Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil

Daquiado, Aileen Rose; Kuppusamy, Saranya; Kim, Song Yeob; Kim, Jang Hwan; Yoon, Young-Eun; Kim, Pil Joo; Oh, Sung-Hwan; Kwak, Youn‐Sig; Lee, Yong-Bok

doi:10.1016/j.apsoil.2016.08.006

Cited by 60 publications

(35 citation statements)

References 33 publications

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“…Increasing the N input to soils can have various adverse effects on soil quality in agriculture [12], including a decrease in microbial functional diversity [13]. Long-term fertilizer experiments have shown that soil microbial biomass and community composition respond differently to N fertilization [14], although Daquiado et al [1] indicated that long-term fertilization had no significant effect on soil microbial community structure in paddy soil.…”

Section: Introductionmentioning

confidence: 99%

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Effects of Reclaimed Water Irrigation on Microbial Diversity and Composition of Soil with Reducing Nitrogen Fertilization

Guo

Xiao

et al. 2018

Water

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Reclaimed water (RW) is an alternative water resource that has been utilized all over the world, but its environmental effects are not fully understood. Soil biodiversity is an important indicator of soil tolerance and resilience. In the present study, the impact of RW irrigation on the microbial community diversity and chemical properties of topsoil was investigated by monitoring nitrogen (N) rates. Tomato plants were grown on plots which had been irrigated with reclaimed water for 5 years with varying levels of N fertilization (N270, 270 kg ha −1 ; N216, 216 kg ha −1 ; N189, 189 kg ha −1 ; and N135, 135 kg ha −1 ). Soil bacterial community composition was analyzed by PCR amplification of the 16S rDNA gene and Illumina MiSeq high-throughput sequencing technology of a total of 770,066 quality sequences. The results showed that long-term RW irrigation altered the bacterial composition of soil in an N-dependent manner. RW irrigation increased the abundances of Gemmatimonadetes, Actinobacteria, Firmicutes, and Nitrospirae in soils. The Chao, ACE, and H indices revealed no significant difference under RW irrigation with varying levels of N fertilization. The tomato yield and partial factor productivity from applied N for RN216 increased significantly under RW irrigation with reducing N fertilization. RW irrigation increased the yield of tomato and the abundance of functional microorganisms, which eventually improved the practice of irrigating with reclaimed municipal wastewater. Meanwhile, the potential environmental and health risks of long-term RW irrigation warrant further investigation.

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Section: Introductionmentioning

confidence: 99%

“…The diversity and composition of soil microbial communities directly affects soil ecosystems and nutrient cycling [1]. Appropriate community structure, with diversity and high variability of microorganisms, is an important factor for sustaining ecosystems and ensuring soil productivity [2,3].…”

Section: Introductionmentioning

confidence: 99%

Effects of Reclaimed Water Irrigation on Microbial Diversity and Composition of Soil with Reducing Nitrogen Fertilization

Guo

Xiao

et al. 2018

Water

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“…Members of Actinobacteria and Proteobacteria are known to be the dominant phyla in soil, and are supposed to be involved in the degradation of organic matter 49 , the production of secondary metabolites 50 , P solubilization and N 2 fixation, thus playing an essential role in nutrient cycling 51 , in the enhancement of soil fertility and crop productivity 52 , and in plant growth promotion 53,54 . These physiological traits could be considered at the base of the biostimulant activity of the strains belonging to these phyla 26 .…”

Section: Discussionmentioning

confidence: 99%

Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard

Gamalero

Bona

Novello

et al. 2020

Sci Rep

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The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. pinot noir rhizosphere in a vineyard subjected to integrated pest management. the aim of this work is to characterize the bacteriome of V. vinifera cv. pinot noir in a conventionally managed vineyard using a metabarcoding approach. comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed. open Scientific RepoRtS | (2020) 10:6453 | https://doi.org/10.1038/s41598-020-63154-w www.nature.com/scientificreports www.nature.com/scientificreports/ On the other hand, the microbiota associated to grapevine is affected by the chemical treatments applied in conventional viticulture; negative effects on soil microbial communities are induced by the use of fungicides 20,21 , by acidification of the soil following the fertilizer application 22,23 , and by pesticide application 24 . Altogether, these practices can result in modification of the dynamic interactions between grapevines and microorganisms.More recently, the grapevine microbiota has been placed at the center of the investigation aiming at understanding the possible beneficial effects of microorganisms on grape production. Thanks to culture-independent methods, and especially to the recent advances in next-generation sequencing methods, the complexity of the grapevine/rhizosphere microbial community has been deeply explored. In a previous work 25 , we characterized, by a metabarcoding approach, the bacteriome of the roots of V. vinifera cv. Pinot Noir, in a vineyard subjected to integrated pest management (IPM), looking at the shifts induced by the plant phenological stage and/or by the presence of the plant itself. The main result of that work was that the bacterial community, dominated by Actinobacteria, Proteobacteria, Gemmatimonadetes and Bacteroidetes, responds more intensely to the rhizosphere effect than to the phenological stage of the plant.In a further study, we used a metaproteome approach in order to characterize the microbial community associated to this IPM vineyard soil and to the ro...

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“…This is consistent with the observations of Chen et al [36] where Methylobacterium and Thiobacillus were the dominant members in mine tailings. Previously, Methylococcales abundance was also reported in an organic fertilizer, and it may also indicate contamination with hydrocarbons [37,38].…”

Section: Discussionmentioning

confidence: 97%

“…Therefore, Thiobacillus spp. have frequently been reported as a dominant species in the mining environment [37,41]. The heavy metal-tolerant genera including Thiobacillus may have an ability to survive in highly contaminated soils.…”

Section: Discussionmentioning

confidence: 99%

Bacterial community analysis of stabilized soils in proximity to an exhausted mine

Park

Lee

Kim³

et al. 2018

Environmental Engineering Research

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Soil stabilization is a soil remediation technique that reduces the mobility of heavy metals in soils. Although it is a well-established technique, it is nonetheless essential to perform a follow-up chemical assessment via a leaching test to evaluate the immobilization of heavy metals in the soil matrix. Unfortunately, a standard chemical assessment is not sufficient for evaluation of the biological functional state of stabilized soils slated for agricultural use. Therefore, it is useful to employ a pyrosequencing-based microbial community analysis for the purpose. In this study, a recently stabilized site in the proximity of an exhausted mine was analyzed for bacterial diversity, richness, and relative abundance as well as the effect of environmental factors. Based on the Shannon and Chao1 indices and rarefaction curves, the results showed that the stabilized layer exhibited lower bacterial diversity than control soils. The prevalence of dominant bacterial populations was examined in a hierarchical manner. Relatively high abundances of Proteobacteria and Methylobacter tundripaludum were observed in the stabilized soil. In particular, there was substantial abundance of the Methylobacter genus, which is known for its association with heavy metal contamination. The study demonstrated the efficacy of (micro)biological assessment for aiding in the understanding and post-management of stabilized soils.

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Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil

Cited by 60 publications

References 33 publications

Effects of Reclaimed Water Irrigation on Microbial Diversity and Composition of Soil with Reducing Nitrogen Fertilization

Effects of Reclaimed Water Irrigation on Microbial Diversity and Composition of Soil with Reducing Nitrogen Fertilization

Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard

Bacterial community analysis of stabilized soils in proximity to an exhausted mine

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