Antipathogenic Activity of Acroporid Bacterial Symbionts Against Brown Band Disease-Associated Bacteria

2021 ◽  
Vol 16 (2) ◽  
pp. 65-74
Author(s):  
Rosa Amalia ◽  
Diah Ayuningrum ◽  
Agus Sabdono ◽  
Ocky Karna Radjasa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
16S Rrna Gene Sequences ◽  
Coral Diseases ◽  
Associated Bacteria ◽  
Brown Band ◽  
The 16S Rrna Gene ◽  
Brown Band Disease

The coral reefs’ condition in most regions in Indonesia has been declining due to coral diseases, such as Brown Band Disease (BrBD). A treatment for BrBD involves the use of biological control agents that have antagonistic properties against disease-causing agents. This study aimed to isolate bacteria from healthy hard coral, those associated with BrBD, and those that had bioactivities against BrBD. Sampling and identification of corals and BrBD were carried out in March 2015 at the Marine National Park of Karimunjawa. Bacteria from healthy and infected corals were isolated and purified. The isolates were subjected to antipathogenic assay using overlay and agar diffusion methods. Finally, molecular identification of active bacteria was carried out using the 16S rRNA gene amplification. As many as 57 bacterial isolates were obtained from healthy coral, as well as four bacterial isolates from coral with BrBD symptoms. A total of 15 bacterial isolates (26%) showed antipathogenic activity against BrBD-associated bacteria. Three isolates with the strongest antipathogenic activities, i.e., GAMSH 3, KASH 6, and TAPSH 1 were identified by 16S rRNA gene sequences. The results showed that they were aligned to Virgibacillus marismortui (97%), Oceanobacillus iheyensis (97%), and Bacillus cereus (96%), respectively.

scholarly journals Variovorax gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4335-4340 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gossypium Hirsutum ◽  
Dna Hybridization ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
The 16S Rrna Gene

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

scholarly journals Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

Description of Sandaracinobacter Hominis Sp. Nov., Isolated From Human Skin

2021 ◽  
Author(s):  
Ping-hua Qu ◽  
Hai-min Luo ◽  
Jun-hui Feng ◽  
Lei Dong ◽  
Song Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Skin Sample ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Separate Branch ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

Abstract Strain SZY PN-1T, representing a novel Gram-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, was isolated from a skin sample of a healthy Chinese people. Growth of SZY PN-1T optimally occurred at pH 7.0, at 30 ºC and tolerate up to 1.0 % (w/v) NaCl. According to the absorption spectrum, carotenoid was present in the cells. Comparative analysis of the 16S rRNA gene revealed that strain SZY PN-1T shared high similarities with Sandaracinobacter sibiricus RB16-17T (97.1 %) and Sandaracinobacter neustonicus JCM 30734T (96.6 %), respectively. Phylogenetic analysis of 16S rRNA gene sequences together with protein-concatamer tree showed that SZY PN-1T formed a separate branch within the genus Sandaracinobacter. The DNA G+C content of the strain SZY PN-1T was 65.0 % (genome). The polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, two sphingoglycolipids, diphosphatidylglycerol, five unidentified glycolipids and seven unidentified lipids. The predominant fatty acids (> 10.0 %) were identified as C18:1 ω7c and/or C18:1 ω6c, C17:1 ω6c, C16:1 ω7c and/or C16:1 ω6c. The major respiratory quinone was ubiquinone Q-10. Based on the phenotypic and genotypic features, we proposed Sandaracinobacter hominis sp. nov. with type strain SZY PN-1T (= KCTC 82150T = NBRC 114675T).

scholarly journals Resuscitation of eleven-year VBNC Citrobacter

2008 ◽  
Vol 6 (4) ◽  
pp. 565-568 ◽  
Author(s):  
Amel Dhiaf ◽  
Amina Bakhrouf ◽  
Karl-Paul Witzel
Keyword(s):  
Growth Factors ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Strain ◽  
Rrna Gene ◽  
Citrobacter Freundii ◽  
16S Rrna Gene Sequences ◽  
High Degree ◽  
Degree Of Similarity ◽  
The 16S Rrna Gene

Citrobacter freundii strain WA1 was stressed by incubation in seawater microcosms for eleven years. After two years of starvation, no culturable strain was observed. Incubation of samples in nutrient-rich broth medium not supplemented with growth factors, however, allowed resuscitation of VBNC cells so that subsequent plating yielded observable colonies for significantly extended periods of time. Recovery of VBNC Citrobacter freundii was obtained by incubation in nutrient broth even after eleven years of starvation. To see whether the samples contained the same strain of Citrobacter freundii inoculated 11 years ago. The complete 16S rRNA gene was PCR amplified and sequenced from initial, stressed and revived strains of Citrobacter freundii strain WA1.The 16S rRNA gene sequences from eleven-year stressed strains were homologous with a high degree of similarity to the GenBank reference strain and were identical to each other.

scholarly journals Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow’s milk

2012 ◽  
Vol 62 (2) ◽  
pp. 322-329 ◽  
Author(s):  
William J. Wolfgang ◽  
An Coorevits ◽  
Jocelyn A. Cole ◽  
Paul De Vos ◽  
Michelle C. Dickinson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New York State ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Clinical Specimens ◽  
The 16S Rrna Gene

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA–DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α l-Lys–Gly–d-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062T  = DSM 23544T  = CCUG 59649T  = LMG 26022T) is proposed.

scholarly journals ‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1890-1899 ◽  
Author(s):  
Nigel A. Harrison ◽  
Robert E. Davis ◽  
Carlos Oropeza ◽  
Ericka E. Helmick ◽  
María Narváez ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cocos Nucifera ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Lethal Yellowing ◽  
The 16S Rrna Gene

In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus Phytoplasma ’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus Phytoplasma ’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.

Description of a tropical new species of Wilmottia (Oscillatoriales, Cyanobacteria) and considerations about the monophyly of W. murrayi

Phytotaxa ◽  
2017 ◽  
Vol 307 (1) ◽  
pp. 43 ◽  
Author(s):  
NÁTHALI MARIA MACHADO-DE-LIMA ◽  
MARIÉLLEN DORNELLES MARTINS ◽  
LUIS H. Z. BRANCO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Morphological Similarity ◽  
16S Rrna Gene Sequences ◽  
Climatic Range ◽  
Low Sensitivity ◽  
Consistent Information ◽  
The 16S Rrna Gene ◽  
Brazilian Populations

The genus Wilmottia was described based on polyphasic studies of Phormidium murrayi populations that revealed them not closely related to other Phormidium species, despite their morphological similarity. The genus contained one species, W. murrayi, found exclusively in cold and temperate areas of the world. Other species morphologically similar to Phormidium were expected to pertain to Wilmottia, but the genus remained unispecific until now. During a survey of Cyanobacteria in Brazil, 11 strains morphologically similar to Wilmottia from southern and southeastern regions were isolated in unicyanobacterial cultures and submitted to polyphasic evaluation (morphological, ecological and molecular studies). The populations studied presented homogeneous morphology (trichomes cylindrical, straight and not attenuated) and were found inhabiting quite diverse environments (freshwater, wet soil and barks of trees). The molecular analyses based on 16S rRNA gene sequences placed the 11 studied strains in two distinct clusters inside the highly supported Wilmottia clade. The 16S-23S ITS marker was very variable and did not provide consistent information to improve the differentiation among the strains. The characteristics of the Brazilian populations, essentially the genetic ones, resulted in the recognition of a new cryptic species of Wilmottia (W. stricta) and indicated a wider distribution for W. murrayi. Such distribution would comprehend a wide climatic range (from polar to tropical) and occurrence in very distinct habitats (aquatic and aerophytic). The possible explanations to that scenario would be the low sensitivity of 16S rRNA gene as marker for distinguishing species inside of this complex of strains or W. murrayi actually represents a case of ubiquitous species. The addition of other genes or whole genome sequencing could be the way to reach a more confident answer. Wilmottia reveals a very intricate phylogeny according to the 16S rRNA gene and more studies are recommended to confirm its monophyly.

scholarly journals Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.

2011 ◽  
Vol 61 (4) ◽  
pp. 969-973 ◽  
Author(s):  
Liping Wang ◽  
Qiliang Lai ◽  
Yuanyuan Fu ◽  
Hua Chen ◽  
Wanpeng Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Chromosomal Dna ◽  
16S Rrna Gene Sequences ◽  
Pr China ◽  
The 16S Rrna Gene

A taxonomic study was carried out on strain 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T  = LMG 25227T  = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T  = KCTC 22740T  = JCM 16344T).

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