J. Bloem

Relationships between soil texture, physical protection of organic matter, soil biota, and C and N mineralization in grassland soils.

Abstract The effect of soil type on carbon (C) and nitrogen (N) mineralization rates in grassland soils was investigated along with the physical and biological soil characteristics that may have caused the observed differences in mineralization rates between soil types. The percentage of mineralized organic N was higher in sandy soils than in loams and clays; this was not observed for C. In loams and clays small pores constituted a higher percentage of the total pore space than in sandy soils. Two mechanisms of physical protection of organic N were distinguished. In clay soils physical protection of organic material by its location in small pores was the main mechanism. In sandy soils, however, organic material was protected by its association with clay particles. In loams both mechanisms played a role. The protected organic material associated with clay particles consisted of amorphous undefined material that did not stain with acridine orange, indicating a high degree of decomposition, while the non-protected organic material present in the sand fraction consisted of plant debris that stained intensely with acridine orange. Physically protected organic matter had a lower C/N ratio than organic matter that was not physically protected. Grazing pressure on bacteria by bacterivorous nematodes was higher in sandy soils than in loams and clays. This coincided with a higher N mineralization rate per bacterium. The C/N ratio of the microbial biomass was higher in sandy soils than in loams and clays and was positively correlated with the N mineralization rate per unit of microbial biomass N. This is in agreement with the concepts of food webs that N mineralization is positively correlated with the C/N ratio of the consumer (bacteria) for a given sol|C/N ratio of the substrate (organic matter). It is not yet clear which of the factors investigated are the most important in determining N mineralization rates in grassland soils.

Microbiological methods for assessing soil quality

This book provides a selection of microbiological methods that are already applied in regional or national soil quality monitoring programs. It is split into two parts: part one gives an overview of approaches to monitoring, evaluating and managing soil quality. Part two provides a selection of methods, which are described in sufficient detail to use the book as a practical handbook in the laboratory. The methods are described in chapters on soil microbial biomass and numbers, soil microbial activity, soil microbial diversity and community composition, and plant-microbe interactions and soil quality.

Simulation of nitrogen mineralization in the belowground food webs of two winter wheat fields.

Food webs in conventional (high-input) and integrated (reduced-input) farming systems were simulated to estimate the contribution of soil microbes and soil fauna to nitrogen mineralization during the growing season. Microbes accounted for approximately 95% of the biomass and 70% of total nitrogen mineralization in both management practices. Among the soil fauna, amoebae and bacterivorous nematodes were the most important contributors to nitrogen mineralization. The contribution of nematodes showed more temporal and spatial variability than the contribution of amoebae. The model calculated nitrogen mineralization rates close to the observed rates for both fields and depth layers. In the integrated plot there were relatively high rates of mineralization in the 0-10 cm layer compared with the 10-25 cm layer, whereas in the conventional plot no differences were observed between depth layers (...)

Bacterial diversity in agricultural soils during litter decomposition

ABSTRACT Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.

Microbial numbers and activity in dried and rewetted arable soil under integrated and conventional management

Abstract During an 8-week microplot experiment, effects of moisture regime and farm management on microbial numbers and activity were studied. Under integrated management (reduced input farming), bacterial numbers, O 2 consumption and N mineralization, respectively, were 1.6, 2.1 and 1.8 times higher than under conventional management (high input farming). These differences may be attributed to 1.3 and 1.4 times higher contents of organic matter and total N in the integrated microplots. One month of drying from a water potential of −0.03 to −0.12 MPa, and subsequent rewetting to −0.01 MPa, did not affect bacterial numbers significantly. However, the relatively small decrease in water potential caused a significant decrease in O 2 consumption and N mineralization. After rewetting, respiration increased from 1.3 to 1.5 fold, and N mineralization from 3 to 5 fold. Concurrently, the frequency of dividing-divided cells (FDDC) increased from 10 to 16% in the conventional and to 23% in the integrated microplots. This suggests that the FDDC, which is determined by direct microscopy and requires no incubation, can be used as an index of in situ bacterial growth rate in soil. For marine bacteria, mathematical relationships have been established between specific growth rate (μ) and FDDC. If it is assumed that these relationships are also valid for soil bacteria, FDDCs of 16 and 23%, respectively, may indicate specific growth rates of about 1 and 2 day −1 . Bacterial production rates based on FDDC (8.5–45 μg C g −1 day −1 ) were 3–8 times higher than those based on O 2 consumption rates determined by 2-week incubations. Uncertainties of the methods are discussed.

Effects of tylosin as a disturbance on the soil microbial community

Abstract The effect of a strong temporary disturbance on the soil microbial community was investigated and the ability of the community to show resilience with respect to bacterial diversity and structure was examined. Soil was treated with the antibiotic tylosin and incubated for 2 months. After 3 weeks, the added tylosin and its degradation products had disappeared. During incubation, the populations of bacteria, fungi and protozoa in the soil responded to the tylosin treatment; the changes in the population sizes being strongest the first 2 weeks after treatment, after which it diminished. The diversity (number and abundance) of colony morphotypes decreased temporarily following the disturbance whereas a more permanent change in diversity was revealed investigating amplified 16S rDNA sequences from total community DNA by DGGE. The community structure (PCA) based on both colony morphology, DGGE and sole carbon source utilisation obtained by Ecoplates® was altered due to the tylosin treatment throughout the experiment. The DGGE was the most sensitive method. Differences in diversity and community structure found by this method were maintained for 2 months. However, the results were highly dependent on the DNA-extraction procedure. We have shown that diversity as a composite community parameter can attain its original value following the disturbance, whereas changes in community structure were permanent. It is therefore important to focus on community structure and not only on diversity, when evaluating the effect of disturbances on soil populations in relation to system functioning.

Dynamics of microorganisms, microbivores and nitrogen mineralisation in winter wheat fields under conventional and integrated management☆

Abstract To reduce environmental problems, integrated farming has been proposed, which may involve a considerable reduction of fertiliser-N input. A reduced fertiliser-N input must be compensated for by a higher N mineralisation from organic matter. To reduce losses and to facilitate optimal use of the N mineralised for crop growth, knowledge of the effects of management on soil orgaisms and on their role in N cycling is needed. Therefore, biomass and activity of bacteria, biomasses of fungi, bacterivorous amoebae, flagellates and nematodes, and in situ N mineralisation were monitored during a full year in a winter wheat field under conventional management (CONV) and integrated management (INT). Fungal biomass was about 100-fold lower than bacterial biomass. The average bacterial biomass was not significantly higher in INT than in CONV, whereas amoebae and nematodes were 64% and 22% higher, respectively. Average N mineralisation was 30% higher in INT. The differences are attributed to the approximately 30% higher organic matter content of INT. Bacterial biomass and frequency of dividing-divided cells (FDDC) were relatively low in December and January, probably owing to temperatures just above 0°C. At about 5°C in February and March, relatively high FDDC values and a doubling of bacteria occurred. During summer, FDDC values were relatively low and bacterial numbers were stable, probably owing to nutrient limitation. After harvest and skim ploughing, rapid increases in FDDC and bacteria were found. In the non-fumigated INT field, protozoan peaks coincided with the bacterial peak, whereas in CONV bacterivorous fauna were drastically reduced by soil fumigation. Nevertheless, the bacterial peaks were similar in CONV and INT, indicating that bacteria were not controlled by bacterivores. Nitrogen mineralisation was relatively low in winter. The increased bacterial growth in February and March, and in September appeared to enhance immobilisation rather than mineralisation of N. During the growing season from April to the end of August, bacterial growth was relatively low and N mineralisation was relatively high. This probably resulted from bacterivore feeding and from substrate- or nutrient-limited bacteria with a low growth efficiency. Considerable mineralisation rates after harvest confirmed the need for measures to stimulate immobilisation during periods without crop uptake.

Short-term and long-term effects of bacterivorous nematodes and nematophagous fungi on carbon and nitrogen mineralization in microcosms

A microcosm experiment was carried out to quantify the effects of organisms at various trophic levels on C and N mineralization after the addition of crop residues to arable soil. The effects of the bacterivorous nematodes Rhabditis sp. and Acrobeloides bütschlii and of the nematophagous fungi Arthrobotrys oligospora und Drechmeria coniospora on soil respiration and N mineralization were measured over 6 months at 20°C. In the presence of nematodes, C mineralization was increased during the first month and subsequently reduced; N mineralization was increased during the first 2 months and then reduced. The results support the assumption that nematodes influence C mineralization mainly indirectly by affecting bacterial activity, and N mineralization mainly directly by mineralizing bacterial biomass. A. oligospora contributed directly to C mineralization. The effect of both fungi on N mineralization was indirect and resulted from the reduction in the numbers of nematodes. The results showed that the effects of nematodes and nematophagous fungi and the mechanisms behind the effects may vary strongly in time, and are correlated with the type of organic matter decomposed.

Enumeration and biovolume determination of microbial cells – a methodological review and recommendations for applications in ecological research

Abstract. A review of direct counts of micro-organisms is presented, which describes the evaluation of different techniques and applications of microscopic methods for enumeration, biovolume and biomass measurement. New staining techniques and their applications are discussed as well as methods to distinguish individual cell properties. Attention is paid to data analysis and error propagation, which is widely neglected during quantitative studies in microbial ecology. Comparisons to other methods are made in order to evaluate methods of direct microscopy with respect to their great importance for environmental descriptions and analyses.

Within-trophic group interactions of bacterivorous nematode species and their effects on the bacterial community and nitrogen mineralization

Knowledge of the interactions between organisms within trophic groups is important for an understanding of the role of biodiversity in ecosystem functioning. We hypothesised that interactions between bacterivorous nematodes of different life history strategies would affect nematode population development, bacterial community composition and activity, resulting in increased N mineralization. A microcosm experiment was conducted using three nematode species (Bursilla monhystera, Acrobeloides nanus and Plectus parvus). All the nematode species interacted with each other, but the nature and effects of these interactions depended on the specific species combination. The interaction between B. monhystera and A. nanus was asymmetrically competitive (0,−), whereas that between B. monhystera and P. parvus, and also A. nanus and P. parvus was contramensal (+, −). The interaction that affected microcosm properties the most was the interaction between B. monhystera and P. parvus. This interaction affected the bacterial community composition, increased the bacterial biomass and increased soil N mineralization. B. monhystera and P. parvus have the most different life history strategies, whereas A. nanus has a life history strategy intermediate to those of B. monhystera and P. parvus. We suggest that the difference in life history strategies between species of the same trophic group is of importance for their communal effect on soil ecosystem processes. Our results support the idiosyncrasy hypothesis on the role of biodiversity in ecosystem functioning.