Editing Mangrove (section)

===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 />