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

This paper reviews the current knowledge of microbial processes affecting C sequestration in agroecosystems. The microbial contribution to soil C storage is directly related to microbial community dynamics and the balance between formation and degradation of microbial byproducts. Soil microbes also indirectly influence C cycling by improving soil aggregation, which physically protects soil organic matter (SOM). Consequently, the microbial contribution to C sequestration is governed by the interactions between the amount of microbial biomass, microbial community structure, microbial byproducts, and soil properties such as texture, clay mineralogy, pore-size distribution, and aggregate dynamics. The capacity of a soil to protect microbial biomass and microbially derived organic matter (MOM) is directly and/or indirectly (i.e., through physical protection by aggregates) related to the reactive properties of clays. However, the stabilization of MOM in the soil is also related to the efficiency with which microorganisms utilize substrate C and the chemical nature of the byproducts they produce. Crop rotations, reduced or no-tillage practices, organic farming, and cover crops increase total microbial biomass and shift the community structure toward a more fungal-dominated community, thereby enhancing the accumulation of MOM. A quantitative and qualitative improvement of SOM is generally observed in agroecosystems favoring a fungal-dominated community, but the mechanisms leading to this improvement are not completely understood. Gaps within our knowledge on MOM-C dynamics and how they are related to soil properties and agricultural practices are identified.

/pdf/bacterial-and-fungal-contributions-to-carbon-sequestration-3i9a4yeaey.pdf

Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems

Bacterial gene transfer by natural genetic transformation in the environment.

Phosphorus (P) is one of the major plant growth-limiting nutrients although it is abundant in soils in both inorganic and organic forms. Phosphate solubilizing micro-organisms (PSMs) are ubiquitous in soils and could play an important role in supplying P to plants in a more environmentally friendly and sustainable manner. Although solubilization of P compounds by microbes is very common under laboratory conditions, results in the field have been highly variable. This variability has hampered the large-scale use of PSMs in agriculture. Many reasons have been suggested for this variability, but none of them have been extensively investigated. In spite of the importance of PSMs in agriculture, the detailed biochemical and molecular mechanisms of P solubilization are not known. Recent work in our laboratory has shown that the conditions employed to isolate PSMs do not reflect soil conditions and that PSMs capable of effectively releasing P from soil are not so highly abundant as was suggested in earlier studies. These studies have also indicated that the mineral phosphate solubilizing (mps) ability of microbes could be linked to specific genes, and that these genes are present even in non P solubilizing bacteria. Understanding the genetic basis of P solubilization could help in transforming more rhizosphere-competent bacteria into PSMs. Further research should also focus on the microbial solubilization of iron (Fe) and aluminum (Al) phosphates, as well as mobilization of the organic phosphate reserves present in the soils.

Role of soil microorganisms in improving P nutrition of plants

Interest in biological control of plant pathogens has been stimulated in recent years by trends in agriculture towards greater sustainability and public concern about the use of hazardous pesticides There is now unequivocal evidence that antibiotics play a key role in the suppression of various soilborne plant pathogens by antagonistic microorganisms The significance of antibiotics in biocontrol, and more generally in microbial interactions, often has been questioned because of the indirect nature of the supporting evidence and the perceived constraints to antibiotic production in rhizosphere environments Reporter gene systems and bio-analytical techniques have clearly demonstrated that antibiotics are produced in the spermosphere and rhizosphere of a variety of host plants Several abiotic factors such as oxygen, temperature, specific carbon and nitrogen sources, and microelements have been identified to influence antibiotic production by bacteria biocontrol agents Among the biotic factors that may play a determinative role in antibiotic production are the plant host, the pathogen, the indigenous microflora, and the cell density of the producing strain This review presents recent advances in our understanding of antibiotic production by bacterial biocontrol agents and their role in microbial interactions

Antibiotic production by bacterial biocontrol agents

The survival of Pseudomonas fluorescens cells encapsulated in alginate beads and colonization of wheat roots was studied in soil microcosms inoculated with the cells in alginate beads of varying composition. Cells encapsulated in beads and introduced into a non-sterile loamy sand survived better than cells added directly to the same soil. A recovery/growth step for the bead-encapsulated cells was added before they were introduced into the soil, in an attempt to obtain optimal population levels in the soil. Further, bacterial populations that grew to the highest density in the beads subsequently showed the highest survival levels in soil. The addition of 3% skim milk, or 3% skim milk and 3% bentonite clay to all bead types consistently resulted in the highest survival of the encapsulated cells in soil. Root colonization by P. fluorescens was generally not impaired by the encapsulation in alginate. One week after inoculation into the soil, encapsulated cells in the various bead types were able to colonize the wheat rhizoplane at high population levels, similar to or exceeding those found when free cells were inoculated. In a second root colonization experiment the wheat rhizoplane was also efficiently colonized 7 weeks after the inoculant cells had been introduced into the soil in different bead types. In both assays, the cells encapsulated in beads amended with skim milk plus bentonite clay showed the highest root colonization rates. It is clear, therefore, that alginate-mediated establishment of inoculants can improve inoculant effectiveness.

Survival of, and root colonization by, alginate-encapsulated Pseudomonas fluorescens cells following introduction into soil

Survival studies with rhizobia introduced into loamy sand showed that a kaolinite amendment of the soil improved the survival of Rhizobium, and that bentonite had a very strong positive effect on rhizobial survival. The survival level was significantly higher in soil amended with 10% than with 5% bentonite. The amount of water present in the bentonite amended soil had a significant influence on rhizobial survival; in drier soil, survival levels were highest. For the loamy sand, the loamy sand amended with 5 and 10% bentonite or with 10% kaolinite, the number of rhizobial cells surviving on day 57 after introducing 2.5–5.0×107 cells g−1 dry soil could be described using the distribution of pores from three size classes in a mathematical relationship. Pores with necks 6 μm had a negative effect.

A determination of protective microhabitats for bacteria introduced into soil

Bentonite clay was used to improve the survival of Rhizobium leguminosarum biovar trifolii cells introduced into soil. Adding 5% bentonite clay to a loamy sand before inoculation markedly improved bacterial survival through the creation of large amounts of protective microhabitats. However, amending loamy sand with 5% bentonite clay also had a strong influence on soil physical properties. We therefore studied different introduction methods, with the aim of applying less bentonite, but maintaining high bacterial survival levels similar to those found with 5% bentonite. Using starved cells instead of a freshly grown culture slightly increased survival in a loamy sand in the absence of bentonite. In the presence of bentonite, no positive effects on survival due to the use of starved cells could be found. Soil-adapted rhizobia survived better in unamended and bentonite-amended loamy sand than freshly cultured rhizobia. However, this was only the case in soil containing up to 1 % bentonite. The previously found high survival levels using 5% bentonite could not be reached. Mixing a fresh rhizobial culture or freeze-dried cells with bentonite clay before introduction into soil was very successful in enhancing bacterial survival. Only 1% of bentonite was necessary to reach survival levels comparable to those found previously, after mixing 5% bentonite with loamy sand before inoculation. It was concluded that when bacteria and bentonite were mixed prior to inoculation, the clay offered protection at the site of introduction, resulting in a more efficient use of bentonite for enhancing bacterial survival.

Improvements to the use of bentonite clay as a protective agent, increasing survival levels of bacteria introduced into soil

Metabolic activity of Flavobacterium strain P25 during starvation and after introduction into bulk soil and the rhizosphere of wheat

Bentonite clay strongly hampered the activity of the flagellate Bodo soltans in liquid culture, and thereby improved the survival of Rhizobium. A possible coating of bacteria and/or flagellates did not seem to play a part in protecting rhizobia from flagellates. Bentonite did not release any substances toxic to B. saltans during the incubation period. It is suggested that, in liquid cultures, bentonite clay increases the minimum level to which rhizobia can be predated upon, thereby giving rise to the presence of higher rhizobial cell concentrations at the end of the incubation period.

Protection of Rhizobium by bentonite clay against predation by flagellates in liquid cultures

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