scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

scholarly journals Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes

2021 ◽  
Author(s):  
Felipe Bastida ◽  
David J. Eldridge ◽  
Carlos García ◽  
G. Kenny Png ◽  
Richard D. Bardgett ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Soil Carbon ◽  
Soil Microbial Communities ◽  
Ecosystem Functions ◽  
Arid Environments ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil C ◽  
Soil Microbial ◽  
Biomass Ratio

AbstractThe relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity–biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.

scholarly journals Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning

2020 ◽  
Author(s):  
Cameron Wagg ◽  
Yann Hautier ◽  
Sarah Pellkofer ◽  
Samiran Banerjee ◽  
Bernhard Schmid ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Ecosystem Functioning ◽  
Temporal Dynamics ◽  
Temporal Stability ◽  
Soil Microbial Communities ◽  
Ecosystem Functions ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

AbstractTheoretical and empirical advances have revealed the importance of biodiversity for stabilizing ecosystem functions through time. Yet despite the global degradation of soils, how the loss of soil microbial diversity can de-stabilizes ecosystem functioning is unknown. Here we experimentally quantified the contribution diversity and the temporal dynamics in the composition of soil microbial communities to the temporal stability of four key ecosystem functions related to nutrient and carbon cycling. Soil microbial diversity loss reduced the temporal stability of all ecosystem functions and was particularly strong when over 50% of microbial taxa were lost. The stabilizing effect of soil biodiversity was linked to asynchrony among microbial taxa whereby different soil fungi and bacteria were associated with different ecosystem functions at different times. Our results emphasize the need to conserve soil biodiversity in order to ensure the reliable provisioning of multiple ecosystems functions that soils provide to society.

scholarly journals Impact of Soil Disinfestation on Fungal and Bacterial Communities in Soil With Cucumber Cultivation

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Wang ◽  
Yujie Jin ◽  
Ping Han ◽  
Jianjun Hao ◽  
Hongyu Pan ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Enzymatic Activities ◽  
Soil Treatment ◽  
Total Carbon ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
The Difference

Soil treatment with disinfectants has been used for controlling soilborne phytopathogens. Besides suppressing specific pathogens, how these disinfectants impact soil health, especially soil microbial communities, is yet to be systemically determined. The objectives of this study were to examine the effects of three representative disinfectants, including the dazomet fumigant, fenaminosulf fungicide, and kasugamycin antibiotic on chemical properties, enzymatic activities, and microbial communities in soil for cucumber cultivation. Results showed that 14 days after soil treatment with these chemicals, residual content of dazomet and kasugamycin quickly declined in soil and were undetectable, while fenaminosulf residues were found at 0.48 ± 0.01 mg/kg. Total nitrogen and total carbon increased in soil after dazomet treatment. Urease and sucrase activities were significantly restrained after disinfectant application. The disinfectants did not significantly change the taxon of predominant bacteria and fungi but altered the relative abundance and diversity of soil microbiome, as well as microbial interspecific relationships. Moreover, cucumber cultivation enhanced the overall soil microbial diversity and enzymatic activities, which diminished the difference of soil microbiome among four treatments. The difference in soil microbial diversity among the four treatments became smaller after planting cucumber. Thus, soil microbial communities were affected by soil disinfectants and gradually recovered by cucumber application.

scholarly journals Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Cameron Wagg ◽  
Yann Hautier ◽  
Sarah Pellkofer ◽  
Samiran Banerjee ◽  
Bernhard Schmid ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Ecosystem Functioning ◽  
Temporal Stability ◽  
Soil Microbial Communities ◽  
Ecosystem Functions ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial ◽  
Plant Soil ◽  
Soil Mesocosms

Theoretical and empirical advances have revealed the importance of biodiversity for stabilizing ecosystem functions through time. Despite the global degradation of soils, whether the loss of soil microbial diversity can destabilize ecosystem functioning is poorly understood. Here, we experimentally quantified the contribution of soil fungal and bacterial communities to the temporal stability of four key ecosystem functions related to biogeochemical cycling. Microbial diversity enhanced the temporal stability of all ecosystem functions and this pattern was particularly strong in plant-soil mesocosms with reduced microbial richness where over 50% of microbial taxa were lost. The stabilizing effect of soil biodiversity was linked to asynchrony among microbial taxa whereby different soil fungi and bacteria promoted different ecosystem functions at different times. Our results emphasize the need to conserve soil biodiversity for the provisioning of multiple ecosystem functions that soils provide to the society.

Soil microbial communities from olive cultivars are shaped by seasonality and geographical scales

2020 ◽  
Author(s):  
Manuel Anguita-Maeso ◽  
Juan C. Rivas ◽  
Guillermo León ◽  
Cristina Estudillo ◽  
Juan A. Navas-Cortés ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Agricultural Practices ◽  
Illumina Miseq ◽  
Plant Health ◽  
Soil Microbiome ◽  
Sequencing Data ◽  
Soil Biodiversity ◽  
Soil Microbial ◽  
Olive Varieties

<p>Soil biodiversity is essential to sustain healthy ecosystems supporting the maintenance of the environment and agricultural practices. Soils provide vital habitat for microorganisms which play determinant roles through organic matter transformation and nutrient cycling, which have a great impact in agriculture and food production and climate regulation. Understanding soil microbiome is becoming a relevant matter for supporting plant productivity and plant health. Unravelling the function and structure of microbial communities prevailing in soils is essential for a better understanding of plant development. However, the vast majority of soil microorganisms remain unknown and their variability at regional and temporal seasonal scale is still an unexplored field. In this study, soils associated to the rhizosphere of three olive varieties were sampled during autumn 2018 and spring 2019 in three olive orchards with differences in physicochemical soil characteristics and climate, located in the provinces of Jaén, Córdoba and Málaga, in Andalusia, Southern Spain. Bacterial and fungal populations were analysed using Illumina MiSeq platform to determine the structure and diversity of soil microbial communities and how those environmental factors may affect them. Sequencing data resulted in a total of 730 bacteria OTUs, distributed in 23 phyla and 312 genera while there were 553 fungal OTUs divided in 8 phyla and 280 genera. <em>Proteobacteria</em> was the most abundant bacterial phylum across olive orchard location (30.37%-5.52%) followed by <em>Actinobacteria</em> (10.72%-5.49%) and <em>Bacteroidetes</em> (7.73%-0.89%). There was circa 50% abundance reduction of these phyla on samples taken in autumn compared to that sampled in the spring. Unique bacterial genera differed according to field location in Jaén (72), Córdoba (45) and Málaga (48) while the shared bacteria genera among plots was 82. Fungi results showed <em>Ascomycota</em> (49.13%-3.13%) and <em>Basidiomycota</em> (25.64%-2.79%) as the two most abundant phyla in all olive orchards. A reduction on the abundance of <em>Ascomycota</em> was noticed on samples from autumn to spring (37.84% and 20.42%, respectively), while <em>Basidiomycota</em> displayed a distinct behavior (11.89% to 20.27%). Exclusive fungal genera varied from Jaén (50), Córdoba (7) and Málaga (14), whereas the core fungal genera among fields was 28. This information can contribute to generate new knowledge regarding temporal and spatial scale insights on soil microbiome associated to olive crop that may be considered to increase plant health and soil biodiversity.</p><p>Study supported by Projects 01LC1620 SOILMAN, XF-ACTORS 727987 (EU-H2020) and AGL2016-75606-R (MICINN Spain and FEDER-EU).</p>

scholarly journals Do Bioinoculants Affect Resident Microbial Communities? A Meta-Analysis

2021 ◽  
Vol 3 ◽  
Author(s):  
Calvin Cornell ◽  
Vasilis Kokkoris ◽  
Andrew Richards ◽  
Christina Horst ◽  
Daniel Rosa ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Meta Analysis ◽  
Soil Microbial Communities ◽  
Sustainable Land Use ◽  
Plant Performance ◽  
Soil Microbiome ◽  
Clear Understanding ◽  
Soil Microbial Diversity ◽  
Soil Microbial

There is a global industry built upon the production of “bioinoculants,” which include both bacteria and fungi. The recent increase in bioinoculant uptake by land users coincides with a drive for more sustainable land use practices. But are bioinoculants sustainable? These microbes are believed to improve plant performance, but knowledge of their effect on resident microbial communities is scant. Without a clear understanding of how they affect soil microbial communities (SMC), their utility is unclear. To assess how different inoculation practices may affect bioinoculant effects on SMC, we surveyed the existing literature. Our results show that bioinoculants significantly affect soil microbial diversity and that these effects are mediated by inoculant type, diversity, and disturbance regime. Further, these changes to soil microbes affect plant outcomes. Knowledge that these products may influence crop performance indirectly through changes to soil microbial diversity attests to the importance of considering the soil microbiome when assessing both bioinoculant efficacy and threats to soil ecosystems.

scholarly journals Soil microbial diversity in organic and non-organic pasture systems

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11184
Author(s):  
Mohan Acharya ◽  
Amanda J. Ashworth ◽  
Yichao Yang ◽  
Joan M. Burke ◽  
Jung Ae Lee ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Bacterial Species ◽  
Soil Microbiome ◽  
Organic Soils ◽  
Pasture Management ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Organic Systems ◽  
Microbiome Diversity

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

scholarly journals Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Shuo Jiao ◽  
Weimin Chen ◽  
Gehong Wei
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Chemical Contamination ◽  
Plant Interactions ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Microbial Responses ◽  
Legume Plants ◽  
Functional Profiles

ABSTRACT A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion. IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.

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 Erosion reduces soil microbial diversity, network complexity and multifunctionality

2021 ◽  
Author(s):  
Liping Qiu ◽  
Qian Zhang ◽  
Hansong Zhu ◽  
Peter B. Reich ◽  
Samiran Banerjee ◽  
...  
Keyword(s):  
Soil Erosion ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Negative Impact ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Relative Abundances ◽  
The Impact

AbstractWhile soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

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