The Root-Associated Microbial Community of the World's Highest Growing Vascular Plants

Abstract

Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.

Keywords: Plant-associated bacteria; Subnival soil; Upward migration; Vascular plants.

Fig. 1

Six vascular plant species discovered at 6150 m.a.s.l.: Draba alshehbazii, Draba altaica, Ladakiella klimesii, Poa attenuata, Saussurea gnaphalodes and Waldheimia tridactylites

Fig. 2

Observed richness (S), a non-parametric richness estimation (Ace) and a parametric richness estimation (using CathAll). Means and standard errors in the different plant species and the soil sample. Errors were propagated from the standard errors associated with each replicate. Values were calculated for each sample using bootstrapped subsampling at 1000 iterations. Samples sharing one of the letters appearing next to the symbols are not significantly different (p < 0.05)

Fig. 3

Shannon–Wiener, inverse Simpson and Berger–Parker diversity indices. Means and standard errors in the different plant species and the soil sample. Errors were propagated from the errors associated with each replicate. Values were calculated for each sample using bootstrapped subsampling of the sequences at 1000 iterations. Samples sharing one of the letters appearing next to the symbols are not significantly different (p < 0.05)

Fig. 4

Taxonomic classification and relative abundances of sequences recovered from the root and soil samples. Representative sequences of each OTU classified at the bacterial order level. Colours of the heat map indicate the cumulative relative abundance of all sequences in a sample classified to a particular order. Grouping (bold lines) separates each sample, whilst numbers on the X-axis indicate replicates. Unclassified: sequences with <70 % classification agreement. Rare: all taxa comprising each <1 % of the sequences

Fig. 5

Sample clustering to metacommunities together with a heat map of the root-associated and soil bacterial OTU dataset with hierarchical clustering. Heat map shows the root-associated and soil bacterial OTU abundances (square-root-transformed), with samples grouped according to the metacommunity from which they most likely have originated. The mean of the Dirichlet component for that mixture is shown to the right of each metacommunity. Only the first 30 OTUs are shown, those with the greatest variability across metacommunities (see Table S2 for details)