Changes in soil microbial community structure and function following degradation in a temperate grassland

2020 ◽  
Author(s):  
Yang Yu ◽  
Lang Zheng ◽  
Yijun Zhou ◽  
Weiguo Sang ◽  
Jianing Zhao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Temperate Grassland ◽  
Grassland Degradation ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Soil Bacterial

Abstract Aims Grassland degradation represents a major challenge in grassland productivity. This process has dramatic impacts on energy flows and soil nutrient dynamics and therefore may directly or indirectly influence soil microbes residing in surface soils. Here we aim to (1) examine changes in soil microbial composition, diversity, and functionality in response to different levels of grassland degradation (i.e., non-degraded, moderately degraded and severely degraded) in a temperate grassland in Inner Mongolia, and (2) elucidate biotic and abiotic factors that are responsible to these changes. Methods The composition structure of soil microbial community was determined by high-throughput sequencing. The functionality of bacterial communities was examined using the tool of FAPROTAX while functional guilds of fungal communities was quantified using the FUNGuild Pipeline. Important Findings Grassland degradation significantly decreased soil bacterial diversity but had no effect on fungal diversity. Belowground biomass, soil organic carbon, and total nitrogen were positively related to changes in diversity of bacterial community. Grassland degradation significantly increased the relative abundance of Chloroflexi (from 2.48% to 8.40%), and decreased Firmicutes (from 3.62% to 1.08%) of bacterial community. Degradation also significantly increased the relative abundance of Glomeromycota (from 0.17% to 1.53%), and decreased Basidiomycota (from 19.30% to 4.83%) of fungal community. The relative abundance of pathogenic fungi (Didymella and Fusarium) decreased significantly in response to degradation. In addition, degradation had a significant impact on putative functionality of soil bacteria related to soil carbon and nitrogen cycling. Our results suggest that soil bacterial community was more sensitive than fungal community in response to degradation in this temperate grassland.

scholarly journals Short-Term Effects of Different Forest Management Methods on Soil Microbial Communities of a Natural Quercus aliena var. acuteserrata Forest in Xiaolongshan, China

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 161 ◽  
Author(s):  
Pan Wan ◽  
Gongqiao Zhang ◽  
Zhonghua Zhao ◽  
Yanbo Hu ◽  
Wenzhen Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Forest Management ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Short Term ◽  
Soil Microbial

One of the aims of sustainable forest management is to preserve the diversity and resilience of ecosystems. Unfortunately, changes in the soil microbial communities after forest management remain unclear. We analyzed and compared the soil microbial community of a natural Quercus aliena var. acuteserrata forest after four years of four different management methods using high-throughput sequencing technology. The forest management methods were close-to-nature management (CNFM), structure-based forest management (SBFM), secondary forest comprehensive silviculture (SFCS) and unmanaged control (CK). The results showed that: (1) the soil microbial community diversity indices were not significantly different among the different management methods. (2) The relative abundance of Proteobacteria in the SBFM treatment was lower than in the CK treatment, while the relative abundance of Acidobacteria in the SBFM was significantly higher than that in the CK treatment. The relative abundance of Ascomycota was highest in the CNFM treatment, and that of Basidiomycota was lowest in the CNFM treatment. However, the relative abundance of dominant bacterial and fungal phyla was not significantly different in CK and SFCS. (3) Redundancy analysis (RDA) showed that the soil organic matter (SOM), total nitrogen (TN), and available nitrogen (AN) significantly correlated with the bacterial communities, and the available potassium (AK) was the only soil nutrient, which significantly correlated with the composition of the fungal communities. The short-term SBFM treatment altered microbial bacterial community compositions, which may be attributed to the phyla present (e.g., Proteobacteria and Acidobacteria), and the short-term CNFM treatment altered microbial fungal community compositions, which may be attributed to the phyla present (e.g., Ascomycota and Basidiomycota). Furthermore, soil nutrients could affect the dominant soil microbial communities, and its influence was greater on the bacterial community than on the fungal community.

scholarly journals Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration

2011 ◽  
Vol 77 (17) ◽  
pp. 6158-6164 ◽  
Author(s):  
Natasha C. Banning ◽  
Deirdre B. Gleeson ◽  
Andrew H. Grigg ◽  
Carl D. Grant ◽  
Gary L. Andersen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Ecosystem Restoration ◽  
Community Structures ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Edaphic Variables

ABSTRACTSoil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

scholarly journals Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

2021 ◽  
Vol 12 (1) ◽  
pp. 157-172
Author(s):  
Shankar G. Shanmugam ◽  
Normie W. Buehring ◽  
Jon D. Prevost ◽  
William L. Kingery
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Production System ◽  
Soil Microbial Community ◽  
Production Systems ◽  
Bacterial Community Composition ◽  
Soybean Production ◽  
Soil Microbial ◽  
Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

scholarly journals Transformation of Soil Microbial Community Structure and Rhizoctonia-Suppressive Potential in Response to Apple Roots

1999 ◽  
Vol 89 (10) ◽  
pp. 920-927 ◽  
Author(s):  
Mark Mazzola
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Burkholderia Cepacia ◽  
Soil Microbial Communities ◽  
Apple Trees ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Orchard Soil

Changes in the composition of soil microbial communities and relative disease-suppressive ability of resident microflora in response to apple cultivation were assessed in orchard soils from a site possessing trees established for 1 to 5 years. The fungal community from roots of apple seedlings grown in noncultivated orchard soil was dominated by isolates from genera commonly considered saprophytic. Plant-pathogenic fungi in the genera Phytophthora, Pythium, and Rhizoctonia constituted an increasing proportion of the fungal community isolated from seedling roots with increasing orchard block age. Bacillus megaterium and Burkholderia cepacia dominated the bacterial communities recovered from noncultivated soil and the rhizosphere of apple seedlings grown in orchard soil, respectively. Populations of the two bacteria in their respective habitats declined dramatically with increasing orchard block age. Lesion nematode populations did not differ among soil and root samples from orchard blocks of different ages. Similar changes in microbial communities were observed in response to planting noncultivated orchard soil to five successive cycles of ‘Gala’ apple seedlings. Pasteurization of soil had no effect on apple growth in noncultivated soil but significantly enhanced apple growth in third-year orchard block soil. Seedlings grown in pasteurized soil from the third-year orchard block were equal in size to those grown in noncultivated soil, demonstrating that suppression of plant growth resulted from changes in the composition of the soil microbial community. Rhizoctonia solani anastomosis group 5 (AG 5) had no effect on growth of apple trees in noncultivated soil but significantly reduced the growth of apple trees in soil from third-year orchard soil. Changes in the ability of the resident soil microflora to suppress R. solani AG 5 were associated with reductions in the relative populations of Burkholderia cepacia and Pseudomonas putida in the rhizosphere of apple.

scholarly journals Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions

2020 ◽  
Author(s):  
Ruth Schmidt ◽  
Xiao-Bo Wang ◽  
Paolina Garbeva ◽  
Étienne Yergeau
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Ammonia Oxidizers ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Fungal Community Structure

AbstractNitrapyrin is one of the most common nitrification inhibitors that are used to retain N in the ammonia form in soil to improve crop yields and quality. Whereas the inhibitory effect of nitrapyrin is supposedly specific to ammonia oxidizers, in view of the keystone role of this group in soils, nitrapyrin could have far-reaching impacts. Here, we tested the hypothesis that nitrapyrin leads to large shifts in soil microbial community structure, composition, diversity and functions, beyond its effect on ammonia-oxidizers. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH4NO3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice, DNA was extracted, the 16S rRNA gene and ITS region were amplified and sequenced to follow shifts in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. As expected, sampling date and plant compartment had overwhelming effects on the microbial communities. However, within these strong effects, we found statistically significant effects of nitrapyrin on the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and on several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling date significantly influenced the profiles observed. Our results point out far-reaching effects of nitrapyrin on soil and plant associated microbial communities, well beyond its predicted direct effect on ammonia-oxidizers. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions.

scholarly journals Effects of Trichoderma asperellum 6S-2 on Apple Tree Growth and Replanted Soil Microbial Environment

2022 ◽  
Vol 8 (1) ◽  
pp. 63
Author(s):  
Haiyan Wang ◽  
Rong Zhang ◽  
Yunfei Mao ◽  
Weitao Jiang ◽  
Xuesen Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Gene Copy ◽  
Available Phosphorus ◽  
Trichoderma Asperellum ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Trichoderma asperellum strain 6S-2 with biocontrol effects and potential growth-promoting properties was made into a fungal fertilizer for the prevention of apple replant disease (ARD). 6S-2 fertilizer not only promoted the growth of Malus hupehensis Rehd seedlings in greenhouse and pot experiments, but also increased the branch elongation growth of young apple trees. The soil microbial community structure changed significantly after the application of 6S-2 fertilizer: the relative abundance of Trichoderma increased significantly, the relative abundance of Fusarium (especially the gene copy numbers of four Fusarium species) and Cryptococcus decreased, and the relative abundance of Bacillus and Streptomyces increased. The bacteria/fungi and soil enzyme activities increased significantly after the application of 6S-2 fertilizer. The relative contents of alkenes, ethyl ethers, and citrullines increased in root exudates of M. hupehensis Rehd treated with 6S-2 fertilizer and were positively correlated with the abundance of Trichoderma. The relative contents of aldehydes, nitriles, and naphthalenes decreased, and they were positively correlated with the relative abundance of Fusarium. In addition, levels of ammonium nitrogen (NH4-N), nitrate nitrogen (NO3-N), available phosphorus (AP), available potassium (AK), organic matter (SOM), and pH in rhizosphere soil were also significantly related to changes in the microbial community structure. In summary, the application of 6S-2 fertilizer was effective in alleviating some aspects of ARD by promoting plant growth and optimizing the soil microbial community structure.

scholarly journals Survival Rates of Microbial Communities from Livestock Waste to Soils: A Comparison between Compost and Digestate

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Maiko Akari ◽  
Yoshitaka Uchida
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Survival Rates ◽  
Chemical Fertilizer ◽  
Livestock Waste ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Livestock waste-based products, such as composted manure, are often used in crop production systems. The products’ microbial characteristics differ depending on animal waste treatment methods used (e.g., biogas production/composting). The question remains whether different livestock waste-based products differently impact soil microbiota. A pot experiment with five treatments (control, chemical fertilizer, digestate + chemical fertilizer, wheat straw compost + chemical fertilizer, and woodchip compost + chemical fertilizer) was conducted to compare the survival rates of microbial communities from digestate and composted manure, after their application to agricultural soil. Potatoes were planted in each pot. The changes in soil pH, the concentration of ammonium and nitrate, and the microbial community properties were monitored after 1, 6, 10, and 14 weeks of the application of livestock waste-based products. The application of composted manure, especially woodchip compost, showed a relatively more extensive impact on the soil microbial community structure than the other treatments. Woodchip compost contained a relatively more abundant and diverse bacterial community than digestate, and its family-level bacterial community structure was similar to that of the soil. These characteristics might determine the extent of the impact of livestock waste-based products on soil microbial communities. Digestate markedly influenced the inorganic nitrogen concentrations in soils but did not affect the soil microbial community. In conclusion, the survival rate of microbes of livestock waste-based products varies depending on the product type. Further investigation is needed to fully understand their impact on soils’ microbial functions.

scholarly journals Molecular Biology-Based Analysis of the Interactive Effect of Nickel and Xanthates on Soil Bacterial Community Diversity and Structure

2019 ◽  
Vol 11 (14) ◽  
pp. 3888
Author(s):  
Prudence Bararunyeretse ◽  
Yan Zhang ◽  
Hongbing Ji
Keyword(s):  
Microbial Community ◽  
Molecular Biology ◽  
Bacterial Community ◽  
Soil Microbial Community ◽  
Bacterial Species ◽  
Interactive Effect ◽  
Soil Bacterial Community ◽  
Community Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Metals and mineral flotation collector’s toxicity to the soil living system greatly compromise the sustainability of mining and ore processing. Their effects on the soil microbial community, the most active soil component, remain less understood and addressed particularly with regards to xanthates and their combination with metals. This study analyzed the interactive effects of Ni and xanthates, potassium ethyl xanthate and sodium isopropyl xanthate, on the soil bacterial community through an efficient molecular biology-based technique, the Miseq (Illumina). Both soil microbial community diversity and structure were more affected by xanthates than by Ni. The five most dominant phyla, representing 96.31% of the whole bacterial community, comprised Proteobacteria (54.16%), Firmicutes (17.51%), Actinobacteria (15.59%), Acidobacteria (4.87%), and Chloroflexi (4.16%). Different soil treatments exhibited greater difference in the species abundance/dominance than in the species numbers. Proteobacteria was the most dominant in the presence of xanthates, individually or in mixtures with nickel, while Firmicutes exhibited its highest proportion in the Ni/xanthate-treated samples. The most abundant and proportionally different bacterial species between different treatments were presented. The most abundant bacterial strains identified should be explored more for their potential application in biomining and for the prediction and biologically-based treatment and remediation of Ni and xanthate-contaminated systems.

scholarly journals Near-natural transformation of Pinus tabuliformis better improve soil nutrients and soil microbial community

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12098
Author(s):  
You Yin ◽  
Qiuli Li ◽  
Haitao Du
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Soil Microbial Community ◽  
Natural Transformation ◽  
Pinus Tabulaeformis ◽  
Soil Microbial Diversity ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Pinus Tabuliformis ◽  
Soil Bacterial

Pinus tabulaeformis plantations have been established around northern China to restore degraded land and provide timber or fuelwood. In recent years, widely distributed monoculture P. tabulaeformis forests have been transformed into mixed forests due to various ecological problems. However, the current research on the influence of near-natural transformation of P. tabulaeformis on soil microbial diversity and community composition remains limited. Therefore, we examined the effect of forest conversion from monoculture Pinus tabuliformis (PT) to P. tabuliformis-Armeniaca vulgaris (PTAU), P. tabuliformis - Robinia pseudoacacia (PTRP), P. tabuliformis - Vitex negundo L. var. heterophylla (PTVN) forests on soil microbial community diversity and composition. The results indicated that compared to PT, PTAU, PTVN, and PTRP could enhance the soil pH, TC, TN, AN, and AK in different degrees, the most obvious in PTAU. Near-natural transformation of P. tabuliformis could improve soil bacterial Pielou_e index, and Simpson index, as well as soil fungal Chao1 index. Proteobacteria and Ascomycota were the dominant soil microbial community at the phylum level. What’s more, both soil bacterial and fungal community among PT, PTAU, PTRP and PTVN showed clear different, and PTAU obviously altered the soil microbial community structure. Proteobacteria was the predominant group in PT, while, Gemmatimonadetes enriched in PTVN. Ascomycota was the predominant group in PTAU, while, Basidiomycota was the predominant group in PTRP. Near-natural transformation of P. tabuliformis could change soil microbial community via altering soil characteristics. In brief, our research results revealed the influence of tree composition and soil nutrient availability on soil microbial diversity and composition, and provided management guidance for introduction soil microbial community in forest protection and management.

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