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Plants rely on microorganisms to mobilize organically and inorganically bound sulfur (S) and phosphorus (P) in which the plant can then readily utilize. The aim of this study was to investigate the role of S- and P-mobilizing bacteria in plant growth promotion in biochar-amended soil, which has been rarely investigated so far. Pot experiments of Lolium perenne were established on S and P limited soil with 1% or 2% biochar ( Miscanthus × giganteus) or without biochar (control) for a period of 126 days. Both biochar amendments resulted in significant plant growth promotion. Rhizobacteria capable of growing with (1) S from aromatic sulfonates, (2) P from phosphate esters, (3) P from phosphonates, and (4) P from tri-calcium phosphates as sole source of S or P, respectively, were significantly more abundant in the biochar treatments. 16S r RNA gene-based rhizobacteria community analysis revealed a significant biochar treatment effect. Abundance of nematodes feeding on bacteria was also significantly increased in the biochar treatments. Diversity analysis of rhizospheric asfA and phnJ genes revealed broad sequence diversities in bacterial sulfonate and phosphonate-mineralizing capabilities. These findings suggest that biochar amendment enhances microbially mediated nutrient mobilization of S and P resulting in improved plant growth. [ABSTRACT FROM AUTHOR]

BACKGROUND Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long-term field experiment which divides conventional and organic agriculture into component pest-control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis ( DGGE) to characterise soil microbial communities in plots used for onion ( Allium cepa L.) cultivation. RESULTS Microbial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest-control treatment plots. CONCLUSION Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. © 2013 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

The impact of earthworms (Metaphire guillelmi) on nematode and enchytraeid abundance was investigated in soil with added maize (Zea mays L., 'suyu 19') residues in a laboratory experiment. Soil mixed with maize residues and earthworms was placed inside a mesh bag of different mesh size (1 mm or 5 µm), and then surrounded by an outside laver of soil mixed only with maize residues (i.e., no earthworms). The 1-mm diam. mesh would allow the movements of nematodes, enchytraeids, and soluble nutrients between the inner and outer soil but prevent the movements of earthworms. While the 5-µm diam. mesh would prevent the migration of earthworms, nematodes, and enchytraeids. The presence of earthworms significantly decreased the abundance of nematodes and enchytraieds in the inner soils of the different mesh-size treatments compared with that in the outer soils during the 7-wk incubation, except for enchytraeids at 1 wk. The presence of earthworms increased protozoan abundance in the inner soil. There was no significant difference in microbial biomass C between inner and outer soils at the end of experiment. Thus, abundant food resources (microbial biomass and protozoa) in the presence of earthworms indicate that competition for food and forced migration was not the main mechanism for decreased enchytraeid and nematode abundance. [ABSTRACT FROM AUTHOR]

The article discusses a study on the effects of bacterial-feeding nematodes on plant growth. For the study, researchers examined the impact of various nematode species on the activity of auxin-producing rhizobacteria and rice root growth. They found that rice seedlings cultivated in soils woth bacterial-feeding nematodes developed a more highly branched and longer root system.

Re-vegetation of trace element contaminated soils can alter the pH and chelating capacity in the rhizosphere, increasing the mobility of pollutants, which, in turn, may impact on rhizosphere ecology. In this study a short-term pot experiment was carried out in order to investigate the multi-factorial effects of: buffering capacity (sandy-loam and loam soils); pollutant load (0%, 1.3%, and 4% of pyrite sludge), and the presence/absence of plant (Lolium perenne L. and Medicago sativa L.) on the mobility of trace elements, soil biochemical functionality (hydrolase activities), and biological diversity (bacterial and nematode communities). The experiment was carried out with representative soils from the Guadiamar basin (SW Spain), an area where the Aznalcóllar mining spill affected over 4000ha. Results indicated that the development of rhizospheres in polluted soils (coarse-textured) increases the mobilization of trace elements. In general the presence of roots has stimulatory effects on soil quality indicators such as hydrolase activities and both bacterial and nematode communities. However, the presence of high amount of metals interferes with these beneficial effects. This study provided evidence about the complexity of the impact of growing plants on trace element polluted soils. Trace element mobilization, hydrolase activities and bacterial and nematode communities in the rhizosphere are dependent on plant species, soil type, and pollution dose. [Copyright &y& Elsevier]

Abstract: Molecular techniques offer an alternative to time-consuming traditional methods of faunal identification based on morphology. The first stage in developing a molecular technique is to have a robust method to extract DNA. Here methods are assessed using nematodes as a model faunal group. A traditional DNA extraction, with proteinase K digestion followed by phenol chloroform extraction; sodium hydroxide extraction; and physical disruption, followed by utilisation of one of four proprietary PCR purification kits were tested for nematode DNA extraction. Nematode communities were isolated from a range of habitats (arable agriculture, sand dune, coniferous forest, permanent pasture and moorland). Template DNA concentration was measured and PCR-amplification performed to test the suitability of the extracts for downstream molecular applications. DNA extraction with phenol chloroform purification consistently yielded high-quality template DNA as did the DNA extraction followed by the Purelink PCR purification kit. T-RFLP based on a single enzyme digest was sufficient to discriminate between nematode communities extracted from all five habitats. In addition, T-RFLP demonstrated that there was little difference in perceived nematode community composition following amplification of DNA extract purified through either the Qiaquick or Purelink kits. Physical disruption of tissue followed by purification through a kit provides a rapid, reliable and relatively inexpensive method of DNA extraction, yielding high-quality template. We suggest that kit suitability should be tested for each habitat under investigation as there may be a limited bias between kits for the community DNA extracted. Application of high-throughput molecular techniques to soil microfauna increases their potential to be used as indicators in routine monitoring of soil health. [Copyright &y& Elsevier]

Microinvertebrate abundance was measured, together with forest soil properties and litter components in eight plots dominated by beech and birch during May to August 2001. The results were analysed using ANOVA, stepwise regression and correlation analysis. Both protozoa and nematodes were analysed according to their functional groups. The protozoa were flagellates, ciliates and naked amoebae, and the nematodes were microbial and plant feeding nematodes. Moisture levels were between 28% and 33% in soil, and 50% to 70% in litter. Population numbers were very variable between sites and dates, and showed variable levels between May and July followed by a significant increase in August. ANOVA showed significant site and date effects, mainly in the litter. Stepwise regression models and correlation analysis revealed a number of interactions among separate groups of protozoa and nematodes, as well as their interrelations with fungi and bacteria. In addition, statistical analysis of soil data revealed a number of microfaunal relationships with soil pH, moisture and organic content, whilst in the field layer a number of significant interactions with specific forest litter fractions were found. The results have revealed particularly high levels of microfaunal abundance in the litter fraction compared to the soil, with flagellates and microbial feeding nematodes showing the highest levels among the trophic groups studied. These data compare well with other studies in similar ecosystems. The invertebrates present appear to be concentrated in hotspots of biological activity. In soil, they may predominantly have been confined to the rhizosphere. In the litter, their numbers may have been enhanced by nutrient availability, which may have increased throughout the study period owing to the gradual progress of decomposition facilitated by the combination of faunal, bacterial and fungal activity. [ABSTRACT FROM AUTHOR]

Summary: Soils from field sites at Foulum (DK), Narbons (FR) and Varois (FR) planted with genetically modified maize expressing either the insecticidal Bacillus thuringiensis protein (Bt) or herbicide tolerance (HT), as described elsewhere in this volume, were analysed for nematodes, protozoa and microbial community structure. These analyses were mirrored in single-species testing and in mesocosm experiments, and were coordinated with field samples taken for microarthropods, enchytraeids and earthworms so allowing for cross-comparison and a better understanding of the results observed in the field. Over the first 2 years of the field experiments (in 2002 and 2003), the effect of Bt-maize was within the normal variation expected in these agricultural systems. Sampling in 2004 and 2005 was expanded to include the effects of tillage (i.e. reduced tillage versus conventional tillage) and also the use of HT-maize. Tillage had major effects regardless of soil type (Varois or Foulum), with reduced-tillage plots having a greater abundance of microfauna and a different microbial community structure (measured both by phospholipid fatty-acid analysis (PLFA) and by community-level physiological profiling (CLPP)) from conventionally tilled plots. Grass, as a contrasting cropping system to maize, also had an effect regardless of soil type and resulted in greater microfaunal abundance and an altered microbial community structure. Differences in crop management, which for the Bt-maize was removal of the insecticide used to control European corn borer and for HT-maize was a change in herbicide formulation, were only tested at single sites. There were differences in microbial community structure (CLPP but not PLFA) and sporadic increases in protozoan abundance under the Bt-crop management. The HT-maize cropping system, which covered a shorter period and only one site, showed little change from the conventional system other than an altered microbial community structure (as measured by PLFA only) at the final harvest. The Bt-trait had a minimal impact, with fewer amoebae at Foulum in May 2003, fewer nematodes at Foulum in May 2004 but more protozoa at Varois in October 2002 and an altered microbial community structure (PLFA) at Foulum in August 2005. These were not persistent effects and could not be distinguished from varietal effects. Based on the field evaluations of microfauna and microorganisms, we conclude that there were no soil ecological consequences for these communities associated with the use of Bt- or HT-maize in place of conventional varieties. Other land management options, such as tillage, crop type and pest management regime, had significantly larger effects on the biology of the soil than the type of maize grown. [Copyright &y& Elsevier]

Abstract: Responses of nematode assemblages and soil function (short-term decomposition) in restored and degraded soil following an experimental disturbance (copper, chloroform, heat or drying) were monitored for 65 days. We tested the hypotheses: restoration enhanced the measured soil parameters; stability to disturbance was higher in degraded soil due to induced tolerance; and whether changes of the nematode assemblage were related to soil function. Even after disturbance, greater nematode abundance (>150 vs >10 per 100g soil), nematode richness (D′>1.0 vs >0.4) and function (>1.0 vs >0.05mg CO2 g−1 week−1) were maintained in restored than in degraded soil, respectively. An increase in nematode enrichment index (from 60 to >75) following all disturbances was attributed to the relatively high abundance of tolerant fungivores. The greater stability of the nematode structure index in degraded soil following heat and drying (120% and 125% respectively of the control), than in restored soil (90% and 30% of control) was due to a higher proportion of tolerant omnivores and carnivores. Thus some higher trophic level nematodes, with high c–p values, were tolerant to disturbance. However, stability of function was greater for restored than degraded soil, with a reduction over time in the degraded soil regardless of disturbance type. The differences in the responses of nematodes and soil function to disturbance suggest that nematodes could provide complementary insights into soil stability. [Copyright &y& Elsevier]

Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology. [ABSTRACT FROM AUTHOR]

In terrestrial ecosystems decomposing cadavers act as resource patches affecting nutrient cycling and soil communities, but the effects on soil communities are not well known. In this study we investigated nematode community response to decomposing pig cadavers ( Sus scrofa ) over a one-year period. As nematodes play key roles in soil food webs and are known to respond to disturbances and nutrient enrichment, we hypothesised that they would respond to decomposing cadavers and that this response would change over time. We compared the temporal patterns of nematode density and community structure under pig cadavers, either placed directly on the ground or hung 1 m aboveground (for effects of cadaveric fluids only), with two controls, i.e., bare soil and bags filled with soil placed on the ground (fake pigs – for microclimatic effects only). In the control and fake pig treatments nematode densities, community patterns and maturity indices did not change significantly. In contrast, density increased significantly underneath the ground and hanging pigs two weeks after the beginning of the experiment, and nematode family richness, Simpson diversity and maturity index were significantly reduced in the cadaver treatments. Most nematode families responded negatively to cadavers with the notable exceptions of Rhabditidae, Neodiplogasteridae and Diplogasteroididae. The latter two were found exclusively underneath the decomposing cadavers and are promising bioindicators of vertebrate cadaver decomposition. Even though diversity, density and communities were recovering after one year, the impact of cadavers was still significant for the maturity index. These contrasting patterns illustrate how decomposing cadavers contribute to increasing local biodiversity and suggest that soil nematodes could be used as a tool to document the presence of a decomposing cadaver, or to estimate the time elapsed since death (post-mortem interval). Patterns should, however, be compared in different settings and seasons before such a tool can be validated. [ABSTRACT FROM AUTHOR]

Previous results from a long-term grassland trial, located in south-east Ireland indicated conserved (homeostatic) nutrient stoichiometry of the soil microbial biomass despite widely varying soil C:N:P ratios. To determine whether this was associated with a change in microbial community structure, rather than a change in microbial physiology, this study characterized the responses of below-ground microbial and nematode community structure to P fertilization. The trial site maintained a range of P fertilisation rates (0-30 kg P ha−1 yr−1) which had been applied since 1968 and soil samples were collected in spring 2009, autumn 2010 and spring 2011. The microbial biomass demonstrated homeostatic stoichiometry over all sampling occasions, particularly of the C:P ratio, despite a 50-fold difference in soil solution C:P ratio. However, microbial and nematode community structure also varied with P fertilisation, indicating that nutrient ratios are maintained even though there were changes in microbial community structure. P fertilization induced a shift from fungal to bacterial dominated decomposition pathways, as indicated by the proportion of bacterial-feeding to fungal-feeding nematodes and bacterial: fungal phospholipid fatty acids (PLFAs). The altered microbial community structure was considered to result from bottom-up control of nutrient quality and quantity by altered vegetation structure and fertilizer inputs, as well as top-down pressures from the nematode community. [ABSTRACT FROM AUTHOR]

Abstract: Plant-mediated effects of aboveground herbivory on the belowground ecosystem are well documented, but less attention has been paid to agro-ecosystems and in particular how crop cultivars with different traits (i.e. resistance to pests) shape such interactions. A fully factorial experiment was conducted using four rice cultivars with different insect-resistance, with and without the aboveground herbivore Nilaparvata lugens (brown planthopper), and to test two hypotheses (1) aboveground herbivory affects the soil microbial biomass and nematode community by altering plant performance and soil resource availability and (2) herbivory effects will depend on cultivar resistance traits. Our results suggested that cultivar resistance mediated both herbivory intensity and herbivore effects on plant performance. N. lugens decreased the availability of soil resources (soluble sugars, amino acids, organic acids, dissolved organic carbon and nitrogen), microbial biomass and percentages of bacterivores when feeding on a susceptible cultivar but increased them in a resistant cultivar. However, total nematode abundance and the percentage of plant-parasitic nematodes responded in the opposite way, increasing under a susceptible cultivar and decreasing under a resistant cultivar. The development of plant-parasites under resistant cultivars before aboveground herbivory might contribute to their resistance traits. Our findings provide evidence that N. lugens significantly reversed the pattern of soil resource availability, microbial biomass and nematode community structure (abundance and trophic composition) across cultivars with distinct resistance. In the presence of aboveground pests, the agronomic use of resistant rice cultivars could also control populations of plant-parasites and promote soil resource availability, further extended to higher trophic level of soil food web. [Copyright &y& Elsevier]