Deciphering Rhizosphere Microbiome Assembly of Castanea henryi in Plantation and Natural Forest

Based on the importance and sensitivity of microbial communities to changes in the forest ecosystem, soil microorganisms can be used to indicate the health of the forest system. The metagenome sequencing was used to analyze the changes of microbial communities between natural and plantation Castanea henryi forests for understanding the effect of forest types on soil microbial communities. Our result showed the soil microbial diversity and richness were higher in the natural forests than in the plantation. Proteobacteria, Actinobacteria, and Acidobacteria are the dominant categories in the C. henryi rhizosphere, and Proteobacteria and Actinobacteria were significantly enriched in the natural forest while Acidobacteria was significantly enriched in the plantation. Meanwhile, the functional gene diversity and the abundance of functions in the natural forest were higher than that of the plantation. Furthermore, we found that the microbial network in the natural forests had more complex than in the plantation. We also emphasized the low-abundance taxa may play an important role in the network structure. These results clearly showed that microbial communities, in response to different forest types, provide valuable information to manipulate microbiomes to improve soil conditions of plantation.

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Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth

Applied and Environmental Microbiology ◽

10.1128/aem.02523-18 ◽

2019 ◽

Vol 85 (6) ◽

Cited By ~ 5

Author(s):

Shuo Jiao ◽

Weimin Chen ◽

Gehong Wei

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Soil Microbiome ◽

Chemical Contamination ◽

Plant Interactions ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Microbial Responses ◽

Legume Plants ◽

Functional Profiles

ABSTRACT A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion. IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.

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Effect of Soil Layer and Plant–Soil Interaction on Soil Microbial Diversity and Function after Canopy Gap Disturbance

Forests ◽

10.3390/f9110680 ◽

2018 ◽

Vol 9 (11) ◽

pp. 680 ◽

Cited By ~ 5

Author(s):

Xuan Yu ◽

Lin Yang ◽

Shixuan Fei ◽

Zitong Ma ◽

Ruqian Hao ◽

...

Keyword(s):

Microbial Communities ◽

Enzyme Activities ◽

Soil Layer ◽

Soil Microbial Communities ◽

Gap Size ◽

Pine Plantation ◽

Soil Microbial Diversity ◽

Chinese Pine ◽

Soil Microbial ◽

Microbial Plfas

Gaps by thinning can have different microclimatic environments compared to surrounding areas, depending on the size of the gap. In addition, gaps can play important roles in biological dynamics, nutrient cycling, and seedling regeneration. The impacts of gap size on soil microbial communities and enzyme activities in different soil layers in Chinese pine plantations are not well understood. Here, we created gaps of 45 m2 (small, G1), 100 m2 (medium, G2), and 190 m2 (large, G3) by thinning unhealthy trees in an aged (i.e., 50 years old) monoculture Chinese pine plantation in 2010. Soil samples were collected in 2015. The total, bacterial, Gram-positive (G+), and Gram-negative (G−) phospholipid fatty acid (PLFA) profiles were highest in medium gaps in both the organic and mineral layers. These indicesdecreased sharply as gap size increased to 190 m2, and each of the detected enzyme activities demonstrated the same trend. Under all the gap size managements, abundances of microbial PLFAs and enzyme activities in the organic layers were higher than in the mineral layers. The soil layer was found to have a stronger influence on soil microbial communities than gap size. Redundancy analysis (RDA) based on the three systems with different gap sizes showed that undergrowth coverage, diversity, soil total nitrogen (TN), total organic carbon (TOC), and available phosphorus (AT) significantly affected soil microbial communities. Our findings highlighted that the effect of gap size on soil microenvironment is valuable information for assessing soil fertility. Medium gaps (i.e., 100 m2) have higher microbial PLFAs, enzyme activity, and soil nutrient availability. These medium gaps are considered favorable for soil microbial communities and fertility studied in a Chinese pine plantation managed on the Loess Plateau.

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Utilization of carbon sources by the soil microbial communities of different forest types in subtropical Australia

Acta Ecologica Sinica ◽

10.5846/stxb201103270392 ◽

2012 ◽

Vol 32 (9) ◽

pp. 2819-2826

Author(s):

鲁顺保 LU Shunbao ◽

郭晓敏 GUO Xiaomin ◽

芮亦超 RUI Yichao ◽

周小奇 ZHOU Xiaoqi ◽

陈成榕 CHEN Chengrong ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Forest Types ◽

Soil Microbial ◽

Subtropical Australia

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Soil Microbial Activity and Diversity in Response to Soil Chemical Factors in Agricultural Soils

Journal of Tropical Soils ◽

10.5400/jts.2019.v24i1.43-51 ◽

2019 ◽

Vol 24 (1) ◽

pp. 43

Author(s):

Lily Ishak ◽

Philip Hugh Brown

Keyword(s):

Microbial Communities ◽

Agricultural Soils ◽

Soil Health ◽

Soil Microbial Communities ◽

Soil Microbial Activity ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Microbial Responses ◽

Chemical Factors ◽

Microbial Groups

The role of microbial communities in maintaining soil health is mostly influenced by chemical condition of soil. Microbial communities vary in response to soil chemical factors. The contradictive results from previous findings emphasise that it is difficult to define a pattern of the influence of soil chemical factors on soil microbial diversity and activity. The aim of the study was to assess soil microbial responses to soil chemical factors in agricultural soils. Composite soil (Dermosol order) samples taken from 16 commercial crop sites in Bundaberg, Queensland, Australia, were chemically and biologically analysed. It was found that bacterial and fungal activity and diversity were significantly affected by soil EC, SOM and NO3-N content, but were not influenced by soil pH, CEC, and Ca:Mg ratio. The diversity of bacterial and fungal communities displayed a positive linear relationship with soil EC, whereas the activity and diversity of these two microbial groups and SOM displayed a significant quadratic relationship. The finding suggested that microbial community was predominantly influenced by SOM content.

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Microbial community diversity in the soil of Barrientos Island estimated by RAPD and Biolog Ecoplate methods

Progress In Microbes & Molecular Biology ◽

10.36877/pmmb.a0000046 ◽

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.

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Development of soil microbial communities for promoting sustainability in agriculture and a global carbon fix

10.7287/peerj.preprints.789 ◽

2015 ◽

Author(s):

David Johnson ◽

Joe Ellington ◽

Wesley Eaton

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Soil Conditions ◽

Management Approach ◽

Total System ◽

Soil C ◽

Soil Microbial ◽

Respiration Rates ◽

Agriculture Management

The goals of this research were to explore alternative agriculture management practices in both greenhouse and field trials that do not require the use of synthetic and/or inorganic nutrient amendments but instead would emulate mechanisms operating in natural ecosystems, between plant and Soil Microbial Communities (SMC), for plant nutrient acquisition and growth. Greenhouse plant-growth trials, implementing a progression of soil conditions with increasing soil carbon (C) (C= 0.14% to 5.3%) and associated SMC population with increasing Fungal to Bacterial ratios (F:B) ( from 0.04 to 3.68), promoted a) increased C partitioning into plant shoot and plant fruit partitions (m=4.41, r2=0.99), b) significant quantities of plant photosynthate, 49%-97% of Total System New C (CTSN), partitioned towards increasing soil C c) four times reduction in soil C respiration (CR) as F:B ratios increased, starting with 44% of initial treatment soil C content respired in bacterial-dominant soils (low F:B), to 11% of soil C content respired in higher fertility fungal-dominant soils (Power Regression, r2=0.90; p=0.003). Plant growth trials in fields managed for increased soil C content and enhanced SMC population and structure (increased F:B) demonstrated: a) dry aboveground biomass production rates (g m-2) of ~1,980 g in soils initiating SMC enhancement (soil C=0.87, F:B= 0.80) with observed potentials of 8,450 g in advanced soils (soil C=7.6%, F:B=4.3) b) a 25-times increase in active soil fungal biomass and a ~7.5 times increase in F:B over a 19 month application period to enhance SMC and c) reduced soil C respiration rates, from 1.25 g C m-2 day-1 in low fertility soils (soil C= 0.6%, F:B= 0.25) with only a doubling of respiration rates to 2.5 g C m-2 day-1 in a high-fertility soil with an enhanced SMC (F:B= 4.3) and >7 times more soil C content (soil C= 7.6%). Enhancing SMC population and F:B structure in a 4.5 year agricultural field study promoted annual average capture and storage of 10.27 metric tons soil C ha-1 year -1 while increasing soil macro-, meso- and micro-nutrient availability offering a robust, cost-effective carbon sequestration mechanism within a more productive and long-term sustainable agriculture management approach.

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Management and Soil Conditions Influence Common Scab Severity on Potato Tubers Via Indirect Effects on Soil Microbial Communities

Phytopathology ◽

10.1094/phyto-06-19-0223-r ◽

2020 ◽

Vol 110 (5) ◽

pp. 1049-1055

Author(s):

Emily W. Lankau ◽

Dianne Xue ◽

Rachel Christensen ◽

Amanda J. Gevens ◽

Richard A. Lankau

Keyword(s):

Microbial Communities ◽

Indirect Effects ◽

Common Scab ◽

Soil Microbial Communities ◽

Farm Management ◽

Equation Modeling ◽

Soil Conditions ◽

Potato Market ◽

Soil Microbial ◽

Soil Bacterial

Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.

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Peanut/Cotton Intercropping Increases Productivity and Economic Returns by Regulating Nutrient Accumulation and Soil Microbial Communities Under both Normal and Saline Soil Conditions

10.21203/rs.3.rs-1145699/v1 ◽

2021 ◽

Author(s):

Wei Xie ◽

Kai Zhang ◽

Xiaoying Wang ◽

Xiaoxia Zou ◽

Xiaojun Zhang ◽

...

Keyword(s):

Microbial Communities ◽

Crop Yield ◽

Bacterial Abundance ◽

Saline Soil ◽

Soil Microbial Communities ◽

Soil Conditions ◽

Nutrient Accumulation ◽

Economic Returns ◽

Soil Microbial ◽

Functional Features

Abstract Background Intercropping has been widely adopted by farmers for it often enhances crop productivity and economic returns; however, the underpinning mechanisms from the perspective of belowground interspecific interactions are only partly understood especially when intercropping under saline soil conditions. By using permeable (100 µm) and impermeable (solid) root barriers in a multi-site field experiment, we aimed to study the impact of root-root interactions on nutrient accumulation, soil microbial communities, crop yield, and economic returns in a peanut/cotton intercropping system under non-saline, secondary-saline, and coastal saline soil conditions. Results The results indicate that intercropping (IC) decreased the peanut pods yield while increased the seed cotton yield, and consequently enhanced the economic returns compared with monoculture of peanut (MP) and cotton (MC). The higher accumulations of nutrients such as nitrogen (N), phosphorus (P), and potassium (K) were also observed in IC not only in the soil but also in vegetative tissues and reproductive organs. Bacterial community structure analysis under normal growth conditions reveals that IC dramatically altered the soil bacterial abundance composition in both peanut and cotton strips of the top soil whereas the bacterial diversity was barely affected compared with MP and MC. At blossom-needling stage, the metabolic functional features of the bacterial communities such as fatty acid biosynthesis, lipoic acid metabolism, peptidoglycan biosynthesis, and biosynthesis of ansamycins were significantly enriched in MP compared with other treatments. Conversely, these metabolic functional features were dramatically depleted in MP while significantly enriched in IC at podding stage. Permeable root barrier treatments (NC-P and NC-C) counteracted the benefits of IC and the side effects were more pronounced in impermeable treatments (SC-P and SC-C). Conclusion Peanut/cotton intercropping increases crop yield as well as economic returns under non-saline, secondary-saline, and coastal saline soil conditions probably by modulating the soil bacterial abundance composition and accelerating nutrients accumulation.

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