Field-scale monitoring of nitrate leaching in agriculture: assessment of three methods.

Deterioration of groundwater quality due to nitrate loss from intensive agricultural systems can only be mitigated if methods for in-situ monitoring of nitrate leaching under active farmers' fields are available. In this study, three methods were used in parallel to evaluate their spatial and temporal differences, namely ion-exchange resin-based Self-Integrating Accumulators (SIA), soil coring for extraction of mineral N (Nmin) from 0 to 90 cm in Mid-October (pre-winter) and Mid-February (post-winter), and Suction Cups (SCs) complemented by a HYDRUS 1D model. The monitoring, conducted from 2017 to 2020 in the Gäu Valley in the Swiss Central Plateau, covered four agricultural fields. The crop rotations included grass-clover leys, canola, silage maize and winter cereals. The monthly resolution of SC samples allowed identifying a seasonal pattern, with a nitrate concentration build-up during autumn and peaks in winter, caused by elevated water percolation to deeper soil layers in this period. Using simulated water percolation values, SC concentrations were converted into fluxes. SCs sampled 30% less N-losses on average compared to SIA, which collect also the wide macropore and preferential flows. The difference between Nmin content in autumn and spring was greater than nitrate leaching measured with either SIA or SCs. This observation indicates that autumn Nmin was depleted not only by leaching but also by plant and microbial N uptake and gaseous losses. The positive correlation between autumn Nmin content and leaching fluxes determined by either SCs or SIA suggests autumn Nmin as a useful relative but not absolute indicator for nitrate leaching. In conclusion, all three monitoring techniques are suited to indicate N leaching but represent different transport and cycling processes and vary in spatio-temporal resolution. The choice of monitoring method mainly depends (1) on the project's goals and financial budget and (2) on the soil conditions. Long-term data, and especially the combination of methods, increase process understanding and generate knowledge beyond a pure methodological comparison.

Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long-term field experiments.

Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life-history groups are used for calculating food web indices, i.e., maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high-throughput amplicon sequencing to investigate the effects of tillage (conventional vs. reduced) and organic matter addition (low vs. high) on nematode communities and food web indices in 10 European long-term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality.

Soil phoD and phoX alkaline phosphatase gene diversity responds to multiple environmental factors.

Alkaline phosphatases such as PhoD and PhoX are important in organic phosphorus cycling in soil. We identified the key organisms harboring the phoD and phoX genes in soil and explored the relationships between environmental factors and the phoD- and phoX-harboring community structures across three land uses located in arid to temperate climates on two continents using 454-sequencing. phoD was investigated using recently published primers, and new primers were designed to study phoX in soil. phoD was found in 1 archaeal, 13 bacterial and 2 fungal phyla, and phoX in 1 archaeal and 16 bacterial phyla. Dominant phoD-harboring phyla were Actinobacteria, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes and Proteobacteria, while abundant phoX-harboring phyla were Acidobacteria, Actinobacteria, Chloroflexi, Planctomycetes, Proteobacteria and Verrucomicrobia. Climate, soil group, land use and soil nutrient concentrations were the common environmental drivers of both community structures. In addition, the phoX-harboring community structure was affected by pH. Despite differences in environmental factors, the dominant phyla in the phoD-harboring community remained similar in all samples, while the composition of phoX differed substantially between the samples. This study shows that the composition of phoD and phoX is governed by the same environmental drivers but that phoD and phoX occur partly in different phyla.

An inter-laboratory comparison of gaseous and liquid fumigation based methods for measuring microbial phosphorus (Pmic) in forest soils with differing P stocks.

In an inter-laboratory trial, gaseous ("CFE") and liquid fumigation ("Resin") based methods for measuring microbial phosphorus (Pmic) were compared, based on the analysis of soil samples from five forests, which differ in their P stocks. Both methods reliably detected the same Pmic gradient in the different soils. However, when the individual recovery rates of spiked P were taken into account, the "CFE" based methods consistently generated higher Pmic values (factor 2) compared to the "Resin" based approaches.

phoD Alkaline Phosphatase Gene Diversity in Soil.

Phosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution of phoD genes using whole-genome and metagenome databases. phoD alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity of phoD, we developed a new set of primers which targets phoD genes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 different phoD operational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalent phoD genes identified in these soils were affiliated with the orders Actinomycetales (13 to 35%), Bacillales (1 to 29%), Gloeobacterales (1 to 18%), Rhizobiales (18 to 27%), and Pseudomonadales (0 to 22%). The primers also amplified phoD genes from additional orders, including Burkholderiales, Caulobacterales, Deinococcales, Planctomycetales, and Xanthomonadales, which represented the major differences in phoD composition between samples, highlighting the singularity of each community. Additionally, the phoD bacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity of phoD in soil and represent a valuable tool for the study of phoD alkaline phosphatase in environmental samples.

Fertilization strategies affect phosphorus forms and release from soils and suspended solids.

The release of phosphorus from soils in surface runoff is strongly influenced by fertilizer inputs and contributes significantly to agriculturally driven eutrophication. This work evaluated the forms and availability of P in bulk soils and suspended solids (SS) produced by a water dispersion test that mimics the action of rain events and/or irrigation. This test was applied on soils cultivated with maize and fertilized with mineral N, P, and K (NPK); mineral P and K (PK); bovine slurry and P (S); or manure and P (M) for 15 yr. The P surplus in the treated soils was in the order NPK < PK < S < M. Forms and availability of P were analyzed in bulk soils, and their respective SS (<20 µm) by the Hedley sequential P fractionation method and the isotopic exchange kinetics. The labile forms increased according to P surplus and represented up to 15 and 25% of total P in the bulk soil and in the SS, respectively, indicating a selective enrichment of the more labile P forms in the erodible particles. Exchangeability of P from SS was rapid and intense as a result of a shift of P solution equilibrium at the increased water/solid ratio and a larger accumulation of more labile P in the detached particles than in the bulk soil. Phosphorus saturation of iron and aluminum oxides and the enrichment of fertilizer-derived P salts in the suspended solids control P forms and exchangeability for mineral fertilizer treatments, whereas in M soil carbon content assumed a key role.

Oxygen isotopes unravel the role of microorganisms in phosphate cycling in soils.

Phosphorus (P) is considered the ultimate limiting nutrient for plants in most natural systems and changes in the distribution of inorganic and organic P forms during soil development have been well documented. In particular, microbial activity has been shown to be an important control on P cycling but its contribution in building up the pool of plant-available P during soil development is still poorly quantified. To determine the importance of different biological processes on P cycling, we analyzed the isotopic composition of oxygen in phosphate (δ(18)O-Pi) from the parent material, soil microorganisms, the available P pool, and from the vegetation along a 150-year soil chronosequence of a glacier forefield. Our results show that at all sites, δ(18)O-Pi of microbial Pi is within the range expected for the temperature-dependent equilibrium between phosphate and water. In addition, the isotopic signature of available Pi is close to the signature of microbial Pi, independently of the contribution of parent material Pi, vegetation Pi or Pi released from organic matter mineralization. Thus, we show that phosphate is cycled through soil microorganisms before being released to the available pool. This isotopic approach demonstrates for the first time in the field and over long time scales, and not only through controlled experiments, the role of the microbial activity in cycling of P in soils.