scholarly journals Biodiversity of major bacterial groups in association with agarwood (Aquilaria crassna) in Khanh Hoa province, Vietnam

2014 ◽  
Vol 6 (2) ◽  
pp. 132-137 ◽  
Author(s):  
Thi Thanh Tra Nguyen ◽  
Van Duy Nguyen

Agarwood mainly formed by Aquilaria species is an economically and pharmaceutically important natural product used for the production of incense, perfumes and traditional medicines in Asia. Endophytic bacteria are potentially important in producing pharmaceutical compounds found in the plants. The aim of this research is to isolate, classify and identify major endophytic bacteria groups associated with agarwood of Aquilaria crassna species in Khanh Hoa province, Vietnam. Agarwood samples were collected and surface-sterilized, and total endophytic bacteria were isolated on Tryptic Soy Agar by the spread plate method. Major bacterial groups were classified according to the Bergey’s system. The 16S rRNA gene fragments were amplified using PCR method, and bacterial isolates were identified using this gene sequence similarity based method. The results showed that from 0.121 g of agarwood, total 26 bacterial isolates were purified and divided into 7 separated groups, in which the group II of Gram-positive spore-forming bacteria was the most dominant. Especially, two dominant strains, T14 of group II, and T15 of group VII, were identified as Bacillus pumilus and Alcaligenes faecalis, respectively. To our knowledge, it is the first time that biodiversity of bacterial endophytes associated with agarwood from Aquilaria crassna in Vietnam has been reported, which requires of further study to understand the relationship of endophytic bacteria to agarwood-producing Aquilaria crassna species as well as explore their potential applications towards the development of valuable bioactive compounds. Trầm hương, chủ yếu được tạo ra từ các loài cây Dó (Aquilaria), là một sản phẩm tự nhiên có giá trị kinh tế và y học đã được sử dụng để sản xuất hương, nước hoa và các dược phẩm truyền thống ở châu Á. Vi khuẩn nội cộng sinh thực vật được cho là một nguồn quan trọng cho các dược phẩm có nguồn gốc thực vật. Mục tiêu của nghiên cứu này là nhằm phân lập, phân loại và định danh các nhóm vi khuẩn chính trên Trầm hương Khánh Hòa, Việt Nam. Các mẫu Trầm hương được thu nhận và vô trùng bề mặt dùng để phân lập vi khuẩn tổng số trên môi trường TSA bằng phương pháp trải đĩa. Các nhóm vi khuẩn chính được phân loại dựa theo hệ thống chuẩn Bergey. Đoạn gen mã hóa 16S rRNA được khuếch đại bằng phương pháp PCR, và các chủng vi khuẩn được định danh bằng phép so sánh độ tương đồng trình tự của đoạn gen này. Kết quả cho thấy từ 0,121 g mẫu trầm hương, chúng tôi đã phân lập được 26 chủng vi khuẩn và phân chúng vào 7 nhóm chính, trong đó nhóm II bao gồm các vi khuẩn Gram dương sinh bào tử là nhóm chiếm ưu thế nhất. Đặc biệt, có 2 chủng ưu thế là chủng T14 thuộc nhóm II và chủng T15 thuộc nhóm VII đã được định danh tương ứng là Bacillus pumilus và Alcaligenes faecalis. Đây là nghiên cứu đầu tiên về đa dạng sinh học của các nhóm vi khuẩn chính trên Trầm hương Khánh Hòa. Vì vậy, cần có những nghiên cứu tiếp theo nhằm tìm hiểu mối quan hệ giữa các vi khuẩn nội cộng sinh với cây Dó bầu (Aquilaria crassna) tạo trầm cũng như khai thác những ứng dụng tiềm năng của các vi khuẩn này theo hướng phát triển các hoạt chất sinh học có giá trị.

2006 ◽  
Vol 56 (8) ◽  
pp. 1735-1740 ◽  
Author(s):  
Masataka Satomi ◽  
Myron T. La Duc ◽  
Kasthuri Venkateswaran

Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA–DNA hybridization showed only 54–66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA–DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36bT (=ATCC BAA-1126T=NBRC 100820T).


2005 ◽  
Vol 55 (1) ◽  
pp. 315-320 ◽  
Author(s):  
Sirilak Namwong ◽  
Somboon Tanasupawat ◽  
Thitapha Smitinont ◽  
Wonnop Visessanguan ◽  
Takuji Kudo ◽  
...  

Eight strains of aerobic, spore-forming, Gram-positive, moderately halophilic bacteria were isolated from sauce (nam-pla and bu-du) produced in Thailand by the fermentation of fish. They grew optimally in the presence of 10 % NaCl, at 37 °C and pH 7·0. A diagnostic diamino acid, meso-diaminopimelic acid, was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were found to be the major polar lipid components. The DNA G+C content was 42–43 mol%. These bacteria were further divided into two groups based on phenotypic characteristics and DNA–DNA similarities. Three strains of Group I were highly affiliated to the type strain of Lentibacillus salicampi in terms of phenotypic characterization and DNA–DNA similarities (96–102 %); accordingly, they were identified as strains of L. salicampi. A representative strain of Group II, strain IS40-3T, was most closely related to L. salicampi in terms of 16S rRNA-based phylogenetic analysis, although five strains of Group II could be distinguished from L. salicampi by means of several phenotypic properties, low 16S rRNA gene sequence similarity (95·2 %) and low DNA–DNA similarities (12–32 %). Therefore, the Group II strains should be included in a novel species of the genus Lentibacillus, for which the name Lentibacillus juripiscarius sp. nov. is proposed. The type strain is IS40-3T (=JCM 12147T=PCU 229T=TISTR 1535T).


2003 ◽  
Vol 69 (9) ◽  
pp. 5503-5511 ◽  
Author(s):  
Annette Summers Engel ◽  
Natuschka Lee ◽  
Megan L. Porter ◽  
Libby A. Stern ◽  
Philip C. Bennett ◽  
...  

ABSTRACT Hydrogen sulfide-rich groundwater discharges from springs into Lower Kane Cave, Wyoming, where microbial mats dominated by filamentous morphotypes are found. The full-cycle rRNA approach, including 16S rRNA gene retrieval and fluorescence in situ hybridization (FISH), was used to identify these filaments. The majority of the obtained 16S rRNA gene clones from the mats were affiliated with the “Epsilonproteobacteria” and formed two distinct clusters, designated LKC group I and LKC group II, within this class. Group I was closely related to uncultured environmental clones from petroleum-contaminated groundwater, sulfidic springs, and sulfidic caves (97 to 99% sequence similarity), while group II formed a novel clade moderately related to deep-sea hydrothermal vent symbionts (90 to 94% sequence similarity). FISH with newly designed probes for both groups specifically stained filamentous bacteria within the mats. FISH-based quantification of the two filament groups in six different microbial mat samples from Lower Kane Cave showed that LKC group II dominated five of the six mat communities. This study further expands our perceptions of the diversity and geographic distribution of “Epsilonproteobacteria” in extreme environments and demonstrates their biogeochemical importance in subterranean ecosystems.


2018 ◽  
Vol 31 (2) ◽  
pp. 315-325 ◽  
Author(s):  
MARIA CAMILA DE BARROS SILVA LEITE ◽  
ARTHUR PRUDÊNCIO DE ARAUJO PEREIRA ◽  
ADIJAILTON JOSÉ DE SOUZA ◽  
FERNANDO DINI ANDREOTE ◽  
FERNANDO JOSÉ FREIRE ◽  
...  

ABSTRACT Cassava is mostly planted in sandy soils which are usually of low fertility, thereby making it necessary to perform beneficial associations with microorganisms that can promote their growth. In this perspective, the possibility of selecting bacterial isolates efficient in promoting the growth of the culture is evident, which can provide subsidies for future inoculants. The objective of this study was to isolate, identify, select and evaluate the genetic diversity of endophytic bacteria in roots and stems of cassava grown in Garanhuns - PE, with features involved in promoting plant growth. The isolation was performed on culture medium semisolid LGI-P. The selected isolates were evaluated for the potential to fix N2, as the ability to produce indole acetic acid, for their ability to solubilize inorganic phosphate and produce exopolysaccharides. Some bacterial isolates had their 16S rRNA gene sequenced by the Sanger method. A total of 52 endophytic bacteria isolates were obtained from cassava. Regarding the potential to fix N2, 15% of the isolates were positive. As for the production of IAA, 78% of the isolates produced this phytohormone in a medium with increased L-tryptophan. Approximately 31% of the isolates were able to solubilize inorganic phosphate and 60% had exopolysaccharide. The identification of 19 isolates allowed the grouping into six bacterial genera, namely: Achromobacter, Bacillus, Burkholderia, Enterobacter, Pantoea and Pseudomonas. Cassava plants grown in Garanhuns - PE present interaction with different groups of endophytic bacteria and there are bacterial groups with several characteristics involved in promoting plant growth.


2019 ◽  
Vol 20 (5) ◽  
Author(s):  
WARZATULLISNA WARZATULLISNA ◽  
LENNI FITRI ◽  
YULIA SARI ISMAIL

Abstract. Warzatullisna, Fitri L, Ismail YS. 2019. Potential of endophytic bacteria from rice root as potassium solvent. Biodiversitas 20: 1303-1308. Endophytic bacteria live in plant tissues and known to have many benefits for plant growth. One function of endophytic bacteria are known to be able to dissolve potassium. Potassium is one of the macronutrients that plays an important role in plant growth and development. This study aims to obtain endophytic bacterial isolates from the roots of rice plants (Oryza sativa L.) which have potential as potassium solvents, identify the endophytic bacteria in morphologically and physiologically, and analysis of the selected isolate 16S rRNA genes. Selected endophytic bacterial isolates from the test of dissolving potassium on medium Alexandrov, measured clear zone using calipers and continued with biochemical tests using KIT DL-96E also identified based on 16S rRNA gene and compared for their close relationship with reference strains available in the Bank Genes. Based on the isolation results, 7 isolates from the roots of rice were obtained. Six isolates of endophytic bacteria were able to dissolve potassium. EPK3 isolates were the isolates that are capable of dissolving the highest potassium in Alexandrov media with a 17.9 mm potassium dissolution index. EPK3 isolates also produce inhibit the growth of Xanthomonas oryzae with a 1.2 mm inhibition zone. Physiological identification showed that EPK3 isolates were Enterobacter cloaceae bacteria with 93.79% of similarity. Based on the 16SrRNA gene showed that EPK3 isolates were closely related to E. cloaceae strain SBP-8 with similarity rate is 99%.


2021 ◽  
Vol 11 (1) ◽  
pp. 24
Author(s):  
Usep Suhendar ◽  
Siti Mahyuni ◽  
Sogandi Sogandi

The increase in infectious diseases caused by pathogenic bacteria impacts the increase in the incidence of pathogenic bacteria to antibiotics. This study aimed to find candidates for the endophytic bacterial isolates of kasturi mango, which have antibacterial potential. After being tested against the pathogenic bacteria, Bacterial isolates showed potential activity using the disc diffusion method. The observations of five endophytic bacterial isolates from the leaves of Kasturi mango, namely L1, L2, L3, L4, and L5, showed that L2 was the most potential compared to other isolates. The formation of a clear zone indicates the inhibitory activity. Molecular identification was carried out by PCR amplification on the 16S rRNA gene. Furthermore, the L2 isolate was identified as Enterobacter cloacae with a 99% sequence similarity. Subsequent tests on several bacteria, including S. mutans ATCC 31987, S. aureus ATCC 25323, E. coli ATCC 25922 and Shigella dysenteriae ATCC 13313. All isolates showed an inhibition zone in the five bacteria.Keywords: Endophyte, Kasturi Mango, AntibacterialABSTRAKIdentifikasi molekuler isolat bakteri endofit daun mangga Kasturi (Mangifera casturi Kosterm) dan analisis aktivitas antibakteriMeningkatnya angka kejadian penyakit menular yang diakibatkan oleh bakteri patogen berdampak pada meningkatknya kemampuan resistensi bakteri patogen terhadap antibiotik. Penelitian ini bertujuan untuk mendapatkan kandidat isolat bakteri endofit daun mangga kasturi yang memiliki aktivitas sebagai antibakteri. Isolat bakteri yang telah diujikan terhadap bakteri patogen Propionibacterium acnes menunjukkan aktivitas potensial dengan menggunakan metode difusi cakram. Hasil pengamatan dari lima isolat bakteri endofit dari daun mangga kasturi yaitu L1, L2, L3, L4, dan L5 menunjukan L2 yang paling potensial dibandingkan isolat yang lain. Aktivitas penghambatan ditunjukkan dengan terbentuknya zona bening. Identifikasi molekuler dilakukan dengan amplifikasi PCR pada gen 16S rRNA. Selanjutnya, isolat L2 diidentifikasi sebagai Enterobacter cloacae dengan kemiripan urutan 99%.  Pengujian berikutnya dilakukan terhadap beberapa bakteri diantaranya bakteri S. mutans ATCC 31987, S. aureus ATCC 25323, E. coli ATCC 25922 dan S. dysenteriae ATCC 13313. Semua isolat menujukkan adanya zona hambat pada kelima bakteri tersebut.Kata Kunci: Endofit, Mangga Kasturi, Antibakteri


2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  

© 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).


2021 ◽  
Vol 9 (7) ◽  
pp. 1448
Author(s):  
Lei Gao ◽  
Jinbiao Ma ◽  
Yonghong Liu ◽  
Yin Huang ◽  
Osama Abdalla Abdelshafy Mohamad ◽  
...  

Endophytes associated with halophytes may contribute to the host’s adaptation to adverse environmental conditions through improving their stress tolerance and protecting them from various soil-borne pathogens. In this study, the diversity and antifungal activity of endophytic bacteria associated with halophytic samples growing on the shore of the western Aral Sea in Uzbekistan were investigated. The endophytic bacteria were isolated from the nine halophytic samples by using the culture-dependent method and identified according to their 16S rRNA gene sequences. The screening of endophytic bacterial isolates with the ability to inhibit pathogenic fungi was completed by the plate confrontation method. A total of 289 endophytic bacterial isolates were isolated from the nine halophytes, and they belong to Firmicutes, Actinobacteria, and Proteobacteria. The predominant genera of the isolated endophytic bacteria were Bacillus, Staphylococcus, and Streptomyces, accounting for 38.5%, 24.7%, and 12.5% of the total number of isolates, respectively. The comparative analysis indicated that the isolation effect was better for the sample S8, with the highest diversity and richness indices. The diversity index of the sample S7 was the lowest, while the richness index of samples S5 and S6 was the lowest. By comparing the isolation effect of 12 different media, it was found that the M7 medium had the best performance for isolating endophytic bacteria associated with halophytes in the western Aral Sea Basin. In addition, the results showed that only a few isolates have the ability to produce ex-enzymes, and eight and four endophytic bacterial isolates exhibited significant inhibition to the growth of Valsa mali and Verticillium dahlia, respectively. The results of this study indicated that halophytes are an important source for the selection of microbes that may protect plant from soil-borne pathogens.


Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.


Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.


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