Soil microbial response to silicate fertilization reduces bioavailable arsenic in contaminated paddies

Das, Suvendu; Hwang, Hyun Young; Song, Hyeon Ji; Cho, Song Rae; Nostrand, Joy D. Van

doi:10.1016/j.soilbio.2021.108307

Cited by 23 publications

(6 citation statements)

References 35 publications

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“…Yang et al indicated that soil microbial diversity had a strong effect on tobacco wilt disease level [ 34 ]. In addition, any modifications in soil microbial community assemblages will have a cascade of effects on soil structure and nutrient cycling, including soil aggregate stability and decomposition processes [ 35 , 36 ]. The results of biodiversity measurement showed that the phyla Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi were dominant bacteria, which are consistently predominant bacteria in tillage soil [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

Ling

Qiao

et al. 2022

BMC Microbiol

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Background Organic mulch is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulch and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulch on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulch. Results Organic mulch could significantly suppress the disease incidence in the litchi plantation, and with a reduction of 37.74% to 85.66%. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, significantly higher bacterial and fungal community diversity indexes were found in organic mulch soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils. Conclusions Thus, we believe that organic mulch has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

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Section: Discussionmentioning

confidence: 99%

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

Ling

Qiao

et al. 2022

BMC Microbiol

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“…To determine the potential differences in the bacterial and fungal communities across compartments and chromium-added treatments, a heatmap of Spearman's rank correlation was generated using the package “gpplot” (Oksanen et al, 2012) in R (v3.6.2) based on Bray-Curtis dissimilarity. Canonical discriminant analysis (CDA) was performed to calculate the environmental factors that have the most remarkable influence on the microbial and fungal communities by CANOCO 5.0 (Biometrics Wageningen, Netherlands) [ 72 , 73 ]. LEfSe analysis was applied using the version at https://huttenhower.sph.harvard.edu/galaxy/ [ 74 ].…”

Section: Methodsmentioning

confidence: 99%

Effects of cadmium contamination on bacterial and fungal communities in Panax ginseng-growing soil

Sun

Jin

et al. 2022

BMC Microbiol

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Background Cadmium (Cd) contamination in soil poses a serious safety risk for the development of medicine and food with ginseng as the raw material. Microorganisms are key players in the functioning and service of soil ecosystems, but the effects of Cd-contaminated ginseng growth on these microorganisms is still poorly understood. To study this hypothesis, we evaluated the effects of microorganisms and Cd (0, 0.25, 0.5, 1.0, 2.0, 5.0, and 10.0 mg kg-1 of Cd) exposure on the soil microbial community using Illumina HiSeq high-throughput sequencing. Results Our results indicated that Cd-contaminated soil affected the soil microbial diversity and composition, and bacterial diversity was affected more than fungal diversity in Cd-contaminated soil, especially according to Shannon indices. The abundance of the soil microbial community decreased and the composition changed according to the relative abundances at the phylum level, including those of Saccharibacteria and Gemmatimonadetes in bacteria and Mortierellomycota in fungi. The LEfSe algorithm was used to identify active biomarkers, and 45 differentially abundant bacterial taxonomic clades and 16 differentially abundant fungal taxonomic clades were identified with LDA scores higher than 4.0. Finally, a heatmap of Spearman's rank correlation coefficients and canonical discriminant analysis (CDA) indicated that some key biomarkers, Arenimonas, Xanthomonadales, Nitrosomonadaceae, Methylophilales, Caulobacterales, Aeromicrobium, Chitinophagaceae, Acidimicrobiales, Nocardioidaceae, Propionibacteriales, Frankiales, and Gemmatimonadaceae, were positively correlated with the total and available Cd (p<0.05) but negatively correlated with AK, AP, and pH (p<0.05) in the bacterial community. Similarly, in the fungal community, Tubaria, Mortierellaceae, and Rhizophagus were positively correlated with the total and available Cd but negatively correlated with AK, AP, TK, and pH. Conclusion Cd contamination significantly affected microbial diversity and composition in ginseng-growing soil. Our findings provide new insight into the effects of Cd contamination on the microbial communities in ginseng-growing soil.

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“…Thus, likelihood of microbial exposure to As and other nutrients appears to be a major factor driving the microbial assemblage toward specialists in As-resistance and nutrient cycling at the root-plaque. Other reports demonstrated similar mechanism of As-contamination influencing the metabolic coupling of As-transforming with Fe-cycling (Muehe et al, 2016;Yi et al, 2019), with S-cycling microorganisms (Das et al, 2021) and with metabolism of C, N, and P (Dunivin et al, 2019;Das et al, 2021).…”

Section: Discussionmentioning

confidence: 65%

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations

et al. 2021

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Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of AsIII and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

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Soil microbial response to silicate fertilization reduces bioavailable arsenic in contaminated paddies

Cited by 23 publications

References 35 publications

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

Effects of cadmium contamination on bacterial and fungal communities in Panax ginseng-growing soil

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations

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