Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis

2006 ◽  
Vol 109 (1-2) ◽  
pp. 79-87 ◽  
Author(s):  
S HARUTA ◽  
S UENO ◽  
I EGAWA ◽  
K HASHIGUCHI ◽  
A FUJII ◽  
...  
2010 ◽  
Vol 40 (12) ◽  
pp. 2384-2397 ◽  
Author(s):  
Tiina Rajala ◽  
Mikko Peltoniemi ◽  
Taina Pennanen ◽  
Raisa Mäkipää

We investigated the fungal communities inhabiting decaying logs in a seminatural boreal forest stand in relation to host tree species, stage of decay, density, diameter, moisture, C to N ratio, Klason lignin content, and water- and ethanol-soluble extractives. Communities were profiled using denaturing gradient gel electrophoresis fingerprinting of the rDNA ITS1 region coupled with sequencing of fungal DNA extracted directly from the wood. In addition, polypore fruit bodies were inventoried. Logs from different tree species had different fungal communities and different physicochemical properties (e.g., C to N ratio, density, ethanol extractives, and diameter). Ascomycetes comprised a larger portion of communities inhabiting deciduous birch ( Betula spp.) and European aspen ( Populus tremula L.) logs compared with those living on coniferous Norway spruce ( Picea abies (L.) Karst.) and Scots pine ( Pinus sylvestris L.). A relationship between mycelial community structure and density of decaying spruce logs suggested a succession of fungi with mass loss of wood. The fruit body inventory underestimated fungal diversity in comparison with the culture-free denaturing gradient gel electrophoresis analysis that also detected inconspicuous but important species inhabiting decaying wood.


2009 ◽  
Vol 55 (4) ◽  
pp. 375-387 ◽  
Author(s):  
Amy Novinscak ◽  
Nadine J. DeCoste ◽  
Céline Surette ◽  
Martin Filion

Composting is a microbial process that converts organic waste into a nutrient-rich end product used in horticultural and agricultural applications. The diversity and long-term succession of microorganisms found in composted biosolids has been less characterized than other composts. In this study, bacterial and fungal communities found in composted biosolids aging from 1 to 24 months were studied using denaturing gradient gel electrophoresis (DGGE) and sequencing. The results revealed high levels of diversity, where 53 bacterial species belonging to 10 phyla and 21 fungal species belonging to 4 phyla were identified. Significant differences were observed when comparing the bacterial DGGE patterns of young compost samples, whereas no differences were observed in samples over 8 months. For fungal patterns, no significant differences were observed during the first 4 months of composting, but the diversity then significantly shifted until 24 months. The results indicate that patterns of bacterial species vary during the first few months of composting, whereas fungal patterns generally vary throughout the whole process, except during early stages. The description of the main microbial groups found in composted biosolids could find various applications, including the discovery of biotechnologically relevant microorganisms and the development of novel markers allowing quantitative monitoring of key microorganisms.


2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.


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