Soil Chemical Analysis

Few microorganisms are as versatile as Escherichia coli. An important member of the normal intestinal microflora of humans and other mammals, E. coli has also been widely exploited as a cloning host in recombinant DNA technology. But E. coli is more than just a laboratory workhorse or harmless intestinal inhabitant; it can also be a highly versatile, and frequently deadly, pathogen. Several different E. coli strains cause diverse intestinal and extraintestinal diseases by means of virulence factors that affect a wide range of cellular processes.

Pathogenic Escherichia coli

Several microbes promote plant growth, and many microbial products that stimulate plant growth have been marketed. In this review we restrict ourselves to bacteria that are derived from and exert this effect on the root. Such bacteria are generally designated as PGPR (plant-growth-promoting rhizobacteria). The beneficial effects of these rhizobacteria on plant growth can be direct or indirect. This review begins with describing the conditions under which bacteria live in the rhizosphere. To exert their beneficial effects, bacteria usually must colonize the root surface efficiently. Therefore, bacterial traits required for root colonization are subsequently described. Finally, several mechanisms by which microbes can act beneficially on plant growth are described. Examples of direct plant growth promotion that are discussed include (a) biofertilization, (b) stimulation of root growth, (c) rhizoremediation, and (d) plant stress control. Mechanisms of biological control by which rhizobacteria can promote plant growth indirectly, i.e., by reducing the level of disease, include antibiosis, induction of systemic resistance, and competition for nutrients and niches.

Plant-growth-promoting rhizobacteria.

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

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

/pdf/soil-bacterial-and-fungal-communities-across-a-ph-gradient-17pkwmnjwv.pdf

Soil bacterial and fungal communities across a pH gradient in an arable soil.

Summary The relationships between bacterial community diver- sity and stability were investigated by perturbing soils, with naturally differing levels of diversity, to equivalent toxicity using copper sulfate and benzene. Benzene amendment led to large decreases in total bacterial numbers and biomass in both soils. Benzene amendment of an organo-mineral/improved pasture soil altered total soil bacterial community structure but, unlike amendment of the mineral/arable soil, maintained genetic diversity, based on polymerase chain reaction-denaturing gradient gel electrophore- sis (PCR-DGGE ) analysis targeting DNA and RNA, until week 9 of the perturbation experiment. Assuming equivalent toxicity, the genetic diversity of the natu- rally more diverse soil was more resistant to benzene perturbation than the less diverse soil. The broad scale function (mineralization of 14 C-labelled wheat shoot) of both benzene- and copper-treated soil com- munities was unaffected. However, narrow niche func- tion (mineralization of 14 C-labelled 2,4-dichlorophenol) was impaired for both benzene-polluted soils. The organo-mineral soil recovered this function by the end of the experiment but the mineral soil did not, sug- gesting greater resilience in the more diverse soil. Despite a large reduction in bacterial numbers and biomass in the copper-treated soils, only small differ- ences in bacterial community diversity were observed by week 9 in the copper-polluted soils. The overall community structure was little altered and functional- ity, measured by mineralization rates, remained unchanged. This suggested a non-selective pressure and a degree of genetic and functional resistance to copper perturbation, despite a significant reduction in bacterial numbers and biomass. However, initial shifts in physiological profiles of both copper-polluted soils were observed but rapidly returned to those of the controls. This apparent functional recovery, accompanied by an increase in culturability, possibly reflects adaptation by the surviving communities to perturbation. The findings indicate that, although soil communities may be robust, relationships between diversity and stability need to be considered in devel- oping a predictive understanding of response to envi- ronmental perturbations.

https://www.abdn.ac.uk/staffpages/uploads/mbi010/Environmental%20Microbiology%207,%20301-313.pdf

Bacterial diversity promotes community stability and functional resilience after perturbation

A potential for heterotrophic nitrification was identified in soil from a mature conifer forest and from a clear-cut site. Potential rates of NO2− production were determined separately from those of NO3− by using acetylene to block autotrophic NH4+ oxidation and chlorate to block NO2− oxidation to NO3− in soil slurries. Rates of NO2− production were similar in soil from the forest and the clear-cut site and were strongly inhibited by acetylene. The rate of NO3− production was much greater than that of NO2− production, and NO3− production was not significantly affected by acetylene or chlorate. Nitrate production was partially inhibited by cycloheximide, but was not significantly reduced by streptomycin. Neither the addition of ammonium nor the addition of peptone stimulated NO3− production. 15N labeling of the NH4+ pool demonstrated that NO3− was not coming from NH4+. The potential for heterotrophic nitrification in these forest soils was greater than that for autotrophic nitrification.

Identification of heterotrophic nitrification in a sierran forest soil.

Direct effects of increased above-ground CO2 concentration on soil microbial processes are unlikely, due to the high pCO2 of the soil atmosphere in most terrestrial ecosystems. However, below- ground microbial processes are likely to be affected through altered plant inputs at elevated CO2. A major component of plant input is derived from litter fall and root turnover. Inputs also derive from rhizodeposition (loss of C-compounds from active root systems) which may account for up to 40% of photoassimilate. This input fuels the activity of complex microbial communities around roots. These communities are centrally important not only to plant–microbe interactions and consequent effects on plant growth, but also, through their high relative activity and abundance, to microbially mediated processes in soil generally. This review focuses on approaches to measure C-flow from roots, in particular, as affected by increased atmospheric CO2 concentration. The available evidence for impacts on microbial communities inhabiting this niche, which constitutes an interface for possible perturbations on terrestrial ecosystems through the influence of environmental change, will also be discussed. While methodologies for measuring effects of increased CO2 concentration on plant growth, physiology and C-partitioning are abundant and widely reported, there is relatively little information on plant-mediated effects on soil microbial communities and processes. Importantly, many studies have also neglected to recognize that any secondary effects on microbial communities may have profound effects on plant parameters measured in relation to environmental change. We critically review approaches which have been used to measure rhizodeposition under conditions of increased atmospheric CO2 concentration, and then consider evidence for changes in microbial communities and processes, and the methodologies which have been recently developed, and are appropriate to study such changes.

Effect of elevated CO2 on rhizosphere carbon flow and soil microbial processes

Net nitrification rates tend to be low or negligible in the forest floor of many coniferous forests of North-East Scotland. The most likely process controls are substrate availability, pH, allelopathy, water potential, nutrient status and temperature. These are discussed in relation to field and laboratory studies of net and potential rates of nitrification. Fungi make up by far the largest part of the nitrifier community in the coniferous forest floor. Very little is known about the distribution and activity of autotrophs in these systems, although it is certain that in vitro evidence suggesting autotrophs cannot nitrify at pH levels characteristic of coniferous forest soils is unrealistic. Because of the metabolic diversity of nitrifying fungi, a variety of organic and inorganic nitrification pathways may exist in coniferous forests. The possible involvement of free radicles in fungal nitrification in coniferous forest soils is also suggested. A complete understanding of nitrification in coniferous forest soils can only result from field characterisation of N flux such as through the use of 15N. This must be combined with ecophysiological characterisation of the organisms involved in order that the complexity of nitrification in coniferous forest soils can be resolved.

Nitrification in coniferous forest soils.

The perennial bunchgrassEhrharta calycina was grown with and without V.A.M. fungal infection (Glomus fasciculatum) in a sandy loam exposed to a range of acidic and heavy metal depositions. Heavy metals (Cu, Ni, Pb, Zn, Fe, and Co) were applied in simulated rain (pH 3.0, 4.0, and 5.6) at deposition rates approximating those observed to result from smelter efluents. Metal concentrations in the roots and shoots of mycorrhizal plants were greater than those of non-mycorrhizal plants. Mycorrhizal enhancement of plant metal uptake increased with greater acidity and higher heavy metal content of treatment. The growth of mycorrhizal plants was reduced compared to non-mycorrhizal plants when metal depostion was combined with simulated acid rain. We propose that mycorrhizal enhancement of heavy metal uptake caused reduced growth in plants exposed to acidic and heavy metal depositions.

Kenneth Stuart Killham

Papers

Bacterial diversity promotes community stability and functional resilience after perturbation

Identification of heterotrophic nitrification in a sierran forest soil.

Effect of elevated CO2 on rhizosphere carbon flow and soil microbial processes

Nitrification in coniferous forest soils.

Vesicular arbuscular mycorrhizal mediation of grass response to acidic and heavy metal depositions