Bacterial Diversity and Interaction Networks of Agave lechuguilla Rhizosphere Differ Significantly From Bulk Soil in the Oligotrophic Basin of Cuatro Cienegas

Abstract

Due to the environmental conditions presented in arid zones, it is expected to have a high influence of deterministic processes over the community assemblages. Symbiotic interactions with microorganisms could increase colonization and survival of plants in difficult conditions, independent of the plants physiological and morphological characteristics. In this context, the microbial communities associated to plants that inhabit these types of areas can be a good model to understand the community assembly processes. We investigated the influence of stochastic and deterministic processes in the assemblage of rhizosphere microbial communities of Agave lechuguilla and bulk soil on the Cuatro Cienegas Basin, a site known for its oligotrophic conditions. We hypothesize that rhizospheric microbial communities of A. lechuguilla differ from those of bulk soil as they differ in physicochemical properties of soil and biotic interactions, including not only the plant, but also their microbial co-occurrence networks, it is expected that microbial species usually critical for plant growth and health are more common in the rhizosphere, whereas in the bulk soil microbial species related to the resistance to abiotic stress are more abundant. In order to confirm this hypothesis, 16S rRNA gene was sequenced by Illumina from rhizospheric and bulk soil samples in two seasons, also the physicochemical properties of the soil were determined. Our results showed differences in bacterial diversity, community composition, potential functions, and interaction networks between the rhizosphere samples and the ones from bulk soil. Although community structure arises from a complex interplay between deterministic and stochastic forces, our results suggest that A. lechuguilla recruits specific rhizospheric microbes with functional traits that benefits the plant through growth promotion and nutrition. This selection follows principally a deterministic process that shapes the rhizospheric microbial communities, directed by the plant modifications around the roots but also subjected to the influence of other environmental variables, such as seasonality and soil properties. Interestingly, keystone taxa in the interactions networks, not necessarily belong to the most abundant taxonomic groups, but they have an important role by their functional traits and keeping the connections on the community network.

Keywords: agave microbiome; community assembly; functional traits; keystone species; microbial co-occurrence.

Figure 1

Heatmap constructed using the relative abundance of the identified phyla in all samples. The intensity of red color represents relative abundance. Superior dendogram is the result of the clustering analysis using Bray Curtis dissimilarity index, each sample is colored according to their origin, rhizosphere (green) or bulk soil (brown).

Figure 2

Relative abundance of functional guilds participating in nutrient cycles, traits conferring stress tolerance, and traits conferring environmental adaptation in rhizosphere and bulk soil. Asterisks indicate significant differences. Bars represent standard errors.

Figure 3

NMDS analysis using relative abundance at a genus level. Arrows indicate the physicochemical properties that resulted in a significant relationship with the microbial community.

Figure 4

Interaction networks found for Rhizosphere and bulk soil over two seasons. The size of the nodes represents the importance in the network, i.e. the bigger the node is the more connections it has with other OTUs. Red rows are negative interactions, while blue rows are positive interactions. The color of each node represents the community to which it belongs.