scholarly journals Host specificity determines the assemblage of root endophytic bacteria of plants growing in metal contaminated soil

2018 ◽  
Author(s):  
Wenbin Song ◽  
Yicong Wang ◽  
Tao Li ◽  
Di Liu ◽  
Meiyan Zhu ◽  
...  
Keyword(s):  
16S Rdna ◽  
Host Specificity ◽  
Endophytic Bacteria ◽  
Invasive Plant ◽  
Endemic Plant ◽  
Clone Libraries ◽  
Rdna Sequences ◽  
Culture Independent ◽  
Ageratina Adenophora ◽  
Lead Zinc

The diversity of endophytic bacteria colonizing the roots of an invasive plant, a pioneer plant, and an endemic plant from varied plant communities developing in a lead-zinc mine tailing pond, southwestern China, was analyzed by the culture-independent method. A total of 1650 16S rDNA sequences were screened for the establishment of four clone libraries, from the pure stands of Arthraxon hispidus (LS-Ah) and Ageratina adenophora (LS-Aa), and a mixed stand of A. adenophora (LC-Aa) and Alnus nepalensis (LC-An) (co-dominant community), respectively. Phylogenetic analysis revealed that the sequences were clustered into at least 17 phylogroups, which consisted of alpha, beta, gamma, delta subclasses of the Proteobacteria, Tenericutes, Bacteroidetes, Chloroflexi, Actinobacteria, Spirochaetes, Chlamydiae, Firmicutes, Deinococcus-Thermus, Planctomycetes, Nitrospirae, Gemmatimonadetes and unclassified bacteria Candidatus Saccharibacteria. The dominant phylum was Proteobacteria (50.49% of the total clones), and the dominant genus was Candidatus Phytoplasma (19.94% of the total clones). The invasive plant (A. adenophora) accumulated more parasitic endophytic bacteria (Phytoplasma) than the other two native plants. Phylogenetic structures of the four 16S rDNA clone libraries were distinct with their similarity indices being less than 0.5. The results also revealed that the dominant phyla and dominant genera in the four clone libraries varied a lot, and the endemic grass harbored a higher diversity of endophytic bacteria than the pioneer and invasive plants, the host-specificity took a more important role in shaping the endophytic bacteria community than the habitats in the metal stressed environment.

scholarly journals Host specificity determines the assemblage of root endophytic bacteria of plants growing in metal contaminated soil

2018 ◽  
Author(s):  
Wenbin Song ◽  
Yicong Wang ◽  
Tao Li ◽  
Di Liu ◽  
Meiyan Zhu ◽  
...  
Keyword(s):  
16S Rdna ◽  
Host Specificity ◽  
Endophytic Bacteria ◽  
Invasive Plant ◽  
Endemic Plant ◽  
Clone Libraries ◽  
Rdna Sequences ◽  
Culture Independent ◽  
Ageratina Adenophora ◽  
Lead Zinc

The diversity of endophytic bacteria colonizing the roots of an invasive plant, a pioneer plant, and an endemic plant from varied plant communities developing in a lead-zinc mine tailing pond, southwestern China, was analyzed by the culture-independent method. A total of 1650 16S rDNA sequences were screened for the establishment of four clone libraries, from the pure stands of Arthraxon hispidus (LS-Ah) and Ageratina adenophora (LS-Aa), and a mixed stand of A. adenophora (LC-Aa) and Alnus nepalensis (LC-An) (co-dominant community), respectively. Phylogenetic analysis revealed that the sequences were clustered into at least 17 phylogroups, which consisted of alpha, beta, gamma, delta subclasses of the Proteobacteria, Tenericutes, Bacteroidetes, Chloroflexi, Actinobacteria, Spirochaetes, Chlamydiae, Firmicutes, Deinococcus-Thermus, Planctomycetes, Nitrospirae, Gemmatimonadetes and unclassified bacteria Candidatus Saccharibacteria. The dominant phylum was Proteobacteria (50.49% of the total clones), and the dominant genus was Candidatus Phytoplasma (19.94% of the total clones). The invasive plant (A. adenophora) accumulated more parasitic endophytic bacteria (Phytoplasma) than the other two native plants. Phylogenetic structures of the four 16S rDNA clone libraries were distinct with their similarity indices being less than 0.5. The results also revealed that the dominant phyla and dominant genera in the four clone libraries varied a lot, and the endemic grass harbored a higher diversity of endophytic bacteria than the pioneer and invasive plants, the host-specificity took a more important role in shaping the endophytic bacteria community than the habitats in the metal stressed environment.

scholarly journals Bacteria and methanogen community in the rumen fed different levels of grass-legume silages

2019 ◽  
Vol 20 (4) ◽  
pp. 1055-1062 ◽  
Author(s):  
RONI RIDWAN ◽  
IMAN RUSMANA ◽  
YANTYATI WIDYASTUTI ◽  
KOMANG G. WIRYAWAN ◽  
BAMBANG PRASETYA ◽  
...  
Keyword(s):  
16S Rdna ◽  
Population Distribution ◽  
Rumen Fluid ◽  
Pennisetum Purpureum ◽  
Relative Distribution ◽  
Bacterial Populations ◽  
Rdna Sequences ◽  
Methanogen Community ◽  
Culture Independent ◽  
Different Levels

Abstract. Ridwan R, Rusmana I, Widyastuti Y, Wiryawan KG, Prasetya B, Sakamoto M, Ohkuma M. 2019. Bacteria and methanogen community in the rumen fed different levels of grass-legume silages. Biodiversitas 20: 1055-1062. This study aimed to investigate the effects of dietary grass-legume silages on the microbial community by using a culture-independent approach. Treatments consisted of R0: 50% Pennisetum purpureum and 50 % concentrate; R1: 20% P. purpureum, 50 % concentrate, and 30% grass-legumes silage; R2: 20% P. purpureum, 35 % concentrate, and 45% grass-legumes silage; and R3; 20% P. purpureum, 20 % concentrate, and 60% grass-legumes silage. The rumen fluid obtained from fistulated cattle was used for T-RFLP, 16S rDNA clone library, and qPCR analyses. The results indicated that bacterial diversity was dominated by Bacteroidetes, Firmicutes, and methanogen by Methanobacteriales, based on partial 16S rDNA sequences. The microbial communities were dominated by Prevotella brevis, P. ruminicola, Succiniclasticum ruminis, and Methanobrevibacter ruminantium, M. smithi, M. thueri, and M. millerae. The increasing silage diet in a rumen suppressed methanogenesis by reducing population distribution of Methanobacteriales, directly or indirectly, by reducing the diversity of bacterial populations. Generally, the increase silage in the diet changed the bacterial and methanogen community. Grass-legume silage diets of less than 45% are potential for ruminant diet to reduce methane production by a decrease of 4% in the relative distribution of methanogens in the rumen.

Culture-independent phylogenetic analysis of the faecal flora of the rat

2003 ◽  
Vol 49 (10) ◽  
pp. 589-601 ◽  
Author(s):  
S P.J Brooks ◽  
M McAllister ◽  
M Sandoz ◽  
M L Kalmokoff
Keyword(s):  
16S Rdna ◽  
Comparative Sequence Analysis ◽  
Gram Positive ◽  
Faecal Flora ◽  
Comparative Sequence ◽  
Gram Positive Bacteria ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Culture Independent ◽  
Cultured Bacteria

The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides–Cytophaga phylum. Several clones within this new group were related to 16S rDNA sequences previously identified from mouse faeces. Lactobacilli were the most abundant Gram-positive species, representing 23% of the total clones but only 7% of OTUs. The remaining Gram-positive clones were distributed among the Clostridium coccoides group (9%), the Clostridium leptum subgroup (18%), and throughout the low GC Gram-positive bacteria (13%). The majority of OTUs (63/69 or 91%) were less than 97% homologous to previously cultured bacteria. Faecal samples were also cultured using a variety of anaerobic media. With the exception of the lactobacilli, the cultured isolates demonstrated low species diversity and poorly reflected the population, as defined through comparative sequence analysis.Key words: rat, faeces, 16S rDNA, phylogenetic, cultured bacteria.

scholarly journals Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Parisa Soltan-Alinejad ◽  
Javad Rafinejad ◽  
Farrokh Dabiri ◽  
Piero Onorati ◽  
Olle Terenius ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Coi Gene ◽  
Diagnostic Tools ◽  
Morphological Identification ◽  
Species Determination ◽  
Important Species ◽  
Mitochondrial Markers ◽  
12S Rdna ◽  
Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Sarcocystis Attenuati N. Sp. (Apicomplexa: Sarcocystidae) Infecting the Asian Gray Shrew, Crocidura Attenuata (Insectivora: Soricidae), in China

2021 ◽  
Author(s):  
junjie hu ◽  
Jun Sun ◽  
Yanmei Guo ◽  
Hongxia Zeng ◽  
Yunzhi Zhang ◽  
...  
Keyword(s):  
Host Specificity ◽  
Definitive Host ◽  
18S Rdna ◽  
Common Species ◽  
Molecular Characteristics ◽  
Intermediate Hosts ◽  
Parasite Life Cycle ◽  
Rdna Sequences ◽  
Transmission Electron ◽  
18S Rdna Sequences

Abstract Background: There are limited data on Sarcocystis in insectivores. The Asian gray shrew, Crocidura attenuata, is one of the most common species of insectivores in the family Soricidae distributed in South Asia and Southeast Asia. To date, Sarcocystis has never been recorded in this host.Methods: Tissues from 42 Asian gray shrews were collected in China in 2017 and 2018. Sarcocysts were observed using light (LM) and transmission electron microscopy (TEM). To complete the parasite life cycle, muscle tissues of the host infected with sarcocysts were force-fed to two beauty rat snakes, Elaphe taeniura. Individual sarcocysts from different Asian gray shrews and oocysts/sporocysts isolated from the small intestines and feces of the experimental snakes were selected for DNA extraction, and seven genetic markers, including two nuclear loci (18S rDNA and ITS1), three mitochondrial genes (cox1, cox3 and cytb), and two apicoplastic genes (rpoB and clpC), were amplified, sequenced and analyzed.Results: Sarcocysts were found in 17 of 42 (40.5%) Asian gray shrews. Under LM, the microscopic sarcocysts were exhibited saw-tooth-like protrusions measuring 3.3–4.5 μm. Ultrastructurally, the sarcocyst wall contained numerous lancet- or leaf-like villous protrusions, similar to type 9h. The experimental beauty rat snakes shed oocysts/sporcysts measuring 11.9–16.7 × 9.2–10.6 μm with a prepatent period of 10 to 11 days. Comparing these sequences with those previously deposited in GenBank revealed that the 18S rDNA sequences and cox1 sequences shared the highest similarity with those of S. scandentiborneensis recorded in tree shrews, Tuaia minor and T. tana (i.e., 97.6–98.3% and 100% identity, respectively). Phylogenetic analysis based on 18S rDNA, ITS1 or cox1 sequences revealed that this parasite formed an independent clade with Sarcocystis spp. that utilize small animals as intermediate hosts and snakes as the known or presumed definitive host. On the basis of morphological and molecular characteristics and host specificity, the parasite was proposed as a new species, named S. attenuati.Conclusions: Sarcocysts were recorded in Asian gray shrews for the first time. The sarcocysts were characterized morphologically and molecularly. The 18S rDNA and cox1 sequences of S. attenuati, named in the present study, shared the highest identities with those of S. scandentiborneensis. However, the sarcocysts of the two species of Sarcocystis were quite different under LM and TEM. Based on experimental infection, beauty rat snakes have been proven to be a definitive host of S. attenuati. As more species of Sarcocystis from insectivores and other small mammals are properly morphologically and molecularly characterized, we may gain a better understanding of the biodiversity, host specificity and evolution of Sarcocystis in the future.

scholarly journals Isolation and Identification of Hydrocarbon-Degrading Bacteria that Tolerant to Saponin of Sapindus Rarak Plant

2019 ◽  
Vol 4 (1) ◽  
pp. 79-88
Author(s):  
Evi Octaviany ◽  
Suharjono Suharjono ◽  
Irfan Mustafa
Keyword(s):  
Crude Oil ◽  
16S Rdna ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Isolation And Identification ◽  
Rdna Sequences ◽  
Degrading Bacteria ◽  
16S Rdna Sequences ◽  
Petroleum Contaminated Soil ◽  
Cell Densities

A commercial saponin as biosurfactant can reduce the surface tension of water and increase of hydrocarbon degradation. However, this saponin can be toxic to some hydrocarbonoclastic bac-teria. This study aimed to obtain bacterial isolates that were tolerant and incapable to degrade saponin, and to identify them based on 16S rDNA sequence. Bacteria were isolated from petroleum contaminated soil in Wonocolo Village, Bojonegoro Regency, East Java, Indonesia. The soil samples were acclimated using Bushnell-Haas (BH) broth with 0.5% crude oil at room temperature for 3 weeks. The culture was spread onto BH agar incubated at 30°C for 7 days. The first screened, isolates were grown in nutrient broth with addition of sap-onin 0%, 8%, and 12% (v/v) then incubated at 30°C for three days. The bacterial cell density was measured using a spectrophotometer. Second screened, the isolates were grown on BH broth with addition of 0.5% saponin as a sole carbon source, and their cell densities were measured. The selected isolates were identified based on 16S rDNA sequences. Among 34 bacterial isolates, nine isolates were tol-erant to 12% saponin. Three bacterial isolates IHT1.3, IHT1.5, and IHT3.24 tolerant to high concentration of saponin and did not use this substance as growth nutrition. The IHT1.3, IHT1.5, and IHT3.24 isolates were identified as Ochrobactrum pseudogrignonense (99% similarity), Pseudomonas mendocina (99%), and Ochrobactrum pi-tuitosum; (97%), respectively. Those three selected isolates are good candidates as hydrocarbon-degrading bacteria to bioremediation of soil contaminated crude oil. However, the combined activity of bacteria and saponin to degrade hydrocarbon needs further study. 

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