Agronomy for Sustainable Development

, Volume 31, Issue 1, pp 205–215

Role of pathogens, signal recalcitrance, and organisms shifting for ecosystem recuperation. A review

Review Article


Nature ability to adapt to ecosystem changes such as cultivation depends upon microbial interactions with plant, animals and humans. A such organisation is made possible in particular by signal exchanges, horizontal and vertical transfers of genetic material from one organism to another, the efficient use of pathogens and environment in food web interactions, the ability to metabolic modifications of shifting, and the potential to assume dormancy under unfavorable conditions. So far industrial agriculture has led to pollution and declines of biodiversity and soil carbon. The biodiversity of agricultural fields can be improved by several processes such as DNA-uptake; viruses and horizontal gene transfers; animals carrying propagules, spores, cysts and seeds from less disrupted environments; and sexual reproduction. Within weeks soil water retention capacity, nutrients availability, communication, and high biomass production is improved. In less perturbed but unfertilized, shifting cultivation systems a return to original productivities needs about 50 years.


genetic-chemical signals environmental cues informational ecology self-organisation host-control biofilms anabolism catabolism defence cryptobiosis food web interactions 


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  1. Addiscott T.M. (1995) Entropy and sustainability, Eur. J. Soil Sci. 46, 161–168.Google Scholar
  2. Ausubel F.M. (2005) Are innate immune signaling pathways in plants and animals conserved? Nature Immunol. 6, 973–979.Google Scholar
  3. Badri D.V., Vivanco J.M. (2009) Regulation and function of root exudates, Plant Cell Environ. 32, 666–681.PubMedGoogle Scholar
  4. Bahn M., Schmitt M., Siegwolf R., Richter A., Brüggemann N. (2009) Does photosynthesis affect grassland soil-respired CO2 and is carbon isotope composition on a diurnal timescale? New Phytol.182, 451–460.PubMedGoogle Scholar
  5. Benckiser G. (1979) Umwandlung und Verwertbarkeit relativperistenter, organischer Verbindungen im Zuge der anaeroben Atmung (Denitrifikation) am Beispiel von Polyäthylensorbitanmonooleat, Phthalsäuredi-n-butylester, Hexachlorbenzol und Abwasserkonzentrat, Dissertation University of Stuttgart-Hohenheim, Germany, Hochschul-Verlag, Freiburg.Google Scholar
  6. Benckiser G. (1996) In situ Bestimmung von Denitrifikationsverlusten auf unterschiedlichen landwirtschaftlichen Nutzflächen mit der Acetylen-Inhibierungstechnik, VDLUFA-Schriftenreihe 41.Google Scholar
  7. Benckiser G. (1997) Organic inputs and soil metabolism. In: Benckiser G. (Ed.) Fauna in soil cosystems — recycling processes, nutrient fluxes, and agricultural production, Marcel Dekker, New York, pp. 7–62.Google Scholar
  8. Benckiser G. (2007a) Principles behind order and sustainability in natural successions and agriculture, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 349–388.Google Scholar
  9. Benckiser G. (2007b) Growth, denitrification and nitrate ammonification of the rhizobial strain TNAU 14 in presence and absence of C2H4 and C2H2, Annu. Rev. Microbiol. 57, 509–514.Google Scholar
  10. Benckiser G. (2010) Ants and sustainable agriculture, A review, Agron. Sustain. Dev. 30, 191–199.Google Scholar
  11. Benckiser G., Schnell S. (2007) Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton.Google Scholar
  12. Ben-Jacob E. (2003) Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment, Philos. Trans. Math. Phys. Eng. Sci. (The Royal Society) 361, 1283–1312.Google Scholar
  13. Biemont C., Vieira C. (2007) Schrott-DNA — Mitspieler der Evolution Spektr. Wiss. Mai, 44–49.Google Scholar
  14. Billi D., Wright D.J., Helm R.F., Prickett D., Potts M., Crowe J.H. (2000) Engineering desiccation tolerance in Escherichia coli, Appl. Environ. Microbiol. 66, 1680–1684.PubMedGoogle Scholar
  15. Bonkowski M. (2004) Protozoa and plant growth: the microbial loop in soil revisited, New Phytol. 162, 617–631.Google Scholar
  16. Bottomley P.J., Myrold D.D. (2007) Biological N Inputs, in: Soil Microbiology, Ecology, and Biochemistry, 3rd ed., Paul E.A. (Ed.), Academic Press, Amsterdam, pp. 365–386.Google Scholar
  17. Branda S.S., Chu F., Kearns D.B., Losick R., Kolter R. (2006) A major protein component of the Bacillus subtilis biofilm matrix, Mol. Microbiol. 59, 1226–1229.Google Scholar
  18. Brundrett M. C. (2009) Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis, Plant Soil 320, 37–77.Google Scholar
  19. Brune A. (2006) Symbiotic associations between termites and prokaryotes, in: Dworkin M. et al. (Eds.), The Prokaryotes, 3rd ed., Springer, New York, pp. 439–474.Google Scholar
  20. Buckley D.H., Schmidt T.M. (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems, Environ. Microbiol. 5, 441–452.PubMedGoogle Scholar
  21. Cabello P., Roldan M.D., Moreno-Vivian C. (2004) Nitrate reduction and the nitrogen cycle in archaea, Microbiol. 150, 3527–3546.Google Scholar
  22. Caesar-TonThat T.C., Caesar A.J., Gaskin J.F., Sainju U.M., Busscher W.J. (2007) Taxonomic diversity of predominant culturable bacteria associated withmicroaggregates from two different agroecosystems and their ability to aggregate soil in vitro, Appl. Soil Ecol. 36, 10–21.Google Scholar
  23. Cleeg C.D., Ritz K., Griffiths B.S. (2000) % G+C profiling and cross hybridization of microbial DNA reveals great variation in belowground community structure in UK upland grasslands, Appl. Soil Ecol. 14, 125–134.Google Scholar
  24. Crawford J.W., Harris J.A., Ritz K., Young I.M. (2005) Towards an evolutionary ecology of life in soil, Trends Ecol. Evol. 20, 81–87.PubMedGoogle Scholar
  25. Crutzen P.J., Mosier A.R., Smith K.A., Winiwarter W. (2007) N2O release from agribiofuel production negates global warming reduction by replacing fossil fuels, Atmos. Chem. Phys. Dis. 7, 11191–11205. Scholar
  26. Darby C., Hsu J.W., Ghori N., Falkow S. (2002) Plaque bacteria biofilm blocks food intake, Nature 417, 243–244.PubMedGoogle Scholar
  27. De Beer D. (1999) Use of micro-electrodes to measure in situ microbial activities in biofilms, sediments and microbial mats, in: Akkermans A.O.L. et al. (Eds.), Molecular Microbiology Ecology Manual. Kluwer, Amsterdam, pp. 1–23.Google Scholar
  28. De Vries S., Schröder I. (2002) Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases, Biochem. Soc. Trans. 30, 662–667.PubMedGoogle Scholar
  29. Esperschütz J., Buegger F., Winkler J.B., Munch J.C., Schloter M., Gattinger A. (2009) Microbial response to exudates in the rhizosphere of young beech trees (Fagus sylvatica L.) after dormancy, Soil Biol. Biochem. 41, 1976–1985.Google Scholar
  30. Esser G. (1994) Eingriffe der Landwirtschaft in den Kohlenstoffkreislauf, in: Schutz der Erdatmosphäre, Enquete-Kommission des 12. Deutschen Bundestages (Ed.), Economica, Bonn, p. 135.Google Scholar
  31. FAO (1999) Agricultural Biodiversity, in: FAO Conference Background Paper No. 1, Multifunctional Character of Agriculture and Land, Maastricht, Sept. 1999.Google Scholar
  32. Falk M.W., Wuertz S. (2007) Diversity of biofilms and their formation processes, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 21–39.Google Scholar
  33. Falkowski P.G., Fenchel T., Delong E.F. (2008) The microbial engines that drive earth’s biochemical cycles, Science 320, 1034–1039.PubMedGoogle Scholar
  34. Fargione J., Hill J., Tilman T., Polasky S., Hawthrone P. (2008) Land clearing and the biofuel carbon debt, Science 319, 1235–1238.PubMedGoogle Scholar
  35. Franken P., George E. (2007) Diversity of arbuscular mycorrhizal fungi, in: Benckiser G., Schnell S. (Eds.), Biodiversity in agricultural production systems, Taylor & Francis, Boca Raton, pp. 189–203.Google Scholar
  36. Fuchs G. (2007) Allgemeine Mikrobiologie Georg Thieme, Stuttgart.Google Scholar
  37. Ganapathy S., Sengupta S., Wawrzyniak P.K., Huber V., Buda F., Baumeister U., Würthner F., de Groot H.J.M. (2009) Zinc chlorins for artificial light-harvesting self-assemble into antiparallel stacks forming a microcrystalline solid-state material, Proc. Natl. Acad. Sci. USA 106, 11472–11477.PubMedGoogle Scholar
  38. Goddard M.R., Charles H., Godfray J., Burt A. (2005) Sex increases the efficacy of natural selection in experimental yeast populations, Nature 434, 636–639.PubMedGoogle Scholar
  39. Goldenfeld N., Woese C. (2007) Biology’s next revolution, Nature 445, 369.PubMedGoogle Scholar
  40. Gómez-Gómez L., Boller T. (2002) Flagellin perception: a paradigm for innate immunity, Trends Plant Sci. 7, 251–256. Scholar
  41. Grayston S.J., Camppbell C.D., Bardgett R.D., Mawdsley J.L., Clegg C.D., Ritz K., Griffith S., Rodwell J.S., Edwards S.J., Davies W.J., Elston D.J., Millard P. (2004) Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques, Appl. Soil Ecol. 25, 63–84.Google Scholar
  42. Green J.L., Holmes A.J., Westoby M., Oliver I., Briscoe D., Dangerfield M., Gillings M., Beattie A.J. (2004) Spatial scaling of microbial eukaryote diversity, Nature 432, 747–749.PubMedGoogle Scholar
  43. Hansel C.M., Fendorf S., Sutton K., Newville M. (2001) Characterization of Fe plaque and associated metals on the roots of mine-waste impacted aquatic plants, Environ. Sci. Technol. 35, 3863–3868.PubMedGoogle Scholar
  44. Hartmann A., Smalla K., Soerensen J. (2007) Microbial diversity in the rhizosphere: highly resolving molecular methodology to study plant-beneficial rhizosphere bacteria, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, CRC, Taylor & Francis, Boca Raton, pp. 101–130.Google Scholar
  45. Hengge R. (2009) Principles of c-di-GMP signalling in bacteria, Nature Rev. Microbiol. 7, 263–273.Google Scholar
  46. Holliger C., Wohlfarth G., Diekert G. (1999) Reductive dechlorination in the energy metabolism of anaerobic bacteria, FEMS Microbiol. Rev. 22, 383–398.Google Scholar
  47. Honermeier B. (2007) Diversity in crop production systems, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems Taylor & Francis, Boca Raton, pp. 1–20.Google Scholar
  48. Jäckel U., Kämpfer P. (2007) Microbial communities introduced through organic amendments and by air-transport into agricultural soils, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 69–80.Google Scholar
  49. John M., Rubick R., Schmitz R.P.H., Rakoczy J., Schubert T., Diekert G. (2009) Retentive memory of bacteria: Long-term regulation of dehalorespiration in Sulfurospirillum multivorans, J. Bacteriol. 191, 1650–1655.PubMedGoogle Scholar
  50. Jones C.G., Guitierrez J.L., Groffman P.M., Shachak F.G. (2006) Linking ecosystem engineers to soil processes: a frame work using the Jenny State Factor Equation, Eur. J. Soil Biol. 42, 39–53.Google Scholar
  51. Jones D.L., Nguyen C., Finlay R.D. (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface, Plant Soil 321, 5–33.Google Scholar
  52. Jones J.D.G., Dangl J.L. (2006) The plant immune system, Nature 444, 323–329.PubMedGoogle Scholar
  53. Kandeler E., Dick R.P. (2007) Soil enzymes: spatial distribution and function in agroecosystems, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 263–286.Google Scholar
  54. Karch H., Tarr P., Bielaszewska M. (2005) Enterohaemorrhagic Escherichia coli in human medicine, Int. J. Med. Microbiol. 295, 405–418.PubMedGoogle Scholar
  55. Kessin R.H., Gundersen G.G., Zaydfudim V., Grimson M. (1996) How cellular slime molds evade nematodes, Proc. Natl. Acad. Sci. USA 93, 4857–4861.PubMedGoogle Scholar
  56. Knight J. (2004) Microbiology gaining ground after lean years, Nature 429, 332.PubMedGoogle Scholar
  57. Kolter R., Greenberg E.P. (2006) The superficial life of microbes, Nature 441, 300–302.PubMedGoogle Scholar
  58. Kool D.M., Müller C., Wrage N., Oenema O., van Groeningen J.W. (2009) Oxygen exchange between nitrogen oxides and H2O can occur during nitrifier pathways, Soil Biol. Biochem. 41, 1632–1641.Google Scholar
  59. Kubicek S., O’sullivan R.J., August E.M., Hickey E.R., Zhang Q., Teodoro M.L., Rea S., Mechtler K., Kowalski J.A., Homon C.A., Kelly T.A., Jenuwein T. (2007) Reversal of H3K9me2 by a smallmolecule inhibitor for the G9a histone methyltransferase, Mol. Cell 25, 473–481.PubMedGoogle Scholar
  60. Lal R. (2009) Soils and world food security, Soil Tillage Res. 102, 1–4.Google Scholar
  61. Leon M., Yaryura P.M., Montecchia M.S., Hernandez A.I., Correa O.S., Pucheu N.L., Kerber N.L., Garcıa A.F. (2009) Antifungal activity of selected indigenous Pseudomonas and Bacillus from the Soybean Rhizosphere, Hind. Publ. Corp. Int. J. Microbiol., article ID 572049.Google Scholar
  62. Leon-Reyes A., Spoel S.H., de Lange E.S., Abe H., Kobayashi M., Tsuda S., Millenaar F.F., Welschen R.A.M., Ritsema T., Pieterse C.M.J. (2009) Ethylene modulates the role of Nonexpressor of Pathogenesis-related genes 1 in cross talk between salicylate and jasmonate signaling1 [W][OA], Plant Physiol. 149, 1797–1809.PubMedGoogle Scholar
  63. Leubner-Metzger G. (2005) b-1,3-Glucanase gene expression in lowhydrated seeds as a mechanism for dormancy release during tobacco after-ripening, Plant J. 41, 133–145.PubMedGoogle Scholar
  64. Lundberg J.O., Weitzberg E., Cole J.A., Benjamin N. (2004) Opinion: Nitrate, bacteria and human health, Nat. Rev. Microbiol. 2, 593–602.PubMedGoogle Scholar
  65. Makeshin F. (1997) Earthworms (Lumbricidae, Oligochaeta): important promoters of soil development and soil fertility, in: Benckiser G. (Ed.), Fauna in soil cosystems — recycling processes, nutrient fluxes, and agricultural production, Marcel Dekker, New York, pp. 173–223.Google Scholar
  66. Maharning A.R., Mills A.A.S., Adl S.M. (2009) Soil community changed during secondary succession to naturalised grasslands, Appl. Soil Ecol. 41, 137–141.Google Scholar
  67. Maherali H., Klironomonas J.N. (2007) Influence of phylogeny on fungal communities assembly and ecosystem functioning, Science 316, 1746–1748.PubMedGoogle Scholar
  68. Maraun M., Visser S., Scheu S. (1998) Oribatid mites enhance the recovery of the microbial community after a strong disturbance, Appl. Soil Ecol. 9, 175–181.Google Scholar
  69. Marie C., Broughton W.J., Deakin W.J. (2001) Rhizobium type III secretion systems: legume charmers or alarmers? Cur. Opin. Plant Biol. 4, 336–342.Google Scholar
  70. Martin W., Rujan T., Richly E., Hansen A., Cornelsen S., Lins T., Leister D., Stoebe B., Hasegawa M., Penny D. (2002) From the Cover: Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus, PNAS 99, 12246–12251.PubMedGoogle Scholar
  71. Martinez-Inigo M.J., Perez-Sanz A., Ortiz I., Alarcón R., Garcia P., Lobo M.C. (2009) Bula soil and rhizosphere bacterial community PCRDGGE profiles and [beta]-galactosidase activity as indicators of biological quality in soils contaminated by heavy metals and cultivated with Silene vulgaris (Moench) Garcke, Chemosphere 75, 1376–1381.PubMedGoogle Scholar
  72. Mashburn L.M., Whiteley M. (2005) Membrane vesicles traffic signals and facilitated group activities in a prokaryote, Nature 437, 422–425.PubMedGoogle Scholar
  73. Matasuyama T., Kaneda K., Nakagawa K., Isa K., Hara-Hotta H., Yano I. (1992) A novel extracelluar cyclic lipopeptide which promotes flagellum-dependent amd-independent spreading growth of Serratia marcescens, J. Bact. 174, 1769–1776.Google Scholar
  74. Mauch-Mani B., Metraux J.P. (1998) Salicylic acid and systemic acquired resistance to pathogen attack, Ann. Bot. 82, 535–540.Google Scholar
  75. McCulley R.L., Burke L.C. (2004) Microbial community composition across the Great Plains: landscape versus reginal variability, Appl. Environ. Microbiol. 70, 4554–4559.Google Scholar
  76. Moore J.C., Simpson R.T., McCann K.S., de Ruiter P.C. (2007) Food web interactions and modeling, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 385–398.Google Scholar
  77. Morris C.E., Monier J.M. (2003) The ecological significance of biofilm formation by plant-associated bacteria, Ann. Rev. Phytopathol. 41, 429–453.Google Scholar
  78. Naeem S. (1998) Species redundancy and ecosystem reliability, Conserv. Biol. 12, 39–45.Google Scholar
  79. Nannipieri P., Ascher M., Ceccherini L., Landi G., Pietramellara G., Renella G. (2003) Microbial diversity and soil functions, Eur. J. Soil Sci. 54, 655–670.Google Scholar
  80. Oberholzer H.R., Höper H. (2007) Soil quality assessment and longterm field observation with emphasis on biological soil characteristics, In: Benckiser G., Schnell S. (eds), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 399–424.Google Scholar
  81. O’Toole G. A. (2004) Jekyll or hide, Nature 432, 680–681.PubMedGoogle Scholar
  82. Ottow J.C.G. (1997) Abbaukinetik und Peristenz von Fremdstoffen in Böden, in: Ottow J.C.G., Bidlingmeier W. (Eds.), Umweltbiotechnologie. Gustav Fischer, Stuttgart.Google Scholar
  83. Parry S., Renault P., Chenu C., Lensi R. (1999) Denitrification in pasture and cropped soil clods as affected by pore space structure, Soil Biol. Biochem. 31, 493–501.Google Scholar
  84. Paterson E., Osler G., Dawson L.A., Gebbing T., Sim A., Ord B. (2008) Labile and recalcitrant plant fractions are utilised by distinct microbial communities in soil: independent of the presence of roots and mycorrhizal fungi, Soil Biol. Biochem. 40, 1103–1113.Google Scholar
  85. Price P.B., Sowers T. (2004) Temperature dependence of metabolic rates for microbial growth, maintance and survival, PNAS 101, 4631–4636.PubMedGoogle Scholar
  86. Rao C.V., Wolf D.M., Arkin A.P. (2002) Control, exploitation and tolerance of intracellular noise, Nature 420, 231–237.PubMedGoogle Scholar
  87. Ratering S., Benckiser G., Schnell S. (2007) Metabolic diversity of microorganisms in agricultural soils, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 287–316.Google Scholar
  88. Ravishankara A.R., Daniel J.S., Portmann R.W. (2009) Nitrous oxide (N2O): the dominant ozon-depleting substance emitted in the 21st century, Science 326, 123–125.PubMedGoogle Scholar
  89. Rubi J.M. (2008) The long arm of the second law, Sci. Am. 299, 40–45.Google Scholar
  90. Ruiz M., Aguiriano E., Carillo J.M. (2008) Effects of N fertilization on yield for low-input production in Spanish wheat landraces (Triticum turgidum L. and Triticum monococcum L.), Plant Breed 127, 20–23.Google Scholar
  91. Rumpho M.E., Worful J.M., Lee J., Kannan K., Tyler M.S., Bhattacharya D., Moustafa A., Manhart J.R. (2008) From the Cover: Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica, PNAS 105, 17867–17871.PubMedGoogle Scholar
  92. Santner A., Estelle M. (2009) Recent advances and emerging trends in plant hormone signaling, Nature 459, 1071–1078.PubMedGoogle Scholar
  93. Scheublin T.R., Ridgway K.P., Young J.P.W., van der Heijden M.G.A. (2004) Nonlegume, legume and root nodulesharbour different arbuscular mycorrhizal fungal communities, Appl. Environ. Microbiol. 70, 6240–6246.PubMedGoogle Scholar
  94. Schmeisser H., Stockigt C., Raasch F., Wingender C., Timmis K.N., Wenderoth D.F., Flemming H.C., Liesegang H., Schmitz R.A., Jaeger K.E., Streit W.R. (2003) Metagenome survey of biofilms in drinking-water networks, Appl. Environ. Microbiol. 69, 7298–7309.PubMedGoogle Scholar
  95. Schroeckh V., Scherlach K., Nützmann H.W., Shelest E., Schmidt-Heck W., Schuemann J., Martin K., Hertweck C., Brakhage A.A. (2009) Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans, PNAS 106, 14558–14563.PubMedGoogle Scholar
  96. Searchinger T., Heimlich R., Houghton R.A., Dong F., Elboid A., Fabiosa J., Tokgoz S., Hayes D., Yu T.H. (2008) Use of US croplands for biofuels increases greenhouse gases through emissions from landuse change, Science 319, 238–240.Google Scholar
  97. Seki K., Horikawa D.D. (2007) Diversity of Tardigrada, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 237–248.Google Scholar
  98. Shaw L.J., Morris P., Hooker J.E. (2006) Perception and modification of plant flavonoid signals by rhizosphere microorganisms, Environ. Microbiol. 8, 1867–1880.PubMedGoogle Scholar
  99. Singh B.K., Nunan N., Ridgway K.P., McNicol J., Young P.W., Daniel T.J., Prosser J.I., Millard P. (2009) The relationship between assemblages of mycorrhizal fungi and bacteria on grass roots, Environ. Microbiol. 10, 534–541.Google Scholar
  100. Singh J.S., Kashyap A.K. (2006) Dynamics of viable nitrifier community, N-mineralization and nitrification in seasonally dry tropical forests and savanna, Microbiol. Res. 161, 253–259.Google Scholar
  101. Singh P.K., Parsek M.R., Greenberg E.P., Welsh M.J. (2002) A component of innate immunity prevents bacterial biofilm development, Nature 417, 552–555.PubMedGoogle Scholar
  102. Sourijik V., Berg H.C. (2004) Functional integration between receptors in bacterial chemotaxis, Nature 428, 437–441.Google Scholar
  103. Stein E., Molitor, A., Kogel K.H., Waller F. (2008) Systemic resistance in Arabidopsis con ferred by the mycorrhizal fungus Piriformospora indica requires jasmonic acid signaling and the cytoplasmic function of NPR1, Plant Cell Physiol. 49, 1747–1751.PubMedGoogle Scholar
  104. Stone F.M., Coulter C.B. (1932) Porphyrin compounds derived from bacteria, J. Gen. Physiol. 20, 629–639.Google Scholar
  105. Suttle C. (2005) The viriosphere: the greatest biological diversity on earth and driver of global processes, Environ. Microbiol. 7, 472–485.Google Scholar
  106. Tamiaki H., Kimura H.S., Kimura T. (2003) Self-aggregation of synthetic zinc21-hydroxy-121/131-oxo-porphyrins, Tetrahedron 59, 7423–7435.Google Scholar
  107. Tashiro M., Ciborowski P., Klenk H.D., Pulverer G., Rott R. (1987) Role of Staphylococcus protease in the development of influenca pneumonia, Nature 325, 536–537.PubMedGoogle Scholar
  108. Tebbe C.C., Schloter M. (2007) Discerning the diversity of soil prokaryotes (bacteria and archaea) and their impact on agriculture, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 81–100.Google Scholar
  109. Tippkötter R., Eickhorst T., Taubner H., Gredner B., Rademaker G. (2009) Detection of soil water in macropores of undisturbed soil using microfocus X-ray tube computerized tomography (mCT), Soil Tillage Res. 105, 12–20.Google Scholar
  110. Trofymow J.A., Coleman D.C., Cambardella C. (1987) Rates of rhizodeposition and ammonium depletion in the rhizosphere of axenic oat roots, Plant Soil 97, 333–344.Google Scholar
  111. Valentine D.L. (2007) Adaption to energy stress dictates the ecology and evolution of the archaea, Nature Rev. Microbiol. 5, 316–323.Google Scholar
  112. Van der Heijden M.G.A., Bardgett R.D., van Straalen N.M. (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems, Ecol. Lett. 11, 296–310.PubMedGoogle Scholar
  113. Vogel H.J., Babel U. (2007) Soil space diversity and its dynamics: qualitative and quantitative considereations, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems Taylor & Francis, Boca Raton, pp. 41–68.Google Scholar
  114. Vogel T.M., Pascal S., Jansson J.K., Hirsch P.R., Tiedje J.M., van Elsas J.D., Bailey M.J., Nalin R., Philippot L. (2009) TerGenome: a consortium for sequencing of a soil metagenome, Nature Rev. Microbiol. 7, 252.Google Scholar
  115. Von Lützow M., Kögel-Knabner I., Ekschmitt K., Flessa H., Guggenberger G., Matzner E., Marschner B. (2007) SOM fractionation methods: Relevance to functional pools and to stabilization mechanisms, Soil Biol. Biochem. 39, 2183–2207.Google Scholar
  116. Walter A., Silk W.K., Schurr U. (2009) Environmental effects on spatial and temporal patterns of leaf and root growth, Ann. Rev. Plant Biol. 60, 279–304.Google Scholar
  117. Wardle D. (2002) Communities and ecosystems, Princeton University Press, New York, p. 342.Google Scholar
  118. Whalen J.K., Fox C.A. (2007) Diversity of lumbricid earthworms in temperate ecosystems, in: Benckiser G., Schnell S. (Eds.), Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton, pp. 249–261.Google Scholar
  119. Wolfe N.D., Dunavan C.P., Diamond J. (2007) Origins of major human infectious diseases, Nature 447, 279–283.PubMedGoogle Scholar
  120. Yoon S.S., Hennigan R.F., Hilliard G.M., Ochsner U.A., Parvatiyar K., Kamani M.C., Allen H.L., DeKievit T.R., Gardner P.R., Schwab U., Rowe J.J., Iglewski B.H., McDermott T.R., Mason R. P., Wozniak D.J., Hancock R.E.W., Parsek M.R., Noah T.L., Boucher R.C., Hassett D.J. (2002) Pseudomonas aeruginosa anaerobic respiration in biofilms: Relationships to cystic fibrosis pathogenesis, Dev. Cell 3, 593–603.PubMedGoogle Scholar

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© INRA and Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Institute of Applied MicrobiologyJustus-Liebig UniversityGiessenGermany
  2. 2.Ecology and Evolutionary BiologyTulane UniversityNew OrleansUSA

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