Microbial Flow Within an Air-Phyllosphere-Soil Continuum

Abstract

The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.

Keywords: airborne microbial community; leaf microbiota; microcosm; phyllosphere; source tracking.

FIGURE 1

Schematic of the equipment used in the current study for plant cultivation and identifying the source of microbial communities.

FIGURE 2

The percentage of microbial communities at phylum (A) and family (B) level, calculated by the average of replicates. “M” represents the chamber 1 samples (with extra outdoor microbes) and “NM” represents chamber 2 samples (without extra microbes). AM, PCM, PSOM, SCM, and SSOM represents the air, phyllosphere, and soil of Allium schoenoprasum and Sonchus oleraceus samples, respectively, in chamber 1 (with external airborne microbes). The ANM, PCNM, PSONM, SCNM, and SSONM represents the air, phyllosphere, and soil of A. schoenoprasum and S. oleraceus samples, respectively, in chamber 2 (without external airborne microbes).

FIGURE 3

Dissimilarity analysis of microbial OTUs, phyla, and families for all samples. “M” represents chamber 1 samples (with extra outdoor microbes) and “NM” represents chamber 2 samples (without extra microbes). (A) Cluster diagram at OTU level. (B,C) The Principal Coordinate Analysis (PCoA) is based on the Bray-Curtis distance for microbial phylum and family, respectively. Different colors represent different habitats, while different shapes indicate each chamber.

FIGURE 4

Venn diagram at OTU level for the two chambers. “M” represents chamber 1 samples (with extra outdoor microbes) and “NM” represents chamber 2 samples (without extra microbes). AM and ANM, PCN and PCNM, PSOM and PSONM represent the air, phyllosphere, and soil samples of Allium schoenoprasum and Sonchus oleraceus in chambers 1 and 2 (with or without extra airborne microbes), respectively. (A,C) represent the overview of shared OTUs between air, phyllosphere, and soil samples in chamber 1; (B,D) represent shared OTUs between air, phyllosphere, and soil samples in chamber 2. (E–G) represent shared microbial OTUs between AM and ANM, PCN and PCNM, PSOM and PSONM, respectively.

FIGURE 5

Fast expectation-maximization microbial source tracking (FEAST) analysis for chamber 1 (A) and chamber 2 (B) based on OTUs level. Direction of the arrows represents the source-sink relationships, and percentages represent the contribution that each source provides.