scholarly journals Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics

2019 ◽  
Author(s):  
Mahdi Ghanbari ◽  
Mansooreh Jami ◽  
Mohsen Shahriari Moghadam ◽  
Konrad J. Domig
Keyword(s):  
16S Rrna ◽  
Habitat Restoration ◽  
Marine Pollution ◽  
Mangrove Ecosystem ◽  
Rrna Gene ◽  
Mangrove Forests ◽  
North West ◽  
The North ◽  
Marine Habitats ◽  
16S Rrna Metagenomics

AbstractWith an area of 390 hectares, the mangrove forests of Nayband Bay are the widest mangrove communities above 27 degrees latitude in the Persian Gulf. They are the last dense, extensive structures of these ecosystems found in the north-west Indian Ocean. Growing industrial activities near the Nayband Bay and the consequent marine pollution has resulted in damage and threatened different marine habitats in recent years. To date, a comprehensive description of the microbial life in the mangrove ecosystem that has been exposed to oil contamination is lacking. This information could significantly contribute to a better overview of the function and resilience of the ecosystem. This work represents a first effort to better understand the Nayband Bay mangrove microbiology by applying 16S rRNA metagenomics. A total of 65,408 readings from the V3–V4 16S rRNA gene regions were obtained from 24 sediment samples, each measuring 440 bp. Most sequences belonged to members of the Proteobacteria phylum (mainly γ-Proteobacteria); however, members of the Bacteroidetes phylum (mainly Flavobacteriia) were also well represented in the samples. We discovered that the community of this ecosystem strongly exhibit typical structures of oil-contaminated marine environments. This is likely due to the growing industrial activity in the area and its consequent marine polluting effects. The use of practicable and applicable bioremediation protocols for habitat restoration in this valuable area is needed.

Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family Pseudonocardiaceae

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2813-2818 ◽  
Author(s):  
Zhan-Feng Xia ◽  
Tong-Wei Guan ◽  
Ji-Sheng Ruan ◽  
Ying Huang ◽  
Li-Li Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
The Family

A novel filamentous actinomycete strain, designated TRM 46004T, was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64′ N 89° 26′ E), north-west China. The isolate was characterized using a polyphasic approach. The isolate formed abundant aerial mycelium with few branches and vegetative mycelium, occasionally twisted and coiled; spherical sporangia containing one to several spherical spores developed at the ends of short sporangiophores on aerial mycelium. The G+C content of the DNA was 65.2 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and xylose, galactose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H10). The major fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 46004T formed a distinct lineage within the family Pseudonocardiaceae and showed 91.7–96.1 % 16S rRNA gene sequence similarity with members of the family Pseudonocardiaceae . On the basis of the evidence from this polyphasic study, a novel genus and species, Longimycelium tulufanense gen. nov., sp. nov., are proposed. The type strain of Longimycelium tulufanense is TRM 46004T ( = CGMCC 4.5737T = NBRC 107726T).

Report on four deep-water barnacles (Cirripedia, Thoracica) from the north west Pacific, with remarks on Trianguloscalpellum regium (Wyville-Thomson, 1873)

Zootaxa ◽  
2019 ◽  
Vol 4565 (2) ◽  
pp. 201 ◽  
Author(s):  
ZHIBIN GAN ◽  
XINZHENG LI
Keyword(s):  
16S Rrna ◽  
Deep Water ◽  
Mariana Trench ◽  
North West ◽  
The North ◽  
Deep Water Species ◽  
First Time ◽  
Distribution Record ◽  
Water Species ◽  
New Distribution

Four deep-water species of stalked barnacles were collected by the manned submersibles Jiaolong and Shenhaiyongshi during recent expeditions. Trianguloscalpellum regium (Wyville-Thomson, 1873), collected from the Mariana Trench at a depth of 5,462 m, represents a new distribution record. Glyptelasma gigas (Annandale, 1916), Poecilasma litum Pilsbry, 1907 and Poecilasma obliqua Hoek, 1907, collected from the South China Sea, are recorded for the first time from a mud volcano environment. Detailed photographs of these four species are presented and their partial sequences of 16S rRNA and mt COI genes are provided. 

scholarly journals Bacteroidales Diversity in Ring-Billed Gulls (Laurus delawarensis) Residing at Lake Michigan Beaches

2009 ◽  
Vol 75 (6) ◽  
pp. 1525-1533 ◽  
Author(s):  
Sonja N. Jeter ◽  
Colleen M. McDermott ◽  
Patricia A. Bower ◽  
Julie L. Kinzelman ◽  
Melinda J. Bootsma ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Lake Michigan ◽  
Rrna Gene ◽  
Fecal Indicator ◽  
Fecal Samples ◽  
Operational Taxonomic Units ◽  
The North ◽  
The Family ◽  
Sample Representation

ABSTRACT This study investigated the occurrence and diversity of Bacteroidales fecal bacteria in gulls residing in the Great Lakes region. Members of this bacterial order have been widely employed as human and bovine host-specific markers of fecal pollution; however, few studies have focused on gulls, which can be a major source of fecal indicator bacteria and pathogens at beaches. We found a low but consistent occurrence of Bacteroidales in gulls at five beaches in three different counties spanning the Wisconsin shoreline of Lake Michigan. The percentages of gulls positive for Bacteroidales were 4 to 8% at beaches in the southern part of the state and 8 to 50% at beaches in the north. Sequencing of 931 clones from seven gull Bacteroidales 16S rRNA gene libraries revealed a large amount of diversity in both individual and pooled gull fecal samples. Two libraries constructed from pooled gull fecal samples (n = 5 and n = 6) did not have a greater richness of sequences than individual samples, suggesting that even within a single gull diversity is high and an extensive sequencing effort is needed to characterize the populations. Estimates of the numbers of operational taxonomic units (OTUs) for the libraries obtained using different similarity levels revealed a large amount of microdiveristy with a limited number of OTUs at the 95% similarity level. Gull sequences were clustered by the beach from which they were collected, suggesting that there were geographic effects on the distribution of Bacteriodales. More than 53% of the 16S rRNA gene sequences from gulls at the southern beaches were associated with the family Porphyromonadaceae, primarily the genus Parabacteroides, whereas sequences from gulls at the northern beaches were comprised of Bacteroidaceae and Prevotellaceae sequences. Comparison of gull sequences with sequences from goose, canine, raccoon, and sewage sources revealed distinct clusters of closely related gull sequences; however, these sequences were widely dispersed across a dendrogram that included all other sources, including previously characterized gull Bacteroidales from other studies, suggesting that geographic influence or simply sample representation plays a greater role in the observed population structure than strictly the host gut environment.

scholarly journals Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats

2011 ◽  
Vol 61 (6) ◽  
pp. 1418-1424 ◽  
Author(s):  
Manuela Filippini ◽  
Andres Kaech ◽  
Urs Ziegler ◽  
Homayoun C. Bagheri
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The North ◽  
Gram Staining

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3T represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3T ( = DSM 22564T  = CCUG 58137T).

scholarly journals Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus)

2010 ◽  
Vol 60 (4) ◽  
pp. 892-895 ◽  
Author(s):  
José Luis Balcázar ◽  
José Pintado ◽  
Miquel Planas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Positive Staining ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
North West ◽  
Hippocampus Guttulatus

A Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1T) was isolated from faeces of wild long-snouted seahorses (Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1T grew at 10–30 °C and pH 5.5–9 (optimally at 20 °C and pH 7.2) and with 0–7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1T was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5aT (96.6 %), B. shackletonii LMG 18435T (96.0 %) and B. isabeliae CVS-8T (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1 ω11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1T to the genus Bacillus. Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1T represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1T (=DSM 21539T =LMG 24668T).

scholarly journals Aerobic Anoxygenic Photosynthesis in Roseobacter Clade Bacteria from Diverse Marine Habitats

2003 ◽  
Vol 69 (9) ◽  
pp. 5051-5059 ◽  
Author(s):  
Martin Allgaier ◽  
Heike Uphoff ◽  
Andreas Felske ◽  
Irene Wagner-Döbler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marker Gene ◽  
Bacterial Photosynthesis ◽  
Rrna Gene ◽  
Physiological Level ◽  
Anoxygenic Photosynthesis ◽  
Marine Habitats ◽  
Dinoflagellate Cultures ◽  
Aerobic Anoxygenic Photosynthesis

ABSTRACT The marine Roseobacter clade comprises several genera of marine bacteria related to the uncultured SAR83 cluster, the second most abundant marine picoplankton lineage. Cultivated representatives of this clade are physiologically heterogeneous, and only some have the capability for aerobic anoxygenic photosynthesis, a process of potentially great ecological importance in the world's oceans. In an attempt to correlate phylogeny with ecology, we investigated the diversity of Roseobacter clade strains from various marine habitats (water samples, biofilms, laminariae, diatoms, and dinoflagellate cultures) by using the 16S rRNA gene as a phylogenetic marker gene. The potential for aerobic anoxygenic photosynthesis was determined on the genetic level by PCR amplification and sequencing of the pufLM genes of the bacterial photosynthesis reaction center and on the physiological level by detection of bacteriochlorophyll (Bchl) a. A collection of ca. 1,000 marine isolates was screened for members of the marine Roseobacter clade by 16S rRNA gene-directed multiplex PCR and sequencing. The 42 Roseobacter clade isolates found tended to form habitat-specific subclusters. The pufLM genes were detected in two groups of strains from dinoflagellate cultures but in none of the other Roseobacter clade isolates. Strains within the first group (the DFL-12 cluster) also synthesized Bchl a. Strains within the second group (the DFL-35 cluster) formed a new species of Roseovarius and did not produce Bchl a under the conditions investigated here, thus demonstrating the importance of genetic methods for screening of cultivation-dependent metabolic traits. The pufL genes of the dinoflagellate isolates were phylogenetically closely related to pufL genes from Betaproteobacteria, confirming similar previous observations which have been interpreted as indications of gene transfer events.

scholarly journals Amycolatopsis salitolerans sp. nov., a filamentous actinomycete isolated from a hypersaline habitat

2012 ◽  
Vol 62 (1) ◽  
pp. 23-27 ◽  
Author(s):  
Tong-Wei Guan ◽  
Zhan-Feng Xia ◽  
Shu-Kun Tang ◽  
Nan Wu ◽  
Zheng-Jun Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
West China ◽  
North West ◽  
Actinomycete Strain

A novel actinomycete strain, designated TRM F103T, was isolated from a hypersaline habitat of the Tarim basin in Xinjiang province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Amycolatopsis and was most closely related to Amycolatopsis halophila YIM 93223T (99.3 % 16S rRNA gene sequence similarity). However, DNA–DNA relatedness between these two strains, based on triplicate experiments, was only 31.6 %. The isolate contained meso-diaminopimelic acid and ribose, glucose and galactose as the major whole-cell sugars. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C16 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and glucosamine-containing phospholipids. The G+C content of the genomic DNA was 66.4 mol%. The phenotypic data clearly distinguished the isolate from its closest relatives. The combined phylogenetic, chemotaxonomic and phenotypic data indicate that the isolate represents a novel species of the genus Amycolatopsis. The proposed name is Amycolatopsis salitolerans sp. nov., with TRM F103T ( = JCM 15899T = CCTCC AB 208326T) as the type strain.

scholarly journals Zhihengliuella halotolerans gen. nov., sp. nov., a novel member of the family Micrococcaceae

2007 ◽  
Vol 57 (5) ◽  
pp. 1018-1023 ◽  
Author(s):  
Yu-Qin Zhang ◽  
Peter Schumann ◽  
Li-Yan Yu ◽  
Hong-Yu Liu ◽  
Yue-Qin Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molar Ratio ◽  
Rrna Gene ◽  
West China ◽  
Qinghai Province ◽  
North West ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Unknown Phospholipid

The actinobacterial strain YIM 70185T was isolated from a saline soil sample collected from Qinghai province, north-west China, and subjected to a taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed 93.5–96.4 % similarity to members of related genera in the family Micrococcaceae. In the phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70185T formed a separate clade next to the genera Micrococcus and Citricoccus within the family Micrococcaceae. The peptidoglycan type was A4α, l-lys–l-ala–l-Glu. Cell-wall sugars contained glucose and tyvelose. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown glycolipid. The menaquinones were MK-9, MK-10 and MK-8 (molar ratio 5 : 2 : 1). The major fatty acids were ai-C15 : 0 and i-C15 : 0 and the DNA G+C content was 66.5 mol%. These chemotaxonomic profiles supported the assignment of strain YIM 70185T to a novel genus within the family Micrococcaceae. The name Zhihengliuella halotolerans gen. nov., sp. nov. is proposed. The type strain of Zhihengliuella halotolerans is YIM 70185T (=DSM 17364T=KCTC 19085T).

scholarly journals Georgenia halophila sp. nov., a halophilic actinobacterium isolated from a salt lake

2010 ◽  
Vol 60 (6) ◽  
pp. 1317-1421 ◽  
Author(s):  
Shu-Kun Tang ◽  
Yun Wang ◽  
Jae-Chan Lee ◽  
Kai Lou ◽  
Dong-Jin Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
North West ◽  
Diamino Acid ◽  
Unknown Phospholipid ◽  
Phosphatidylinositol Mannosides

A Gram-stain-positive actinobacterium, designated strain YIM 93316T, was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 10–45 °C, at pH 6–9 and in the presence of 1–15 % (w/v) NaCl, but no growth was observed in the absence of NaCl. The cell-wall diamino acid contained alanine, glutamine and lysine with peptidoglycan type A4α. Polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The predominant menaquinone was MK-8(H4). The major fatty acids were anteiso-C15 : 0 and anteiso-C15 : 1. The DNA G+C content of strain YIM 93316T was 70.1 mol%. Chemotaxonomic properties supported the affiliation of strain YIM 93316T to the genus Georgenia, and this was supported by phylogenetic analysis based on 16S rRNA gene sequences. Levels of 16S rRNA gene sequence similarity between strain YIM 93316T and Georgenia thermotolerans TT02-04T, Georgenia ruanii YIM 004T and Georgenia muralis 1A-CT were 96.6, 96.5 and 96.3 %, respectively. Data from fatty acid, physiological and biochemical tests allowed the clear phenotypic differentiation of strain YIM 93316T from recognized members of the genus Georgenia. On the basis of evidence from the present polyphasic study, strain YIM 93316T is considered to represent a novel species of the genus Georgenia, for which the name Georgenia halophila sp. nov. is proposed. The type strain is YIM 93316T (=DSM 21365T =CCTCC AB 208144T).

Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

Phytotaxa ◽  
2017 ◽  
Vol 307 (4) ◽  
pp. 263
Author(s):  
T. BHUVANESHWARI ◽  
M. SHYLAJANACIYAR ◽  
P. ARUL PRAKASAM ◽  
K. EZHILMARAN ◽  
L. KARTHICK ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Evolutionary Relationship ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Internal Transcribed Spacer Region ◽  
Ultrastructural Studies ◽  
Marine Habitats

Cyanobacteria, the primordial oxygenic photosynthetic prokaryotes encompass a wide spectrum of morphologies and ecologies. The diversity of twelve marine unicellular cyanobacteria isolated from different marine habitats was analyzed morphologically. The evolutionary relationship among the investigated strains was examined by phylogenetic analysis of nearly complete 16S rRNA gene and 16-23S internal transcribed spacer region. Phylogenetic analysis of both 16S rRNA genes and internal spacer regions exhibited coherent clustering patterns. The genetic relatedness of the investigated strains was largely congruent with morphology-based taxonomic groupings. All the investigated strains possess both the types of tRNA (tRNAIle and tRNAAla) in their 16-23S internal spacer regions and significantly varied GC contents and spacer sequence lengths. Further, ultrastructural studies provide a more valuable insight into the cyanobacterial taxa studied. Our study helps to apply the polyphasic approach (use of morphology, ultra-structure, ecology, and molecular analysis of complete 16S rRNA genes and 16-23S internal spacer regions) to resolve taxonomic ambiguities and provide a fairly robust cyanobacterial classification system among the unicellular forms studied.

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