Characteristics of the rhizosphere bacterial community across different cultivation years in saline–alkaline paddy soils of Songnen Plain of China

2018 ◽  
Vol 64 (12) ◽  
pp. 925-936 ◽  
Author(s):  
Juntao Cui ◽  
Yanan Li ◽  
Chengyu Wang ◽  
Kyung Seok Kim ◽  
Tianye Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Paddy Soils ◽  
Community Diversity ◽  
Soil Conditions ◽  
Alkaline Soil ◽  
Songnen Plain ◽  
Soil Microbial Diversity ◽  
Soil Microbial

The characteristics of the rhizosphere microbial community across different cultivation years (from 1, 3, 5, 15, 20, and 50 years) in saline–alkaline paddy soils in Songnen Plain of China were investigated based on sequence variation of 16S rDNA using Illumina MiSeq sequencing. The results showed that the microbial community diversity varied across cultivation years, showing higher diversity in cultivation years >15 than in cultivation years <15. The dominant microbial community of the rhizosphere was mainly composed of Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. Furthermore, soil microbial diversity appeared to be affected directly by changes in soil properties corresponding to cultivated years. Diversity of Proteobacteria decreased as cultivated years increased; however, that of Acidobacteria showed the opposite direction. In addition, the soil microbial communities were clustered into two main groups: one from the sites cultivated for fewer than 15 years, and the other from the sites cultivated for more than 15 years. The abundance of nitrogen-fixing microorganisms in the soil sample was significantly higher in soils cultivated for under 15 years than in those cultivated for over 15 years (P < 0.05). Moreover, there was an obvious negative correlation between the cultivated years and Methanosarcina. Our findings on the dynamics of microbial community and its specific function in response to variable soil conditions are important for understanding and improving physical and chemical characteristics of saline–alkaline soil in Songnen Plain of China.

scholarly journals Organic Mulching Can Suppress Litchi Downy Blight Through Modification of Soil Microbial Community Structure and Functional Potentials

2021 ◽  
Author(s):  
Dandan Xu ◽  
Jinfeng Ling ◽  
Pinggen Xi ◽  
Yani Zeng ◽  
Jianfan Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Management Practice ◽  
Disease Incidence ◽  
Soil Microbial Communities ◽  
Community Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Pests And Diseases

Abstract Organic mulching 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 mulching and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulching on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulching. Our results showed that organic mulching could decrease the disease incidence in the litchi plantation. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, higher bacterial and fungal community diversity indexes were found in organic mulching 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. Thus, we believe that organic mulching has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

scholarly journals Microbial community diversity in the soil of Barrientos Island estimated by RAPD and Biolog Ecoplate methods

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Learn-Han Lee ◽  
Vengadesh Letchumanan ◽  
Nurul-Syakima Ab Mutalib ◽  
Yoke Kqueen Cheah
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Soil Microbial Communities ◽  
Community Diversity ◽  
Soil Microbial Diversity ◽  
Microbial Community Diversity ◽  
Soil Microbial ◽  
Biolog Ecoplate

The diversity of soil microbial communities at Barrientos Island with  differents soil characteristics were evaluated using PCR-based method random amplified polymorphic DNA (RAPD) and community level physiological profiles (CLPP) of Biolog Ecoplate. The soils were selected from 17 different locations around Barrientos Island inhabited by different breeders. Shannon-Weaver index and multivariate analysis were performed to characterize variations of soil microbial communities. Both RAPD and CLPP methods exhibited that most soils with different type of rookery and characteristics could possibly affect the DNA sequence diversity and soil microbial diversity. The abandoned type of rookery had the highest Shannon-Weaver index as exhibited by soil sample 445 (3.4 for RAPD) and 450 (3.09 for CLPP). Higher coefficients of DNA sequence similarity were found in soil samples colonized by similar breeders, like soil 442 and 446 (both were active Chinstrap rookery) shared highest similarity in DNA sequences (73.53). The cluster analysis of RAPD profiles by UPGMA and principle component analysis (PCA) of Biolog Ecoplate exhibited similar influence of type of rookery and soil condition towards soil microbial community diversity. The results may suggest that the change in microbial community DNA composition is accompanied with the change in microbial functional properties.

scholarly journals Organic Mulching can Suppress Litchi Downy Blight Through Modification of Soil Microbial Community Structure and Functional Potentials

2021 ◽  
Author(s):  
Dandan Xu ◽  
Jinfeng Ling ◽  
Fang Qiao ◽  
Pinggen Xi ◽  
Yani Zeng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Management Practice ◽  
Disease Incidence ◽  
Soil Microbial Communities ◽  
Community Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Pests And Diseases

Abstract Background: Organic mulching 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 mulching and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulching on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulching. Results: Organic mulching could decrease the disease incidence in the litchi plantation. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, higher bacterial and fungal community diversity indexes were found in organic mulching 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 mulching has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

Alleviating Continuous Monocropping Obstacle in Melon: Biological Elimination of Phenolic Acid

2020 ◽  
Author(s):  
Huiqin Xie ◽  
Yongli Ku ◽  
Xiangna Yang ◽  
Le Cao ◽  
Xueli Mei ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Phenolic Acids ◽  
Fruit Quality ◽  
High Performance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Continuous Cropping ◽  
Soil Microbial

Abstract Background: Melon (Cucumis melo L.) is one of the most important fruit crops grown in China. However, the yield and quality of melon have significantly declined under continuous cropping. Phenolic acids are believed to be associated with the continuous monocropping obstacle (CMO) and can influence plant microbe interactions. Coumaric acid (CA) is one of the major phenolic acids found in melon root exudates. The objectives of this study were to estimate the elimination of CA by the soil bacterium K3 as well as its effects on mitigating melon CMO. CA degradation was investigated by monitoring the CA retained in the growth medium using high performance liquid chromatography (HPLC). The effects of CA and K3 on rhizosphere soil microbial communities were investigated by the spread plate method and Illumina MiSeq sequencing. Furthermore, the effects of CA and K3 on melon seedling growth were measured under potted conditions. The changes in soil enzymes and fruit quality under K3 amendment were examined in a greenhouse experiment. Result:The results suggest that the addition of CA had the same result as the CMO, such as deterioration of the microbial community and slower growth of melon plants. HPLC and microbial analysis showed that K3 had a pronounced ability to decompose CA and could improve the soil microbial community environment. Soil inoculation with K3 agent could significantly improve the fruit quality of melon.Conclusion: Our results show that the effects of K3 in the soil are reflected by changes in populations and diversity of soil microbes and suggest that deterioration of microbial communities in soil might be associated with the growth constraint of melon in continuous monoculture systems.

scholarly journals Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

2020 ◽  
Vol 66 (4) ◽  
pp. 263-273
Author(s):  
Julien Saavedra-Lavoie ◽  
Anne de la Porte ◽  
Sarah Piché-Choquette ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Co Oxidation ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Oxidative Capacity ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microcosms ◽  
Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

scholarly journals Dazomet application suppressed watermelon wilt by the altered soil microbial community

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Feiying Zhu ◽  
Jiling Xiao ◽  
Yi Zhang ◽  
Lin Wei ◽  
Zhihuai Liang
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Plant Immunity ◽  
Soil Phosphorus ◽  
Illumina Miseq ◽  
Control Group ◽  
Soil Microbial Diversity ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Available Soil Phosphorus

AbstractFusarium wilt disease causes severe decline of watermelon yield and quality. Researches have been reported that soil fumigation with dazomet can help control crop disease. Firstly, we discovered that the dazomet application suppressed watermelon wilt in field experiment compared to the control group. While the importance of microbial community in regulating plant health has been rising up, we therefore focused on examining the soil microbial diversity at six different sampling times after dazomet application by using Illumina MiSeq platform. Remarkably, our research results showed that some beneficial microbial genera have been altered, and these beneficial microbial genera have dominated the entire community, such as Nitrolancea, Pseudomonas and Penicillium after dazomet application. Instead, the relative abundance of Fusarium genus and the pathogen FON (Fusarium oxysporum f. sp. niveum, FON) had the decreased. As there was a significant accumulation of AP (available soil phosphorus) after dazomet application, we noticed that the beneficial microbes as Bacillus, Nitrolancea, Paenibacillus and Penicillium have significant positive correlation with AP but negatively related to morbidity. Together, these results demonstrate that the altered soil microbial community structure by dazomet application is critical to suppress watermelon Fusarium wilt. Thus, our results will drive investigations aimed to deploy interaction of microbiota contribute and plant immunity.

scholarly journals The Responses of Soil Microbial to Changed Rainfall and Increased Temperature in Desert Grassland in Northern China

2021 ◽  
Author(s):  
Yi Zhang ◽  
Ying-Zhong Xie ◽  
Hong-Bin Ma ◽  
Juan Zhang ◽  
Le Jing ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Respiration ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Response Strategy ◽  
Desert Grassland ◽  
Soil Microbial Diversity ◽  
Soil Microbial

Abstract Background: The study evaluates how rainfall change and temperature increase affect microbial communities in the desert grassland of Ningxia Autonomous Region, China to explore the soil microbial community and the relationships among the soil microbial community, chemical properties, soil respiration (SR) and plant biomass under the climate change. We established the field experiment with five levels of rainfall by rainout shelters and two levels of temperature by Open-Top Chamber (OTC). Results: The effect of temperature to soil microbial communities is not significant, but with the continuous increase of rainfall, the microbial community gradually increases. Soil microbial diversity negatively correlated with soil CO2 flux. The α-diversity of microbial communities positively correlated with above-living biomass (ALB) and soil temperature (ST), but negatively correlated with root biomass (RB). Conclusions: Both rainfall and temperature’s rising do not promote the soil community α-diversity, but it can promote soil microbial community β-diversity. Soil microbial communities show resistance to rainfall changing. Soil respiration (SR) will limit soil microbial diversity. Soil organic carbon (SOC), soil total nitrogen (STN), and soil total phosphorus (STP) will promote soil microbial abundance and diversity. ALB and ST will promote the soil α-diversity, but the effect of RB to soil microbial is opposite. These findings maybe provide a reliable theoretical basis for formulating a reasonable response strategy in desert steppe ecosystems.

Differences in soil microbial response to anthropogenic disturbances in Sanjiang and Momoge Wetlands, China

2019 ◽  
Author(s):  
Jing Wei ◽  
Jie Gao ◽  
Na Wang ◽  
Ying Liu ◽  
Yuwan Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Salt Marsh ◽  
Total Nitrogen ◽  
Soil Microbial Communities ◽  
Anthropogenic Disturbances ◽  
Community Diversity ◽  
Total Carbon ◽  
Freshwater Wetland ◽  
Soil Microbial

Abstract To understand the response of soil microbial communities in different types of wetlands to anthropogenic disturbances, this study focused on a freshwater wetland (Sanjiang Wetland) and a salt marsh (Momoge Wetland) and sampled cultivated, degraded, and natural soils in these wetlands. High-throughput sequencing was applied to characterize the soil microbial community composition, and physicochemical properties, including pH, total nitrogen, total carbon, and soil water content (SWC), were measured. The results revealed that the total nitrogen, total carbon, and SWC were significantly lower in disturbed soil in the freshwater wetland but higher in the salt marsh. Generally, under anthropogenic disturbances, microbial community diversity decreased in the freshwater wetland and increased in the salt marsh. The bacterial community structure in the salt marsh was more sensitive than that in the freshwater wetland, while the fungal community structure in the freshwater wetland was more susceptible than that in the salt marsh. The results of indicator value analyses revealed specific issues in two wetlands, such as methane generation and anoxic conditions. This study shows that soil microbiomes in two types of wetlands respond differently to human activities, which implies that the type of native wetlands should be considered in the exploitation of wetlands.

scholarly journals Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ai-Zi Tong ◽  
Wei Liu ◽  
Qiang Liu ◽  
Guang-Qing Xia ◽  
Jun-Yi Zhu
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Panax Ginseng ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Continuous Cropping ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Borne Pathogens

Abstract Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.

scholarly journals Plants species' influence on rhizosphere microbial communities depends on N availability

2021 ◽  
Author(s):  
Teal S Potter ◽  
Amber C Churchill ◽  
William D Bowman ◽  
Brian L Anacker
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Plant Species ◽  
Soil Microbes ◽  
Plant Traits ◽  
Soil Microbial Communities ◽  
Community Change ◽  
Soil Conditions ◽  
Growth Responses ◽  
Soil Microbial

Purpose: Plants and soil microbes both influence how ecosystems respond to environmental change. Yet, we lack the ability to generalize how plants and soil microbes influence each other in the same or varying soil conditions. This limitation thwarts ecologists' ability to understand and predict effects of environmental changes such and elevated anthropogenic nitrogen (N) deposition. Accordingly, we examined the specificity of plant species' influence on soil microbial community composition. Methods: We tested (1) whether congeneric grass species have unique effects on soil microbial communities, (2) how relative abundances of microbial taxa can be explained by Poa phylogeny, plant traits, and range-wide traits (annual temperature and soil pH), and (3) whether N addition alters associations between Poa species and soil microbes, and (4) whether the magnitude of microbial community change in response to elevated N can be explained by plant growth responses to N. We conducted a greenhouse experiment with seven Poa species and native soils. Results: We found that individual Poa species were associated with different soil fungi but similar soil bacteria. Differences in microbial composition were not attributable to Poa phylogeny, plant traits, or range-wide traits. Nitrogen addition enhanced the unique effects of Poa species on fungal and bacterial community compositions. Conclusion: These results demonstrate how ecological interactions of related plant species vary depending on resource supply, revealing important context dependency for accurately predicting microbially-mediated nutrient cycling and ecosystem responses to changes in nutrient availability.

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