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 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 Pyrosequencing Assessment of Soil Microbial Communities in Organic and Conventional Potato Farms

Plant Disease ◽  
2010 ◽  
Vol 94 (11) ◽  
pp. 1329-1335 ◽  
Author(s):  
Akifumi Sugiyama ◽  
Jorge M. Vivanco ◽  
Sastry S. Jayanty ◽  
Daniel K. Manter
Keyword(s):  
Microbial Community ◽  
Genetic Distance ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Quantitative Polymerase Chain Reaction ◽  
Soil Microbial Communities ◽  
Pythium Ultimum ◽  
Community Diversity ◽  
Organic Farms ◽  
Conventional Farms

Organic farming is frequently touted as being beneficial to soil health by increasing microbial community diversity; however, contradictory results exist in the literature. In this study, we compared several organic and conventional potato farms in Colorado for differences in soil nutrients and microbial communities using 454 pyrosequencing of the 18S ribosomal RNA gene. Organic farms showed a slightly higher diversity and evenness within the microbial community compared with conventional farms. No difference in the number of observed or estimated total operational taxonomic units (OTUs) was observed between management strategies. However, the relative abundance of 16 OTUs (3% genetic distance) differed between the organic and conventional farms, with seven increasing and nine decreasing in organic farms. A variety of known potato fungal pathogens (e.g., Alternaria spp., Ulocladium spp., and Pythium ultimum) were detected in the soil, including three different OTUs (3% genetic distance) with a high homology to the early blight pathogen Alternaria solani. Relative abundance for Alternaria spp. was higher in conventional farms (relative abundance 30.15 versus 7.8%), whereas the relative abundance for P. ultimum was higher in organic farms (relative abundance 0.25 versus 0.05%). Quantitative polymerase chain reaction, using primers specific for A. solani, Phoma foveata, and Pythium ultimum, yielded similar results to the pyrosequencing, validating the use of pyrosequencing data for the quantification of OTU relative abundances.

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.

scholarly journals Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3937 ◽  
Author(s):  
Miranda H. Hengy ◽  
Dean J. Horton ◽  
Donald G. Uzarski ◽  
Deric R. Learman
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Bottom Water ◽  
Community Diversity ◽  
Freshwater Lakes ◽  
Microbial Community Diversity ◽  
Physical And Chemical ◽  
Beaver Island

Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.

scholarly journals Characteristics of Microbial Communities of Pachygrontha antennata (Hemiptera: Pachygronthidae) in Relation to Habitat Variables

2019 ◽  
Vol 16 (23) ◽  
pp. 4668
Author(s):  
Jae-Yeon Kang ◽  
Yong-Su Kwon ◽  
Gilsang Jeong ◽  
Injung An ◽  
Soyeon Park
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Urban Areas ◽  
Environmental Variables ◽  
Environmental Heterogeneity ◽  
Community Diversity ◽  
Microbial Community Diversity ◽  
Highly Correlated ◽  
Agricultural Areas ◽  
Habitat Variables

The microbial community interacts with the environment and the health and immune function of its host both directly and indirectly. However, very few studies about microbial communities have considered habitat and external environmental variables. This study examined environmental influences on the microbial community of Pachygrontha antennata, which is found in various habitats (e.g., urban, forested, and agricultural areas). The results demonstrated that the composition of the microbial community differed according to land use, while the bacterial diversity did not. In urban areas with high environmental heterogeneity, microbial community diversity tended to be high. Furthermore, bacteria in forests and agricultural areas (e.g., Paraburkholderia, Burkholderia) have been found to be highly correlated with habitat variables. Therefore, we suggest that habitat variables should be considered in future symbiotic studies.

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 Slope Aspect Affects The Soil Microbial Communities In Karst Tiankeng Negative Landforms

2021 ◽  
Author(s):  
Cong Jiang ◽  
Wei Shui ◽  
Su-Feng Zhu ◽  
Jie Feng
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Large Scale ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Slope Aspect ◽  
Soil Conditions ◽  
Metagenomic Sequencing ◽  
Soil Microbial

Abstract Background: Karst tiankeng is a large-scale negative surface terrain, and slope aspect affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated. Methods: In this study, metagenomic sequencing technology was used to analyzed the soil microbial communities and metabolic function on the shady and sunny slopes of karst tiankeng. Results: The Shannon-Wiener diversity of microbial communities on shady slopes was significantly higher than that on shady slopes. Shady and sunny slopes have similar microbial community composition, but there are differences in abundance. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOM and pH). Conclusions: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.

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