scholarly journals Genetic Diversity and Host Range of Rhizobia Nodulating Lotus tenuis in Typical Soils of the Salado River Basin (Argentina)

2008 ◽  
Vol 75 (4) ◽  
pp. 1088-1098 ◽  
Author(s):  
Mar�a Julia Estrella ◽  
Socorro Mu�oz ◽  
Mar�a Jos� Soto ◽  
Oscar Ruiz ◽  
Juan Sanju�n
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Range ◽  
River Basin ◽  
Rrna Gene ◽  
Narrow Host Range ◽  
Salado River

ABSTRACT A total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating Lotus tenuis in typical soils of the Salado River Basin. A high level of genetic diversity was revealed by repetitive extragenic palindromic PCR, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters A and B, after 16S rRNA restriction fragment length polymorphism analysis. Cluster A strains appeared to be related to the genus Mesorhizobium, whereas cluster B was related to the genus Rhizobium. 16S rRNA sequence and phylogenetic analysis further supported the distribution of most of the symbiotic isolates in either Rhizobium or Mesorhizobium: the only exception was isolate BA135, whose 16S rRNA gene was closely related to the 16S rRNA gene of the genus Aminobacter. Most Mesorhizobium-like isolates were closely related to Mesorhizobium amorphae, Mesorhizobium mediterraneum, Mesorhizobium tianshanense, or the broad-host-range strain NZP2037, but surprisingly few isolates grouped with Mesorhizobium loti type strain NZP2213. Rhizobium-like strains were related to Rhizobium gallicum, Rhizobium etli, or Rhizobium tropici, for which Phaseolus vulgaris is a common host. However, no nodC or nifH genes could be amplified from the L. tenuis isolates, suggesting that they have rather divergent symbiosis genes. In contrast, nodC genes from the Mesorhizobium and Aminobacter strains were closely related to nodC genes from narrow-host-range M. loti strains. Likewise, nifH gene sequences were very highly conserved among the Argentinian isolates and reference Lotus rhizobia. The high levels of conservation of the nodC and nifH genes suggest that there was a common origin of the symbiosis genes in narrow-host-range Lotus symbionts, supporting the hypothesis that both intrageneric horizontal gene transfer and intergeneric horizontal gene transfer are important mechanisms for the spread of symbiotic capacity in the Salado River Basin.

scholarly journals Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA

2007 ◽  
Vol 74 (2) ◽  
pp. 495-502 ◽  
Author(s):  
Dhritiman Ghosh ◽  
Krishnakali Roy ◽  
Kurt E. Williamson ◽  
David C. White ◽  
K. Eric Wommack ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Bacteria ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Viral Dna

ABSTRACT Bacteriophages are very abundant in the biosphere, and viral infection is believed to affect the activity and genetic diversity of bacterial communities in aquatic environments. Lysogenic conversion, for example, can improve host fitness and lead to phage-mediated horizontal gene transfer. However, little is known about lysogeny and transduction in the soil environment. In this study we employed atrazine-impregnated Bio-Sep beads (a cell immobilization matrix) to sample active microbiota from soils with prior pesticide exposure history. Once recovered from soil, the bead communities were induced with mitomycin C (MC), and viral and bacterial abundances were determined to evaluate the incidence of inducible prophage in soil bacteria. The inducible fraction calculated within bead communities was high (ca. 85%) relative to other studies in aquatic and sedimentary environments. Moreover, the bacterial genes encoding 16S rRNA and trzN, a chlorohydrolase gene responsible for dehalogenation of atrazine, were detected by PCR in the viral DNA fraction purified from MC-induced bead communities. A diverse collection of actinobacterial 16S rRNA gene sequences occurred within the viral DNA fraction of induced, water-equilibrated beads. Similar results were observed in induced atrazine-equilibrated beads, where 77% of the cloned sequences were derived from actinobacterial lineages. Heterogeneous 16S rRNA gene sequences consisting of fragments from two different taxa were detected in the clone libraries. The results suggest that lysogeny is a prevalent reproductive strategy among soil bacteriophages and that the potential for horizontal gene transfer via transduction is significant in soil microbial communities.

scholarly journals Epipelic cyanobacterial diversity in Pinang River basin, Malaysia, revealed by 16S-based metagenomic approach

Algologia ◽  
2021 ◽  
Vol 31 (1) ◽  
pp. 93-113
Author(s):  
A.R. Nur Fadzliana ◽  
◽  
W.O. Wan Maznah ◽  
S.A.M. Nor ◽  
Choon Pin Foong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
River Basin ◽  
Sequence Data ◽  
Diversity Index ◽  
Saline Water ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Cyanobacterial Community ◽  
Upstream Station

Cyanobacteria are the most widespread group of photosynthetic prokaryotes. They are primary producers in a wide variety of habitats and are able to thrive in harsh environments, including polluted waters; therefore, this study was conducted to explore the cyanobacterial populations inhabiting river tributaries with different levels of pollution. Sediment samples (epipelon) were collected from selected tributaries of the Pinang River basin. Air Terjun (T1) and Air Itam rivers (T2) represent the upper streams of Pinang River basin, while Dondang (T3) and Jelutong rivers (T4) are located at in the middle of the river basin. The Pinang River (T5) is located near the estuary and is subjected to saline water intrusion during high tides. Cyanobacterial community was determined by identifying the taxa via 16S rRNA gene amplicon sequence data. 16S rRNA gene amplicons generated from collected samples were sequenced using illumina Miseq, with the targeted V3 and V4 regions yielding approximately 1 mln reads per sample. Synechococcus, Phormidium, Arthronema and Leptolyngbya were found in all samples. Shannon-Weiner diversity index was highest (H’ = 1.867) at the clean upstream station (T1), while the moderately polluted stream (T3) recorded the lowest diversity (H’ = 0.399), and relatively polluted stations (T4 and T5) recorded fairly high values of H’. This study provides insights into the cyanobacterial community structure in Pinang River basin via cultivation-independent techniques using 16S rRNA gene amplicon sequence. Occurrence of some morphospecies at specific locations showed that the cyanobacterial communities are quite distinct and have specific ecological demands. Some species which were ubiquitous might be able to tolerate varied environmental conditions.

Genetic diversity of vaginal lactobacilli from women in different countries based on 16S rRNA gene sequences

2002 ◽  
Vol 92 (3) ◽  
pp. 451-459 ◽  
Author(s):  
S.I. Pavlova ◽  
A.O. Kilic ◽  
S.S. Kilic ◽  
J.-S. So ◽  
M.E. Nader-Macias ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Vaginal Lactobacilli

DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities

1992 ◽  
Vol 100 (1-3) ◽  
pp. 59-65 ◽  
Author(s):  
Paul A. Rochelle ◽  
John C. Fry ◽  
R. John Parkes ◽  
Andrew J. Weightman
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Deep Sediment

ARDRA and Identification of Intestinal Aerobic Bacteria from 4th Instar Larvae of Dendrolimu. kikuchii

2012 ◽  
Vol 518-523 ◽  
pp. 5523-5527
Author(s):  
Wu Xian Zhang ◽  
Jin Hua Wang ◽  
You He Sun ◽  
Biao Li ◽  
Zhi Xiong
Keyword(s):  
Genetic Diversity ◽  
Bacillus Subtilis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Enzyme Digestion ◽  
Aerobic Bacteria ◽  
Rrna Gene ◽  
Accession Number ◽  
16S Rrna Gene Sequences

Genetic diversity of 11 intestinal aerobic bacteria isolated from Dendrolimu. kikuchii was analysed, using PCR and ARDRA which used enzyme digestion of cloned 16S rRNA gene sequences. The results showed that 11 strains could be divided into 6 groups on 84% similarity level, it indicated that the intestinal aerobic bacteria genetic diversity was abundant. Sequencing the 6 representative strains’ 16S rDNA and submitting to GenBank, the accession number being JQ308104 to JQ308109 respectively. The 6 strains belonged to Klebsiella sp., Lysinibacillus sp., Brevibacillus sp., Bacillus subtilis, Gamma Proteobacterium and Brevibacillus limnophilus.

scholarly journals Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia

2005 ◽  
Vol 55 (4) ◽  
pp. 1439-1452 ◽  
Author(s):  
Endalkachew Wolde-meskel ◽  
Zewdu Terefework ◽  
Åsa Frostegård ◽  
Kristina Lindström
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Genes ◽  
Partial Sequence ◽  
23S Rrna ◽  
Southern Ethiopia ◽  
Rrna Gene ◽  
Pcr Rflp ◽  
23S Rrna Gene

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR–RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100 % similar to those of previously described species and 34 were novel sequences with 94–99 % similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

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