Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain
- PDF / 2,105,373 Bytes
- 13 Pages / 595.276 x 790.866 pts Page_size
- 14 Downloads / 171 Views
PLANT MICROBE INTERACTIONS
Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain Jonathan R. Dickey 1
&
James A. Fordyce 1 & Sarah L. Lebeis 2
Received: 26 October 2019 / Accepted: 31 August 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system. Keywords Rhizosphere microbiomes . 16S rRNA amplicon sequencing . Indicator species analysis . Hill numbers . Alpha diversity . Salvia
Introduction Plants transform the soil that surrounds their roots (i.e., the rhizosphere) with primary metabolites like amino acids, secondary metabolites like alkaloids, and macronutrients through litter deposition [1]. Rhizosphere modifications by plants influence critical relationships with microorganisms, such as fungi and bacteria, which utilize the rhizosphere niche [2]. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00248-020-01594-7) contains supplementary material, which is available to authorized users. * Jonathan R. Dickey [email protected] 1
Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996, USA
2
Department of Microbiology, The University of Tennessee, 307 Ken and Blaire Mossman Bldg., Knoxville, TN 37996, USA
Data Loading...
