scholarly journals Penapisan dan Identifikasi Bakteri Penghasil Agarase dari Sampel Sedimen Laut Bara Caddi, Sulawesi Selatan

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Dewi Seswita Zilda ◽  
Gintung Patantis ◽  
Mada Triandala Sibero ◽  
Yusro Nuri Fawzya
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Marine Bacteria ◽  
Solid Medium ◽  
Rrna Gene ◽  
Clear Zone ◽  
Sediment Samples ◽  
South Sulawesi ◽  
The 16S Rrna Gene

Agarase adalah enzim yang mampu menghidrolisis agar menjadi oligoagar yang sudah banyak diaplikasikan dalam industri kesehatan dan kosmetik. Bakteri laut merupakan mikroba yang paling banyak dilaporkan sebagai sumber untuk isolasi bakteri penghasil agarase. Penelitian ini bertujuan untuk melakukan penapisan, isolasi, dan identifikasi bakteri penghasil agarase dari sedimen laut. Sampel sedimen diambil dari pantai Pulau Bara Caddi, Sulawesi Selatan. Penapisan dilakukan menggunakan media air laut yang ditambahkan tripton 0,5%, ekstrak ragi 0,1%, dan agar 2%. Identifikasi dilakukan dengan amplifikasi gen 16S rRNA. Sebanyak 45 isolat berhasil dimurnikan, 16 diantaranya merupakan bakteri penghasil agarase. Pola zona bening yang terbentuk terlihat berbeda-beda, hal ini diduga disebabkan oleh perbedaan jenis agarase yang dihasilkan oleh masing-masing isolat. Hasil penelitian menunjukkan bahwa terdapat 4 genera bakteri yang memiliki kemiripan yang tinggi dengan 16 isolat bakteri penghasil agarase yang terdapat pada sampel sedimen yaitu Vibrio, Alteromonas, Salinivibrio, dan Marinobacter. Vibrio merupakan genus yang paling dominan diikuti oleh Alteromonas dan hanya satu isolat yang menunjukkan kesamaan dengan Salinivibrio dan Marinobacter. ABSTRACTAgarase is an enzyme that hydrolyze agar into agaro oligosaccharide which have been applied in health and cosmetic industries. Marine bacteria are the most widely reported microbes as a source for isolation of agarase-producing bacteria. This work was aimed to screen, isolate, and identify the agarase-producing bacteria from marine sediment. The sediment samples were collected from the sea around Bara Caddi Island, South Sulawesi. The screening of agarase-producing bacteria was carried out using seawater media containing 0.5% tryptone, 0.1 % yeast extract with 2 % agar. The identification of the bacteria obtained was carried out by amplification of the 16S rRNA gene. A total of 45 isolates were successfully purified, 16 of which were agarase-producing bacteria. The clear zone formed on solid medium by some isolates showed different pattern which may be caused by the type of agarase produced by each isolate. The results showed that there were 4 genera of bacteria which similar to the 16 isolates agarase-producing bacteria found in sediment samples i.e. Vibrio, Alteromonas, Salinivibrio, and Marinobacter. Vibrio is the most dominant genus followed by Alteromonas and only one isolate showed similarity to Salinivibrio and Marinobacter.

Pontibacter flavimaris sp. nov., of the family Hymenobacteraceae, isolated from marine sediment

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Di Liu ◽  
Qin Xiong ◽  
Juanjuan Zhao ◽  
Zhenjuan Fang ◽  
Guishan Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A Gram-stain-negative, ovoid or rod-shaped, non-flagellated, motile-by-gliding and aerobic bacteria, designated S10-8T, was isolated from marine sediment of the Yellow Sea. Colonies of strain S10-8T had a pink-red pigmentation and its cells were approximately 0.5–0.8 μm×1.0–2.5 μm in size. Growth occurred at 10–45 °C (optimally at 33–37 °C), in the presence of 0–12.0 % NaCl (optimally at 2.0–5.0 %, w/v) and at pH 5.0–8.5 (optimally at pH 7.0–7.5). Phylogenetic analysis of the 16S rRNA gene indicated that strain S10-8T is a member of the genus Pontibacter within the family Hymenobacteraceae , and the 16S rRNA gene sequence similarity of strain S10-8T to its closest relative Pontibacter actiniarum KCTC 12367T was 96.9 %. Strain S10-8T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B) and iso-C15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The size of the draft genome was 4 623 791 bp and the G+C content was 53.5 mol%. There were low DNA-DNA hybridization values (<48.3±5.2 %) and average nucleotide identity values (<86.5 %) between strain S10-8T and the most closely related recognized Pontibacter species. Therefore, we propose a novel species in the genus Pontibacter to accommodate the novel isolate: Pontibacter flavimaris sp. nov. (type strain S10-8T=KCTC 42769T=ACCC 19859T).

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Diagnosis of Fulminant Pneumonia Caused by Legionella pneumophila Serogroup 8 with the Sequence Analysis of the 16S rRNA Gene

2011 ◽  
Vol 225 (1) ◽  
pp. 65-69 ◽  
Author(s):  
Toshinori Kawanami ◽  
Kazuhiro Yatera ◽  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Masamizu Kunimoto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Legionella Pneumophila ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

2014 ◽  
Vol 81 (1) ◽  
pp. 48-58 ◽  
Author(s):  
Brandee L. Stone ◽  
Nathan M. Russart ◽  
Robert A. Gaultney ◽  
Angela M. Floden ◽  
Jefferson A. Vaughan ◽  
...  
Keyword(s):  
Lyme Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Dakota ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Content Type ◽  
Intergenic Spacer Region ◽  
Grand Forks ◽  
The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

Clover proliferation phytoplasma: ‘Candidatus Phytoplasma trifolii’

2004 ◽  
Vol 54 (4) ◽  
pp. 1349-1353 ◽  
Author(s):  
Chuji Hiruki ◽  
Keri Wang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Strain ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Beet Leafhopper ◽  
Signature Sequences ◽  
Elm Yellows ◽  
The 16S Rrna Gene

Clover proliferation phytoplasma (CPR) is designated as the reference strain for the CP phylogenetic group or subclade, on the basis of molecular analyses of genomic DNA, the 16S rRNA gene and the 16S–23S spacer region. Other strains related to CPR include alfalfa witches'-broom (AWB), brinjal little leaf (BLL), beet leafhopper-transmitted virescence (BLTV), Illinois elm yellows (ILEY), potato witches'-broom (PWB), potato yellows (PY), tomato big bud in California (TBBc) and phytoplasmas from Fragaria multicipita (FM). Phylogenetic analysis of the 16S rRNA gene sequences of BLL, CPR, FM and ILEY, together with sequences from 16 other phytoplasmas that belong to the ash yellows (AshY), jujube witches'-broom (JWB) and elm yellows (EY) groups that were available in GenBank, produced a tree on which these phytoplasmas clearly clustered as a discrete group. Three subgroups have been classified on the basis of sequence homology and the collective RFLP patterns of amplified 16S rRNA genes. AWB, BLTV, PWB and TBBc are assigned to taxonomic subgroup CP-A, FM belongs to subgroup CP-B and BLL and ILEY are assigned to subgroup CP-C. Genetic heterogeneity between different isolates of AWB, CPR and PWB has been observed from heteroduplex mobility assay analysis of amplified 16S rRNA genes and the 16S–23S spacer region. Two unique signature sequences that can be utilized to distinguish the CP group from others were present. On the basis of unique properties of the DNA from clover proliferation phytoplasma, the name ‘Candidatus Phytoplasma trifolii’ is proposed for the CP group.

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