scholarly journals Peer Review #2 of "Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification (v0.1)"

2018 ◽  
Keyword(s):  
Bacterial Community ◽  
Peer Review ◽  
High Throughput ◽  
Soil Bacterial Community ◽  
Absolute Abundance ◽  
Soil Bacterial

scholarly journals Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4514 ◽  
Author(s):  
Jun Lou ◽  
Li Yang ◽  
Haizhen Wang ◽  
Laosheng Wu ◽  
Jianming Xu
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Laboratory Strain ◽  
Soil Bacterial Community ◽  
Absolute Abundance ◽  
Internal Reference ◽  
Biodegradation Study ◽  
Soil Bacterial

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

scholarly journals Soil bacterial community and functions directly respond to grazing exclusion in a Leymus chinensis steppe of Inner Mongolia, China

2020 ◽  
Author(s):  
Han-Wen Deng ◽  
Xin-Fu Bai ◽  
Ping Zhu ◽  
Yu-Meng Lu ◽  
Lei Ji ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Inner Mongolia ◽  
Soil Bacterial Community ◽  
Leymus Chinensis ◽  
Absolute Abundance ◽  
Ecological Functions ◽  
Grazing Exclusion ◽  
The Absolute ◽  
Soil Bacterial

Abstract Background Grazing exclusion is a common grassland management strategy for restoring degraded grasslands. Its effectiveness on optimizing plant species community, increasing vegetation diversity and biomass, improving soil fertility, has been widely documented in literatures. However, little is known on the responses of the absolute abundance and the ecological functions of soil bacterial community to long-term grazing exclusion. Result In this study, the absolute abundance, diversity, and ecological functions of soil bacterial community were determined by the high-throughput absolute quantitative sequencing technology on a long-term grazing exclusion (40 years, GE) area and three free grazing areas (FGs) within a Leymus chinensis steppe of Inner Mongolia, China, and analyzed the driving forces leading to the variations in soil bacterial community and functions. Our results showed that there was significantly higher soil bacterial abundance in the GE than the FGs along with corresponding variations in vegetation and soil properties. With the decrease of vegetation aboveground biomass, the absolute abundance of soil bacterial community also decreased. Among the phyla of the soil bacterial communities, the relative abundances of Chloroflexi and Firmicutes phyla were especially lower, and that of Verrucomicrobia phylum was higher in the GE than the FGs; the absolute abundances of Euryarchaeota and Microgenomates phyla were especially higher in the GE than the FGs. Conclusions This study suggested that long-term grazing exclusion significantly increased the absolute abundance, changed soil bacterial composition, and especially enhanced bacterial motility and chemotaxis. In particular, soil organic matter was the important agent to influence and connect vegetation and soil. This work will enrich our understanding of the responses of absolute abundance, diversity, and function of the soil bacterial community to long-term grazing exclusion, and help the evaluation of grassland degradation degree and restoration strategy effectiveness.

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