Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm (Elaeis guineensis) via High-Throughput Sequencing

Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.

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

Microbiome ◽

10.1186/s40168-020-00892-z ◽

2020 ◽

Vol 8 (1) ◽

Cited By ~ 2

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.

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

10.21203/rs.3.rs-18216/v1 ◽

2020 ◽

Author(s):

Chengyuan Tao ◽

Rong Li ◽

Wu Xiong ◽

Zongzhuan Shen ◽

Shanshan Liu ◽

...

Keyword(s):

Microbial Communities ◽

Organic Fertilizer ◽

Soil Microbial Communities ◽

Plant Diseases ◽

Disease Suppression ◽

Organic Fertilizers ◽

Soil Microbiome ◽

Pseudomonas Spp ◽

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. We further observed that disease suppression in these treatments could be linked to impacts on the resident soil microbial communities, with noted increases in specific Pseudomonas spp.. The link between Bacillus amendment and indigenous Pseudomonas spp. was further examined using pot experiments and biofilm assays. 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.

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Changes in Bacterial and Fungal Community of Soil under Treatment of Pesticides

Agronomy ◽

10.3390/agronomy12010124 ◽

2022 ◽

Vol 12 (1) ◽

pp. 124

Author(s):

Rostislav Streletskii ◽

Angelika Astaykina ◽

George Krasnov ◽

Victor Gorbatov

Keyword(s):

Fungal Community ◽

Large Scale ◽

High Throughput Sequencing ◽

Soil Microbial Communities ◽

Illumina Miseq ◽

Soil Microbiome ◽

Soil Microbial ◽

Large Scale Assessment ◽

Integral Methods ◽

State Registration

Experiments were carried out in soil microcosms with the treatment of pesticide formulations—imidacloprid, benomyl, and metribuzin in single and tenfold application rates. For additional stimulation of microorganisms, a starch–mineral mixture was added to some variants. For all samples, high-throughput sequencing on the Illumina MiSeq platform of the V4 (16S rRNA) and ITS1 (18S rRNA) fragments was carried out. As a result, it was possible to establish the characteristic changes in the structure of the soil fungal and bacterial communities under pesticides application. The application of pesticides was accompanied by dramatic shifts in alfa-diversity of the fungal community. The phylum Basidiomycota was likely to be involved in the degradation of pesticides. The changes in the relative abundance of the genera Terrabacter, Kitasatospora, Streptomyces, Sphingomonas, Apiotrichum, Solicoccozyma, Gamsia, and Humicola can be proposed as an indicator of pesticide contamination. It is suggested to use these markers for large-scale assessment of the effect of pesticides on soil microbial communities instead of classical integral methods, including within the framework of state registration of pesticides. It is also recommended to research the effect of pesticides on the soil microbiome during artificially initiated successions using the additional source of carbon.

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

10.21203/rs.3.rs-18216/v2 ◽

2020 ◽

Author(s):

Chengyuan Tao ◽

Rong Li ◽

Wu Xiong ◽

Zongzhuan Shen ◽

Shanshan Liu ◽

...

Keyword(s):

Microbial Communities ◽

Organic Fertilizer ◽

Soil Microbial Communities ◽

Plant Diseases ◽

Disease Suppression ◽

Organic Fertilizers ◽

Soil Microbiome ◽

Pseudomonas Spp ◽

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.

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Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation

Applied and Environmental Microbiology ◽

10.1128/aem.02992-18 ◽

2019 ◽

Vol 85 (7) ◽

Cited By ~ 6

Author(s):

Liangliang Liu ◽

Xinqi Huang ◽

Jun Zhao ◽

Jinbo Zhang ◽

Zucong Cai

Keyword(s):

Disease Incidence ◽

Critical Role ◽

Soil Microbial Communities ◽

Disease Suppression ◽

Soil Environment ◽

Soilborne Diseases ◽

Abiotic Environment ◽

Soil Disinfestation ◽

Soil Microbial ◽

Microbial Agents

ABSTRACTMany agricultural soil management strategies have been shown to be effective in preventing soilborne diseases. However, their underlying mechanisms of action remain unknown. In this study, we used reductive soil disinfestation (RSD), also named anaerobic soil disinfestation (ASD) and biological soil disinfestation (BSD), as a representative method for disease management and cucumber damping-off diseased soil as a model system to identify the disease-suppressive agents in artificially managed soil. The results showed that RSD created a soil environment that was different from that of the diseased soil, where the pH level and the carbon content were greater. Heat treatment and pathogen or soil microbiota self- and cross-reinoculations resulted in the expansion of various soil microbial communities harbored by the two soil environments, as well as various disease incidences. Environmental factors were the primary determinant of the reassembled bacterial community, followed by initial microbiota, whereas initial microbiota was the key driver of the reassembled fungal community. The relative abundances of the bacterial orderSphingobacterialesand fungal order Sordariales, as well as their affiliated generaSphingobacterium, unclassified genus withinSphingobacteriaceae,Zopfiella, and unclassified genera within Lasiosphaeriaceae and Chaetomiaceae, were negatively correlated with disease incidence and positively associated with RSD-conditioned soil environment. Furthermore, we validated that both the microbial disease-suppressive agent and its adapted abiotic environment contributed to disease suppression. Our results elucidate the abiotic and biotic foundations of soilborne disease suppression under artificial management and highlight that the abiotic environment is as important as the microbial agents in disease suppression.IMPORTANCEMost defined systems have identified microbial elements as the primary factors determining disease suppression, but the involvement of the soil abiotic environment is less defined. The significance of this work is that the soil abiotic environment plays a critical role in the establishment of the soil microbial community and key microbial agents that directly contribute to the prevention of soilborne diseases. We highlight the importance of the soil abiotic environment in disease suppression. Furthermore, we provide a framework for the characterization of disease-suppressing agents in artificially managed soil. These results will gradually close the gap in knowledge on soil environment-microbe interactions.

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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

Microorganisms ◽

10.3390/microorganisms9071400 ◽

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.

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EFFECT OF MICRONUTRIENTS-ENRICHED FERTILIZERS ON BASAL STEM ROT DISEASE INCIDENCE AND SEVERITY ON OIL PALM (ELAEIS GUINEENSIS JACQ.) SEEDLINGS

American Journal of Applied Sciences ◽

10.3844/ajassp.2014.1841.1859 ◽

2014 ◽

Vol 11 (10) ◽

pp. 1841-1859 ◽

Cited By ~ 6

Author(s):

Fabien Fonguimgo Tengoua ◽

Mohamed M. Hanafi ◽

A. S. Idris ◽

Kadir Jugah ◽

Jamaludin Nurul Mayziatul Azwa ◽

...

Keyword(s):

Oil Palm ◽

Elaeis Guineensis ◽

Disease Incidence ◽

Stem Rot ◽

Basal Stem Rot ◽

Rot Disease

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Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0025 ◽

2020 ◽

Author(s):

Jane Oja ◽

Sakeenah Adenan ◽

Abdel-Fattah Talaat ◽

Juha Alatalo

Keyword(s):

Microbial Communities ◽

High Throughput ◽

Mycorrhizal Fungi ◽

High Throughput Sequencing ◽

Soil Microbial Communities ◽

Arbuscular Mycorrhizal ◽

Soil Microbial ◽

Fungal Abundance ◽

Novel Approach ◽

Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

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Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽

10.1128/msystems.00645-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.02523-18 ◽

2019 ◽

Vol 85 (6) ◽

Cited By ~ 5

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.

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