The Minimal Rhizosphere Microbiome

Abstract

The rhizosphere provides a home to numerous (micro) organisms that in turn may affect plant growth, development, and tolerance to abiotic and biotic stresses. How plants shape the rhizosphere microbiome has been subject of many past and present studies with the ultimate goal to identify plant genetic traits that select and support beneficial microorganisms. Novel 'omics technologies have provided more in-depth knowledge of the diversity and functioning of the rhizosphere microbiome and significant advances are being made to uncover mechanisms, genes and metabolites involved in the multitrophic interactions in the rhizosphere. To better understand this intriguing complexity, both reductionists' and systems ecology approaches are needed to identify the biotic and abiotic factors involved in microbiome assembly. Here, different strategies are discussed to re-shape the rhizosphere microbiome in favour of microbial consortia that promote root development and plant growth, and that prevent the proliferation of pests and diseases. IntroductionCurrently more than one third of the crop yields worldwide are lost due to abiotic and biotic stress factors, such as drought, salinity, pests and diseases. Future increases in crop yields will have to be achieved on sub-optimal soils with reduced input of fertilizers and pesticides ('more with less'). These challenges have increased the awareness of the importance of the plant microbiome (i.e. the collective communities of microorganisms on and in plants, their genomes and interactions) for improved and sustainable agricultural practices. Plants are colonized by an astounding number of microorganisms that can have profound effects on seed germination, plant growth and development, nutrition, diseases and productivity. In this context, plants can be viewed as superorganisms that rely in part on their microbiome for specific functions J. M. Raaijmakers ( )

Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere

“…The niche differentiation among these plant compartments with substantially distinct micro-environments can explain this topological distinction. In the rhizosphere, the nutrients including volatile organic compounds, trace elements, and other metabolites deposited by plant roots are able to attract abundant microorganisms including fungi, making the rhizosphere to be one of the most dynamic interfaces on the earth (Philippot et al, 2013; Raaijmakers, 2015). Resource and food availabilities are important drivers of both macro- and microbiological network structures (Zhou et al, 2011; Foster et al, 2012).…”

“…Rhizosphere, which is a narrow zone surrounding the plant roots, is a hot-spot of microbial activity and interactions (Raaijmakers, 2015; Wang et al, 2017). The rhizosphere microbial community harbors members that exert neutral, deleterious, or beneficial effects on their host plants, but are all part of the complex food web sustained by large amount of carbon and other nutrients released by plant roots (Raaijmakers et al, 2009; Raaijmakers, 2015). Therefore, the rhizosphere is akin to a battlefield where the complex microbial community members interact with each other and influence the outcome of pathogen infection and host health and growth (Raaijmakers et al, 2009).…”

Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

“…To our knowledge there are no plant breeding strategies yet that have evaluated plant lines for their broad interaction with the rhizosphere microbiome. In this regard, it has been speculated to design a minimal rhizosphere microbiome ( Raaijmakers, 2015 ), in analogy to the minimal genome ( Juhas et al, 2011 ), with the final aim to select only these microorganisms (or traits) which are proficient for soil remediation and plant health.…”

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems

“…The complex plant-associated microbial community, also referred to as the “second genome of the plant”, is crucial for plant health, growth and development 13 . Previous work investigating microbial communities associated with growing media has mainly focused on the absence of pathogenic bacteria and fungi 14 .…”