Editing Mangrove (section)

==Mangrove microbiome==
{{see also|Plant microbiome}}

[[Plant microbiome]]s play crucial roles in the health and productivity of mangroves.<ref name=Purahong2018>{{cite journal |doi = 10.3389/fpls.2018.01563|doi-access = free|title = Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. Actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants|year = 2018|last1 = Purahong|first1 = Witoon|last2 = Orrù|first2 = Luigi|last3 = Donati|first3 = Irene|last4 = Perpetuini|first4 = Giorgia|last5 = Cellini|first5 = Antonio|last6 = Lamontanara|first6 = Antonella|last7 = Michelotti|first7 = Vania|last8 = Tacconi|first8 = Gianni|last9 = Spinelli|first9 = Francesco|journal = Frontiers in Plant Science|volume = 9|page = 1563|pmid = 30464766|pmc = 6234494}}</ref> Many researchers have successfully applied knowledge acquired about plant [[microbiome]]s to produce specific [[wikt:inocula|inocula]] for crop protection.<ref>{{Cite journal |last1=Afzal |first1=A. |last2=Bano |first2=A. |date=2008 |title=Rhizobium and phosphate solubilizing bacteria improve the yield and phosphorus uptake in wheat (''Triticum aestivum'') |url=https://www.researchgate.net/publication/228684375 |journal=International Journal of Agriculture and Biology (Pakistan) |volume=10 |issue=1 |pages=85–88 |issn=1560-8530 |eissn=1814-9596}}</ref><ref name=Busby2017 /> Such inocula can stimulate plant growth by releasing phytohormones and enhancing uptake of some mineral nutrients (particularly phosphorus and nitrogen).<ref name=Busby2017>{{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 | doi-access=free }}</ref><ref name=Berendsen2012>{{cite journal |doi = 10.1016/j.tplants.2012.04.001|title = The rhizosphere microbiome and plant health|year = 2012|last1 = Berendsen|first1 = Roeland L.|last2 = Pieterse|first2 = Corné M.J.|last3 = Bakker|first3 = Peter A. H. M.|journal = Trends in Plant Science|volume = 17|issue = 8|pages = 478–486|pmid = 22564542| bibcode=2012TPS....17..478B |hdl = 1874/255269| s2cid=32900768 |hdl-access = free}}</ref><ref name="Bringel2016">{{Cite journal |last1=Bringel |first1=Françoise |last2=Couée |first2=Ivan |year=2015 |title=Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics |journal=Frontiers in Microbiology |volume=06 |page=486 |doi=10.3389/fmicb.2015.00486 |pmc=4440916 |pmid=26052316 |doi-access=free}}</ref> However, most of the plant microbiome studies have focused on the model plant ''[[Arabidopsis thaliana]]'' and economically important crop plants, such as [[rice]], [[barley]], [[wheat]], [[maize]] and [[soybean]]. There is less information on the microbiomes of tree species.<ref name=Purahong2018 /><ref name=Busby2017 /> Plant microbiomes are determined by plant-related factors (e.g., [[genotype]], organ, species, and health status) and environmental factors (e.g., land use, climate, and nutrient availability).<ref name=Purahong2018 /><ref name="Bringel2016" /> Two of the plant-related factors, plant species and genotypes, have been shown to play significant roles in shaping [[rhizosphere]] and plant microbiomes, as tree genotypes and species are associated with specific [[microbial communities]].<ref name=Berendsen2012 /> Different plant organs also have specific microbial communities depending on plant-associated factors (plant genotype, available nutrients, and organ-specific physicochemical conditions) and environmental conditions (associated with aboveground and underground surfaces and disturbances).<ref name="Coleman-Derr2016">{{cite journal |doi = 10.1111/nph.13697|title = Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species|year = 2016|last1 = Coleman-Derr|first1 = Devin|last2 = Desgarennes|first2 = Damaris|last3 = Fonseca-Garcia|first3 = Citlali|last4 = Gross|first4 = Stephen|last5 = Clingenpeel|first5 = Scott|last6 = Woyke|first6 = Tanja|last7 = North|first7 = Gretchen|last8 = Visel|first8 = Axel|last9 = Partida-Martinez|first9 = Laila P.|last10 = Tringe|first10 = Susannah G.|journal = New Phytologist|volume = 209|issue = 2|pages = 798–811|pmid = 26467257|pmc = 5057366}}</ref><ref>{{cite journal |doi = 10.1186/s40168-018-0413-8|title = The Populus holobiont: Dissecting the effects of plant niches and genotype on the microbiome|year = 2018|last1 = Cregger|first1 = M. A.|last2 = Veach|first2 = A. M.|last3 = Yang|first3 = Z. K.|last4 = Crouch|first4 = M. J.|last5 = Vilgalys|first5 = R.|last6 = Tuskan|first6 = G. A.|last7 = Schadt|first7 = C. W.|journal = Microbiome|volume = 6|issue = 1|page = 31|pmid = 29433554|pmc = 5810025 | doi-access=free }}</ref><ref>{{cite journal |doi = 10.1111/nph.13760|title = Disentangling the factors shaping microbiota composition across the plant holobiont|year = 2016|last1 = Hacquard|first1 = Stéphane|journal = New Phytologist|volume = 209|issue = 2|pages = 454–457|pmid = 26763678| hdl=11858/00-001M-0000-002B-166F-5 |doi-access = free}}</ref><ref name=Purahong2019 />

===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>

===Suggestions for future mangrove microbial diversity research===
Despite many research advancements in mangrove sediment bacterial metagenomics
diversity in various conditions over the past few years, bridging the research gap and
expanding our knowledge towards the relationship between microbes mainly constituted of bacteria and its nutrient cycles in the mangrove sediment and direct and indirect impacts on mangrove growth and stand-structures as coastal barriers and other ecological service providers. Thus, based on studies by Lai et al.'s systematic review, here they suggest sampling improvements and a fundamental environmental index for future reference.<ref name="A Systematic Review of the Physicoc"/>

===Mangrove virome===
[[File:Caudovirales.svg|thumb|upright=1.5|[[Phage]]s are viruses that infect bacteria, such as cyanobacteria. Shown are the [[virion]]s of different families of [[Caudovirales|tailed phages]]: ''[[Myoviridae]]'', ''Podoviridae'' and ''Siphoviridae'']]
{{see also|Virome|Marine viruses}}

[[File:Phylogenetic tree of Caudovirales from mangrove virome contigs.webp|thumb|upright=1.5|right|Phylogenetic tree of tailed phages found in the mangrove virome.<ref name=Jin2019>{{cite journal |doi = 10.1186/s40168-019-0675-9|title = Diversities and potential biogeochemical impacts of mangrove soil viruses|year = 2019|last1 = Jin|first1 = Min|last2 = Guo|first2 = Xun|last3 = Zhang|first3 = Rui|last4 = Qu|first4 = Wu|last5 = Gao|first5 = Boliang|last6 = Zeng|first6 = Runying|journal = Microbiome|volume = 7|issue = 1|page = 58|pmid = 30975205|pmc = 6460857 | doi-access=free }} [[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> [[Reference sequence]]s are coloured black, and [[virome]] [[contig]]s are indicated with varied colours. The scale bar represents half amino acid substitution per site.]]

[[Mangrove forest]]s are one of the most carbon-rich biomes, accounting for 11% of the total input of terrestrial carbon into oceans. [[Virus]]es are thought to significantly influence local and global [[biogeochemical cycle]]s, though as of 2019, little information was available about the community structure, genetic diversity, and ecological roles of viruses in mangrove ecosystems.<ref name=Jin2019 />

Viruses are the most abundant biological entities on earth, present in virtually all ecosystems.<ref>{{cite journal |doi = 10.1038/nature04160|title = Viruses in the sea|year = 2005|last1 = Suttle|first1 = Curtis A.|journal = Nature|volume = 437|issue = 7057|pages = 356–361|pmid = 16163346|bibcode = 2005Natur.437..356S|s2cid = 4370363}}</ref><ref>{{cite journal |doi = 10.1073/pnas.1305956110|title = Twelve previously unknown phage genera are ubiquitous in global oceans|year = 2013|last1 = Holmfeldt|first1 = K.|last2 = Solonenko|first2 = N.|last3 = Shah|first3 = M.|last4 = Corrier|first4 = K.|last5 = Riemann|first5 = L.|last6 = Verberkmoes|first6 = N. C.|last7 = Sullivan|first7 = M. B.|journal = Proceedings of the National Academy of Sciences|volume = 110|issue = 31|pages = 12798–12803|pmid = 23858439|pmc = 3732932|bibcode = 2013PNAS..11012798H|doi-access = free}}</ref> By [[Viral lysis|lysing]] their hosts, that is, by rupturing their cell membranes, viruses control host abundance and affect the structure of host communities.<ref>{{cite journal |doi = 10.3389/fmicb.2014.00355|doi-access = free|title = Environmental bacteriophages: Viruses of microbes in aquatic ecosystems|year = 2014|last1 = Sime-Ngando|first1 = TÃ©Lesphore|journal = Frontiers in Microbiology|volume = 5|page = 355|pmid = 25104950|pmc = 4109441}}</ref> Viruses also influence their host diversity and evolution through [[horizontal gene transfer]], [[Natural selection#Arms races|selection for resistance]] and manipulation of [[bacterial metabolisms]].<ref name="Breitbart2012">{{cite journal |doi = 10.1146/annurev-marine-120709-142805|title = Marine Viruses: Truth or Dare|year = 2012|last1 = Breitbart|first1 = Mya|journal = Annual Review of Marine Science|volume = 4|pages = 425–448|pmid = 22457982|bibcode = 2012ARMS....4..425B}}</ref><ref>{{cite journal |doi = 10.1128/mBio.00893-17|title = Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions|year = 2017|last1 = He|first1 = Tianliang|last2 = Li|first2 = Hongyun|last3 = Zhang|first3 = Xiaobo|journal = mBio|volume = 8|issue = 4|pmid = 28698277|pmc = 5513705}}</ref><ref>{{cite journal |doi = 10.1073/pnas.1319778111|title = Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses|year = 2014|last1 = Hurwitz|first1 = B. L.|last2 = Westveld|first2 = A. H.|last3 = Brum|first3 = J. R.|last4 = Sullivan|first4 = M. B.|journal = Proceedings of the National Academy of Sciences|volume = 111|issue = 29|pages = 10714–10719|pmid = 25002514|pmc = 4115555|bibcode = 2014PNAS..11110714H|doi-access = free}}</ref> Importantly, [[marine virus]]es affect local and global [[biogeochemical cycle]]s through the release of substantial amounts of [[organic carbon]] and nutrients from hosts and assist microbes in driving biogeochemical cycles with [[auxiliary metabolic genes]] (AMGs).<ref>{{cite journal |doi = 10.1126/science.1252229
|title = Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
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}}</ref><ref name=Roux2016>{{cite journal |doi = 10.1038/nrmicro.2017.113|title = Algal virus boosts nitrogen uptake in the ocean|year = 2017|last1 = York|first1 = Ashley|journal = Nature Reviews Microbiology|volume = 15|issue = 10|page = 573|pmid = 28900307|s2cid = 19473466|doi-access = free}}</ref><ref>{{cite journal |doi = 10.1038/nature19366|title = Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses|year = 2016|last1 = Roux|first1 = Simon|last2 = Brum|first2 = Jennifer R.|last3 = Dutilh|first3 = Bas E.|last4 = Sunagawa|first4 = Shinichi|last5 = Duhaime|first5 = Melissa B.|last6 = Loy|first6 = Alexander|last7 = Poulos|first7 = Bonnie T.|last8 = Solonenko|first8 = Natalie|last9 = Lara|first9 = Elena|last10 = Poulain|first10 = Julie|last11 = Pesant|first11 = Stéphane|last12 = Kandels-Lewis|first12 = Stefanie|last13 = Dimier|first13 = Céline|last14 = Picheral|first14 = Marc|last15 = Searson|first15 = Sarah|last16 = Cruaud|first16 = Corinne|last17 = Alberti|first17 = Adriana|last18 = Duarte|first18 = Carlos M.|last19 = Gasol|first19 = Josep M.|last20 = Vaqué|first20 = Dolors|last21 = Bork|first21 = Peer|last22 = Acinas|first22 = Silvia G.|last23 = Wincker|first23 = Patrick|last24 = Sullivan|first24 = Matthew B.|journal = Nature|volume = 537|issue = 7622|pages = 689–693|pmid = 27654921|bibcode = 2016Natur.537..689.|hdl = 1874/341494|s2cid = 54182070|hdl-access = free}}</ref><ref name=Jin2019 />

It is presumed that AMGs augment viral-infected host metabolism and facilitate the production of new viruses.<ref name= Breitbart2012 /><ref>{{cite journal |doi = 10.1038/nature08060|title = Viruses manipulate the marine environment|year = 2009|last1 = Rohwer|first1 = Forest|last2 = Thurber|first2 = Rebecca Vega|journal = Nature|volume = 459|issue = 7244|pages = 207–212|pmid = 19444207|bibcode = 2009Natur.459..207R|s2cid = 4397295}}</ref> AMGs have been extensively explored in [[marine cyanophage]]s and include genes involved in photosynthesis, carbon turnover, phosphate uptake and stress response.<ref>{{cite journal |doi = 10.1371/journal.pbio.0040234|title = Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts|year = 2006|last1 = Sullivan|first1 = Matthew B.|last2 = Lindell|first2 = Debbie|author-link2=Debbie Lindell|last3 = Lee|first3 = Jessica A.|last4 = Thompson|first4 = Luke R.|last5 = Bielawski|first5 = Joseph P.|last6 = Chisholm|first6 = Sallie W.|journal = PLOS Biology|volume = 4|issue = 8|pages = e234|pmid = 16802857|pmc = 1484495 | doi-access=free }}</ref><ref>{{cite journal |doi = 10.1073/pnas.1102164108|title = Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism|year = 2011|last1 = Thompson|first1 = L. R.|last2 = Zeng|first2 = Q.|last3 = Kelly|first3 = L.|last4 = Huang|first4 = K. H.|last5 = Singer|first5 = A. U.|last6 = Stubbe|first6 = J.|last7 = Chisholm|first7 = S. W.|journal = Proceedings of the National Academy of Sciences|volume = 108|issue = 39|pages = E757–E764|pmid = 21844365|pmc = 3182688|doi-access = free}}</ref><ref>{{cite journal |doi = 10.1016/j.cub.2011.11.055|title = Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation|year = 2012|last1 = Zeng|first1 = Qinglu|last2 = Chisholm|first2 = Sallie W.|journal = Current Biology|volume = 22|issue = 2|pages = 124–128|pmid = 22244998|s2cid = 7692657|doi-access = free| bibcode=2012CBio...22..124Z |hdl = 1721.1/69047|hdl-access = free}}</ref><ref>{{cite journal |doi = 10.1038/ismej.2013.4|title = Structure and function of a cyanophage-encoded peptide deformylase|year = 2013|last1 = Frank|first1 = Jeremy A.|last2 = Lorimer|first2 = Don|last3 = Youle|first3 = Merry|last4 = Witte|first4 = Pam|last5 = Craig|first5 = Tim|last6 = Abendroth|first6 = Jan|last7 = Rohwer|first7 = Forest|last8 = Edwards|first8 = Robert A.|last9 = Segall|first9 = Anca M.|last10 = Burgin|first10 = Alex B.|journal = The ISME Journal|volume = 7|issue = 6|pages = 1150–1160|pmid = 23407310|pmc = 3660681| bibcode=2013ISMEJ...7.1150F }}</ref> Cultivation-independent metagenomic analysis of viral communities has identified additional AMGs that are involved in motility, central carbon metabolism, photosystem I, energy metabolism, iron–sulphur clusters, anti-oxidation and sulphur and nitrogen cycling.<ref name=Roux2016 /><ref>{{cite journal |doi = 10.1371/journal.pbio.0050016|title = The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families|year = 2007|last1 = Yooseph|first1 = Shibu|last2 = Sutton|first2 = Granger|last3 = Rusch|first3 = Douglas B.|last4 = Halpern|first4 = Aaron L.|last5 = Williamson|first5 = Shannon J.|last6 = Remington|first6 = Karin|last7 = Eisen|first7 = Jonathan A.|last8 = Heidelberg|first8 = Karla B.|last9 = Manning|first9 = Gerard|last10 = Li|first10 = Weizhong|last11 = Jaroszewski|first11 = Lukasz|last12 = Cieplak|first12 = Piotr|last13 = Miller|first13 = Christopher S.|last14 = Li|first14 = Huiying|last15 = Mashiyama|first15 = Susan T.|last16 = Joachimiak|first16 = Marcin P.|last17 = Van Belle|first17 = Christopher|last18 = Chandonia|first18 = John-Marc|last19 = Soergel|first19 = David A.|last20 = Zhai|first20 = Yufeng|last21 = Natarajan|first21 = Kannan|last22 = Lee|first22 = Shaun|last23 = Raphael|first23 = Benjamin J.|last24 = Bafna|first24 = Vineet|last25 = Friedman|first25 = Robert|last26 = Brenner|first26 = Steven E.|last27 = Godzik|first27 = Adam|last28 = Eisenberg|first28 = David|last29 = Dixon|first29 = Jack E.|last30 = Taylor|first30 = Susan S.|journal = PLOS Biology|volume = 5|issue = 3|pages = e16|pmid = 17355171|pmc = 1821046|display-authors = 1 | doi-access=free }}</ref><ref>{{cite journal |doi = 10.1038/nature06810|title = Functional metagenomic profiling of nine biomes|year = 2008|last1 = Dinsdale|first1 = Elizabeth A.|last2 = Edwards|first2 = Robert A.|last3 = Hall|first3 = Dana|last4 = Angly|first4 = Florent|last5 = Breitbart|first5 = Mya|last6 = Brulc|first6 = Jennifer M.|last7 = Furlan|first7 = Mike|last8 = Desnues|first8 = Christelle|last9 = Haynes|first9 = Matthew|last10 = Li|first10 = Linlin|last11 = McDaniel|first11 = Lauren|last12 = Moran|first12 = Mary Ann|last13 = Nelson|first13 = Karen E.|last14 = Nilsson|first14 = Christina|last15 = Olson|first15 = Robert|last16 = Paul|first16 = John|last17 = Brito|first17 = Beltran Rodriguez|last18 = Ruan|first18 = Yijun|last19 = Swan|first19 = Brandon K.|last20 = Stevens|first20 = Rick|last21 = Valentine|first21 = David L.|last22 = Thurber|first22 = Rebecca Vega|last23 = Wegley|first23 = Linda|last24 = White|first24 = Bryan A.|last25 = Rohwer|first25 = Forest|journal = Nature|volume = 452|issue = 7187|pages = 629–632|pmid = 18337718|bibcode = 2008Natur.452..629D|s2cid = 4421951}}</ref><ref>{{cite journal |doi = 10.1016/j.tim.2016.06.006|title = Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean|year = 2016|last1 = Rosenwasser|first1 = Shilo|last2 = Ziv|first2 = Carmit|last3 = Creveld|first3 = Shiri Graff van|last4 = Vardi|first4 = Assaf|journal = Trends in Microbiology|volume = 24|issue = 10|pages = 821–832|pmid = 27395772}}</ref> Interestingly, a recent analysis of Pacific Ocean Virome data identified niche-specialised AMGs that contribute to depth-stratified host adaptations.<ref>{{cite journal |doi = 10.1038/ismej.2014.143|title = Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome|year = 2015|last1 = Hurwitz|first1 = Bonnie L.|last2 = Brum|first2 = Jennifer R.|last3 = Sullivan|first3 = Matthew B.|journal = The ISME Journal|volume = 9|issue = 2|pages = 472–484|pmid = 25093636|pmc = 4303639| bibcode=2015ISMEJ...9..472H }}</ref> Given that microbes drive global biogeochemical cycles, and viruses infect a large fraction of microbes at any given time,<ref>{{cite journal |doi = 10.1128/MMBR.64.1.69-114.2000|title = Virioplankton: Viruses in Aquatic Ecosystems|year = 2000|last1 = Wommack|first1 = K. Eric|last2 = Colwell|first2 = Rita R.|journal = Microbiology and Molecular Biology Reviews|volume = 64|issue = 1|pages = 69–114|pmid = 10704475|pmc = 98987}}</ref> viral-encoded AMGs must play important roles in global biogeochemistry and microbial metabolic evolution.<ref name=Jin2019 />

Mangrove forests are the only woody [[halophyte]]s that live in salt water along the world's subtropical and tropical coastlines. Mangroves are one of the most productive and ecologically important ecosystems on earth. The rates of primary production of mangroves equal those of tropical humid evergreen forests and coral reefs.<ref name= Alongi2012>{{cite journal |doi = 10.4155/cmt.12.20|title = Carbon sequestration in mangrove forests|year = 2012|last1 = Alongi|first1 = Daniel M.|journal = Carbon Management|volume = 3|issue = 3|pages = 313–322|s2cid = 153827173|doi-access = free| bibcode=2012CarM....3..313A }}</ref> As a globally relevant component of the carbon cycle, mangroves sequester approximately 24 million metric tons of carbon each year.<ref name= Alongi2012 /><ref>{{cite journal |doi = 10.1007/s00114-001-0283-x|title = Relevance of mangroves for the production and deposition of organic matter along tropical continental margins|year = 2002|last1 = Jennerjahn|first1 = Tim C.|last2 = Ittekkot|first2 = Venugopalan|journal = Naturwissenschaften|volume = 89|issue = 1|pages = 23–30|pmid = 12008969|bibcode = 2002NW.....89...23J|s2cid = 33556308}}</ref> Most mangrove carbon is stored in soil and sizable belowground pools of dead roots, aiding in the conservation and recycling of nutrients beneath forests.<ref>{{cite journal |doi = 10.1007/s00468-002-0206-2|title = Nutrient partitioning and storage in arid-zone forests of the mangroves Rhizophora stylosa and Avicennia marina|year = 2003|last1 = Alongi|first1 = Daniel M.|last2 = Clough|first2 = Barry F.|last3 = Dixon|first3 = Paul|last4 = Tirendi|first4 = Frank|journal = Trees|volume = 17| issue=1 |pages = 51–60| bibcode=2003Trees..17...51A |s2cid = 23613917}}</ref> Although mangroves cover only 0.5% of the earth's coastal area, they account for 10–15% of the coastal sediment carbon storage and 10–11% of the total input of terrestrial carbon into oceans.<ref>{{cite journal |doi = 10.1146/annurev-marine-010213-135020|title = Carbon Cycling and Storage in Mangrove Forests|year = 2014|last1 = Alongi|first1 = Daniel M.|journal = Annual Review of Marine Science|volume = 6|pages = 195–219|pmid = 24405426|bibcode = 2014ARMS....6..195A|doi-access = free}}</ref> The disproportionate contribution of mangroves to carbon sequestration is now perceived as an important means to counterbalance greenhouse gas emissions.<ref name=Jin2019 />

[[File:Avicennia marina chloroplast genome.png|thumb|upright=1.5|Circular representation of the chloroplast genome for the grey mangrove, ''[[Avicennia marina]]''<ref name=Natarajan2021>{{cite journal | last1=Natarajan | first1=Purushothaman | last2=Murugesan | first2=Ashok Kumar | last3=Govindan | first3=Ganesan | last4=Gopalakrishnan | first4=Ayyaru | last5=Kumar | first5=Ravichandiran | last6=Duraisamy | first6=Purushothaman | last7=Balaji | first7=Raju | last8=Shyamli | first8=Puhan Sushree | last9=Parida | first9=Ajay K. | last10=Parani | first10=Madasamy | title=A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina | journal=Communications Biology | publisher=Springer Science and Business Media LLC | volume=4 | issue=1 | date=8 July 2021 | page=851 | issn=2399-3642 | doi=10.1038/s42003-021-02384-8| pmid=34239036 | pmc=8266904 }} [[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>]]

Despite the ecological importance of the mangrove ecosystem, knowledge of mangrove biodiversity is notably limited. Previous reports mainly investigated the biodiversity of mangrove fauna, flora, and bacterial communities.<ref>{{cite journal |doi = 10.1111/j.1574-6941.2008.00519.x|title = Exploring the diversity of bacterial communities in sediments of urban mangrove forests|year = 2008|last1 = Marcial Gomes|first1 = Newton C.|last2 = Borges|first2 = Ludmila R.|last3 = Paranhos|first3 = Rodolfo|last4 = Pinto|first4 = Fernando N.|last5 = Mendonã§a-Hagler|first5 = Leda C. S.|last6 = Smalla|first6 = Kornelia|journal = FEMS Microbiology Ecology|volume = 66|issue = 1|pages = 96–109|pmid = 18537833| bibcode=2008FEMME..66...96M | s2cid=40733636 }}</ref><ref>{{cite journal |doi = 10.1371/journal.pone.0038600|doi-access = free|title = The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics|year = 2012|last1 = Andreote|first1 = Fernando Dini|last2 = Jiménez|first2 = Diego Javier|last3 = Chaves|first3 = Diego|last4 = Dias|first4 = Armando Cavalcante Franco|last5 = Luvizotto|first5 = Danice Mazzer|last6 = Dini-Andreote|first6 = Francisco|last7 = Fasanella|first7 = Cristiane Cipola|last8 = Lopez|first8 = Maryeimy Varon|last9 = Baena|first9 = Sandra|last10 = Taketani|first10 = Rodrigo Gouvêa|last11 = De Melo|first11 = Itamar Soares|journal = PLOS ONE|volume = 7|issue = 6|pages = e38600|pmid = 22737213|pmc = 3380894|bibcode = 2012PLoSO...738600A}}</ref><ref>{{Cite book|url=https://books.google.com/books?id=EgvLwAEACAAJ&q=%22Species+diversity+in+ecological+communities:+historical+and+geographical+perspectives%22|title = Species Diversity in Ecological Communities: Historical and Geographical Perspectives|isbn = 9780226718231|last1 = Ricklefs|first1 = Robert E.|last2 = Schluter|first2 = Dolph|year = 1993| publisher=University of Chicago Press }}</ref> Particularly, little information is available about viral communities and their roles in mangrove soil ecosystems.<ref>{{cite journal |doi = 10.1016/j.tim.2017.12.004|title = The 'Neglected' Soil Virome – Potential Role and Impact|year = 2018|last1 = Pratama|first1 = Akbar Adjie|last2 = Van Elsas|first2 = Jan Dirk|journal = Trends in Microbiology|volume = 26|issue = 8|pages = 649–662|pmid = 29306554|s2cid = 25057850}}</ref><ref>{{cite journal |doi = 10.1146/annurev-virology-101416-041639|title = Viruses in Soil Ecosystems: An Unknown Quantity within an Unexplored Territory|year = 2017|last1 = Williamson|first1 = Kurt E.|last2 = Fuhrmann|first2 = Jeffry J.|last3 = Wommack|first3 = K. Eric|last4 = Radosevich|first4 = Mark|journal = Annual Review of Virology|volume = 4|issue = 1|pages = 201–219|pmid = 28961409|doi-access = free}}</ref> In view of the importance of viruses in structuring and regulating host communities and mediating element biogeochemical cycles, exploring viral communities in mangrove ecosystems is essential. Additionally, the intermittent flooding of sea water and resulting sharp transition of mangrove environments may result in substantially different genetic and functional diversity of bacterial and viral communities in mangrove soils compared with those of other systems.<ref>{{cite journal |doi = 10.1007/s00227-006-0377-2|title = Recovery of novel bacterial diversity from mangrove sediment|year = 2007|last1 = Liang|first1 = Jun-Bin|last2 = Chen|first2 = Yue-Qin|last3 = Lan|first3 = Chong-Yu|last4 = Tam|first4 = Nora F. Y.|last5 = Zan|first5 = Qi-Jie|last6 = Huang|first6 = Li-Nan|journal = Marine Biology|volume = 150|issue = 5|pages = 739–747| bibcode=2007MarBi.150..739L |s2cid = 85384181}}</ref><ref name=Jin2019 />

===Genome sequencing===
* ''Rhizophoreae'' as revealed by [[whole-genome sequencing]]<ref name=Xu2017>{{cite journal | last1=Xu | first1=Shaohua | last2=He | first2=Ziwen | last3=Zhang | first3=Zhang | last4=Guo | first4=Zixiao | last5=Guo | first5=Wuxia | last6=Lyu | first6=Haomin | last7=Li | first7=Jianfang | last8=Yang | first8=Ming | last9=Du | first9=Zhenglin | last10=Huang | first10=Yelin | last11=Zhou | first11=Renchao | last12=Zhong | first12=Cairong | last13=Boufford | first13=David E | last14=Lerdau | first14=Manuel | last15=Wu | first15=Chung-I | last16=Duke | first16=Norman C. | last17=Shi | first17=Suhua | title=The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing | journal=National Science Review | publisher=Oxford University Press (OUP) | volume=4 | issue=5 | date=5 June 2017 | issn=2095-5138 | doi=10.1093/nsr/nwx065 | pages=721–734| pmid=31258950 | pmc=6599620 }}</ref>

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