Does plant diversity determine the diversity of the rhizosphere microbial community?

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Close connection and mutual influence in this communication allow to talk about the self-adjusting “plant-rhizosphere community” system, which should be be studied in connection. Diversity estimation is one of the ways of describing both bacterial and plant communities. Based on the literature, there are two assumptions of how the diversity of plant communities related to the diversity of bacterial communities: 1) an increase in the species richness of plants leads to an increase in the number of available micro-niches, and increasing of microbial diversity, 2) an increase in the species richness of plants is accompanied by the predominant development of bacteria from highly productive specific taxa and decreasing in the diversity of microorganisms. Experimental studies show controversial results. We analyzed field sites (rye crop field and two fallow sites), using DNA isolation of both the plant root mass (followed by sequencing of the ITS1 region) and rhizosphere microorganisms (followed by sequencing of the 16s rDNA V4 region). This allowed us to 1) accurately determine the abundance and taxonomic position of plant communities; 2) extract information about both plant and microbial communities from the same sample. There was no correlation between alpha-diversity indices of plants and rhizosphere communities. Alpha-diversity connection should be explored in similar plant communities, such as synusia. We hypothesize, that the significant differences in plant abundances lead to significant changes in exudation profiles, and the loss of diversity connection. The beta-diversity between rhizosphere communities and plant communities is highly correlated, in particular in terms of the abundance of taxa. This can be explained by a potential correlation (as reported in the literature) or by the presence of statistical artifacts.

119 PCR and agarose gel electrophoresis. Sequencing of the V4 variable region of the 16S rRNA gene 120 was performed on an Illumina MiSEQ sequencer, using the primers F515 121 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACTACVSGGGTATCTAAT) [23]. 122 Plant DNA from roots was isolated using mechanical destruction in liquid nitrogen, followed 123 by phenol extraction; the quality of the DNA was also checked via agarose gel electrophoresis.

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The general processing of sequences was carried out in R 3.6.4, using the dada2 (v. 1 and PLANiTS [28] were used. 130 The main alpha-and beta-metrics were calculated using the phyloseq and picante [29] 131 packages. For the mean p-distance in a library, we used the home-brew script with following steps: 132 1) make multiple alignment for reference sequences; 2) extract p-value for every pair of sequence; 133 3) multiple this p-value to abundance of both seqences; 3) sum all values. Correlations between 134 diversity indices were calculated using Spearman correlation.  144 (provided in the S1 Table) corresponded with the composition structure according to ITS1 145 sequencing (Fig 1A).   166 Acidobacteria (Blastocatellales), and Actinobacteria (Pseudonocardiales) were more abundant.
For all samples, the most common alpha-diversity indices, observed OTUs, Shannon, 168 Simpson, mpd (mean pairwise distance), and p-dist (mean p-distance, restored from alignment, see 169 Materials and Methods), were calculated at different taxonomic levels (Fig 3).

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The plant communities were highly diverse at different levels and indices ( Fig 3A). The 173 observed OTU index was not useful because of the presence of weedy plants in the rye crop.
174 Weighted indices, such as mpd or p-dist, were more suitable; the differences between sample sites 175 were significant for both indices up to the order level.

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The bacterial communities were less diverse. The observed OTUs as well as the p-dist and 177 mpd indices showed that communities from the PolyC site were more diverse, mostly at low 178 taxonomical levels (OTUs, genus). Interestingly, samples from rye roots (MonoR) were 179 significantly less diverse at phylum level, whereas at other taxonomical ranks, there were no such 180 differences.

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For each index on the OTU taxonomic level, the correlation between plant diversity indices 182 and microbial diversity indices was calculated. We observed no significant correlations between 183 plant and rhizosphere microbial diversity.  193 communities, from plants and from rhizospheres, formed their own clusters (Fig 3B).

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The correlation between the distance matrix in plant and bacterial communities was high for 195 the Bray distance (R = 0.866, p = 0.01) and not significant for the weighted UniFrac index. Fig 5   196 shows the results of the beta-distance correlation, excluding the intra-cluster distance (distance 197 between repeats of the same sample).  Fig 3A), with variations in abundance; it therefore seems logical that the exudomes of 223 these communities also will differ not in the number of different spectra but in their weights. In

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In this study, using modern approaches, we found no correlation between different alpha-