scholarly journals Stenotrophomonas-Like Bacteria Are Widespread Symbionts in Cone Snail Venom Ducts

2017 ◽  
Vol 83 (23) ◽  
Author(s):  
Joshua P. Torres ◽  
Maria Diarey Tianero ◽  
Jose Miguel D. Robes ◽  
Jason C. Kwan ◽  
Jason S. Biggs ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Invertebrates ◽  
The Philippines ◽  
Biological Study ◽  
Snail Species ◽  
Rrna Gene ◽  
Cone Snail ◽  
The World ◽  
Cone Snails

ABSTRACT Cone snails are biomedically important sources of peptide drugs, but it is not known whether snail-associated bacteria affect venom chemistry. To begin to answer this question, we performed 16S rRNA gene amplicon sequencing of eight cone snail species, comparing their microbiomes with each other and with those from a variety of other marine invertebrates. We show that the cone snail microbiome is distinct from those in other marine invertebrates and conserved in specimens from around the world, including the Philippines, Guam, California, and Florida. We found that all venom ducts examined contain diverse 16S rRNA gene sequences bearing closest similarity to Stenotrophomonas bacteria. These sequences represent specific symbionts that live in the lumen of the venom duct, where bioactive venom peptides are synthesized. IMPORTANCE In animals, symbiotic bacteria contribute critically to metabolism. Cone snails are renowned for the production of venoms that are used as medicines and as probes for biological study. In principle, symbiotic bacterial metabolism could either degrade or synthesize active venom components, and previous publications show that bacteria do indeed contribute small molecules to some venoms. Therefore, understanding symbiosis in cone snails will contribute to further drug discovery efforts. Here, we describe an unexpected, specific symbiosis between bacteria and cone snails from around the world.

Redescription of the brackish water crab Ptychognathus glaber Stimpson, 1858 based on the topotypic material from the Ogasawara Islands and new record of P. lipkei N.K. Ng, 2010 from Japan (Decapoda: Brachyura: Varunidae)

Zootaxa ◽  
2021 ◽  
Vol 5048 (1) ◽  
pp. 58-76
Author(s):  
TOMOYUKI KOMAI ◽  
TADAFUMI MAENOSONO ◽  
TOSHIFUMI SAEKI ◽  
TOHRU NARUSE
Keyword(s):  
16S Rrna ◽  
Genetic Analysis ◽  
16S Rrna Gene ◽  
New Record ◽  
The Philippines ◽  
Rrna Gene ◽  
Ryukyu Islands ◽  
Ogasawara Islands ◽  
The Ryukyu Islands ◽  
Mitochondrial 16S Rrna Gene

Examination of material from various Japanese localities clarified that the estuarine crab Ptychognathus glaber Stimpson, 1858 is possibly restricted to the Ogasawara Islands, Japan. Specimens from the Ryukyu Islands, thought to represent P. glaber, actually represent P. lipkei N.K. Ng, 2010 instead, previously known only from Cebu, the Philippines. Ptychognathus glaber is redescribed in detail, and differentiating characters between it and P. lipkei are reassessed. Previous literature records of P. glaber are reviewed in the light of our findings. Genetic analysis using partial sequences of the mitochondrial 16S rRNA gene suggests that P. glaber is genetically closer to P. ishii Sakai, 1939 than to P. lipkei, and thus P. ishii is also compared morphologically with P. glaber.  

Down into the Earth: microbial diversity of the deepest cave of the world

Biologia ◽  
2015 ◽  
Vol 70 (8) ◽  
Author(s):  
Ieva Kieraite-Aleksandrova ◽  
Vilius Aleksandrovas ◽  
Nomeda Kuisiene
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Independent Method ◽  
Rrna Gene ◽  
Sampling Depth ◽  
First Report ◽  
The Earth ◽  
The World

AbstractIn our work, microbial diversity of Krubera-Voronja cave was evaluated in the view of the frequency of human visits in different locations as well as the sampling depth. Sampling in this cave was performed at depths of 220 m to 1640 m. Cultivation-independent method, namely barcoded pyrosequencing of 16S rRNA gene, was used for this analysis. Our results demonstrated high bacterial diversity at the phylum and genus levels. We have shown that the bacterial diversity at the phylum level depends on both the sampling depth and the frequency of human visits in Krubera-Voronja cave. Frequently visited locations were more diverse at the phylum level than the rarely visited branches. The total number of bacterial genera both per phylum and per sample correlated with the frequency of human visits but not with the sampling depth. Some genera, found in Krubera-Voronja cave, seem to be absent or very rare in other caves. The present study represents the first report on the microbial diversity in Krubera-Voronja cave

scholarly journals Shewanella affinis sp. nov., isolated from marine invertebrates

2004 ◽  
Vol 54 (4) ◽  
pp. 1089-1093 ◽  
Author(s):  
Elena P. Ivanova ◽  
Olga I. Nedashkovskaya ◽  
Tomoo Sawabe ◽  
Natalia V. Zhukova ◽  
Galina M. Frolova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Marine Invertebrates ◽  
Sequence Similarity ◽  
Tween 20 ◽  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
North West

Four marine bacterial strains, designated KMM 3587T, KMM 3586, KMM 3821 and KMM 3822, were isolated from the sipuncula Phascolosoma japonicum, a common inhabitant of Troitza Bay in the Gulf of Peter the Great (Sea of Japan region), and from an unidentified hydrocoral species collected in Makarov Bay (Iturup Islands), Kuril Islands, North-West Pacific Ocean. The strains were characterized to clarify their taxonomic position. 16S rRNA gene sequences of KMM 3587T and KMM 3586 indicated 99 % similarity to Shewanella colwelliana. Despite such a high level of 16S rRNA gene sequence similarity, DNA–DNA hybridization experiments demonstrated only 45–52 % binding with DNA of S. colwelliana ATCC 39565T. The DNA G+C contents of the novel strains were 45 mol% and the shared level of DNA hybridization was conspecific (81–97 %), indicating that they represent a single genospecies. The novel strains were mesophilic (able to grow at 10–34 °C), neutrophilic and haemolytic, and able to degrade gelatin, casein and Tween 20, 40 and 80, but not starch, agar, elastin, alginate or chitin. The major fatty acids were i13 : 0, i15 : 0, 16 : 0, 16 : 1ω7 and 17 : 1ω8 (68·9 % of total). The major isoprenoid quinones were Q7 (47–62 %) and Q8 (26–47 %). Eicosapentaenoic acid was produced in minor amounts. Based on these data, the strains are assigned to a novel species, Shewanella affinis sp. nov. (type strain KMM 3587T=CIP 107703T=ATCC BAA-642T).

scholarly journals Lake Superior Supports Novel Clusters of Cyanobacterial Picoplankton

2007 ◽  
Vol 73 (12) ◽  
pp. 4055-4065 ◽  
Author(s):  
Natalia V. Ivanikova ◽  
Linda C. Popels ◽  
R. Michael L. McKay ◽  
George S. Bullerjahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Lake Superior ◽  
Abundant Species ◽  
Rrna Gene ◽  
Neighbor Joining ◽  
16S Rrna Gene Sequences ◽  
The World ◽  
Gene Data ◽  
The 16S Rrna Gene

ABSTRACT Very little is known about the biodiversity of freshwater autotrophic picoplankton (APP) in the Laurentian Great Lakes, a system comprising 20% of the world's lacustrine freshwater. In this study, the genetic diversity of Lake Superior APP was examined by analyzing 16S rRNA gene and cpcBA PCR amplicons from water samples. By neighbor joining, the majority of 16S rRNA gene sequences clustered within the “picocyanobacterial clade” consisting of freshwater and marine Synechococcus and Prochlorococcus. Two new groups of Synechococcus spp., the pelagic Lake Superior clusters I and II, do not group with any of the known freshwater picocyanobacterial clusters and were the most abundant species (50 to 90% of the sequences) in samples collected from offshore Lake Superior stations. Conversely, at station Portage Deep (PD), located in a nearshore urbanized area, only 4% of the sequences belonged to these clusters and the remaining clones reflected the freshwater Synechococcus diversity described previously at sites throughout the world. Supporting the 16S rRNA gene data, the cpcBA library from nearshore station PD revealed a cosmopolitan diversity, whereas the majority of the cpcBA sequences (97.6%) from pelagic station CD1 fell within a unique Lake Superior cluster. Thus far, these picocyanobacteria have not been cultured, although their phylogenetic assignment suggests that they are phycoerythrin (PE) rich, consistent with the observation that PE-rich APP dominate Lake Superior picoplankton. Lastly, flow cytometry revealed that the summertime APP can exceed 105 cells ml−1 and suggests that the APP shifts from a community of PE and phycocyanin-rich picocyanobacteria and picoeukaryotes in winter to a PE-rich community in summer.

scholarly journals Investigation of Oscillatoria spongeliae-Dominated Bacterial Communities in Four Dictyoceratid Sponges

2005 ◽  
Vol 71 (11) ◽  
pp. 7366-7375 ◽  
Author(s):  
Christian P. Ridley ◽  
D. John Faulkner ◽  
Margo G. Haygood
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Marine Invertebrates ◽  
Marine Sponges ◽  
Sponge Species ◽  
Epithelial Tissue ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Oscillatoria Spongeliae

ABSTRACT Certain species of marine sponges in the order Dictyoceratida harbor large populations of the cyanobacterial symbiont Oscillatoria spongeliae in the mesohyl (interior) of the sponge. We show that in four of these sponge species (Lamellodysidea herbacea, Lamellodysidea chlorea, Lendenfeldia chondrodes, and Phyllospongia papyracea) from Palau there is a consistent community of α-proteobacteria in addition to O. spongeliae that fall within the Rhodobacter group based on 16S rRNA gene analysis. Some of the α-proteobacteria in Lendenfeldia chondrodes and P. papyracea but not in the Lamellodysidea spp. contained site-specific insertions in the 16S rRNA gene. Reverse transcription-PCR experiments demonstrated that the largest insertion found in this study (63 bp) is present in the mature rRNA. Lendenfeldia chondrodes was the only sponge found to have another cyanobacterium in the tissue, a Synechocystis sp. We found that the Synechocystis sp. was present in both the pinacoderm (surface epithelial tissue) and mesohyl, in contrast to O. spongeliae, which was only found in the mesohyl through the use of specific fluorescence in situ hybridization experiments. Of the four sponge species, only P. papyracea was found to contain a significant number of γ-proteobacteria. These results demonstrate that O. spongeliae-dominated bacterial communities in different sponge species can vary considerably and increase our understanding of the bacterial communities found in marine invertebrates.

scholarly journals IDENTIFICATION OF POTENTIAL DIESEL OIL-DEGRADING BACTERIA ISOLATED FROM MANADO SEA PORT BASED ON 16S rRNA GENE

2014 ◽  
Vol 14 (2) ◽  
pp. 73
Author(s):  
Olivia H Abram ◽  
Trina E Tallei ◽  
Edwin De Queljoe ◽  
Beivy J Kolondam
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Salt Water ◽  
Klebsiella Oxytoca ◽  
Diesel Oil ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Environmental Threat ◽  
Degrading Bacteria ◽  
The World

ABSTRACT  Petroleum contamination and its derivate in ecosystem are considered as environmental threat all over the world. Some microorganisms exhibit potential to degrade hydrocarbon in contaminated environments. This study aims at identifying potential diesel oil-degrading bacteria grown on artificial media. Bacteria isolated from Manado Sea port were grown in nutrient agar containing artificial diesel oil plus salt water and diesel oil only, respectively. The growing bacteria were isolated and each of them was grown separately to obtain pure isolate. Three bacterial isolates namely AO2, OA3 and OA4 were identified using 16S rRNA gene as Pseudomonas aeroginosa, Klebsiella oxytoca, and Citrobacter sp, respectively. Keywords: diesel oil, diesel oil-degrading bacteria, Manado Sea Port, 16S rRNA gene IDENTIFIKASI BAKTERI YANG BERPOTENSI SEBAGAI PENDEGRADASI MINYAK DIESEL DI ISOLASI DARI PELABUHAN LAUT MANADO   ABSTRAK   Kontaminasi minyak bumi dan turunannya dalam ekosistem dianggap sebagai ancaman lingkungan di seluruh dunia. Beberapa mikroorganisme menunjukkan potensi yang dapat menurunkan hidrokarbon dalam lingkungan yang terkontaminasi. Penelitian ini bertujuan untuk mengidentifikasi bakteri yang berpotensi sebagai pendegradasi minyak yang tumbuh pada media buatan. Bakteri diisolasi dari pelabuhan laut Manado dan ditumbuhkan dalam media NA yang mengandung minyak diesel dengan penambahan air garam buatan dan minyak diesel tanpa air garam buatan. Bakteri yang tumbuh diisolasi dan masing-masing ditanam secara terpisah untuk mendapatkan isolat murni. Tiga isolat bakteri yaitu AO2, AO3 dan AO4 yang telah diidentifikasi menggunakan 16S rRNA gen secara berturut-turut adalah  Pseudomonas aeroginosa, Klebsiella oxytoca, dan Citrobacter sp. Kata kunci: minyak diesel, bakteri pendegradasi minyak diesel, Pelabuhan Laut Manado, gen 16S rRNA

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

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).

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