Differences in Soil Bacterial Community Compositions in Paddy Fields under Organic and Conventional Farming Conditions

Suzuki, Kazuki; Takemura, Manami; Miki, Takaaki; Nonaka, Manabu; Harada, Naoki

doi:10.1264/jsme2.me18101

Cited by 12 publications

(7 citation statements)

References 14 publications

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“…Altogether, these observations suggest that rice cultivation and associated treatments, such as fertilization, encourage the proliferation of certain species, which are uniquely adapted and functionally relevant in mineralizing nutrients in the rice-cultivated soil environment compared to the fallow soils and to the 5mR soils, which were not actively managed for the short five months off-season duration. Our observations of fluctuating bacterial species richness and diversity in fields with different rice cultivation status or time points is similar to findings from studies investigating bacterial communities in rice agroecosystem during rice plant developmental stages [110,111], under different farming conditions [112] and for wild and cultivated rice cultivars [113].…”

Section: Discussionsupporting

confidence: 87%

Assessing the Impact of Rice Cultivation and Off-Season Period on Dynamics of Soil Enzyme Activities and Bacterial Communities in Two Agro-Ecological Regions of Mozambique

et al. 2021

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Soil ecosystem perturbation due to agronomic practices can negatively impact soil productivity by altering the diversity and function of soil health determinants. Currently, the influence of rice cultivation and off-season periods on the dynamics of soil health determinants is unclear. Therefore, soil enzyme activities (EAs) and bacterial community compositions in rice-cultivated fields at postharvest (PH) and after a 5-month off-season period (5mR), and fallow-fields (5-years-fallow, 5YF; 10-years-fallow, 10YF and/or one-year-fallow, 1YF) were assessed in two agroecological regions of Mozambique. EAs were mostly higher in fallow fields than in PH, with significant (p < 0.05) differences detected for β-glucosidase and acid phosphatase activities. Only β-glucosidase activity was significantly (p < 0.05) different between PH and 5mR, suggesting that β-glucosidase is responsive in the short-term. Bacterial diversity was highest in rice-cultivated soil and correlated with NO3−, NH4+ and electrical conductivity. Differentially abundant genera, such as Agromyces, Bacillus, Desulfuromonas, Gaiella, Lysobacter, Micromonospora, Norcadiodes, Rubrobacter, Solirubrobacter and Sphingomonas were mostly associated with fallow and 5mR fields, suggesting either negative effects of rice cultivation or the fallow period aided their recovery. Overall, rice cultivation and chemical parameters influenced certain EAs and shaped bacterial communities. Furthermore, the 5-month off-season period facilitates nutrient recovery and proliferation of plant-growth-promoting bacteria.

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Section: Discussionsupporting

confidence: 87%

Assessing the Impact of Rice Cultivation and Off-Season Period on Dynamics of Soil Enzyme Activities and Bacterial Communities in Two Agro-Ecological Regions of Mozambique

et al. 2021

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“…A meta-analysis and meta-regression confirmed that organic farming also enhanced soil microbial abundance and activity [25]. In addition, the soil bacterial community compositions were different in paddy fields under organic and conventional farming conditions [26]. In short, the diversity of soil microbial communities (bacterial communities) is complex and different s in various agricultural ecosystem.…”

Section: Introductionmentioning

confidence: 79%

WITHDRAWN: Differences in the soil bacterial community under organic farming and conventional farming modes revealed by 16S rDNA sequencing

Yang

Fang

et al. 2020

Preprint

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Background The bacterial communities is complex and different in various agricultural ecosystem. In this study, high-throughput Illumina MiSeq sequencing was conducted to assess the differences in soil bacterial communities between organic farming and conventional farming modes. Results A total of 3, 919 operational taxonomic units were identified and classified as 26 phyla, 42 classes, 78 orders, 120 families, 281 genera. The dominant genera were Lysobacter , Pseudomonas , Massilia , Pseudarthrobacter , Ferruginibacter , Flavobacterium , Flavisolibacter , Brevundimonas , Haliangium and Sphingomonas . Analysis of soil bacterial diversity showed that the soil under the organic farming had a greater bacterial diversity than that under the conventional farming. Linear discriminant analysis effect size analysis showed that the major bacterial groups identified in the soil sample CK1 (2015.4) and CK6 (2017.10) under conventional farming mode were largely different from those in the soil sample O6 (2017.10) under organic farming mode. Redundancy analysis demonstrated that available nitrogen was the most important factor regulating bacterial composition under the organic farming mode, followed by soil rapidly available phosphorous and potassium. Massilia , Pseudomonas , Lysobacter and Pseudarthrobacter abundances showed a strong positive correlation with the content of available nitrogen. Conclusions Organic farming could improve soil organic matter, available nitrogen, rapidly available phosphorus and retard soil acidification. This modification of soil can directly or indirectly relate to the bacterial communities in soil. The shifts of bacterial communities were complicated and dynamic with respect to all sorts of the measures of cultivation and management under organic farming mode.

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“…Little is known about the root microbial community associated with nature farming and its plant growth-promoting potential under low-input conditions, and no study has been performed on the root microbial community of naturally farmed rice plants in Japan. A previous study reported that rice fields managed with organic farming practices have a distinct bacterial community composition compared with that of conventionally farmed fields (Suzuki et al, 2019). The root microbial abundance was significantly higher in organically managed crops than in conventionally managed crops (Lenc et al, 2015), and a higher abundance of nutrition-related bacteria was observed (Wang et al, 2016).…”

Section: Introductionmentioning

confidence: 90%

Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits

Sinong

Yasuda

Nara³

et al. 2021

Front. Sustain. Food Syst.

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A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.

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Differences in Soil Bacterial Community Compositions in Paddy Fields under Organic and Conventional Farming Conditions

Cited by 12 publications

References 14 publications

Assessing the Impact of Rice Cultivation and Off-Season Period on Dynamics of Soil Enzyme Activities and Bacterial Communities in Two Agro-Ecological Regions of Mozambique

Assessing the Impact of Rice Cultivation and Off-Season Period on Dynamics of Soil Enzyme Activities and Bacterial Communities in Two Agro-Ecological Regions of Mozambique

WITHDRAWN: Differences in the soil bacterial community under organic farming and conventional farming modes revealed by 16S rDNA sequencing

Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits

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