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

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.

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

Phytopathology ◽

10.1094/phyto.1999.89.10.920 ◽

1999 ◽

Vol 89 (10) ◽

pp. 920-927 ◽

Cited By ~ 84

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.

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

Journal of Plant Ecology ◽

10.1093/jpe/rtaa102 ◽

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.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.631882 ◽

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.

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STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽

10.18860/elha.v1i4.1785 ◽

2012 ◽

Vol 1 (4) ◽

Author(s):

Prihastuti Prihastuti

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Microbial Communities ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Organic Soil ◽

Plant Type ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Wide Range

Soils are made up of organic and an organic material. The organic soil component contains all the living creatures in the soil and the dead ones in various stages of decomposition. Biological activity in soil helps to recycle nutrients, decompose organic matter making nutrient available for plant uptake, stabilize humus, and form soil particles. The extent of the diversity of microbial in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microbial is involved in important soil functions. That ecologically managed soils have a greater quantity and diversity of soil microbial. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. The fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to their complexity of the microbial interactions in soil, including interactions between microbial and soil and microbial and plants. The basic premise of organic soil stewardship is that all plant nutrients are present in the soil by maintaining a biologically active soil environment. The diversity of microbial communities has on ecological function and resilience to disturbances in soil ecosystems. Relationships are often observed between the extent of microbial diversity in soil, soil and plant quality and ecosystem sustainability. Agricultural management can be directed toward maximizing the quality of the soil microbial community in terms of disease suppression, if it is possible to shift soil microbial communities.Keywords: structure, microbial, implication, sustainable agriculture

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Distinct assembly processes and determinants of soil microbial communities between farmland and grassland in arid and semiarid areas

Applied and Environmental Microbiology ◽

10.1128/aem.01010-21 ◽

2021 ◽

Author(s):

Aiai Xu ◽

Jie Liu ◽

Zhiying Guo ◽

Changkun Wang ◽

Kai Pan ◽

...

Keyword(s):

Microbial Community ◽

Variable Selection ◽

Microbial Communities ◽

Soil Microbial Community ◽

Environmental Gradient ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Semiarid Areas ◽

Arid And Semiarid Areas ◽

Arid And Semiarid

It is critical to identify the assembly processes and determinants of soil microbial communities to better predict soil microbial responses to environmental change in arid and semiarid areas. Here, soils from 16 grassland-only, 9 paired grassland and farmland, and 16 farmland-only sites were collected across the central Inner Mongolia Plateau covering a steep environmental gradient. Through analyzing the paired samples, we discovered that land uses had strong effects on soil microbial communities, but weak effects on their assembly processes. For all samples, although no environmental variables were significantly correlated with the net relatedness index (NRI), both the nearest taxon index (NTI) and the β-nearest taxon index (βNTI) were most related to mean annual precipitation (MAP). With the increase of MAP, soil microbial taxa at the tips of the phylogenetic tree were more clustered, and the contribution of determinism increased. Determinism (48.6%), especially variable selection (46.3%), and stochasticity (51.4%) were almost equal in farmland, while stochasticity (75.0%) was dominant in grassland. Additionally, Mantel tests and redundancy analyses (RDA) revealed that the main determinants of soil microbial community structure were MAP in grassland, but mean annual temperature (MAT) in farmland. MAP and MAT were also good predictors of the community composition (the top 200 dominant OTUs) in grassland and farmland, respectively. Collectively, in arid and semiarid areas, soil microbial communities were more sensitive to environmental change in farmland than in grassland, and unlike the major impact of MAP on grassland microbial communities, MAT was the primary driver of farmland microbial communities. Importance As one of the most diverse organisms, soil microbes play indispensable roles in many ecological processes in arid and semiarid areas with limited macrofaunal and plant diversity, yet the mechanisms underpinning soil microbial community are not fully understood. In this study, soil microbial communities were investigated along a 500 km transect covering a steep environmental gradient across farmland and grassland in the areas. The results showed that precipitation was the main factor mediating the assembly processes. Determinism was more influential in farmland, and variable selection of farmland was twice that of grassland. Temperature mainly drove farmland microbial communities, while precipitation mainly affected grassland microbial communities. These findings provide new information about the assembly processes and determinants of soil microbial communities in arid and semiarid areas, consequently improving the predictability of the community dynamics, which have implications for sustaining soil microbial diversity and ecosystem functioning, particularly under global climate change conditions.

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Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

Microorganisms ◽

10.3390/microorganisms8060834 ◽

2020 ◽

Vol 8 (6) ◽

pp. 834

Author(s):

Naihui Li ◽

Danmei Gao ◽

Xingang Zhou ◽

Shaocan Chen ◽

Chunxia Li ◽

...

Keyword(s):

Community Structure ◽

Organic Carbon ◽

Bacterial Community ◽

Soil Organic Carbon ◽

Microbial Communities ◽

Fungal Community ◽

Soil Microbial Communities ◽

Tomato Seedling ◽

Soil Microbial ◽

Potato Onion

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

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

10.1101/2020.07.21.205765 ◽

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.

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Short-Term Effects of Cover Grass on Soil Microbial Communities in an Apple Orchard on the Loess Plateau

Forests ◽

10.3390/f12121787 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1787

Author(s):

Pan Wan ◽

Ruirui He

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Soil Microbial Community ◽

Apple Orchard ◽

Moderate Intensity ◽

The Loess Plateau ◽

Soil Microbial ◽

Low Intensity ◽

The Given

Grass cover may improve soil environmental conditions in apple orchards. However, the mechanisms for how the soil microbial community changes after cover grass treatments are not well understood. In this study, we analyzed soil properties, microbial community diversity and composition in an apple orchard after being covered with native wild grasses for 3 years on the Loess Plateau, China. The ratios of cover grass were 0% (no cover, NC), 20% (low-intensity cover, LIC), 40% (moderate-intensity cover, MIC1), 60% (moderate-intensity cover, MIC2) and 80% (high-intensity cover, HIC). Meanwhile, the relationships between soil nutrients, cover grass properties, and microbial communities was analyzed by redundancy analysis and Pearson correlations. The results showed that cover grass altered the bacterial community composition, and significant changes at the phylum level were mainly caused by Proteobacteria, Bacteroidetes and Chloroflexi. Compared with NC, the abundance of Proteobacteria was lower in LIC, and the abundance of Bacteroidetes was lower in LIC, MIC1 and MIC2, while that of Chloroflexi was higher in LIC. LIC and MIC1 were the only cover grass intensities that altered the soil fungal community composition; there were no significant differences at the phylum level. The changes in the soil microbial community at the given phyla may be related to the change in soil available nitrogen content caused by cover grass. 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; soil copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) were found to be at lower abundance in the low-intensity cover grass.

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Liming Alters the Soil Microbial Community and Extracellular Enzymatic Activities in Temperate Coniferous Forests

Forests ◽

10.3390/f12020190 ◽

2021 ◽

Vol 12 (2) ◽

pp. 190

Author(s):

Sangsub Cha ◽

Yong Suk Kim ◽

Ah Lim Lee ◽

Dong-Hyeon Lee ◽

Namin Koo

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Bacterial Community ◽

Soil Ph ◽

Fungal Community ◽

Anthropogenic Activities ◽

Soil Microbial Communities ◽

Lime Treatment ◽

Soil Microbial

Soil acidification caused by anthropogenic activities adversely affects forest ecosystems by altering soil pH, which is an important factor in soil quality and function. Liming is one suggested way to solve this problem. This study was performed to evaluate the effects of liming in acidic forest soils by determining soil microbial biomass, microbial community structure, and extracellular enzyme activities associated with carbon, nitrogen, and phosphorus cycling. Lime treatment increased soil pH by up to 40%, significantly increased organic matter (OM) content at some sites, and altered the enzyme activity of the soil. With liming, the microbial biomass appeared to be affected by the chemical properties of the soil, such as pH, Ca2+, Mg2+, K+, and exchangeable aluminum (Ale) levels, although there were no significant differences at the site level. Enzymatic activity was found to be affected by pH, Ca2+, Mg2+, electrical conductivity (EC), and Ale; and acid phosphatase (AP) and phenol oxidase (POX) activity were significantly affected by lime treatment. AP activity decreased from 0.62 to 0.66, and POX activity increased from 1.75 to 3.00 in part of the sites. The bacterial community richness was influenced by pH as a direct effect of lime treatment. The fungal community richness was associated with changes in K+ that were not due to lime treatment. The bacterial community structure was affected by soil OM, total nitrogen (TN), pH, and Ca2+; and the fungal community structure was affected by pH, Mg2+, and K+. In conclusion, changes in soil environmental conditions by liming can affect soil microbial communities and functions through direct or indirect processes, further changing ecosystem processes.

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The soil microbial community alters patterns of selection on flowering time and fitness related traits in Ipomoea purpurea

10.1101/672691 ◽

2019 ◽

Author(s):

Lindsay Chaney ◽

Regina S. Baucom

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Flowering Time ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Morning Glory ◽

Evolutionary Processes ◽

Soil Microbial ◽

Ipomoea Purpurea ◽

Evolutionary Response

ABSTRACTPremise of the studyPlant flowering time plays an important role in plant fitness and thus evolutionary processes. Soil microbial communities are diverse and have a large impact, both positive and negative, on the host plant. However, owing to few available studies, how the soil microbial community may influence the evolutionary response of plant populations is not well understood. Here we sought to uncover if below-ground microbial communities act as an agent of selection on flowering and growth traits in the common morning glory, Ipomoea purpurea.MethodsWe performed a controlled greenhouse experiment in which genetic lines of I. purpurea were planted into either sterilized soils, or soils that were sterilized and re-inoculated with the microbial community from original field soil. This allowed us to directly test the influence of alterations to the microbial community on plant growth, flowering, and fitness, as well as assess patterns of selection in both soil microbial environments.ResultsWe found that a more complex soil microbial community resulted in larger plants that produced more flowers. Selection strongly favored earlier flowering when plants were grown in the complex microbial environment than compared to sterilized soil. Additionally, we uncovered a pattern of negative correlational selection on growth rate and flowering time, indicating that selection favored different combinations of growth and flowering traits in the simplified versus complex soil community.ConclusionsTogether these results suggest the soil microbial community is a selective agent on flowering time and ultimately that soil microbial community influences important plant evolutionary processes.

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