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

Biodegradation aspects of Polycyclic Aromatic Hydrocarbons (PAHs): A review

Mechanisms of membrane toxicity of hydrocarbons.

The intent of this review is to provide an outline of the microbial degradation of polycyclic aromatic hydrocarbons. A catabolically diverse microbial community, consisting of bacteria, fungi and algae, metabolizes aromatic compounds. Molecular oxygen is essential for the initial hydroxylation of polycyclic aromatic hydrocarbons by microorganisms. In contrast to bacteria, filamentous fungi use hydroxylation as a prelude to detoxification rather than to catabolism and assimilation. The biochemical principles underlying the degradation of polycyclic aromatic hydrocarbons are examined in some detail. The pathways of polycyclic aromatic hydrocarbon catabolism are discussed. Studies are presented on the relationship between the chemical structure of the polycyclic aromatic hydrocarbon and the rate of polycyclic aromatic hydrocarbon biodegradation in aquatic and terrestrial ecosystems.

Biodegradation of polycyclic aromatic hydrocarbons

Carvacrol, (+)-carvone, thymol, and trans-cinnamaldehyde were tested for their inhibitory activity against Escherichia coli O157:H7 and Salmonella typhimurium. In addition, their toxicity to Photobacterium leiognathi was determined, utilizing a bioluminescence assay. Their effects on the cell surface were investigated by measuring the uptake of 1-N-phenylnaphthylamine (NPN), by measuring their sensitization of bacterial suspensions toward detergents and lysozyme, and by analyzing material released from cells upon treatment by these agents. Carvacrol, thymol, and trans-cinnamaldehyde inhibited E. coli and S. typhimurium at 1-3 mM, whereas (+)-carvone was less inhibitory. trans-Cinnamaldehyde was the most inhibitory component toward P. leiognathi. Carvacrol and thymol disintegrated the outer membrane and released outer membrane-associated material from the cells to the external medium; such release by (+)-carvone or trans-cinnamaldehyde was negligible. Of the tested components, carvacrol and thymol decreased the intracellular ATP pool of E. coli and also inreased extracellular ATP, indicating disruptive action on the cytoplasmic membrane.

Characterization of the action of selected essential oil components on gram-negative bacteria

A Rhodococcus species, designated strain UW1, was isolated from contaminated soil using conventional enrichment and isolation techniques. The isolate was able to use pyrene as sole source of carbon and energy; it mineralized 72% of the pyrene within 2 weeks. During growth a metabolite was detected in the culture fluid and further characterized by UV- and mass spectrometry. There is evidence that this metabolite resulted from a recyclization of the direct meta-ring-fission product of pyrene after dihydroxylation in either the 1,2- or 4,5-position. At pH 7.0 and 30°C Rhodococcus sp. UW1 showed a maximum degradation rate of 0.08 mg pyrene/ml per day, while growing with a doubling time of 30 h. The activity of the initial dioxygenase system was characterized by measuring the oxygen-consumption rates of pyrene-induced resting cells, the maxima of which occurred at pH 7.2 and 45°C. Rhodococcus sp. UW1 could also use phenathrene, anthracene, fluoranthene and chrysene as sole sources of carbon and energy, whereas naphthalene, dibenzofuran, fluorene and dibenzothiophene were only co-metabolized.

Degradation of pyrene byRhodococcus sp. UW1

The inhibition of the exponential growth of Escherichia coli K-12 by different phenolic compounds was examined. Cells entrapped in calcium alginate showed a greater tolerance than cells grown in suspension. The extent of inhibition of growth of the immobilized cells depended on the period of growth in the gel matrix. After the addition of bacteriostatic concentrations of phenol or 4-chlorophenol, a dose-dependent efflux of metabolites such as ATP and of K+ ions was elicited. Provided that glucose was supplied as an energy substrate, a reaccumulation of K+ ions at low phenol concentrations was observed. The restoration of the membrane gradient for K+ always preceded the continuation of growth in the presence of the toxic compounds. Compared with free cells, those cells immobilized and grown in alginate suffered a smaller loss of cations after the addition of 4-chlorophenol. The reestablishment of gradients was observed at higher concentrations of the pollutants with entrapped cells than with free cells. Corresponding to the increase in tolerance, the membrane damage was reduced in cells grown in immobilized form for longer times. These data offer a mechanistic explanation of the protection of immobilized microorganisms from phenolic solvents. The data point to the membrane as an important cell component in the toxicity of these pollutants.

Influence of phenols on growth and membrane permeability of free and immobilized Escherichia coli.

A Pseudomonas sp. which was isolated from phenol-containing soil was immobilized in alginate and polyacrylamide-hydrazide (PAAH) and cultivated in a special airlift fermenter.

Degradation of phenol by polymer entrapped microorganisms

The phenol degradation by Candida sp. and Pseudomonas sp. immobilized on activated carbon was investigated. Thanks to its great adsorptive surface, activated carbon is suited as supporting material for microorganisms and also provides a high adsorption capacity for phenol.

Phenol degradation by microorganisms adsorbed on activated carbon

The antibacterial activity of phenol was determined by measuring inhibition of exponentially growing free and immobilized cells of Escherichia coli, Pseudomonas putida and Staphylococcus aureus. Immobilization of microorganisms in calcium alginate beads reduced the growth inhibition caused by bacteriostatic concentrations of phenol. The increase in phenol tolerance occurred at different culture conditions and growth rates of the cells. The strength of the effect, however, was found to correlate with the formation of colonies in the gel matrix. Dissolution of gel beads led to a substantial loss of the protection against phenol of immobilized-grown cells.

Hans-Jürgen Rehm

Papers

Degradation of pyrene byRhodococcus sp. UW1

Influence of phenols on growth and membrane permeability of free and immobilized Escherichia coli.

Degradation of phenol by polymer entrapped microorganisms

Phenol degradation by microorganisms adsorbed on activated carbon

Protection of bacteria against toxicity of phenol by immobilization in calcium alginate