Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots: A morphological and metabarcoding approach

Abstract

Soil biodiversity plays a key regulation role in the ecosystem services that underpin regenerative sustainable agriculture. It can be impacted by agricultural management techniques, both positively (through measures such as compost application) and negatively (through, for example, application of synthetic nitrogen). As one of the most numerous members of the soil biota, nematodes are well established as indicators for the soil food web. However, compost application also includes the addition of nematodes present in compost and their subsequent survival in soil is unknown. Nematode communities within the compost applied to soil, and nematode communities in the soil of a multi-year rotational cropping field trial in Melle (Belgium) were studied using morphological and metabarcoding techniques. Compost (C) and nitrogen fertilizer (NF) treated plots were compared. Three replicate plots were investigated for each of the following treatments: C application only; C and NF application; NF only; no C and no NF (control). Plots were sampled six times between 2015-2017, before and after C or NF were added each spring and after crop harvest (except for 2017). NF treatment resulted in a significant decrease of fungal feeding and predatory nematodes, while herbivorous nematodes were positively affected. Remarkably, we did not find compost addition to exert any noticeable effects on the soil nematode community. The morphological and metabarcoding data resulted in different results of the nematode community composition. However, trends and patterns in the two data sets were congruent when observed with NMDS plots and using the nematode maturity index. Metabarcoding of individual compost nematode taxa demonstrated that nematodes originating from compost did not persist in soil.

Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions

“…Approximately nine variable regions of eukaryotic SSU genes have been suggested as potential DNA barcodes by Hugerth et al [ 38 ] and Hadziavdic et al [ 37 ]; several metabarcoding studies of isolated terrestrial nematode communities have been reported. In many of these, the V7–V8 region (region 4 in this study) of the SSU gene amplified by the primer set including NF1 and 18Sr2b has been preferentially used as a DNA barcode [ 20 , 22 , 30 – 33 , 36 , 56 ] ( S1 Fig ). The V1–V2 (here, region 1) [ 36 ], V4–V5 (here, region 2) [ 21 , 32 , 57 , 58 ], and V9 [ 58 ] regions have also been used for DNA barcoding of nematodes ( S1 Fig ).…”

“…There have been several reports of taxonomic analyses of nematodes in forest [ 33 , 58 , 60 – 71 ] and agricultural field [ 11 , 13 , 15 – 17 , 19 – 22 , 30 , 72 ] soils. Studies on forest soils have shown that bacteria, plant, and fungus feeders occupy significant fractions of the nematode communities despite varied proportions by the sampling sites, periods, and environmental status of forests [ 33 , 62 , 68 , 70 ].…”

“…Nematode communities in agricultural fields have also been reported to contain mainly bacteria, fungus, and plant feeders, with minor groups of omnivores and predators [ 11 , 13 , 15 – 17 , 19 – 22 , 30 , 72 ]. However, the proportions of feeding groups in agricultural soils can be modified by tillage [ 15 , 20 , 21 ], fertilizers and compost treatments [ 13 , 15 – 17 , 19 , 20 , 22 ], or crop cultivation [ 16 , 17 ]. A prior investigation, in which Sanger-based DNA barcoding of individual nematodes from soybean-cultivated agricultural soils using a 900 bp-region encompassing regions 1 and 2 as a barcode ( S1 Fig ) allowed for the identification of 13 rOTUs, which were mainly classified to the Rhabditida-derived bacteria feeders [ 26 ].…”

“…Nematodes play a crucial role in the nutrient cycling of soil biota and influence plant growth [ 7 ]. Nematode taxonomic compositions vary by ecosystem type [ 8 , 9 ] and are influenced by various factors such as food availability and abundance, physical and chemical parameters (e.g., pH, temperature) [ 10 , 11 ], soil properties [ 11 , 12 ], and agricultural conditions (e.g., tillage, cultivated plants, fertilizers) [ 13 – 22 ]. These characteristics strongly indicate that the taxonomic composition and abundance of nematodes can be used as an indicator for biological conditions in soils [ 2 , 23 – 25 ].…”

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene

“…Nematodes play crucial roles in the nutrient cycling of soil biota and influence plant growth [4,5]. Nematode taxonomic compositions vary by ecosystem type [6] and are influenced by various factors such as food, temperature, humidity, pH and nutrients in soils [7], soil properties [7,8], cultivated plants [9], tillage [10], and fertilizers [11,12]. These characteristics strongly indicate that the taxonomic composition of nematodes can be used as an excellent indicator for assessing biological, chemical, and nutrient status in soils [13,14].…”