Open Access

Illumina MiSeq Analysis and Comparison of Freshwater Microalgal Communities on Ulleungdo and Dokdo Islands


Cite

Ahmadjian V. The lichen alga Trebouxia: does it occur free-living? Plant Syst Evol. 1987;158(2-4):243–247. https://doi.org/10.1007/BF00936348AhmadjianV.The lichen alga Trebouxia: does it occur free-living?Plant Syst Evol.1987;158(2-4):243247. https://doi.org/10.1007/BF0093634810.1007/BF00936348Search in Google Scholar

Bates SS, Bird CJ, Freitas ASW, Foxall R, Gilgan M, Hanic LA, Johnson GR, McCulloch AW, Odense P, Pocklington R, et al. Pennate diatom Nitzschia pungens as the primary source of domoic acid, a toxin in shellfish from eastern Prince Edward Island, Canada. Can J Fish Aquat Sci. 1989 Jul;46(7):1203–1215. https://doi.org/10.1139/f89-156BatesSSBirdCJFreitasASWFoxallRGilganMHanicLAJohnsonGRMcCullochAWOdensePPocklingtonR, Pennate diatom Nitzschia pungens as the primary source of domoic acid, a toxin in shellfish from eastern Prince Edward Island, Canada. Can J Fish Aquat Sci.1989Jul;46(7):12031215. https://doi.org/10.1139/f89-15610.1139/f89-156Search in Google Scholar

Bellinzoni AM, Caneva G, Ricci S. Ecological trends in travertine colonisation by pioneer algae and plant communities. Int Bio deterior Biodegradation. 2003 Apr;51(3):203–210. https://doi.org/10.1016/S0964-8305(02)00172-5BellinzoniAMCanevaGRicciS.Ecological trends in travertine colonisation by pioneer algae and plant communities. Int Bio deterior Biodegradation.2003Apr;51(3):203210. https://doi.org/10.1016/S0964-8305(02)00172-510.1016/S0964-8305(02)00172-5Search in Google Scholar

Berner RA. Weathering, plants, and the long-term carbon cycle. Geochim Cosmochim Acta. 1992 Aug;56(8):3225–3231. https://doi.org/10.1016/0016-7037(92)90300-8BernerRA.Weathering, plants, and the long-term carbon cycle. Geochim Cosmochim Acta.1992Aug;56(8):32253231. https://doi.org/10.1016/0016-7037(92)90300-810.1016/0016-7037(92)90300-8Search in Google Scholar

Booth WE. Algae as pioneers in plant succession and their importance in erosion control. Ecology. 1941 Jan;22(1):38–46. https://doi.org/10.2307/1930007BoothWE.Algae as pioneers in plant succession and their importance in erosion control. Ecology.1941Jan;22(1):3846. https://doi.org/10.2307/193000710.2307/1930007Search in Google Scholar

Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 2009 Oct;184(2):449–456. https://doi.org/10.1111/j.1469-8137.2009.03003.xBuéeMReichMMuratCMorinENilssonRHUrozSMartinF.454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol.2009Oct;184(2):449456. https://doi.org/10.1111/j.1469-8137.2009.03003.x10.1111/j.1469-8137.2009.03003.x19703112Search in Google Scholar

Busse MD, Beattie SE, Powers RF, Sanchez FG, Tiarks AE. Microbial community responses in forest mineral soil to com paction, organic matter removal, and vegetation control. Can J For Res. 2006 Mar;36(3):577–588. https://doi.org/10.1139/x05-294BusseMDBeattieSEPowersRFSanchezFGTiarksAE.Microbial community responses in forest mineral soil to com paction, organic matter removal, and vegetation control. Can J For Res.2006Mar;36(3):577588. https://doi.org/10.1139/x05-29410.1139/x05-294Search in Google Scholar

Canovas S, Picot B, Casellas C, Zulkifi H, Dubois A, Bontoux J. Seasonal development of phytoplankton and zooplankton in a high-rate algal pond. Water Sci Technol. 1996 Mar;33(7):199–206. https://doi.org/10.2166/wst.1996.0139CanovasSPicotBCasellasCZulkifiHDuboisABontouxJ.Seasonal development of phytoplankton and zooplankton in a high-rate algal pond. Water Sci Technol.1996Mar;33(7):199206. https://doi.org/10.2166/wst.1996.013910.2166/wst.1996.0139Search in Google Scholar

Cardinale BJ, Matulich KL, Hooper DU, Byrnes JE, Duffy E, Gamfeldt L, Balvanera P, O’Connor MI, Gonzalez A. The functional role of producer diversity in ecosystems. Am J Bot. 2011 Mar;98(3):572–592. https://doi.org/10.3732/ajb.1000364CardinaleBJMatulichKLHooperDUByrnesJEDuffyEGamfeldtLBalvaneraPO’ConnorMIGonzalezA.The functional role of producer diversity in ecosystems. Am J Bot.2011Mar;98(3):572592. https://doi.org/10.3732/ajb.100036410.3732/ajb.100036421613148Search in Google Scholar

Chang KI, Kim YB, Suk MS, Byun SK. Hydrography around Dokdo. Ocean Polar Res. 2002 Dec 31;24(4):369–389. https://doi.org/10.4217/OPR.2002.24.4.369ChangKIKimYBSukMSByunSK.Hydrography around Dokdo. Ocean Polar Res.2002Dec 31;24(4):369389. https://doi.org/10.4217/OPR.2002.24.4.36910.4217/OPR.2002.24.4.369Search in Google Scholar

Chen W, Zhang CK, Cheng Y, Zhang S, Zhao H. A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS One. 2013 Aug 13;8(8):e70837. https://doi.org/10.1371/journal.pone.0070837ChenWZhangCKChengYZhangSZhaoH.A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS One.2013Aug 13;8(8):e70837. https://doi.org/10.1371/journal.pone.007083710.1371/journal.pone.0070837Search in Google Scholar

Chen Z, Lei X, Zhang B, Yang L, Zhang H, Zhang J, Li Y, Zheng W, Tian Y, Liu J, et al. First report of Pseudobodo sp., a new pathogen for a potential energy-producing algae: Chlorella vul garis cultures. PLoS One. 2014 Mar 5;9(3):e89571. https://doi.org/10.1371/journal.pone.0089571ChenZLeiXZhangBYangLZhangHZhangJLiYZhengWTianYLiuJ, First report of Pseudobodo sp., a new pathogen for a potential energy-producing algae: Chlorella vul garis cultures. PLoS One.2014Mar 5;9(3):e89571. https://doi.org/10.1371/journal.pone.008957110.1371/journal.pone.0089571Search in Google Scholar

Chiao JS, Sheng WG, Cheng XB. [An important mission for microbiologists in the new century-cultivation of the unculturable microorganisms]. Sheng Wu Gong Cheng Xue Bao. 2004 Sep;20(5):641–645.ChiaoJSShengWGChengXB.[An important mission for microbiologists in the new century-cultivation of the unculturable microorganisms]. Sheng Wu Gong Cheng Xue Bao.2004Sep;20(5):641645.Search in Google Scholar

Claassen S, du Toit E, Kaba M, Moodley C, Zar HJ, Nicol MP. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods. 2013 Aug;94(2):103–110. https://doi.org/10.1016/j.mimet.2013.05.008ClaassenSdu ToitEKabaMMoodleyCZarHJNicolMP.A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods.2013Aug;94(2):103110. https://doi.org/10.1016/j.mimet.2013.05.00810.1016/j.mimet.2013.05.008Search in Google Scholar

Daniel GF, Chamberlain AHL, Jones EBG. Ultrastructural observations on the marine fouling diatom Amphora. Helgol Meeresunters. 1980 Jun;34(2):123–149. https://doi.org/10.1007/BF01984035DanielGFChamberlainAHLJonesEBG.Ultrastructural observations on the marine fouling diatom Amphora. Helgol Meeresunters.1980Jun;34(2):123149. https://doi.org/10.1007/BF0198403510.1007/BF01984035Search in Google Scholar

Djukic I, Zehetner F, Mentler A, Gerzabek MH. Microbial commu nity composition and activity in different Alpine vegetation zones. Soil Biol Biochem. 2010 Feb;42(2):155–161. https://doi.org/10.1016/j.soilbio.2009.10.006DjukicIZehetnerFMentlerAGerzabekMH.Microbial commu nity composition and activity in different Alpine vegetation zones. Soil Biol Biochem.2010Feb;42(2):155161. https://doi.org/10.1016/j.soilbio.2009.10.00610.1016/j.soilbio.2009.10.006Search in Google Scholar

Falconer IR. Algal Toxins in Seafood and Drinking Water. London (UK): Academic Press; 2012.FalconerIR.Algal Toxins in Seafood and Drinking Water.London (UK): Academic Press; 2012.Search in Google Scholar

Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012 May;6(5):1007–1017. https://doi.org/10.1038/ismej.2011.159FiererNLauberCLRamirezKSZaneveldJBradfordMAKnightR.Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J.2012May;6(5):10071017. https://doi.org/10.1038/ismej.2011.15910.1038/ismej.2011.159Search in Google Scholar

Goldman JC, Shapiro J. Letter: Carbon dioxide and pH: effect on species succession of algae. Science. 1973 Oct 19;182(4109):306–307. https://doi.org/10.1126/science.182.4109.306GoldmanJCShapiroJ.Letter: Carbon dioxide and pH: effect on species succession of algae. Science.1973Oct 19;182(4109):306307. https://doi.org/10.1126/science.182.4109.30610.1126/science.182.4109.306Search in Google Scholar

Han X, Wang R, Liu J, Wang M, Zhou J, Guo W. Effects of vegetation type on soil microbial community structure and catabolic diversity assessed by polyphasic methods in North China. J Environ Sci (China). 2007 Jan;19(10):1228–1234. https://doi.org/10.1016/S1001-0742(07)60200-9HanXWangRLiuJWangMZhouJGuoW.Effects of vegetation type on soil microbial community structure and catabolic diversity assessed by polyphasic methods in North China. J Environ Sci (China).2007Jan;19(10):12281234. https://doi.org/10.1016/S1001-0742(07)60200-910.1016/S1001-0742(07)60200-9Search in Google Scholar

Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004 Dec 01;68(4):669–685. https://doi.org/10.1128/MMBR.68.4.669-685.2004HandelsmanJ.Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev.2004Dec 01;68(4):669685. https://doi.org/10.1128/MMBR.68.4.669-685.200410.1128/MMBR.68.4.669-685.200453900315590779Search in Google Scholar

Havens K, DeCosta J. Freshwater plankton community succession during experimental acidification. Arch. Hydrobiol. 1987;111:37–65.HavensKDeCostaJ.Freshwater plankton community succession during experimental acidification. Arch. Hydrobiol.1987;111:3765.10.1127/archiv-hydrobiol/111/1987/37Search in Google Scholar

Heck KL Jr, van Belle G, Simberloff D. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology. 1975 Oct;56(6):1459–1461. https://doi.org/10.2307/1934716HeckKLJrvan BelleGSimberloffD.Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology.1975Oct;56(6):14591461. https://doi.org/10.2307/193471610.2307/1934716Search in Google Scholar

Hudon C, Bourget E. The effect of light on the vertical structure of epibenthic diatom communities. Bot Mar. 1983;26(7):317–330. https://doi.org/10.1515/botm.1983.26.7.317HudonCBourgetE.The effect of light on the vertical structure of epibenthic diatom communities. Bot Mar.1983;26(7):317330. https://doi.org/10.1515/botm.1983.26.7.31710.1515/botm.1983.26.7.317Search in Google Scholar

Jackson TA. Study of the ecology of pioneer lichens, mosses, and algae on recent Hawaiian lava flows. Pac Sci. 1971;25:22–32.JacksonTA.Study of the ecology of pioneer lichens, mosses, and algae on recent Hawaiian lava flows. Pac Sci.1971;25:2232.Search in Google Scholar

Johnson MTJ, Agrawal AA. The ecological play of predator-prey dynamics in an evolutionary theatre. Trends Ecol Evol. 2003 Nov; 18(11):549–551. https://doi.org/10.1016/j.tree.2003.09.001JohnsonMTJAgrawalAA.The ecological play of predator-prey dynamics in an evolutionary theatre. Trends Ecol Evol.2003Nov; 18(11):549551. https://doi.org/10.1016/j.tree.2003.09.00110.1016/j.tree.2003.09.001Search in Google Scholar

Jung SY, Byun JG, Park SH, Oh SH, Yang JC, Jang JW, Chang KS, Lee YM. The study of distribution characteristics of vascular and naturalized plants in Dokdo, South Korea. J Asia-Pac Biodivers. 2014 Jun;7(2):e197–e205. https://doi.org/10.1016/j.japb.2014.03.011JungSYByunJGParkSHOhSHYangJCJangJWChangKSLeeYM.The study of distribution characteristics of vascular and naturalized plants in Dokdo, South Korea. J Asia-Pac Biodivers.2014Jun;7(2):e197e205. https://doi.org/10.1016/j.japb.2014.03.01110.1016/j.japb.2014.03.011Search in Google Scholar

Kaczmarska I, Reid C, Moniz M. Diatom taxonomy: morphology, molecules and barcodes. Paper presented at: Proceedings of the 1st Central-European Diatom meeting 2007: Botanic Garden and Botanical Museum Berlin-Dahlem FU-Berlin; 2007. p. 69–72.KaczmarskaIReidCMonizM.Diatom taxonomy: morphology, molecules and barcodes. Paper presented at: Proceedings of the 1st Central-European Diatom meeting 2007: Botanic Garden and Botanical MuseumBerlin-Dahlem FU-Berlin; 2007. p. 6972.10.3372/cediatom.114Search in Google Scholar

Kim CH, Park JW, Lee MH, Park CH. Detailed bathymetry and submarine terraces in the coastal area of the Dokdo volcano in the Ulleung Basin, the East Sea (Sea of Japan). J Coast Res. 2013 Jan 02;65:523–528. https://doi.org/10.2112/SI65-089.1KimCHParkJWLeeMHParkCH.Detailed bathymetry and submarine terraces in the coastal area of the Dokdo volcano in the Ulleung Basin, the East Sea (Sea of Japan). J Coast Res.2013Jan 02;65:523528. https://doi.org/10.2112/SI65-089.110.2112/SI65-089.1Search in Google Scholar

Kim MH, Oh YJ, Kim CS, Han MS, Lee JT, Na YE. The flora and vegetation distribution in Dokdo. Korean J Environ Agric. 2007 Mar 27;26(1):85–93. https://doi.org/10.5338/KJEA.2007.26.1.085KimMHOhYJKimCSHanMSLeeJTNaYE.The flora and vegetation distribution in Dokdo. Korean J Environ Agric.2007Mar 27;26(1):8593. https://doi.org/10.5338/KJEA.2007.26.1.08510.5338/KJEA.2007.26.1.085Search in Google Scholar

Kim YE, Yoon H, Kim M, Nam YJ, Kim H, Seo Y, Lee GM, Ja Kim Y, Kong WS, Kim JG, et al. Metagenomic analysis of bacterial communities on Dokdo Island. J Gen Appl Microbiol. 2014; 60(2):65–74. https://doi.org/10.2323/jgam.60.65KimYEYoonHKimMNamYJKimHSeoYLeeGMJa KimYKongWSKimJG, Metagenomic analysis of bacterial communities on Dokdo Island. J Gen Appl Microbiol.2014; 60(2):6574. https://doi.org/10.2323/jgam.60.6510.2323/jgam.60.6524859864Search in Google Scholar

Knight IT. Molecular genetic methods for detection and identi fication of viable but nonculturable microorganisms. In: Colwell RR, Grimes DJ, editors. Nonculturable Microorganisms in the Environment. Boston: (MA, USA): Springer; 2000. p. 77–85. https://doi.org/10.1007/978-1-4757-0271-2_6KnightIT.Molecular genetic methods for detection and identi fication of viable but nonculturable microorganisms. In: ColwellRRGrimesDJ, editors. Nonculturable Microorganisms in the Environment. Boston: (MA, USA): Springer; 2000. p. 7785. https://doi.org/10.1007/978-1-4757-0271-2_610.1007/978-1-4757-0271-2_6Search in Google Scholar

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013 Sep 01;79(17):5112–5120. https://doi.org/10.1128/AEM.01043-13KozichJJWestcottSLBaxterNTHighlanderSKSchlossPD.Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol.2013Sep 01;79(17):51125120. https://doi.org/10.1128/AEM.01043-1310.1128/AEM.01043-13375397323793624Search in Google Scholar

Krustok I, Truu J, Odlare M, Truu M, Ligi T, Tiirik K, Nehrenheim E. Effect of lake water on algal biomass and microbial community structure in municipal wastewater-based lab-scale photobioreactors. Appl Microbiol Biotechnol. 2015 Aug;99(15):6537–6549. https://doi.org/10.1007/s00253-015-6580-7KrustokITruuJOdlareMTruuMLigiTTiirikKNehrenheimE.Effect of lake water on algal biomass and microbial community structure in municipal wastewater-based lab-scale photobioreactors. Appl Microbiol Biotechnol.2015Aug;99(15):65376549. https://doi.org/10.1007/s00253-015-6580-710.1007/s00253-015-6580-725895091Search in Google Scholar

Lange K, Liess A, Piggott JJ, Townsend CR, Matthaei CD. Light, nutrients and grazing interact to determine stream diatom community composition and functional group structure. Freshw Biol. 2011 Feb;56(2):264–278. https://doi.org/10.1111/j.1365-2427.2010.02492.xLangeKLiessAPiggottJJTownsendCRMatthaeiCD.Light, nutrients and grazing interact to determine stream diatom community composition and functional group structure. Freshw Biol.2011Feb;56(2):264278. https://doi.org/10.1111/j.1365-2427.2010.02492.x10.1111/j.1365-2427.2010.02492.xSearch in Google Scholar

Lee YG, Kim BJ, Park GU, Ahn BY. Characteristics of precipitation and temperature at Ulleung-do and Dok-do, Korea for recent four years (2005~2008). J. Environ. Sci. Int. 2010 Sep 30;19(9):1109–1118. https://doi.org/10.5322/JES.2010.19.9.1109LeeYGKimBJParkGUAhnBY.Characteristics of precipitation and temperature at Ulleung-do and Dok-do, Korea for recent four years (2005~2008). J. Environ. Sci. Int.2010Sep 30;19(9):11091118. https://doi.org/10.5322/JES.2010.19.9.110910.5322/JES.2010.19.9.1109Search in Google Scholar

Lehman JT. Release and cycling of nutrients between planktonic algae and herbivores. Limnol Oceanogr. 1980 Jul;25(4):620–632. https://doi.org/10.4319/lo.1980.25.4.0620LehmanJT.Release and cycling of nutrients between planktonic algae and herbivores. Limnol Oceanogr.1980Jul;25(4):620632. https://doi.org/10.4319/lo.1980.25.4.062010.4319/lo.1980.25.4.0620Search in Google Scholar

Li W, Fu L, Niu B, Wu S, Wooley J. Ultrafast clustering algorithms for metagenomic sequence analysis. Brief Bioinform. 2012 Nov 01;13(6):656–668. https://doi.org/10.1093/bib/bbs035LiWFuLNiuBWuSWooleyJ.Ultrafast clustering algorithms for metagenomic sequence analysis. Brief Bioinform.2012Nov 01;13(6):656668. https://doi.org/10.1093/bib/bbs03510.1093/bib/bbs035350492922772836Search in Google Scholar

Littler MM, Littler DS. An undescribed fungal pathogen of reef-forming crustose corraline algae discovered in American Samoa. Coral Reefs. 1998 Jul 7;17(2):144. https://doi.org/10.1007/s003380050108LittlerMMLittlerDS.An undescribed fungal pathogen of reef-forming crustose corraline algae discovered in American Samoa. Coral Reefs.1998Jul 7;17(2):144. https://doi.org/10.1007/s00338005010810.1007/s003380050108Search in Google Scholar

Luddington IA, Kaczmarska I, Lovejoy C. Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS One. 2012 Sep 21;7(9):e45664. https://doi.org/10.1371/journal.pone.0045664LuddingtonIAKaczmarskaILovejoyC.Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS One.2012Sep 21;7(9):e45664. https://doi.org/10.1371/journal.pone.004566410.1371/journal.pone.0045664344864623029169Search in Google Scholar

Martin JL, Haya K, Burridge LE, Wildish DJ. Nitzschia pseudo-delicatissima – a source of domoic acid in the Bay of Fundy, eastern Canada. Mar Ecol Prog Ser. 1990;67:177–182. https://doi.org/10.3354/meps067177MartinJLHayaKBurridgeLEWildishDJ.Nitzschia pseudo-delicatissima – a source of domoic acid in the Bay of Fundy, eastern Canada. Mar Ecol Prog Ser.1990;67:177182. https://doi.org/10.3354/meps06717710.3354/meps067177Search in Google Scholar

Mayer J, Dokulil MT, Salbrechter M, Berger M, Posch T, Pfister G, Kirschner AK, Velimirov B, Steitz A, Ulbricht T. Seasonal successions and trophic relations between phytoplankton, zooplankton, ciliate and bacteria in a hypertrophic shallow lake in Vienna, Austria. Hydrobiologia. 1997;342:165–174. https://doi.org/10.1023/A:1017098131238MayerJDokulilMTSalbrechterMBergerMPoschTPfisterGKirschnerAKVelimirovBSteitzAUlbrichtT.Seasonal successions and trophic relations between phytoplankton, zooplankton, ciliate and bacteria in a hypertrophic shallow lake in Vienna, Austria. Hydrobiologia.1997;342:165174. https://doi.org/10.1023/A:101709813123810.1023/A:1017098131238Search in Google Scholar

Merilä P, Malmivaara-Lämsä M, Spetz P, Stark S, Vierikko K, Derome J, Fritze H. Soil organic matter quality as a link between microbial community structure and vegetation composition along a successional gradient in a boreal forest. Appl Soil Ecol. 2010 Oct;46(2):259–267. https://doi.org/10.1016/j.apsoil.2010.08.003MeriläPMalmivaara-LämsäMSpetzPStarkSVierikkoKDeromeJFritzeH.Soil organic matter quality as a link between microbial community structure and vegetation composition along a successional gradient in a boreal forest. Appl Soil Ecol.2010Oct;46(2):259267. https://doi.org/10.1016/j.apsoil.2010.08.00310.1016/j.apsoil.2010.08.003Search in Google Scholar

Metting F. Biodiversity and application of microalgae. J Ind Microbiol. 1996;17:477–489.MettingF.Biodiversity and application of microalgae. J Ind Microbiol.1996;17:477489.10.1007/BF01574779Search in Google Scholar

Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010 Jun 01;2010(6):pdb.prot5448. https://doi.org/10.1101/pdb.prot5448MeyerMKircherM.Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc.2010Jun 01;2010(6):pdb.prot5448. https://doi.org/10.1101/pdb.prot544810.1101/pdb.prot544820516186Search in Google Scholar

Nam YJ, Kim H, Lee JH, Yoon H, Kim JG. Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands. J Gen Appl Microbiol. 2015;61(3):67–74. https://doi.org/10.2323/jgam.61.67NamYJKimHLeeJHYoonHKimJG.Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands. J Gen Appl Microbiol.2015;61(3):6774. https://doi.org/10.2323/jgam.61.6710.2323/jgam.61.6726227909Search in Google Scholar

Niu B, Fu L, Sun S, Li W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 2010;11(1):187. https://doi.org/10.1186/1471-2105-11-187NiuBFuLSunSLiW.Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics.2010;11(1):187. https://doi.org/10.1186/1471-2105-11-18710.1186/1471-2105-11-187287455420388221Search in Google Scholar

Park SJ, Song IG, Park SJ, Lim DO. [The flora and vegetation of Dokdo Island in Ulleung-gun, Gyeongsanbuk-do]. Korean J Environ Ecol. 2010;24(3):264–278.ParkSJSongIGParkSJLimDO.[The flora and vegetation of Dokdo Island in Ulleung-gun, Gyeongsanbuk-do]. Korean J Environ Ecol.2010;24(3):264278.Search in Google Scholar

Piercey-Normore MD. The lichen-forming ascomycete Evernia meso morpha associates with multiple genotypes of Trebouxia jamesii. New Phytol. 2006 Jan;169(2):331–344. https://doi.org/10.1111/j.1469-8137.2005.01576.xPiercey-NormoreMD.The lichen-forming ascomycete Evernia meso morpha associates with multiple genotypes of Trebouxia jamesii. New Phytol.2006Jan;169(2):331344. https://doi.org/10.1111/j.1469-8137.2005.01576.x10.1111/j.1469-8137.2005.01576.x16411936Search in Google Scholar

Porter KG. The plant-animal interface in freshwater ecosystems: microscopic grazers feed differentially on planktonic algae and can influence their community structure and succession in ways that are analogous to the effects of herbivores on terrestrial plant communities. Am Sci. 1977;65:159–170.PorterKG.The plant-animal interface in freshwater ecosystems: microscopic grazers feed differentially on planktonic algae and can influence their community structure and succession in ways that are analogous to the effects of herbivores on terrestrial plant communities. Am Sci.1977;65:159170.Search in Google Scholar

Post AF, Dubinsky Z, Wyman K, Falkowski PG. Kinetics of light-intensity adaptation in a marine planktonic diatom. Mar Biol. 1984;83(3):231–238. https://doi.org/10.1007/BF00397454PostAFDubinskyZWymanKFalkowskiPG.Kinetics of light-intensity adaptation in a marine planktonic diatom. Mar Biol.1984;83(3):231238. https://doi.org/10.1007/BF0039745410.1007/BF00397454Search in Google Scholar

Pradeep V, Van Ginkel S, Park S, Igou T, Yi C, Fu H, Johnston R, Snell T, Chen Y. Use of copper to selectively inhibit Brachionus calyciflorus (Predator) growth in Chlorella kessleri (Prey) mass cultures for algae biodiesel production. Int J Mol Sci. 2015 Aug 31;16(9):20674–20684. https://doi.org/10.3390/ijms160920674PradeepVVan GinkelSParkSIgouTYiCFuHJohnstonRSnellTChenY.Use of copper to selectively inhibit Brachionus calyciflorus (Predator) growth in Chlorella kessleri (Prey) mass cultures for algae biodiesel production. Int J Mol Sci.2015Aug 31;16(9):2067420684. https://doi.org/10.3390/ijms16092067410.3390/ijms160920674461322526404247Search in Google Scholar

Prowse GA, Talltng JF. The seasonal growth and succession of plankton algae in the White Nile. Limnol Oceanogr. 1958 Apr;3(2):222–238. https://doi.org/10.4319/lo.1958.3.2.0222ProwseGATalltngJF.The seasonal growth and succession of plankton algae in the White Nile. Limnol Oceanogr.1958Apr;3(2):222238. https://doi.org/10.4319/lo.1958.3.2.022210.4319/lo.1958.3.2.0222Search in Google Scholar

Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, et al. Viral and microbial community dynamics in four aquatic environments. ISME J. 2010 Jun;4(6):739–751. https://doi.org/10.1038/ismej.2010.1Rodriguez-BritoBLiLWegleyLFurlanMAnglyFBreitbartMBuchananJDesnuesCDinsdaleEEdwardsR, Viral and microbial community dynamics in four aquatic environments. ISME J.2010Jun;4(6):739751. https://doi.org/10.1038/ismej.2010.110.1038/ismej.2010.120147985Search in Google Scholar

Round FE. The taxonomy of the Chlorophyta. Brit Phycol Bull. 1963 Dec;2(4):224–235. https://doi.org/10.1080/00071616300650061RoundFE.The taxonomy of the Chlorophyta. Brit Phycol Bull.1963Dec;2(4):224235. https://doi.org/10.1080/0007161630065006110.1080/00071616300650061Search in Google Scholar

Sar EA, Sunesen I, Goya AB, Lavigne AS, Tapia E, García C, Lagos N. First report of diarrheic shellfish toxins in mollusks from Buenos Aires province (Argentina) associated with Dinophysis spp.: evidence of okadaic acid, dinophysistoxin-1 and their acylderi vatives. Bol Soc Argent Bot. 2012;47:5–14.SarEASunesenIGoyaABLavigneASTapiaEGarcíaCLagosN.First report of diarrheic shellfish toxins in mollusks from Buenos Aires province (Argentina) associated with Dinophysis spp.: evidence of okadaic acid, dinophysistoxin-1 and their acylderi vatives. Bol Soc Argent Bot.2012;47:514.Search in Google Scholar

Sarma SSS, Trujillo-Hernández HE, Nandini S. Population growth of herbivorous rotifers and their predator (Asplanchna) on urban wastewaters. Aquat Ecol. 2003;37(3):243–250. https://doi.org/10.1023/A:1025896703470SarmaSSSTrujillo-HernándezHENandiniS.Population growth of herbivorous rotifers and their predator (Asplanchna) on urban wastewaters. Aquat Ecol.2003;37(3):243250. https://doi.org/10.1023/A:102589670347010.1023/A:1025896703470Search in Google Scholar

Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 2005;6(8):229. https://doi.org/10.1186/gb-2005-6-8-229SchlossPDHandelsmanJ.Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol.2005;6(8):229. https://doi.org/10.1186/gb-2005-6-8-22910.1186/gb-2005-6-8-229127362516086859Search in Google Scholar

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing micro bial communities. Appl Environ Microbiol. 2009 Dec 01; 75(23):7537–7541. https://doi.org/10.1128/AEM.01541-09SchlossPDWestcottSLRyabinTHallJRHartmannMHollisterEBLesniewskiRAOakleyBBParksDHRobinsonCJ, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing micro bial communities. Appl Environ Microbiol.2009Dec 01; 75(23):75377541. https://doi.org/10.1128/AEM.01541-0910.1128/AEM.01541-09278641919801464Search in Google Scholar

Shin H, Park S, Kang K, Yoo J. The establishment of conservation area and conservation strategy in Ulnung Island. Korean J Environ Ecol. 2004;18:221–230.ShinHParkSKangKYooJ.The establishment of conservation area and conservation strategy in Ulnung Island. Korean J Environ Ecol.2004;18:221230.Search in Google Scholar

Shokralla S, Spall JL, Gibson JF, Hajibabaei M. Next-generation sequencing technologies for environmental DNA research. Mol Ecol. 2012 Apr;21(8):1794–1805. https://doi.org/10.1111/j.1365-294X.2012.05538.xShokrallaSSpallJLGibsonJFHajibabaeiM.Next-generation sequencing technologies for environmental DNA research. Mol Ecol.2012Apr;21(8):17941805. https://doi.org/10.1111/j.1365-294X.2012.05538.x10.1111/j.1365-294X.2012.05538.x22486820Search in Google Scholar

Sohn YK. Geology of Tok Island, Korea: eruptive and depositional processes of a shoaling to emergent island volcano. Bull Volcanol. 1995 Feb;56(8):660–674. https://doi.org/10.1007/BF00301469SohnYK.Geology of Tok Island, Korea: eruptive and depositional processes of a shoaling to emergent island volcano. Bull Volcanol.1995Feb;56(8):660674. https://doi.org/10.1007/BF0030146910.1007/BF00301469Search in Google Scholar

Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, Richards TA. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010 Mar;19 Suppl 1:21–31. https://doi.org/10.1111/j.1365-294X.2009.04480.xStoeckTBassDNebelMChristenRJonesMDMBreinerHWRichardsTA.Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol.2010Mar;19 Suppl 1:2131. https://doi.org/10.1111/j.1365-294X.2009.04480.x10.1111/j.1365-294X.2009.04480.x20331767Search in Google Scholar

Streit WR, Schmitz RA. Metagenomics – the key to the uncultured microbes. Curr Opin Microbiol. 2004 Oct;7(5):492–498. https://doi.org/10.1016/j.mib.2004.08.002StreitWRSchmitzRA.Metagenomics – the key to the uncultured microbes. Curr Opin Microbiol.2004Oct;7(5):492498. https://doi.org/10.1016/j.mib.2004.08.00210.1016/j.mib.2004.08.00215451504Search in Google Scholar

Sturm M, Schroeder C, Bauer P. SeqPurge: highly-sensitive adapter trimming for paired-end NGS data. BMC Bioinformatics. 2016 Dec;17(1):208. https://doi.org/10.1186/s12859-016-1069-7SturmMSchroederCBauerP.SeqPurge: highly-sensitive adapter trimming for paired-end NGS data. BMC Bioinformatics.2016Dec;17(1):208. https://doi.org/10.1186/s12859-016-1069-710.1186/s12859-016-1069-7486214827161244Search in Google Scholar

Tragin M, Zingone A, Vaulot D. Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta. Environ Microbiol. 2018 Feb;20(2):506–520. https://doi.org/10.1111/1462-2920.13952TraginMZingoneAVaulotD.Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta. Environ Microbiol.2018Feb;20(2):506520. https://doi.org/10.1111/1462-2920.1395210.1111/1462-2920.1395228984410Search in Google Scholar

Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol. 2010 Oct 15;44(20):7777–7782. https://doi.org/10.1021/es101500zUnnoTJangJHanDKimJHSadowskyMJKimOSChunJHurHG.Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol.2010Oct 15;44(20):77777782. https://doi.org/10.1021/es101500z10.1021/es101500z20853824Search in Google Scholar

Vitousek PM, Cassman K, Cleveland C, Crews T, Field CB, Grimm NB, Howarth RW, Marino R, Martinelli L, Rastetter EB. Towards an ecological understanding of biological nitrogen fixation. In: Boyer EW, Howarth RW, editors. The nitrogen cycle at regional to global scales. Dordrecht (Germany): Springer; 2002. p. 1–45. https://doi.org/10.1007/978-94-017-3405-9_1VitousekPMCassmanKClevelandCCrewsTFieldCBGrimmNBHowarthRWMarinoRMartinelliLRastetterEB.Towards an ecological understanding of biological nitrogen fixation. In: BoyerEWHowarthRW, editors. The nitrogen cycle at regional to global scales. Dordrecht (Germany): Springer; 2002. p. 145. https://doi.org/10.1007/978-94-017-3405-9_110.1007/978-94-017-3405-9_1Search in Google Scholar

Vo ATE, Jedlicka JA. Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples. Mol Ecol Resour. 2014 Nov;14(6):1183–1197. https://doi.org/10.1111/1755-0998.12269VoATEJedlickaJA.Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples. Mol Ecol Resour.2014Nov;14(6):11831197. https://doi.org/10.1111/1755-0998.1226910.1111/1755-0998.1226924774752Search in Google Scholar

Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol. 2007 Nov;9(11):2707–2719. https://doi.org/10.1111/j.1462-2920.2007.01383.xWegleyLEdwardsRRodriguez-BritoBLiuHRohwerF.Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol.2007Nov;9(11):27072719. https://doi.org/10.1111/j.1462-2920.2007.01383.x10.1111/j.1462-2920.2007.01383.x17922755Search in Google Scholar

Yoshida T, Hairston NG Jr, Ellner SP. Evolutionary trade-off between defence against grazing and competitive ability in a simple unicellular alga, Chlorella vulgaris. Proc R Soc Lond B Biol Sci. 2004 Sep 22;271(1551):1947–1953. https://doi.org/10.1098/rspb.2004.2818YoshidaTHairstonNGJrEllnerSP.Evolutionary trade-off between defence against grazing and competitive ability in a simple unicellular alga, Chlorella vulgaris. Proc R Soc Lond B Biol Sci.2004Sep 22;271(1551):19471953. https://doi.org/10.1098/rspb.2004.281810.1098/rspb.2004.2818169180415347519Search in Google Scholar

Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000 Feb;7(1-2):203–214. https://doi.org/10.1089/10665270050081478ZhangZSchwartzSWagnerLMillerW.A greedy algorithm for aligning DNA sequences. J Comput Biol.2000Feb;7(1-2):203214. https://doi.org/10.1089/1066527005008147810.1089/1066527005008147810890397Search in Google Scholar

eISSN:
2544-4646
Language:
English
Publication timeframe:
4 times per year
Journal Subjects:
Life Sciences, Microbiology and Virology