Soil bacteria and archaea first evolved as principal inhabitants of primordial environments, and then in association with fungi, plants and animals as new environments emerged. Thus, transitions occurred, which did not correspond to a replacement of ancient processes by new ones, but to a superposition or accretion of processes. The maintenance of primordial environments depends on the development of complexity to compensate for the effects of increasing diversity. Much of the persistence that is observed along the biological history of soils depends on symbiogenesis, which might be understood in terms, not of natural selection among biological systems, but of natural maintenance.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Akiyama K, Hayashi H (2006) Strigolactones: chemical signals for fungal symbionts and parasitic weeds in plant roots. Ann Bot 97:925-931
Akiyama K, Matsuzaki K, Hayashi H (2005) Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435:824-827
Albrecht C, Geurts R, Bisseling T (1999) Legume nodulation and mycorrhizae formation; two extremes in host specificity meet. EMBO J 18:281-288
Andersson SGE, Kurland CG (1998) Reductive evolution of resident genomes. Trends Microbiol 6:263-268
Ané J-M, Kiss, GB, Riely, BK et al. (2004) Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303:1364-1367
Artursson V, Jansson JK (2003) Use of bromodeoxyuridine immunocapture to identify active bac-teria associated with arbuscular mycorrhizal hyphae. Appl Environ Microbiol 69:6208-6215
Artursson V, Finlay RD, Jansson JK (2006) Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environ Microbiol 8:1-10
Banfield JF, Barker WW, Welch SA, Taunton A (1999) Biological impact on mineral dissolution: Application of the lichen model to understanding mineral weathering in the rhizosphere. Proc Natl Acad Sci USA 96:3404-3411
Battistuzzi F, Feijao A, Hedges SB (2004) A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 4:44
Beaulieu J-P, Bennett DP, Fouqué P et al. (2006) Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing. Nature 439:437-440
Beller HR, Chain PSG, Letain TE et al. (2006) The genome sequence of the obligately chemo-lithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 188:1473-1488
Belnap J (2003) The world at your feet: desert biological soil crusts. Front Ecol Environ 1:181-189 Bern M, Goldberg D (2005) Automatic selection of representative proteins for bacterial phylog-eny. BMC Evol Biol 5:34
Beukes NJ, Dorland H, Gutzmer J, Nedachi M, Ohmoto H (2002) Tropical laterites, life on land, and the history of atmospheric oxygen in the Paleoproterozoic. Geology 30:491-494
Bianciotto V, Bonfante P (2002) Arbuscular mycorrhizal fungi: a specialised niche for rhizospheric and endocellular bacteria. Antonie van Leeuwenhoek 81:365-371
Bianciotto V, Andreotti S, Balestrini R, Bonfante P, Perotto S (2001) Mucoid mutants of the bio-control strain Pseudomonas fluorescens CHA0 show increased ability in biofilm formation on mycorrhizal and nonmycorrhizal carrot roots. Mol Plant Microbe Interact 14:255-260
Bonfante P (2003) Plants, mycorrhizal fungi and endobacteria: a dialog among cells and genomes. Biol Bull 204:215-220
Bouwmeester HJ, Roux C, Lopez-Raez JA, Bécard G (2007) Rhizosphere communication of plants, parasitic plants and AM fungi. Trends Plant Sci 12:224-230
Brencic A, Angert ER, Winans SC (2005) Unwounded plants elicit Agrobacterium vir gene induc-tion and T-DNA transfer: transformed plant cells produce opines yet are tumour free. Mol Microbiol 57:1522-1531
Brocks JJ, Logan GA, Buick R, Summons RE (1999) Archean molecular fossils and the early rise of eukaryotes. Science 285:1033-1036
Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281-285
Brune A, Friedrich M (2000) Microecology of the termite gut: structure and function on a micro-scale. Curr Opin Microbiol 3:263-269
Büdel B, Weber B, Kühl M, Pfanz H, Sültemeyer D, Wessels D (2004) Reshaping of sandstone surfaces by cryptoendolithic cyanobacteria: bioalkalization causes chemical weathering in arid landscapes. Geobiology 2:261-268
Buscot F (2005) What are soils? In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions. Springer, Berlin Heidelberg New York, pp 3-17
Bywater RP, Conde-Frieboes K (2005) Did life begin on the beach? Astrobiology 5:568-574
Cabello P, Roldán MD, Moreno-Vivián C (2004) Nitrate reduction and the nitrogen cycle in archaea. Microbiology 150:3527-3546
Canbäck B, Tamas I, Andersson SGE (2004) A phylogenomic study of endosymbiotic bacteria. Mol Biol Evol 21:1110-1122
Canfield DE (2006) Gas with an ancient history. Nature 440:426-427
Canfield DE, Habicht KS, Thamdrup B (2000) The Archean sulfur cycle and the early history of atmospheric oxygen. Science 288:658-661
Carroll RL (2001) The origin and early radiation of terrestrial vertebrates. J Paleont 75:1202-1213
Castresana J, Moreira D (1999) Respiratory chains in the last common ancestor of living organisms. J Mol Evol 49:453-460
Catling DC, Zahnle KJ, McKay C (2001) Biogenic methane, hydrogen escape, and the irreversible oxidation of early Earth. Science 293:839-843
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287
Crawford JW, Harris JA, Ritz K, Young IM (2005) Towards an evolutionary ecology of life in soil. Trends Ecol Evol 20:81-87
Crispim CA, Gaylarde PM, Gaylarde CC (2003) Algal and cyanobacterial biofilms on calcareous historic buildings. Curr Microbiol 46:79-82
Davey ME, O’Toole GA (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64:847-867
Davis EL, Mitchum MG (2005) Nematodes. Sophisticated parasites of legumes. Plant Physiol 137:1182-1188
de Boer W, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: Impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29:795-811
Denison RF, Kiers ET (2004) Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgo-ing symbiosis. FEMS Microbiol Lett 237:187-193
Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolu-tion: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 101:15386-15391
Egert M, Wagner B, Lemke T, Brune A, Friedrich MW (2003) Microbial community structure in midgut and hindgut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera:Scarabaeidae). Appl Environ Microbiol 69:6659-6668
Eldredge N, Gould SJ (1972) Punctuated equilibria: an alternative to phyletic gradualism. In: Schopf TJM (ed) Models in paleobiology. Freeman, Cooper, San Francisco, pp 82-115
Elshahed MS, Senko JM, Najar FZ et al. (2003) Bacterial diversity and sulfur cycling in a mes-ophilic sulfide-rich spring. Appl Environ Microbiol 69:5609-5621
Endre G, Kereszt A, Kevei Z, Mihacea S, Kaló P, Kiss GB (2002) A receptor kinase gene regulat-ing symbiotic nodule development. Nature 417:962-966
Ferguson GP, Datta A, Baumgartner J, Roop RM II, Carlson RW, Walker GC (2004) Similarity to peroxisomal-membrane protein family reveals that Sinorhizobium and Brucella BacA affect lipid-A fatty acids. Proc Natl Acad Sci USA 101:5012-5017
ffrench-Constant R, Waterfield N, Daborn P et al. (2003) Photorhabdus: towards a functional genomic analysis of a symbiont and pathogen. FEMS Microbiol Rev 26:433-456
Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J (2001) Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl Environ Microbiol 67:2873-2882
Gargas A, DePriest PT, Grube M, Tehler A (1995) Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268:1492-1495
Gaylarde CC, Gaylarde PM (2005) A comparative study of the major microbial biomass of bio-films on exteriors of buildings in Europe and Latin America. Int Biodeterior Biodegrad 55:131-139
Genre A, Chabaud M, Timmers T, Bonfante P, Barker DG (2005) Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infec-tion. Plant Cell 17:3489-3499
Gevertz D, Telang AJ, Voordouw G, Jenneman GE (2000) Isolation and characterization of strains CVO and FWKO B, two novel nitrate-reducing, sulfide-oxidizing bacteria isolated from oil field brine. Appl Environ Microbiol 66:2491-2501
Gilbert OM, Foster KR, Mehdiabadi NJ, Strassmann JE, Queller DC (2007) High relatedness maintains multicellular cooperation in a social amoeba by controlling cheater mutants. Proc Natl Acad Sci USA 104:8913-8917
Giraud E, Moulin L, Vallenet D et al. (2007) Legumes symbioses: absence of nod genes in photo-synthetic bradyrhizobia. Science 316:1307-1312
Gorbushina AA, Krumbein WE (2005) Role of microorganisms in wear down of rocks and miner-als. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions. Springer, Berlin Heidelberg New York, pp 59-84
Grassineau NV, Nisbet EG, Bickle MJ et al. (2001) Antiquity of the biological sulphur cycle: evi-dence from sulphur and carbon isotopes in 2700 million-year-old rocks of the Belingwe Belt, Zimbabwe. Proc R Soc Lond B 268:113-119
Guerrero R, Piqueras M, Berlanga M (2002) Microbial mats and the search for minimal ecosys-tems. Int Microbiol 5:177-188
Guest H (1994) Discovery of the heliobacteria. Photosynth Res 41:17-21
Güimil S, Chang H-S, Zhu T et al. (2005) Comparative transcriptomics of rice reveals an ancient pattern of response to microbial colonization. Proc Natl Acad Sci USA 102:8066-8070
Gutzmer J, Beukes NJ (1998) Earliest laterites and possible evidence for terrestrial vegetation in the Early Proterozoic. Geology 26:263-266
Haaijer SCM, Van der Welle MEW, Schmid MC, Lamers LPM, Jetten MSM, Op den Camp HJM (2006) Evidence for the involvement of betaproteobacterial Thiobacilli in the nitrate-dependent oxidation of iron sulfide minerals. FEMS Microbiol Ecol 58:439-448
Harb OS, Gao L-Y, Kwaik YA (2000) From protozoa to mammalian cells: a new paradigm in the life cycle of intracellular bacterial pathogens. Environ Microbiol 2:251-265
Harrison MJ (2005) Signaling in the arbuscular mycorrhizal symbiosis. Annu Rev Microbiol 59:19-42
Hawksworth DL (1988) The fungal partner. In: Galun M (ed) CRC handbook of lichenology. CRC Press, Boca Raton, FL., pp 35-38
He J, Baldini RL, Deziel E et al. (2004a) The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc Natl Acad Sci USA 101:2530-2535
He SY, Nomura K, Whittam TS (2004b) Type III protein secretion mechanism in mammalian and plant pathogens. Biochim Biophys Acta 1694:181-206
Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evi-dence for the early colonization of land by fungi and plants. Science 293:1129-1133
Hedges SB (2002) The origin and evolution of model organisms. Nat Rev Genet 3:838-849
Hentschel U, Steinert M, Hacker J (2000) Common molecular mechanisms of symbiosis and pathogenesis. Trends Microbiol 8:226-231
Herzenberg LA, Herzenberg LA (1989) Toward a layered immune system. Cell 59:953-954
Hirsch AM, Lum MR, Downie JA (2001) What makes the rhizobia-legume symbiosis so special? Plant Physiol 127:1484-1492
Hoeft SE, Kulp TR, Stolz JF, Hollibaugh JT, Oremland RS (2004) Dissimilatory arsenate reduction with sulfide as electron donor: experiments with Mono Lake water and isolation of strain MLMS-1, a chemoautotrophic arsenate respirer. Appl Environ Microbiol 70:2741-2747
Holland HD (2002) Volcanic gases, black smokers, and the great oxidation event. Geochim Cosmochim Acta 66:3811-3826
Hollibaugh JT, Budinoff C, Hollibaugh RA, Ransom B, Bano N (2006) Sulfide oxidation coupled to arsenate reduction by a diverse microbial community in a soda lake. Appl Environ Microbiol 72:2043-2049
Horn MA, Drake HL, Schramm A (2006) Nitrous oxide reductase genes (nosZ) of denitrifying microbial populations in soil and the earthworm gut are phylogenetically similar. Appl Environ Microbiol 72:1019-1026
Horodyski RJ, Knauth LPS (1994) Life on land in the Precambrian. Science 263:494-498
Hughes KA, Lawley B (2003) A novel Antarctic microbial endolithic community within gypsum crusts. Environ Microbiol 5:555-565
Jackson CR, Dugas SL (2003) Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol Biol 3:18 Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16 S rRNA and 16 S rRNA genes. Appl Environ Microbiol 72:1719-1728
Jargeat P, Cosseau C, Ola’h B et al. (2004) Isolation, free-living capacities, and genome structure of “Candidatus Glomeribacter gigasporarum,” the endocellular bacterium of the mycorrhizal fungus Gigaspora margarita. J Bacteriol 186:6876-6884
Karandashov V, Bucher M (2005) Symbiotic phosphate transport in arbuscular mycorrhizas. Trends Plant Sci 10:22-29
Kasting JF, Catling D (2003) Evolution of a habitable planet. Annu Rev Astron Astrophys 41:429-463
Kelly DP, Shergill JK, Lu W-P, Wood AP (1997) Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie van Leeuwenhoek 71:95-107
Kennedy M, Droser M, Mayer LM, Pevear D, Mrofka D (2006) Late Precambrian oxygenation; inception of the clay mineral factory. Science 311:1446-1449
Kistner C, Winzer T, Pitzschke A et al. (2005) Seven Lotus japonicus genes required for transcrip-tional reprogramming of the root during fungal and bacterial symbiosis. Plant Cell 17:2217-2229
Klasson L, Andersson SGE (2004) Evolution of minimal-gene-sets in host-dependent bacteria. Trends Microbiol 12:37-43
Kluge M (2002) A fungus eats a cyanobacterium: the story of the Geosiphon pyriformis endocya-nosis. Biol Environ 102B:11-14
Kooijman SALM, Hengeveld R (2005) The symbiontic nature of metabolic evolution. In: Reydon TAC, Hemerik L (eds) Current themes in theoretical biology. Springer, Berlin Heidelberg New York, pp 159-202
Kühl M, Jørgensen BB (1992) Microsensor measurements of sulfate reduction and sulfide oxida-tion in compact microbial communities of aerobic biofilms. Appl Environ Microbiol 58:1164-1174
Kurland CG, Andersson SGE (2000) Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64:786-820
Kurland CG, Collins LJ, Penny D (2006) Genomics and the irreducible nature of eukaryote cells. Science 312:1011-1014
LeVier K, Phillips RW, Grippe VK, Roop RM II, Walker GC (2000) Similar requirements of a plant symbiont and a mammalian pathogen for prolonged intracellular survival. Science 287:2492-2493
Lévy J, Bres C, Geurts R et al. (2004) A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303:1361-1364
Liengen T (1999) Environmental factors influencing the nitrogen fixation activity of free-living terrestrial cyanobacteria from a high arctic area, Spitsbergen. Can J Microbiol 45:573-581
Lloret L, Martínez-Romero E (2005) Evolución y filogenia de Rhizobium. Rev Latinoameric Microbiol 47:43-60
Lodwig EM, Hosie AHF, Bourdes A et al. (2003) Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. 422:722-726
Lutzoni F, Pagel M (1997) Accelerated evolution as a consequence of transitions to mutualism. Proc Natl Acad Sci USA 94:11422-11427
Lutzoni F, Pagel M, Reeb V (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937-940
Lynch M (2006) The origins of eukaryotic gene structure. Mol Biol Evol 23:450-468
Mancinelli RL, McKay CP (1988) The evolution of nitrogen cycling. Origins Life Evol Biosphere 18:311-325
Margulis L (1970) Origin of eukaryotic cells. Yale University Press, New Haven
Megonigal JP, Hines ME, Visscher PT (2005) Anaerobic metabolism: linkages to trace gases and aerobic processes. In: Schlesinger WH (ed) Biogeochemistry, vol 8, Treatise on geochemistry (eds Holland HD, Turekian KK). Elsevier-Pergamon, Oxford
Miyamoto T, Kawahara M, Minamisawa K (2004) Novel endophytic nitrogen-fixing clostridia from the grass Miscanthus sinensis as revealed by terminal restriction fragment length poly-morphism analysis. Appl Environ Microbiol 70:6580-6586
Molmeret M, Horn M, Wagner M, Santic M, Abu Kwaik Y (2005) Amoebae as training grounds for intracellular bacterial pathogens. Appl Environ Microbiol 71:20-28
Moran NA, Plague GR (2004) Genomic changes following host restriction in bacteria. Curr Opin Genet Dev 14:627-633
Morris CE, Monier J-M (2003) The ecological significance of biofilm formation by plant-associated bacteria. Annu Rev Phytopathol 41:429-453
Müller-Hill B (2006) What is life? The paradigm of DNA and protein cooperation at high local concentrations. Mol Microbiol 60:253-255
Neumeister B, Reiff G, Faigle M, Dietz K, Northoff H, Lang F (2000) Influence of Acanthamoeba castellanii on intracellular growth of different Legionella species in human monocytes. Appl Environ Microbiol 66:914-919
Nisbet EG, Fowler CMR (1999) Archaean metabolic evolution of microbial mats. Proc R Soc Lond B 266:2375-2382
Nisbet EG, Sleep NH (2001) The habitat and nature of early life. Nature 409:1083-1091
Nürnberger T, Brunner F, Kemmerling B, Piater L (2004) Innate immunity in plants and animals: Striking similarities and obvious differences. Immunol Rev 198:249-266
Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1099
Oremland RS, Stolz JF (2003) The ecology of arsenic. Science 300:939-944
Ormerod JG, Kimble LK, Nesbakken T, Torgersen YA, Woese CR, Madigan MT (1996) Heliophilum fasciatum gen. nov. sp. nov. and Heliobacterium gestii sp. nov.: Endospore-forming heliobacteria from rice field soils. Arch Microbiol 165:226-234
Padan E (1979) Facultative anoxygenic photosynthesis in cyanobacteria. Annu Rev Plant Physiol 30:27-40
Paerl HW, Pinckney JL (1996) A mini-review of microbial consortia: their roles in aquatic produc-tion and biogeochemical cycling. Microb Ecol 31:225-247
Parniske M (2000) Intracellular accommodation of microbes by plants: a common developmental program for symbiosis and disease? Curr Opin Plant Biol 3:320-328
Peters V, Conrad R (1995) Methanogenic and other strictly anaerobic bacteria in desert soil and other oxic soils. Appl Environ Microbiol 61:1673-1676
Phillips DA, Ferris H, Cook DR, Strong DR (2003) Molecular control points in rhizosphere food webs. Ecology 84:816-826
Pisani D, Poling L, Lyons-Weiler M, Hedges S (2004) The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol 2:1. DOI: 10.1186/1741-7007-2-1
Pitman AR, Jackson RW, Mansfield JW, Kaitell V, Thwaites R, Arnold DL (2005) Exposure to host resistance mechanisms drives evolution of bacterial virulence in plants. Curr Biol 15:2230-2235
Ramey BE, Koutsoudis M, von Bodman SB, Fuqua C (2004) Biofilm formation in plant-microbe associations. Curr Opin Microbiol 7:602-609
Raven JA (2002) The evolution of cyanobacterial symbioses. Biol Environ 102B:3-6
Raven JA, Edwards D (2001) Roots: evolutionary origins and biogeochemical significance. J Exp Bot 52:381-401
Raymond J, Segrè D (2006) The effect of oxygen on biochemical networks and the evolution of complex life. Science 311:1764-1767
Read DJ, Duckett JG, Francis R, Ligrone R, Russell A (2000) Symbiotic fungal associations in “lower” land plants. Phil Trans R Soc Lond B 355:815-831
Retallack GJ (2001) Soils of the past. An introduction to paleopedology, 2nd edn. Blackwell Science, Oxford
Retallack GJ (2003) Soils and global change in the carbon cycle over geological time. In: Drever JI (ed) Treatise on geochemistry, vol 5. Elsevier, Amsterdam, pp 581-605
Rippka R (1988) Recognition and identification of cyanobacteria. Method Enzymol 167:28-67
Roossinck MJ (2005) Symbiosis versus competition in plant virus evolution. Nat Rev Micro 3:917-924
Rudgers JA, Mattingly WB, Koslow JM (2005) Mutualistic fungus promotes plant invasion into diverse communities. Oecologia 144:463-471
Rye R, Holland HD (1998) Paleosols and the evolution of atmospheric oxygen: a critical review. Am J Sci 298:621-672
Saffo MB (2002) Themes from variation: probing the commonalities of symbiotic associations. Integr Comp Biol 42:291-294
Saikkonen K, Wäli P, Helander M, Faeth SH (2004) Evolution of endophyte-plant symbioses. Trends Plant Sci 9:275-280
Sánchez-Baracaldo P, Hayes PK, Blank CE (2005) Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach. Geobiology 3:145-165
Scholl E, Thorne J, McCarter J, Bird DMcK (2003) Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol 4:R39
Schulz B, Boyle C (2005) The endophytic continuum. Mycol Res 109:661-686 Schüßler A (2000) Glomus claroideum forms an arbuscular mycorrhiza-like symbiosis with the hornwort Anthoceros punctatus. Mycorrhiza 10:15-21
Schüßler A (2002) Molecular phylogeny, taxonomy, and evolution of Geosiphon pyriformis and arbuscular mycorrhizal fungi. Plant Soil 244:75-83
Schüßler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota: phylog-eny and evolution. Mycol Res 105:1413-1421
Selosse M-A, Le Tacon F (1998) The land flora: a phototroph-fungus partnership? Trends Ecol Evolut 13:15-20
Shen Y, Buick R, Canfield DE (2001) Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410:77-81
Sprenger W, van Belzen M, Rosenberg J, Hackstein J, Keltjens J (2000) Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int J Syst Evol Microbiol 50:1989-1999
Stacey G, Libault M, Brechenmacher L, Wan J, May GD (2006) Genetics and functional genomics of legume nodulation. Curr Opin Plant Biol 9:110-121
Stevenson AK, Kimble LK, Woese CR, Madigan MT (1997) Characterization of new phototrophic heliobacteria and their habitats. Photosynth Res 53:1-12
Stracke S, Kistner C, Yoshida S et al. (2002) A plant receptor-like kinase required for both bacte-rial and fungal symbiosis. Nature 417:959-962
Strobel G (2006) Muscodor albus and its biological promise. J Indust Microbiol Biotechnol 33:514-522
Szczyglowski K, Amyot L (2003) Symbiosis, inventiveness by recruitment? Plant Physiol 131:935-940
Tamas I, Klasson L, Canback B et al. (2002) 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:2376-2379
Teske A, Dhillon A, Sogin ML (2003) Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation. Biol Bull 204:186-191
Thompson JN, Nuismer SL, Gomulkiewicz R (2002) Coevolution and maladaptation. Integr Comp Biol 42:381-387
Tiedje J, Sexstone A, Parkin T, Revsbech N (1984) Anaerobic processes in soil. Plant Soil 76:197-212
Tokuda G, Yamaoka I, Noda H (2000) Localization of symbiotic clostridia in the mixed segment of the termite Nasutitermes takasagoensis (Shiraki). Appl Environ Microbiol 66:2199-2207
Tomov AT, Tsvetkova ED, Tomova IA, Michailova LI, Kassovski VK (1999) Persistence and multiplication of obligate anaerobe bacteria in amoebae under aerobic conditions. Anaerobe 5:19-23
Towe KM, Catling D, Zahnle K, McKay C (2002) The problematic rise of Archean oxygen. Science 295:1419-1421
Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki Y (2006) Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440:516-519
Velicer GJ (2003) Social strife in the microbial world. Trends Microbiol 11:330-337
Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434:1011-1014
Waller F, Achatz B, Baltruschat H et al. (2005) The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield. Proc Natl Acad Sci USA 102:13386-13391
Warscheid T, Braams J (2000) Biodeterioration of stone: a review. Int Biodeterior Biodegrad 46:343-368
Watanabe Y, Martini JEJ, Ohmoto H (2000) Geochemical evidence for terrestrial ecosystems 2.6 billion years ago. Nature 408:574-578
Weerasinghe RR, Bird DMcK, Allen NS (2005) Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus. Proc Natl Acad Sci USA 102:3147-3152
Wellman CH, Osterloff PL, Mohiuddin U (2003) Fragments of the earliest land plants. Nature 425:282-285
Wernegreen J, Moran N (1999) Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol Biol Evol 16:83-97
Winiecka-Krusnella J, Linder E (2001) Bacterial infections of free-living amoebae. Res Microbiol 152:613-619
Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99:8742-8747
Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1:8
Wren BW (2000) Microbial genome analysis: insights into virulence, host adaptation and evolu-tion. Nat Rev Genet 1:30-39
Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE (2000) Molecular evidence for the early evolution of photosynthesis. Science 289:1724-1730
Yoneyama K, Takeuchi Y, Yokota T (2001) Production of clover broomrape seed germination stimulants by red clover root requires nitrate but is inhibited by phosphate and ammonium. Physiol Planta 112:25-30
Young IM, Crawford JW (2004) Interactions and self-organization in the soil-microbe complex. Science 304:1634-1637
Young IM, Ritz K (2000) Tillage, habitat space and function of soil microbes. Soil Tillage Res 53:201-213
Yuan X, Xiao S, Taylor TN (2005) Lichen-like symbiosis 600 million years ago. Science 308:1017-1020
Zhu J, Oger PM, Schrammeijer B, Hooykaas PJJ, Farrand SK, Winans SC (2000) The bases of crown gall tumorigenesis. J Bacteriol 182:3885-3895
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Dion, P. (2008). Reconstructing Soil Biology. In: Nautiyal, C.S., Dion, P. (eds) Molecular Mechanisms of Plant and Microbe Coexistence. Soil Biology, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75575-3_3
Download citation
DOI: https://doi.org/10.1007/978-3-540-75575-3_3
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75574-6
Online ISBN: 978-3-540-75575-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)