Meiofaunal diversity in the Atlantic Forest soil: A quest for nematodes in a native reserve using eukaryotic metabarcoding analysis

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

“…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 ). The regions 1 (V1–V2), 2 (V4), 3 (V5–V7), and 4 (V7–V8) in this study were analyzed for their capabilities in the DNA barcoding of individual nematodes isolated from the copse soil, as published by Kenmotsu et al [ 28 ]; region 4 was indicated as a suitable barcode of the SSU gene.…”

“…A large fraction of the sequence reads from the isolated nematodes were often occupied by non-nematode species in previous MiSeq-assisted amplicon sequencing. Approximately 5% of the total reads were only derived from the phyrum Nematode in the metabarcoding using the eukaryotic universal primers for the V4 and V9 regions and the nematodes from the forest soils, and most of the reads was derived from Fungi and Rhizaria [ 58 ]. Treonis et al investigated the taxa of nematode communities from different types of agricultural soils by amplicon sequencing using NF1-18Sr2b primers with the Miseq platform [ 20 ].…”

“…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 ].…”

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

“…Pothula and colleagues have examined the impact of agricultural intensification and urbanization on soil nematode communities using 111 published articles and examined the richness and abundance of 5 trophic groups in 5 different environmental soils including forest [ 50 ], indicating that the order of abundance was herbivores (plant feeders) > bacterivores > fungivores and omnivores > predators despite high variation. So far, several taxonomic studies on soil nematode communities in forest soils have been known and were performed using morphogenic and sequence-based approaches over the world (Brazil [ 51 ], Canada [ 52 ], China [ 53 – 56 ], Germany [ 57 ], Japan [ 58 , 59 ], Slovakia [ 60 ], Sweden [ 61 ], USA [ 62 ]). These studies have shown that bacterial feeders, plant feeders, and fungivores often occupied significant fractions of the nematode communities in forest soils.…”

“…A relatively high abundance of bacterial feeders has been commonly found; however, their proportions varied by the sampling sites and periods [58,62], age [56], and environmental status of the forests [25,52,55] or treatments such as clear-cut harvesting and fertilization [61,63]. Omnivores and predators were found in relatively minor fractions of soil nematodes in forest soils except in natural re-establishing subtropical forest [54] and coastal fir and pine forests [51,58]. In contrast, our results showed that fungal and plant feeders dominated and the abundance of bacterial feeders significantly decreased in the nematode community in copse soils.…”