Effects of Living Cover on the Soil Microbial Communities and Ecosystem Functions of Hazelnut Orchards

Living cover is an important management measure for orchards in China, and has certain influences on soil properties, microorganisms, and the micro-ecological environment. However, there are few studies on the effects of living cover on the soil changes in hazelnut orchards. In this study, we compared the soils of living cover treatments with Vulpia myuros and the soils of no cover treatments, and analyzed the observed changes in soil properties, microorganisms, and microbial functions by using high-throughput ITS rDNA and 16S rRNA gene Illumina sequencing. The results demonstrated that the total organic carbon content in the 20–40 cm deep soils under the living cover treatments increased by 32.87 and 14.82% in May and July, respectively, compared with those under the no cover treatments. The living cover treatment with V. myuros also significantly increased the contents of total phosphorus (TP), total nitrogen (TN), available phosphorus (AP), and available potassium (AK) in the soil samples. Moreover, the influence of seasons was not as significant as that of soil depth. The living cover treatment also significantly improved the soil enzyme activity levels. The results demonstrated that Ascomycota, Mortierellomycota and Basidiomycota were the dominant fungal phyla in all samples, while Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, and Chloroflexi were the dominant bacterial phyla, but the different treatments impacted the compositions of fungal and bacterial communities. Principal component analysis (PCA) showed that living cover with V. myuros significantly changed the soil fungal community structures whereas the bacterial community structures may be more sensitive to seasonal changes. At the microbial functional level, the living cover treatment increased the fungal operational taxonomic units (OTUs) of symbiotrophs and decreased that of pathotrophs. According to this study, we believe that the application of a living cover with V. myuros has a favorable regulating influence on soil properties, microbial communities and microbial function. This treatment can also reduce the use of herbicides, reduce the cost of orchard management, and store more carbon underground to achieve sustainable intensification of production in hazelnut orchards, so it can be considered as a management measure for hazelnut orchards.

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Effects of living cover on the soil microbial communities and ecosystem functions of hazelnut orchard

10.21203/rs.3.rs-84985/v1 ◽

2020 ◽

Author(s):

Wenxu Ma ◽

Zhen Yang ◽

Sihao Hou ◽

Qinghua Ma ◽

Lisong Liang ◽

...

Keyword(s):

Community Structure ◽

Soil Properties ◽

Soil Enzymes ◽

Soil Depth ◽

Soil Microbial Communities ◽

Ecosystem Functions ◽

Rrna Gene ◽

Organic Carbon Content ◽

Microbial Function ◽

Management Measure

Abstract Background: Living covers are an important management measure for orchards in China, which has a certain influence on soil properties, microorganisms and micro-ecological environment. However, there are few studies on the effects of living covers on the soil changes in hazelnut orchard. In this study, we compared living cover treatment by Vulpia myuros and no cover treatment, and analyzed the changes on the soil properties, microorganisms and microbial function by using high-throughput ITS rDNA and 16S rRNA gene Illumina sequencing. Results: The consequences demonstrated that the total organic carbon content of living cover treatment in the 20-40 cm soils increased by 32.87 % and 14.82 % respectively in May and July compared with no cover treatment, and living cover treatment by Vulpia myuros can also significantly increased the contents of total phosphorus (TP), total nitrogen (TN), available phosphorus (AP) and available potassium (AK) in the soil samples. Moreover, the influence of seasons is not as significant as that of soil depth. The living cover treatment significantly improved the soil enzymes activity levels. Among the four kind of soil enzymes, the soil invertase activity of living cover treatment was 50.94 % greater than that of no cover treatment in 0-20 cm soils and 52.17 % in 20-40 cm soils in May. The consequences demonstrated that Ascomycota, Mortierellomycota and Basidiomycota were the dominant fungal phylum in all samples, while Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi were the dominant bacterial phylum, but different treatments impacted the composition of fungal and bacterial communities. Principal component analysis (PCA) showed that living cover with Vulpia myuros significantly changed the soil fungal community structure whereas the bacterial community structure may be more sensitive to seasonal changes. At the microbial functional level, the pathotrophs, saprotrophs and symbiotrophs accounted for approximately 36.69 %, 49.80 % and 2.59 % of no cover treatment fungal OTUs respectively whereas in living cover treatment was 19.76 %, 41.51 % and 6.89 %. Conclusions: According to this study, we believe that the living cover with Vulpia myuros has a favorable regulating influence on soil properties, microbial community and microbial function, and can be considered as a management measure for hazelnut orchards management.

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Syringic acid inhibited cucumber seedling growth and changed rhizosphere microbial communities

Plant Soil and Environment ◽

10.17221/924/2013-pse ◽

2014 ◽

Vol 60 (No. 4) ◽

pp. 158-164 ◽

Cited By ~ 7

Author(s):

Zhou XG ◽

Wu FZ ◽

Xiang WS

Keyword(s):

Microbial Communities ◽

Seedling Growth ◽

Fungal Community ◽

Root Exudation ◽

Soil Microbial Communities ◽

Syringic Acid ◽

Plant Residue ◽

Rrna Gene ◽

Cucumber Seedling ◽

Community Structures

Phenolic compounds enter soil as a result of root exudation and plant residue decomposition, but their impacts on soil microbial communities are poorly understood. In this experiment, effects of syringic acid on cucumber rhizosphere microbial communities were evaluated. Rhizosphere bacterial and fungal community structures and abundances were analyzed with PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR, respectively. Results showed that syringic acid inhibited cucumber seedling growth at concentrations of 0.05 to 0.2 μmol/g soil, and increased rhizosphere soil dehydrogenase activity, microbial biomass carbon content, bacterial 16S rRNA gene and fungal ITS rRNA gene densities, and decreased the bacteria-to-fungi ratio at concentrations of 0.02 to 0.2 μmol/g soil. Syringic acid also changed rhizosphere bacterial and fungal community structures: it decreased the richness, evenness, and diversity indices of rhizosphere bacterial community but had no significant influences on that of fungal community, indicating that syringic acid had different influence on bacterial and fungal communities. Taken together, these results showed that syringic acid inhibited cucumber growth and altered rhizosphere microbial communities, suggesting that syringic acid plays some role in the communication between plants and soil microorganisms.

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The Impacts of Different Green Manure on Soil Microbial Communities and Crop Health

10.20944/preprints201609.0056.v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Hongwu Yang ◽

Jiaojiao Niu ◽

Jiemeng Tao ◽

Yabing Gu ◽

Chao Zhang ◽

...

Keyword(s):

Soil Properties ◽

Microbial Communities ◽

Soil Nutrients ◽

Green Manure ◽

Soil Microbial Communities ◽

Disease Rate ◽

Rrna Gene ◽

Soil Microbial ◽

Tobacco Disease ◽

Crop Health

Green manure could improve soil nutrients and crop production, playing a significant role in sustainable agriculture. However, the impacts of green manure on crop health and the roles soil microbial communities play in the process haven’t been clarified clearly yet. In this study, we investigated soil microbial community composition and structure in four tobacco farmlands, which were treated with different green manure (control, ryegrass, pea and rape), using 16S rRNA gene amplicons sequencing. Results showed that green manure had significant impacts on soil properties, microbial communities and tobacco health. First, soil total C, N and Ca content increased significantly in groups treated with green manure than control. Second, soil community diversity was significantly higher in groups treated with green manure. Third, green manure especially ryegrass, decreased tobacco disease (bacterial wilt) rate dramatically, and the process might be mediated by soil microbial communities. On the one hand, several microbial populations were found to be potentially disease inducible or suppressive. For example, the abundances of Dokdonella and Rhodanobacter were positively correlated to tobacco disease rate, while Acidobacteira_Gp4 and Gp6 had negative correlations with tobacco disease. On the other hand, soil microbial communities were shaped by soil properties (e.g., pH, C and N content). In conclusion, our research showed that green manure could increase soil nutrients directly, and further improve tobacco health mediated by soil microorganisms, which may shed light on revealing interactions among soil properties, microorganisms and plants.

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Effects of Heavy Metals/Metalloids and Soil Properties on Microbial Communities in Farmland in the Vicinity of a Metals Smelter

Frontiers in Microbiology ◽

10.3389/fmicb.2021.707786 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xuewu Hu ◽

Jianlei Wang ◽

Ying Lv ◽

Xingyu Liu ◽

Juan Zhong ◽

...

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Soil Properties ◽

Microbial Communities ◽

Soil Ph ◽

Contaminated Soils ◽

High Throughput Sequencing ◽

Available Phosphorus ◽

Rrna Gene ◽

Multiple Heavy Metals

Microorganisms play a fundamental role in biogeochemical cycling and are highly sensitive to environmental factors, including the physiochemical properties of the soils and the concentrations of heavy metals/metalloids. In this study, high-throughput sequencing of the 16S rRNA gene was used to study the microbial communities of farmland soils in farmland in the vicinity of a lead–zinc smelter. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes were the predominant phyla in the sites of interest. Sphingomonas, Gemmatimonas, Lysobacter, Flavisolibacter, and Chitinophaga were heavy metal-/metalloid-tolerant microbial groups with potential for bioremediation of the heavy metal/metalloid contaminated soils. However, the bacterial diversity was different for the different sites. The contents of heavy metal/metalloid species and the soil properties were studied to evaluate the effect on the soil bacterial communities. The Mantel test revealed that soil pH, total cadmium (T-Cd), and available arsenic played a vital role in determining the structure of the microbial communities. Further, we analyzed statistically the heavy metals/metalloids and the soil properties, and the results revealed that the microbial richness and diversity were regulated mainly by the soil properties, which correlated positively with organic matter and available nitrogen, while available phosphorus and available potassium were negatively correlated. The functional annotation of the prokaryotic taxa (FAPROTAX) method was used to predict the function of the microbial communities. Chemoheterotrophy and airborne chemoheterotrophy of the main microbial community functions were inhibited by soil pH and the heavy metals/metalloids, except in the case of available lead. Mantel tests revealed that T-Cd and available zinc were the dominant factors affecting the functions of the microbial communities. Overall, the research indicated that in contaminated soils, the presence of multiple heavy metals/metalloids, and the soil properties synergistically shaped the structure and function of the microbial communities.

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Combined Effect of Laboratory-Simulated Fire and Chromium Pollution on Microbial Communities in an Agricultural Soil

Biology ◽

10.3390/biology10070587 ◽

2021 ◽

Vol 10 (7) ◽

pp. 587

Author(s):

Ida Rascio ◽

Maddalena Curci ◽

Concetta Eliana Gattullo ◽

Anna Lavecchia ◽

Mohammad Yaghoubi Khanghahi ◽

...

Keyword(s):

Soil Properties ◽

Microbial Communities ◽

Relative Abundance ◽

Agricultural Soil ◽

Crop Residues ◽

Soil Microbial Communities ◽

Soil Conditions ◽

Rrna Gene ◽

Bacterial Strains ◽

Soil Microbial

Fire events in agricultural soils can modify not only soil properties but also the structure of soil microbial communities, especially in soils containing high concentrations of potentially toxic elements (PTEs). The recolonization of burned soils can in fact favor the proliferation of certain microorganisms, more adaptable to post-fire soil conditions and higher PTE availability, over others. In this study, we simulated with laboratory experiments the microbial recolonization of an agricultural soil containing high Cr concentrations after heating at 500 °C for 30 min, to mimic the burning of crop residues. Changes in soil properties and Cr speciation were assessed, as well as soil microbial structure by means of 16S rRNA gene sequencing. Both altered soil conditions and increased Cr availability, especially Cr(VI), appeared to be responsible for the reduction in species diversity in heated soils and the proliferation of Firmicutes. Indeed, already after 3 days from the heat treatment, Firmicutes increased from 14% to 60% relative abundance. In particular, Paenibacillus was the most abundant genus identified after the simulation, with an average relative abundance of 40%. These bacteria are known to be good fire-responders and Cr-tolerant. These results could be useful to identify bacterial strains to be used as bioindicators of altered environments and for the recovery of fire-impacted polluted sites.

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Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽

10.3390/agronomy11010173 ◽

2021 ◽

Vol 11 (1) ◽

pp. 173

Author(s):

Huiling Guan ◽

Jiangwen Fan ◽

Haiyan Zhang ◽

Warwick Harris

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Soil Depth ◽

Phospholipid Fatty Acid ◽

Soil Microbial Communities ◽

Deep Soil ◽

Soil System ◽

Soil Microbial ◽

Total Soil ◽

Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

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Improvement of Tea (Camellia sinensis L.) Soil Properties by Growing Different Green Crops

The Agriculturists ◽

10.3329/agric.v12i2.21729 ◽

2015 ◽

Vol 12 (2) ◽

pp. 34-38 ◽

Cited By ~ 1

Author(s):

Ashim Kumar Saha ◽

Apu Biswas ◽

Abdul Qayyum Khan ◽

Md. Mohashin Farazi ◽

Md. Habibur Rahman

Keyword(s):

Organic Carbon ◽

Soil Properties ◽

Total Nitrogen ◽

Soil Ph ◽

Nutritional Value ◽

Soil Health ◽

Critical Value ◽

Available Phosphorus ◽

Organic Carbon Content

Long-term tea cultivation has led to degradation of the soil. Old tea soils require rehabilitation for restoring soil health. Soil rehabilitation by growing different green crops can break the chain of monoculture of tea. An experiment was conducted at The Bangladesh Tea Research Institute (BTRI) Farm during 2008-2011 to find out the efficiency of different green crops on the improvement of soil properties. Four green crops such as Guatemala, Citronella, Mimosa and Calopogonium were grown to develop the nutritional value of the degraded tea soil. Soil samples were collected and analyzed before and at the end of experiment. Soil pH was increased in all four green crops treated plots with the highest increase in Citronella treated plots (from 4.1 to 4.5). Highest content of organic carbon (1.19%) and total nitrogen (0.119%) were found in Mimosa and Calopogonium treated plots, respectively. Concentration of available phosphorus, calcium and magnesium in all green crops treated plots were above the critical values, while available potassium content was above the critical value in Guatemala, Citronella and Mimosa treated plots. Changes in soil pH and available potassium were significant, while changes in organic carbon content, total nitrogen and available calcium were insignificant. Changes in available phosphorus and magnesium were significant. The Agriculturists 2014; 12(2) 34-38

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Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

Frontiers in Microbiology ◽

10.3389/fmicb.2021.742000 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marc Crampon ◽

Coralie Soulier ◽

Pauline Sidoli ◽

Jennifer Hellal ◽

Catherine Joulian ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Treated Wastewater ◽

Rrna Gene ◽

Sequencing Data ◽

Rrna Gene Sequencing

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

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Associations between human impacts and forest soil microbial communities

Elem Sci Anth ◽

10.1525/elementa.005 ◽

2020 ◽

Vol 8 (1) ◽

Author(s):

Yongjian Chen ◽

Jialiang Kuang ◽

Pandeng Wang ◽

Wensheng Shu ◽

Albert Barberán

Keyword(s):

Microbial Communities ◽

Forest Soil ◽

Human Activity ◽

Eastern China ◽

Soil Microbial Communities ◽

Nitrifying Bacteria ◽

Rrna Gene ◽

Internal Transcribed Spacer Region ◽

Soil Microbial ◽

Soil Variables

We are living in a new epoch—the Anthropocene, in which human activity is reshaping global biodiversity at an unprecedented rate. Increasing efforts are being made toward a better understanding of the associations between human activity and the geographic patterns in plant and animal communities. However, similar efforts are rarely applied to microbial communities. Here, we collected 472 forest soil samples across eastern China, and the bacterial and fungal communities in those samples were determined by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer region, respectively. By compiling human impact variables as well as climate and soil variables, our goal was to elucidate the association between microbial richness and human activity when climate and soil variables are taken into account. We found that soil microbial richness was associated with human activity. Specifically, human population density was positively associated with the richness of bacteria, nitrifying bacteria and fungal plant pathogens, but it was negatively associated with the richness of cellulolytic bacteria and ectomycorrhizal fungi. Together, these results suggest that the associations between geographic variations of soil microbial richness and human activity still persist when climate and soil variables are taken into account and that these associations vary among different microbial taxonomic and functional groups.

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Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France

PLoS ONE ◽

10.1371/journal.pone.0252216 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0252216

Author(s):

Laurie Dunn ◽

Christophe Lang ◽

Nicolas Marilleau ◽

Sébastien Terrat ◽

Luc Biju-Duval ◽

...

Keyword(s):

Microbial Biomass ◽

Soil Properties ◽

Microbial Communities ◽

Soil Microorganisms ◽

Soil Microbial Communities ◽

Partial Least Square ◽

Farming Practices ◽

Soil Microbial ◽

Bacterial Richness ◽

Over Time

According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.

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