Skip to main content

Advertisement

SpringerLink
Log in

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

  • Review Article
  • Published:
Agronomy for Sustainable Development Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Addiscott T.M. (1995) Entropy and sustainability, Eur. J. Soil Sci. 46, 161–168.

    Google Scholar 

  • Ausubel F.M. (2005) Are innate immune signaling pathways in plants and animals conserved? Nature Immunol. 6, 973–979.

    CAS  Google Scholar 

  • Badri D.V., Vivanco J.M. (2009) Regulation and function of root exudates, Plant Cell Environ. 32, 666–681.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

  • Benckiser G. (1996) In situ Bestimmung von Denitrifikationsverlusten auf unterschiedlichen landwirtschaftlichen Nutzflächen mit der Acetylen-Inhibierungstechnik, VDLUFA-Schriftenreihe 41.

  • 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 

  • 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 

  • 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.

    CAS  Google Scholar 

  • Benckiser G. (2010) Ants and sustainable agriculture, A review, Agron. Sustain. Dev. 30, 191–199.

    CAS  Google Scholar 

  • Benckiser G., Schnell S. (2007) Biodiversity in Agricultural Production Systems, Taylor & Francis, Boca Raton.

    Google Scholar 

  • 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 

  • Biemont C., Vieira C. (2007) Schrott-DNA — Mitspieler der Evolution Spektr. Wiss. Mai, 44–49.

  • 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.

    PubMed  CAS  Google Scholar 

  • Bonkowski M. (2004) Protozoa and plant growth: the microbial loop in soil revisited, New Phytol. 162, 617–631.

    Google Scholar 

  • 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 

  • 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 

  • 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.

    CAS  Google Scholar 

  • 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 

  • Buckley D.H., Schmidt T.M. (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems, Environ. Microbiol. 5, 441–452.

    PubMed  Google Scholar 

  • Cabello P., Roldan M.D., Moreno-Vivian C. (2004) Nitrate reduction and the nitrogen cycle in archaea, Microbiol. 150, 3527–3546.

    CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    PubMed  Google Scholar 

  • 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. www.atmos-chem-phys-discuss.net/7/11191/2007/.

    Google Scholar 

  • Darby C., Hsu J.W., Ghori N., Falkow S. (2002) Plaque bacteria biofilm blocks food intake, Nature 417, 243–244.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  Google Scholar 

  • 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 

  • 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 

  • FAO (1999) Agricultural Biodiversity, in: FAO Conference Background Paper No. 1, Multifunctional Character of Agriculture and Land, Maastricht, Sept. 1999.

  • 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 

  • Falkowski P.G., Fenchel T., Delong E.F. (2008) The microbial engines that drive earth’s biochemical cycles, Science 320, 1034–1039.

    PubMed  CAS  Google Scholar 

  • Fargione J., Hill J., Tilman T., Polasky S., Hawthrone P. (2008) Land clearing and the biofuel carbon debt, Science 319, 1235–1238.

    PubMed  CAS  Google Scholar 

  • 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 

  • Fuchs G. (2007) Allgemeine Mikrobiologie Georg Thieme, Stuttgart.

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Goldenfeld N., Woese C. (2007) Biology’s next revolution, Nature 445, 369.

    PubMed  CAS  Google Scholar 

  • Gómez-Gómez L., Boller T. (2002) Flagellin perception: a paradigm for innate immunity, Trends Plant Sci. 7, 251–256. http://plants.trends.com.

    PubMed  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • Hengge R. (2009) Principles of c-di-GMP signalling in bacteria, Nature Rev. Microbiol. 7, 263–273.

    CAS  Google Scholar 

  • Holliger C., Wohlfarth G., Diekert G. (1999) Reductive dechlorination in the energy metabolism of anaerobic bacteria, FEMS Microbiol. Rev. 22, 383–398.

    Google Scholar 

  • 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.

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • Jones J.D.G., Dangl J.L. (2006) The plant immune system, Nature 444, 323–329.

    PubMed  CAS  Google Scholar 

  • 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 

  • Karch H., Tarr P., Bielaszewska M. (2005) Enterohaemorrhagic Escherichia coli in human medicine, Int. J. Med. Microbiol. 295, 405–418.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Knight J. (2004) Microbiology gaining ground after lean years, Nature 429, 332.

    PubMed  CAS  Google Scholar 

  • Kolter R., Greenberg E.P. (2006) The superficial life of microbes, Nature 441, 300–302.

    PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Lal R. (2009) Soils and world food security, Soil Tillage Res. 102, 1–4.

    Google Scholar 

  • 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.

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Lundberg J.O., Weitzberg E., Cole J.A., Benjamin N. (2004) Opinion: Nitrate, bacteria and human health, Nat. Rev. Microbiol. 2, 593–602.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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 

  • Maherali H., Klironomonas J.N. (2007) Influence of phylogeny on fungal communities assembly and ecosystem functioning, Science 316, 1746–1748.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Mashburn L.M., Whiteley M. (2005) Membrane vesicles traffic signals and facilitated group activities in a prokaryote, Nature 437, 422–425.

    PubMed  CAS  Google Scholar 

  • 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 

  • Mauch-Mani B., Metraux J.P. (1998) Salicylic acid and systemic acquired resistance to pathogen attack, Ann. Bot. 82, 535–540.

    CAS  Google Scholar 

  • 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 

  • 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 

  • Morris C.E., Monier J.M. (2003) The ecological significance of biofilm formation by plant-associated bacteria, Ann. Rev. Phytopathol. 41, 429–453.

    CAS  Google Scholar 

  • Naeem S. (1998) Species redundancy and ecosystem reliability, Conserv. Biol. 12, 39–45.

    Google Scholar 

  • 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 

  • 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 

  • O’Toole G. A. (2004) Jekyll or hide, Nature 432, 680–681.

    PubMed  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Price P.B., Sowers T. (2004) Temperature dependence of metabolic rates for microbial growth, maintance and survival, PNAS 101, 4631–4636.

    PubMed  CAS  Google Scholar 

  • Rao C.V., Wolf D.M., Arkin A.P. (2002) Control, exploitation and tolerance of intracellular noise, Nature 420, 231–237.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • Rubi J.M. (2008) The long arm of the second law, Sci. Am. 299, 40–45.

    Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Santner A., Estelle M. (2009) Recent advances and emerging trends in plant hormone signaling, Nature 459, 1071–1078.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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 

  • Shaw L.J., Morris P., Hooker J.E. (2006) Perception and modification of plant flavonoid signals by rhizosphere microorganisms, Environ. Microbiol. 8, 1867–1880.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • Sourijik V., Berg H.C. (2004) Functional integration between receptors in bacterial chemotaxis, Nature 428, 437–441.

    Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Stone F.M., Coulter C.B. (1932) Porphyrin compounds derived from bacteria, J. Gen. Physiol. 20, 629–639.

    Google Scholar 

  • Suttle C. (2005) The viriosphere: the greatest biological diversity on earth and driver of global processes, Environ. Microbiol. 7, 472–485.

    Google Scholar 

  • Tamiaki H., Kimura H.S., Kimura T. (2003) Self-aggregation of synthetic zinc21-hydroxy-121/131-oxo-porphyrins, Tetrahedron 59, 7423–7435.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    CAS  Google Scholar 

  • Valentine D.L. (2007) Adaption to energy stress dictates the ecology and evolution of the archaea, Nature Rev. Microbiol. 5, 316–323.

    CAS  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • 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.

  • 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.

    CAS  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • Wardle D. (2002) Communities and ecosystems, Princeton University Press, New York, p. 342.

    Google Scholar 

  • 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 

  • Wolfe N.D., Dunavan C.P., Diamond J. (2007) Origins of major human infectious diseases, Nature 447, 279–283.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Applied Microbiology, Justus-Liebig University, Heinrich Buff-Ring 26-32, Giessen, Germany

    Gero Benckiser

  2. Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118-5698, USA

    Stuart S. Bamforth

Authors
  1. Gero Benckiser
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stuart S. Bamforth
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gero Benckiser.

About this article

Cite this article

Benckiser, G., Bamforth, S.S. Role of pathogens, signal recalcitrance, and organisms shifting for ecosystem recuperation. A review. Agronomy Sust. Developm. 31, 205–215 (2011). https://doi.org/10.1051/agro/2010024

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1051/agro/2010024

Keywords

Search

Navigation