https://libpls.net/publication/PLS_basic_2001.pdf

PLS-regression: a basic tool of chemometrics

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

A method is described for the rapid and objective estimation of the amount of carbon in the living, non-resting microbial biomass of soils. The method, which is based on the initial respiratory response of microbial populations to amendment with an excess of a carbon and energy source, was quantified using an expanded version of Jenkinson's technique.

The simultaneous application of the two methods to 50 soil samples showed a highly significant correlation (r = 0.96) between both. From this correlation it could be deduced that at 22°C, a substrate-induced maximal respiratory rate of 1 ml CO2· h−1 corresponds to c. 40 mg microbial biomass C. Evidence supporting these results was obtained from pure culture studies. The various soil types investigated were collected from agricultural as well as forest sites and they contained between 15 and 240 mg microbial C·100g dry soil−1. The respiratory method provides reproducible estimates of biomass size within 1–3 h after soil amendment. It can be combined without difficulty with a selective inhibition method for determination of bacterial and fungal contributions to soil metabolism.

A physiological method for the quantitative measurement of microbial biomass in soils

Organic acids, such as malate, citrate and oxalate, have been proposed to be involved in many processes operating in the rhizosphere, including nutrient acquisition and metal detoxification, alleviation of anaerobic stress in roots, mineral weathering and pathogen attraction. A full assessment of their role in these processes, however, cannot be determined unless the exact mechanisms of plant organic acid release and the fate of these compounds in the soil are more fully understood. This review therefore includes information on organic acid levels in plants (concentrations, compartmentalisation, spatial aspects, synthesis), plant efflux (passive versus active transport, theoretical versus experimental considerations), soil reactions (soil solution concentrations, sorption) and microbial considerations (mineralization). In summary, the release of organic acids from roots can operate by multiple mechanisms in response to a number of well-defined environmental stresses (e.g., Al, P and Fe stress, anoxia): These responses, however, are highly stress- and plant-species specific. In addition, this review indicates that the sorption of organic acids to the mineral phase and mineralisation by the soil's microbial biomass are critical to determining the effectiveness of organic acids in most rhizosphere processes.

Organic acids in the rhizosphere: a critical review

Summary
Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high-resolution techniques with which to detect inactive and active microbial cells in the soil matrix.

Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function.

The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13C- and 12C-DNA, both extracted from soil treated with a 13C source, by density-gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13C-DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C-substrate added to soil.

/pdf/microbial-diversity-and-soil-functions-3p2xvso2y0.pdf

Microbial diversity and soil functions

We review the current knowledge on biodiversity in soils, its role in ecosystem processes, its importance for human purposes, and its resilience against stress and disturbance. The number of existing species is vastly higher than the number described, even in the macroscopically visible taxa, and biogeographical syntheses are largely lacking. A major effort in taxonomy and the training of a new generation of systematists is imperative. This effort has to be focussed on the groups of soil organisms that, to the best of our knowledge, play key roles in ecosystem functioning. To identify such groups, spheres of influence (SOI) of soil biota - such as the root biota, the shredders of organic matter and the soil bioturbators - are recognized that presumably control ecosystem processes, for example, through interactions with plants. Within those SOI, functional groups of soil organisms are recognized. Research questions of the highest urgency are the assignment of species to functional groups and determining the redundancy of species within functional groups. These priorities follow from the need to address the extent of any loss of functioning in soils, associated with intensive agriculture, forest disturbance, pollution of the environment, and global environmental change. The soil biota considered at present to be most at risk are species-poor functional groups among macrofaunal shredders of organic matter, bioturbators of soil, specialized bacteria like nitrifiers and nitrogen fixers, and fungiforming mycorrhizas. An experimental approach in addressing these research priorities is needed, using longterm and large-scale field experiments and modern methods of geostatistics and geographic information systems. (Less)

/pdf/biodiversity-and-ecosystem-functioning-in-soil-1euzplxjp1.pdf

Biodiversity and ecosystem functioning in soil

The use of phospholipid and neutral lipid fatty-acids to estimate biomass of arbuscular mycorrhizal fungi in soil

A method for vital staining of fungal mycelium with fluorescein diacetate (FDA) is described. In experiments with pure cultures, good correlation was obtained between relative staining efficiency, growth rate, and respiration. FDA thus appears to be a true vital stain, in that it stains only metabolically active mycelia. In fresh soil suspensions stained with FDA, brightly fluorescent hyphae and portions of hyphae were observed. The applicability of the method for measurement of active mycelium in the soil is discussed.

Vital staining of fungi in pure cultures and in soil with fluorescein diacetate

Microbial biomass and soil respiration rate decreased after application of 150 kg NH4NO3–N∙ha−1 to different coniferous forest podzols. The decrease was already found 3 months after fertilization and was still evident after 3–5 years. Changes in pH, organic matter, or water content in the soils could not explain the decreases. In laboratory experiments, several unfertilized forest soils were treated with 2 mg of NH4NO3–N or of urea–nitrogen∙g wet soil−1. The ammonium nitrate addition resulted in severe depressions of the respiration rates during and up to 175 days of incubation and the decrease was evident after about 1 week. The urea treatment initially increased the respiration rate of the soils, but this appeared to be a transitory effect.

Bengt Söderström

Papers

Biodiversity and ecosystem functioning in soil

The use of phospholipid and neutral lipid fatty-acids to estimate biomass of arbuscular mycorrhizal fungi in soil

Vital staining of fungi in pure cultures and in soil with fluorescein diacetate

Decrease in soil microbial activity and biomasses owing to nitrogen amendments

Effects of experimental acidification and liming on soil organisms and decomposition in a Scots pine forest