Soil amendment with biochar is evaluated globally as a means to improve soil fertility and to mitigate climate change. However, the effects of biochar on soil biota have received much less attention than its effects on soil chemical properties. A review of the literature reveals a significant number of early studies on biochar-type materials as soil amendments either for managing pathogens, as inoculant carriers or for manipulative experiments to sorb signaling compounds or toxins. However, no studies exist in the soil biologyliterature that recognize the observed largevariations ofbiochar physico-chemical properties. This shortcoming has hampered insight into mechanisms by which biochar influences soil microorganisms, fauna and plant roots. Additional factors limiting meaningful interpretation of many datasets are the clearly demonstrated sorption properties that interfere with standard extraction procedures for soil microbial biomass or enzyme assays, and the confounding effects of varying amounts of minerals. In most studies, microbial biomass has been found to increase as a result of biochar additions, with significant changes in microbial community composition and enzyme activities that may explain biogeochemical effects of biochar on element cycles, plant pathogens, and crop growth. Yet, very little is known about the mechanisms through which biochar affects microbial abundance and community composition. The effects of biochar on soil fauna are even less understood than its effects on microorganisms, apart from several notable studies on earthworms. It is clear, however, that sorption phenomena, pH and physical properties of biochars such as pore structure, surface area and mineral matter play important roles in determining how different biochars affect soil biota. Observations on microbial dynamics lead to the conclusion of a possible improved resource use due to co-location of various resources in and around biochars. Sorption and therebyinactivation of growth-inhibiting substances likelyplaysa rolefor increased abundance of soil biota. No evidence exists so far for direct negative effects of biochars on plant roots. Occasionally observed decreases in abundance of mycorrhizal fungi are likely caused by concomitant increases in nutrient availability,reducing theneedfor symbionts.Inthe shortterm,therelease ofavarietyoforganic molecules from fresh biochar may in some cases be responsible for increases or decreases in abundance and activity of soil biota. A road map for future biochar research must include a systematic appreciation of different biochar-types and basic manipulative experiments that unambiguously identify the interactions between biochar and soil biota.

http://www.css.cornell.edu/faculty/lehmann/pictures/publ/SoilBiolBiochem%2043,%201812–1836,%202011%20Lehmann.pdf

Biochar effects on soil biota – A review

Trichoderma spp. are free-living fungi that are common in soil and root ecosystems. Recent discoveries show that they are opportunistic, avirulent plant symbionts, as well as being parasites of other fungi. At least some strains establish robust and long-lasting colonizations of root surfaces and penetrate into the epidermis and a few cells below this level. They produce or release a variety of compounds that induce localized or systemic resistance responses, and this explains their lack of pathogenicity to plants. These root-microorganism associations cause substantial changes to the plant proteome and metabolism. Plants are protected from numerous classes of plant pathogen by responses that are similar to systemic acquired resistance and rhizobacteria-induced systemic resistance. Root colonization by Trichoderma spp. also frequently enhances root growth and development, crop productivity, resistance to abiotic stresses and the uptake and use of nutrients.

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Trichoderma species--opportunistic, avirulent plant symbionts.

The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.

Going back to the roots: the microbial ecology of the rhizosphere.

Particular bacterial strains in certain natural environments prevent infectious diseases of plant roots. How these bacteria achieve this protection from pathogenic fungi has been analysed in detail in biocontrol strains of fluorescent pseudomonads. During root colonization, these bacteria produce antifungal antibiotics, elicit induced systemic resistance in the host plant or interfere specifically with fungal pathogenicity factors. Before engaging in these activities, biocontrol bacteria go through several regulatory processes at the transcriptional and post-transcriptional levels.

/pdf/biological-control-of-soil-borne-pathogens-by-fluorescent-4524lno10w.pdf

Biological control of soil-borne pathogens by fluorescent pseudomonads

Pathogenic microorganisms affecting plant health are a major and chronic threat to food production and ecosystem stability worldwide As agricultural production intensified over the past few decades, producers became more and more dependent on agrochemicals as a relatively reliable method of crop

Use of Plant Growth-Promoting Bacteria for Biocontrol of Plant Diseases: Principles, Mechanisms of Action, and Future Prospects

http://www.plantpath.cornell.edu/labs/enelson/PDFs/Hill_et_al_2000.pdf

Methods for assessing the composition and diversity of soil microbial communities

▪ Abstract The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for tes...

/pdf/microbial-dynamics-and-interactions-in-the-spermosphere-1vty3nu5iy.pdf

Microbial dynamics and interactions in the spermosphere.

The development and dispersal of seeds as well as their transition to seedlings represent perhaps the most critical stages of a plant’s life cycle The endophytic and epiphytic microbial interactions that take place in, on, and around seeds during these stages of the plant’s life cycle may have profound impacts on plant ecology, health, and productivity While our understanding of the seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now being made This review explores the microbial associations with seeds through various stages of the plant life cycle, beginning with the earliest stages of seed development on the parent plant and continuing through the development and establishment of seedlings in soil This review represents a broad synthesis of the ecological and agricultural literature focused on seed-microbe interactions as a means of better understanding how these interactions may ultimately influence plant ecology, health, and productivity in both natural and agricultural systems Our current understanding of seed-microbe associations will be discussed, with an emphasis on recent findings that specifically highlight the emerging contemporary understanding of how seed-microbe associations may ultimately impact plant health and productivity The diversity and dynamics of seed microbiomes represent the culmination of complex interactions with microbes throughout the plant life cycle The richness and dynamics of seed microbiomes is revealing exciting new opportunities for research into plant-microbe interactions Often neglected in plant microbiome studies, the renaissance of inquiry into seed microbiomes is offering exciting new insights into how the diversity and dynamics of the seed microbiome with plant and soil microbiomes as well as the microbiomes of dispersers and pollinators It is clear that the interactions taking place in and around seeds indeed have significant impacts on plant health and productivity in both agricultural and natural ecosystems

/pdf/the-seed-microbiome-origins-interactions-and-impacts-3lsd8z1y4q.pdf

The seed microbiome: Origins, interactions, and impacts

Evaluation de l'antagonisme de diverses especes fongiques vis-a-vis de R. dans des composts et dans des milieux amendes avec des composts d'ecorce de feuillus

Effects of Fungal Antagonists and Compost Age on Suppression of Rhizoctonia Damping-Off in Container Media Amended with Composted Hardwood Bark

Plant pathogenic fungi survive in soils in a quiescent state. In order for many root-pathogen interactions to be initiated, dormant propagules must be activated by molecules present in seed and root exudates. Without the release of such stimulatory molecules, the majority of root infections do not occur. Currently, little is known about the specific molecules involved in stimulating propagule germination and initiating root-pathogen interactions. Although certain molecules can be shown to elicit germination responses in vitro, responses of propagules reared on conventional culture media do not always reflect the responses of those formed on plant tissues in soil. Consequently, it is not possible to extend conclusions from laboratory determinations of the role of specific exudate molecules in stimulating fungal propagule germination to soil systems. The interaction of Pythium species with germinating seeds has served as a model system to answer questions about propagule behavior and the role of exudate stimulant molecules in establishing root-fungus interactions. The potential role of both volatile and water-soluble molecules in stimulating propagule germination are discussed.

Eric B. Nelson

Papers

Methods for assessing the composition and diversity of soil microbial communities

Microbial dynamics and interactions in the spermosphere.

The seed microbiome: Origins, interactions, and impacts

Effects of Fungal Antagonists and Compost Age on Suppression of Rhizoctonia Damping-Off in Container Media Amended with Composted Hardwood Bark

Exudate molecules initiating fungal responses to seeds and roots