Abstract
The microbiome is known to influence plant fitness and differs significantly between plant compartments. To characterize the communities associated with different plant compartments, it is necessary to separate plant tissues in a manner that is suitable for microbiome analysis. Here, we describe a standardized protocol for sampling the microbiomes associated with bulk soil, the apical and basal ectorhizosphere, the apical and ectorhizosphere, the rhizome, pseudostem, and leaves of Musa spp. The approach can easily be modified for work with other plants.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Santoyo G, Moreno-Hagelsieb G, del Carmen Orozco-Mosqueda M, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183:92–99
Kudoyarova GR, Vysotskaya LB, Arkhipova TN, Kuzmina LY, Galimsyanova NF, Sidorova LV et al (2017) Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants. Acta Physiol Plant 39:1–8
Berg M, Koskella B (2018) Nutrient- and dose-dependent microbiome-mediated protection against a plant pathogen. Curr Biol 28:2487–2492
Kim Y-C, Glick BR, Bashan Y, Ryu C-M (2012) Enhancement of plant drought tolerance by microbes. In: Plant responses to drought stress. Springer, Berlin, p 383
Evelin H, Kapoor R, Giri B (2009) Arbuscular mycorrhizal fungi in alleviation of salt stress: a review. Ann Bot 104:1263–1280
Coleman-derr D, Desgarennes D, Fonseca-garcia C, Gross S, Clingenpeel S, Woyke Y et al (2016) Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol 209:798–811
Watt M, Hugenholtz P, White R, Vinall K (2006) Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ Microbiol 8:871–884
van Vuurde JWL, Schippers B (1980) Bacterial colonisation of seminal wheat roots. Soil Biol Biochem 12:559–565
Olsson S, Baath E, Soderstrom B (1987) Growth of Verticillium dahliae Kleb. hyphae and of bacteria along the roots of rape (Brassica napus L.) seedlings. Can J Microbiol 39:916–919
Parke JL, Moen R, Rovira AD, Bowen GD (1986) Soil water affects the rhizosphere distribution of a seed-borne biological control agent, Pseudomonas fluorescens. Soil Biol Biochem 18:583–588
Deangelis KM, Brodie EL, DeSantis TZ, Andersen GL, Lindow SE, Firestone MK (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–178
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Birt, H.W.G., Pattison, A.B., Dennis, P.G. (2021). Sampling Microbiomes Associated with Different Plant Compartments. In: Carvalhais, L.C., Dennis, P.G. (eds) The Plant Microbiome. Methods in Molecular Biology, vol 2232. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1040-4_2
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1040-4_2
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1039-8
Online ISBN: 978-1-0716-1040-4
eBook Packages: Springer Protocols