scholarly journals Host-Symbiont Relationships in Hydrothermal Vent Gastropods of the Genus Alviniconcha from the Southwest Pacific

2006 ◽  
Vol 72 (2) ◽  
pp. 1388-1393 ◽  
Author(s):  
Yohey Suzuki ◽  
Shigeaki Kojima ◽  
Takenori Sasaki ◽  
Masae Suzuki ◽  
Takashi Utsumi ◽  
...  
Keyword(s):  
Hydrothermal Vent ◽  
Tricarboxylic Acid Cycle ◽  
Distinct Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
New Host ◽  
Southwest Pacific ◽  
Bacterial Endosymbionts ◽  
Host Lineage ◽  
Manus Basin

ABSTRACT Hydrothermal vent gastropods of the genus Alviniconcha are unique among metazoans in their ability to derive their nutrition from chemoautotrophic γ- and ε-proteobacterial endosymbionts. Although host-symbiont relationships in Alviniconcha gastropods from the Central Indian Ridge in the Indian Ocean and the Mariana Trough in the Western Pacific have been studied extensively, host-symbiont relationships in Alviniconcha gastropods from the Southwest Pacific remain largely unknown. Phylogenetic analysis using mitochondrial cytochrome c oxidase subunit I gene sequences of host gastropods from the Manus, North Fiji, and Lau Back-Arc Basins in the Southwest Pacific has revealed a new host lineage in a Alviniconcha gastropod from the Lau Basin and the occurrence of the host lineage Alviniconcha sp. type 2 in the Manus Basin. Based on 16S rRNA gene sequences of bacterial endosymbionts, two γ-proteobacterial lineages and one ε-proteobacterial lineage were identified in the present study. The carbon isotopic compositions of the biomass and fatty acids of the gastropod tissues suggest that the γ- and ε-proteobacterial endosymbionts mediate the Calvin-Benson cycle and the reductive tricarboxylic acid cycle, respectively, for their chemoautotrophic growth. Coupling of the host and symbiont lineages from the three Southwest Pacific basins revealed that each of the Alviniconcha lineages harbors different bacterial endosymbionts belonging to either the γ- or ε-Proteobacteria. The host specificity exhibited in symbiont selection provides support for the recognition of each of the host lineages as a distinct species. The results from the present study also suggest the possibility that Alviniconcha sp. types 1 and 2 separately inhabit hydrothermal vent sites approximately 120 m apart in the North Fiji Basin and 500 m apart in the Manus Basin.

scholarly journals New record of the hydrothermal vent-endemic polychaete Archinome jasoni Borda et al., 2013 (Annelida, Amphinomidae) from the Northwest Pacific

Check List ◽  
2019 ◽  
Vol 15 (3) ◽  
pp. 523-526
Author(s):  
Naoto Jimi ◽  
Chong Chen ◽  
Kajihara Hiroshi
Keyword(s):  
Hydrothermal Vent ◽  
New Record ◽  
Okinawa Trough ◽  
First Record ◽  
Northwest Pacific ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Sequences ◽  
Southwest Pacific ◽  
28S Rrna Gene

The hydrothermal vent-endemic polychaete Archinome jasoni Borda et al., 2013 is known from the Atlantic, Indian, and Southwest Pacific oceans. In this study, we report A. jasoni from Okinawa Trough, Japan, which represents the first record of this species and the genus from the Northwest Pacific. We determined 16S and 28S rRNA gene sequences from 1 of the 7 specimens collected. We compared our Northwest Pacific specimens to specimens from the Southwest Pacific, Atlantic, and Indian oceans, and our specimen was genetically most closely related to individuals from the Southwest Pacific.

scholarly journals Unique clade of alphaproteobacterial endosymbionts induces complete cytoplasmic incompatibility in the coconut beetle

2017 ◽  
Vol 114 (23) ◽  
pp. 6110-6115 ◽  
Author(s):  
Shun-ichiro Takano ◽  
Midori Tuda ◽  
Keiji Takasu ◽  
Naruto Furuya ◽  
Yuya Imamura ◽  
...  
Keyword(s):  
Cytoplasmic Incompatibility ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Biological Control Agent ◽  
Illumina Miseq ◽  
Distinct Species ◽  
Rrna Gene ◽  
Asian Clade ◽  
The Pacific ◽  
Bacterial Endosymbionts ◽  
Unique Clade

Maternally inherited bacterial endosymbionts in arthropods manipulate host reproduction to increase the fitness of infected females. Cytoplasmic incompatibility (CI) is one such manipulation, in which uninfected females produce few or no offspring when they mate with infected males. To date, two bacterial endosymbionts,WolbachiaandCardinium, have been reported as CI inducers. OnlyWolbachiainduces complete CI, which causes 100% offspring mortality in incompatible crosses. Here we report a third CI inducer that belongs to a unique clade of Alphaproteobacteria detected within the coconut beetle,Brontispa longissima. This beetle comprises two cryptic species, the Asian clade and the Pacific clade, which show incompatibility in hybrid crosses. Different bacterial endosymbionts, a unique clade of Alphaproteobacteria in the Pacific clade andWolbachiain the Asian clade, induced bidirectional CI between hosts. The former induced complete CI (100% mortality), whereas the latter induced partial CI (70% mortality). Illumina MiSeq sequencing and denaturing gradient gel electrophoresis patterns showed that the predominant bacterium detected in the Pacific clade ofB. longissimawas this unique clade of Alphaproteobacteria alone, indicating that this endosymbiont was responsible for the complete CI. Sex distortion did not occur in any of the tested crosses. The 1,160 bp of 16S rRNA gene sequence obtained for this endosymbiont had only 89.3% identity with that ofWolbachia, indicating that it can be recognized as a distinct species. We discuss the potential use of this bacterium as a biological control agent.

scholarly journals Methanofervidicoccus abyssi gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea

2019 ◽  
Vol 69 (4) ◽  
pp. 1225-1230 ◽  
Author(s):  
Sanae Sakai ◽  
Yoshihiro Takaki ◽  
Masayuki Miyazaki ◽  
Miyuki Ogawara ◽  
Katsunori Yanagawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Hydrothermal Vent ◽  
Caribbean Sea ◽  
Spreading Center ◽  
Amino Acid Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Hydrogenotrophic Methanogen ◽  
Link Type

A novel hydrogenotrophic methanogen, strain HHBT, was isolated from a deep-sea hydrothermal vent chimney sample collected from Beebe Vent Field at the Mid-Cayman Spreading Center, Caribbean Sea. The cells were non-motile regular to irregular cocci possessing several flagella. The novel isolate grew at 60–80 °C, pH 5.0–7.4 and with 1–4 % of NaCl (w/v). The isolate utilized H2/CO2 as the only substrates for growth and methane production. The results of phylogenetic analyses of both 16S rRNA and mcrA gene sequences and comparative genome analysis indicated that HHBT represented a member of the order Methanococcales , and was closely related to the members of the genera Methanothermococcus and Methanotorris . The most closely related species were Methanothermococcus okinawensis IH1T and Methanotorris igneus Kol 5T in comparison of 16S rRNA gene sequences (each with 93 % identity), and Methanotorris formicicus Mc-S-70T in the case of deduced amino acid sequence similarity of mcrA genes (92 % similarity). The ANI and AAI values between HHBT and the members of the genera Methanothermococcus and Methanotorris were 69–72 % and 66–70 %, respectively. Although many of the morphological and physiological characteristics were quite similar between HHBT and the species of the genera Methanothermococcus and Methanotorris , they were distinguishable by the differences in susceptibility to antibiotics, formate utilization, growth temperature and NaCl ranges. On the basis of these phenotypic, phylogenetic and genomic properties, we propose that strain HHBT represents a novel species, of a novel genus, Methanofervidicoccus abyssi gen. nov., sp. nov. The type strain is HHBT (=JCM 32161T=DSM 105918T).

Streptomyces turgidiscabies and Streptomyces reticuliscabiei: one genomic species, two pathogenic groups

2006 ◽  
Vol 56 (12) ◽  
pp. 2771-2776 ◽  
Author(s):  
K. Bouchek-Mechiche ◽  
L. Gardan ◽  
D. Andrivon ◽  
P. Normand
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Common Scab ◽  
Distinct Species ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Streptomyces Turgidiscabies ◽  
Almost All

Three strains of Streptomyces reticuliscabiei and two strains of Streptomyces turgidiscabies were analysed, together with reference and type strains of other Streptomyces species, for phenotypic traits, DNA–DNA relatedness, comparison of 16S rRNA gene sequences and presence of necrotic protein gene (nec1) homologues in order to clarify their phylogenetic relationships. A numerical analysis of phenotypic characteristics showed that S. reticuliscabiei and S. turgidiscabies belong to the same cluster and share almost all morphological and biochemical traits that are important in the identification of Streptomyces species. DNA–DNA hybridization and phylogenetic comparisons of 16S rRNA gene sequences confirmed that the two species are genomically closely related. In contrast, pathological data showed that S. turgidiscabies and S. reticuliscabiei cause two distinct diseases. Gene homologues of nec1 were detected in S. turgidiscabies and other common scab species (Streptomyces scabiei, Streptomyces europaeiscabiei and Streptomyces stelliscabiei), but not in S. reticuliscabiei. To avoid confusion between agents causing separate diseases, it is proposed that the existing distinct species names are retained: S. turgidiscabies involved in common scab and S. reticuliscabiei involved in netted scab.

scholarly journals Microplate Subtractive Hybridization To Enrich for Bacteroidales Genetic Markers for Fecal Source Identification

2005 ◽  
Vol 71 (6) ◽  
pp. 3179-3183 ◽  
Author(s):  
Linda K. Dick ◽  
Michael T. Simonich ◽  
Katharine G. Field
Keyword(s):  
Water Resource Management ◽  
Management Strategies ◽  
Human Health Risk ◽  
Subtractive Hybridization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Specific Primers ◽  
New Host ◽  
One Step ◽  
Or Gene

ABSTRACT The ability to identify sources of fecal pollution plays a key role in the analysis of human health risk and the implementation of water resource management strategies. One approach to this problem involves the identification of bacterial lineages or gene sequences that are found exclusively in a particular host species or group. We used subtractive hybridization to enrich for target host-specific fecal Bacteroidales rRNA gene fragments that were different from those of very closely related reference (subtracter) host sources. Target host rRNA gene fragments were hybridized to subtracter rRNA gene fragments immobilized in a microplate well, and target sequences that did not hybridize were cloned and sequenced for PCR primer design. The use of microplates for DNA immobilization resulted in a one-step subtractive hybridization in which the products could be directly amplified with PCR. The new host-specific primers designed from subtracted target fragments differentiated among very closely related Bacteroidales rRNA gene sequences and distinguished between similar fecal sources, such as elk and cow or human and domestic pet (dog).

scholarly journals Molecular characterization and phylogenetic assessment of a few Dioscorea (Dioscoreaceae) species of North-East India

2019 ◽  
Vol 79 (01) ◽  
Author(s):  
Nilofer Sheikh ◽  
Yogendra Kumar ◽  
A. K. Misra
Keyword(s):  
Molecular Characterization ◽  
Distinct Species ◽  
18S Rrna Gene ◽  
Marker Genes ◽  
Rrna Gene ◽  
Rbcl Gene ◽  
Eastern Region ◽  
Gene Sequences ◽  
Sequence Characterization ◽  
North East

Dioscorea spp. or yam are consumed by the indigenous peoples of North-Eastern region of India as a substitute for potato and most of the species are also used in traditional medicine. North-East region is one of the hotspot for Dioscorea species growing in wild habitat which has not been characterized or identified. In the present study, eight morphologically distinct species of Dioscorea belonging to section Enantiophyllum, Botryosicyos and Opsophyton were subjected to molecular characterization and phylogenetic assessment using three marker genes (18S rDNA, matK and rbcL). The results of sequence characterization of the these genes revealed that 18S rRNA gene was highly conserved than matK and rbcL gene sequences and hence 18Sr RNA gene can be used as better candidates for species delimitation. The phylogenetic analysis of the combined molecular gene sequences also showed that the species belonging to section Enantiophyllum were monophyletic in origin.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

scholarly journals Distribution and recombination of Wolbachia endosymbionts in Korean coleopteran insects

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Gilsang Jeong ◽  
Taeman Han ◽  
Haechul Park ◽  
Soyeon Park ◽  
Pureum Noh
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Surface Protein ◽  
Rrna Gene ◽  
Infection Frequency ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Endosymbiotic Bacteria ◽  
Molecular Machinery ◽  
Broad Scale

Abstract Background Wolbachia are among the most prevalent endosymbiotic bacteria and induce reproductive anomalies in various invertebrate taxa. The bacterium has huge impacts on host reproductive biology, immunity, evolution, and molecular machinery. However, broad-scale surveys of Wolbachia infections at the order scale, including the order Coleoptera, are limited. In this study, we investigated the Wolbachia infection frequency in 201 Coleopteran insects collected in Korea. Results A total of 26 species (12.8%) belonging to 11 families harbored Wolbachia. The phylogenetic trees of based on partial 16S rRNA gene sequences and partial Wolbachia surface protein (wsp) gene sequences were largely incongruent to that of their hosts. This result confirms that Wolbachia evolved independently from their hosts, Conclusion Phylogenetic trees suggest that complex horizontal gene transfer and recombination events occurred within and between divergent Wolbachia subgroups.

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