Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness

Dignam, Bryony E.A.; O’Callaghan, Maureen; Condron, Leo M.; Raaijmakers, Jos M.; Kowalchuk, George A.; Wakelin, Steve

doi:10.1016/j.soilbio.2019.05.020

Cited by 30 publications

(18 citation statements)

References 68 publications

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“…Labile organic carbon also had an indirect positive effect on biodiversity conservation through its stimulation of the active part of the microbial community (i.e., soil respiration), and on disease regulation/suppression through its stimulation of the competitive ability of the microbial community (viz., microbial biomass carbon and MSIR) against the pathogen. This latter finding is consistent with Dignam et al [103] who found that higher carbon availability selected for a richer and more competitive and suppressive community controlling Rhizoctonia solani. Likewise, Bastida et al [104] demonstrated the key position of labile carbon measured as DOC in the multifunctionality of soil microbial communities.…”

Section: Linking Soil Quality Indicators With Ecosystem Processes Andsupporting

confidence: 91%

Novel soil quality indicators for the evaluation of agricultural management practices: a biological perspective

Bongiorno¹

2020

Front. Agr. Sci. Eng.

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Developments in soil biology and in methods to characterize soil organic carbon can potentially deliver novel soil quality indicators that can help identify management practices able to sustain soil productivity and environmental resilience. This work aimed at synthesizing results regarding the suitability of a range of soil biological and biochemical properties as novel soil quality indicators for agricultural management. The soil properties, selected through a published literature review, comprised different labile organic carbon fractions [hydrophilic dissolved organic carbon, dissolved organic carbon, permanganate oxidizable carbon (POXC), hot water extractable carbon and particulate organic matter carbon], soil disease suppressiveness measured using a Pythium-Lepidium bioassay, nematode communities characterized by amplicon sequencing and qPCR, and microbial community level physiological profiling measured with MicroResp TM. Prior studies tested the sensitivity of each of the novel indicators to tillage and organic matter addition in ten European long-term field experiments (LTEs) and assessed their relationships with pre-existing soil quality indicators of soil functioning. Here, the results of these previous studies are brought together and interpreted relative to each other and to the broader body of literature on soil quality assessment. Reduced tillage increased carbon availability, disease suppressiveness, nematode richness and diversity, the stability and maturity of the food web, and microbial activity and functional diversity. Organic matter addition played a weaker role in enhancing soil quality, possibly due to the range of composition of the organic matter inputs used in the LTEs. POXC was the indicator that discriminated best between soil management practices, followed by nematode indices based on functional characteristics. Structural equation modeling shows that POXC has a central role in nutrient retention/supply, carbon sequestration, biodiversity conservation, erosion control and disease regulation/suppression. The novel indicators proposed here have great potential to improve existing soil quality assessment schemes. Their feasibility of application is discussed and needs for future research are outlined.

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Section: Linking Soil Quality Indicators With Ecosystem Processes Andsupporting

confidence: 91%

Novel soil quality indicators for the evaluation of agricultural management practices: a biological perspective

Bongiorno¹

2020

Front. Agr. Sci. Eng.

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“…Phylogenetically diverse soil microorganisms have been associated with plant disease suppression (Raaijmakers and Mazzola, 2012; Dignam et al ., 2019). Among these organisms, Pseudomonas spp.…”

Section: Discussionmentioning

confidence: 99%

“…It is notable that compared with the other soils in this study, Boteva soil is characterized by higher amounts of organic carbon. Although plant residue management was shown to significantly influence the community structure of Pseudomonas genus between treatments, 80% of observed differences in Pseudomonas community structure was attributed to changes in soil organic matter (Dignam et al ., 2019). Increased Pseudomonas diversity as evidenced by the Shannon index, in addition to microbial activity, soil organic matter and availability of carbon, distinguished low disease (suppressive) soils from high disease (conducive soils) (Dignam et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Eleven structurally diverse CLPs were associated with the cocoyam rhizosphere at Boteva. to microbial activity, soil organic matter and availability of carbon, distinguished low disease (suppressive) soils from high disease (conducive soils) (Dignam et al, 2019). It should be noted that in the volcanic soils of Cameroon, soil suppressiveness is lost if cocoyam is cultivated continuously for a period of more than 5 years (Adiobo et al, 2007) as exemplified by Ekona and Maumu soils.…”

Section: Nature Of Disease Suppression In Boteva Soil-microbial Compementioning

confidence: 99%

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Cyclic lipopeptide‐producing Pseudomonas koreensis group strains dominate the cocoyam rhizosphere of a Pythium root rot suppressive soil contrasting with P. putida prominence in conducive soils

Oni

Geudens

Onyeka

et al. 2020

Environmental Microbiology

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Pseudomonas isolates from tropical environments have been underexplored and may form an untapped reservoir of interesting secondary metabolites. In this study, we compared Pseudomonas and cyclic lipopeptide (CLP) diversity in the rhizosphere of a cocoyam root rot disease (CRRD) suppressive soil in Boteva, Cameroon with those from four conducive soils in Cameroon and Nigeria. Compared with other soils, Boteva andosols were characterized by high silt, organic matter, nitrogen and calcium. Besides, the cocoyam rhizosphere at Boteva was characterized by strains belonging mainly to the P. koreensis and P. putida (sub)groups, with representations in the P. fluorescens, P. chlororaphis, P. jessenii and P. asplenii (sub)groups. In contrast, P. putida isolates were prominent in conducive soils. Regarding CLP diversity, Boteva was characterized by strains producing 11 different CLP types with cocoyamide A producers, belonging to the P. koreensis group, being the most abundant. However, putisolvin III-V producers were the most dominant in the rhizosphere of conducive soils in both Cameroon and Nigeria. Furthermore, we elucidated the chemical structure of putisolvin derivatives-putisolvin III-V, and described its biosynthetic gene cluster. We show that high Pseudomonas and metabolic diversity may be driven by microbial competition, which likely contributes to soil suppressiveness to CRRD.

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“…These authors have evaluated the maximum benefit for plant productivity and disease suppression against P. aphanidermatum damping-off in a cucumber cropping system. Other authors have focused their interest on the impact of manipulated rhizospheres in an organic farming system by long-term supplementation of plant residues in combination with BCAs [65]. They provided new insights on the beneficial effects regarding the SOM oxysporum-infested soil and watermelon-waste-amended soil to assess the potential role of the new microbiome in plant health and Fusarium wilt suppression in a watermelon cropping system [158].…”

Section: Soil Microbiota Disturbance For Increasing Soil Disease Suppmentioning

confidence: 99%

Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies

Corato

2020

Chem. Biol. Technol. Agric.

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Soil microbiota plays a key role in suppressing soil-borne plant pathogens improving the natural soil suppressiveness. Microbiome disturbance triggers specific perturbation to change and shape the soil microbial communities’ network for increasing suppression against phytopathogens and related diseases. Very important goals have been reached in manipulation of soil microbiota through agronomical practices based on soil pre-fumigation, organic amendment, crop rotation and intercropping. Nevertheless, to limit inconsistencies, drawbacks and failures related to soil microbiota disturbance, a detailed understanding of the microbiome shifts during its manipulation is needed under the light of the microbiome-assisted strategies. Next-generation sequencing often offers a better overview of the soil microbial communities during microbiomes manipulation, but sometime it does not provide information related to the highest taxonomic resolution of the soil microbial communities. This review work reports and discusses the most reliable findings in relation to a comprehensive understanding of soil microbiota and how its manipulation can improve suppression against soil-borne diseases in organic farming systems. Role and functionality of the soil microbiota in suppressing soil-borne pathogens affecting crops have been basically described in the first section of the paper. Characterization of the soil microbiomes network by high-throughput sequencing has been introduced in the second section. Some relevant findings by which soil microbiota manipulation can address the design of novel sustainable cropping systems to sustain crops’ health without use (or reduced use) of synthetic fungicides and fumigants have been extensively presented and discussed in the third and fourth sections, respectively, under the light of the new microbiome-assisted strategies. Critical comparisons on the next-generation sequencing have been provided in the fifth section. Concluding remarks have been drawn in the last section.

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Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness

Cited by 30 publications

References 68 publications

Novel soil quality indicators for the evaluation of agricultural management practices: a biological perspective

Novel soil quality indicators for the evaluation of agricultural management practices: a biological perspective

Cyclic lipopeptide‐producing Pseudomonas koreensis group strains dominate the cocoyam rhizosphere of a Pythium root rot suppressive soil contrasting with P. putida prominence in conducive soils

Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies

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