Bryan S. Griffiths

Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques.

This study aimed to characterise soil microbial community structure and function in temperate upland grassland ecosystems. We compared the use of community level physiological profiles (CLPP), phospholipid fatty acid (PLFA) profiles and community DNA (%G+C base distribution) approaches to quantify soil microbial community structure and potential activity across a gradient of three upland grassland types at 10 geographically distinct sites within the UK. Soil microbial biomass (Cmic) was highest in unimproved (U4a) and lowest in improved (MG6) grasslands. In contrast, potential soil microbial activity (carbon utilisation) was greatest in the improved and lowest in the semi-improved (U4b) grasslands. PLFA and culturing revealed that the soil microbial community shifted from one favouring fungi to one favouring bacteria as grassland improvement increased. Canonical variate analysis (CVA) of the CLPP and PLFA data differentiated microbial communities from the grassland types and sites and the separation between grasslands was greater using PLFA than CLPP. Discrimination between grasslands was mainly due to the presence of higher concentrations of fatty acids typical for Gram −ve bacteria in improved grasslands and actinomycete and fungal fatty acids in the semi and unimproved grasslands. CVA of the %G+C data gave less discrimination of the microbial communities than the other two methods. Correlation analysis of the CVA data for each microbial analysis showed a small, but significant, level of matching between the CLPP and PLFA data suggesting these two analyses may be reporting on similar members of the microbial community. Correlation between microbial community structure and soil physio-chemical properties indicated that PLFA were highly correlated with calcium, phosphorus, sodium, nitrogen and organic matter content and pH. CLPP were highly correlated with sodium and organic matter content and pH, while %G+C content correlated with pH. Correlation between microbial community structure and plant community structure indicated that fatty acids typical for Gram −ve bacteria were highly correlated with the presence of Lolium perenne and Trifolium repens and all microbial PLFA with the presence of Vaccinium myrtillus. Correlation of plant species with CLPP indicated that the presence of a number of rushes, shrubs, herbs and grasses influenced the metabolic profiles of the microbial communities from these grasslands. The presence of herbs were found to be highly correlated with certain %G+C classes within the community DNA.

Insights into the resistance and resilience of the soil microbial community.

Soil is increasingly under environmental pressures that alter its capacity to fulfil essential ecosystem services. To maintain these crucial soil functions, it is important to know how soil microorganisms respond to disturbance or environmental change. Here, we summarize the recent progress in understanding the resistance and resilience (stability) of soil microbial communities and discuss the underlying mechanisms of soil biological stability together with the factors affecting it. Biological stability is not solely owing to the structure or diversity of the microbial community but is linked to a range of other vegetation and soil properties including aggregation and substrate quality. We suggest that resistance and resilience are governed by soil physico-chemical structure through its effect on microbial community composition and physiology, but that there is no general response to disturbance because stability is particular to the disturbance and soil history. Soil stability results from a combination of biotic and abiotic soil characteristics and so could provide a quantitative measure of soil health that can be translated into practice.

Plant root proliferation in nitrogen–rich patches confers competitive advantage

Plants respond strongly to environmental heterogeneity, particularly below ground, where spectacular root proliferations in nutrient–rich patches may occur. Such ‘foraging’ responses apparently maximize nutrient uptake and are now prominent in plant ecological theory. Proliferations in nitrogen–rich patches are difficult to explain adaptively, however. The high mobility of soil nitrate should limit the contribution of proliferation to N capture. Many experiments on isolated plants show only a weak relation between proliferation and N uptake. We show that N capture is associated strongly with proliferation during interspecific competition for finite, locally available, mixed N sources, precisely the conditions under which N becomes available to plants on generally infertile soils. This explains why N–induced root proliferation is an important resource–capture mechanism in N–limited plant communities and suggests that increasing proliferation by crop breeding or genetic manipulation will have a limited impact on N capture by well–fertilized monocultures.

Impact of protozoan grazing on bacterial community structure in soil microcosms.

ABSTRACT The influence of grazing by a mixed assemblage of soil protozoa (seven flagellates and one amoeba) on bacterial community structure was studied in soil microcosms amended with a particulate resource (sterile wheat roots) or a soluble resource (a solution of various organic compounds). Sterilized soil was reinoculated with mixed soil bacteria (obtained by filtering and dilution) or with bacteria and protozoa. Denaturing gradient gel electrophoresis (DGGE) of PCR amplifications of 16S rRNA gene fragments, as well as community level physiological profiling (Biolog plates), suggested that the mixed protozoan community had significant effects on the bacterial community structure. Excising and sequencing of bands from the DGGE gels indicated that high-G+C gram-positive bacteria closely related to Arthrobacter spp. were favored by grazing, whereas the excised bands that decreased in intensity were related to gram-negative bacteria. The percentages of intensity found in bands related to high G+C gram positives increased from 4.5 and 12.6% in the ungrazed microcosms amended with roots and nutrient solution, respectively, to 19.3 and 32.9% in the grazed microcosms. Protozoa reduced the average bacterial cell size in microcosms amended with nutrient solution but not in the treatment amended with roots. Hence, size-selective feeding may explain some but not all of the changes in bacterial community structure. Five different protozoan isolates (Acanthamoeba sp., two species of Cercomonas, Thaumatomonas sp., and Spumella sp.) had different effects on the bacterial communities. This suggests that the composition of protozoan communities is important for the effect of protozoan grazing on bacterial communities.

Microbial-feeding nematodes and protozoa in soil: Their effectson microbial activity and nitrogen mineralization in decomposition hotspots and the rhizosphere

Food web studies from a range of ecosystems have demonstrated that the fauna contributes about 30% of total net nitrogen mineralization. This results mainly from the activities of microbial-feeding microfauna (nematodes and protozoa). Microbial and microfaunal activity is concentrated at spatially discrete and heterogeneously distributed organic substrates, including the rhizosphere. The dynamics of microfauna and their effect on nutrient cycling and microbial processes at these sites is reviewed. The potential manipulation of microfauna, either as an experimental tool to further understand soil microbial ecology or as a practical means of managing nutrient flows in agroecosystems, is discussed.

Nutrient inflow and root proliferation during the exploitation of a temporally and spatially discrete source of nitrogen in soil

To obtain nutrients mineralised from organic matter in the soil, plants have to respond to its heterogeneous distribution. We measured the timing of nitrogen uptake by wheat from a localised, 15N labelled organic residue in soil, as well as the timing of changes in root length density. We calculated the rates of N uptake per unit root length (inflows) for roots growing through the residue and for the whole root system. A stimulated local inflow appeared to be the main mechanism of exploitation of the residue N during the first five days of exploitation. 8% of the N that the plants would ultimately obtain from the residue was captured in this period. Roots then proliferated in the residue. This, together with a rapidly declining N inflow, contributed to the capture, over the next seven days, of 63% of the N that the plants derived from the residue. After that time, massive root proliferation occurred in the residue, but relatively little further N was captured.

Functional stability, substrate utilisation and biological indicators of soils following environmental impacts

Abstract Stability of a soil property to perturbation comprises both resistance and resilience. Resistance is defined as the ability of the soil to withstand the immediate effects of perturbation, and resilience the ability of the soil to recover from perturbation. Functional stability is used here to describe the stability of a biological function to perturbation, rather than the stability of physical structure or chemical properties. The function chosen for this study was the short-term decomposition of added plant residues, and the perturbations were copper and heat stresses. Previous studies had shown that functional stability was reduced greatly in soils with experimentally reduced biodiversity. The objective of this study was to determine the relative sensitivity of functional stability and potential indicators of biological status to detect alteration of field soils by various environmental impacts. Functional stability, protozoan populations and substrate mineralisation kinetics, were measured on paired soils with: high or low plant species diversity; hydrocarbon pollution or not; extensive or intensive agricultural management practices. Substrate mineralisation kinetics were poorly related to the soil’s antecedent conditions and were stimulated significantly by hydrocarbon pollution. Protozoan populations were potentially useful for detecting differences within soil type, but will require greater taxonomic input to be most useful. Functional stability, particularly resistance, was able to quantify differences between and within soils. The potential development of the technique in relation to soil health is discussed.

The Relationship between Microbial Community Structure and Functional Stability, Tested Experimentally in an Upland Pasture Soil

Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure. One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10−2, 10−4, 10−6, or 10−8 dilution of a soil suspension prepared from unsterilized soil. Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed. In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined. Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored. The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands. These shifts in microbial community structure were associated with a reduction in functional stability. The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies. RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation. We conclude that the functional stability of decomposition is related to specific components of the microbial community.

Spatial structure in soil chemical and microbiological properties in an upland grassland

We characterised the spatial structure of soil microbial communities in an unimproved grazed upland grassland in the Scottish Borders. A range of soil chemical parameters, cultivable microbes, protozoa, nematodes, phospholipid fatty acid (PLFA) profiles, community-level physiological profiles (CLPP), intra-radical arbuscular mycorrhizal community structure, and eubacterial, actinomycete, pseudomonad and ammonia-oxidiser 16S rRNA gene profiles, assessed by denaturing gradient gel electrophoresis (DGGE) were quantified. The botanical composition of the vegetation associated with each soil sample was also determined. Geostatistical analysis of the data revealed a gamut of spatial dependency with diverse semivariograms being apparent, ranging from pure nugget, linear and non-linear forms. Spatial autocorrelation generally accounted for 40-60% of the total variance of those properties where such autocorrelation was apparent, but accounted for 97% in the case of nitrate-N. Geostatistical ranges extending from approximately 0.6-6 m were detected, dispersed throughout both chemical and biological properties. CLPP data tended to be associated with ranges greater than 4.5 m. There was no relationship between physical distance in the field and genetic similarity based on DGGE profiles. However, analysis of samples taken as close as 1 cm apart within a subset of cores suggested some spatial dependency in community DNA-DGGE parameters below an 8 cm scale. Spatial correlation between the properties was generally weak, with some exceptions such as between microbial biomass C and total N and C. There was evidence for scale-dependence in the relationships between properties. PLFA and CLPP profiling showed some association with vegetation composition, but DGGE profiling did not. There was considerably stronger association between notional sheep urine patches, denoted by soil nutrient status, and many of the properties. These data demonstrate extreme spatial variation in community-level microbiological properties in upland grasslands, and that despite considerable numeric ranges in the majority of properties, overarching controlling factors were not apparent.

Food preferences of earthworms for soil fungi.

Summary Soil fungi are considered to be an important food source for earthworms. Selection experiments were carried out in order to study the preferences of earthworm species for a variety of soil fungi. Nine fungal species ( Cladosporium cladosporioides, Rhizoctonia solani, Mucor sp., Trichoderma viride, Fusarium nivale, Phlebia radiata, Glaeophyllum trabeum, Coniophora puteana, Coriolus versicolor ) were grown separately in centrifuge tubes on sterilized sand with potato dextrose. Tubes containing different fungal species, 8–9 per experiment, were arranged in a food choice arena. The preference for the fungi of 5 different earthworm species ( Lumbricus terrestris, Lumbricus castaneus, Aporrectodea caliginosa, Aporrectodea rosea, Octolasion cyaneum ) was tested by adding one specimen per chamber. Removal of sand from the tubes within 6 days was used as the indicator of preference by earthworms. The food preference of earthworms irrespective of ecological group followed a general pattern. F. nivale and C. cladosporioides were the preferred fungal species, followed by fast-growing species such as Mucor sp. and R. solani. In contrast, basidiomycetes were generally refused. The epigeic species L. rubellus had the strongest preference for a single fungal species, in contrast the endogeic species A. rosea fed more evenly on different fungal species. We conclude that early successional fungal species are used as cues by earthworms to detect fresh organic resources in soil.