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

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

Forests ◽

10.3390/f10020161 ◽

2019 ◽

Vol 10 (2) ◽

pp. 161 ◽

Cited By ~ 4

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.

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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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Apple Root stocks and Pre-plant Soil Treatments Alter Soil Microbial Community Composition in a New York Orchard

HortScience ◽

10.21273/hortsci.40.4.1128c ◽

2005 ◽

Vol 40 (4) ◽

pp. 1128C-1128

Author(s):

Shengrui Yao ◽

Ian A. Merwin ◽

Janice E. Thies

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Soil Microbial Community ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Growth And Yield ◽

Soil Microbial ◽

Plant Soil ◽

Soil Microbial Community Composition

Apple (Malu ×domestica) replant disease (ARD) is a soil-borne disease syndrome of complex etiology that occurs worldwide when establishing new orchards in old fruit-growing sites. Methyl bromide (MB) has been an effective soil fumigant to control ARD, but safer alternatives to MB are needed. We evaluated soil microbial communities, tree growth, and fruit yield for three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and five clonal rootstocks (M7, M26, CG6210, CG30, and G16), in an apple replant site at Ithaca, N.Y. Molecular fingerprinting (PCR-DGGE) techniques were used to study soil microbial community composition of root-zone soil of the different soil treatments and rootstocks. Tree caliper, shoot growth, and yield were measured annually from 2002–04. Among the five rootstocks we compared, trees on CG6210 had the most growth and yield, while trees on M26 had the least growth and yield. Soil treatments altered soil microbial communities during the year after pre-plant treatments, and each treatment was associated with distinct microbial groups in hierarchical cluster analyses. However, those differences among fungal and bacterial communities diminished during the second year after planting, and soil fungal communities equilibrated faster than bacterial communities. Pre-plant soil treatments altered bulk-soil microbial community composition, but those shifts in soil microbial communities had no obvious correlation with tree performance. Rootstock genotypes were the dominant factor in tree performance after 3 years of observations, and different rootstocks were associated with characteristic bacterial, pseudomonad, fungal, and oomycetes communities in root-zone soil.

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

10.21203/rs.3.rs-192228/v1 ◽

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.

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Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0112 ◽

2020 ◽

Vol 375 (1794) ◽

pp. 20190112 ◽

Cited By ~ 6

Author(s):

Richard D. Bardgett ◽

Tancredi Caruso

Keyword(s):

Climate Change ◽

Microbial Community ◽

Microbial Communities ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Climate Extremes ◽

Alternative States ◽

Community Responses ◽

Extrinsic Factors ◽

Soil Microbial

A major challenge for advancing our understanding of the functional role of soil microbial communities is to link changes in their structure and function under climate change. To address this challenge requires new understanding of the mechanisms that underlie the capacity of soil microbial communities to resist and recover from climate extremes. Here, we synthesize emerging understanding of the intrinsic and extrinsic factors that influence the resistance and resilience of soil microbial communities to climate extremes, with a focus on drought, and identify drivers that might trigger abrupt changes to alternative states. We highlight research challenges and propose a path for advancing our understanding of the resistance and resilience of soil microbial communities to climate extremes, and of their vulnerability to transitions to alternative states, including the use of trait-based approaches. We identify a need for new approaches to quantify resistance and resilience of soil microbial communities, and to identify thresholds for transitions to alternative states. We show how high-resolution time series coupled with gradient designs will enable detecting response patterns to interacting drivers. Finally, to account for extrinsic factors, we suggest that future studies should use environmental gradients to track soil microbial community responses to climate extremes in space and time. This article is part of the theme issue ‘Climate change and ecosystems: threats, opportunities and solutions’.

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Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

Nature Communications ◽

10.1038/s41467-021-25675-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Alberto Canarini ◽

Hannes Schmidt ◽

Lucia Fuchslueger ◽

Victoria Martin ◽

Craig W. Herbold ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Soil Microbial Community ◽

Net Primary Productivity ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Drought Event ◽

Soil Processes ◽

Soil Microbial ◽

Ecological Memory

AbstractClimate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

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Unravelling the Functional Diversity of the Soil Microbial Community of Chinese Fir Plantations of Different Densities

Forests ◽

10.3390/f9090532 ◽

2018 ◽

Vol 9 (9) ◽

pp. 532 ◽

Cited By ~ 6

Author(s):

Chaoqun Wang ◽

Lin Xue ◽

Yuhong Dong ◽

Yihui Wei ◽

Ruzhen Jiao

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Functional Diversity ◽

Soil Microbial Community ◽

Diversity Index ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Stand Density ◽

Chinese Fir ◽

Soil Microbial

The structure and function of forest ecosystems are directly or indirectly affected by their stand density. However, what effect the density of Chinese fir plantations has on the functional diversity of the soil microbial community remains unclear. The microbial metabolic functional diversity of soils sampled at the topsoil (0–20 cm) of 35-year-old Chinese fir plantations of five initial densities (D1: 1667 stems∙hm−2, D2: 3333 stems∙hm−2, D3: 5000 stems∙hm−2, D4: 6667 stems∙hm−2, and D5: 10,000 stems∙hm−2) was studied by using Biolog ECO technology. The results showed that the soil pH, oxidizable organic carbon (SOOC), available N (AN), available P (AP), and available K (AK) contents all showed a gradual increase from D1 to D4 and a decrease from D4 to D5, while the number of culturable bacteria and total microorganisms, the average well color development (AWCD) values for the single carbon substrate and six types of carbon sources used by the microbial community, as well as the Shannon-Wiener diversity index (H’), Pielou evenness index (J), and McIntosh Diversity Index (U), were the opposite, suggesting that low-densities favored C and N mineralization and the nutrient cycle. The density of Chinese fir plantations had a significant effect on the use of carbohydrates, amino acids, carboxylic acids, and phenolic acids by the soil microbial community, but it had no significant effect on the use of polymers (p < 0.05). Principal component analysis (PCA) revealed that carbohydrates, polymers, and phenolic acids were sensitive carbon sources that caused differences in the metabolic functions of soil microbial communities in Chinese fir plantations. Redundancy analysis (RDA) showed that physicochemical factors have a significant influence on the metabolic function of soil microbial communities (RDA1 and RDA2 explained >85% variance). The changes in density affected the soil physicochemical properties, the composition, and the metabolic functional diversity of microbial communities in Chinese fir plantations, which is certainly useful for the stand density regulation of Chinese fir plantations.

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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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