Using high-throughput sequencing quantitatively to investigate soil nematode community composition in a steppe-forest ecotone

Du, Xiaofang; Li, Yingbin; Han, Xu; Ahmad, Wasim; Li, Qi

doi:10.1016/j.apsoil.2020.103562

Cited by 46 publications

(31 citation statements)

References 43 publications

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“…Region 1 covered both V1 and V2 hypervariable regions, and region 2 spanned the V4 regions of the eukaryotic 18S rDNA sequences reported by Hugerth et al [38]. Both PCR target regions have been used in previous DNA barcode analyses of nematode communities using the next-generation sequencer Roche 454 [20,21,26,39] or Illumina MiSeq [22,23,25,27,28,40,41]. Regions 2 and 3 were newly examined in this study and spanned the V4 region and the V5-V7 regions, respectively ( Fig 1B).…”

Section: Experimental Design and Nematode Isolation From Copse Soilsmentioning

confidence: 84%

“…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].…”

Section: Detection Of Svs and Taxonomic Analyses Of Nematode Isolatesmentioning

confidence: 99%

“…In the past decade, the extensive advancement of DNA sequencing technology has transformed from the "one-by-one DNA barcoding" method using Sanger sequencing of a PCR amplicon from an individual organism, to the "DNA metabarcoding" method using NGS-assisted massive sequencing of an amplicon from a complex community. Currently, several studies concerning the DNA metabarcoding of terrestrial [20][21][22][23][24][25] and marine nematodes [26][27][28] have been conducted using deep sequencing of SSU-derived amplicons. However, potential regions of the SSU gene that would be most suitable for NGS-based DNA metabarcoding have not been investigated in detail yet.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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Nematodes are representative soil metazoans with diverged species that play crucial roles in nutrient recycling in the pedosphere. Qualitative and quantitative information on nematode communities is useful for assessing soil quality, and DNA barcode-mediated taxonomic analysis is a powerful tool to investigate taxonomic compositions and changes in nematode communities. Here, we investigated four regions (regions 1-4) of the 18S small subunit ribosomal RNA (SSU) gene as PCR targets of deep amplicon sequencing for the taxonomic profiling of individual soil nematodes. We determined the sequence variants (SVs) of 4 SSU regions for 96 nematodes (total 384 amplicons) isolated from copse soils and assigned their taxonomy using the QIIME2 software with dada2 or deblur algorithm and the SILVA database. Dada2 detected approximately 2-fold more nematode-derived SVs than deblur, and a larger number of SVs were obtained in regions 1 and 4 than those in other regions. These results and sufficient reference sequence coverage in region 4 indicated that DNA barcoding using a primer set for region 4 followed by dada2-based analysis would be most suitable for soil nematode taxonomic analysis. Eighteen SSU-derived operational taxonomic units (rOTUs) were obtained from 68 isolates, and their orders were determined based on the phylogenetic trees built by four regional sequences of rOTUs and 116 nematode reference species as well as the BLASTN search. The majority of the isolates were derived from three major orders Dorylaimida (6 rOTUs, 51.5% in 68 isolates), Rhabditida (4 rOTUs, 29.4%), and Triplonchida (7 rOTUs, 17.6%). The predicted feeding types of the isolates were fungivores (38.2% in total nematodes), plant feeders (32.4%), and 14.7% for both bacterivores and omnivores/predators. Additionally, we attempted to improve the branch structure of phylogenetic trees by using long nucleotide sequences artificially prepared by connecting regional sequences, but the effect was limited.

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Section: Experimental Design and Nematode Isolation From Copse Soilsmentioning

confidence: 84%

Section: Detection Of Svs and Taxonomic Analyses Of Nematode Isolatesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…The meadow steppe was treated as grassland with moderate disturbance of human activity due to the mowing each year (Cao et al 2019;Yan et al 2016). The grassland from forest-steppe ecotone was selected as the natural grassland with little disturbance and human activity (Du et al 2020). We hypothesized that grassland degradation will have negative influences on soil quality and soil biotic communities, with lower SQI index and diversity of soil biotic community observed in the degraded grassland compared with the meadow steppe and grassland from the forest-steppe ecotone.…”

Section: Introductionmentioning

confidence: 99%

Effect of grassland degradation on soil quality and soil biotic community in a semi-arid temperate steppe

Han

et al. 2020

Ecol Process

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Grasslands provide a number of ecosystem services for human society. Degradation of grasslands results in the loss of biodiversity and leads to the deterioration of ecosystem functions. In order to accurately assess the influence of grassland degradation on belowground ecosystems, we conducted experiments on a temperate steppe with different levels of degradation and investigated the influence of degradation on soil quality and soil biotic communities. Our results showed that grassland degradation significantly decreased soil quality, with lower values of soil quality index (SQI) observed in the degraded grassland than the meadow steppe and the grassland from the forest-steppe ecotone. Changes in the SQI along the grassland degradation gradient were positively correlated with soil carbon stock and the aboveground biomass, and negatively correlated with the root shoot ratio. Nematode trophic diversity and the ratio of fungal to bacterial PLFA were lower in the degraded grassland than the grassland from the forest-steppe ecotone. The dissimilarities in soil microbial and nematode community composition increased with the changes in soil quality index. Our results indicate that soil quality index based on the minimum data sets could effectively assess the influence of grassland degradation on soil biodiversity and ecosystem function. In order to effectively restore degraded grasslands, the key contributors to the soil quality, such as soil carbon, should be taken on priority basis for revitalizing the soil biodiversity and ecosystem function.

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“…Nitrogen enrichment caused by nitrogen deposition is one of the main reasons leading to species extinction and changes in species composition in grassland ecosystems (Zhang et al, 2014). Shifts in plant composition has an important mediation effect on soil bacteria, fungi and their consumers (Bezemer et al, 2010;Zhang et al, 2015;Du et al, 2020). Nematodes, as the most important microbial predators in soil, are good indicators for evaluating the structure and function of soil food webs because they are closely related to the soil environment and are sensitive to habitat disturbance (Yeates, 2003;Bardgett and van der Putten, 2014).…”

Section: Introductionmentioning

confidence: 99%

Mowing did not mitigate the negative effects of nitrogen deposition on soil nematode community in a temperate steppe

Liang

et al. 2020

Soil Ecol. Lett.

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Soil nematodes are the most numerous components of the soil fauna in terrestrial ecosystems. The occurrence and abundance of nematode trophic groups determine the structure and function of soil food webs. However, little is known about how nitrogen deposition and land-use practice (e.g. mowing) affect soil nematode communities. We investigated the main and interactive effects of nitrogen addition and mowing on soil nematode diversity and biomass carbon in nematode trophic groups in a temperate steppe in northern China. Nitrogen addition and mowing significantly decreased the abundance of soil nematodes and trophic diversity but had no effects on nematode richness and the Shannon-Wiener diversity. Nitrogen addition influenced soil nematode communities through decreasing soil pH. Mowing influenced soil nematode communities through decreasing soil moisture. Nitrogen addition enhanced the bacterial energy channel but mowing promoted fungal energy channel in the soil micro-food web. Our study emphasizes that ecosystem function supported by soil organisms can be greatly influenced by nitrogen deposition, and mowing cannot mitigate the negative effects of nitrogen deposition on soil food webs.

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Using high-throughput sequencing quantitatively to investigate soil nematode community composition in a steppe-forest ecotone

Cited by 46 publications

References 43 publications

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

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

Effect of grassland degradation on soil quality and soil biotic community in a semi-arid temperate steppe

Mowing did not mitigate the negative effects of nitrogen deposition on soil nematode community in a temperate steppe

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