Michael Bonkowski

Protozoa, Nematoda and Lumbricidae in the rhizosphere of Hordelymus europaeus (Poaceae): faunal interactions, response of microorganisms and effects on plant growth

Interactions among protozoa (mixed cultures of ciliates, flagellates and naked amoebae), bacteria-feeding nematodes (Pellioditis pellio Schneider) and the endogeic earthworm species Aporrectodea caliginosa (Savigny) were investigated in experimental chambers with soil from a beechwood (Fagus sylvatica L.) on limestone. Experimental chambers were planted with the grass Hordelymus europeaus L. (Poaceae) and three compartments separated by 45-μm mesh were established: rhizosphere, intermediate and non-rhizosphere. The experiment lasted for 16 weeks and the following parameters were measured at the end of the experiment: shoot and root mass of H. europaeus, carbon and nitrogen content in shoots and roots, density of ciliates, amoebae, flagellates and nematodes, microbial biomass (SIR), basal respiration, streptomycin sensitive respiration, ammonium and nitrate contents, phosphate content of soil compartments. In addition, leaching of nutrients (nitrogen and phosphorus) and leachate pH were measured at regular intervals in leachate obtained from suction cups in the experimental chambers. Protozoa stimulated the recovery of nitrifying bacteria following defaunation (by chloroform fumigation) and increased nitrogen losses as nitrate in leachate. In contrast, protozoa and nematodes reduced leaching of phosphate, an effect ascribed to stimulation of microbial growth early in the experiment. Earthworms strongly increased the amount of extractable mineral nitrogen whereas it was strongly reduced by protozoa and nematodes. Both protozoa and nematodes reduced the stimulatory effect of earthworms on nitrogen mineralization. Microbial biomass, basal respiration, and numbers of protozoa and nematodes increased in the vicinity of the root. Protozoa generally caused a decrease in microbial biomass whereas nematodes and earthworms reduced microbial biomass only in the absence of protozoa. None of the animals studied significantly affected basal respiration, but specific respiration of microorganisms (O2 consumption per unit biomass) was generally higher in animal treatments. The stimulatory effect of nematodes and earthworms, however, occurred only in the absence of protozoa. The sensitivity of respiration to streptomycin suggested that protozoa selectively grazed on bacterial biomass but the bacterial/fungal ratio appeared to be unaffected by grazing of P. pellio. Earthworms reduced root biomass of H. europaeus, although shoot biomass remained unaffected, and concentrations of nitrogen in shoots and particularly in roots were strongly increased by earthworms. Both nematodes and protozoa increased plant biomass, particularly that of roots. This increase in plant biomass was accompanied by a marked decrease in nitrogen concentrations in roots and to a lesser extent in shoots. Generally, the effects of protozoa on plant growth considerably exceeded those of nematodes. It is concluded that nematodes and protozoa stimulated plant growth by non-nutritional effects, whereas the effects of earthworms were caused by an increase in nutrient supply to H. europaeus.

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.

Soil networks become more connected and take up more carbon as nature restoration progresses

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.

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.

Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana

We constructed an experimental model system to study the effects of grazing by a common soil amoeba, Acanthamoeba castellanii, on the composition of bacterial communities in the rhizosphere of Arabidopsis thaliana. Amoebae showed distinct grazing preferences for specific bacterial taxa, which were rapidly replaced by grazing tolerant taxa in a highly reproducible way. The relative proportion of active bacteria increased although bacterial abundance was strongly decreased by amoebae. Specific bacterial taxa had disappeared already two days after inoculation of amoebae. The decrease in numbers was most pronounced in Betaproteobacteria and Firmicutes. In contrast, Actinobacteria, Nitrospira, Verrucomicrobia and Planctomycetes increased. Although other groups, such as betaproteobacterial ammonia oxidizers and Gammaproteobacteria did not change in abundance, denaturing gradient gel electrophoresis with specific primers for pseudomonads (Gammaproteobacteria) revealed both specific changes in community composition as well as shifts in functional genes (gacA) involved in bacterial defence responses. The resulting positive feedback on plant growth in the amoeba treatment confirms that bacterial grazers play a dominant role in structuring bacteria–plant interactions. This is the first detailed study documenting how rapidly protozoan grazers induce shifts in rhizosphere bacterial community composition.

Do soil protozoa enhance plant growth by hormonal effects

We investigated changes in root morphology of watercress seedlings (Lepidium sativum L.) and effects on the composition of the rhizosphere bacterial community to test the hypothesis that rhizosphere protozoa affect plant growth by a grazing-induced stimulation of plant growth-promoting rhizobacteria. The presence of Acanthamoebae (Protozoa: Amoebida) induced changes in root morphology of watercress seedlings as soon as the root protruded from the seed. The root system was greater and more branched. These changes resembled hormonal effects and were accompanied by an increase in the proportion of auxin, indolyl-3-acetic acid (IAA) producing rhizosphere bacteria. IAA did not originate from amoebal metabolism, but resulted from changes in the composition and activity of the microbial community. Therefore, amoebae affected both the functioning and turnover of rhizosphere microoganisms. We propose a new mechanism based on hormonal effects of protozoa on root growth. Protozoa function as bacteria-mediated mutualists promoting plant growth by hormonal feed-back mechanisms and nutrient effects based on nutrient release from grazed bacterial biomass, i.e. the microbial-loop.

Substrate heterogeneity and microfauna in soil organic ‘hotspots’ as determinants of nitrogen capture and growth of ryegrass

In this study we simultaneously manipulated the patchiness of complex organic resources and the composition of microfaunal populations (protozoa and nematodes) in soil, to influence microbial mineralization processes and to elucidate the underlying mechanisms of nutrient acquisition from decomposing plant residues by ryegrass plants. Hotspot treatments of decreasing patchiness were established by filling laboratory microcosms with defaunated soil and adding labelled ( 13 C, 15 N) grass residues as 1-layer, 4-layer or completely mixed within the soil. Microfaunal treatments were set up by inoculation of the soil with either protozoa or bacterivorous nematodes, a combination of both or neither (control). The microcosms were planted with surface sterile ryegrass seedlings. Growth of ryegrass plants was enhanced by both, increasing patchiness of the organic matter in soil (1-layer > 4-layer > mixed) and microfloral‐microfaunal interactions (protozoa C nematodes D protozoa > nematodes > control). The presence of microfauna enhanced the decomposition of hotspot material. Protozoan grazing in particular increased the availability of N in soil and leaching water and led to a concomitant increase in plant growth. While root foraging in organic hotspots enhanced the spatial coupling of mineralization and plant uptake, microfaunal grazing increased the temporal coupling of nutrient release and plant uptake. Consequently the greatest plant biomass was found in treatments combining aggregation of organic material in patches and the presence of microfauna. ©2000 Elsevier Science B.V. All rights reserved.

Rhizosphere fauna: the functional and structural diversity of intimate interactions of soil fauna with plant roots

For decades, the term “rhizosphere fauna” has been used as a synonym to denote agricultural pests among root herbivores, mainly nematodes and insect larvae. We want to break with this constrictive view, since the connection between plants and rhizosphere fauna is far more complex than simply that of resource and consumer. For example, plant roots have been shown to be neither defenceless victims of root feeders, nor passive recipients of nutrients, but instead play a much more active role in defending themselves and in attracting beneficial soil microorganisms and soil fauna. Most importantly, significant indirect feed-backs exist between consumers of rhizosphere microorganisms and plant roots. In fact, the majority of soil invertebrates have been shown to rely profoundly on the carbon inputs from roots, breaking with the dogma of soil food webs being mainly fueled by plant litter input from aboveground. In this review we will highlight areas of recent exciting progress and point out the black boxes that still need to be illuminated by rhizosphere zoologists and ecologists.

Interactions between earthworms and soil protozoa: A trophic component in the soil food web

Abstract Earthworms and protozoa are, in terms of biomass, the most important groups of soil fauna in beech forests on limestone in southern Lower Saxonia (Germany). To investigate the effect of high protozoan numbers on earthworm distribution, a multiple choice feeding experiment was set up in fumigated soil, reinoculated with different numbers of naked amoebae, protozoa commonly found in that soil. Distribution of Aporrectodea caliginosa (Savigny) after 1 wk was correlated with numbers of amoebae in soil. Other experiments confirmed digestion of protozoa by earthworms. The weight gain of young A. caliginosa in soil with amoebae was twice that in soil without protozoa. Direct observations of fresh cast material confirmed that active protozoa were digested by A. caliginosa. Lower protozoan numbers in faeces of Octolasion lacteum (Orley) than in the surrounding soil were found by dilution series, indicating grazing on the active part of soil protozoa by earthworms. The experiments provide evidence that A. caliginosa is actively searching for places with high protozoan densities and that protozoa may play a significant role in earthworm nutrition.

Soil protozoa and forest tree growth : non-nutritional effects and interaction with mycorrhizae

Mycorrhizal (Lactarius rufus Fr.) and non-mycorrhizal Norway spruce seedlings (Picea abies Karst.) were grown in a sand culture and inoculated with protozoa (naked amoebae and flagellates) extracted from native forest soil or with protozoa grown on agar cultures. A soil suspension from which the protozoa were eliminated by filtration or chloroform fumigation was used as a control. After 19 weeks of growth in a climate chamber at 20–22°C, the seedlings were harvested. Protozoa reduced the number of bacterial colony-forming units extracted from the rhizoplane of both non-mycorrhizal and mycorrhizal seedlings and significantly increased seedling growth. However, concentrations of mineral nutrients in needles were not increased in seedlings with protozoan treatment. It is concluded that the increased growth of seedling was not caused by nutrients released during amoebal grazing on rhizosphere micro-organisms. The protozoa presumably affected plant physiological processes, either directly, via production of phytohormones, or indirectly, via modification of the structure and performance of the rhizosphere microflora and their impact on plant growth. Mycorrhizal colonization significantly increased the abundance of naked amoebae at the rhizoplane. Our observations indicate that protozoa in the rhizosphere interact significantly with mycorrhizae.