Agricultural habitats are dominated by rapidly evolving nematodes revealed through phylogenetic comparative methods

Gong, Xin; Chen, Xiaoyun; Geisen, Stefan; Zhang, Jingru; Zhu, Huimin; Hu, Feng; Liu, Manqiang

doi:10.1016/j.soilbio.2021.108183

Cited by 17 publications

(3 citation statements)

References 71 publications

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“…In addition, recent studies suggest that in nature, Pristionchus nematodes live in complex ecosystems with competing nematode species ( Herrmann et al 2006 ; Meyer et al 2017 ; Gong et al 2021 ; Renahan and Sommer 2021 ). In this context, cellulases might provide P. pacificus more pronounced ecological advantages.…”

Section: Discussionmentioning

confidence: 99%

Horizontally Acquired Cellulases Assist the Expansion of Dietary Range inPristionchusNematodes

Han

Sieriebriennikov

Susoy

et al. 2022

Molecular Biology and Evolution

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Horizontal gene transfer (HGT) enables the acquisition of novel traits via non-Mendelian inheritance of genetic material. HGT plays a prominent role in the evolution of prokaryotes, whereas in animals, HGT is rare and its functional significance is often uncertain. Here, we investigate horizontally acquired cellulase genes in the free-living nematode model organism Pristionchus pacificus. We show that these cellulase genes i) are likely of eukaryotic origin, ii) are expressed, iii) have protein products that are secreted and functional, and iv) result in endo-cellulase activity. Using CRISPR/Cas9, we generated an octuple cellulase mutant, which lacks all eight cellulase genes and cellulase activity altogether. Nonetheless, this cellulase null mutant is viable and therefore allows a detailed analysis of a gene family that was horizontally acquired. We show that the octuple cellulase mutant has associated fitness costs with reduced fecundity and slower developmental speed. Furthermore, by using various Escherichia coli K-12 strains as a model for cellulosic biofilms, we demonstrate that cellulases facilitate the procurement of nutrients from bacterial biofilms. Together, our analysis of cellulases in Pristionchus provides comprehensive evidence from biochemistry, genetics, and phylogeny, which supports the integration of horizontally acquired genes into the complex life history strategy of this soil nematode.

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Section: Discussionmentioning

confidence: 99%

Horizontally Acquired Cellulases Assist the Expansion of Dietary Range inPristionchusNematodes

Han

Sieriebriennikov

Susoy

et al. 2022

Molecular Biology and Evolution

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“…Recently, SILVA and PR2 databases have been successfully used in a number of nematode studies (Sapkota and Nicolaisen, 2015;Kerfahi et al, 2016;Geisen et al, 2018;Schuelke et al, 2018;Bongiorno et al, 2019;Wilschut et al, 2019;Sikder et al, 2020;Gong et al, 2021). However, studies on how the choice of reference database may influence nematode taxonomic classification and phylogenic results are lacking entirely.…”

Section: Comparison Of Reference Databasesmentioning

confidence: 99%

Optimising high-throughput sequencing data analysis, from gene database selection to the analysis of compositional data: a case study on tropical soil nematodes

Wang,

Schneider,

Hartke

et al. 2024

Front. Ecol. Evol.

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IntroductionHigh-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data, providing a very powerful tool to analyze biodiversity of soil organisms. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databases, controversial sequence similarity thresholds for delimitating taxa, and downstream compositional data analysis. MethodsHere, we use HTS data from a soil nematode biodiversity experiment to explore standardized HTS data processing procedures. We compared the taxonomic assignment performance of two main rDNA reference databases (SILVA and PR2). We tested whether the same ecological patterns are detected with Amplicon Sequence Variants (ASV; 100% similarity) versus classical Operational Taxonomic Units (OTU; 97% similarity). Further, we tested how different HTS data normalization methods affect the recovery of beta diversity patterns and the identification of differentially abundant taxa.ResultsAt this time, the SILVA 138 eukaryotic database performed better than the PR2 4.12 database, assigning more reads to family level and providing higher phylogenetic resolution. ASV- and OTU-based alpha and beta diversity of nematodes correlated closely, indicating that OTU-based studies represent useful reference points. For downstream data analyses, our results indicate that loss of data during subsampling under rarefaction-based methods might reduce the sensitivity of the method, e.g. underestimate the differences between nematode communities under different treatments, while the clr-transformation-based methods may overestimate effects. The Analysis of Compositions of Microbiome with Bias Correction approach (ANCOM-BC) retains all data and accounts for uneven sampling fractions for each sample, suggesting that this is currently the optimal method to analyze compositional data.DiscussionOverall, our study highlights the importance of comparing and selecting taxonomic reference databases before data analyses, and provides solid evidence for the similarity and comparability between OTU- and ASV-based nematode studies. Further, the results highlight the potential weakness of rarefaction-based and clr-transformation-based methods. We recommend future studies use ASV and that both the taxonomic reference databases and normalization strategies are carefully tested and selected before analyzing the data.

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“…It could weaken top-down control by decreasing the abundance of predators which are sensitive to disturbances (Köhl et al, 2014;Murrell and Barton, 2017). The limited resource supply could cause nematode diversity and footprint reduction in agricultural habitats, compared with natural ecosystems (Gong et al, 2021;Zhang et al, 2017). Simultaneously, monoculture could stimulate the plant parasitic nematodes which is a potential threat to agriculture (Decraemer and Hunt, 2006).…”

Section: Introductionmentioning

confidence: 99%

Precipitation regulated soil nematode community and footprint in cropland ecosystems

Guan

Hao

et al. 2023

Soil Ecol. Lett.

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Nematode abundance and footprint show unimodal patterns with precipitation levels.• MAP governed nematode diversity along the precipitation gradient of agroecosystem.• Soil pH determined nematode abundance and footprint in low precipitation levels. Precipitation plays a crucial role in global biodiversity change across terrestrial ecosystems. Precipitation is proven to affect soil organism diversity in natural ecosystems. However, how precipitation change affects the function of the soil nematode community remains unclear in cropland ecosystems. Here, we tested soil nematode communities from different precipitation sites (300 mm to 900 mm) of the agricultural ecosystem. The abundance of total nematodes, fungivores, and plant parasites, together with the footprint of fungivores was significantly affected by mean annual precipitation (MAP) in cropland ecosystem. Plant parasites diversity and footprint showed negative relationships with MAP. The random forest suggested plant parasite footprint was the most responsive to MAP. The structural equation model revealed that MAP affected nematode abundance and footprint indirectly via soil pH; nematode diversity was affected by MAP directly. We conclude that precipitation could act as the main selection stress for nematode diversity among the large gradient of agricultural ecosystems. However, the soil pH may act as a stress factor in determining nematode community and carbon flow in the soil food web. Our study emphasized that using nematode value by trophic group would provide a deep understanding of nematode response to precipitation in cropland ecosystems.

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Agricultural habitats are dominated by rapidly evolving nematodes revealed through phylogenetic comparative methods

Cited by 17 publications

References 71 publications

Horizontally Acquired Cellulases Assist the Expansion of Dietary Range inPristionchusNematodes

Horizontally Acquired Cellulases Assist the Expansion of Dietary Range inPristionchusNematodes

Optimising high-throughput sequencing data analysis, from gene database selection to the analysis of compositional data: a case study on tropical soil nematodes

Precipitation regulated soil nematode community and footprint in cropland ecosystems

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