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

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

The rhizosphere microbiome and plant health

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

The cell content of 12 bacterial phospholipid fatty acids (PLFA) was determined in bacteria extracted from soil by homogenization/centrifugation. The bacteria were enumerated using acridine orange direct counts. An average of 1.40×10-17 mol bacterial PLFA cell-1 was found in bacteria extracted from 15 soils covering a wide range of pH and organic matter contents. With this factor, the bacterial biomass based on PLFA analyses of whole soil samples was calculated as 1.0–4.8 mg bacterial C g-1 soil C. The corresponding range based on microscopical counts was 0.3–3.0 mg bacterial C g-1 soil C. The recovery of bacteria from the soils using homogenization/centrifugation was 2.6–16% (mean 8.7%) measured by PLFA analysis, and 12–61% (mean 26%) measured as microscopical counts. The soil content of the PLFA 18:2ω6 was correlated with the ergosterol content (r=0.92), which supports the use of this PLFA as an indicator of fungal biomass. The ratio 18:2ω6 to bacterial PLFA is therefore suggested as an index of the fungal:bacterial biomass ratio in soil. An advantage with the method based on PLFA analyses is that the same technique and even the same sample is used to determine both fungi and bacteria. The fungal:bacterial biomass ratio calculated in this way was positively correlated with the organic matter content of the soils (r=0.94).

The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil

Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). Rhizobacteria-mediated induced systemic resistance (ISR) has been demonstrated against fungi, bacteria, and viruses in Arabidopsis, bean, carnation, cucumber, radish, tobacco, and tomato under conditions in which the inducing bacteria and the challenging pathogen remained spatially separated. Bacterial strains differ in their ability to induce resistance in different plant species, and plants show variation in the expression of ISR upon induction by specific bacterial strains. Bacterial determinants of ISR include lipopolysaccharides, siderophores, and salicylic acid (SA). Whereas some of the rhizobacteria induce resistance through the SA-dependent SAR pathway, others do not and require jasmonic acid and ethylene perception by the plant for ISR to develop. No consistent host plant alterations are associated with the induced state, but upon challenge inoculation, resistance responses are accelerated and enhanced. ISR is effective under field conditions and offers a natural mechanism for biological control of plant disease.

/pdf/systemic-resistance-induced-by-rhizosphere-bacteria-13ehvnz7fj.pdf

Systemic resistance induced by rhizosphere bacteria

Broad spectrum biological control of diseases caused by soilborne plant pathogens such as Pythium, Phytophthora, and Rhizoctonia solani requires the introduction into or presence of edaphic sources of organic nutrients in soil for sustenance of biocontrol agents. The decomposition level of organic matter critically affects the composition of bacterial taxa as well as the populations and activities of biocontrol agents. Competition, antibiosis, parasitism, and systemic induced resistance are all affected. Highly stabilized sources of Sphagnum peat consistently fail to support sustained biological control, even when inoculated with biocontrol agents. Composts, on the other hand, can serve as an ideal food base for biocontrol agents and offer an opportunity to introduce and establish specific biocontrol agents into soils, which in turn leads to sustained biological control based on the activities of microbial communities.

BIOCONTROL WITHIN THE CONTEXT OF SOIL MICROBIAL COMMUNITIES: A Substrate-Dependent Phenomenon.

Environmental problems caused by disposal of organic wastes in landfills and streams or by incineration have forced man to examine alternative procedures. For example, burning of tree bark was a nuisance because of associated air pollution problems. This waste has now been turned into a resource through development of profitable composting processes and efficient energy retrieval systems. S ludges are removed from waste waters at a major cost to taxpayers and industries to reduce pollution of streams. Compo sting is chosen in­ creasingly as the least objectionable treatment process for these wastes; thus sludges provide another type of compost. Finally, with the increase in size of farms, the composting process has become a practical procedure for treatment of manures because it allows storage of a stabilized product until a time of year when its market value is highest. I n China, Japan, and other parts of the Orient, composts have been used in agriculture with beneficial effects for years (58). In the West, however, utilization of composts is a relatively recent phenomenon. During the past two decades several reports have discussed suppressive effects of composts to a variety of soilborne plant pathogens. Most of this literature is on ornamental crops. Only a few diseases of vegetable and field crops are controlled with

Basis for the control of soilborne plant pathogens with composts

Composts offer unique opportunities to examine fundamental interactions between plant pathogens, biocontrol agents, soil organic matter and plant roots. These organic amendments can be prepared reproducibly and have the potential to provide consistent biological control of plant diseases. Foliar as well as root pathogens may be affected by composts. Unfortenately, many factors control these beneficial effects. Heat exposure during composting kills or inactivates pathogens if the process is monitored properly. Biocontrol agents with the exception of Bacillus spp. also are killed by this heat treatment, however. Thus, biocontrol agents largely must recolonize composts after peak heating. The raw feedstock, the composting environment, as well as conditions during curing and utilization affect the potential for recolonization of composts by biocontrol agents and the induction of disease suppression. In practice, controlled inoculation of compost with biocontrol agents has proved necessary to induce consistent levels of suppression.

/pdf/suppression-of-plant-diseases-by-composts-221amgfen4.pdf

Suppression of Plant Diseases by Composts

If moist food scraps are placed in a container and left to sit for a week or two, the end product is likely to be a smelly \" slop \" that attracts flies. Given the proper conditions, these same food scraps can be composted to produce a material that looks and smells like rich soil and can be used to enhance soil texture and productivity. So, what are these conditions that promote composting? The physical and chemical conditions that should be maintained in a compost heap seem logical if you think about what compost really is — a big pile of food for billions of minute organisms. These microorganisms have certain chemical requirements, primarily carbon for energy, nitrogen to build proteins, and oxygen for respiration. Interacting with these are physical requirements, such as aeration to maintain optimal oxygen levels while not depleting the moisture necessary for microbial growth. This chapter begins with an overview of the chemical, physical, and biological changes that occur during thermophilic composting, thereby providing an example of how several sciences can be integrated in the study of composting. This overview is followed by more detailed, separate sections on compost chemistry, physics, and biology. Much of the information in the chemistry and physics sections focuses on thermophilic composting. The biology section includes a discussion of the microbes that are present in all types of composting, and of the diversity of invertebrates that live in outdoor and some worm composting systems. The information presented here reflects the current body of scientific knowledge regarding composting. Much remains unknown, leaving a variety of intriguing questions for future research. Some of these questions are identified as Research Possibilities, sprinkled in italics throughout the text. We hope they will provide the inspiration for students to ask a much wider range of questions, and to design their own original research.

Harry A. J. Hoitink

Papers

BIOCONTROL WITHIN THE CONTEXT OF SOIL MICROBIAL COMMUNITIES: A Substrate-Dependent Phenomenon.

Basis for the control of soilborne plant pathogens with composts

Suppression of Plant Diseases by Composts

The Science of Composting

Science and engineering of composting: design, environmental, microbiological and utilization aspects