Plant microbiome

Plants live in association with diverse microorganisms, collectively called the microbiome. These microbes live either inside (endosphere) or outside (episphere) of plant tissues. Microbes play important roles in the ecology and physiology of plants. "The core plant microbiome is thought to comprise keystone microbial taxa that are important for plant fitness and established through evolutionary mechanisms of selection and enrichment of microbial taxa containing essential functions genes for the fitness of the plant holobiont."

Overview

Microbiome in plant ecosystem

Schematic plant and plant-associated microbiota colonizing different niches on and inside the plant tissue. All the above-ground plant parts together, called the phyllosphere, are a continuously evolving habitat due to ultraviolet (UV) radiation and altering climatic conditions. It is primarily composed of leaves. Below-ground plant parts, mainly roots, are generally influenced by soil properties. Harmful interactions affect the plant growth through pathogenic activities of some microbiota members (left side). On the other hand, beneficial microbial interactions promote plant growth (right side).

The study of the association of plants with microorganisms precedes that of the animal and human microbiomes, notably the roles of microbes in nitrogen and phosphorus uptake. The most notable examples are plant root-arbuscular mycorrhizal (AM) and legume-rhizobial symbioses, both of which greatly influence the ability of roots to uptake various nutrients from the soil. Some of these microbes cannot survive in the absence of the plant host (the ‘obligate symbionts’ including viruses, some bacteria and fungi), which provides space, oxygen, proteins, and carbohydrates to the microorganisms. The association of AM fungi with plants has been known since 1842, and over 80 % of land plants are found associated with them. It is thought that AM fungi helped in the domestication of plants. Traditionally, culturable microbes have been used for plant-microbe interaction studies with the enormous unculturable microbes remain uninvestigated and consequently, our knowledge of the roles of these unculturable microbes remains largely unknown.

Unraveling the types and outcomes of plant-microbe interactions has received considerable interest among ecologists, evolutionary biologists, plant biologists, and agronomists. Recent developments in meta-omics and the establishment of large collections of microorganisms have dramatically increased our knowledge of the plant microbiome composition and diversity. The sequencing of marker genes of entire microbial communities, referred to as metagenomics, sheds light on the phylogenetic diversity of the microbiomes of plants. It also adds to the knowledge of the major biotic and abiotic factors responsible for shaping plant microbiome community assemblages.

Plant microbiota

Diverse microbial communities of characteristic microbiota are part of plant microbiomes, and are found on the outside surfaces and in the internal tissues of the host plant, as well as in the surrounding soil.

Rhizosphere microbiome

Microbial consortia naturally formed
on the roots of Arabidopsis thaliana

Scanning electron microscopy pictures of root surfaces from natural A. thaliana populations showing the complex microbial networks formed on roots.
a) Overview of an A. thaliana root (primary root) with numerous root hairs. b) Biofilm-forming bacteria. c) Fungal or oomycete hyphae surrounding the root surface. d) Primary root densely covered by spores and protists. e, f) Protists, most likely belonging to the Bacillariophyceae class. g) Bacteria and bacterial filaments. h, i) Different bacterial individuals showing great varieties of shapes and morphological features.

See also: Rhizosphere

The rhizosphere comprises the 1–10 mm zone of soil immediately surrounding the roots that is under the influence of the plant through its deposition of root exudates, mucilage and dead plant cells. A diverse array of organisms specialize in living in the rhizosphere, including bacteria, fungi, oomycetes, nematodes, algae, protozoa, viruses, and archaea. The most frequently studied beneficial rhizosphere organisms are mycorrhizae, rhizobium bacteria, plant growth promoting rhizobacteria (PGPR), and biocontrol microbes. Gans and Wolinsky projected that one gram of soil could harbor more than a million distinct bacterial genomes. İnceoğlu and Al-Soud reported 55,121 OTUs (operational taxonomic units) from the potato rhizosphere. Among the prokaryotes in the rhizosphere, the most frequent bacteria are within the Acidobacteria, Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, and Firmicutes. In some studies, no significant differences were reported in the microbial community composition between the bulk soil (soil not attached to the plant root) and rhizosphere soil. Certain bacterial groups (e. g. Actinobacteria, Xanthomonadaceae) are less abundant in the rhizosphere than in nearby bulk soil .

Mycorrhizal fungi are abundant members of the rhizosphere community, and have been found in over 200,000 plant species, and are estimated to associate with over 80% of all plants. These mycorrhizae–root associations play profound roles in land ecosystems by regulating nutrient and carbon cycles. Mycorrhizae are integral to plant health because they provide up to 80 % of N and P requirements. In return, the fungi obtain carbohydrates and lipids from host plants. Recent studies of arbuscular mycorrhizal fungi using sequencing technologies show greater between-species and within-species diversity than previously known.

Phyllosphere microbiome

A leaf from a healthy Arabidopsis plant (left) and a leaf from a dysbiosis mutant plant (right)

See also: Phyllosphere

The aerial surface of a plant (stem, leaf, flower, fruit) is called the phyllosphere and is considered comparatively nutrient poor when compared to the rhizosphere and endosphere. The environment in the phyllosphere is more dynamic than the rhizosphere and endosphere environments. Microbial colonizers are subjected to diurnal and seasonal fluctuations of heat, moisture, and radiation. In addition, these environmental elements affect plant physiology (such as photosynthesis, respiration, water uptake etc.) and indirectly influence microbiome composition. Rain and wind also cause temporal variation to the phyllosphere microbiome. Overall, there remains high species richness in phyllosphere communities. Fungal communities are highly variable in the phyllosphere of temperate regions and are more diverse than in tropical regions. There can be up to 107 microbes per cm2 present on leaf surfaces of plants, and thus the bacterial population of the phyllosphere on a global scale is estimated to be 1026 cells. The population size of the fungal phyllosphere is likely to be smaller [25]. Phyllosphere microbes from different plants appear to be somewhat similar at high levels of taxa, but at the lower levels taxa there remain significant differences. This indicates that microorganisms may need finely tuned metabolic adjustment to survive in phyllosphere environment. Proteobacteria seems to be the dominant colonizers, with Bacteroidetes and Actinobacteria also predominant in phyllospheres. Although there are similarities between the rhizosphere and soil microbial communities, very low similarity has been reported between phyllosphere communities and those in open air.

Endosphere microbiome

Some microorganisms, such as endophytes, penetrate and occupy the plant internal tissues, forming the endospheric microbiome. The AM and other endophytic fungi are the dominant colonizers of the endosphere. Bacteria, and to some degree Archaea, are important members of endosphere communities. Some of these endophytic microbes interact with their host and provide obvious benefits to plants. Unlike the rhizosphere and the rhizoplane, the endospheres harbor highly specific microbial communities. The root endophytic community can be very distinct from that of the adjacent soil community. In general, diversity of the endophytic community is lower than the diversity of the microbial community outside the plant. The identity and diversity of the endophytic microbiome of above-and below-ground tissues may also differ within the plant.

Reference books

• Saleem M (2015) Microbiome Community Ecology: Fundamentals and Applications Springer. ISBN 9783319116655.
• Kumar V, Prasad R, Kumar M and Choudhary DK (2019) Microbiome in Plant Health and Disease: Challenges and Opportunities Springer. ISBN 9789811384950.

• Kumar, Vivek; Prasad, Ram; Kumar, Manoj; Choudhary, Devendra K. (10 August 2019). Microbiome in Plant Health and Disease: Challenges and Opportunities. ISBN 9789811384950.

• Grube, Martin; Schloter, Michael; Smalla, Kornelia; Berg, Gabriele (22 January 2015). The plant microbiome and its importance for plant and human health. ISBN 9782889193783. PMID 25278934.

• Egamberdieva, Dilfuza; Ahmad, Parvaiz (6 February 2018). Plant Microbiome: Stress Response. ISBN 9789811055140.

• Castiglione, Stefano; Cicatelli, Angela; Ferrol, Nuria; Rozpadek, Piotr (22 August 2019). Effects of Plant-Microbiome Interactions on Phyto- and Bio-Remediation Capacity. ISBN 9782889459322.

• Castiglione, Stefano; Cicatelli, Angela; Ferrol, Nuria; Rozpadek, Piotr (22 August 2019). Effects of Plant-Microbiome Interactions on Phyto- and Bio-Remediation Capacity. ISBN 9782889459322.

• Carvalhais, Lilia C.; Dennis, Paul G. (30 December 2020). The Plant Microbiome: Methods and Protocols. ISBN 9781071610398.

• Kumar, Vivek; Prasad, Ram; Kumar, Manoj; Choudhary, Devendra K. (10 August 2019). Microbiome in Plant Health and Disease: Challenges and Opportunities. ISBN 9789811384950.

• Solanki, Manoj Kumar; Kashyap, Prem Lal; Ansari, Rizwan Ali; Kumari, Baby (28 August 2020). Microbiomes and Plant Health: Panoply and Their Applications. ISBN 9780128226018.

• Yadav, Ajar Nath (2020). Advances in Plant Microbiome and Sustainable Agriculture: Diversity and Biotechnological Applications. ISBN 9789811532085.

• Varma, Ajit. Plant Microbiome Paradigm. ISBN 9783030503956.
• Doty, Sharon Lafferty (21 September 2017). Functional Importance of the Plant Microbiome: Implications for Agriculture, Forestry and Bioenergy. ISBN 9783319658971.

• Yadav (2020). Advances in Plant Microbiome and Sustainable Agriculture. ISBN 9789811532047.

• Antwis, Rachael E.; Harrison, Xavier A.; Cox, Michael J. (12 March 2020). Microbiomes of Soils, Plants and Animals: An Integrated Approach. ISBN 9781108473712.

• Varma, Ajit; Tripathi, Swati; Prasad, Ram (20 October 2020). Plant Microbiome Paradigm. ISBN 9783030503949.

• Rosenberg, Eugene; Zilber-Rosenberg, Ilana (31 January 2014). The Hologenome Concept: Human, Animal and Plant Microbiota. ISBN 9783319042411.

• Yadav, Ajar Nath; Singh, Joginder; Rastegari, Ali Asghar; Yadav, Neelam (6 March 2020). Plant Microbiomes for Sustainable Agriculture. ISBN 9783030384531.