AUTHOR=Orr Jamie N. , Neilson Roy , Freitag Thomas E. , Roberts David M. , Davies Keith G. , Blok Vivian C. , Cock Peter J. A. 

TITLE=Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2020

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.01763

DOI=10.3389/fpls.2019.01763

ISSN=1664-462X

ABSTRACT=<p><italic>Pasteuria</italic> spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly species-specific nematode suppression may be observed in soils containing a sufficiently high density of <italic>Pasteuria</italic> spp. spores. This suppression is enacted by the bacteria <italic>via</italic> inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of <italic>Pasteuria</italic> spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile <italic>Pasteuria</italic> spp. and nematode communities in parallel. We have investigated <italic>Pasteuria</italic> spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the <italic>Pasteuria</italic> spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that <italic>Pasteuria</italic> spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to <italic>Pasteuria hartismeri</italic>, a species first described parasitizing <italic>Meloidogyne ardenensis</italic>, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a <italic>Pasteuria</italic>-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and <italic>Pratylenchus</italic> spp. encumbered by <italic>Pasteuria</italic> spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the <italic>Pasteuria</italic> spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of <italic>Pasteuria</italic> species from eDNA.</p>