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

Many physical, chemical, mineralogical, and biological soil properties can be affected by forest fires. The effects are chiefly a result of burn severity, which consists of peak temperatures and duration of the fire. Climate, vegetation, and topography of the burnt area control the resilience of the soil system; some fire-induced changes can even be permanent. Low to moderate severity fires, such as most of those prescribed in forest management, promote renovation of the dominant vegetation through elimination of undesired species and transient increase of pH and available nutrients. No irreversible ecosystem change occurs, but the enhancement of hydrophobicity can render the soil less able to soak up water and more prone to erosion. Severe fires, such as wildfires, generally have several negative effects on soil. They cause significant removal of organic matter, deterioration of both structure and porosity, considerable loss of nutrients through volatilisation, ash entrapment in smoke columns, leaching and erosion, and marked alteration of both quantity and specific composition of microbial and soil-dwelling invertebrate communities. However, despite common perceptions, if plants succeed in promptly recolonising the burnt area, the pre-fire level of most properties can be recovered and even enhanced. This work is a review of the up-to-date literature dealing with changes imposed by fires on properties of forest soils. Ecological implications of these changes are described.

/pdf/effects-of-fire-on-properties-of-forest-soils-a-review-1ymllzm5e7.pdf

Effects of fire on properties of forest soils: a review

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

Until recently, the common view of the terrestrial nitrogen cycle had been driven by two core assumptions—plants use only inorganic N and they compete poorly against soil microbes for N. Thus, plants were thought to use N that microbes “left over,” allowing the N cycle to be divided cleanly into two pieces—the microbial decomposition side and the plant uptake and use side. These were linked by the process of net mineralization. Over the last decade, research has changed these views. N cycling is now seen as being driven by the depolymerization of N-containing polymers by microbial (including mycorrhizal) extracellular enzymes. This releases organic N-containing monomers that may be used by either plants or microbes. However, a complete new conceptual model of the soil N cycle needs to incorporate recent research on plant–microbe competition and microsite processes to explain the dynamics of N across the wide range of N availability found in terrestrial ecosystems. We discuss the evolution of thinking abou...

Nitrogen mineralization: challenges of a changing paradigm

Although it is generally accepted that plant community composition is key for predicting rates of ecosystem processes in the face of global change, microbial community composition is often ignored in ecosystem modeling. To address this issue, we review recent experiments and assess whether microbial community composition is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the composition of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in composition are often associated with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community composition into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiological traits, and disturbance responses. These relationships will determine how readily microbial community composition can be used to predict the responses of ecosystem processes to global change.

https://www.pnas.org/content/pnas/105/Supplement_1/11512.full.pdf

Resistance, resilience, and redundancy in microbial communities

The phospholipid fatty acid (PLFA) pattern was analyzed in a forest humus and in an arable soil experimentally polluted with Cd, Cu, Ni, Pb, or Zn at different concentrations. In both soil types, there were gradual changes in the PLFA patterns for the different levels of metal contamination. The changes in the forest soil were similar irrespective of which metal was used, while in the arable soil the changes due to Cu contamination differed from those due to the other metals. Several PLFAs reacted similarly to the metal amendments in the two soil types, while others showed different responses. In both soils, the metal pollution resulted in a decrease in the iso-branched PLFAs i15:0 and i17:0 and in the monounsaturated 16:1ω5 and 16:1ω7c fatty acids, while increases were found for i16:0, the branched br17:0 and br18:0, and the cyclopropane cy17:0 fatty acids. In the forest soil, the methyl branched PLFAs 10Me16:0, 10Me17:0, and 10Me18:0 increased in metal-polluted soils, indicating an increase in actinomycetes, while in the arable soil a decrease was found for 10Me16:0 and 10Me18:0 in response to most metals. The bacterial PLFAs 15:0 and 17:0 increased in all metal-contaminated samples in the arable soil, while they were unaffected in the forest soil. Fatty acid 18:2ω6, which is considered to be predominantly of fungal origin, increased in the arable soil, except in the Cu-amended samples, in which it decreased instead. Effects on the PLFA patterns were found at levels of metal contamination similar to or lower than those at which effects on ATP content, soil respiration, or total amount of PLFAs had occurred.

Phospholipid Fatty Acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals.

The effects of lime and wood-ash on the microbial community structure were evaluated by analyzing the phospholipid fatty acid (PLFA) composition of soils from two areas in the south of Sweden. A pine forest was amended with lime or ash at two concentrations, and a spruce forest was limed at one concentration. The treatments were carried out 5–6 years before sampling and raised the pH from approx. 4.0 to values between 4.8 and 7.0. At both sites there was a difference in the PLFA composition between the treated plots and the controls. The changes found were similar at both sites and correlated to the pH changes. No difference was found between limed plots and those treated with wood-ash. The methyl-branched fatty acids i15:0, i16:0 and 10Me16:0, the monounsaturated fatty acids 16: 1ω 7t and 18: 1ω 9, the cyclopropane fatty acid cy 19:0, and the saturated fatty acid 20:0 were more abundant in the control plots. In the plots with the highest pH there was a three-fold increase in the fatty acid 16: lω 5. An increase was also found for the fatty acids i14:0, 16:lω9, 16:lω 7c, cy17:0, 18:lω 7 and 10Me18:0. No effect on 18:2ω6 was found. The changes in PLFA pattern indicated that the increased pH caused a shift in the bacterial community to more Gram-negative and fewer Gram-positive bacteria, while the amount of fungi was unaffected. The increase in 10Me18:0 in limed soils indicated an increase in actinomycetes.

Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis

The determination of the phospholipid fatty acid (PLFA) pattern of soil organisms has become one of the most commonly used methods to study microbial community structure. Here we recapitulate the background of our work applying the PLFA method to soil in the early 1990s. We also stress that although the PLFA method was, and still is, a rapid and sensitive method to detect changes in the microbial community in soil, as with all popular methods it can be misused. We discuss problems in PLFA interpretation, the extent of turn-over of PLFAs in soil, and the flawed use of diversity indices to evaluate PLFA patterns.

/pdf/use-and-misuse-of-plfa-measurements-in-soils-59wa49lhbu.pdf

Åsa Frostegård

Papers

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

Phospholipid Fatty Acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals.

Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis

Use and misuse of PLFA measurements in soils

Microbial biomass measured as total lipid phosphate in soils of different organic content