Plant microbiome

File:Microbiome in plant ecosystem.jpg Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].]]

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 (obligate symbionts include viruses and 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.{{cite journal |doi = 10.1007/s00572-004-0307-4|title = A history of research on arbuscular mycorrhiza|year = 2004|last1 = Koide|first1 = Roger T.|last2 = Mosse|first2 = Barbara|journal = Mycorrhiza|volume = 14|issue = 3|pages = 145–163|pmid = 15088135| bibcode=2004Mycor..14..145K |s2cid = 1809402}} It is thought AM fungi helped in the domestication of plants.Dastogeer, K.M., Tumpa, F.H., Sultana, A., Akter, M.A. and Chakraborty, A. (2020) "Plant microbiome–an account of the factors that shape community composition and diversity". Current Plant Biology: 100161. {{doi|10.1016/j.cpb.2020.100161}}. 50px Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].

File:Arbuscular mycorrhizal root tuber.GIF is being colonized by an arbuscular mycorrhizal fungus (AMF)]]

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Traditionally, plant-microbe interaction studies have been confined to culturable microbes. The numerous microbes that could not be cultured have remained uninvestigated, so knowledge of their roles is largely unknown. The possibilities of unraveling the types and outcomes of these plant-microbe interactions has generated considerable interest among ecologists, evolutionary biologists, plant biologists, and agronomists.{{cite journal |doi = 10.1146/annurev-arplant-050312-120106|title = Structure and Functions of the Bacterial Microbiota of Plants|year = 2013|last1 = Bulgarelli|first1 = Davide|last2 = Schlaeppi|first2 = Klaus|last3 = Spaepen|first3 = Stijn|last4 = Van Themaat|first4 = Emiel Ver Loren|last5 = Schulze-Lefert|first5 = Paul|journal = Annual Review of Plant Biology|volume = 64| issue=1 |pages = 807–838|pmid = 23373698| bibcode=2013AnRPB..64..807B }}{{cite journal |doi = 10.1186/gb-2013-14-6-209|title = The plant microbiome|year = 2013|last1 = Turner|first1 = Thomas R.|last2 = James|first2 = Euan K.|last3 = Poole|first3 = Philip S.|journal = Genome Biology|volume = 14|issue = 6|page = 209|pmid = 23805896|pmc = 3706808 | doi-access=free }} Recent developments in multiomics and the establishment of large collections of microorganisms have dramatically increased 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.

The composition of microbial communities associated with different plant species is correlated with the phylogenetic distance between the plant species, that is, closely related plant species tend to have more alike microbial communities than distant species.{{Cite journal |last1=Abdelfattah |first1=Ahmed |last2=Tack |first2=Ayco J. M. |last3=Wasserman |first3=Birgit |last4=Liu |first4=Jia |last5=Berg |first5=Gabriele |last6=Norelli |first6=John |last7=Droby |first7=Samir |last8=Wisniewski |first8=Michael |title=Evidence for host–microbiome co-evolution in apple |journal=New Phytologist |year=2021 |volume=234 |issue=6 |pages=2088–2100 |language=en |doi=10.1111/nph.17820 |pmid=34823272 |pmc=9299473 |s2cid=244661193 |issn=1469-8137}} The composition of these microbiomes is dynamic and can be modulated by the environment and by climatic conditions.{{Cite journal |last1=Saati-Santamaría |first1=Zaki |last2=Vicentefranqueira |first2=Rocío |last3=Kolařik |first3=Miroslav |last4=Rivas |first4=Raúl |last5=García-Fraile |first5=Paula |date=2023-07-22 |title=Microbiome specificity and fluxes between two distant plant taxa in Iberian forests |journal=Environmental Microbiome |volume=18 |issue=1 |page=64 |doi=10.1186/s40793-023-00520-x |doi-access=free |pmid=37481564 |pmc=10363313 |bibcode=2023EMicb..18...64S |issn=2524-6372|hdl=10366/154277 |hdl-access=free }} The focus of plant microbiome studies has been directed at model plants, such as Arabidopsis thaliana, as well as important economic crop species including barley (Hordeum vulgare), corn (Zea mays), rice (Oryza sativa), soybean (Glycine max), wheat (Triticum aestivum), whereas less attention has been given to fruit crops and tree species.{{cite journal |doi = 10.1371/journal.pbio.2001793|title = Research priorities for harnessing plant microbiomes in sustainable agriculture|year = 2017|last1 = Busby|first1 = Posy E.|last2 = Soman|first2 = Chinmay|last3 = Wagner|first3 = Maggie R.|last4 = Friesen|first4 = Maren L.|last5 = Kremer|first5 = James|last6 = Bennett|first6 = Alison|last7 = Morsy|first7 = Mustafa|last8 = Eisen|first8 = Jonathan A.|last9 = Leach|first9 = Jan E.|last10 = Dangl|first10 = Jeffery L.|journal = PLOS Biology|volume = 15|issue = 3|pages = e2001793|pmid = 28350798|pmc = 5370116|s2cid = 6434145 | doi-access=free }}

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{{see also|microbiota}}

Cyanobacteria are an example of a microorganism which widely interacts in a symbiotic manner with land plants.{{cite journal |doi = 10.1046/j.1469-8137.1999.00352.x|title = Colonization of wheatpara-nodules by the N2-fixing cyanobacterium Nostocsp. Strain 2S9B|year = 1999|last1 = Gantar|first1 = M.|last2 = Elhai|first2 = J.|journal = New Phytologist|volume = 141|issue = 3|pages = 373–379|doi-access = free}}{{cite journal |doi = 10.1007/s003740000243|title = Mechanical damage of roots provides enhanced colonization of the wheat endorhizosphere by the dinitrogen-fixing cyanobacterium Nostoc sp. Strain 2S9B|year = 2000|last1 = Gantar|first1 = M.|journal = Biology and Fertility of Soils|volume = 32|issue = 3|pages = 250–255| bibcode=2000BioFS..32..250G |s2cid = 7590731}}{{cite journal |doi = 10.1111/nph.13870|title = The mechanisms whereby the green alga Chlorella ohadii , isolated from desert soil crust, exhibits unparalleled photodamage resistance|year = 2016|last1 = Treves|first1 = Haim|last2 = Raanan|first2 = Hagai|last3 = Kedem|first3 = Isaac|last4 = Murik|first4 = Omer|last5 = Keren|first5 = Nir|last6 = Zer|first6 = Hagit|last7 = Berkowicz|first7 = Simon M.|last8 = Giordano|first8 = Mario|last9 = Norici|first9 = Alessandra|last10 = Shotland|first10 = Yoram|last11 = Ohad|first11 = Itzhak|last12 = Kaplan|first12 = Aaron|journal = New Phytologist|volume = 210|issue = 4|pages = 1229–1243|pmid = 26853530|doi-access = free| bibcode=2016NewPh.210.1229T }}{{cite journal |doi = 10.1186/s12870-018-1588-7|title = Molecular characterization of eukaryotic algal communities in the tropical phyllosphere based on real-time sequencing of the 18S rDNA gene|year = 2018|last1 = Zhu|first1 = Huan|last2 = Li|first2 = Shuyin|last3 = Hu|first3 = Zhengyu|last4 = Liu|first4 = Guoxiang|journal = BMC Plant Biology|volume = 18|issue = 1|page = 365|pmid = 30563464|pmc = 6299628 | doi-access=free | bibcode=2018BMCPB..18..365Z }} Cyanobacteria can enter the plant through the stomata and colonise the intercellular space, forming loops and intracellular coils.{{cite journal |doi = 10.1016/j.revpalbo.2008.06.006|title = Endophytic cyanobacteria in a 400-million-yr-old land plant: A scenario for the origin of a symbiosis?|year = 2009|last1 = Krings|first1 = Michael|last2 = Hass|first2 = Hagen|last3 = Kerp|first3 = Hans|last4 = Taylor|first4 = Thomas N.|last5 = Agerer|first5 = Reinhard|last6 = Dotzler|first6 = Nora|journal = Review of Palaeobotany and Palynology|volume = 153|issue = 1–2|pages = 62–69| bibcode=2009RPaPa.153...62K }} Anabaena spp. colonize the roots of wheat and cotton plants.{{cite journal |doi = 10.1007/s12223-009-0007-8|title = Physiological characterization and electron microscopic investigation of cyanobacteria associated with wheat rhizosphere|year = 2009|last1 = Karthikeyan|first1 = N.|last2 = Prasanna|first2 = R.|last3 = Sood|first3 = A.|last4 = Jaiswal|first4 = P.|last5 = Nayak|first5 = S.|last6 = Kaushik|first6 = B. D.|journal = Folia Microbiologica|volume = 54|issue = 1|pages = 43–51|pmid = 19330544|s2cid = 23420342}}{{cite journal |doi = 10.1007/s10811-014-0322-6|title = Analysing the colonisation of inoculated cyanobacteria in wheat plants using biochemical and molecular tools|year = 2015|last1 = Babu|first1 = Santosh|last2 = Prasanna|first2 = Radha|last3 = Bidyarani|first3 = Ngangom|last4 = Singh|first4 = Rajendra|journal = Journal of Applied Phycology|volume = 27| issue=1 |pages = 327–338| bibcode=2015JAPco..27..327B |s2cid = 17353123}}{{cite journal |doi = 10.1002/jobm.201400591|title = Deciphering the factors associated with the colonization of rice plants by cyanobacteria|year = 2015|last1 = Bidyarani|first1 = Ngangom|last2 = Prasanna|first2 = Radha|last3 = Chawla|first3 = Gautam|last4 = Babu|first4 = Santosh|last5 = Singh|first5 = Rajendra|journal = Journal of Basic Microbiology|volume = 55|issue = 4|pages = 407–419|pmid = 25515189|s2cid = 5401526}} Calothrix sp. has also been found on the root system of wheat. Monocots, such as wheat and rice, have been colonised by Nostoc spp.,{{cite journal |doi = 10.1111/j.1469-8137.1991.tb00031.x|title = Colonization of wheat (Triticum vulgare L.) by N2-fixing cyanobacteria: II. An ultrastructural study|year = 1991|last1 = Gantar|first1 = M.|last2 = Kerby|first2 = N. W.|last3 = Rowell|first3 = P.|journal = New Phytologist|volume = 118|issue = 3|pages = 485–492|doi-access = }}{{cite journal |doi = 10.1007/s11104-010-0488-x|title = Association of non-heterocystous cyanobacteria with crop plants|year = 2010|last1 = Ahmed|first1 = Mehboob|last2 = Stal|first2 = Lucas J.|last3 = Hasnain|first3 = Shahida|journal = Plant and Soil|volume = 336|issue = 1–2|pages = 363–375| bibcode=2010PlSoi.336..363A |s2cid = 21309970|url = http://dare.uva.nl/personal/pure/en/publications/association-of-nonheterocystous-cyanobacteria-with-crop-plants(a90f9b12-6bd1-47cc-87c4-389ab649d969).html}}{{cite journal |doi = 10.1007/s00284-013-0408-4|title = Root Colonization and Phytostimulation by Phytohormones Producing Entophytic Nostoc sp. AH-12|year = 2013|last1 = Hussain|first1 = Anwar|last2 = Hamayun|first2 = Muhammad|last3 = Shah|first3 = Syed Tariq|journal = Current Microbiology|volume = 67|issue = 5|pages = 624–630|pmid = 23794014|s2cid = 14704537}}{{cite journal |doi = 10.3389/fpls.2015.00046|doi-access = free|title = Effect of IAA on in vitro growth and colonization of Nostoc in plant roots|year = 2015|last1 = Hussain|first1 = Anwar|last2 = Shah|first2 = Syed T.|last3 = Rahman|first3 = Hazir|last4 = Irshad|first4 = Muhammad|last5 = Iqbal|first5 = Amjad|journal = Frontiers in Plant Science|volume = 6|page = 46|pmid = 25699072|pmc = 4318279}} In 1991, Ganther and others isolated diverse heterocystous nitrogen-fixing cyanobacteria, including Nostoc, Anabaena and Cylindrospermum, from plant root and soil. Assessment of wheat seedling roots revealed two types of association patterns: loose colonization of root hair by Anabaena and tight colonization of the root surface within a restricted zone by Nostoc.

File:Microbial colonization of the phyllosphere and rhizosphere.jpg Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].}} Microbial colonisation occurs both in the above-ground part of the plant (phyllosphere), as well as the below-ground part (rhizosphere). (A) The microbial colonisation on the leaf takes place on the leaf surface (epiphytes) from air-borne and soil-borne inocula and the inner leaf part (endophytes). Microbial colonisation can lead to exogenous intraspecies biofilm formation on the leaf surface. (B) Microbe–microbe interactions occur between interspecies and interkingdoms, referred to as quorum sensing. Quorum-sensing molecules impacting microbial recognition and biofilm formation on leaves. (C) Pathogenic microbes colonize host plants by means of their virulence. The genetic make-up of both the host and pathogen contributes to disease progression. However, other microbes in the host phyllosphere can influence this plant–pathogen interaction by either facilitation or antagonism. (D) Plant immune responses are of specific interest as host–microbe interactions shaping the phyllosphere microbiome. Non-host-adapted pathogens are involved in PAMP-triggered immunity (PTI) and recognised via pattern recognition receptors (PRRs). Host-adapted microbes are recognised via nucleotide-binding leucine-rich repeat receptors (NLRs), summarised in effector-triggered immunity (ETI).]]

File:The plant microbiome.jpg

File:Leaf and root colonization by cyanobacteria.jpg with land plants{{hsp}}{{cite journal | last1=Lee | first1=Sang-Moo | last2=Ryu | first2=Choong-Min | title=Algae as New Kids in the Beneficial Plant Microbiome | journal=Frontiers in Plant Science | publisher=Frontiers Media SA | volume=12 | date=4 Feb 2021 | issn=1664-462X | doi=10.3389/fpls.2021.599742 | page=599742| pmid=33613596 | pmc=7889962 | doi-access=free }} 50px Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].}} (1) Cyanobacteria enter the leaf tissue through the stomata and colonize the intercellular space, forming a cyanobacterial loop.
(2) On the root surface, cyanobacteria exhibit two types of colonization pattern; in the root hair, filaments of Anabaena and Nostoc species form loose colonies, and in the restricted zone on the root surface, specific Nostoc species form cyanobacterial colonies.
(3) Co-inoculation with 2,4-D and Nostoc spp. increases para-nodule formation and nitrogen fixation. A large number of Nostoc spp. isolates colonize the root endosphere and form para-nodules.]]

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File:Associations in the rhizosphere between plant roots, microbes and root exudates.jpg Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].}}]]

{{see also|Root microbiome|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.{{cite journal |doi = 10.1007/s11104-008-9885-9|title = Rhizosphere: Biophysics, biogeochemistry and ecological relevance|year = 2009|last1 = Hinsinger|first1 = Philippe|last2 = Bengough|first2 = A. Glyn|last3 = Vetterlein|first3 = Doris|last4 = Young|first4 = Iain M.|journal = Plant and Soil|volume = 321|issue = 1–2|pages = 117–152| bibcode=2009PlSoi.321..117H |s2cid = 8997382}} A diverse array of organisms specialize in living in the rhizosphere, including bacteria, fungi, oomycetes, nematodes, algae, protozoa, viruses, and archaea.{{cite journal |doi = 10.1007/s11104-009-0013-2|title = Rhizosphere fauna: The functional and structural diversity of intimate interactions of soil fauna with plant roots|year = 2009|last1 = Bonkowski|first1 = Michael|last2 = Villenave|first2 = Cécile|last3 = Griffiths|first3 = Bryan|journal = Plant and Soil|volume = 321|issue = 1–2|pages = 213–233| bibcode=2009PlSoi.321..213B |s2cid = 35701713}}

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|quote = "Experimental evidence underlines the importance of the root microbiome in plant health and it is becoming increasingly clear that the plant is able to control the composition of its microbiome. It stands to reason that those plants that manage their microbiome in a way that is beneficial to their reproductive success will be favored during evolutionary selection. It appears that such selective pressure has brought about many specific interactions between plants and microbes, and evidence is accumulating that plants call for microbial help in time of need."

|source = – Berendsen et al, 2012{{hsp}}

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File:Microbial consortia naturally formed on the roots of Arabidopsis thaliana.webp 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.]]

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.{{cite journal |doi = 10.1111/nph.13288|title = Mycorrhizal ecology and evolution: The past, the present, and the future|year = 2015|last1 = Van Der Heijden|first1 = Marcel G. A.|last2 = Martin|first2 = Francis M.|last3 = Selosse|first3 = Marc-André|last4 = Sanders|first4 = Ian R.|journal = New Phytologist|volume = 205|issue = 4|pages = 1406–1423|pmid = 25639293|doi-access = | bibcode=2015NewPh.205.1406V | hdl=1874/329560 |hdl-access = free}} 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 the nitrogen and phosphorus requirements. In return, the fungi obtain carbohydrates and lipids from host plants.{{cite journal |doi = 10.1016/j.tplants.2017.05.008|title = Diet of Arbuscular Mycorrhizal Fungi: Bread and Butter?|year = 2017|last1 = Rich|first1 = Mélanie K.|last2 = Nouri|first2 = Eva|last3 = Courty|first3 = Pierre-Emmanuel|last4 = Reinhardt|first4 = Didier|journal = Trends in Plant Science|volume = 22|issue = 8|pages = 652–660|pmid = 28622919| bibcode=2017TPS....22..652R |url = http://doc.rero.ch/record/305034/files/rei_dam.pdf}} Recent studies of arbuscular mycorrhizal fungi using sequencing technologies show greater between-species and within-species diversity than previously known.{{cite journal |doi = 10.5941/MYCO.2013.41.3.121|title = Diversity of Arbuscular Mycorrhizal Fungi and Their Roles in Ecosystems|year = 2013|last1 = Lee|first1 = Eun-Hwa|last2 = Eo|first2 = Ju-Kyeong|last3 = Ka|first3 = Kang-Hyeon|last4 = Eom|first4 = Ahn-Heum|journal = Mycobiology|volume = 41|issue = 3|pages = 121–125|pmid = 24198665|pmc = 3817225}}

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The most frequently studied beneficial rhizosphere organisms are mycorrhizae, rhizobium bacteria, plant-growth promoting rhizobacteria (PGPR), and biocontrol microbes. It has been projected that one gram of soil could contain more than one million distinct bacterial genomes,{{cite journal |doi = 10.1126/science.1112665|title = Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil|year = 2005|last1 = Gans|first1 = J.|last2 = Wolinsky|first2 = M.|last3 = Dunbar|first3 = J.|journal = Science|volume = 309|issue = 5739|pages = 1387–1390|pmid = 16123304|bibcode = 2005Sci...309.1387G|s2cid = 130269020}} and over 50,000 OTUs (operational taxonomic units) have been found within the potato rhizosphere.{{cite journal |doi = 10.1371/journal.pone.0023321|title = Comparative Analysis of Bacterial Communities in a Potato Field as Determined by Pyrosequencing|year = 2011|last1 = i̇Nceoğlu|first1 = Özgül|last2 = Al-Soud|first2 = Waleed Abu|last3 = Salles|first3 = Joana Falcão|last4 = Semenov|first4 = Alexander V.|last5 = Van Elsas|first5 = Jan Dirk|journal = PLOS ONE|volume = 6|issue = 8|pages = e23321|pmid = 21886785|pmc = 3158761|bibcode = 2011PLoSO...623321I|doi-access = free}} Among the prokaryotes in the rhizosphere, the most frequent bacteria are within the Acidobacteriota, Pseudomonadota, Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota.{{cite journal |doi = 10.1038/nature11336|title = Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota|year = 2012|last1 = Bulgarelli|first1 = Davide|last2 = Rott|first2 = Matthias|last3 = Schlaeppi|first3 = Klaus|last4 = Ver Loren Van Themaat|first4 = Emiel|last5 = Ahmadinejad|first5 = Nahal|last6 = Assenza|first6 = Federica|last7 = Rauf|first7 = Philipp|last8 = Huettel|first8 = Bruno|last9 = Reinhardt|first9 = Richard|last10 = Schmelzer|first10 = Elmon|last11 = Peplies|first11 = Joerg|last12 = Gloeckner|first12 = Frank Oliver|last13 = Amann|first13 = Rudolf|last14 = Eickhorst|first14 = Thilo|last15 = Schulze-Lefert|first15 = Paul|journal = Nature|volume = 488|issue = 7409|pages = 91–95|pmid = 22859207|bibcode = 2012Natur.488...91B|s2cid = 4393146}}{{cite journal |doi = 10.1111/j.1758-2229.2009.00117.x|title = Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil|year = 2010|last1 = Uroz|first1 = Stéphane|last2 = Buée|first2 = Marc|last3 = Murat|first3 = Claude|last4 = Frey-Klett|first4 = Pascale|last5 = Martin|first5 = Francis|journal = Environmental Microbiology Reports|volume = 2|issue = 2|pages = 281–288|pmid = 23766079| bibcode=2010EnvMR...2..281U }} 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.{{cite journal |doi = 10.1038/nature11237|title = Defining the core Arabidopsis thaliana root microbiome|year = 2012|last1 = Lundberg|first1 = Derek S.|last2 = Lebeis|first2 = Sarah L.|last3 = Paredes|first3 = Sur Herrera|last4 = Yourstone|first4 = Scott|last5 = Gehring|first5 = Jase|last6 = Malfatti|first6 = Stephanie|last7 = Tremblay|first7 = Julien|last8 = Engelbrektson|first8 = Anna|last9 = Kunin|first9 = Victor|last10 = Rio|first10 = Tijana Glavina del|last11 = Edgar|first11 = Robert C.|last12 = Eickhorst|first12 = Thilo|last13 = Ley|first13 = Ruth E.|last14 = Hugenholtz|first14 = Philip|last15 = Tringe|first15 = Susannah Green|last16 = Dangl|first16 = Jeffery L.|journal = Nature|volume = 488|issue = 7409|pages = 86–90|pmid = 22859206|pmc = 4074413|bibcode = 2012Natur.488...86L}}{{cite journal |doi = 10.1073/pnas.1321597111|title = Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives|year = 2014|last1 = Schlaeppi|first1 = K.|last2 = Dombrowski|first2 = N.|last3 = Oter|first3 = R. G.|last4 = Ver Loren Van Themaat|first4 = E.|last5 = Schulze-Lefert|first5 = P.|journal = Proceedings of the National Academy of Sciences|volume = 111|issue = 2|pages = 585–592|pmid = 24379374|pmc = 3896156|bibcode = 2014PNAS..111..585S|s2cid = 13806811|doi-access = free}} Certain bacterial groups (e.g. Actinomycetota, Xanthomonadaceae) are less abundant in the rhizosphere than in nearby bulk soil .

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{{main|Endosphere}}

Some microorganisms, such as endophytes, penetrate and occupy the plant internal tissues, forming the endospheric microbiome. The arbuscular mycorrhizal and other endophytic fungi are the dominant colonizers of the endosphere.{{cite journal |doi = 10.1007/s00248-012-0053-7|title = Exploring Biodiversity in the Bacterial Community of the Mediterranean Phyllosphere and its Relationship with Airborne Bacteria|year = 2012|last1 = Vokou|first1 = Despoina|last2 = Vareli|first2 = Katerina|last3 = Zarali|first3 = Ekaterini|last4 = Karamanoli|first4 = Katerina|last5 = Constantinidou|first5 = Helen-Isis A.|last6 = Monokrousos|first6 = Nikolaos|last7 = Halley|first7 = John M.|last8 = Sainis|first8 = Ioannis|journal = Microbial Ecology|volume = 64|issue = 3|pages = 714–724|pmid = 22544345| bibcode=2012MicEc..64..714V |s2cid = 17291303}} 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.{{cite journal |doi = 10.1016/j.envexpbot.2017.08.008|title = Metabolic responses of endophytic Nicotiana benthamiana plants experiencing water stress|year = 2017|last1 = Dastogeer|first1 = Khondoker M.G.|last2 = Li|first2 = Hua|last3 = Sivasithamparam|first3 = Krishnapillai|last4 = Jones|first4 = Michael G.K.|last5 = Du|first5 = Xin|last6 = Ren|first6 = Yonglin|last7 = Wylie|first7 = Stephen J.|journal = Environmental and Experimental Botany|volume = 143|pages = 59–71| bibcode=2017EnvEB.143...59D |url = https://researchrepository.murdoch.edu.au/id/eprint/38407/}}{{cite journal |doi = 10.1111/j.1469-8137.2009.02773.x|title = Fungal endophytes: Diversity and functional roles|year = 2009|last1 = Rodriguez|first1 = R. J.|last2 = White Jr|first2 = J. F.|last3 = Arnold|first3 = A. E.|last4 = Redman|first4 = R. S.|journal = New Phytologist|volume = 182|issue = 2|pages = 314–330|pmid = 19236579|doi-access = free| bibcode=2009NewPh.182..314R }} 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.

{{main|Phyllosphere}}

File:Healthy and unhealthy leaf.png plant (left) and a leaf from a dysbiosis mutant plant (right){{cite news |last1=He |first1=Sheng-Yang |title=When plants and their microbes are not in sync, the results can be disastrous |url=https://theconversation.com/when-plants-and-their-microbes-are-not-in-sync-the-results-can-be-disastrous-143802 |work=The Conversation |date=28 August 2020}}]]

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.{{cite book |doi = 10.1007/978-0-585-34164-4_10|chapter = Role of Immigration and Other Processes in Determining Epiphytic Bacterial Populations|title = Aerial Plant Surface Microbiology|year = 1996|last1 = Lindow|first1 = Steven E.|pages = 155–168|isbn = 978-0-306-45382-3}}

Interactions between plants and their associated microorganisms in many of these microbiomes can play pivotal roles in host plant health, function, and evolution.{{cite journal |doi = 10.1146/annurev-ecolsys-102710-145039|title = Microbially Mediated Plant Functional Traits|year = 2011|last1 = Friesen|first1 = Maren L.|last2 = Porter|first2 = Stephanie S.|last3 = Stark|first3 = Scott C.|last4 = von Wettberg|first4 = Eric J.|last5 = Sachs|first5 = Joel L.|last6 = Martinez-Romero|first6 = Esperanza|journal = Annual Review of Ecology, Evolution, and Systematics|volume = 42|pages = 23–46}} The leaf surface, or phyllosphere, harbours a microbiome comprising diverse communities of bacteria, fungi, algae, archaea, and viruses.{{cite journal |doi = 10.1016/j.mib.2019.10.002|title = A brief from the leaf: Latest research to inform our understanding of the phyllosphere microbiome|year = 2019|last1 = Leveau|first1 = Johan HJ|journal = Current Opinion in Microbiology|volume = 49|pages = 41–49|pmid = 31707206|s2cid = 207946690}}{{cite journal |last1=Ruinen |first1=J. |title=Occurrence of Beijerinckia Species in the 'Phyllosphere' |journal=Nature |date=February 1956 |volume=177 |issue=4501 |pages=220–221 |doi=10.1038/177220a0 |bibcode=1956Natur.177..220R |language=en |issn=1476-4687}} Interactions between the host plant and phyllosphere bacteria have the potential to drive various aspects of host plant physiology.{{cite journal|last1=Vogel|first1=Christine|author-link=Christine Vogel|last2=Bodenhausen|first2=Natacha|last3=Gruissem|first3=Wilhelm|last4=Vorholt|first4=Julia A.|year=2016|title=The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health|url=https://www.zora.uzh.ch/id/eprint/131259/1/PMID27306148.pdf|journal=New Phytologist|volume=212|issue=1|pages=192–207|doi=10.1111/nph.14036|pmid=27306148|bibcode=2016NewPh.212..192V |hdl=20.500.11850/117578|hdl-access=free}}{{cite journal |doi = 10.1007/s00792-018-1015-x|title = Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere|year = 2018|last1 = Cid|first1 = Fernanda P.|last2 = Maruyama|first2 = Fumito|last3 = Murase|first3 = Kazunori|last4 = Graether|first4 = Steffen P.|last5 = Larama|first5 = Giovanni|last6 = Bravo|first6 = Leon A.|last7 = Jorquera|first7 = Milko A.|journal = Extremophiles|volume = 22|issue = 3|pages = 537–552|pmid = 29492666|s2cid = 4320165}}{{cite journal |doi = 10.1128/genomeA.00019-18|title = Draft Genome Sequence of Plant Growth-Promoting and Drought-Tolerant Bacillus altitudinis FD48, Isolated from Rice Phylloplane|year = 2018|last1 = Kumaravel|first1 = Sowmya|last2 = Thankappan|first2 = Sugitha|last3 = Raghupathi|first3 = Sridar|last4 = Uthandi|first4 = Sivakumar|journal = Genome Announcements|volume = 6|issue = 9|pmid = 29496824|pmc = 5834328}} However, as of 2020 knowledge of these bacterial associations in the phyllosphere remains relatively modest, and there is a need to advance fundamental knowledge of phyllosphere microbiome dynamics.{{cite journal |doi = 10.1002/ajb2.1229|title = Decrypting the phyllosphere microbiota: Progress and challenges|year = 2019|last1 = Laforest-Lapointe|first1 = Isabelle|last2 = Whitaker|first2 = Briana K.|journal = American Journal of Botany|volume = 106|issue = 2|pages = 171–173|pmid = 30726571|doi-access = free}}

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.{{cite journal |doi = 10.1128/AEM.05565-11|title = Geographical Location Determines the Population Structure in Phyllosphere Microbial Communities of a Salt-Excreting Desert Tree|year = 2011|last1 = Finkel|first1 = Omri M.|last2 = Burch|first2 = Adrien Y.|last3 = Lindow|first3 = Steven E.|last4 = Post|first4 = Anton F.|last5 = Belkin|first5 = Shimshon|journal = Applied and Environmental Microbiology|volume = 77|issue = 21|pages = 7647–7655|pmid = 21926212|pmc = 3209174|bibcode = 2011ApEnM..77.7647F}} There can be up to 107 microbes per square centimetre present on the leaf surfaces of plants, and the bacterial population of the phyllosphere on a global scale is estimated to be 10²⁶ cells.{{cite journal |doi = 10.1038/nrmicro2910|title = Microbial life in the phyllosphere|year = 2012|last1 = Vorholt|first1 = Julia A.|journal = Nature Reviews Microbiology|volume = 10|issue = 12|pages = 828–840|pmid = 23154261|s2cid = 10447146|hdl = 20.500.11850/59727|hdl-access = free}} The population size of the fungal phyllosphere is likely to be smaller.{{cite journal |doi = 10.1128/AEM.69.4.1875-1883.2003|title = Microbiology of the Phyllosphere|year = 2003|last1 = Lindow|first1 = Steven E.|last2 = Brandl|first2 = Maria T.|journal = Applied and Environmental Microbiology|volume = 69|issue = 4|pages = 1875–1883|pmid = 12676659|pmc = 154815|bibcode = 2003ApEnM..69.1875L|s2cid = 2304379}}

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 microorganisms may need finely tuned metabolic adjustment to survive in phyllosphere environment. Pseudomonadota seems to be the dominant colonizers, with Bacteroidota and Actinomycetota also predominant in phyllospheres.{{cite journal |doi = 10.1371/journal.pone.0056329|title = Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana|year = 2013|last1 = Bodenhausen|first1 = Natacha|last2 = Horton|first2 = Matthew W.|last3 = Bergelson|first3 = Joy|author-link3=Joy Bergelson|journal = PLOS ONE|volume = 8|issue = 2|pages = e56329|pmid = 23457551|pmc = 3574144|bibcode = 2013PLoSO...856329B|doi-access = free}} Although there are similarities between the rhizosphere and soil microbial communities, very little similarity has been found between phyllosphere communities and microorganisms floating in open air (aeroplankton).

The assembly of the phyllosphere microbiome, which can be strictly defined as epiphytic bacterial communities on the leaf surface, can be shaped by the microbial communities present in the surrounding environment (i.e., stochastic colonisation) and the host plant (i.e., biotic selection). However, although the leaf surface is generally considered a discrete microbial habitat,{{cite journal |doi = 10.1007/s00248-016-0738-4|title = Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest|year = 2016|last1 = Stone|first1 = Bram W. G.|last2 = Jackson|first2 = Colin R.|journal = Microbial Ecology|volume = 71|issue = 4|pages = 954–961|pmid = 26883131| bibcode=2016MicEc..71..954S |s2cid = 17292307}}{{cite journal |doi = 10.1111/j.1462-2920.2010.02258.x|title = The ecology of the phyllosphere: Geographic and phylogenetic variability in the distribution of bacteria on tree leaves|year = 2010|last1 = Redford|first1 = Amanda J.|last2 = Bowers|first2 = Robert M.|last3 = Knight|first3 = Rob|last4 = Linhart|first4 = Yan|last5 = Fierer|first5 = Noah|journal = Environmental Microbiology|volume = 12|issue = 11|pages = 2885–2893|pmid = 20545741|pmc = 3156554| bibcode=2010EnvMi..12.2885R }} there is no consensus on the dominant driver of community assembly across phyllosphere microbiomes. For example, host-specific bacterial communities have been reported in the phyllosphere of co-occurring plant species, suggesting a dominant role of host selection.{{cite journal |doi = 10.1186/s40168-016-0174-1|title = Host species identity, site and time drive temperate tree phyllosphere bacterial community structure|year = 2016|last1 = Laforest-Lapointe|first1 = Isabelle|last2 = Messier|first2 = Christian|last3 = Kembel|first3 = Steven W.|journal = Microbiome|volume = 4|issue = 1|page = 27|pmid = 27316353|pmc = 4912770 | doi-access=free }}

Conversely, microbiomes of the surrounding environment have also been reported to be the primary determinant of phyllosphere community composition.{{cite journal |doi = 10.1128/mBio.02527-14|title = The Soil Microbiome Influences Grapevine-Associated Microbiota|year = 2015|last1 = Zarraonaindia|first1 = Iratxe|last2 = Owens|first2 = Sarah M.|last3 = Weisenhorn|first3 = Pamela|last4 = West|first4 = Kristin|last5 = Hampton-Marcell|first5 = Jarrad|last6 = Lax|first6 = Simon|last7 = Bokulich|first7 = Nicholas A.|last8 = Mills|first8 = David A.|last9 = Martin|first9 = Gilles|last10 = Taghavi|first10 = Safiyh|last11 = Van Der Lelie|first11 = Daniel|last12 = Gilbert|first12 = Jack A.|journal = mBio|volume = 6|issue = 2|pmid = 25805735|pmc = 4453523}}{{cite journal |doi = 10.1128/AEM.00888-12|title = Distance-Decay Relationships Partially Determine Diversity Patterns of Phyllosphere Bacteria on Tamrix Trees across the Sonoran Desert|year = 2012|last1 = Finkel|first1 = Omri M.|last2 = Burch|first2 = Adrien Y.|last3 = Elad|first3 = Tal|last4 = Huse|first4 = Susan M.|last5 = Lindow|first5 = Steven E.|last6 = Post|first6 = Anton F.|last7 = Belkin|first7 = Shimshon|journal = Applied and Environmental Microbiology|volume = 78|issue = 17|pages = 6187–6193|pmid = 22752165|pmc = 3416633|bibcode = 2012ApEnM..78.6187F}} As a result, the processes that drive phyllosphere community assembly are not well understood but unlikely to be universal across plant species. However, the existing evidence does indicate that phyllosphere microbiomes exhibiting host-specific associations are more likely to interact with the host than those primarily recruited from the surrounding environment.{{cite journal |doi = 10.1073/pnas.1216057111|title = Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest|year = 2014|last1 = Kembel|first1 = S. W.|last2 = O'Connor|first2 = T. K.|last3 = Arnold|first3 = H. K.|last4 = Hubbell|first4 = S. P.|last5 = Wright|first5 = S. J.|last6 = Green|first6 = J. L.|journal = Proceedings of the National Academy of Sciences|volume = 111|issue = 38|pages = 13715–13720|pmid = 25225376|pmc = 4183302|bibcode = 2014PNAS..11113715K|s2cid = 852584|doi-access = free}}{{cite journal |doi = 10.1128/AEM.00133-11|title = Protection of Arabidopsis thaliana against Leaf-Pathogenic Pseudomonas syringae by Sphingomonas Strains in a Controlled Model System|year = 2011|last1 = Innerebner|first1 = Gerd|last2 = Knief|first2 = Claudia|last3 = Vorholt|first3 = Julia A.|journal = Applied and Environmental Microbiology|volume = 77|issue = 10|pages = 3202–3210|pmid = 21421777|pmc = 3126462|bibcode = 2011ApEnM..77.3202I}}{{cite journal |doi = 10.1186/s40168-020-00844-7|title = Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest|year = 2020|last1 = Lajoie|first1 = Geneviève|last2 = Maglione|first2 = Rémi|last3 = Kembel|first3 = Steven W.|journal = Microbiome|volume = 8|issue = 1|page = 70|pmid = 32438916|pmc = 7243311 | doi-access=free }}

The search for a core microbiome in host-associated microbial communities is a useful first step in trying to understand the interactions that may be occurring between a host and its microbiome.{{cite journal |doi = 10.1111/j.1462-2920.2011.02585.x |title = Beyond the Venn diagram: The hunt for a core microbiome |year = 2012 |last1 = Shade |first1 = Ashley |last2 = Handelsman |first2 = Jo |journal = Environmental Microbiology |volume = 14 |issue = 1 |pages = 4–12 |pmid = 22004523 |doi-access = free |bibcode = 2012EnvMi..14....4S }}{{cite journal |doi = 10.1186/s40168-020-00875-0|title = Microbiome definition re-visited: Old concepts and new challenges|year = 2020|last1 = Berg|first1 = Gabriele|last2 = Rybakova|first2 = Daria|last3 = Fischer|first3 = Doreen|last4 = Cernava|first4 = Tomislav|last5 = Vergès|first5 = Marie-Christine Champomier|last6 = Charles|first6 = Trevor|last7 = Chen|first7 = Xiaoyulong|last8 = Cocolin|first8 = Luca|last9 = Eversole|first9 = Kellye|last10 = Corral|first10 = Gema Herrero|last11 = Kazou|first11 = Maria|last12 = Kinkel|first12 = Linda|last13 = Lange|first13 = Lene|last14 = Lima|first14 = Nelson|last15 = Loy|first15 = Alexander|last16 = MacKlin|first16 = James A.|last17 = Maguin|first17 = Emmanuelle|last18 = Mauchline|first18 = Tim|last19 = McClure|first19 = Ryan|last20 = Mitter|first20 = Birgit|last21 = Ryan|first21 = Matthew|last22 = Sarand|first22 = Inga|last23 = Smidt|first23 = Hauke|last24 = Schelkle|first24 = Bettina|last25 = Roume|first25 = Hugo|last26 = Kiran|first26 = G. Seghal|last27 = Selvin|first27 = Joseph|last28 = Souza|first28 = Rafael Soares Correa de|last29 = Van Overbeek|first29 = Leo|last30 = Singh|first30 = Brajesh K.|journal = Microbiome|volume = 8|issue = 1|page = 103|pmid = 32605663|pmc = 7329523|display-authors = 15 | doi-access=free }} The prevailing core microbiome concept is built on the notion that the persistence of a taxon across the spatiotemporal boundaries of an ecological niche is directly reflective of its functional importance within the niche it occupies; it therefore provides a framework for identifying functionally critical microorganisms that consistently associate with a host species.{{cite journal |doi = 10.1038/nature07540|title = A core gut microbiome in obese and lean twins|year = 2009|last1 = Turnbaugh|first1 = Peter J.|last2 = Hamady|first2 = Micah|last3 = Yatsunenko|first3 = Tanya|last4 = Cantarel|first4 = Brandi L.|last5 = Duncan|first5 = Alexis|last6 = Ley|first6 = Ruth E.|last7 = Sogin|first7 = Mitchell L.|last8 = Jones|first8 = William J.|last9 = Roe|first9 = Bruce A.|last10 = Affourtit|first10 = Jason P.|last11 = Egholm|first11 = Michael|last12 = Henrissat|first12 = Bernard|last13 = Heath|first13 = Andrew C.|last14 = Knight|first14 = Rob|last15 = Gordon|first15 = Jeffrey I.|journal = Nature|volume = 457|issue = 7228|pages = 480–484|pmid = 19043404|pmc = 2677729|bibcode = 2009Natur.457..480T}}

Divergent definitions of "core microbiome" have arisen across scientific literature with researchers variably identifying "core taxa" as those persistent across distinct host microhabitats{{hsp}}{{cite journal |doi = 10.1111/1462-2920.14031|title = Field study reveals core plant microbiota and relative importance of their drivers|year = 2018|last1 = Hamonts|first1 = Kelly|last2 = Trivedi|first2 = Pankaj|last3 = Garg|first3 = Anshu|last4 = Janitz|first4 = Caroline|last5 = Grinyer|first5 = Jasmine|last6 = Holford|first6 = Paul|last7 = Botha|first7 = Frederik C.|last8 = Anderson|first8 = Ian C.|last9 = Singh|first9 = Brajesh K.|journal = Environmental Microbiology|volume = 20|issue = 1|pages = 124–140|pmid = 29266641|s2cid = 10650949|doi-access = | bibcode=2018EnvMi..20..124H }}{{cite journal |doi = 10.1186/s40168-019-0624-7|title = Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.)|year = 2019|last1 = Cernava|first1 = Tomislav|last2 = Erlacher|first2 = Armin|last3 = Soh|first3 = Jung|last4 = Sensen|first4 = Christoph W.|last5 = Grube|first5 = Martin|last6 = Berg|first6 = Gabriele|journal = Microbiome|volume = 7|issue = 1|page = 13|pmid = 30696492|pmc = 6352427 | doi-access=free }} and even different species. Given the functional divergence of microorganisms across different host species{{hsp}} and microhabitats,{{cite journal |doi = 10.1111/1462-2920.12695|title = Spatial structuring of bacterial communities within individual Ginkgo bilobatrees|year = 2015|last1 = Leff|first1 = Jonathan W.|last2 = Del Tredici|first2 = Peter|last3 = Friedman|first3 = William E.|last4 = Fierer|first4 = Noah|journal = Environmental Microbiology|volume = 17|issue = 7|pages = 2352–2361|pmid = 25367625| bibcode=2015EnvMi..17.2352L }} defining core taxa sensu stricto as those persistent across broad geographic distances within tissue- and species-specific host microbiomes, represents the most biologically and ecologically appropriate application of this conceptual framework.{{cite journal |last1=Hernandez-Agreda |first1=Alejandra |last2=Gates |first2=Ruth D. |last3=Ainsworth |first3=Tracy D. |author-link3=Tracy Ainsworth |year=2017 |title=Defining the Core Microbiome in Corals' Microbial Soup |journal=Trends in Microbiology |volume=25 |issue=2 |pages=125–140 |doi=10.1016/j.tim.2016.11.003 |pmid=27919551}} Tissue- and species-specific core microbiomes across host populations separated by broad geographical distances have not been widely reported for the phyllosphere using the stringent definition established by Ruinen.

The flowering tea tree commonly known as mānuka is indigenous to New Zealand.{{cite journal |doi = 10.1080/0028825X.2005.9512966|title = A review of Leptospermum scoparium(Myrtaceae) in New Zealand|year = 2005|last1 = Stephens|first1 = J. M. C.|last2 = Molan|first2 = P. C.|last3 = Clarkson|first3 = B. D.|journal = New Zealand Journal of Botany|volume = 43|issue = 2|pages = 431–449|s2cid = 53515334|doi-access = free| bibcode=2005NZJB...43..431S }} Mānuka honey, produced from the nectar of mānuka flowers, is known for its non-peroxide antibacterial properties.{{cite journal |doi = 10.1046/j.1365-2672.2002.01761.x|title = The sensitivity to honey of Gram-positive cocci of clinical significance isolated from wounds|year = 2002|last1 = Cooper|first1 = R.A.|last2 = Molan|first2 = P.C.|last3 = Harding|first3 = K.G.|journal = Journal of Applied Microbiology|volume = 93|issue = 5|pages = 857–863|pmid = 12392533|s2cid = 24517001|doi-access = }}{{cite journal |doi = 10.3109/01913123.2016.1154914|title = How methylglyoxal kills bacteria: An ultrastructural study|year = 2016|last1 = Rabie|first1 = Erika|last2 = Serem|first2 = June Cheptoo|last3 = Oberholzer|first3 = Hester Magdalena|last4 = Gaspar|first4 = Anabella Regina Marques|last5 = Bester|first5 = Megan Jean|journal = Ultrastructural Pathology|volume = 40|issue = 2|pages = 107–111|pmid = 26986806|hdl = 2263/52156|s2cid = 13372064|hdl-access = free}} Microorganisms have been studied in the mānuka rhizosphere and endosphere.{{cite journal |doi = 10.1017/S0953756297005765|title = Leaf endophytes of manuka (Leptospermum scoparium)|year = 1998|last1 = Johnston|first1 = Peter R.|journal = Mycological Research|volume = 102|issue = 8|pages = 1009–1016}}{{cite journal |doi = 10.1080/0028825X.2006.9513025|title = Checklist of fungi on teatree (Kunzeaand Leptospermumspecies) in New Zealand|year = 2006|last1 = McKenzie|first1 = E. H. C.|last2 = Johnston|first2 = P. R.|last3 = Buchanan|first3 = P. K.|journal = New Zealand Journal of Botany|volume = 44|issue = 3|pages = 293–335|s2cid = 84538904|doi-access = free| bibcode=2006NZJB...44..293M }}{{cite journal |doi = 10.1007/s13199-017-0506-3|title = Arbuscular mycorrhizal fungi associated with Leptospermum scoparium (Mānuka): Effects on plant growth and essential oil content|year = 2018|last1 = Wicaksono|first1 = Wisnu Adi|last2 = Sansom|first2 = Catherine E.|last3 = Eirian Jones|first3 = E.|last4 = Perry|first4 = Nigel B.|last5 = Monk|first5 = Jana|last6 = Ridgway|first6 = Hayley J.|journal = Symbiosis|volume = 75| issue=1 |pages = 39–50| bibcode=2018Symbi..75...39W |s2cid = 4819178}} Earlier studies primarily focussed on fungi, and a 2016 study provided the first investigation of endophytic bacterial communities from three geographically and environmentally distinct mānuka populations using fingerprinting techniques and revealed tissue-specific core endomicrobiomes.{{cite journal |last1=Wicaksono |first1=Wisnu Adi |last2=Jones |first2=E. Eirian |author-link2=Eirian Jones |last3=Monk |first3=Jana |last4=Ridgway |first4=Hayley J. |year=2016 |title=The Bacterial Signature of Leptospermum scoparium (Mānuka) Reveals Core and Accessory Communities with Bioactive Properties |journal=PLOS ONE |volume=11 |issue=9 |pages=e0163717 |bibcode=2016PLoSO..1163717W |doi=10.1371/journal.pone.0163717 |pmc=5038978 |pmid=27676607 |doi-access=free}}

File:Differential abundance of taxa in manuka phyllosphere.png on the left illustrates how the composition of OTUs in the mānuka phyllosphere and associated soil communities differed significantly. No core soil microbiome was detected.
(B) The chart on the right shows how OTUs in phyllosphere and associated soil communities differed in relative abundances.]]

A 2020 study identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. The results demonstrated the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka.

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| footer = Mānuka is a flowering scrub. The chart shows an abundance-occupancy distribution identifying core phyllosphere taxa in non-rarefied (green) and rarefied (purple) datasets. Each point represents a taxon plotted by its mean logarithmic relative abundance and occupancy. Taxa (pink) with an occupancy of 1 (i.e., detected in all 89 phyllosphere samples) were considered members of the core microbiome.{{cite journal |doi = 10.1371/journal.pone.0237079|title = A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand|year = 2020|last1 = Noble|first1 = Anya S.|last2 = Noe|first2 = Stevie|last3 = Clearwater|first3 = Michael J.|last4 = Lee|first4 = Charles K.|journal = PLOS ONE|volume = 15|issue = 8|pages = e0237079|pmid = 32790769|pmc = 7425925|bibcode = 2020PLoSO..1537079N|doi-access = free}} 50px Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License]. 50px Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].

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| image2 = Relative abundance of core phyllosphere taxa in the mānuka phyllosphere (crop).png

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{{main|Spermosphere}}

Plant seeds can serve as natural vectors for vertical transmission of their beneficial endophytes, such as those that confer disease resistance. A 2021 research paper explained, "It makes sense that their most important symbionts would be vertically transmitted through seed rather than gambling that all of the correct soil-dwelling microbes might be available at the germination site."{{cite journal |last1=Johnston-Monje |first1=David |last2=Gutierrez |first2=Janneth P |last3=Lopez-Lavalle |first3=Luis A B |title=Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes |journal=Frontiers in Microbiology |date=2021 |volume=12 |doi=10.3389/fmicb.2021.737616 |doi-access=free |pmid=34745040 |pmc=8569520 }}

The new paradigm regarding mutualistic fungi and bacterial transmission via the seeds of host plants has been fostered largely by research pertaining to plants of agricultural value.{{cite journal |last1=War |first1=Aadil Farooq |last2=Bashir |first2=Iqra |last3=Reshi |first3=Zafar A. |last4=Kardol |first4=Paul |last5=Rashid |first5=Irfan |title=Insights into the seed microbiome and its ecological significance in plant life |journal=Microbiological Research |date=April 2023 |volume=269 |doi=10.1016/j.micres.2023.127318 |pmid=36753851 |s2cid=256563377|doi-access=free }} Rice seeds were found to entail high microbial diversity, with the greatest diversity inhabiting the embryo rather than the pericarp.{{cite journal |last1=Matsumoto |first1=Haruna |last2=Fan |first2=Xiaoyan |last3=Wang |first3=Yue |last4=Kusstatscher |first4=Peter |last5=Duan |first5=Jie |last6=Wu |first6=Sanling |last7=Chen |first7=Sunlu |last8=Qiao |first8=Kun |last9=Wang |first9=Yiling |last10=Ma |first10=Bin |last11=Zhu |first11=Guonian |last12=Hashidoko |first12=Yasuyuki |last13=Berg |first13=Gabriele |last14=Cernava |first14=Tomislav |last15=Wang |first15=Mengcen |title=Bacterial seed endophyte shapes disease resistance in rice |journal=Nature Plants |date=4 January 2021 |volume=7 |issue=1 |pages=60–72 |doi=10.1038/s41477-020-00826-5 |pmid=33398157 |bibcode=2021NatPl...7...60M |s2cid=230508404 }} Fungi of genus Fusarium transmitted via seeds were found to be dominant members of the microbiome within the stems of maize. This facet of the plant microbiome came to be known as the seed microbiome.{{cite journal |last1=Nelson |first1=Eric B |title=REVIEW: The seed microbiome: Origins, interactions, and impacts |journal=Plant and Soil |date=2018 |volume=422 |pages=7–34 |doi=10.1007/s11104-017-3289-7}}

Forestry researchers have also begun to identify members of the seed microbiome pertaining to valuable tree species. Vertical transmission of fungal and bacterial mutualists was confirmed in 2021 for the acorns of oak trees.{{Cite journal| last1=Abdelfattah|first1=Ahmed|last2=Wisniewski|first2=Michael|last3=Schena|first3=Leonardo|last4=Tack|first4=Ayco J. M.|title=Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root|journal=Environmental Microbiology|year=2021|volume=23|issue=4|pages=2199–2214|language=en|doi=10.1111/1462-2920.15392|pmid=33427409|issn=1462-2920|doi-access=free| bibcode=2021EnvMi..23.2199A}}{{Cite web|title=Seeds transfer their microbes to the next generation|url=https://www.eurekalert.org/pub_releases/2021-01/su-stt012121.php|access-date=2021-01-21|website=EurekAlert! AAAS|language=en}} If the research on oaks turns out to apply to other tree species, it will be understood that the above-soil portions of a plant (the phyllosphere) obtain nearly all of their beneficial fungi from those carried in the seed. In contrast, the roots (the rhizosphere) acquire only a small fraction of their mutualists from the seed. Most arrive via the surrounding soil, and this includes their vital associations with arbuscular mycorrhizal fungi.

Microbial species consistently found in plant seeds are known as the "core microbiome." Benefits to the host plant include their ability to assist in the production of antimicrobial compounds, detoxification, nutrient uptake, and growth-promoting activities. Discerning the functions of symbiotic microbes in seeds is shifting the agricultural paradigm away from seed breeding and preparation that traditionally sought to minimize the presence of fungal and bacterial propagules. The likelihood that a microbe found within a seed is mutualistic is now a routine presumption. Such partners may contribute to "seed dormancy and germination, environmental adaptation, resistance and tolerance against diseases, and growth promotion."{{cite journal | last1=Abdelfattah |first1=Ahmed |last2=Tack |first2=Ayco J.M. |last3=Lobato |first3=Carolina |last4=Wassermann |first4=Birgit |last5=Berg |first5=Gabriele |title=From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome |journal=Trends in Microbiology |date=April 2023 |volume=31 |issue=4 |pages=346–355 |doi=10.1016/j.tim.2022.10.009 | pmid=36481186 |doi-access=free }}

Application of the new understanding of beneficial microbes inhabiting seeds has been suggested for use beyond agriculture and for biodiversity conservation. A citizen group advocating for northward assisted migration of an endangered tree in the USA has pointed to the seed microbiome paradigm shift as a reason for the official institutions to lift their ban on seed transfer beyond the ex situ conservation plantings in northern Georgia.{{cite web |last1=Barlow |first1=Connie |title=Published Documents on Endangerment Causes of Torreya taxifolia in Florida |url=https://www.torreyaguardians.org/extinction-papers.html |website=Torreya Guardians |access-date=22 February 2024}}

{{main|Plant holobiont}}

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a holobiont. Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments.{{cite journal |last1=Hassani |first1=M. Amine |last2=Durán |first2=Paloma |last3=Hacquard |first3=Stéphane | title = Microbial interactions within the plant holobiont | journal=Microbiome | volume = 6 | issue = 1 | pages = 58 |date = March 2018 | pmid = 29587885 | doi = 10.1186/s40168-018-0445-0 | pmc = 5870681 | doi-access = free }} 50px Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].

• Biomass partitioning
• Mangrove microbiome
• Phytobiome

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Category:Microbiomes

Category:Plants