Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition

Abstract

While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.

Keywords: bacteria biodiversity; environmental interactions; microbial ecology; nutrient acquisition; plant holobiont.

Figure 1

Main types of plant habitats colonised by microorganisms, s.l.—sensu lato; s.s—sensu stricto; (a) general microhabitats; (b) leaf microhabitats; (c) rhizosphere s.l. microhabitats (Graphic elements from u/nnnn (ipuzzle. pl) and Berkshire Community College Bioscience Image Library (CC0, via Flickr) were used).

Figure 2

Schematic representation of the four eco-evolutionary processes shaping community assembly, using soil and plant-associated communities as examples, inspired by schemes by Cordovez et al. [88]; (a) dispersal, a spatial process with both deterministic and stochastic properties; (b) selection, representing deterministic changes in the community composition; (c) ecological drift, representing stochastic changes in taxa abundance; (d) diversification, representing evolutionary change (see text for more information).

Figure 3

Three groups of symbiotic N2-fixers (graphic elements from PNGWing (non-commercial DMCA), Pixabay (CC0), PhyloPic (CC0) and Nefronus (CC BY-SA 4.0, via Wikimedia Commons) were used).

Figure 4

Examples of siderophores belonging to different groups. Inside the circles, the functional groups based on which the siderophores are classified are shown (in the case of mixed-typed siderophores, these are example groups). Graphics from the MetaCyc database [213] were used.

Figure 5

The depiction of negative frequency-dependent selection based on schemes of Morris et al. and Kramer et al. [207,221].