Search

The separate and collective role of soil nematodes and protists at community level in soil biogeochemical processes remains poorly quantified due to the lack of appropriate methodologies to study them independently from other soil biota under conditions emulating natural soil. Here we present a methodological exploration for the selective removal of nematodes and protists using gamma irradiation and the subsequent reinoculation with metazoan-free soil powder inoculum that allows reconstructing a complex microbial food web comprising the native microflora and soil protist communities, without other fauna. Nematodes, and culturable flagellates and ciliates were removed from 6 kGy onwards, while a small fraction of the amoebae survived (8% of the entire protist population) at 16 kGy but were totally removed at 27 kGy. Reinoculation with pulverized soil powder successfully established a protist community of similar size and composition as the control soil as assessed by both amplicon sequencing-based detection and microscopic observation after cultivation. A viable native microflora community remained from 6 to 16 kGy doses, but microbial activity was completely inhibited at 27 kGy. We suggest that, in ecological relevant experiments where selective removal of nematodes or other fauna is the purpose and protist community is meant to be kept intact, gamma irradiation needs to be followed routinely by soil powder inoculation in order to restore the suppressed protist community. This experiment also opens up new perspectives for studying the ecological roles of the entire protist community or specific groups thereof (flagellates and ciliates) in real soil and in the presence of a viable native microflora community.

Sustainable agriculture requires the careful optimization of the use of organic amendments to improve soil fertility while minimizing any harmful environmental effects. To understand the events that occur in soil after the addition of different organic amendments, we evaluated the nitrogen (N) mineralization dynamics in soil after adding organic amendments, and evaluated changes in the microbial population. The four organic amendments were fresh dairy cattle manure, fresh white clover, vegetable, fruit, and yard waste compost, and poplar tree compost. The N mineralization potential of each organic amendment was determined by analyzing total mineral nitrogen during a 97-day laboratory incubation experiment. Soils amended with clover released 240 μg N g −1 soil during the 97-day incubation, more than twice as much as that released from soils amended with manure or composts (76–100 μg N g −1 soil). At the end of the incubation, the net N mineralization in clover-amended soils was 54%, more than five times higher than that in soils amended with composts or manure (4%–9%). Nitrogen was mineralized faster in clover-amended soil (1.056 μg N g −1 soil day −1 ) than in soil amended with composts (0.361–0.417 μg N g −1 soil day −1 ). The microbial biomass carbon content was higher in clover-amended soil than in the soils amended with manure or composts. We monitored changes in the microbial population in amended soils by a phospholipid fatty acid (PLFA) analysis. On day 97, there were higher concentrations of total PLFAs in soils with organic amendments (e.g., 14.41 nmol g −1 in clover-amended soil) than in control soil without amendments (9.84 nmol g −1 ). Bacteria (Gram-positive and Gram-negative), actinomycetes, and fungi were more abundant in clover-amended soils than soils amended with manure or composts. The N mineralization potential varied among the four organic amendments. Therefore, the timing of application and the type of organic amendment should be matched to the nutrient needs of the crop.

Gamma irradiation is becoming a potential tool in soil ecological studies as it gives a possibility to vary a dose that selectively kills the target organism. It makes minimum changes in soil biochemical properties as compared to autoclaving and freezing. Although gamma irradiation has often been used in studying the roles of nematodes on nutrient cycling, the recommended doses to eliminate nematodes still lead to a nutrient flush, and are less reproducible. Given that the indirect effect of gamma irradiation is through radiolysis, the same dose might have a different effect on the soil biochemical properties as the soil moisture content changes. Thus, an optimal dose that eliminates nematodes needs to be determined taking the moisture content of the soil sample at the time of irradiation into consideration. We conducted an incubation experiment for about three months during which the effects of a range of low gamma irradiation doses (0, 1, 3 and 5 kGy) at different moisture content (air dried, 50% water filled pore space (WFPS), 80%WFPS) were tested on nematode abundance and selected soil biochemical properties. Leaching with water immediately after irradiation at 50%WFPS, was used to assess to what extent it would remove N from the flush. The results showed that as the moisture content of the soil increases from 50%WFPS to 80%WFPS, nematode abundance, enzyme activities and total mineral N concentrations decreased during most of the incubation period at each irradiation dose. Increasing the moisture content, however, did not make significant changes in total phospholipid fatty acid concentrations in all levels of irradiations except at 3 kGy. These findings indicate the effects of gamma irradiation on soil biological and chemical properties vary depending on the moisture content of the soil at the time irradiation. Moreover, the moisture content of the soil at the time of gamma irradiation need to be considered during optimizing gamma irradiation as a tool in selective sterilization or defaunation. In the current experimental set up, the application of 3 kGy at 80%WFPS at the time of irradiation eradicated nematodes and left a comparable microbial abundance and community structure to the unirradiated CTR. Leaching the 50%WFPS samples irradiated at 5 kGy dose immediately after irradiation generally significantly reduced both NH 4 + -N and NO 3 − -N concentrations, but NH + 4 -N concentration remained higher compared to the unirradiated CTR. This indicates that leaching with water only partly reduced the nutrient flush and underlines the need to test additional methods to reduce the nutrient flush further.

Soil quality in vegetable cropping systems is seriously threatened by intensive tillage and fertilization practices and by limited crop rotations. Inclusion of cover crops, compost application and reduced tillage may help to sustain soil quality. A three-year field trial was set up on horticultural land to explore the combined effects of compost amendment at three rates (0, 15 and 45 Mg ha−1 year−1) and tillage practices (reduced tillage versus conventional ploughing) on soil quality. Cover crop was not a factor in the experiment, but cover crops were included in the rotation for reasons of good agricultural practice. The highest compost dose supported the initial level of total organic carbon in the arable layer. The decrease in pH in the arable layer was considerably limited by compost application, irrespective of the dose applied. Reduced tillage resulted in a favorable stratification for different soil quality indicators both by placement of organic inputs near the soil surface and by a reduction of leaching of base cations and organic carbon compounds. Differences between tillage practices and compost doses were most striking in the 0–10 cm soil layer. Compost application at the highest rate enhanced organic C content by 16% compared to the content in the non-amended soil. Reduced tillage induced a 13% higher organic C content in the 0–10 cm soil layer than that in the underlying 10–30 cm layer. Combining reduced tillage and recurrent compost application resulted in a different soil microbial community structure in the 0–10 cm surface layer, as revealed by phospholipid fatty acids analysis. Total microbial biomass was 44% higher under reduced compared to conventional tillage and increased by 27% due to compost application at a rate of 45 Mg ha−1 year−1. Fungal biomass doubled in the surface layer by reduced tillage. Actinomycetes and arbuscular mycorrhizal fungi were favored by both reduced tillage and compost application. Conversion to reduced tillage allowed for sustaining crop production in this intensive vegetable cropping system. Compost application and reduced tillage counteracted soil degradation.

We compared the effect of organic and conventional farming practices on soil microbial dynamics in West Java, Indonesia. A secondary forest was included to obtain natural reference values. On the organic farms, soil fertility is maintained mainly with composted organic matter in contrast to conventional farmers who combine fresh manure and chemical fertilizers, and typically apply large amounts of pesticides. Parameters measured were dehydrogenase, β-glucosidase, acid phosphomonoesterase and β-glucosaminidase activity, microbial biomass C (MBC) and microbial community composition by phospholipid fatty acid analysis. A strong negative impact of intensive chemical fertilizer and pesticide use on soil enzyme activities was demonstrated. Dehydrogenase and β-glucosidase activities were correlated with soil organic matter content and pH. β-glucosidase activity under organic management approached that under forest, while MBC and dehydrogenase activity remained higher under forest. The composition of the soil microbial community strongly differed between forest and cultivated soil, a clear difference in composition was also observed between conventional and organic farming. Dehydrogenase activity and C16:1ω5c, marker fatty acid for arbuscular mycorrhizal fungi, appeared to be particularly suited as indicators of the impact of management on soil quality and on the soil microbial community.