Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Primers used in this study.

Article Snippet: Taxonomy was assigned to ZOTUs using UCLUST ( ) via assign-taxonomy.py in QIIME v1.91 ( ) to cluster ZOTU sequences iteratively between 100% and 90% identity to our curated Pasteuria spp. reference database for 16S rRNA gene products and to the SILVA-132 database ( ) for the 18S rRNA gene products.

Techniques: Sequencing

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Boxplots of Pasteuria penetrans (A) and P. hartismeri (B) 16S rRNA gene template copy number vs the merged paired read copy number ul −1 of product added to the final sequencing pool. Spearman's rank correlation is given as Rho and p. Loess curve of best fit is given as the blue trend line with dark grey shading representing uncertainty in this fit with a 95% confidence interval. Template copy number, representing the number of plasmids in each PCR reaction carrying the target gene, was log transformed as each input copy number was an order of magnitude greater or less than the next smallest or largest.

Article Snippet: Taxonomy was assigned to ZOTUs using UCLUST ( ) via assign-taxonomy.py in QIIME v1.91 ( ) to cluster ZOTU sequences iteratively between 100% and 90% identity to our curated Pasteuria spp. reference database for 16S rRNA gene products and to the SILVA-132 database ( ) for the 18S rRNA gene products.

Techniques: Sequencing, Transformation Assay

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Maximum likelihood phylogeny and pairwise sequence identity heatmap of Pasteuria spp. taxonomic reference sequences used in primer design and Pasteuria spp. ZOTU taxonomic assignment.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques: Sequencing

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Map of distribution of the most abundant Pasteuria spp. ZOTUs across both NSIS2 (circles) and ESFN (triangles) datasets. Plot points are colored by ZOTU and sized as a function of the total number of merged read pairs recovered for that ZOTU µl −1 of product added to the final pool from the corresponding sample.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: NDMS ordination plot of NSIS2 Pasteuria spp. community composition. Points are colored by soil horizon where L = litter; H = humus; O = peaty material formed under wet, anaerobic conditions; and A = mineral horizon formed at or near the surface showing accumulation and incorporation of organic matter. Points are sized by the total number of merged read pairs µl −1 of PCR product added to the final pool from the corresponding sample. Stress = 0.245235.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Environmental variables with a statistically significant relationship to Pasteuria spp. community ordination before or after Benjamini-Hochberg correction.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Spearman’s rank correlation of soil properties with statistically significant correlation to Pasteuria spp. community composition.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: The top three most abundant Pasteuria spp. ZOTUs in the ESFN dataset and respective metazoan ZOTU Spearman’s rank correlations which were statistically significant after Benjamini-Hochberg correction.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: (A) 400x magnification Pratylenchus spp. recovered from ESFN soil with Pasteuria spp. endospore attached (position indicated by red arrow). (B) 1000x magnification of Pratylenchus spp. recovered from ESFN soil with Pasteuria spp. endospore attached (position indicated by red arrow). (C) 1000x magnification of free living non-parasitic nematode recovered from ESFN soil with several Pasteuria spp. endospores attached (positions indicated by red arrows). (D) 1000x magnification of fluorescence image of Pratylenchus spp. recovered from ESFN soil with Pasteuria spp. endospore attached (position indicated by blue arrow), showing anti- Pasteuria penetrans antibody recognition.

Article Snippet: Of these ZOTUs 75 (50.7%) were at least 90% similar to curated Pasteuria spp. reference sequences and only one sequence returned a best hit as low as 92% similarity.

Techniques: Fluorescence