Community Structure and Soil pH Determine Chemoautotrophic Carbon Dioxide Fixation in Drained Paddy Soils

Long, Xiaojing; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K.; Zhu, Yan

doi:10.1021/acs.est.5b00506

Cited by 79 publications

(26 citation statements)

References 38 publications

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“…However, we observed that there was no significant correlation between AP and the top 50 bacterial genera. In a previous study, bacterial abundance was positively associated with soil pH [19], and pH differences were the main factor influencing soil archaeal diversity and community structure in the tropical zone and chemoautotrophic carbon dioxide fixation in drained paddy soils [62, 63]. Environmental factors clearly affected the bacterial community in this study and were the main reason for their differences in abundance.…”

Section: Discussionsupporting

confidence: 48%

High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

Zhang

Shen

et al. 2019

PLoS ONE

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Potential environmental risks of genetically modified (GM) crops have raised concerns. To better understand the effect of transgenic rice on the bacterial community in paddy soil, a field experiment was carried out using pairs of rice varieties from two subspecies (indica and japonica) containing bar transgene with herbicide resistance and their parental conventional rice. The 16S rRNA gene of soil genomic DNA from different soil layers at the maturity stage was sequenced using high-throughput sequencing on the Illumina MiSeq platform to explore the microbial community diversity among different rice soils. There were no significant differences in diversity indices between transgenic japonica rice and its sister conventional rice (japonica pair) among different soil layers, but, significant differences was observed between transgenic indica rice and its conventional rice (indica pair) in the topsoil layer around concentrated rice roots according to the ace diversity index. Though the japonica rice soil and indica rice soil were shared several key genera, including Rivibacter, Anaeromyxobacter, Roseomonas, Geobacter, Thiobacillus, Clostridium, and Desulfobulbus, the primary bacterial genera in indica rice soil were different from those in japonica rice. Synechococcus and Dechloromonas were present in japonica rice samples, while Chloronema, Flexibacter, and Blastocatella were observed in indica rice soil. Moreover, the abundance of genera between GM and non-GM varieties in japonica rice was significantly different from indica rice, and several bacterial communities influenced these differences. Anaerovorax was more abundant in transgenic japonica rice soil than conventional rice soil, while it was deficient in transgenic indica rice soil compared to conventional rice soil, and opposite responses to Deferrisoma were in that of indica rice. Thus, we concluded that transgenic indica and japonica rice had different effects on soil bacteria compared with their corresponding sister conventional rice. However, these composition and abundance difference only occurred for a few genera but had no effect on the primary genera and soil characteristics were mainly contributed to these differences. Thus, differences in bacterial community structure can be ignored when evaluating the impacts of transgenic rice in the complex soil microenvironment.

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Section: Discussionsupporting

confidence: 48%

High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

Zhang

Shen

et al. 2019

PLoS ONE

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“…These results are similar to the ones found in our study. Soil TOC and cbbl abundance exhibited a significant positive correlation, in line with the view that soil organic carbon and pH are the most significant factors influencing the community composition, abundance, and activity of the cbbl bacteria(Yuan et al 2012;Long et al 2015). The value of soil pH was also significantly correlated with the abundance of AOB and nifH.…”

supporting

confidence: 81%

Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol

Wang

et al. 2019

Can. J. Microbiol.

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Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.

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“…Table 4). They were the most significant factors influencing the community composition, abundance, and activity of the cbbl bacteria [51][52]. The above results show that different nitrogen fertilization rates can change the soil nutrient content, and changes of soil nutrients could promote the abundance of nutrient cycling microbial changed, and different soil nutrients can affect different functional microbes.…”

Section: Relative Abundance Of Functional Microbialmentioning

confidence: 81%

Effects of Long-Term Nitrogen Fertilizer Application on Rhizosphere Microorganisms under Different Soil Types

Wang

et al. 2019

Pol. J. Environ. Stud.

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The application of nitrogen fertilizers can improve the soil environment and influence the nutrition and quality of plants; there are also significant impacts of soil types on soil microbial communities. Research on the coupling effects between the rates of nitrogen fertilizer and the soil types on soil microbial metabolic activities under field conditions are currently lacking. In this study, we investigated the effect of five different N fertilization rates on three types of soils (meadow black, alluvial, and sandy soil) that were over 8-year-long planted maize. Illumina Miseq sequencing methods were used to characterize the soil microbial communities. Real-time PCR were adopted to calculate the relative abundance of N, C, and P-cycling functional microbial. Results indicated that different N rates can significantly change soil available nutrients and effectively reduce soil pH. The structure of the soil bacterial communities and diversity did not change after the fertilization of N during the study period. However, it can be found that soil types can substantially influence the structure of bacterial communities in soil, meanwhile, there was a significant correlation between pH and the composition of bacterial communities. Although the composition of the soil microbial community did not influence the fertilization rate of N, they can be indirectly affected by pH. There was significant difference (P<0.05) in the relative abundances of the nutrient cycling functional genes of the rhizosphere soil under different nitrogen levels, with nitrogen application and soil type the main influencing factors. The results showed that the excessive application of N fertilizer did not increase the yields of maize, thus it is important to investigate the reasonable fertilization rates of N fertilizer to protect the ecological balance of crop soils.

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Community Structure and Soil pH Determine Chemoautotrophic Carbon Dioxide Fixation in Drained Paddy Soils

Cited by 79 publications

References 38 publications

High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol

Effects of Long-Term Nitrogen Fertilizer Application on Rhizosphere Microorganisms under Different Soil Types

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