메뉴 건너뛰기




Volumn 217, Issue 1, 2018, Pages 453-466

Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify

Author keywords

15N isotope; Azolla; denitrification; ditch water microbiome; metagenome; N2 fixation; Nostoc; Rhizobiales

Indexed keywords

BACTERIUM; DENITRIFICATION; ENDOPHYTE; FERN; GENE EXPRESSION; GENOMICS; GREENHOUSE GAS; METABOLISM; NITROGEN FIXATION;

EID: 85035311947     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.14843     Document Type: Article
Times cited : (28)

References (65)
  • 1
    • 84907963715 scopus 로고    scopus 로고
    • Cyanobacterial–plant symbioses
    • In, Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Fabiano T, eds., Berlin, Germany, Spring
    • Adams DG, Bergman B, Nierzwicki-Bauer S, Duggan PS, Rai AN, Schüßler A. 2013. Cyanobacterial–plant symbioses. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Fabiano T, eds. The prokaryotes. Berlin, Germany: Springer, 359–400.
    • (2013) The prokaryotes , pp. 359-400
    • Adams, D.G.1    Bergman, B.2    Nierzwicki-Bauer, S.3    Duggan, P.S.4    Rai, A.N.5    Schüßler, A.6
  • 2
    • 84926474687 scopus 로고    scopus 로고
    • 2 fixation in legumes: incidence for N balance of legume-based cropping systems in Europe
    • 2 fixation in legumes: incidence for N balance of legume-based cropping systems in Europe. Ecosphere 6: 1–24.
    • (2015) Ecosphere , vol.6 , pp. 1-24
    • Anglade, J.1    Billen, G.2    Garnier, J.3
  • 4
    • 3042531297 scopus 로고
    • Azolla filiculoides as partial replacement for traditional protein supplements in diets for growing-fattening pigs based on sugar cane juice
    • Becerra M, Murgueitio E, Reyes G, Preston TR. 1990. Azolla filiculoides as partial replacement for traditional protein supplements in diets for growing-fattening pigs based on sugar cane juice. Livestock Research for Rural Development 2: 15–22.
    • (1990) Livestock Research for Rural Development , vol.2 , pp. 15-22
    • Becerra, M.1    Murgueitio, E.2    Reyes, G.3    Preston, T.R.4
  • 5
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 6
    • 0342832644 scopus 로고
    • Dinitrogenase reductase (Fe-protein) of nitrogenase in the cyanobacterial symbionts of three Azolla species: localization and sequence of appearance during heterocyst differentiation
    • Braun-Howland EB, Lindblad P, Nierzwicki-Bauer SA, Bergman B. 1988. Dinitrogenase reductase (Fe-protein) of nitrogenase in the cyanobacterial symbionts of three Azolla species: localization and sequence of appearance during heterocyst differentiation. Planta 176: 319–322.
    • (1988) Planta , vol.176 , pp. 319-322
    • Braun-Howland, E.B.1    Lindblad, P.2    Nierzwicki-Bauer, S.A.3    Bergman, B.4
  • 9
    • 84935842989 scopus 로고    scopus 로고
    • Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species
    • Cao HX, Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu GT. 2015. Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Frontiers in Microbiology 6: 526
    • (2015) Frontiers in Microbiology , vol.6 , pp. 526
    • Cao, H.X.1    Schmutzer, T.2    Scholz, U.3    Pecinka, A.4    Schubert, I.5    Vu, G.T.6
  • 11
    • 0026305676 scopus 로고
    • Are bacteria the third partner of the Azolla–Anabaena symbiosis?
    • Carrapiço F. 1991. Are bacteria the third partner of the Azolla–Anabaena symbiosis? Plant and Soil 137: 157–160.
    • (1991) Plant and Soil , vol.137 , pp. 157-160
    • Carrapiço, F.1
  • 12
    • 84859951166 scopus 로고    scopus 로고
    • Azolla as a superorganism: its implication in symbiotic studies
    • In, Seckbach J, Grube M, eds., Dordrecht, the Netherlands, Spring
    • Carrapiço F. 2010. Azolla as a superorganism: its implication in symbiotic studies. In: Seckbach J, Grube M, eds. Symbioses and stress: joint ventures in biology. Dordrecht, the Netherlands: Springer, 225–241.
    • (2010) Symbioses and stress: joint ventures in biology , pp. 225-241
    • Carrapiço, F.1
  • 14
    • 79960872039 scopus 로고    scopus 로고
    • Evaluation of short read metagenomic assembly
    • Charuvaka A, Rangwala H. 2011. Evaluation of short read metagenomic assembly. BMC Genomics 12: S8.
    • (2011) BMC Genomics , vol.12 , pp. S8
    • Charuvaka, A.1    Rangwala, H.2
  • 17
    • 0026565251 scopus 로고
    • Indole-3-acetic acid (IAA) production by Arthrobacter species isolated from Azolla
    • Forni C, Riov J, Caiola MG, Tel-Or E. 1992. Indole-3-acetic acid (IAA) production by Arthrobacter species isolated from Azolla. Microbiology 138: 377–381.
    • (1992) Microbiology , vol.138 , pp. 377-381
    • Forni, C.1    Riov, J.2    Caiola, M.G.3    Tel-Or, E.4
  • 18
    • 85035309172 scopus 로고
    • Effects of antibiotic treatments on Azolla–Anabaena and Arthrobacter
    • In, Polsinelli M, Materassi R, Vincenzini M, eds., Dordrecht, the Netherlands, Spring
    • Forni C, Tel-Or E, Bar E, Caiola MG. 1991. Effects of antibiotic treatments on Azolla–Anabaena and Arthrobacter. In: Polsinelli M, Materassi R, Vincenzini M, eds. Developments in plant and soil sciences. Dordrecht, the Netherlands: Springer, 457–461.
    • (1991) Developments in plant and soil sciences , pp. 457-461
    • Forni, C.1    Tel-Or, E.2    Bar, E.3    Caiola, M.G.4
  • 19
    • 84883240261 scopus 로고    scopus 로고
    • The biochemistry of the metabolic poison propionate 3-nitronate and its conjugate acid, 3-nitropropionate
    • Francis K, Smitherman C, Nishino SF, Spain JC, Gadda G. 2013. The biochemistry of the metabolic poison propionate 3-nitronate and its conjugate acid, 3-nitropropionate. IUBMB Life 65: 759–768.
    • (2013) IUBMB Life , vol.65 , pp. 759-768
    • Francis, K.1    Smitherman, C.2    Nishino, S.F.3    Spain, J.C.4    Gadda, G.5
  • 20
    • 0025919422 scopus 로고
    • Identification of a common cyanobacterial symbiont associated with Azolla spp. through molecular and morphological characterization of free-living and symbiotic cyanobacteria
    • Gebhardt JS, Nierzwicki-Bauer SA. 1991. Identification of a common cyanobacterial symbiont associated with Azolla spp. through molecular and morphological characterization of free-living and symbiotic cyanobacteria. Applied and Environmental Microbiology 57: 2141–2146.
    • (1991) Applied and Environmental Microbiology , vol.57 , pp. 2141-2146
    • Gebhardt, J.S.1    Nierzwicki-Bauer, S.A.2
  • 21
    • 0001486741 scopus 로고    scopus 로고
    • Life history and laboratory host range of Stenopelmus rufinasus, a natural enemy for Azolla filiculoides in South Africa
    • Hill MP. 1998. Life history and laboratory host range of Stenopelmus rufinasus, a natural enemy for Azolla filiculoides in South Africa. BioControl 43: 215–224.
    • (1998) BioControl , vol.43 , pp. 215-224
    • Hill, M.P.1
  • 25
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. 2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Research 38: D355–D360.
    • (2010) Nucleic Acids Research , vol.38 , pp. D355-D360
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 28
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357–359.
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 30
    • 0025720646 scopus 로고
    • Immunocytochemical localization of nitrogenase in bacteria symbiotically associated with Azolla spp
    • Lindblad P, Bergman B, Nierzwicki-Bauer SA. 1991. Immunocytochemical localization of nitrogenase in bacteria symbiotically associated with Azolla spp. Applied and Environmental Microbiology 57: 3637–3640.
    • (1991) Applied and Environmental Microbiology , vol.57 , pp. 3637-3640
    • Lindblad, P.1    Bergman, B.2    Nierzwicki-Bauer, S.A.3
  • 32
    • 79956189425 scopus 로고    scopus 로고
    • Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing
    • Lutz KA, Wang W, Zdepski A, Michael TP. 2011. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnology 11: 54.
    • (2011) BMC Biotechnology , vol.11 , pp. 54
    • Lutz, K.A.1    Wang, W.2    Zdepski, A.3    Michael, T.P.4
  • 33
    • 79956041561 scopus 로고    scopus 로고
    • EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
    • Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF. 2011. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biology 12: R44.
    • (2011) Genome Biology , vol.12 , pp. R44
    • Miller, C.S.1    Baker, B.J.2    Thomas, B.C.3    Singer, S.W.4    Banfield, J.F.5
  • 36
    • 33748111316 scopus 로고    scopus 로고
    • Comparative morphology of reproductive structures in heterosporous water ferns and a reevaluation of the sporocarp
    • Nagalingum NS, Schneider H, Pryer KM. 2006. Comparative morphology of reproductive structures in heterosporous water ferns and a reevaluation of the sporocarp. International Journal of Plant Sciences 167: 805–815.
    • (2006) International Journal of Plant Sciences , vol.167 , pp. 805-815
    • Nagalingum, N.S.1    Schneider, H.2    Pryer, K.M.3
  • 37
    • 77953032413 scopus 로고    scopus 로고
    • Growth of bacteria on 3-nitropropionic acid as a sole source of carbon, nitrogen, and energy
    • Nishino SF, Shin KA, Payne RB, Spain JC. 2010. Growth of bacteria on 3-nitropropionic acid as a sole source of carbon, nitrogen, and energy. Applied and Environmental Microbiology 76: 3590–3598.
    • (2010) Applied and Environmental Microbiology , vol.76 , pp. 3590-3598
    • Nishino, S.F.1    Shin, K.A.2    Payne, R.B.3    Spain, J.C.4
  • 38
    • 0020424297 scopus 로고
    • Regulation of glutamine synthetase activity and synthesis in free-living and symbiotic Anabaena spp
    • Orr J, Haselkorn R. 1982. Regulation of glutamine synthetase activity and synthesis in free-living and symbiotic Anabaena spp. Journal of Bacteriology 152: 626–635.
    • (1982) Journal of Bacteriology , vol.152 , pp. 626-635
    • Orr, J.1    Haselkorn, R.2
  • 43
    • 84987040772 scopus 로고
    • The Azolla and Anabaena symbiosis: endophyte continuity in the Azolla life cycle is facilitated by epidermal trichomes
    • Perkins SK, Peters GA. 1993. The Azolla and Anabaena symbiosis: endophyte continuity in the Azolla life cycle is facilitated by epidermal trichomes. New Phytologist 123: 53–64.
    • (1993) New Phytologist , vol.123 , pp. 53-64
    • Perkins, S.K.1    Peters, G.A.2
  • 48
    • 84906539725 scopus 로고    scopus 로고
    • The combined structural and kinetic characterization of a bacterial nitronate monooxygenase from Pseudomonas aeruginosa PAO1 establishes NMO class I and II
    • Salvi F, Agniswamy J, Yuan H, Vercammen K, Pelicaen R, Cornelis P, Spain JC, Weber IT, Gadda G. 2014. The combined structural and kinetic characterization of a bacterial nitronate monooxygenase from Pseudomonas aeruginosa PAO1 establishes NMO class I and II. Journal of Biological Chemistry 289: 23764–23775.
    • (2014) Journal of Biological Chemistry , vol.289 , pp. 23764-23775
    • Salvi, F.1    Agniswamy, J.2    Yuan, H.3    Vercammen, K.4    Pelicaen, R.5    Cornelis, P.6    Spain, J.C.7    Weber, I.T.8    Gadda, G.9
  • 51
    • 84896548779 scopus 로고    scopus 로고
    • Herbivory eliminates fitness costs of mutualism exploiters
    • Simonsen AK, Stinchcombe JR. 2014. Herbivory eliminates fitness costs of mutualism exploiters. New Phytologist 202: 651–661.
    • (2014) New Phytologist , vol.202 , pp. 651-661
    • Simonsen, A.K.1    Stinchcombe, J.R.2
  • 52
    • 33646452163 scopus 로고    scopus 로고
    • Isolation and identification of an epibiotic bacterium associated with heterocystous Anabaena cells
    • Stevenson BS, Waterbury JB. 2006. Isolation and identification of an epibiotic bacterium associated with heterocystous Anabaena cells. Biological Bulletin 210: 73–77.
    • (2006) Biological Bulletin , vol.210 , pp. 73-77
    • Stevenson, B.S.1    Waterbury, J.B.2
  • 53
    • 0001887756 scopus 로고    scopus 로고
    • An overview of endophytic microbes: endophytism defined
    • In, Bacon CW, White JF, eds., New York, NY, USA, Marcel Dekk
    • Stone JK, Bacon CW, White JF. 2000. An overview of endophytic microbes: endophytism defined. In: Bacon CW, White JF, eds. Microbial endophytes. New York, NY, USA: Marcel Dekker, 3–29.
    • (2000) Microbial endophytes , pp. 3-29
    • Stone, J.K.1    Bacon, C.W.2    White, J.F.3
  • 54
    • 84885406698 scopus 로고    scopus 로고
    • GNU Parallel: the command-line power tool
    • Tange O. 2011. GNU Parallel: the command-line power tool. USENIX Magazine 36: 42–47.
    • (2011) USENIX Magazine , vol.36 , pp. 42-47
    • Tange, O.1
  • 59
    • 84928230995 scopus 로고    scopus 로고
    • Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria–plant symbiosis
    • Vigil-Stenman T, Larsson J, Nylander JA, Bergman B. 2015. Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria–plant symbiosis. BMC Genomics 16: 193.
    • (2015) BMC Genomics , vol.16 , pp. 193
    • Vigil-Stenman, T.1    Larsson, J.2    Nylander, J.A.3    Bergman, B.4
  • 63
    • 85006856675 scopus 로고    scopus 로고
    • RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
    • Xie C, Goi CL, Huson DH, Little PF, Williams RB. 2016. RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. BMC Bioinformatics 17: 277.
    • (2016) BMC Bioinformatics , vol.17 , pp. 277
    • Xie, C.1    Goi, C.L.2    Huson, D.H.3    Little, P.F.4    Williams, R.B.5
  • 64
    • 84941755547 scopus 로고    scopus 로고
    • Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
    • Zependa Mendoza ML, Sicheritz-Pontén T, Gilbert MTP. 2015. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Briefings in Bioinformatics 16: 745–758.
    • (2015) Briefings in Bioinformatics , vol.16 , pp. 745-758
    • Zependa Mendoza, M.L.1    Sicheritz-Pontén, T.2    Gilbert, M.T.P.3
  • 65
    • 57449111763 scopus 로고    scopus 로고
    • Cellular responses in the cyanobacterial symbiont during its vertical transfer between plant generations in the Azolla microphylla symbiosis
    • Zheng W, Bergman B, Chen B, Zheng S, Xiang G, Rasmussen U. 2009. Cellular responses in the cyanobacterial symbiont during its vertical transfer between plant generations in the Azolla microphylla symbiosis. New Phytologist 181: 53–61.
    • (2009) New Phytologist , vol.181 , pp. 53-61
    • Zheng, W.1    Bergman, B.2    Chen, B.3    Zheng, S.4    Xiang, G.5    Rasmussen, U.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.