The microbial diversity of a storm cloud as assessed by hailstones

FEMS Microbiology Ecology

Volumn 81, Issue 3, 2012, Pages 684-695

  Temkiv, Tina Šantl ^a   Finster, Kai ^a   Hansen, Bjarne Munk ^a   Nielsen, Niels Woetmann ^b   Karlson, Ulrich Gosewinkel ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b DANISH METEOROLOGICAL INSTITUTE   (Denmark)

Author keywords

Atmospheric chemistry; Bacterial diversity; Biogeography; Cloud borne bacteria; Species evenness; Species richness

Indexed keywords

ATMOSPHERIC CHEMISTRY; BACTERIUM; BARRIER (EQUIPMENT); BIOGEOGRAPHY; CHEMICAL COMPOSITION; CLOUD DROPLET; DISPERSAL; ENVIRONMENTAL STRESS; GROWTH RATE; GROWTH RESPONSE; HAIL; MICROBIAL COMMUNITY; RESIDENCE TIME; SPECIES EVENNESS; SPECIES RICHNESS;

ARTICLE; ATMOSPHERE; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIAL SPORE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLIMATE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGICAL STRESS; PHYSIOLOGY; SLOVENIA;

AIR MICROBIOLOGY; ATMOSPHERE; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIODIVERSITY; CLIMATIC PROCESSES; MOLECULAR SEQUENCE DATA; SLOVENIA; SPORES, BACTERIAL; STRESS, PHYSIOLOGICAL;

BACTERIA (MICROORGANISMS); METHYLOBACTERIUM; OTUS;

EID: 84864633922     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01402.x     Document Type: Article

References (63)

1. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V & Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71: 8966-8969.
2. Ahern HE, Walsh KA, Hill TCJ & Moffet B (2007) Fluorescent pseudomonads isolated from Hebridean cloud and rain water produce biosurfactants but do not cause ice nucleation. Biogeosciences 4: 115-124.
3. Ahrens CD (2009) Meteorology Today. An Introduction to Weather, Climate and the Environment, 9th edn. Brooks/Cole, Belmont.
4. Amato P, Menager M, Sancelme M, Laj P, Mailhot G & Delort AM (2005) Microbial population in cloud water at the Puy de Dome: implications for the chemistry of clouds. Atmos Environ 39: 4143-4153.
5. Amato P, Parazols M, Sancelme M, Laj P, Mailhot G & Delort AM (2007a) Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dôme: major groups and growth abilities at low temperatures. FEMS Microbiol Ecol 59: 242-254.
6. Amato P, Demeer F, Melaouhi A, Fontanella S, Martin-Biesse AS, Sancelme M, Laj P & Delort AM (2007b) A fate for organic acids, formaldehyde and methanol in cloud water: their biotransformation by micro-organisms. Atmos Chem Phys 7: 4159-4169.
7. Ariya PA, Nepotchatykh O, Ignatova O & Amyot M (2002) Microbiological degradation of atmospheric organic compounds. Geophys Res Lett 29: 2077-2081.
8. Bauer H, Kasper-Giebl A, Löflund M, Giebl H, Hitzenberger R, Zibuschka F & Puxbaum H (2002) The contribution of bacteria and fungal spores to the organic carbon content of cloud water, precipitation and aerosols. Atmos Res 64: 109-119.
9. Bower CE & Holm-Hansen T (1980) A salicylate-hypochlorit method for determining ammonia in seawater. Can J Fish Aquat Sci 37: 794-798.
10. Bowers RM, Lauber CL, Wiedinmyer C, Hamady M, Hallar AG, Fall R, Knight R & Fierer N (2009) Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei. Appl Environ Microbiol 75: 5121-5130.
11. Burrows SM, Butler T, Jöckel P, Tost H, Kerkweg A, Pöschl U & Lawrence MG (2009) Bacteria in the global atmosphere - Part 2: modeling of emissions and transport between different ecosystems. Atmos Chem Phys Discuss 9: 9281-9297.
12. Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T & Geigl EM (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS ONE 5: e13042 doi:10.1371/journal.pone.0013042.
13. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
14. Colwell RK (2006) EstimateS: statistical estimation of species richness and shared species from samples. Version 8. Communities. Microb Ecol 42: 150-158.
15. Corpe WA & Rheem S (1989) Ecology of the methylotrophic bacteria on living leaf surfaces. FEMS Microbiol Ecol 62: 243-250.
16. Delort A-M, Vaïtilingom M, Amato P, Sancelme M, Parazols M, Mailhot G, Laj P & Deguillaume L (2010) A short overview of the microbial population in clouds: potential roles in atmospheric chemistry and nucleation processes. Atmos Res 98: 249-260.
17. Edwards A, Anesio AM, Rassner SM, Sattler B, Hubbard B, Perkins WT, Young M & Griffith GW (2011) Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard. ISME J 5: 150-160.
18. Fahlgren C, Hagstrom Å, Nilsson D & Zweifel UL (2010) Annual variations in the diversity, viability, and origin of airborne bacteria. Appl Environ Microbiol 76: 3015-3025.
19. Fan Z-Y, Li X-R, Mao D-P, Zhu G-F, Wang S-Y & Quan Z-X (2009) Could nested PCR be applicable for the study of microbial diversity? World J Microbiol Biotechnol 25: 1447-1452.
20. Fukui Y & Doskey PV (1998) Air-surface exchange of nonmethane organic compounds at a grassland site: seasonal variations and stressed emissions. J Geophys Res 103: 13153-13168.
21. Fuzzi S, Mandrioli P & Perfetto A (1997) Fog droplets - an atmospheric source of secondary biological aerosol particles. Atmos Environ 31: 287-290.
22. Galbally IE & Kristine W (2002) The production of methanol by flowering plants and the global cycle of methanol. J Atmos Chem 43: 195-229.
23. Graneli W, Carlsson P & Bertilsson S (2004) Bacterial abundance, production and organic carbon limitation in the Southern Ocean (39-621S, 4-14 1E) during the austral summer 1997/1998. Deep-Sea Res Pt II 51: 2569-2582.
24. Herlihy LJ, Galloway JN & Mills AL (1987) Bacterial utilization of formic and acetic acid in rainwater. Atmos Environ 21: 2397-2402.
25. Hill TCJ, Walsh KA, Harris JA & Moffett BF (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43: 1-11.
26. Hill KA, Shepson PB, Galbavy ES, Anastasio C, Kourtev PS, Konopka A & Stirm BH (2007) Processing of atmospheric nitrogen by clouds above a forest environment. J Geophys Res 112: 1-16.
27. Huber T, Faulkner G & Hugenholtz P (2004) Bellerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
28. Kellogg CA & Griffin DW (2006) Aerobiology and the global transport of desert dust. Trends Ecol Evol 21: 638-644.
29. Klappenbach JA, Dunbar JM & Schmidt TM (2000) RNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328-1333.
30. Knief C, Frances L & Vorholt JA (2010) Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and Identification of representative models, including M. extorquens PA1. Microb Ecol 60: 440-452.
31. Kourtev PS, Hill KA, Shepson PB & Konopka A (2011) Atmospheric cloud water contains a diverse bacterial community. Atmos Environ 45: 5399-5405.
32. Lee ZM, Bussema C & Schmidt TM (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37: D489-D493.
33. Lin Y-L (2007) Mesoscale Dynamics. Cambridge University Press, Cambridge, pp. 630.
34. Lindow SE & Brandl MT (2003) Microbiology of the Phyllosphere. Appl Environ Microbiol 69: 1875-1883.
35. Liu Y, Yao T, Zhu L, Jiao N, Liu X, Zeng Y & Jiang H (2009) Bacterial diversity of freshwater Alpine Lake Puma Yumco on the Tibetan Plateau. Geomicrobiol J 26: 131-145.
36. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M & Schleifer KH (1998) Bacterial phylogeny based on comparative sequence analysis (review). Electrophoresis 19: 554-568.
37. Marinoni A, Laj P, Sellegri K & Mailhot G (2004) Cloud chemistry at the Puy de Dome: variability and relationships with environmental factors. Atmos Chem Phys 4: 715-728.
38. Markowski P & Richardson Y (2010) Mesoscale Meteorology in Midlatitudes. Wiley-Blackwell, New York.
39. Maron P-A, Lejon DPH, Carvalho E, Bizet K, Lemanceau P, Ranjard L & Mougel C (2005) Assessing genetic structure and diversity of airborne bacterial communities by DNA fingerprinting and 16S rDNA clone library. Atmos Environ 39: 3687-3695.
40. Marzorati M, Wittebolle L, Boon N, Daffonchio D & Verstraete W (2008) How to get more out of molecular fingerprints: practical tools for microbial ecology. Environ Microbiol 10: 1571-1581.
41. Molouba F, Lorquin J, Willems A, Hoste B, Giraud E, Dreyfus B, Gillis M, de Lajudie P & Masson-Boivin C (1999) Photosynthetic Bradyrhizobia from Aeschynomene spp. Are specific to stem-nodulated species and form a separate 16S ribosomal DNA restriction fragment length polymorphism group. Appl Environ Microbiol 65: 3084-3094.
42. Morris CE, Sands DC, Vinatzerv BA, Glaux C, Guilbaud C, Buffiere A, Yan S, Dominguez H & Thompson BM (2008) The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle. ISME J 2: 1-14.
43. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, Kanigan T, Lewis K & Epstein SS (2010) Use of Ichip for high-throughput in situ cultivation of "Uncultivable" Microbial species. Appl Environ Microbiol 76: 2445-2450.
44. Prosser JI (2010) Replicate or lie. Environ Microbiol 12: 1806-1810.
45. Rastogi R, Wu M, DasGupta I & Fox GE (2009) Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol 9: 208.
46. Reasoner DJ & Geldreich EE (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49: 1-7.
47. Romanovskaya VA, Stolyar SM, Malashenko YR & Dodatko TN (2001) The ways of plant colonization by Methylobacterium strains and properties of these bacteria. Microbiology 70: 221-227.
48. Sattler B, Puxbaum H & Psenner R (2001) Bacterial growth in supercooled cloud droplets. Geophys Res Lett 28: 239-242.
49. Schloss PD & Handelsman J (2005) Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 6: 229.
50. Shrestha PM, Noll M & Liesack W (2007) Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession. Environ Microbiol 9: 2464-2474.
51. Stackebrandt E & Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152-155.
52. Sudtachat N, Ito N, Itakura M, Masuda S, Eda S, Mitsui H, Kawaharada Y & Minamisawa K (2009) Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum. Appl Environ Microbiol 75: 5012-5017.
53. Thomas V, Casson N & Greub G (2007) New Afipia and Bosea strains isolated from various water sources by amoebal co-culture. Syst Appl Microbiol 30: 572-579.
54. Torsvik V, Sørheim R & Goksøyr J (1996) Total bacterial diversity in soil and sediment communities-a review. J Ind Microbiol 17: 170-178.
55. Vaïtilingom M, Amato P, Sancelme M, Laj P, Leriche M & Delort AM (2010) Contribution of microbial activity to carbon chemistry in clouds. Appl Environ Microbiol 76: 23-29.
56. Vaïtilingom M, Charbouillot T, Deguillaume L, Maisonobe R, Parazols M, Amato P, Sancelme M & Delort AM (2011) Atmospheric chemistry of carboxylic acids: microbial implication versus photochemistry. Atmos Chem Phys Discuss 11: 4881-4911.
57. Venter JC, Remington K, Heidelberg JF et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
58. Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol 73: 5261-5267.
59. Weizhong L (2011) CD-HIT Suite: Biological Sequence Clustering and Comparison. http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi.
60. Whittenbury R, Phillips KC & Wilkinson JF (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61: 205-218.
61. Widdel F & Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. The Prokaryotes, 2nd edn (Balows H, Trüper HG, Dworkin M, Harder W & Schleifer KH, eds), pp. 3352-3378. Springer-Verlag, New York.
62. Wittebolle L, Vervaeren H, Verstraete W & Boon N (2008) Quantifying community dynamics of nitrifiers in functionally stable reactors. Appl Environ Microbiol 74: 286-293.
63. Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K, De Vos P, Verstraete W & Boon N (2009) Initial community evenness favors functionality under selective stress. Nature 458: 623-626.