Shifts of the soil microbiome composition induced by plant-plant interactions under increasing cover crop densities and diversities

Abstract

Interspecific and intraspecific competition and facilitation have been a focus of study in plant-plant interactions, but their influence on plant recruitment of soil microbes is unknown. In this greenhouse microcosm experiment, three cover crops (alfalfa, brassica, and fescue) were grown alone, in paired mixtures, and all together under different densities. For all monoculture trials, total pot biomass increased as density increased. Monoculture plantings of brassica were associated with the bacteria Azospirillum spp., fescue with Ensifer adhaerens, and alfalfa with both bacterial taxa. In the polycultures of cover crops, for all plant mixtures, total above-ground alfalfa biomass increased with density, and total above ground brassica biomass remained unchanged. For each plant mixture, differential abundances highlighted bacterial taxa which had not been previously identified in monocultures. For instance, mixtures of all three plants showed an increase in abundance of Planctomyces sp. SH-PL14 and Sandaracinus amylolyticus which were not represented in the monocultures. Facilitation was best supported for the alfalfa-fescue interaction as the total above ground biomass was the highest of any mixture. Additionally, the bulk soil microbiome that correlated with increasing plant densities showed increases in plant growth-promoting rhizobacteria such as Achromobacter xylosoxidans, Stentotrophomonas spp., and Azospirillum sp. In contrast, Agrobacterium tumefaciens, a previously known generalist phytopathogen, also increased with alfalfa-fescue plant densities. This could suggest a strategy by which, after facilitation, a plant neighbor could culture a pathogen that could be more detrimental to the other.

Figure 1

Above ground dry biomass in monoculture for crop densities of one plant total, 24 plants total, and 48 plants total. (a) Alfalfa dry biomass (purple), (c) brassica dry biomass (gold), and (e) fescue dry biomass (green). Constrained Principal Coordinate Analysis (PCoA) using Bray–Curtis distance for comparing bulk soil bacteriomes of increasing crop densities by each individual crop (b) alfalfa, (d) brassica, and (f) fescue. Colors were used to represent increasing densities from 1 plant (red), 24 plants (yellow), and 48 plants (green). Letters (a, b, and c) indicate significant differences between the mean values of plant biomass with (Tukey P < 0.05). Error bars are the SD.

Figure 2

Above ground dry biomass for the alfalfa and brassica crop mixture densities of two plants total, 24 plants total, and 48 plants by (a) total alfalfa (purple), (b) total brassica (gold), and (c) total biomass (alfalfa and brassica). (d) Constrained Principal Coordinate Analysis (PCoA) using Bray–Curtis distance for comparing bulk soil bacteriomes of increasing crop densities of the alfalfa and brassica mixture. Colors were used to represent increasing densities from 2 plants (red), 24 plants (yellow), and 48 plants (green). Letters (a, b, and c) indicate significant differences between the mean values of plant biomass with (Tukey P < 0.05), and ns = not significant differences. Error bars are the SD.

Figure 3

Above ground dry biomass for the alfalfa and fescue crop mixture densities of two plants total, 24 plants total, and 48 plants by (a) total alfalfa (purple), (b) total fescue (green), and (c) total biomass (alfalfa and fescue). (d) Constrained Principal Coordinate Analysis (PCoA) using Bray–Curtis distance for comparing bulk soil bacteriomes of increasing crop densities of the alfalfa and fescue mixture. Colors were used to represent increasing densities from 2 plants (red), 24 plants (yellow), and 48 plants (green). Letters (a, b, and c) indicate significant differences between the mean values of plant biomass with (Tukey P < 0.05). Error bars are the SD.

Figure 4

Above ground dry biomass for the alfalfa and fescue crop mixtures for densities of two plants total, 24 plants total, and 48 plants by (a) total brassica (gold), (b) total fescue (green), and (c) total brassica and fescue. (d) Constrained Principal Coordinate Analysis (PCoA) using Bray–Curtis distance for comparing bulk soil bacteriomes of increasing crop densities of the brassica and fescue mixture. Colors were used to represent increasing densities from 2 plants (red), 24 plants (yellow), and 48 plants (green). Letters (a, b, and c) indicate significant differences between the mean values of plant biomass with (Tukey P < 0.05), and ns = not significant differences. Error bars are the SD.

Figure 5

Above ground dry biomass for the alfalfa, brassica, and fescue crop mixture densities of three plants total, 24 plants total, and 48 plants shown separately by (a) total alfalfa (purple), total brassica (gold), total fescue (green), and (b) total biomass (alfalfa, brassica, and fescue). (d) Constrained Principal Coordinate Analysis (PCoA) using Bray–Curtis distance for comparing bulk soil bacteriomes of increasing crop densities of the alfalfa, brassica, and fescue mixture. Colors were used to represent increasing densities from 3 plants (red), 24 plants (yellow), and 48 plants (green). Letters (a, b, and c) indicate significant differences between the mean values of plant biomass with (Tukey P < 0.05), and ns = not significant differences. Error bars are the SD.