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 ◽  
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 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.

scholarly journals Influence of Peanut, Sorghum, and Soil Salinity on Microbial Community Composition in Interspecific Interaction Zone

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaolong Shi ◽  
Xinhua Zhao ◽  
Jinyao Ren ◽  
Jiale Dong ◽  
He Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Salinity ◽  
Soil Microbial Communities ◽  
Interspecific Interaction ◽  
Community Diversity ◽  
Dominant Factor ◽  
Soil Conditions ◽  
Interaction Zone ◽  
Microbial Community Diversity

Soil microorganisms play important roles in crop production and sustainable agricultural management. However, soil conditions and crop selection are key determining factors for soil microbial communities. This study investigated the effect of plant types and soil salinity on the microbial community of interspecific interaction zone (II) based on the sorghum/peanut intercropping system. Microbial community diversity and composition were determined through PacBio single molecule, real-time sequencing of 16S rDNA and internal transcribed spacer (ITS) genes. Results showed Proteobacteria, Bacteroidota, and Acidobacteriota to be the dominant bacterial phyla in IP, II, and IS, whereas Ascomycota, Basidiomycota, and Mucoromycota were the dominant fungal phyla. Under salt-treated soil conditions, the plants-specific response altered the composition of the microbial community (diversity and abundance). Additionally, the interspecific interactions were also helpful for maintaining the stability and ecological functions of microbial communities by restructuring the otherwise stable core microbiome. The phylogenetic structure of the bacterial community was greatly similar between IP and II while that of the fungal community was greatly similar between IP and IS; however, the phylogenetic distance between IP and IS increased remarkably upon salinity stress. Overall, salinity was a dominant factor shaping the microbial community structure, although plants could also shape the rhizosphere microenvironment by host specificity when subjected to environmental stresses. In particular, peanut still exerted a greater influence on the microbial community of the interaction zone than sorghum.

scholarly journals Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoya Gong ◽  
Jibo Shi ◽  
Xingang Zhou ◽  
Tao Yuan ◽  
Danmei Gao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Soil Microbial Community ◽  
Management Practice ◽  
Soil Microbial Communities ◽  
Pot Experiment ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
And Control

Paddy-upland rotation is an effective agricultural management practice for alleviating soil sickness. However, the effect of varying degrees of flooding on the soil microbial community and crop performance remains unclear. We conducted a pot experiment to determine the effects of two soil water content (SWC) and two flooding durations on the soil microbial community attributes and yield in cucumber. In the pot experiment, cucumber was rotated with cress single (45 days) or double (90 days) under 100 or 80% SWC. Then, the soil microbial were inoculated into sterilized soil to verified the relationship between cucumber growth and microorganisms. The results indicated single cress rotation resulted in a higher cucumber yield than double cress rotation and control. Cress rotation under 80% SWC had higher soil microbial diversity than cress rotation under 100% SWC and control. Flooding duration and SWC led to differences in the structure of soil microbial communities. Under 80% SWC, single cress rotation increased the relative abundance of potentially beneficial microorganisms, including Roseiflexus and Pseudallescheria spp., in cucumber rhizosphere. Under 100% SWC, single cress rotation increased the relative abundance of potentially beneficial bacteria, such as Haliangium spp., and decreased potential pathogenic fungi, such as Fusarium and Monographella spp., compared with double cress rotation and control. Varying degrees of flooding were causing the difference in diversity, structure and composition of soil microbial communities in the cucumber rhizosphere, which have a positive effect on cucumber growth and development.

scholarly journals Soil Microbial Communities Altered by Titanium Ions in Different Agroecosystems of Pitaya and Grape

2021 ◽  
Author(s):  
Yuan He ◽  
Xinrong Ma ◽  
Xin-Yi Hou ◽  
Cai-Xia Li ◽  
Yan Wang
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Foliar Spray ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Significant Difference

Abstract Titanium ions can significantly promote plant growth, but it is unclear whether the application of titanium ions to plants has any effect on the soil microbial community. In this study, we conducted field surveys to determine the effect of titanium ions on soil microbial communities of the pitaya and grape plantations in Panxi area by performing full-length 16S rRNA gene and ITS amplicon sequencing using PacBio Sequel. The results showed that the application of titanium ions significantly altered the composition and structure of soil microbiota. Root irrigation with titanium ions in pitaya garden, the diversity of soil fungi was significantly reduced. Although there was no statistically significant difference, bacterial diversity also declined. While, the foliar spray of titanium ions on grapes greatly reduced the soil microbial diversity. Moreover, the soil microbiota had a core of conserved taxa, and their relative abundances were significantly altered by titanium ions. Moreover, titanium ions enhanced the cooccurrence relationships and probably improved the stability of the soil microbial community. Our results highlight the different responses of bacterial and fungal communities to titanium ions and sites and provides a basis for the application of titanium ions in plant farming.

scholarly journals Short-term effects of cover grass intensity on soil microbial communities in an apple orchard

2020 ◽  
Author(s):  
Pan Wan ◽  
Anzhi Wei
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Apple Orchard ◽  
Community Diversity ◽  
Moderate Intensity ◽  
Microbial Community Diversity ◽  
Soil Microbial

Soil microbiota play an important and diverse roles in horticultural crop nutrition or productivity. However, the soil microbial community composition and the relationships within the taxa in the microbial community populations after cover grass treatments in apple orchards are not well understood. We analysed the microbial community diversity, composition and microbial network of an apple orchard after covering with native wild grasses at different intensities for 2 years in the Loess Plateau, China. The cover grass intensities were 0%, 20%, 40%, 60% and 80%. Soil microbial community diversity was not obviously change by cover grass in the apple orchard. Cover grass altered the microbial bacterial community compositions, their changes exhibited significant differences at the phylum level that were caused by the Proteobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae. However, low-intensity (20%) and moderate-intensity (40%) treatments were the only cover grass intensities that altered the soil fungal community composition; but their changes did not exhibit significant differences at the phylum level. The positive links among the bacterial taxa decreased with the increasing cover intensity, primarily among Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi and Gemmatimonadetes. Although cover grass increased the positive links between fungal taxa, these taxa were reduced with the increasing cover intensity. Here we demonstrate that cover grass changed the soil microbial community, and the changes may be attributed to the given phyla in the bacterial community; furthermore, the antagonistic effect between the soil bacterial and fungal communities was significantly increased by higher coverage than by lower coverage.

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 ◽  
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.

scholarly journals Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil System ◽  
Soil Microbial ◽  
Total Soil ◽  
Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

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