scholarly journals Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques

2005 ◽  
Vol 71 (4) ◽  
pp. 2162-2169 ◽  
Author(s):  
Hideyuki Tamaki ◽  
Yuji Sekiguchi ◽  
Satoshi Hanada ◽  
Kazunori Nakamura ◽  
Nakao Nomura ◽  
...  

ABSTRACT Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.

2009 ◽  
Vol 75 (6) ◽  
pp. 1566-1574 ◽  
Author(s):  
Uma Shankar Sagaram ◽  
Kristen M. DeAngelis ◽  
Pankaj Trivedi ◽  
Gary L. Andersen ◽  
Shi-En Lu ◽  
...  

ABSTRACT The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. “Candidatus Liberibacter asiaticus” was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of “Candidatus Liberibacter asiaticus” in symptomatic leaves. These data implicate “Candidatus Liberibacter asiaticus” as the pathogen responsible for HLB disease.


2014 ◽  
Vol 48 (8) ◽  
pp. 717-728 ◽  
Author(s):  
M. N. Zakaria ◽  
T. Takeshita ◽  
Y. Shibata ◽  
H. Maeda ◽  
N. Wada ◽  
...  

2013 ◽  
Vol 825 ◽  
pp. 50-53 ◽  
Author(s):  
Xing Yu Liu ◽  
Bo Wei Chen ◽  
Jian Kang Wen

The distribution and diversity of bacterial community in Zijinshan commercial non-aeration copper bioheapleaching system operated at pH 0.8 for three years were investigated. The 24 meters high heap was cut off by mechanical digger. On the trapezoidal cross-section of the heap, 9 ore samples were taken from different vertical and horizontal locations and investigated by 16S rRNA gene clone library. Another 3 liquid samples from raffinate solution pond, spray solution pond and pregnant solution pond were also applied to 16S rRNA gene clone library analysis. The retrieved 1166 clone sequences from 12 samples were mainly related to genus Acidithiobacillus (42.36%), genus Leptospirillum (37.73%) and genus Sulfobacillus (6.52%). Relative high amount of heterotrophic bacteria were distributed at the ore surface in the internal part of the heap and in the liquid samples respectively. The retrieved heterotrophic bacterial sequences were mainly related to genus Acidiphilium (accounting 11.11% to 32.00% percent in the liquid samples), genus Acidovorax (accounting 12.37% in A1 sample), genus Pelomonas (accounting 4.17% to 10.31% in several ore samples) and genus Aquabacterium (accounting 10.31% in C2 sample). Bacterial diversity in the heap was increased from the surfcae layer to the interior of the heap. The proportion of genus Leptospirillum horizontally increased from the inner to the outer part while vertically decreased from lower depth (2-3 years leaching time) to higher depth(3-6 month leaching time), and reverse correlation of genus Acidithiobacillus was found in the heap. Our finding indicated that heterotrophic bacteria may play very important roles in the commercial bioheapleaching system, and revealed high distribution of genus Leptospirillum in the outer part of this non-aerated heap.


Microbiology ◽  
2016 ◽  
Vol 85 (3) ◽  
pp. 379-385 ◽  
Author(s):  
Xiumin Zhang ◽  
Zhiyuan Gao ◽  
Mengmeng Zhang ◽  
Fengxia Jing ◽  
Jiao Du ◽  
...  

2006 ◽  
Vol 72 (5) ◽  
pp. 3788-3792 ◽  
Author(s):  
Julie C. Frey ◽  
Jessica M. Rothman ◽  
Alice N. Pell ◽  
John Bosco Nizeyi ◽  
Michael R. Cranfield ◽  
...  

ABSTRACT We describe the bacterial diversity in fecal samples of a wild gorilla by use of a 16S rRNA gene clone library and terminal-restriction fragment length polymorphism (T-RFLP). Clones were classified as Firmicutes, Verrucomicrobia, Actinobacteria, Lentisphaerae, Bacteroidetes, Spirochetes, and Planctomycetes. Our data suggest that fecal populations did not change temporally, as determined by T-RFLP.


2008 ◽  
Vol 13 (3) ◽  
pp. 97-102 ◽  
Author(s):  
HIROKI MATSUI ◽  
RIE TSUCHIYA ◽  
YUKA ISOBE ◽  
HIROTO MAEDA ◽  
MIYO NARITA

2009 ◽  
Vol 75 (22) ◽  
pp. 7287-7290 ◽  
Author(s):  
Shu-Rong Xiang ◽  
Tian-Cui Shang ◽  
Yong Chen ◽  
Ze-Fan Jing ◽  
Tandong Yao

ABSTRACT Dominant bacteria in the different habitats in the Kuytun 51 Glacier were investigated using a 16S rRNA gene clone library sequencing technique. Results showed diverse bacteria on the glacial surface, with the dominant phyla being Proteobacteria, Cyanobacteria, and Bacteroidetes. UniFrac data showed distinct community patterns between the Kuytun and Himalayan Rongbuk glaciers.


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