Evaluation of metabarcoding primers for analysis of soil nematode communities

While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set. We used DNA from 22 nematode taxa, 10 mock communities, 20 soil samples, 4 root samples, and one bulk soil. We amplified the target regions from the DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the Nemf/18Sr2b primer set was superior for detecting soil nematodes compared to the other primer sets based on our sequencing results and on the annotation of our sequence reads at the genus and species ranks. This primer set generated 74% reads of Nematoda origin in the soil samples. Additionally, this primer set did well with the mock communities, detecting all the included specimens. It also worked better in the root samples than the other primer set that was tested. Therefore, we suggest that the Nemf/18Sr2b primer set could be used to study rhizosphere soil and root associated nematodes, and this can be done without an initial nematode extraction step

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history

Interspecies and seasonal variations in macroalgae from the Nordic region: Chemical composition and impacts on rumen fermentation and microbiome assembly

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Data from: High-throughput sequencing of nematode communities from total soil DNA extractions

Background: Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using standard methods such as identification based on morphology and therefore high-throughput sequencing is an attractive alternative. Generally, primers that have been used for generating amplicons for sequencing are not nematode specific and also amplify other groups such as fungi and plantae. Thus a nematode enrichment step must be included that may introduce biases. Results: An amplification strategy, including a new primer, which selectively amplifies nematodes and other metazoans was developed. When this strategy was tested on DNA templates from a set of 22 agricultural soils, we obtained 64.4 % sequences of nematode origin in total, whereas the remaining sequences were almost entirely metazoan. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This amplification and sequencing strategy for assessing nematode diversity was demonstrated to be able to collect a broad taxonomy of nematodes without prior enrichment and thus the method will be highly valuable in ecological studies of nematodes. Keywords: nematode, community, next-generation sequencing, SSU, diversity, 18S, rDN

Host- and Fusarium-Adapted Bacterial Consortia Alter Microbial Community Structures in Arabidopsis Roots and Suppress Fusarium oxysporum

The plant-associated microbiota confers beneficial traits to the plant host by promoting growth and preventing disease. However, it is not fully understood how the host and its associated microbiota interact with pathogens. In this work, we studied how the host plant modulates its associated microbiome to suppress disease. For this, we used two Arabidopsis thaliana lines with different host responses to Fusarium oxysporum f. sp. mathioli (FOM). We isolated bacterial consortia (BCs) from FOM-infected or healthy host plants of the two lines of Arabidopsis and studied their effect on the root-associated microbiota and FOM progression in the following generations of Arabidopsis plants. Root bacterial and fungal communities were profiled using 16S ribosomal RNA and internal transcribed spacer amplicon sequencing, respectively, while quantitative PCR was used for assessment of FOM quantities in shoots of Arabidopsis. Host- or pathogen-adapted BCs significantly reduced FOM quantities in shoots of both the resistant Col-0 and the susceptible Ler-0 Arabidopsis lines. Several bacterial taxa, including Chthoniobacter, Bacillus, Chryseobacterium and Actinoplanes negatively correlated with FOM, suggestive of an antagonistic effect. Furthermore, both host- and pathogen-adapted BCs significantly affected community composition with distinct differentially abundant taxa and co-occurrence network structures. Taken together, our findings suggest that using a subcommunity selection approach is a potential route for exploiting plant-associated rhizosphere microbiomes for engineering disease resilient microbiomes. [Graphic: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license

Improving the nutritional values of yellow mealworm Tenebrio molitor (Coleoptera : Tenebrionidae) larvae as an animal feed ingredient : a review

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