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

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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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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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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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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Soil microbial communities following bush removal in a Namibian savanna

SOIL Discussions ◽

10.5194/soild-2-1393-2015 ◽

2015 ◽

Vol 2 (2) ◽

pp. 1393-1418

Author(s):

J. S. Buyer ◽

A. Schmidt-Küntzel ◽

M. Nghikembua ◽

J. E. Maul ◽

L. Marker

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Microbial Community Structure ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Management Approach ◽

Polymorphism Analysis ◽

Soil Microbial

Abstract. Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

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Soil microbial communities following bush removal in a Namibian savanna

SOIL ◽

10.5194/soil-2-101-2016 ◽

2016 ◽

Vol 2 (1) ◽

pp. 101-110 ◽

Cited By ~ 12

Author(s):

Jeffrey S. Buyer ◽

Anne Schmidt-Küntzel ◽

Matti Nghikembua ◽

Jude E. Maul ◽

Laurie Marker

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Microbial Community Structure ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Management Approach ◽

Polymorphism Analysis ◽

Soil Microbial

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Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration

Applied and Environmental Microbiology ◽

10.1128/aem.00764-11 ◽

2011 ◽

Vol 77 (17) ◽

pp. 6158-6164 ◽

Cited By ~ 126

Author(s):

Natasha C. Banning ◽

Deirdre B. Gleeson ◽

Andrew H. Grigg ◽

Carl D. Grant ◽

Gary L. Andersen ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Fungal Community ◽

Soil Microbial Community ◽

Ecosystem Restoration ◽

Community Structures ◽

Soil Microbial ◽

Soil Bacterial ◽

Edaphic Variables

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

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The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

10.1101/2020.03.31.018416 ◽

2020 ◽

Author(s):

Jingjie Hao ◽

Yen Ning Chai ◽

Raziel A. Ordóñez ◽

Emily E. Wright ◽

Sotirios Archontoulis ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Structure ◽

Soil Depth ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Soil Microbial

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.

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Microbial regulation of soil carbon properties under nitrogen addition and plant inputs removal

PeerJ ◽

10.7717/peerj.7343 ◽

2019 ◽

Vol 7 ◽

pp. e7343

Author(s):

Ran Wu ◽

Xiaoqin Cheng ◽

Wensong Zhou ◽

Hairong Han

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Soil Carbon ◽

Microbial Community Structure ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Nitrogen Addition ◽

Soil Microbial Community Structure ◽

Soil Microbial

Background Soil microbial communities and their associated enzyme activities play key roles in carbon cycling in terrestrial ecosystems. Soil microbial communities are sensitive to resource availability, but the mechanisms of microbial regulation have not been thoroughly investigated. Here, we tested the mechanistic relationships between microbial responses and multiple interacting resources. Methods We examined soil carbon properties, soil microbial community structure and carbon-related functions under nitrogen addition and plant inputs removal (litter removal (NL), root trench and litter removal (NRL)) in a pure Larix principis-rupprechtii plantation in northern China. Results We found that nitrogen addition affected the soil microbial community structure, and that microbial biomass increased significantly once 100 kg ha−1 a−1 of nitrogen was added. The interactions between nitrogen addition and plant inputs removal significantly affected soil bacteria and their enzymatic activities (oxidases). The NL treatment enhanced soil microbial biomass under nitrogen addition. We also found that the biomass of gram-negative bacteria and saprotrophic fungi directly affected the soil microbial functions related to carbon turnover. The biomass of gram-negative bacteria and peroxidase activity were key factors controlling soil carbon dynamics. The interactions between nitrogen addition and plant inputs removal strengthened the correlation between the hydrolases and soil carbon. Conclusions This study showed that nitrogen addition and plant inputs removal could alter soil enzyme activities and further affect soil carbon turnover via microbial regulation. The increase in soil microbial biomass and the microbial regulation of soil carbon both need to be considered when developing effective sustainable forest management practices for northern China. Moreover, further studies are also needed to exactly understand how the complex interaction between the plant and below-ground processes affects the soil microbial community structure.

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Plant genotype controls wetland soil microbial functioning in response to sea-level rise

Biogeosciences ◽

10.5194/bg-18-6133-2021 ◽

2021 ◽

Vol 18 (23) ◽

pp. 6133-6146

Author(s):

Hao Tang ◽

Susanne Liebner ◽

Svenja Reents ◽

Stefanie Nolte ◽

Kai Jensen ◽

...

Keyword(s):

Climate Change ◽

Community Structure ◽

Microbial Community ◽

Sea Level Rise ◽

Sea Level ◽

Microbial Community Structure ◽

Soil Microbial Communities ◽

Litter Breakdown ◽

Plant Genotype ◽

Soil Microbial

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

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