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Chaudhary P, Bhattacharjee A, Khatri S, Dalal RC, Kopittke PM, Sharma S. Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms. Microbiol Res 2024; 289:127880. [PMID: 39236602 DOI: 10.1016/j.micres.2024.127880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 05/23/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024]
Abstract
Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.
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Affiliation(s)
- Priya Chaudhary
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shivani Khatri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ram C Dalal
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Peter M Kopittke
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Shilpi Sharma
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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Andrade L, Chique C, Hynds P, Weatherill J, O'Dwyer J. The antimicrobial resistance profiles of Escherichia coli and Pseudomonas aeruginosa isolated from private groundwater wells in the Republic of Ireland. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120817. [PMID: 36481470 DOI: 10.1016/j.envpol.2022.120817] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The role of the natural environment in the dissemination of antimicrobial resistant bacteria has been increasingly recognised in the literature. However, knowledge surrounding the critical factors and mechanisms mediating their occurrence is still limited, particularly in relatively 'pristine' groundwater environments. In the Republic of Ireland (RoI), a country characterised by high groundwater reliance, household-based (unregulated) wells provide drinking water to 11% of the population. These private wells are generally located in rural areas, where the risk of microbiological contamination is high due to intensive agricultural practices and high reliance on domestic wastewater treatment systems; both of which are also potential sources of antimicrobials and antimicrobial resistant bacteria. Accordingly, the current research sought to elucidate current rates of antimicrobial resistant bacteria and the principal factors associated with their presence in private wells in the RoI. A total of 250 samples (from 132 wells nationwide) were assessed for the presence of faecal (Escherichia coli) and environmental (Pseudomonas aeruginosa) bacteria, with single isolates from each contaminated sample tested phenotypically against 18 and 9 antimicrobials, respectively. Findings show that while 16.7% of E. coli (n = 8/48) were categorically resistant to ≥1 antimicrobial, with a further 79.2% classified as intermediately resistant, no categorical resistance was found among P. aeruginosa isolates (n = 0/6), with just one intermediately resistant isolate detected. Multivariate regression modelling indicates significantly higher odds of resistant E. coli detection in concurrence with elevated cattle density (OR = 1.028, p = 0.032), aligning with findings of highest resistance rates to veterinary antimicrobials (e.g., streptomycin = 14.6%, tetracycline = 12.5%, and ampicillin = 12.5%). Multivariate model results also suggest overland flow culminating in direct wellhead ingress as a primary ingress mechanism for resistant E. coli. Study findings may inform groundwater source protection initiatives and antimicrobial resistance surveillance moving forward.
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Affiliation(s)
- Luisa Andrade
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland.
| | - Carlos Chique
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland; UNEP GEMS/Water Capacity Development Centre, University College Cork, Cork, Ireland
| | - Paul Hynds
- Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Sustainability and Health Institute, Technological University Dublin, Dublin 7, Ireland
| | - John Weatherill
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jean O'Dwyer
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
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Zhu W, Lu X, Hong C, Hong L, Zhu F, Zhang S, Yao Y. Contributions of carbon source, crop cultivation, and chemical property on microbial community assemblage in soil subjected to reductive disinfestation. Front Microbiol 2023; 14:1146207. [PMID: 37032903 PMCID: PMC10081160 DOI: 10.3389/fmicb.2023.1146207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
In agricultural practice, reductive soil disinfestation (RSD) is an effective method for eliminating soil-borne pathogens that depends heavily on carbon source. However, knowledge regarding the assembly of soil microbial communities in RDS-treated soils amended with different carbon sources after continuous crop cultivation is still not well-characterized. RSD treatments were performed on greenhouse soil with six different carbon sources (ethanol, glucose, alfalfa, wheat bran, rice bran, and sugarcane residue), which have different C:N ratios (Org C/N) and easily oxidized carbon contents (Org EOC). After RSD, two consecutive seasons of pepper pot experiments were conducted. Then, the effects of carbon source property, crop cultivation, and soil chemical property on soil microbial community reestablishment, pathogen reproduction, and crop performance were investigated in the RSD-cropping system. Variation partition analysis indicated that carbon source property, crop cultivation, and soil chemical property explained 66.2 and 39.0% of bacterial and fungal community variation, respectively. Specifically, Mantel tests showed that Org C/N, crop cultivation, soil available phosphorus and potassium were the most important factors shaping bacterial community composition, while Org C/N, Org EOC, and crop cultivation were the most important factors shaping fungal community composition. After two planting seasons, the number of cultivable Fusarium was positively correlated with Org EOC, and negatively correlated with soil total organic carbon, Fungal Chao1, and Fungal PC1. Crop yield of complex-carbon soils (Al, Wh, Ri and Su) was negatively affected by Org C/N after the first season, and it was highest in Al, and lower in Et and Su after the second season. Overall, Org EOC and Org C/N of carbon source were vitally important for soil microbe reestablishment, Fusarium reproduction and crop performance. Our findings further broaden the important role of carbon source in the RSD-cropping system, and provide a theoretical basis for organic carbon selection in RSD practice.
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Affiliation(s)
- Weijing Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaolin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chunlai Hong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Leidong Hong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fengxiang Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shuo Zhang
- Ningbo Agricultural and Rural Green Development Center, Ningbo, China
| | - Yanlai Yao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Yanlai Yao,
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Wang Y, He Y, Ding M, Wang Z, Zhou S. Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest. Curr Microbiol 2022; 79:368. [PMID: 36253615 DOI: 10.1007/s00284-022-03049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022]
Abstract
Understanding plant-microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.
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Affiliation(s)
- Yukun Wang
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Yuran He
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Mao Ding
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Zhi Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, Nanjing, 210042, China
| | - Shoubiao Zhou
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China.
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, 241002, China.
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Caradus JR, Goldson SL, Moot DJ, Rowarth JS, Stewart AV. Pastoral agriculture, a significant driver of New Zealand's economy, based on an introduced grassland ecology and technological advances. J R Soc N Z 2021; 53:259-303. [PMID: 39439484 PMCID: PMC11459793 DOI: 10.1080/03036758.2021.2008985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/17/2021] [Indexed: 12/21/2022]
Abstract
The New Zealand economy is export-driven and heavily reliant on the productivity of the pastoral sector. The transformation of native forest and tussock grassland ecologies to temperate grasslands occurred rapidly with the arrival of Europeans. However, this transplanted ecology required the development and use of plant, microbial, animal and management technologies for successful grassland farming. These have enabled New Zealand pastoral agriculture to compete effectively in international markets, without subsidies. The extensive list of plant-based and associated microbial-based adaptations, and the management strategies that have enabled the development of highly productive grasslands are described and reviewed. Credible science is required to inform the debate on the environmental impacts of pasture production to avoid misinformation proliferating. This needs transparent and objective integrity from the science community using funding that seeks no defined or preconceived outcomes. Critically, much of the success of New Zealand pastoral farming has been due to the willingness and ability of farmers to use, adapt, adopt and integrate new ideas and technologies into their farming systems. Historic, current and future challenges, and threats that impact on the productivity and sustainability of pastoral agriculture are described and the means to achieve further technology development to manage these is discussed.
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Affiliation(s)
| | | | - Derrick J. Moot
- Faculty of Agriculture and Life Science, Lincoln University, Canterbury, New Zealand
| | - Jacqueline S. Rowarth
- Faculty of Agriculture and Life Science, Lincoln University, Canterbury, New Zealand
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6
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Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production. Curr Microbiol 2021; 78:1069-1085. [PMID: 33611628 DOI: 10.1007/s00284-021-02375-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/05/2021] [Indexed: 01/29/2023]
Abstract
Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.
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7
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Dong Z, Guo Y, Yu C, Zhixian Z, Rongli M, Deng W, Li Y, Hu X. The dynamics in rhizosphere microbial communities under bacterial wilt resistance by mulberry genotypes. Arch Microbiol 2020; 203:1107-1121. [PMID: 33165874 DOI: 10.1007/s00203-020-02098-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
The contribution of crops and soil microbial community structure and functional diversity in soil-borne diseases control mulberry plant production is still inadequately understood. In this work, a comparative study was undertaken on the microbial abundance, community structure, and functional diversity in the soil rhizosphere between the resistant (Kangqing 10) and the susceptible (Guisang 12) mulberry genotypes. The study deployed the use of dilution plate method, micro-ecology technology, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques. The study aimed at developing better crop management methods for mulberry cultivation as well as preventing and controlling the occurrence and impacts of bacterial wilt on mulberry productivity. The results indicated that the soil rhizosphere microorganisms were more abundant in the normal resistant mulberry genotype than in the normal susceptible mulberry genotype. Carbon source utilization was better in the normal susceptible mulberry genotype. These properties were lower in the sickly resistant mulberry genotype than in the susceptible sickly mulberry genotype. Through the PCR-DGGE, it was shown that the bacterial and fungal community structures of the resistant genotypes were more stable than those of the susceptible genotypes. Through correlation regression analysis, it was shown that the mulberry bacterial wilt significantly contributes to the loss of soil nutrients, particularly organic matter and nitrogen, a possible cause to disrupted balance between the soil microbial community and the loss of soil organic matter. Resistant genotype plants displayed more resistance to bacterial wilt. Therefore, this study recommends the need to promote the cultivation of resistant genotype mulberry for increased yield.
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Affiliation(s)
- Zhaoxia Dong
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Yao Guo
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Cui Yu
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Zhu Zhixian
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Mo Rongli
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wen Deng
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Yong Li
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Xingming Hu
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
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8
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Palojärvi A, Kellock M, Parikka P, Jauhiainen L, Alakukku L. Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate. Front Microbiol 2020; 11:534786. [PMID: 33193124 PMCID: PMC7644446 DOI: 10.3389/fmicb.2020.534786] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/05/2020] [Indexed: 01/28/2023] Open
Abstract
The soil-borne plant pathogens cause serious yield losses and are difficult to control. In suppressive soils, disease incidence remains low regardless of the presence of the pathogen, the host plant, and favorable environmental conditions. The potential to improve natural soil disease suppressiveness through agricultural management practices would enable sustainable and resilient crop production systems. Our aim was to study the impact of autumn tillage methods and crop sequence on the soil carbon status, fungistasis and yield in boreal climate. The disease suppression was improved by the long-term reduced and no tillage management practices with and without crop rotation. Compared to the conventional plowing, the non-inversion tillage systems were shown to change the vertical distribution of soil carbon fractions and the amount of microbial biomass by concentrating them on the soil surface. Crop sequence and the choice of tillage method had a combined effect on soil organic carbon (SOC) sequestration. The improved general disease suppression had a positive correlation with the labile carbon status and microbial biomass. From the most common Fusarium species, the predominantly saprophytic F. avenaceum was more abundant under non-inversion practice, whereas the opposite was true for the pathogenic ones. Our findings furthermore demonstrated the correlation of the soil fungistasis laboratory assay results and the prevalence of the pathogenic test fungus Fusarium culmorum on the crop cereals in the field. Our results indicate that optimized management strategies have potential to improve microbial related soil fungistasis in boreal climate.
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Affiliation(s)
- Ansa Palojärvi
- Natural Resources Institute Finland (Luke), Turku, Finland
| | - Miriam Kellock
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Päivi Parikka
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | - Laura Alakukku
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Hermans SM, Buckley HL, Case BS, Curran-Cournane F, Taylor M, Lear G. Using soil bacterial communities to predict physico-chemical variables and soil quality. MICROBIOME 2020; 8:79. [PMID: 32487269 PMCID: PMC7268603 DOI: 10.1186/s40168-020-00858-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial community composition of over 3000 soil samples from 606 sites in New Zealand. Sites were classified as indigenous forests, exotic forest plantations, horticulture, or pastoral grasslands; soil physico-chemical variables related to soil quality were also collected. The composition of soil bacterial communities was then used to predict the land use and soil physico-chemical variables of each site. RESULTS Soil bacterial community composition was strongly linked to land use, to the extent where it could correctly determine the type of land use with 85% accuracy. Despite the inherent variation introduced by sampling across ~ 1300 km distance gradient, the bacterial communities could also be used to differentiate sites grouped by key physico-chemical properties with up to 83% accuracy. Further, individual soil variables such as soil pH, nutrient concentrations and bulk density could be predicted; the correlations between predicted and true values ranged from weak (R2 value = 0.35) to strong (R2 value = 0.79). These predictions were accurate enough to allow bacterial communities to assign the correct soil quality scores with 50-95% accuracy. CONCLUSIONS The inclusion of biological information when monitoring soil quality is crucial if we wish to gain a better, more accurate understanding of how land management impacts the soil ecosystem. We have shown that soil bacterial communities can provide biologically relevant insights on the impacts of land use on soil ecosystems. Furthermore, their ability to indicate changes in individual soil parameters shows that analysing bacterial DNA data can be used to screen soil quality. Video Abstract.
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Affiliation(s)
- Syrie M Hermans
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 46 Wakefield St, Auckland, 1010, New Zealand
| | - Bradley S Case
- School of Science, Auckland University of Technology, 46 Wakefield St, Auckland, 1010, New Zealand
| | - Fiona Curran-Cournane
- Ministry for the Environment - Manatū Mō Te Taiao, 45 Queen Street, Auckland, 1010, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 401 Grey Street, Hamilton, 3216, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand.
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10
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Abstract
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. 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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11
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Attwood GT, Wakelin SA, Leahy SC, Rowe S, Clarke S, Chapman DF, Muirhead R, Jacobs JME. Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture. Front Nutr 2019; 6:107. [PMID: 31380386 PMCID: PMC6646666 DOI: 10.3389/fnut.2019.00107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles. Here, we summarize the microbiome research that has been done in each of these three environments (soils, forage plants, animals' rumen) and investigate what additional benefits may be possible through understanding the interactions between the various microbiomes. The challenge for future research is to enhance microbiome function by appropriate matching of plant and animal genotypes with the environment to improve the output and environmental sustainability of pastoral agriculture.
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Affiliation(s)
| | | | | | - Suzanne Rowe
- Animal Science, AgResearch, Invermay, New Zealand
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12
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Song GC, Im H, Jung J, Lee S, Jung M, Rhee S, Ryu C. Plant growth‐promoting archaea trigger induced systemic resistance inArabidopsis thalianaagainstPectobacterium carotovorumandPseudomonas syringae. Environ Microbiol 2019; 21:940-948. [DOI: 10.1111/1462-2920.14486] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 11/11/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Geun Cheol Song
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
| | - Hyunjoo Im
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
- Biosystems and Bioengineering ProgramUniversity of Science and Technology Daejeon 34113 South Korea
| | - Jihye Jung
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 South Korea
| | - Soohyun Lee
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
| | - Man‐Young Jung
- Department of MicrobiologyChungbuk National University Cheongju 28644 South Korea
| | - Sung‐Keun Rhee
- Department of MicrobiologyChungbuk National University Cheongju 28644 South Korea
| | - Choong‐Min Ryu
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
- Biosystems and Bioengineering ProgramUniversity of Science and Technology Daejeon 34113 South Korea
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