Editing Mangrove (section)

===Root microbiome===
[[File:Bacterial and fungal community in a mangrove tree.webp|thumb|upright=2|Bacterial and fungal community in a mangrove tree.<ref name=Purahong2019>{{cite journal |doi = 10.3390/microorganisms7120585|doi-access = free|title = First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments|year = 2019|last1 = Purahong|first1 = Witoon|last2 = Sadubsarn|first2 = Dolaya|last3 = Tanunchai|first3 = Benjawan|last4 = Wahdan|first4 = Sara Fareed Mohamed|last5 = Sansupa|first5 = Chakriya|last6 = Noll|first6 = Matthias|last7 = Wu|first7 = Yu-Ting|last8 = Buscot|first8 = François|journal = Microorganisms|volume = 7|issue = 12|page = 585|pmid = 31756976|pmc = 6955992}} [[File:CC-BY icon.svg|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].</ref> Bacterial taxonomic community composition in the rhizosphere soil and fungal taxonomic community composition in all four rhizosphere soil and plant compartments. Information on the fungal ecological functional groups is also provided. Proportions of fungal [[Operational taxonomic unit|OTUs]] (approximate species) that can colonise at least two of the compartments are shown in the left panel.]]
{{see also|Root microbiome}}

Mangrove roots harbour a repertoire of [[microbial taxa]] that contribute to important ecological functions in mangrove ecosystems. Like typical terrestrial plants, mangroves depend upon mutually beneficial interactions with microbial communities.<ref name=Thatoi2013>{{cite journal |doi = 10.1007/s13213-012-0442-7|title = Biodiversity and biotechnological potential of microorganisms from mangrove ecosystems: A review|year = 2013|last1 = Thatoi|first1 = Hrudayanath|last2 = Behera|first2 = Bikash Chandra|last3 = Mishra|first3 = Rashmi Ranjan|last4 = Dutta|first4 = Sushil Kumar|journal = Annals of Microbiology|volume = 63|pages = 1–19|s2cid = 17798850|doi-access = free}}</ref> In particular, microbes residing in developed roots could help mangroves transform nutrients into usable forms before plant assimilation.<ref name=Liu2020>{{cite journal |doi = 10.1016/j.scitotenv.2020.137807|title = Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa|year = 2020|last1 = Liu|first1 = Xingyu|last2 = Yang|first2 = Chao|last3 = Yu|first3 = Xiaoli|last4 = Yu|first4 = Huang|last5 = Zhuang|first5 = Wei|last6 = Gu|first6 = Hang|last7 = Xu|first7 = Kui|last8 = Zheng|first8 = Xiafei|last9 = Wang|first9 = Cheng|last10 = Xiao|first10 = Fanshu|last11 = Wu|first11 = Bo|last12 = He|first12 = Zhili|last13 = Yan|first13 = Qingyun|journal = Science of the Total Environment|volume = 721|page = 137807|pmid = 32179356|bibcode = 2020ScTEn.72137807L|s2cid = 212739128}}</ref><ref>{{cite journal |doi = 10.1038/s41467-018-07343-2|title = The structure and function of the global citrus rhizosphere microbiome|year = 2018|last1 = Xu|first1 = Jin|last2 = Zhang|first2 = Yunzeng|last3 = Zhang|first3 = Pengfan|last4 = Trivedi|first4 = Pankaj|last5 = Riera|first5 = Nadia|last6 = Wang|first6 = Yayu|last7 = Liu|first7 = Xin|last8 = Fan|first8 = Guangyi|last9 = Tang|first9 = Jiliang|last10 = Coletta-Filho|first10 = Helvécio D.|last11 = Cubero|first11 = Jaime|last12 = Deng|first12 = Xiaoling|last13 = Ancona|first13 = Veronica|last14 = Lu|first14 = Zhanjun|last15 = Zhong|first15 = Balian|last16 = Roper|first16 = M. Caroline|last17 = Capote|first17 = Nieves|last18 = Catara|first18 = Vittoria|last19 = Pietersen|first19 = Gerhard|last20 = Vernière|first20 = Christian|last21 = Al-Sadi|first21 = Abdullah M.|last22 = Li|first22 = Lei|last23 = Yang|first23 = Fan|last24 = Xu|first24 = Xun|last25 = Wang|first25 = Jian|last26 = Yang|first26 = Huanming|last27 = Jin|first27 = Tao|last28 = Wang|first28 = Nian|journal = Nature Communications|volume = 9|issue = 1|page = 4894|pmid = 30459421|pmc = 6244077|bibcode = 2018NatCo...9.4894X}}</ref> These microbes also provide mangroves [[phytohormone]]s for suppressing [[phytopathogen]]s<ref name="Durán2018"/> or helping mangroves withstand heat and salinity.<ref name=Thatoi2013 /> In turn, root-associated microbes receive carbon [[metabolite]]s from the plant via root [[exudate]]s,<ref>{{cite journal | last1=Sasse | first1=Joelle | last2=Martinoia | first2=Enrico | last3=Northen | first3=Trent | title=Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? | journal=Trends in Plant Science | publisher=Elsevier BV | volume=23 | issue=1 | year=2018 | issn=1360-1385 | doi=10.1016/j.tplants.2017.09.003 | pages=25–41| pmid=29050989 | bibcode=2018TPS....23...25S | osti=1532289 | s2cid=205455681 | url=https://www.zora.uzh.ch/id/eprint/148899/1/Sasse_TIPS_2017.pdf }}</ref> thus close associations between the plant and microbes are established for their mutual benefits.<ref name= Bais2006>{{cite journal |doi = 10.1146/annurev.arplant.57.032905.105159|title = The Role of Root Exudates in Rhizosphere Interactions with Plants and Other Organisms|year = 2006|last1 = Bais|first1 = Harsh P.|last2 = Weir|first2 = Tiffany L.|last3 = Perry|first3 = Laura G.|last4 = Gilroy|first4 = Simon|last5 = Vivanco|first5 = Jorge M.|journal = Annual Review of Plant Biology|volume = 57|pages = 233–266|pmid = 16669762}}</ref><ref name=Zhuang2020>{{cite journal |doi = 10.1038/s41522-020-00164-6|title = Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale|year = 2020|last1 = Zhuang|first1 = Wei|last2 = Yu|first2 = Xiaoli|last3 = Hu|first3 = Ruiwen|last4 = Luo|first4 = Zhiwen|last5 = Liu|first5 = Xingyu|last6 = Zheng|first6 = Xiafei|last7 = Xiao|first7 = Fanshu|last8 = Peng|first8 = Yisheng|last9 = He|first9 = Qiang|last10 = Tian|first10 = Yun|last11 = Yang|first11 = Tony|last12 = Wang|first12 = Shanquan|last13 = Shu|first13 = Longfei|last14 = Yan|first14 = Qingyun|last15 = Wang|first15 = Cheng|last16 = He|first16 = Zhili|journal = npj Biofilms and Microbiomes|volume = 6|issue = 1|page = 52|pmid = 33184266|pmc = 7665043}} [[File:CC-BY icon.svg|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].</ref>

The taxonomic class level shows that most [[Proteobacteria]] were reported to come from Gammaproteobacteria, followed by Deltaproteobacteria and Alphaproteobacteria. The diverse function and the phylogenic variation of Gammaproteobacteria, which consisted of orders such as Alteromonadales and Vibrionales, are found in marine and coastal regions and are high in abundance in mangrove sediments functioning as nutrient recyclers. Members of Deltaproteobacteria found in mangrove soil are mostly sulfur-related, consisting of [[Desulfobacterales]], [[Desulfuromonadales]], [[Desulfovibrionales]], and Desulfarculales among others.<ref name="A Systematic Review of the Physicoc">{{cite journal |last1=Lai |first1=Jiayong |last2=Cheah |first2=Wee |last3=Palaniveloo |first3=Kishneth |last4=Suwa |first4=Rempei |last5=Sharma |first5=Sahadev |title=A Systematic Review of the Physicochemical and Microbial Diversity of Well-Preserved, Restored, and Disturbed Mangrove Forests: What Is Known and What Is the Way Forward? |journal=Forests |date=16 December 2022 |volume=13 |issue=12 |pages=2160 |doi=10.3390/f13122160 |doi-access=free }}</ref>
Highly diverse microbial communities (mainly [[bacteria]] and [[fungi]]) have been found to inhabit and function in mangrove roots.<ref>{{cite journal |doi = 10.1007/s00468-015-1233-0|title = Mangrove root: Adaptations and ecological importance|year = 2016|last1 = Srikanth|first1 = Sandhya|last2 = Lum|first2 = Shawn Kaihekulani Yamauchi|last3 = Chen|first3 = Zhong|journal = Trees|volume = 30|issue = 2|pages = 451–465| bibcode=2016Trees..30..451S |s2cid = 5471541}}</ref><ref name=Thatoi2013 /><ref>{{cite journal |doi = 10.2307/2261526|jstor = 2261526|title = Soil Physicochemical Patterns and Mangrove Species Distribution--Reciprocal Effects?|last1 = McKee|first1 = Karen L.|journal = Journal of Ecology|year = 1993|volume = 81|issue = 3|pages = 477–487| bibcode=1993JEcol..81..477M }}</ref> For example, [[Diazotroph|diazotrophic bacteria]] in the vicinity of mangrove roots could perform [[biological nitrogen fixation]], which provides 40–60% of the total nitrogen required by mangroves;<ref>{{cite journal |doi = 10.1007/s003740000319|title = The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: An overview|year = 2001|last1 = Holguin|first1 = Gina|last2 = Vazquez|first2 = Patricia|last3 = Bashan|first3 = Yoav|journal = Biology and Fertility of Soils|volume = 33|issue = 4|pages = 265–278| bibcode=2001BioFS..33..265H |s2cid = 10826862}}</ref><ref>{{cite journal |doi = 10.1093/treephys/tpq048|title = Nutrition of mangroves|year = 2010|last1 = Reef|first1 = R.|last2 = Feller|first2 = I. C.|last3 = Lovelock|first3 = C. E.|journal = Tree Physiology|volume = 30|issue = 9|pages = 1148–1160|pmid = 20566581|doi-access = free}}</ref> the soil attached to mangrove roots lacks oxygen but is rich in organic matter, providing an optimal microenvironment for [[sulfate-reducing bacteria]] and [[methanogen]]s,<ref name=Thatoi2013 /> [[lignin]]olytic, [[cellulolytic]], and [[amylolytic]] fungi are prevalent in the mangrove root environment;<ref name=Thatoi2013 /> rhizosphere fungi could help mangroves survive in waterlogged and nutrient-restricted environments.<ref>{{cite journal |doi = 10.1016/j.apsoil.2013.11.009|title = Effects of arbuscular mycorrhizal inoculation and phosphorus supply on the growth and nutrient uptake of Kandelia obovata (Sheue, Liu & Yong) seedlings in autoclaved soil|year = 2014|last1 = Xie|first1 = Xiangyu|last2 = Weng|first2 = Bosen|last3 = Cai|first3 = Bangping|last4 = Dong|first4 = Yiran|last5 = Yan|first5 = Chongling|journal = Applied Soil Ecology|volume = 75|pages = 162–171| bibcode=2014AppSE..75..162X }}</ref> These studies have provided increasing evidence to support the importance of root-associated bacteria and fungi for mangrove growth and health.<ref name=Thatoi2013 /><ref name=Liu2020 /><ref name=Zhuang2020 />

Recent studies have investigated the detailed structure of root-associated microbial communities at a continuous fine-scale in other plants,<ref>{{cite journal | last1=Edwards | first1=Joseph | last2=Johnson | first2=Cameron | last3=Santos-Medellín | first3=Christian | last4=Lurie | first4=Eugene | last5=Podishetty | first5=Natraj Kumar | last6=Bhatnagar | first6=Srijak | last7=Eisen | first7=Jonathan A. | last8=Sundaresan | first8=Venkatesan | title=Structure, variation, and assembly of the root-associated microbiomes of rice | journal=Proceedings of the National Academy of Sciences | volume=112 | issue=8 | date=20 January 2015 | issn=0027-8424 | doi=10.1073/pnas.1414592112 | pages=E911–E920| pmid=25605935 | pmc=4345613 | bibcode=2015PNAS..112E.911E | doi-access=free }}</ref> where a microhabitat was divided into four root compartments: endosphere,<ref name="Durán2018">{{cite journal |doi = 10.1016/j.cell.2018.10.020|title = Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival|year = 2018|last1 = Durán|first1 = Paloma|last2 = Thiergart|first2 = Thorsten|last3 = Garrido-Oter|first3 = Ruben|last4 = Agler|first4 = Matthew|last5 = Kemen|first5 = Eric|last6 = Schulze-Lefert|first6 = Paul|last7 = Hacquard|first7 = Stéphane|journal = Cell|volume = 175|issue = 4|pages = 973–983.e14|pmid = 30388454|pmc = 6218654}}</ref><ref name=Edwards2015 /><ref>{{cite journal |doi = 10.1042/BCJ20180615|title = Interactions between plants and soil shaping the root microbiome under abiotic stress|year = 2019|last1 = Hartman|first1 = Kyle|last2 = Tringe|first2 = Susannah G.|journal = Biochemical Journal|volume = 476|issue = 19|pages = 2705–2724|pmid = 31654057|pmc = 6792034}}</ref> episphere,<ref name="Durán2018"/> rhizosphere,<ref name=Edwards2015>{{cite journal |doi = 10.1073/pnas.1414592112|title = Structure, variation, and assembly of the root-associated microbiomes of rice|year = 2015|last1 = Edwards|first1 = Joseph|last2 = Johnson|first2 = Cameron|last3 = Santos-Medellín|first3 = Christian|last4 = Lurie|first4 = Eugene|last5 = Podishetty|first5 = Natraj Kumar|last6 = Bhatnagar|first6 = Srijak|last7 = Eisen|first7 = Jonathan A.|last8 = Sundaresan|first8 = Venkatesan|journal = Proceedings of the National Academy of Sciences|volume = 112|issue = 8|pages = E911–E920|pmid = 25605935|pmc = 4345613|bibcode = 2015PNAS..112E.911E|doi-access = free}}</ref><ref>{{cite journal |doi = 10.1146/annurev-phyto-082712-102342|title = Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity|year = 2015|last1 = Reinhold-Hurek|first1 = Barbara|last2 = Bünger|first2 = Wiebke|last3 = Burbano|first3 = Claudia Sofía|last4 = Sabale|first4 = Mugdha|last5 = Hurek|first5 = Thomas|journal = Annual Review of Phytopathology|volume = 53|pages = 403–424|pmid = 26243728}}</ref> and nonrhizosphere or [[bulk soil]].<ref>{{cite journal |last1=Liu |first1=Yalong |last2=Ge |first2=Tida |last3=Ye |first3=Jun |last4=Liu |first4=Shoulong |last5=Shibistova |first5=Olga |last6=Wang |first6=Ping |last7=Wang |first7=Jingkuan |last8=Li |first8=Yong |last9=Guggenberger |first9=Georg |last10=Kuzyakov |first10=Yakov |author-link10=Yakov Kuzyakov |last11=Wu |first11=Jinshui |year=2019 |title=Initial utilization of rhizodeposits with rice growth in paddy soils: Rhizosphere and N fertilization effects |journal=Geoderma |volume=338 |pages=30–39 |bibcode=2019Geode.338...30L |doi=10.1016/j.geoderma.2018.11.040 |s2cid=134648694}}</ref><ref>{{cite journal |doi = 10.1016/j.femsec.2003.11.012|title = Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture|year = 2004|last1 = Johansson|first1 = Jonas F.|last2 = Paul|first2 = Leslie R.|last3 = Finlay|first3 = Roger D.|journal = FEMS Microbiology Ecology|volume = 48|issue = 1|pages = 1–13|pmid = 19712426| s2cid=22700384 |doi-access = free| bibcode=2004FEMME..48....1J }}</ref> Moreover, the microbial communities in each compartment have been reported to have unique characteristics.<ref name="Durán2018"/><ref name=Edwards2015 /> Root exudates selectively enrich adapted microbial populations; however, these exudates were found to exert only marginal impacts on microbes in the [[bulk soil]] outside the rhizosphere .<ref name=Sasse2017>{{cite journal |doi = 10.1016/j.tplants.2017.09.003|title = Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?|year = 2018|last1 = Sasse|first1 = Joelle|last2 = Martinoia|first2 = Enrico|last3 = Northen|first3 = Trent|journal = Trends in Plant Science|volume = 23|issue = 1|pages = 25–41|pmid = 29050989| bibcode=2018TPS....23...25S |osti = 1532289| s2cid=205455681 |url = https://www.zora.uzh.ch/id/eprint/148899/1/Sasse_TIPS_2017.pdf}}</ref><ref name= Bais2006 /> Furthermore, it was noted that the root episphere, rather than the rhizosphere, was primarily responsible for controlling the entry of specific microbial populations into the root,<ref name="Durán2018"/> resulting in the selective enrichment of Proteobacteria in the endosphere.<ref name="Durán2018"/><ref name="Ofek-Lalzar2014">{{cite journal |doi = 10.1038/ncomms5950|title = Niche and host-associated functional signatures of the root surface microbiome|year = 2014|last1 = Ofek-Lalzar|first1 = Maya|last2 = Sela|first2 = Noa|last3 = Goldman-Voronov|first3 = Milana|last4 = Green|first4 = Stefan J.|last5 = Hadar|first5 = Yitzhak|last6 = Minz|first6 = Dror|journal = Nature Communications|volume = 5|page = 4950|pmid = 25232638|bibcode = 2014NatCo...5.4950O|doi-access = free}}</ref> These findings provide new insights into the niche differentiation of root-associated microbial communities,<ref name="Durán2018"/><ref name=Sasse2017 /><ref name= Bais2006 /><ref name="Ofek-Lalzar2014"/> Nevertheless, amplicon-based community profiling may not provide the functional characteristics of root-associated microbial communities in plant growth and biogeochemical cycling.<ref>{{cite journal |doi = 10.1007/s13238-020-00724-8|title = A practical guide to amplicon and metagenomic analysis of microbiome data|year = 2021|last1 = Liu|first1 = Yong-Xin|last2 = Qin|first2 = Yuan|last3 = Chen|first3 = Tong|last4 = Lu|first4 = Meiping|last5 = Qian|first5 = Xubo|last6 = Guo|first6 = Xiaoxuan|last7 = Bai|first7 = Yang|journal = Protein & Cell|volume = 12|issue = 5|pages = 315–330|pmid = 32394199|pmc = 8106563}}</ref> Unraveling functional patterns across the four root compartments holds a great potential for understanding functional mechanisms responsible for mediating root–microbe interactions in support of enhancing mangrove ecosystem functioning.<ref name=Zhuang2020 />

The diversity of bacteria in disturbed mangroves is reported to be higher than in
well-preserved mangroves<ref name="A Systematic Review of the Physicoc"/> Studies comparing mangroves in different conservation states show that bacterial composition in disturbed mangrove sediment alters its structure, leading to a functional equilibrium, where the dynamics of chemicals in mangrove soils lead to the remodeling of its microbial structure.<ref>{{cite journal |title=Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity |date=2019 |doi=10.1016/j.marpolbul.2019.03.001 |last1=Cotta |first1=Simone Raposo |last2=Cadete |first2=Luana Lira |last3=Van Elsas |first3=Jan Dirk |last4=Andreote |first4=Fernando Dini |last5=Dias |first5=Armando Cavalcante Franco |journal=Marine Pollution Bulletin |volume=141 |pages=586–594 |pmid=30955771 |bibcode=2019MarPB.141..586C |s2cid=91872087 |url=https://research.rug.nl/en/publications/45e6976e-8216-46e2-a2bb-d23a6158b694 }}</ref>