marinovum of the Alphaproteobacteria. The phylogenetic and chemotaxonomic similarities suggest that strain TF-218T represents a member of the genus Phaeobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain TF-218T differs from the recognized Phaeobacter species. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain TF-218T represents a novel species of the genus Phaeobacter, for which the name Phaeobacter daeponensis sp. nov. is proposed. The type strain is TF-218T (=KCTC 12794T=JCM 13606T).

scholarly journals Taxonomy, ontogeny and molecular phylogeny of Anteholosticha marimonilata spec. nov. (Ciliophora, Hypotrichida) from the Yellow Sea, China

2011 ◽  
Vol 61 (8) ◽  
pp. 2000-2014 ◽  
Author(s):  
Yuan Xu ◽  
Jie Huang ◽  
Xiaozhong Hu ◽  
Khaled A. S. Al-Rasheid ◽  
Weibo Song ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Yellow Sea ◽  
Gene Sequence ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Sequence Information ◽  
Rrna Gene Sequence ◽  
Cortical Granules

The morphology, morphogenesis and molecular phylogeny of the marine ciliated protozoan Anteholosticha marimonilata spec. nov., isolated from mollusc-farming waters of the Yellow Sea, Qingdao, PR China, were investigated using microscopic observations of live and protargol-impregnated specimens and by small subunit rRNA gene sequence analysis. The novel species could be distinguished by the following features: an elongated elliptical body, in vivo size 80–160 µm × 30–50 µm; an adoral zone consisting of about 36 membranelles; three frontal, one parabuccal, one buccal, two frontoterminal and usually two pretransverse ventral cirri; 10–13 transverse cirri; a midventral complex composed of 12–17 pairs of cirri only, terminating in posterior 1/5; four or five dorsal kineties; two types of colourless cortical granules; four to nine moniliform macronuclear nodules and one to three micronuclei, and a contractile vacuole positioned at mid-body. Hitherto, the ontogenesis of the genus Anteholosticha has been regarded as rather diverse, which was confirmed by the morphogenetic processes of this novel species. The most noteworthy feature of A. marimonilata was that the proter retained almost the entire parental adoral zone except for a few proximal membranelles that were renewed in situ. The SSU rRNA gene sequence information clearly discriminated this isolate from its congeners. Molecular phylogenetic analyses demonstrated, with high statistical support, that A. marimonilata branched as a sister lineage to the Nothoholosticha–Pseudokeronopsis clade and hence belongs to the core part of the order Urostylida.

scholarly journals Eionea flava sp. nov., isolated from coastal seawater, and emended description of the genus Eionea

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2975-2979 ◽  
Author(s):  
Kiwoon Baek ◽  
Ahyoung Choi ◽  
Jang-Cheon Cho
Keyword(s):  
Novel Species ◽  
Polar Lipids ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Gram Staining ◽  
Emended Description ◽  
Unknown Phospholipid

A Gram-staining-negative, non-motile, catalase- and oxidase-positive, facultatively aerobic bacterium, designated IMCC1962T was isolated from a surface seawater sample from the Yellow Sea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC1962T belonged to the genus Eionea, forming a robust clade with members of the genus, and was most closely related to Eionea nigra (97.3  % similarity). DNA–DNA relatedness between strain IMCC1962T and Eionea nigra DSM 19752T was 21.8–26.3  %, which indicated strain IMCC1962T represents a novel genomic species of the genus Eionea. The G+C content of the DNA of strain IMCC1962T was 48.7 mol%. The major isoprenoid quinone was ubiquinone Q-8 and major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c (43.4  %), C18 : 1ω7c and/or C18 : 1ω6c (19.3  %) and C16 : 0 (17.2  %). The polar lipids found in strain IMCC1962T were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, unknown phospholipid, and four unknown polar lipids. Strain IMCC1962T and Eionea nigra DSM 19752T differed from each other in diverse phenotypic characteristics including motility, colony colour and enzyme activities. On the basis of phenotypic and genotypic data, strain IMCC1962T ( = KACC 17481T = NBRC 109703T) represents a novel species of the genus Eionea, for which the name Eionea flava sp. nov. is proposed. An emended description of the genus Eionea is also provided.

scholarly journals Gelidibacter sediminis sp. nov., isolated from a sediment sample of the Yellow Sea

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2304-2309 ◽  
Author(s):  
De-Chao Zhang ◽  
Rosa Margesin
Keyword(s):  
Yellow Sea ◽  
Sediment Sample ◽  
Novel Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
16S Rrna Gene Sequences ◽  
Type Strains ◽  
Sequence Similarities ◽  
Combined Data

The Gram-stain-negative, yellow-pigmented, rod-shaped bacterial strain, designated S11-41T, was isolated from a sediment sample of the Yellow Sea in China. The strain was able to grow well over a wide temperature range (1–35 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S11-41T was related to the members of the genus Gelidibacter, sharing highest sequence similarities with the type strains of Geldibacter salicanalis (98.2 %), Geldibacter algens (97.4 %) and Geldibacter mesophilus (96.9 %). The genomic DNA G+C content of strain S11-41T was 39.2 mol%. The predominant cellular fatty acids were iso-C15 : 0 (13.2 %), iso-C17 : 0 3-OH (12.8 %) and iso-C15 : 1 G (12.2 %). Phosphatidylethanolamine was identified as the major polar lipid. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain S11-41T is a representative of a novel species of the genus Gelidibacter, for which we propose the name Gelidibacter sediminis sp. nov. (type strain S11-41T = DSM 28135T = LMG 28076T).

scholarly journals Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ellen S. Cameron ◽  
Philip J. Schmidt ◽  
Benjamin J.-M. Tremblay ◽  
Monica B. Emelko ◽  
Kirsten M. Müller
Keyword(s):  
Microbial Community ◽  
Pathogenic Bacteria ◽  
Graphical Representation ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
Next Generation Sequencing Data ◽  
Diversity Analysis ◽  
Sequencing Data ◽  
Library Size

AbstractAmplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial community analysis that eliminates the challenges associated with lab cultivation and taxonomic identification through microscopy. In water resources management, it can be especially useful to evaluate ecosystem shifts in response to natural and anthropogenic landscape disturbances to signal potential water quality concerns, such as the detection of toxic cyanobacteria or pathogenic bacteria. Amplicon sequencing data consist of discrete counts of sequence reads, the sum of which is the library size. Groups of samples typically have different library sizes that are not representative of biological variation; library size normalization is required to meaningfully compare diversity between them. Rarefaction is a widely used normalization technique that involves the random subsampling of sequences from the initial sample library to a selected normalized library size. This process is often dismissed as statistically invalid because subsampling effectively discards a portion of the observed sequences, yet it remains prevalent in practice and the suitability of rarefying, relative to many other normalization approaches, for diversity analysis has been argued. Here, repeated rarefying is proposed as a tool to normalize library sizes for diversity analyses. This enables (i) proportionate representation of all observed sequences and (ii) characterization of the random variation introduced to diversity analyses by rarefying to a smaller library size shared by all samples. While many deterministic data transformations are not tailored to produce equal library sizes, repeatedly rarefying reflects the probabilistic process by which amplicon sequencing data are obtained as a representation of the amplified source microbial community. Specifically, it evaluates which data might have been obtained if a particular sample’s library size had been smaller and allows graphical representation of the effects of this library size normalization process upon diversity analysis results.

scholarly journals Five Novel Taxa from Freshwater Habitats and New Taxonomic Insights of Pleurotheciales and Savoryellomycetidae

2021 ◽  
Vol 7 (9) ◽  
pp. 711
Author(s):  
Wei Dong ◽  
Rajesh Jeewon ◽  
Kevin D. Hyde ◽  
Er-Fu Yang ◽  
Huang Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Fungal Diversity ◽  
Yunnan Province ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Taxonomic Study ◽  
Freshwater Fungi ◽  
Incertae Sedis ◽  
Freshwater Habitats ◽  
Novel Taxa

Pleurotheciales is the largest order in Savoryellomycetidae with a large proportion of species known from freshwater habitats. In order to investigate the phylogenetic relationships of taxa within Pleurotheciales and contribute to their diversity, submerged wood was collected from freshwater habitats in China (Yunnan Province) and Thailand. Two dematiaceous, sporodochial hyphomycetes and one annulatascales-like ascomycete with unusual morphology as compared to extant ones were discovered. They were subjected to DNA-based phylogenetic analyses and the results revealed three distinct lineages in Savoryellomycetidae. This morpho-phylo taxonomic study supports the establishment of five novel taxa including two novel genera, Obliquifusoideum and Saprodesmium, and three novel species, Coleodictyospora muriformis, Obliquifusoideum guttulatum and Saprodesmium dematiosporum. Coleodictyospora muriformis and S. dematiosporum are placed in Pleurotheciales, while O. guttulatum is referred to Savoryellomycetidae genera incertae sedis. The phylogenetic relationships are also presented for Coleodictyospora and Pseudocoleodictyospora, which raises an intriguing taxonomic issue. These two genera are positioned in two different classes, viz Sordariomycetes and Dothideomycetes, although they are quite similar except for the presence of a conidial sheath. This study expands our knowledge of the fungal diversity of freshwater fungi, and also indicates that Pleurotheciales species are mostly found in freshwater habitats.

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