Editing Endosymbiont (section)

=== Plants ===
All vascular plants harbor endosymbionts or endophytes in this context. They include [[bacteria]], [[Fungus|fungi]], [[virus]]es, [[protozoa]] and even [[microalgae]]. Endophytes aid in processes such as growth and development, nutrient uptake, and defense against biotic and abiotic stresses like [[drought]], [[salinity]], heat, and herbivores.<ref name="Baron 39–55">{{cite journal |vauthors=Baron NC, Rigobelo EC |year=2022 |title=Endophytic fungi: a tool for plant growth promotion and sustainable agriculture |journal=Mycology |volume=13 |issue=1 |pages=39–55 |doi=10.1080/21501203.2021.1945699 |pmc=8856089 |pmid=35186412}}</ref>

Plant symbionts can be categorized into [[Epiphyte|epiphytic]], [[Endophyte|endophytic]], and [[mycorrhiza]]l. These relations can also be categorized as beneficial, [[Mutualism (biology)|mutualistic]], neutral, and [[pathogen]]ic.<ref name="Hardoim 293–320">{{cite journal |display-authors=6 |vauthors=Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A |date=September 2015 |title=The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes |journal=Microbiology and Molecular Biology Reviews |volume=79 |issue=3 |pages=293–320 |doi=10.1128/MMBR.00050-14 |pmc=4488371 |pmid=26136581}}</ref><ref>{{cite journal |vauthors=Khare E, Mishra J, Arora NK |date=2018 |title=Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects |journal=Frontiers in Microbiology |volume=9 |pages=2732 |doi=10.3389/fmicb.2018.02732 |pmc=6249440 |pmid=30498482 |doi-access=free}}</ref> [[Microorganism]]s living as endosymbionts in plants can enhance their host's primary productivity either by producing or capturing important resources.<ref name="Fungal plant endosymbionts alter li">{{cite journal |vauthors=de Sassi C, Müller CB, Krauss J |date=May 2006 |title=Fungal plant endosymbionts alter life history and reproductive success of aphid predators |journal=Proceedings. Biological Sciences |volume=273 |issue=1591 |pages=1301–1306 |doi=10.1098/rspb.2005.3442 |pmc=1560287 |pmid=16720406}}</ref> These endosymbionts can also enhance plant productivity by producing toxic metabolites that aid plant defenses against [[herbivore]]s.<ref>{{cite journal |vauthors=Schardl CL, Leuchtmann A, Spiering MJ |date=2004-06-02 |title=Symbioses of grasses with seedborne fungal endophytes |journal=Annual Review of Plant Biology |volume=55 |issue=1 |pages=315–340 |doi=10.1146/annurev.arplant.55.031903.141735 |pmid=15377223}}</ref><ref>{{Cite journal |vauthors=Hunter MD, Price PW |date=1992 |title=Playing Chutes and Ladders: Heterogeneity and the Relative Roles of Bottom-Up and Top-Down Forces in Natural Communities |url=https://www.jstor.org/stable/1940152 |journal=Ecology |volume=73 |issue=3 |pages=724–732 |bibcode=1992Ecol...73..724H |doi=10.2307/1940152 |issn=0012-9658 |jstor=1940152 |s2cid=54005488}}</ref>

Plants are dependent on [[plastid]] or [[chloroplast]] organelles. The chloroplast is derived from a cyanobacterial primary endosymbiosis that began over one billion years ago. An oxygenic, photosynthetic free-living [[Cyanobacteria|cyanobacterium]] was engulfed and kept by a heterotrophic [[protist]] and eventually evolved into the present intracellular organelle.<ref>{{cite journal |vauthors=Qiu H, Yoon HS, Bhattacharya D |title=Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes |journal=Frontiers in Plant Science |volume=4 |pages=366 |date=September 2013 |pmid=24065973 |pmc=3777023 |doi=10.3389/fpls.2013.00366 |doi-access=free }}</ref> 

Mycorrhizal endosymbionts appear only in [[Fungus|fungi]].

Typically, plant endosymbiosis studies focus on a single category or species to better understand their individual biological processes and functions.<ref>{{cite journal |vauthors=Porras-Alfaro A, Bayman P |title=Hidden fungi, emergent properties: endophytes and microbiomes |journal=Annual Review of Phytopathology |volume=49 |issue=1 |pages=291–315 |date=2011-09-08 |pmid=19400639 |doi=10.1146/annurev-phyto-080508-081831 }}</ref>

==== Fungal endophytes ====
Fungal endophytes can be found in all plant tissues. Fungi living below the ground amidst plant roots are known as [[mycorrhiza]], but are further categorized based on their location inside the root, with prefixes such as ecto, endo, arbuscular, ericoid, etc. Fungal endosymbionts that live in the roots and extend their extraradical [[hyphae]] into the outer [[rhizosphere]] are known as ectendosymbionts.<ref name="Salhi-2022">{{Cite journal |vauthors=Salhi LN, Bustamante Villalobos P, Forget L, Burger G, Lang BF |date=Sep 2022 |title=Endosymbionts in cranberry: Diversity, effect on plant growth, and pathogen biocontrol |journal=Plants, People, Planet |language=en |volume=4 |issue=5 |pages=511–522 |doi=10.1002/ppp3.10290 |s2cid=250548548 |issn=2572-2611|doi-access=free }}</ref><ref>{{cite journal |vauthors=Roth R, Paszkowski U |title=Plant carbon nourishment of arbuscular mycorrhizal fungi |journal=Current Opinion in Plant Biology |volume=39 |pages=50–56 |date=October 2017 |pmid=28601651 |doi=10.1016/j.pbi.2017.05.008 |series=39 Cell signalling and gene regulation 2017 |bibcode=2017COPB...39...50R }}</ref>

===== Arbuscular Mycorrhizal Fungi (AMF) =====
[[Arbuscular mycorrhiza|Arbuscular mycorrhizal fungi]] or AMF are the most diverse plant microbial endosymbionts. With exceptions such as the [[Ericaceae]] family, almost all vascular plants harbor [[Arbuscular mycorrhiza|AMF]] endosymbionts as endo and ecto as well. AMF plant endosymbionts systematically colonize [[Root|plant roots]] and help the plant host acquire soil [[nutrient]]s such as nitrogen. In return it absorbs plant organic carbon products.<ref name="Salhi-2022" /> [[Plant root exudates]] contain diverse secondary metabolites, especially [[flavonoids]] and [[strigolactones]] that act as [[plant communication|chemical signals]] and attracts the AMF.<ref>{{cite journal |vauthors=Oldroyd GE, Harrison MJ, Paszkowski U |title=Reprogramming plant cells for endosymbiosis |journal=Science |volume=324 |issue=5928 |pages=753–754 |date=May 2009 |pmid=19423817 |doi=10.1126/science.1171644 |bibcode=2009Sci...324..753O |s2cid=206518892 }}</ref> AMF ''[[Gigasporaceae|Gigaspora]] margarita'' lives as a plant endosymbiont and also harbors further endosymbiont intracytoplasmic bacterium-like organisms.<ref>{{cite journal |vauthors=Bianciotto V, Bandi C, Minerdi D, Sironi M, Tichy HV, Bonfante P |title=An obligately endosymbiotic mycorrhizal fungus itself harbors obligately intracellular bacteria |journal=Applied and Environmental Microbiology |volume=62 |issue=8 |pages=3005–3010 |date=August 1996 |pmid=8702293 |pmc=168087 |doi=10.1128/aem.62.8.3005-3010.1996 |bibcode=1996ApEnM..62.3005B }}</ref> AMF generally promote plant health and growth and alleviate [[abiotic stress]]es such as salinity, drought, heat, poor nutrition, and [[metal toxicity]].<ref>{{cite journal |vauthors=Begum N, Qin C, Ahanger MA, Raza S, Khan MI, Ashraf M, Ahmed N, Zhang L |display-authors=6 |title=Role of Arbuscular Mycorrhizal Fungi in Plant Growth Regulation: Implications in Abiotic Stress Tolerance |journal=Frontiers in Plant Science |volume=10 |pages=1068 |date=2019 |pmid=31608075 |pmc=6761482 |doi=10.3389/fpls.2019.01068 |doi-access=free }}</ref> Individual AMF species have different effects in different hosts – introducing the AMF of one plant to another plant can reduce the latter's growth.<ref>{{cite journal |vauthors=Herre EA, Mejía LC, Kyllo DA, Rojas E, Maynard Z, Butler A, Van Bael SA |date=March 2007 |title=Ecological implications of anti-pathogen effects of tropical fungal endophytes and mycorrhizae |journal=Ecology |volume=88 |issue=3 |pages=550–558 |bibcode=2007Ecol...88..550H |doi=10.1890/05-1606 |pmid=17503581}}</ref>

===== Endophytic fungi =====
Endophytic fungi in [[Mutualism (biology)|mutualistic]] relations directly benefit and benefit from their host plants. They also can help their hosts succeed in polluted environments such as those contaminated with toxic metals.<ref>{{cite journal |vauthors=Domka AM, Rozpaądek P, Turnau K |title=Are Fungal Endophytes Merely Mycorrhizal Copycats? The Role of Fungal Endophytes in the Adaptation of Plants to Metal Toxicity |journal=Frontiers in Microbiology |volume=10 |pages=371 |date=2019 |pmid=30930857 |pmc=6428775 |doi=10.3389/fmicb.2019.00371 |doi-access=free }}</ref> Fungal [[endophyte]]s are taxonomically diverse and are divided into categories based on mode of transmission, [[biodiversity]], in planta colonization and host plant type.<ref name="Rodriguez-2009">{{cite journal |vauthors=Rodriguez RJ, White JF, Arnold AE, Redman RS |title=Fungal endophytes: diversity and functional roles |journal=The New Phytologist |volume=182 |issue=2 |pages=314–330 |date=Apr 2009 |pmid=19236579 |doi=10.1111/j.1469-8137.2009.02773.x |doi-access=free |bibcode=2009NewPh.182..314R }}</ref><ref>{{Cite journal |vauthors=Purahong W, Hyde KD |date=2011-03-01 |title=Effects of fungal endophytes on grass and non-grass litter decomposition rates |url=https://doi.org/10.1007/s13225-010-0083-8 |journal=Fungal Diversity |language=en |volume=47 |issue=1 |pages=1–7 |doi=10.1007/s13225-010-0083-8 |s2cid=43678079 |issn=1878-9129}}</ref> Clavicipitaceous fungi systematically colonize temperate season grasses. Non-clavicipitaceous fungi colonize higher plants and even roots and divide into subcategories.<ref>{{Cite journal |date=2005-05-24 |title=Evolutionary Development of the Clavicipitaceae |url=https://www.taylorfrancis.com/chapters/edit/10.1201/9781420027891-33/evolutionary-development-clavicipitaceae |journal=The Fungal Community |language=en |pages=525–538 |doi=10.1201/9781420027891-33|isbn=9780429116407 }}</ref> ''[[Aureobasidium]] ''and ''[[Preussia (fungus)|preussia]]'' species of endophytic fungi isolated from ''[[Boswellia sacra]]'' produce [[Indole-3-acetic acid|indole acetic acid]] [[hormone]] to promote plant health and development.<ref>{{cite journal |vauthors=Khan AL, Al-Harrasi A, Al-Rawahi A, Al-Farsi Z, Al-Mamari A, Waqas M, Asaf S, Elyassi A, Mabood F, Shin JH, Lee IJ |display-authors=6 |title=Endophytic Fungi from Frankincense Tree Improves Host Growth and Produces Extracellular Enzymes and Indole Acetic Acid |journal=PLOS ONE |volume=11 |issue=6 |pages=e0158207 |date=2016-06-30 |pmid=27359330 |pmc=4928835 |doi=10.1371/journal.pone.0158207 |bibcode=2016PLoSO..1158207K |doi-access=free }}</ref>

[[Aphid]]s can be found in most plants. Carnivorous [[Coccinellidae|ladybirds]] are aphid predators and are used in [[pest control]]. Plant endophytic fungus ''[[Neotyphodium lolii]]'' produces [[alkaloid]] [[mycotoxin]]s in response to [[aphid]] invasions. In response, ladybird predators exhibited reduced [[fertility]] and abnormal reproduction, suggesting that the mycotoxins are transmitted along the [[food chain]] and affect the [[Predation|predators]].<ref name="Fungal plant endosymbionts alter li"/>

==== Endophytic bacteria ====
Endophytic bacteria belong to a diverse group of plant endosymbionts characterized by systematic colonization of plant tissues. The most common genera include ''[[Pseudomonas]]'', ''[[Bacillus]]'', ''[[Acinetobacter]]'', ''[[Actinobacteria]]'', ''[[Sphingomonas]].'' Some endophytic bacteria, such as ''[[Bacillus amyloliquefaciens]]'', a seed-born endophytic bacteria, produce plant growth by producing [[gibberellins]], which are potent plant growth hormones. ''[[Bacillus amyloliquefaciens]]'' promotes the taller height of [[Transgenic rice|transgenic]] dwarf rice plants.<ref>{{cite journal |vauthors=Shahzad R, Waqas M, Khan AL, Asaf S, Khan MA, Kang SM, Yun BW, Lee IJ |display-authors=6 |title=Seed-borne endophytic Bacillus amyloliquefaciens RWL-1 produces gibberellins and regulates endogenous phytohormones of Oryza sativa |journal=Plant Physiology and Biochemistry |volume=106 |pages=236–243 |date=September 2016 |pmid=27182958 |doi=10.1016/j.plaphy.2016.05.006 |bibcode=2016PlPB..106..236S }}</ref> Some endophytic bacteria genera additionally belong to the [[Enterobacteriaceae]] family.<ref>{{Cite book |last1=Pirttilä |first1=Anna Maria |url={{google books|plainurl=y|id=10MZbnLKRJIC}} |title=Endophytes of Forest Trees: Biology and Applications |last2=Frank |first2=A. Carolin |date=2011-07-11 |publisher=Springer Science & Business Media |isbn=978-94-007-1599-8 |language=en}}</ref> Endophytic bacteria typically colonize the leaf tissues from plant roots, but can also enter the plant through the leaves through leaf [[stomata]].<ref>Senthilkumar et al., 2011</ref> Generally, the endophytic bacteria are isolated from the plant tissues by surface [[Sterilization (microbiology)|sterilization]] of the plant tissue in a sterile environment.<ref>{{Cite journal |vauthors=Quadt-Hallmann A, Kloepper JW, Benhamou N |date=2011-02-10 |title=Bacterial endophytes in cotton: mechanisms of entering the plant |url=https://cdnsciencepub.com/doi/10.1139/m97-081 |journal=Canadian Journal of Microbiology |volume=43 |issue=6 |pages=577–582 |language=en |doi=10.1139/m97-081}}</ref> Passenger endophytic bacteria eventually colonize inner tissue of plant by [[stochastic]] events while True endophytes possess adaptive traits because of which they live strictly in association with plants.<ref>{{cite journal |vauthors=Hardoim PR, van Overbeek LS, Elsas JD |title=Properties of bacterial endophytes and their proposed role in plant growth |language=English |journal=Trends in Microbiology |volume=16 |issue=10 |pages=463–471 |date=October 2008 |pmid=18789693 |doi=10.1016/j.tim.2008.07.008 |url=https://research.rug.nl/en/publications/c4338aca-07f5-4222-9ecc-75142f0dbdab }}</ref> The ''in vitro-''cultivated endophytic [[bacteria]] association with plants is considered a more intimate relationship that helps plants acclimatize to conditions and promotes health and growth. Endophytic bacteria are considered to be plant's essential endosymbionts because virtually all plants harbor them, and these endosymbionts play essential roles in host survival.<ref>{{cite journal |vauthors=Bodył A, Mackiewicz P, Stiller JW |title=The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles? |language=English |journal=Trends in Microbiology |volume=15 |issue=7 |pages=295–296 |date=July 2007 |pmid=17537638 |doi=10.1016/j.tim.2007.05.002 }}</ref> This endosymbiotic relation is important in terms of [[ecology]], [[evolution]] and diversity. Endophytic bacteria such as ''[[Sphingomonas]]'' sp. and ''[[Serratia]]'' sp. that are isolated from arid land plants regulate endogenous [[hormone]] content and promote growth.<ref>{{Cite journal |vauthors=Asaf S, Khan MA, Khan AL, Waqas M, Shahzad R, Kim A, Kang S, Lee I  |date=2017-01-01 |title=Bacterial endophytes from arid land plants regulate endogenous hormone content and promote growth in crop plants: an example of Sphingomonas sp. and Serratia marcescens |journal=Journal of Plant Interactions |language=en |volume=12 |issue=1 |pages=31–38 |doi=10.1080/17429145.2016.1274060 |s2cid=90203067 |issn=1742-9145|doi-access=free |bibcode=2017JPlaI..12...31A }}</ref>

==== Archaea endosymbionts ====
[[Archaea]] are members of most [[microbiome]]s. While archaea are abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome, and play a role in host plant's health, growth and survival amid biotic and abiotic stresses. However, few studies have investigated the role of archaea in plant health and its symbiotic relationships.<ref name="Jung-2020">{{cite journal |vauthors=Jung J, Kim JS, Taffner J, Berg G, Ryu CM |title=Archaea, tiny helpers of land plants |journal=Computational and Structural Biotechnology Journal |volume=18 |pages=2494–2500 |date=2020-01-01 |pmid=33005311 |pmc=7516179 |doi=10.1016/j.csbj.2020.09.005 }}</ref> Most plant endosymbiosis studies focus on fungal or bacteria using [[metagenomic]] approaches.<ref>{{cite journal |vauthors=Taffner J, Cernava T, Erlacher A, Berg G |title=Novel insights into plant-associated archaea and their functioning in arugula (''Eruca sativa'' Mill.) |journal=Journal of Advanced Research |volume=19 |pages=39–48 |date=September 2019 |pmid=31341668 |pmc=6629838 |doi=10.1016/j.jare.2019.04.008 |series=Special Issue on Plant Microbiome |s2cid=155746848 }}</ref>

The characterization of archaea includes crop plants such as [[rice]]<ref>{{cite journal |vauthors=Ma M, Du H, Sun T, An S, Yang G, Wang D |title=Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient |journal=The Science of the Total Environment |volume=650 |issue=Pt 1 |pages=1640–1651 |date=February 2019 |pmid=30054090 |doi=10.1016/j.scitotenv.2018.07.175 |bibcode=2019ScTEn.650.1640M |s2cid=51727014 }}</ref> and [[maize]], but also aquatic plants.<ref name="Jung-2020" /> The abundance of archaea varies by tissue type; for example archaea are more abundant in the [[rhizosphere]] than the [[phyllosphere]] and [[endosphere]].<ref>{{cite journal |vauthors=Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA |display-authors=6 |title=Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice |journal=The ISME Journal |volume=6 |issue=7 |pages=1378–1390 |date=July 2012 |pmid=22189496 |pmc=3379629 |doi=10.1038/ismej.2011.192 |bibcode=2012ISMEJ...6.1378K }}</ref> This archaeal abundance is associated with plant species type, environment and the plant's developmental stage.<ref>{{cite journal |vauthors=Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA |title=Archaea Are Interactive Components of Complex Microbiomes |journal=Trends in Microbiology |volume=26 |issue=1 |pages=70–85 |date=January 2018 |pmid=28826642 |doi=10.1016/j.tim.2017.07.004 }}</ref> In a study on plant [[genotype]]-specific archaeal and bacterial endophytes, 35% of archaeal sequences were detected in overall sequences (achieved using [[amplicon sequencing]] and verified by [[Real-time polymerase chain reaction|real time-PCR]]). The archaeal sequences belong to the phyla ''[[Thaumarchaeota]]'', ''[[Crenarchaeota]],'' and ''[[Euryarchaeota]]''.<ref>{{cite journal |vauthors=Müller H, Berg C, Landa BB, Auerbach A, Moissl-Eichinger C, Berg G |title=Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees |journal=Frontiers in Microbiology |volume=6 |pages=138 |date=2015 |pmid=25784898 |pmc=4347506 |doi=10.3389/fmicb.2015.00138 |doi-access=free }}</ref>