Agogué H, Brink M, Dinasquet J, Herndl GJ (2008) Major gradients in putatively nitrifying and non-nitrifying archaea in the deep North Atlantic. Nature 456:788–792
Article
ADS
PubMed
Google Scholar
Auguet JC, Triadó-Margarit X, Nomokonova N, Camarero L, Casamayor EO (2012) Vertical segregation and phylogenic characterization of ammonia-oxidizing archaea in a deep oligotrophic lake. ISME J 6:1786–1797
Article
CAS
PubMed
PubMed Central
Google Scholar
Casciotti KL, Sigman DM, Hastings MG, Böhlke JK, Hilkert A (2002) Measurement of the oxygen isotopic composition of nitrate in seawater and freshwater using the denitrifier method. Anal Chem 74:4905–4912
Article
CAS
PubMed
Google Scholar
Church MJ, Wai B, Karl DM, DeLong EF (2010) Abundance of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol 12:679–688
Article
CAS
PubMed
PubMed Central
Google Scholar
Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA 106:16428–16433
Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Di HJ, Cameron KC, Shen JP, Winefield CS, O’Ccallaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2:621–624
Article
ADS
CAS
Google Scholar
Enya J, Shinohara H, Yoshida S, Tsukiboshi T, Negishi H, Suyama K, Tsushima S (2007) Culturable leaf-associated bacteria on tomato plants and their potential as biological control agents. Microb Ecol 53:524–536
Article
CAS
PubMed
Google Scholar
Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33:855–869
Article
CAS
PubMed
Google Scholar
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Article
Google Scholar
Fett WF, Osman SF, Dunn MF (1987) Auxin production by plant-pathogenic pseudomonads and xanthomonads. Appl Environ Microbiol 53:1839–1845
CAS
PubMed
PubMed Central
Google Scholar
Finkel OM, Burch AY, Lindow SE, Post AF, Belkin S (2011) Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree. Appl Environ Microbiol 77:7647–7655
Article
CAS
PubMed
PubMed Central
Google Scholar
Finkel OM, Burch AY, Elad T, Huse SM, Lindow SE, Post AF, Belkin S (2012) Distance-decay relationships partially determine diversity patterns of phyllosphere bacteria on Tamrix trees across the Sonoran Desert. Appl Environ Microbiol 78:6187–6193
Article
CAS
PubMed
PubMed Central
Google Scholar
Francis CA, Beman JM, Kuypers MMM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1:19–27
Article
CAS
PubMed
Google Scholar
Fürnkranz M, Wanek W, Richter A, Abell G, Rasche F, Sessitsch A (2008) Nitrogen fixation by phyllosphere bacteria associated with higher plants and their colonizing epiphytes of a tropical lowland rainforest of Costa Rica. ISME J 2:561–570
Article
PubMed
Google Scholar
Gaige E, Dail DB, Hollinger DY, Davidson EA, Fernandez IJ, Sievering H, White A, Halteman W (2007) Changes in canopy processes following whole-forest canopy nitrogen fertilization of a mature spruce-hemlock forest. Ecosystems 10:1133–1147
Article
CAS
Google Scholar
Garten CT Jr (1992) Nitrogen isotope composition of ammonium and nitrate in bulk precipitation and forest throughfall. Int J Anal Chem 47:33–45
Article
CAS
Google Scholar
Granger J, Sigman DM, Prokopenko MG, Lehmann MF, Torrtell PD (2006) A method for nitrite removal in nitrate N and O isotope analyses. Limnol Oceanogr Methods 4:205–212
Article
CAS
Google Scholar
Gruber N, Galloway JN (2008) An earth-system perspective of the global nitrogen cycle. Nature 451:293–296
Article
ADS
CAS
PubMed
Google Scholar
Guerrieri R, Vanguelova EI, Michalski G, Heaton TH, Mencuccini M (2015) Isotopic evidence for the occurrence of biological nitrification and nitrogen deposition processing in forest canopies. Glob Chang Biol 21:4613–4626
Article
PubMed
Google Scholar
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA 105:2134–2139
Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Hayatsu M, Tago K, Saito M (2008) Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci Plant Nutr 54:33–45
Article
CAS
Google Scholar
Herrmann M, Saunders AM, Schramm A (2009) Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sediment. Appl Environ Microbiol 75:3127–3136
Article
CAS
PubMed
PubMed Central
Google Scholar
Hirano SS, Upper CD (2000) Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae—a pathogen, ice nucleus, and epiphyte. Microbiol Mol Biol Rev 64:624–653
Article
CAS
PubMed
PubMed Central
Google Scholar
Hou H, Takamatsu T, Koshikawa MK, Hosomi M (2005) Trace metals in bulk precipitation and throughfall in a suburban area of Japan. Atmos Environ 39:3583–3595
Article
ADS
CAS
Google Scholar
Kendall C (1998) Tracing nitrogen sources and cycling in catchments. In: Kendall C, McDonnell JJ (eds) Isotope tracers in catchment hydrology. Elsevier, Amsterdam, pp 519–576
Chapter
Google Scholar
Kohzu A, Imai A, Nakajima Y, Komatsu K, Kawasaki N, Satou T (2011) An inexpensive auto-injection preprocessing system for N2O by isotope ratio mass spectrometer to measure δ15N and δ18O of nitrate. Radioisotopes 60:231–240 (in Japanese)
Article
CAS
Google Scholar
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809
Article
ADS
CAS
PubMed
Google Scholar
Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883
Article
CAS
PubMed
PubMed Central
Google Scholar
Martens-Habbena M, Berube PM, Urakawa H, de la Torre JR, Sthal DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461:976–979
Article
ADS
CAS
PubMed
Google Scholar
Morris CE, Kinkel LL (2002) Fifty years of phyllosphere microbiology: significant contribution to research in related fields. In: Lindow SE, Hecht-Poinar EI, Elliott V (eds) phyllosphere microbiology. APS Press, St. Paul, pp 365–375
Google Scholar
Müller T, Müller M, Behrendt U (2004) Leucine arylamidase activity in the phyllosphere and the litter layer of a Scots pine forest. FEMS Microbiol Ecol 47:153–159
Article
PubMed
Google Scholar
Nunoura T, Takaki Y, Hirai M, Shimamura S, Makabe A, Koide O, Kikuchi T, Miyazaki J, Koba K, Yoshida N, Sunamura M, Takai K (2015) Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth. Proc Natl Acad Sci USA 112:E1230–E1236
Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Ollivier J, Töwe S, Bannert A, Hai B, Kastl E-M, Meyer A, Su MX, Kleineidam K, Schloter M (2011) Nitrogen turnover in soil and global change. FEMS Microbiol Ecol 78:3–16
Article
CAS
PubMed
Google Scholar
Papen H, Geßler A, Zumbusch E, Rennenberg H (2002) Chemolithoautotrophic nitrifiers in the phyllosphere of a spruce ecosystem receiving high atmospheric nitrogen input. Curr Microbiol 44:56–60
Article
CAS
PubMed
Google Scholar
Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10:2931–2941
Article
CAS
PubMed
Google Scholar
Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12:2885–2893
Article
PubMed
PubMed Central
Google Scholar
Reed DW, Smith JM, Francis CA, Fujita Y (2010) Responses of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groudwater. Appl Environ Microbiol 76:2517–2523
Article
CAS
PubMed
PubMed Central
Google Scholar
Rotthauwe J-H, Witzel K-P, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63:4704–4712
CAS
PubMed
PubMed Central
Google Scholar
Saitou N, Nei N (1987) The neighbor-joining method: a new method for reconstructing phylogenic trees. Mol Biol Evol 4:406–425
CAS
PubMed
Google Scholar
Shi J, Ohte N, Tokuchi N, Imamura N, Nagayama M, Oda T, Suzuki M (2014) Nitrate isotopic composition reveals nitrogen deposition and transformation dynamics along the canopy—soil continuum of a suburban forest in Japan. Rapid Commun Mass Spectrom 28:2539–2549
Article
CAS
PubMed
Google Scholar
Sigman DM, Casciotti KL, Andreani M, Barford C, Galanter M, Böhlke JK (2001) A bacterial method for the nitrogen isotopic analysis of nitrate in seawater and freshwater. Anal Chem 73:4145–4153
Article
CAS
PubMed
Google Scholar
Snider DM, Spoelstra J, Schiff SL, Venkiteswaran JJ (2010) Stable oxygen isotopic ratios of nitrate produced from nitrification: 18O-labeled water incubation of agricultural and temperate forest soils. Environ Sci Technol 44:5358–5364
Article
ADS
CAS
PubMed
Google Scholar
Suda W, Nagasaki A, Shishido M (2009) Powdery mildew—infection changes bacterial community composition in the phyllosphere. Microbes Environ 24:217–223
Article
PubMed
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Article
CAS
PubMed
PubMed Central
Google Scholar
Teuber M, Papen H, Gasche R, Eßmüller TH, Geßler A (2007) The apoplast of Norway spruce (Picea abies) needles as habitat and reaction compartment for autotrophic nitrifiers. In: Sattelmacher B, Horst WJ (eds) The apoplast of higher plants: compartment of storage, transport and reactions. Springer, Dordrecht, pp 405–425
Chapter
Google Scholar
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Article
CAS
PubMed
PubMed Central
Google Scholar
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk H-P, Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985–1995
Article
CAS
PubMed
Google Scholar
Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840
Article
CAS
PubMed
Google Scholar
Woods CL, Hunt SL, Morris DM, Gordon AM (2012) Epiphytes influence the transformation of nitrogen in coniferous forest canopies. Boreal Environ Res 17:411–424
CAS
Google Scholar
Xue D, Botte J, De Baets B, Accoe F, Nestler A, Taylor P, Van Cleemput O, Berglund M, Boeckx P (2009) Present limitations and future prospects of stable isotope methods for nitrate source identification in surface- and groundwater. Water Res 43:1159–1170
Article
CAS
PubMed
Google Scholar
Yang CH, Crowley DE, Borneman J, Keen NT (2001) Microbial phyllosphere populations are more complex than previously realized. Proc Natl Acad Sci USA 98:3889–3894
Article
ADS
CAS
PubMed
PubMed Central
Google Scholar