https://web.science.uu.nl/pmi/publications/PDF/2012/TiPS-Berendsen-2012.pdf

The rhizosphere microbiome and plant health

The loss of organic material from the roots provides the energy for the development of active microbial populations in the rhizosphere around the root. Generally, saproptrophs or biotrophs such as mycorrhizal fungi grow in the rhizosphere in response to this carbon loss, but plant pathogens may also develop and infect a susceptible host, resulting in disease. This review examines the microbial interactions that can take place in the rhizosphere and that are involved in biological disease control. The interactions of bacteria used as biocontrol agents of bacterial and fungal plant pathogens, and fungi used as biocontrol agents of protozoan, bacterial and fungal plant pathogens are considered. Whenever possible, modes of action involved in each type of interaction are assessed with particular emphasis on antibiosis, competition, parasitism, and induced resistance. The significance of plant growth promotion and rhizosphere competence in biocontrol is also considered. Multiple microbial interactions involving bacteria and fungi in the rhizosphere are shown to provide enhanced biocontrol in many cases in comparison with biocontrol agents used singly. The extreme complexity of interactions that can occur in the rhizosphere is highlighted and some potential areas for future research in this area are discussed briefly.

/pdf/microbial-interactions-and-biocontrol-in-the-rhizosphere-1erj9kqzek.pdf

Microbial interactions and biocontrol in the rhizosphere

In addition to their well-recognized roles in plant nutrition and communities, mycorrhizas can influence the key ecosystem process of soil aggregation. Here we review the contribution of mycorrhizas, mostly focused on arbuscular mycorrhizal fungi (AMF), to soil structure at various hierarchical levels: plant community; individual root; and the soil mycelium. There are a suite of mechanisms by which mycorrhizal fungi can influence soil aggregation at each of these various scales. By extension of these mechanisms to the question of fungal diversity, it is recognized that different species or communities of fungi can promote soil aggregation to different degrees. We argue that soil aggregation should be included in a more complete 'multifunctional' perspective of mycorrhizal ecology, and that in-depth understanding of mycorrhizas/soil process relationships will require analyses emphasizing feedbacks between soil structure and mycorrhizas, rather than a uni-directional approach simply addressing mycorrhizal effects on soils. We finish the discussion by highlighting new tools, developments and foci that will probably be crucial in further understanding mycorrhizal contributions to soil structure.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2006.01750.x

Mycorrhizas and soil structure

The loss of organic and inorganic carbon from roots into soil underpins nearly all the major changes that occur in the rhizosphere. In this review we explore the mechanistic basis of organic carbon and nitrogen flow in the rhizosphere. It is clear that C and N flow in the rhizosphere is extremely complex, being highly plant and environment dependent and varying both spatially and temporally along the root. Consequently, the amount and type of rhizodeposits (e.g. exudates, border cells, mucilage) remains highly context specific. This has severely limited our capacity to quantify and model the amount of rhizodeposition in ecosystem processes such as C sequestration and nutrient acquisition. It is now evident that C and N flow at the soil–root interface is bidirectional with C and N being lost from roots and taken up from the soil simultaneously. Here we present four alternative hypotheses to explain why high and low molecular weight organic compounds are actively cycled in the rhizosphere. These include: (1) indirect, fortuitous root exudate recapture as part of the root’s C and N distribution network, (2) direct re-uptake to enhance the plant’s C efficiency and to reduce rhizosphere microbial growth and pathogen attack, (3) direct uptake to recapture organic nutrients released from soil organic matter, and (4) for inter-root and root–microbial signal exchange. Due to severe flaws in the interpretation of commonly used isotopic labelling techniques, there is still great uncertainty surrounding the importance of these individual fluxes in the rhizosphere. Due to the importance of rhizodeposition in regulating ecosystem functioning, it is critical that future research focuses on resolving the quantitative importance of the different C and N fluxes operating in the rhizosphere and the ways in which these vary spatially and temporally.

Carbon flow in the rhizosphere: carbon trading at the soil–root interface

The loss of carbon from roots (rhizodeposition) and the consequent proliferation of microorganisms in the surrounding soil, coupled with the physical presence of a root and processes associated with nutrient uptake, gives rise to a unique zone of soil called the rhizosphere. In this review, we bring together evidence to show that roots can directly regulate most aspects of rhizosphere C flow either by regulating the exudation process itself or by directly regulating the recapture of exudates from soil. Root exudates have been hypothesized to be involved in the enhanced mobilization and acquisition of many nutrients from soil or the external detoxification of metals. With few exceptions, there is little mechanistic evidence from soil-based systems to support these propositions. We conclude that much more integrated work in realistic systems is required to quantify the functional significance of these processes in the field. We need to further unravel the complexities of the rhizosphere in order to fully engage with key scientific ideas such as the development of sustainable agricultural systems and the response of ecosystems to climate change. Contents I. Introduction 460 II. What is rhizodeposition? 460 III. Regulation of rhizodeposition 460 IV. How large is the root exudation C flux? 463 V. How responsive is the root exudation C flux? 463 VI. How responsive is the microbial community to root exudation? 464 VII. The role of root exudates in nutrient acquisition 464 VIII. Mycorrhizal fungi and rhizodeposition 471 IX. Future thoughts 474 Acknowledgements 474 References 474.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2004.01130.x

Plant and mycorrhizal regulation of rhizodeposition

Arbuscular mycorrhizal (AM) fungi can reduce the incidence and importance of plant root diseases caused by pathogens. The mechanisms involved are not well characterized. We used an in vitro experimental system to test the hypothesis that the extraradical mycelium of AM fungi can interfere directly with microorganisms in the mycosphere and directly or indirectly reduce the population of plant pathogens. This system permitted the isolation of soluble substances released by the extraradical mycelium of Glomus intraradices. The AM fungus was grown on Daucus carota transformed roots in one compartment, while only the extraradical mycelium was allowed to grow in a second compartment. A freezing and centrifugation technique was developed for the extraction and concentration of substances present in the compartment containing only the AM fungal mycelium. Four soil-inhabiting microorganisms were selected, and conidial germination (fungi) or growth (bacteria) of these was studied in the presence and absence (control) of the extract. In comparison with the control, the results indicated that both the growth of Pseudomonas chlororaphis and the conidial germination of Trichoderma harzianum were stimulated in the presence of the AM fungal extract. In contrast, conidial germination of Fusarium oxysporum f. sp. chrysanthemi was reduced while the growth of Clavibacter michiganensis subsp. michiganensis was not affected. The measured effects in general were directly correlated with extract concentration. Differences in pH were noted between the extract containing substances released by the AM fungus and the non-AM control, but no significant influence of the pH on growth or conidial germination was noted, confirming that substances released by the AM fungus in the growth medium is the main factor explaining differential growth of the microorganisms tested. The results suggest that direct interactions exist between AM fungi and soil microorganisms, which might lead to changes in microbial equilibrium detrimental to pathogens.

Direct interaction between the arbuscular mycorrhizal fungus Glomus intraradices and different rhizosphere microorganisms

Direct quantification of fungal DNA from soil substrate using real-time PCR.

cDNA sequence and homologies of the "57-kDa" nucleotide-binding subunit of the vacuolar ATPase from Arabidopsis.

The capacity of the arbuscular mycorrhizal fungus Glomus intraradices in reducing the presence of Fusarium solani f. sp. phaseoli in bean plants and the surrounding mycorrhizosphere soil was evaluated in a compartmentalized experimental system. Quantification of the pathogen and the symbiont in plant tissues, the soil regions of the mycorrhizosphere (rhizosphere and mycosphere), and the bulk soil was accomplished using specific polymerase chain reaction (PCR) primers in real-time PCR assays, culture-dependant methods, and microscopic determination techniques. Nonmycorrhizal bean plants infected with the pathogen had distinctive Fusarium root rot symptoms, while infected plants previously colonized by G. intraradices remained healthy. The amount of F. solani f. sp. phaseoli genomic DNA was significantly reduced in mycorrhizal bean plants and in each mycorrhizosphere soil compartment. The presence of G. intraradices in the mycorrhizosphere was not significantly modified, although the mycorrhizal colonization of roots was slightly increased in the presence of the pathogen. The results suggest that the reduced presence of Fusarium as well as root rot symptoms are caused by biotic and/or abiotic modifications of the mycorrhizosphere as a result of colonization with G. intraradices.

/pdf/quantification-of-fusarium-solani-f-sp-phaseoli-in-6ydwqk8lt4.pdf

Quantification of Fusarium solani f. sp. phaseoli in Mycorrhizal Bean Plants and Surrounding Mycorrhizosphere Soil Using Real-Time Polymerase Chain Reaction and Direct Isolations on Selective Media.

Bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is known to cause significant economic losses to tomato production worldwide. Biological control has been proposed as an alternative to current chemical containment methods, which are often inefficient and may leave adverse effects on the environment. However, only little headway has so far been made in developing biocontrol strategies against C. michiganensis subsp. michiganensis. To address this knowledge gap, we investigated the antagonistic capacity of PCA, produced by Pseudomonas sp. LBUM223, and DAPG and HCN, both produced by Pseudomonas sp. LBUM300, on C. michiganensis subsp. michiganensis under in vitro and in planta conditions. Nonsynthesizing isogenic mutants of the producer strains were also developed to further dissect the role of each individual metabolite on C. michiganensis subsp. michiganensis biological control. Novel specific quantitative polymerase chain reaction TaqMan assays allowed quantification of C. michiganensis subsp. michiganensis in tomato plants and rhizospheric soil. Pseudomonas spp. LBUM223 and LBUM300 significantly repressed C. michiganensis subsp. michiganensis growth in vitro, while their respective nonproducing mutants showed less or no significant antagonistic activity. In planta, only Pseudomonas sp. LBUM300 was capable of significantly reducing disease development and C. michiganensis subsp. michiganensis rhizospheric population, suggesting that the production of both DAPG and HCN was involved. In summary, simultaneous DAPG/HCN production by Pseudomonas sp. LBUM300 shows great potential for controlling bacterial canker of tomato.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-11-11-0312

Martin Filion

Papers

Direct interaction between the arbuscular mycorrhizal fungus Glomus intraradices and different rhizosphere microorganisms

Direct quantification of fungal DNA from soil substrate using real-time PCR.

cDNA sequence and homologies of the "57-kDa" nucleotide-binding subunit of the vacuolar ATPase from Arabidopsis.

Quantification of Fusarium solani f. sp. phaseoli in Mycorrhizal Bean Plants and Surrounding Mycorrhizosphere Soil Using Real-Time Polymerase Chain Reaction and Direct Isolations on Selective Media.

Production of DAPG and HCN by Pseudomonas sp. LBUM300 contributes to the biological control of bacterial canker of tomato.