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 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.

Alleviating Continuous Monocropping Obstacle in Melon: Biological Elimination of Phenolic Acid

2020 ◽  
Author(s):  
Huiqin Xie ◽  
Yongli Ku ◽  
Xiangna Yang ◽  
Le Cao ◽  
Xueli Mei ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Phenolic Acids ◽  
Fruit Quality ◽  
High Performance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Continuous Cropping ◽  
Soil Microbial

Abstract Background: Melon (Cucumis melo L.) is one of the most important fruit crops grown in China. However, the yield and quality of melon have significantly declined under continuous cropping. Phenolic acids are believed to be associated with the continuous monocropping obstacle (CMO) and can influence plant microbe interactions. Coumaric acid (CA) is one of the major phenolic acids found in melon root exudates. The objectives of this study were to estimate the elimination of CA by the soil bacterium K3 as well as its effects on mitigating melon CMO. CA degradation was investigated by monitoring the CA retained in the growth medium using high performance liquid chromatography (HPLC). The effects of CA and K3 on rhizosphere soil microbial communities were investigated by the spread plate method and Illumina MiSeq sequencing. Furthermore, the effects of CA and K3 on melon seedling growth were measured under potted conditions. The changes in soil enzymes and fruit quality under K3 amendment were examined in a greenhouse experiment. Result:The results suggest that the addition of CA had the same result as the CMO, such as deterioration of the microbial community and slower growth of melon plants. HPLC and microbial analysis showed that K3 had a pronounced ability to decompose CA and could improve the soil microbial community environment. Soil inoculation with K3 agent could significantly improve the fruit quality of melon.Conclusion: Our results show that the effects of K3 in the soil are reflected by changes in populations and diversity of soil microbes and suggest that deterioration of microbial communities in soil might be associated with the growth constraint of melon in continuous monoculture systems.

scholarly journals Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Chengyuan Tao ◽  
Rong Li ◽  
Wu Xiong ◽  
Zongzhuan Shen ◽  
Shanshan Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Pathogens ◽  
Organic Fertilizer ◽  
Soil Microbial Communities ◽  
Plant Diseases ◽  
Disease Suppression ◽  
Organic Fertilizers ◽  
Soil Microbiome ◽  
Soil Microbial ◽  
Bioorganic Fertilizer

Abstract Background Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. Results To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. Conclusion Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.

scholarly journals Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Arunima Bhattacharjee ◽  
Dusan Velickovic ◽  
Thomas W. Wietsma ◽  
Sheryl L. Bell ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Soil Core ◽  
Soil Microbial ◽  
Functional Relationships ◽  
Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

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 Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

mBio ◽  
2011 ◽  
Vol 2 (4) ◽  
Author(s):  
Jizhong Zhou ◽  
Ye Deng ◽  
Feng Luo ◽  
Zhili He ◽  
Yunfeng Yang
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput ◽  
Network Topology ◽  
Ecosystem Functioning ◽  
Soil Microbial Communities ◽  
Microbial Populations ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Soil Microbial

ABSTRACT Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO2, is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO2 enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO2 levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. IMPORTANCE The interactions among different microbial populations in a community play critical roles in determining ecosystem functioning, but very little is known about the network interactions in a microbial community, owing to the lack of appropriate experimental data and computational analytic tools. High-throughput metagenomic technologies can rapidly produce a massive amount of data, but one of the greatest difficulties is deciding how to extract, analyze, synthesize, and transform such a vast amount of information into biological knowledge. This study provides a novel conceptual framework to identify microbial interactions and key populations based on high-throughput metagenomic sequencing data. This study is among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO2 level. The framework developed will allow microbiologists to address research questions which could not be approached previously, and hence, it could represent a new direction in microbial ecology research.

scholarly journals The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus

2020 ◽  
Author(s):  
Lanying Ma ◽  
Fernando Igne Rocha ◽  
Jaejin Lee ◽  
Jinlyung Choi ◽  
Mauricio Tejera ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
N Fertilizer ◽  
Soil Microbiome ◽  
Stand Age ◽  
Soil Microbial ◽  
Miscanthus Giganteus

Yield of the perennial grass Miscanthus × giganteus has shown an inconsistent and unpredictable response to nitrogen (N) fertilizer, yet fertilization underpins the crop’s environmental and economic sustainability. The interactions among soil microbial communities, N availability, and M. × giganteus and management may explain changes in plant productivity. In this study, soil samples from different stand ages of M. × giganteus in a replicated chronosequence field trial were used to investigate the effects of stand age and N fertilizer rates on microbial community structure. We hypothesized that there is a definable M. × giganteus soil microbiome and that this community varies significantly with stand age and fertilization. Our results showed that the main phyla in soil microbial communities, regardless of plant age, are similar but microbial community structures are significantly different. The variation in observed microbial communities generally decreases in older stand ages. The amount of N fertilizer applied also affected the microbial community structure associated with different aged M. × giganteus. Specifically, the relative abundance of Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Acidobacteria (Subgroup Gp1) increased shortly after fertilization and were more associated with younger M. × giganteus. Further, our results show a significant relationship between bacterial alpha diversity and fertilization rates and that this response is also impacted by stand age. Overall, our results emphasize linkages between microbial community structure, plant age, and fertilization in M. × giganteus.

Bio-Organic Fertilizers Manipulate Abundance Patterns of Rhizosphere Soil Microbial Community Structure To Improve Tomato Productivity

2021 ◽  
Author(s):  
Bintao Li ◽  
Luodi Guo ◽  
Haoming Wang ◽  
Yulong Li ◽  
Hangxian Lai ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Microbial Communities ◽  
Crop Yields ◽  
Organic Fertilizer ◽  
Soil Microbial Communities ◽  
Organic Fertilizers ◽  
Soil Microbiome ◽  
Growth Stages ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Abstract Background Bio-organic fertilizers has been shown to improve crop yields, partially because of the effects on the structure and function in resident soil microbiome. Purpose and methods Whereas, it is unknown if such improvements have been facilitated by the particular action of microbial inoculants, or the compost substrate. To understand the ecological mechanisms to increase crop productivity by bio-organic fertilizers, we conducted a pot experiment tracking soil physicochemical factors and extracellular enzyme activity over two growth stages and variations of soil microbial communities caused by fertilization practices as below: Bacillus subtilis CY1 inoculation, swine compost, and bio-organic fertilizer. Results Results showed that different fertilization measures, especially bio-organic fertilizers, increased soil nutrients, enzyme activity, and the diversity of microbial communities. For quantifying the “effect size” of microbiota manipulation, we discoverd that, respectively, 19.94% and 48.99% of variation in the bacterial and fungal communities could be interpreted using tested fertilization practices. Fertilization-sensitive microbes showed taxonomy diversity and gave responses as guilds of taxa to specific treatments. The microbes exhibited medium to high degree of co-occurrence in the network and could be recruited, directly or indirectly, by B. subtilis CY1, suggesting that bio-organic fertilizer may allow manipulation of influential community members.Conclusion Together we demonstrated that the increase in tomato productivity by bio-organic fertilizer was caused by the synergistic effect of organic fertilizer and beneficial microorganisms, thus providing novel insights into the soil microbiome manipulation strategies of biologically-enhanced organic fertilizers.

scholarly journals Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol

2019 ◽  
Vol 6 (1) ◽  
pp. 181054
Author(s):  
Zhenhua Yu ◽  
Jian Jin ◽  
Yansheng Li ◽  
Yue Yang ◽  
Yue Zhao ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Crop Productivity ◽  
Soya Bean ◽  
Soil Microbial ◽  
Topsoil Layer

Eroded black soils (classified as Mollisols) lead to a thinner topsoil layer, reduced organic carbon storage and declined crop productivity. Understanding the changes in soil microbial communities owing to soil erosion is of vital importance as soil microbial communities are sensitive indicators of soil condition and are essential in soil nutrient cycling. This study used the reconstructed facility with 10, 20 and 30 cm topsoil thickness under no-till soya bean–corn rotation in black soil region of Northeast China. Illumina MiSeq sequencing targeting 16S rRNA, q PCR and soil respiration measurement were performed to assess the changes in soya bean and corn rhizosphere bacterial communities, as well as their abundance and activities due to the topsoil thickness. The results showed that soil bacterial communities from both soya bean and corn were more sensitive to topsoil removal than to soil biogeochemical characteristics. Topsoil depths significantly influenced both soya bean and corn bacterial communities, while they only significantly influenced the bacterial abundance and respiration in corn. We also found that the topsoil depths significantly induced the changes in phyla and genera from both soya bean and corn rhizosphere bacterial community, which aid further understandings on how topsoil layer influences the global nutrient cycling of Mollisols by influencing the change in microbial communities.

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