scholarly journals Initial sample processing can influence the soil microbial metabarcoding surveys, revealed by Leucocalocybe mongolica fairy ring ecosystem

2020 ◽  
Author(s):  
Mingzheng Duan ◽  
Tolgor Bau
Keyword(s):  
High Temperature ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Soil Samples ◽  
Soil Microbial ◽  
Microbial Structures ◽  
Sequencing Quality ◽  
Bacteria And Fungi ◽  
The Impact ◽  
High Temperature Drying

AbstractIn this study, we aimed to investigate the influence of soil preservation approaches, especially cryopreservation and high temperature-drying on the sequencing quality of its microbial community and the background microbial diversity information of fairy ring soil from Leucocalocybe mongolica. Through DNA metabarcoding surveys based on 16S rDNA and ITS barcodes, we observed that the bacterial abundance was notably changed when the soil samples were exposed in room temperature for 4 hours, whereas the fungal composition was not significantly changed. Moreover, the soil samples preserved their major microbial structures even after high temperature-drying for 12 hours, whereas their microbial diversity was influenced. Overall, a total of 9283 and 1871 OTUs were obtained from soil bacteria and fungi, respectively, and we observed that Chthoniobacteraceae and Tricholomataceae were the dominant bacterial and fungal families in the fairy ring soil, respectively. Our study reveals the impact of soil processing methods on the microbial community compositions and contributes to the understanding of fairy ring ecology.

scholarly journals Soil microbial community variation with time and soil depth in Eurasian Steppe (Inner Mongolia, China)

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Hongbin Zhao ◽  
Wenling Zheng ◽  
Shengwei Zhang ◽  
Wenlong Gao ◽  
Yueyue Fan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Temporal And Spatial ◽  
Time Of Year ◽  
Bacteria And Fungi ◽  
The Impact

Abstract Purpose Soil microorganisms play an indispensable role in the material and energy cycle of grassland ecosystems. The abundance of these organisms vary according to environmental factors, such as time of year and soil depth. There have been few studies on the transformation of soil microbial communities in degraded typical steppe according to these temporal and spatial changes. In this study, we analyze the community structure and diversity of soil bacteria and fungi, and the impact of these changing temporal and spatial factors upon the community structure. Methods From May to September 2018, we collected 90 soil samples from different depths (10, 20, and 30 cm) from the typical degraded steppe area of Xilingol. We carried out studies on soil physical and chemical properties and soil microbial diversity using high-throughput sequencing technology. Results We found that depth significantly affected abundance and diversity of bacteria and fungi. Bacteria and fungi diversity at 10 cm was higher than that at 20 cm and 30 cm. The abundance of Acidobacteria, Proteobacteria, Actinomycetes, Ascomycetes, and Basidiomycetes varies significantly with depth. In addition, soil pH increased significantly with increasing depth, while soil organic matter (SOM), available nitrogen (AN), volume water content of soil (VWC), and soil temperature (ST) decreased significantly with increasing depth. Finally, the depth, total organic carbon (TOC), and AN had a significant impact on the bacterial and fungal communities’ abundance (p < 0.05). Conclusions Spatial heterogeneity (in soil depth) is more significant than the time of year (month) in predicting changes in microbial community composition and soil properties. SOM, VWC, and the abundance of Proteobacteria and Actinomycetes positively correlate with soil depth, while pH and the abundance of Acidobacteria, Ascomycetes, and Basidiomycetes negatively correlate with soil depth. We speculate that SOM and VWC account for the variations in the abundance of Acidobacteria and Proteobacteria, while pH causes variations in the abundance of Actinomycetes, Ascomycetes and Basidiomycota.

scholarly journals Microbial Diversity of Reconstituted, Degraded, and Agricultural Soils Assessed by 16S rDNA Multi-Amplicon Sequencing

2022 ◽  
Vol 9 ◽  
Author(s):  
Laura Maretto ◽  
Saptarathi Deb ◽  
Samathmika Ravi ◽  
Claudia Chiodi ◽  
Paolo Manfredi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
16S Rdna ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Biogeochemical Cycle ◽  
Soil Microbial Diversity ◽  
Soil Microbial

The microbial diversity is, among soil key factors, responsible for soil fertility and nutrient biogeochemical cycles, and can be modified upon changes in main soil physicochemical properties and soil pollution. Over the years, many restoration techniques have been applied to restore degraded soils. However, the effect of these approaches on soil microbial diversity is less understood and thus requires more investigation. In this study, we analyzed the impact, on soil microbial diversity of a patented novel technology, used to restore degraded soils. Soil samples were collected from three nearby sites located in Borgotrebbia, Piacenza, Italy, and categorized as reconstituted, degraded, and agricultural soils. After total soil DNA extraction, 16S rDNA multi-amplicon sequencing was carried out using an Ion GeneStudio S5 System to compare soils’ bacterial community profiles. Sequenced reads were processed to assign taxonomy and then key microbial community differences were identified across the sampling sites. Species diversity featured significant abatement at all rank levels in the degraded soil when compared to the agricultural control. The 5 year restoration technique showed full recovery of this index at the genus level but not at the phylum level, displaying a rank-dependent gradient of restored richness. In parallel, the abundance of genes involved in the nitrogen (N) biogeochemical cycle was assessed using quantitative Real-Time PCR (qPCR). Total DNA content was significantly higher (p &lt; 0.05) in degraded (μ = 12.69 ± 2.58 μg g−1) and reconstituted (μ = 11.73 ± 1.65 μg g−1) soil samples when compared to the agricultural soil samples (μ = 2.39 ± 0.50 μg g−1). The taxonomic diversity of each soil site was significantly different, with some instances unique of the agricultural soil even at the phylum level. The analysis of N functional genes showed that the relative abundance of bacterial amoA (p &lt; 0.05) and nosZ (p &lt; 0.01) genes were significantly lower in the agricultural than in the reconstituted and degraded soils. We concluded that the application of the soil reconstitution technique appears to enhance the active microbial community, with distinct diversity and functionality towards genes involved in N biogeochemical cycle, as compared to both the degraded and the agricultural soil.

scholarly journals Effects of Short-Term Rice Straw Return on the Soil Microbial Community

Agriculture ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 561
Author(s):  
Enze Wang ◽  
Xiaolong Lin ◽  
Lei Tian ◽  
Xinguang Wang ◽  
Li Ji ◽  
...  
Keyword(s):  
Microbial Community ◽  
Rice Straw ◽  
Paddy Soil ◽  
Soil Microbial Community ◽  
Short Term ◽  
Soil Microbial ◽  
Microbial Network ◽  
Straw Return ◽  
Bacteria And Fungi ◽  
Main Factor

Rice straw is a byproduct of agricultural production and an important agricultural resource. However, rice straw has not yet been effectively used, and incorrect treatment methods (such as burning in the field) can cause serious damage to the environment. Studies have shown that straw returning is beneficial to soil, but there have been few studies focused on the effect of the amount of short-term straw returned on the soil microbial community. This study evaluates 0%, 50%, 75%, and 100% rice straw returned to the field on whether returning different amounts of straw in the short term would affect the diversity and composition of the soil microbial community and the correlation between bacteria and fungi. The results show that the amount of straw returned to the field is the main factor that triggers the changes in the abundance and composition of the microbial community in the paddy soil. A small amount of added straw (≤ 50% straw added) mainly affects the composition of the bacterial community, while a larger amount of added straw (> 50% straw added) mainly affects the composition of the fungal community. Returning a large amount of straw increases the microbial abundance related to carbon and iron cycles in the paddy soil, thus promoting the carbon and iron cycle processes to a certain extent. In addition, network analysis shows that returning a large amount of straw also increases the complexity of the microbial network, which may encourage more microbes to be niche-sharing and comprehensively improve the ecological environment of paddy soil. This study may provide some useful guidance for rice straw returning in northeast China.

scholarly journals STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽  
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

<p>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.<br />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. <br />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.</p><p>Keywords: structure, microbial, implication, sustainable agriculture<br /><br /></p>

scholarly journals Seasonal Variation in the Rhizosphere and Non-Rhizosphere Microbial Community Structures and Functions of Camellia yuhsienensis Hu

2020 ◽  
Vol 8 (9) ◽  
pp. 1385
Author(s):  
Jun Li ◽  
Ziqiong Luo ◽  
Chenhui Zhang ◽  
Xinjing Qu ◽  
Ming Chen ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Microbial Community ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Pathogen Resistance ◽  
High Yield ◽  
Glutathione Metabolism ◽  
Oilseed Crop ◽  
Soil Microbial ◽  
Bacteria And Fungi

Camellia yuhsienensis Hu, endemic to China, is a predominant oilseed crop, due to its high yield and pathogen resistance. Past studies have focused on the aboveground parts of C. yuhsienensis, whereas the microbial community of the rhizosphere has not been reported yet. This study is the first time to explore the influence of seasonal variation on the microbial community in the rhizosphere of C. yuhsienensis using high-throughput sequencing. The results showed that the dominant bacteria in the rhizosphere of C. yuhsienensis were Chloroflexi, Proteobacteria, Acidobacteria, Actinobacteria, and Planctomycetes, and the dominant fungi were Ascomycota, Basidiomycota, and Mucoromycota. Seasonal variation has significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. A significant increase in bacterial abundance and diversity in the rhizosphere reflected the root activity of C. yuhsienensis in winter. Over the entire year, there were weak correlations between microorganisms and soil physiochemical properties in the rhizosphere. In this study, we found that the bacterial biomarkers in the rhizosphere were chemoorganotrophic Gram-negative bacteria that grow under aerobic conditions, and fungal biomarkers, such as Trichoderma, Mortierella, and Lecanicillium, exhibited protection against pathogens in the rhizosphere. In the rhizosphere of C. yuhsienensis, the dominant functions of the bacteria included nitrogen metabolism, oxidative phosphorylation, glycine, serine and threonine metabolism, glutathione metabolism, and sulfur metabolism. The dominant fungal functional groups were endophytes and ectomycorrhizal fungi of a symbiotroph trophic type. In conclusion, seasonal variation had a remarkable influence on the microbial communities and functions, which were also significantly different in the rhizosphere and non-rhizosphere of C. yuhsienensis. The rhizosphere of C. yuhsienensis provides suitable conditions with good air permeability that allows beneficial bacteria and fungi to dominate the soil microbial community, which can improve the growth and pathogen resistance of C. yuhsienensis.

The Impact of Reclaimed Water Irrigation on Soil Microbial Community Structure

2014 ◽  
Vol 955-959 ◽  
pp. 3635-3639 ◽  
Author(s):  
Ji Hua Wang ◽  
Xue Gong ◽  
Jian Fei Guan ◽  
Hui Yan Xing
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Soil Column ◽  
Reclaimed Water ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact ◽  
Reclaimed Water Irrigation

The reclaimed water treated in a Harbin recycled water plant has been taken as a target of research, by using microbial traditional culture method and tablet coated counting method, discussing the influence of the reclaimed water irrigation on soil microbial community structure through the method of short-term indoor simulated soil column irrigation. The results shows that the reclaimed water irrigation can significantly increase the quantity of bacteria and actinomycetes in the surface 0-20 cm layer soil, but it has little affect on 20-40 cm and 40-60 cm layer soil. Microbial community structure and diversity were changed relatively with the irrigation of reclaimed water, which embodied the increase or decrease of dominant and subdominant groups, the disappearance of non-dominant groups sensitive to reclaimed water, the appear or disappear of the other part of the occasional groups.

scholarly journals Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

2020 ◽  
Vol 66 (4) ◽  
pp. 263-273
Author(s):  
Julien Saavedra-Lavoie ◽  
Anne de la Porte ◽  
Sarah Piché-Choquette ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Co Oxidation ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Oxidative Capacity ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microcosms ◽  
Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

scholarly journals Contrasting soil microbial abundance and diversity on and between pasture drill rows in the third growing season after sowing

2020 ◽  
pp. 1-10 ◽  
Author(s):  
Richard C. Hayes ◽  
Vadakattu V. S. R. Gupta ◽  
Guangdi D. Li ◽  
Mark B. Peoples ◽  
Richard P. Rawnsley ◽  
...  
Keyword(s):  
Subterranean Clover ◽  
Plant Distribution ◽  
Total Carbon ◽  
Microbial Abundance ◽  
Soil Microbial ◽  
The Third ◽  
Fungal Populations ◽  
Abundance And Diversity ◽  
Bacteria And Fungi ◽  
The Impact

Abstract Changed spatial configurations at sowing have been investigated as a strategy to minimize interspecific competition and improve the establishment and persistence of multi-species plantings in pastures, but the impact of this practice on the soil microbiome has received almost no previous research attention. Differences in populations of bacteria and fungi in the surface 10 cm of soil in the third year following pasture establishment were quantified using quantitative polymerase chain reaction and terminal restriction fragment length polymorphism methods. Populations were compared on, and between, drill rows sown to either the perennial grass phalaris (Phalaris aquatica L.), perennial legume lucerne (alfalfa; Medicago sativa L.) or the annual legume subterranean clover (Trifolium subterraneum L.). Results showed that soil microbial abundance and diversity were related to plant distribution across the field at the time of sampling and to soil chemical parameters including total carbon (C), mineral nitrogen (N), pH, and available phosphorus (P), potassium (K) and sulfur (S). Despite the 27-month lag since sowing, pasture species remained concentrated around the original drill row with very little colonization of the inter-row area. The abundance and diversity of bacterial and fungal populations were consistently greater under drill rows associated with higher total C concentrations in the surface soil compared with the inter-row areas. Our results showed that the pH and available nutrients were similar between the subterranean clover drill row and the inter-row, suggesting that soil microbial populations were not impacted directly by these soil fertility parameters, but rather were related to the presence or absence of plants. The abundance of bacteria and fungi were numerically lower under phalaris rows compared to rows sown to legumes. The richness and diversity of fungal populations were lowest between rows where lucerne was planted. Possible explanations for this observation include a lower C:N ratio of lucerne roots and/or a lack of fibrous roots at the soil surface compared to the other species, illustrating the influence of contrasting plant types on the soil microflora community. This study highlights the enduring legacy of the drill row on the spatial distribution of plants well into the pasture phase of a cropping rotation and discusses the opportunity to enhance the microbiome of cropping soils on a large scale during the pasture phase by increasing plant distribution across the landscape.

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