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 < 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 < 0.05) and nosZ (p < 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 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 Insight into the Characteristics of Soil Microbial Diversity during the Ecological Restoration of Mines: A Case Study in Dabaoshan Mining Area, China

2021 ◽  
Vol 13 (21) ◽  
pp. 11684
Author(s):  
Li Fan ◽  
Weiping Zhao ◽  
Wendan Feng ◽  
Ping Mo ◽  
Yunlin Zhao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Physicochemical Properties ◽  
Microbial Diversity ◽  
Ecological Restoration ◽  
Soil Microbial Community ◽  
Mining Area ◽  
Soil Restoration ◽  
Soil Physicochemical Properties ◽  
Soil Microbial Diversity ◽  
Soil Microbial

Soil microorganisms play an important role in regulating a variety of ecological functions. In recent years, the research on ecological restoration after mining has made people more aware of the importance of microbial diversity to ecosystem restoration. The present study investigated the effect of ecological restoration on microbial community structure and its relationship with soil physicochemical properties in the Dabaoshan mining area, China. High throughput sequencing technology was used to analyze and compare the microbial community composition of three types of soil (undamaged area, unrestoration area, and ecological restoration area). The contents of organic carbon, total nitrogen, and total phosphorus were 2.38–12.97 g/kg, 0.39–1.62 g/kg, and 0.99–1.51 g/kg, respectively. In different soil states, undamaged area and ecological restoration area were significantly higher than those in unrestoration area. The results showed that the structure of soil microbial community was significantly correlated with soil physicochemical properties, and formations in the repaired and unrepaired soils were different. Operational Taxonomic Unit (OTU) cluster analysis and diversity index analysis showed that soil microbial community changed at phylum and genus levels. The results showed that at the phylum level, all soil samples contained Firmicutes, Proteobacteria, and actinobacteria. Firmicutes and Proteobacteria of the ecological restoration area (ER1, ER2) were the highest in relative abundance compared with other samples, accounting for more than 45%. Proteobacteria and Acidobacteria were the dominant phylum in the undamaged area (UD), accounting for 32.7% and 22.3%, respectively. It can be seen that soil restoration produced a new dominant population, and Proteobacteria showed an absolute competitive advantage in the mining soil.

scholarly journals Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ai-Zi Tong ◽  
Wei Liu ◽  
Qiang Liu ◽  
Guang-Qing Xia ◽  
Jun-Yi Zhu
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Panax Ginseng ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Continuous Cropping ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Borne Pathogens

Abstract Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.

scholarly journals The Responses of Soil Microbial to Changed Rainfall and Increased Temperature in Desert Grassland in Northern China

2021 ◽  
Author(s):  
Yi Zhang ◽  
Ying-Zhong Xie ◽  
Hong-Bin Ma ◽  
Juan Zhang ◽  
Le Jing ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Respiration ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Response Strategy ◽  
Desert Grassland ◽  
Soil Microbial Diversity ◽  
Soil Microbial

Abstract Background: The study evaluates how rainfall change and temperature increase affect microbial communities in the desert grassland of Ningxia Autonomous Region, China to explore the soil microbial community and the relationships among the soil microbial community, chemical properties, soil respiration (SR) and plant biomass under the climate change. We established the field experiment with five levels of rainfall by rainout shelters and two levels of temperature by Open-Top Chamber (OTC). Results: The effect of temperature to soil microbial communities is not significant, but with the continuous increase of rainfall, the microbial community gradually increases. Soil microbial diversity negatively correlated with soil CO2 flux. The α-diversity of microbial communities positively correlated with above-living biomass (ALB) and soil temperature (ST), but negatively correlated with root biomass (RB). Conclusions: Both rainfall and temperature’s rising do not promote the soil community α-diversity, but it can promote soil microbial community β-diversity. Soil microbial communities show resistance to rainfall changing. Soil respiration (SR) will limit soil microbial diversity. Soil organic carbon (SOC), soil total nitrogen (STN), and soil total phosphorus (STP) will promote soil microbial abundance and diversity. ALB and ST will promote the soil α-diversity, but the effect of RB to soil microbial is opposite. These findings maybe provide a reliable theoretical basis for formulating a reasonable response strategy in desert steppe ecosystems.

scholarly journals Microbial Structure and Diversity in Rhizosphere Soil under Different Forest Types in the Subtropical Zone of China

2021 ◽  
Author(s):  
Liuting Zhou ◽  
Jianjuan Li ◽  
Chen Zhang ◽  
Xinlai Guo ◽  
Wei Chu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Nutrients ◽  
Soil Microbial Community ◽  
Rhizosphere Soil ◽  
Forest Types ◽  
Soil Microbial Diversity ◽  
Subtropical Zone ◽  
Soil Microbial

Abstract The aim of this study was to explore the soil microbial variability within different forest ecosystems (evergreen broad-leaf forest (EBF), coniferous forest (CF), subalpine dwarf forest (SDF) and alpine meadow (AM) at different altitudes in mid-subtropics of China. The phospholipid fatty acid (PLFA) method was used to analyze the microbial communities in rhizosphere soil under different forest types. The relationships were also analyzed between the microbial diversity and soil nutrients. A total of 27 PLFA biomarkers were detected and the PLFA concentrations decreased in the sequence of bacteria > fungus > actinomycete > protozoa in all forest types. The microbial communities in the soil under all forest types were distinct. The predominant microflora in all soils were 18:1ω9c, 16:1ω7c, cy19:0, a17:0 and 18:0. The indexes of Simpson, Shannon-Wiener and Brillouin of soil microbial community diversity in these four forest types all showed a trend of EBF > CF > SDF > AM. According to principal component analyses (PCA), the variable variances of principal components 1 and 2, which were related to the PLFA biomarkers of soil microorganisms, were 67.67% and 17.91%, respectively. Furthermore, the total PLFAs of different soil microbial groups showed a correlation with soil nutrients and enzyme activities in all forest types. The soil microbial diversity gradually decreased in the order of EBF > CF > SDF > AM in the Daiyun Mountains. Different vegetation types affect soil microbial community composition and diversity by changing the soil physicochemical properties and enzyme activity.

Developing nation’s soil microbial community shifts and diversity loss: leading towards major ecological threat

2021 ◽  
pp. 117-121
Author(s):  
Arun Kumar ◽  
Sanjat Kumar Sahu ◽  
Jayanthi J
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Soil Microbial Community ◽  
Food Production ◽  
Agricultural Land ◽  
Developing Nations ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Diversity Loss ◽  
Community Shifts

Nature does not discriminate and has no boundaries; however only developing nations faces huge food security issues and in such circumstances much of importance has been emphasised on food production technologies but studies and research on concealed factor behind food production i.e biogeochemical drivers were largely overlooked. Injudicious agricultural practices; for instance profound use of agrochemicals in continuous and unmonitored way may had already situate many soil microbial species in verge of extinction consequently creating ecological imbalance. With huge land pressure for crop production and lack of upto date technologies of preciseness, most of the developing nation which includes the whole of Africa, almost all Asian countries and numerous other island states faces the agricultural land degradation issues; one of the major reason for such degradation is missing out of ecological drivers i.e soil microbial diversity. Anthropogenic activities application of fertilisers, land use changes (LUC), land intensification, crop diversification, irrigation management etc accelerates the soil microbial community shifts and microbial diversity loss predominately in developing nations. In this short communication, we address the concerns faced by the developing nations to prevent the soil microbial community shift and diversity loss. Also we propose the each exported commodity may have specific tax included which may be utilised by soil scientist from developing nations for studying the current soil microbial shifts and diversity loss due to agriculture management practices more efficiently.

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 Organic Amendments and Sampling Date Influences on Soil Bacterial Community Composition and Their PredictiveFunctional Profiles in an Olive Grove Ecosystem

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1178
Author(s):  
Laura L. de Sosa ◽  
Beatriz Moreno ◽  
Rafael Alcalá Alcalá Herrera ◽  
Marco Panettieri ◽  
Engracia Madejón ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Soil Bacterial Community ◽  
Olive Grove ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
The Impact

A collapse of soil microbial diversity, mainly due to chemical inputs, has been reported to lead to the degradation of conventional agroecosystems. The use of compost from urban and agricultural waste management, in order to achieve a net gain in the storage of C, is an adequate management of agricultural soils, especially in rainfed conditions. However, the great variability of composts of different maturity and origins and of the soils to which they are added limits the ability to predict the impact of these amendments on the dynamics of soil microbial communities. This study was designed to gain insights on the effect of exogenous organic matter management on the soil bacterial community and its contribution to key functions relevant to agricultural soils. To achieve this, two different types of compost (alperujo or biosolids composts) at two doses were used as soil amendments twice for 3 years in a rainfed olive grove ecosystem. A metagenomic analysis was carried out to assess the abundance and composition of the soil bacterial communities and predicted functions. We only detected a minor and transitory effect on the bacterial abundance of the soil, the structure of the community and the potential functions, less related to the dose or the type of compost than to seasonal variations. Although the result suggests that the soil bacteria were highly resilient, promoting community stability and functional resilience after the addition of the two composts, more efforts are necessary to assess not only the resulting soil microbial community after organic fertilization but the intrinsic microbial community within the organic amendment that acts as an inoculum, and to what extent the changes in its dose could lead to the functionality of the soil.

Sign in / Sign up

Export Citation Format

Share Document