Dynamic Microbial Network Structure and Assembly Process in Rhizosphere and Bulk Soils Along a Coniferous Plantation Chronosequence

Abstract Aims: During plantation development, microbial composition and diversity are critical for the establishment of plant diversity and multiple ecosystem functions. Here we aimed to evaluate the impacts of chronosequence and soil compartment on the bacterial and fungal community compositions, species co-occurrence, and assembly processes in forest ecosystem.Methods: Soils were collected in rhizosphere and bulk soils along a Pinus tabulaeformis plantation chronosequence (15, 30 and 60 years old). The bacterial and fungal communities were determined using amplicon sequencing.Results: The effect of stand age on the soil properties and microbial community structures was stronger than the effect of the soil compartment. In all soil samples, the dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Basidiomycota, Ascomycota, and Mortierellomycota were the dominant fungal phyla. Higher turnover rates of soil microbial communities were observed in rhizosphere soil than in bulk soil. Dispersal limitation governed the bacterial and fungal community assembly in all soil samples, and the fungal community was more susceptible to dispersal limitation. The bacterial and fungal keystone species compositions in the rhizosphere had significant positive correlations with the soil total phosphorus and nitrite nitrogen and total nitrogen and total phosphorus, respectively, indicating their importance in soil nitrogen and phosphorus cycling. The complexity of bacterial networks increased along the chronosequence. Fungal network complexity did not show a clear age-related trend but increased from bulk soil to the rhizosphere.Conclusions: During Pinus tabulaeformis plantation development, soil microbial assembly was less environmentally constrained due to an increase in resource availability.

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Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab028 ◽

2021 ◽

Vol 97 (4) ◽

Author(s):

Lucas Dantas Lopes ◽

Jingjie Hao ◽

Daniel P Schachtman

Keyword(s):

Microbial Communities ◽

Plant Species ◽

Soil Ph ◽

Soil Microbial Communities ◽

Bulk Soil ◽

Strong Impact ◽

Alkaline Soil ◽

Alkaline Soils ◽

Soil Microbial ◽

Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

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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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How drought modulates carbon-use efficiency and soil carbon formation in rhizosphere, detritusphere, and bulk soils

10.5194/egusphere-egu2020-13148 ◽

2020 ◽

Author(s):

Noah Sokol ◽

Steve Blazewicz ◽

Megan Foley ◽

Alex Greenlon ◽

Jennifer Pett-Ridge

Keyword(s):

Soil Moisture ◽

Soil Carbon ◽

Soil Microbial Communities ◽

Bulk Soil ◽

Carbon Pools ◽

Carbon Formation ◽

Soil Microbial ◽

Carbon Use Efficiency ◽

Use Efficiency ◽

Soil Carbon Formation

Carbon use efficiency (CUE) is theorized to be positively associated with the formation of microbially-derived, mineral-associated soil carbon.&#160; Yet few empirical studies have directly tested this relationship. Moreover, it is unclear: (1) how differences between distinct soil microbial communities (for example, differences in competitive interactions and/or growth rate among rhizosphere, detritusphere, and bulk soil communities) may yield different relationships between carbon-use efficiency and soil carbon formation, and (2) how microbial ecophysiology &#8211; such as physiological changes induced by drought &#8211; may modulate the strength and/or direction of the CUE-soil carbon relationship.To investigate these questions, we conducted a 12-week 13C tracer study to track the movement of two dominant sources of plant carbon &#8211;&#160;rhizodeposition and root detritus &#8211; into soil microbial communities and carbon pools under normal moisture vs drought conditions. Using a continuous 13CO2-labeling system, we grew the Mediterranean annual grass Avena barbata in controlled growth chambers and measured the formation of organic matter from 13C-enriched rhizodeposition. As the plants grew, we harvested rhizosphere and bulk soil at three time points (4, 8, and 12 weeks) to capture changes in soil carbon pools and microbial community dynamics. In parallel microcosms, we tracked the formation of soil carbon derived from 13C-enriched A. barbata root detritus during 12 weeks of decomposition; harvesting detritusphere and bulk soil at 4,8, and 12 weeks. In all microcosms, we manipulated soil moisture to generate drought (7.8 &#177; 2.1 % soil moisture) and &#8216;normal moisture&#8217; (15.1 &#177; 4.2 % soil moisture) treatments.In all samples (over 150 observations), we measured CUE via the 18O-H2O method, and quantified the formation of different 13C-soil organic carbon pools via density fractionation. Here we will present data on how soil moisture influences CUE in rhizosphere, detritusphere, and bulk soil communities, and whether differences in CUE are correlated with the formation of mineral-associated soil organic carbon. These results will help to illustrate whether CUE acts as a lynchpin variable with predictive power for stable soil carbon formation, or whether other microbial traits may require consideration.&#160;&#160;

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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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Investigation of soil microbiome under the influence of different mulching treatments in northern highbush blueberry

AMB Express ◽

10.1186/s13568-021-01294-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sang In Lee ◽

Jungmin Choi ◽

Hyunhee Hong ◽

Jun Haeng Nam ◽

Bernadine Strik ◽

...

Keyword(s):

Microbial Communities ◽

Functional Properties ◽

Soil Depth ◽

Plant Growth Promoting Rhizobacteria ◽

Soil Samples ◽

Soil Microbiome ◽

Microbial Composition ◽

Soil Microbial ◽

Significant Difference ◽

Plant Growth Promoting

AbstractMicrobial communities on soil are fundamental for the long-term sustainability of agriculture ecosystems. Microbiota in soil would impact the yield and quality of blueberries since microbial communities in soil can interact with the rhizosphere of plant. This study was conducted to determine how different mulching treatments induce changes in soil microbial composition, diversity, and functional properties. A total of 150 soil samples were collected from 5 different mulch treatments (sawdust, green weed mat, sawdust topped with green weed mat, black weed mat, and sawdust topped with black weed mat) at 3 different depths (bottom, middle, and top region of 20 cm soil depth) from 2 different months (June and July 2018). A total of 8,583,839 sequencing reads and 480 operational taxonomic units (OTUs) of bacteria were identified at genus level. Eight different plant growth promoting rhizobacteria (PGPR) were detected, and the relative abundances of Bradyrhizobium, Bacillus, and Paenibacillus were more than 0.1% among all soil samples. Sampling depth and month of soil samples impacted the amount of PGPR, while there were no significant differences based on mulch type. Functional properties of bacteria were identified through PICRUSt2, which found that there is no significant difference between mulch treatment, depth, and month. The results indicated that sampling month and depth of soil impacted the relative abundance of PGPR in soil samples, but there were no significant differences of functional properties and beneficial microbial communities based on mulch type.

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Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1908117117 ◽

2020 ◽

Vol 117 (13) ◽

pp. 7263-7270 ◽

Cited By ~ 1

Author(s):

Kelly Gravuer ◽

Anu Eskelinen ◽

Joy B. Winbourne ◽

Susan P. Harrison

Keyword(s):

Spatial Variability ◽

Spatial Heterogeneity ◽

Soil Microbial Communities ◽

Archaeal Community ◽

Ecosystem Functions ◽

Water Addition ◽

Microbial Composition ◽

Soil Microbial ◽

The Face ◽

And Function

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.

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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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Soil Bacterial and Fungal Composition and Diversity Responses to Seasonal Deer Grazing in a Subalpine Meadow

Diversity ◽

10.3390/d13020084 ◽

2021 ◽

Vol 13 (2) ◽

pp. 84

Author(s):

Andéole Niyongabo Turatsinze ◽

Baotian Kang ◽

Tianqi Zhu ◽

Fujiang Hou ◽

Saman Bowatte

Keyword(s):

Relative Abundance ◽

Soil Microbial Communities ◽

Gansu Province ◽

Total Carbon ◽

Mountain Range ◽

Microbial Composition ◽

Soil Microbial ◽

Β Diversity ◽

Α Diversity ◽

Soil Bacterial

Soil microbial composition and diversity are widely recognized for their role in ecological functioning. This study examined the differences of soil microbial communities between two seasonally grazed grasslands. The study area was in the Gansu red deer farm located on the Qilian Mountain range in the Gansu province of northwestern China. This farm adopted a seasonal rotation grazing system whereby grasslands at higher altitudes are grazed in summer (SG), whilst grasslands at lower altitudes are grazed in winter (WG). The soil bacterial and fungal communities were examined by Illumina MiSeq sequencing. We found that soil water content (SWC), organic carbon (OC), total carbon (TC), and total nitrogen (TN) were significantly higher, whereas the C/N ratio was significantly lower in SG than WG pastures. The α-diversity of bacteria was greater than that of fungi in both pastures, while both bacterial and fungal α-diversity were not significantly different between the pastures. The bacterial β-diversity was significantly different between the pastures, but fungal β-diversity was not. The bacterial phylum Actinobacteria and fungal phylum Ascomycota were dominant in both pastures. The relative abundance of Actinobacteria in soil was significantly higher in WG pastures, whereas the relative abundance of Proteobacteria in soil was significantly higher in SG pastures. Significant correlations between bacterial and fungal phyla and soil properties were observed, but this varied between the two grasslands. This study showed that distinct microbial community structures developed in two pastures within the same geographic location that were grazed in different seasons.

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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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Biochar and Intercropping With Potato–Onion Enhanced the Growth and Yield Advantages of Tomato by Regulating the Soil Properties, Nutrient Uptake, and Soil Microbial Community

Frontiers in Microbiology ◽

10.3389/fmicb.2021.695447 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xingjia He ◽

Hua Xie ◽

Danmei Gao ◽

M. Khashi U. Rahman ◽

Xingang Zhou ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Soil Ph ◽

Fungal Community ◽

Soil Microbial Communities ◽

Pot Experiment ◽

Growth And Yield ◽

Positive Interactions ◽

Soil Microbial ◽

Potato Onion

The application of biochar stimulates the activities of microorganisms that affect soil quality and plant growth. However, studies on the impacts of biochar mainly focus on a monoculture, its effects on interspecific interactions are rarely reported. Here, we investigated the impacts of biochar on tomato/potato–onion intercropped (TO) in a pot experiment. Tomato monoculture (T) and TO were treated with no, 0.3, 0.6, and 1.2% biochar concentrations in a pot experiment. Microbial communities from tomato rhizosphere soil were analyzed by quantitative PCR and Illumina MiSeq. The results showed that compared with the tomato monoculture, 0.6%TO and 1.2%TO significantly increased tomato yield in 2018. TO and 1.2%TO significantly increased plant height and dry weight in 2018 and 2019. Biochar treatments increased soil pH, decreased NO3--N and bulk density, and increased the absorption of N, P, and K by tomato. Bacterial and fungal abundances increased with an increase in biochar concentration, while Bacillus spp. and Pseudomonas spp. abundances showed an “increase-decrease-increase” trend. Biochar had a little effect on bacterial diversities but significantly lowered fungal diversities. TO, 0.6%TO, and 1.2%TO increased the potentially beneficial organisms (e.g., Pseudeurotium and Solirubrobacter) and lowered the potentially pathogenic organisms (e.g., Kribbella and Ilyonectria). Different concentrations of biochar affected the bacterial and fungal community structures. Redundancy analysis indicated that the bacterial community was strongly correlated with soil pH, NO3--N, and EC, while the fungal community was closely related to soil NO3--N and moisture. The network analysis showed that biochar and intercropping affected the symbiosis pattern of the microorganisms and increased the proportion of positive interactions and nitrifying microorganisms (Nitrospirae) in the microbial community. Overall, our results indicated that monoculture and intercropping with biochar improved soil physicochemical states and plant nutrient absorption, and regulated soil microbial communities, these were the main factors to promote tomato growth and increase tomato productivity.

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