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Original Articles

Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulations—a case study from tallgrass prairie

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Pages 1177-1194 | Accepted 07 Oct 2005, Published online: 27 Jan 2017

LITERATURE CITED

  • Allen RG. 2000. Using the FAO-56 dual crop coefficient method over an irrigated region as part of an evapotranspiration intercomparison study. Journal of Hydrology 229:27–41.
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402.
  • Amann RI, Ludwig W, Schkeifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59:143–169.
  • Avis PG, McLaughlin DJ, Dentinger BC, Reich PB. 2003. Long-term increase in nitrogen supply alters above- and below-ground ectomycorrhizal communities and increases the dominance of Russula spp. in a temperate oak savanna. New Phytol 160:239–253.
  • Baltanas A. 1992. On the use of some methods for the estimation of species richness. Oikos 65:484–492.
  • Bentivenga SP, Hetrick BAD. 1992a. The effect of prairie management practices on mycorrhizal symbiosis. Mycologia 84:522–527.
  • ———, ———. 1992b. Seasonal and temperature effects on mycorrhizal activity and dependence of cool- and warm-season tallgrass prairie grases. Can J Bot 70:1596–1602.
  • Borneman J, Hartin RJ. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360.
  • Bowden RD, Davidson E, Savage K, Arabia C, Steudler P. 2004. Chronic nitrogen additions reduce total soil respiration in temperate forest soils at the Harvard Forest. For Ecol Manag 196:43–56.
  • Bowen GD, Rovira AD. 1991. The photosphere—the hidden half of the hidden half. In: Waisel Y, Eshel A, Kafkafi U, eds. The hidden half. New York: Marcel Dekker. p 641–669.
  • Chandler DP, Fredrickson JK, Brockman FJ. 1997. Effect of PCR template concentration on the composition and distribution of total community rDNA clone libraries. Mol Ecol 6:475–482.
  • Claridge AW, Barry SC, Cork SJ, Trappe JM. 2000. Diversity and habitat relationships of hypogeous fungi. II. Factors influencing the occurrence and number of taxa. Biodiversity and conservation 9:175–199.
  • Compton JE, Watrud LS, Porteous LA, DeGrood S. 2004. Response of soil microbial biomass and community composition to chronic nitrogen additions at Harvard Forest. For Ecol Manag 196:143–158.
  • Cooke RC, Rayner ADM. 1984. Ecology of saprobic fungi. London: Longman. 415 p.
  • Cornejo FH, Varela A, Wright SJ. 1994. Tropical forest litter decomposition under seasonal drought: nutrient release, fungi and bacteria. Oikos 70:183–190.
  • Curl EA, Truelove B. 1986. The rhizosphere. New York: Springer Verlag. 228 p.
  • Domsch KH, Gams W, Anderson T-H. 1980. Compendium of soil fungi fungi. New York: Academic Press. 859 p.
  • Easterling DR, Meehl GA, Parmesan C, Chagnon SA, Karl TR, Mearns LO. 2000. Climate extremes: observations, modeling, and impacts. Science 289:2068–2074.
  • Egerton-Warburton LM, Allen EB. 2000. Shifts in arbuscular mycorrhizal communities along an anthropogenic nitrogen deposition gradient. Ecol Appl 10:484–496.
  • Eom A-H, Hartnett DC, Wilson GT, H. FDA. 1999. The effect of fire, mowing and fertilizer amendment on arbuscular mycorrhizas in tallgrass prairie. American Midland Naturalist 142:55–70.
  • Epstein HE, Lauenroth WK, Burke IC, Coffin DP. 1996. Ecological responses of dominant grasses along two climatic gradients in the Great Plains of the United States. Journal of Vegetation Science 7:777–788.
  • Farrelly V, Rainey FA, Stackebrandt E. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 91:2798–2801.
  • Fenn ME, Poth MA, Aber JD, Baron JS, Borman BT, Johnson DW, Lemly AD, McNulty SG, Ryan DF, Stottlemeyr R. 1998. Nitrogen excess in North American ecosystems: predisposing factors, ecosystem responses and management strategies. Ecol Appl 8:706–733.
  • Fog K. 1988. The effect of added nitrogen on the rate of decomposition of organic matter. Biol Rev 63:433–462.
  • Franklin RB, Mills AL. 2003. Multiscale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbial Ecology 44:335–346.
  • Frey SD, Knorr M, Parrent JL, Simpson RT. 2004. Chronic nitrogen enrichment affects the structure and function of the soil microbial community in temperate hardwood and pine forests. For Ecol Manag 196:159–171.
  • Galloway JN, Cowling EB. 2002. Reactive nitrogen and the world: 200 years of change. Ambio 31:64–71.
  • Gray JP, Herwig RP. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62:4049–4059.
  • Groisman PY, Karl TR, Easterling DA, Knight RW, Jamason PF, Hennessy KJ, Suppiah R, Page CM, Wibig J, Fortuniak K, Razuvaev VN, Douglas A, Forland E, Zhai P. 1999. Changes in the probability of heavy precipitation: important indicators of climatic change. Climatic Change 42:243–283.
  • Hawksworth DL. 2001. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432.
  • ———, Rossmann AY. 1997. Where are all the undescribed fungi? Phytopathology 87:888–891.
  • Hooper DU, Johnson L. 1999. Nitrogen limitation in dryland ecosystems: responses to geographical and temporal variation in precipitation. Biogeochemistry 46:247–293.
  • Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774.
  • Hunt J, Boddy L, Randerson PF, Rogers HJ. 2004. An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils. Microbial Ecology 47:385–395.
  • Jensen KD, Beier C, Michelsen A, Emmett BA. 2003. Effects of experimental drought on microbial processes in two temperate heathlands at contrasting water conditions. Applied Soil Ecology 24:165–176.
  • Johnson NC. 1993. Can fertilization of soil select less mutualistic mycorrhizae? Ecol Appl 3:749–757.
  • Jumpponen A. 2005. Soil fungal communities underneath willow canopies on a primary successional glacier forefront: rDNA sequence results can be affeted by primer selection and chimeric data. Microbial Ecology (In press).
  • ———, Trappe JM. 1998. Dark-septate root endophytes: a review with special reference to facultative biotrophic symbiosis. New Phytol 140:295–310.
  • Kent AD, Triplett EW. 2002. Microbial communities and their interactions in soil and rhizosphere ecosystems. Annual Review of Microbiology 56:211–236.
  • Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT. 2004. Methods for studying soil microbial diversity. J Microbiol Meth 58:169–188.
  • Knapp AK, Fay PA, Collins SL, Smith MD, Carlisle JD, Harper CW, Danner BT, Lett MS, McCarron JK. 2002. Rainfall variability, carbon cycling, and plant species diversity in a mesic grassland. Science 298:2202–2205.
  • Kochy M, Wilson SD. 2001. Nitrogen deposition and forest expansion in the northern Great Plains. J Ecol 89:807–817.
  • Kohn LM, Stasovski E. 1990. The mycorrhizal status of plants at Alexandra Fjord, Ellesmere Island, Canada, a high arctic site. Mycologia 82:23–35.
  • Koske RE, Gemma JN, Jackson N. 1997. Mycorrhizal fungi associated with three species of turfgrass. Can J Bot 75:320–332.
  • Kowalchuk GA, Gerards S, Woldendorp JW. 1997. Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis. Appl Environ Microbiol 63:3858–3865.
  • Lauenroth WK, Sala OE. 1992. Long-term forage production of North American shortgrass steppe. Ecol Appl 2:397–403.
  • Lilleskov EA, Fahey TJ, Horton TR, Lovett GM. 2002a. Belowground ectomycorrhizal community change over a nitrogen deposition gradient in Alaska. Ecology 83:104–115.
  • ———, ———, Lovett GM. 2001. Ectomycorrhizal fungal aboveground community change over an atmospheric nitrogen deposition gradient. Ecol Appl 11:2001.
  • ———, Hobbie EA, Fahey TJ. 2002b. Ectomycorrhizal fungal taxa differing in response to nitrogen deposition also differ in pure culture organic nitrogen use and natural abundance of nitrogen isotopes. New Phytol 154:219–231.
  • Lugo MA, González Maza ME, Cabello MN. 2003. Arbuscular mycorrhizal fungi in a mountain grassland II: Seasonal variation of colonization studied, along with its relation to grazing and metabolic host type. Mycologia 95:407–415.
  • Lutgen ER, Muir-Clairmont D, Graham J, Rillig MC. 2003. Seasonality of arbuscular mycorrhizal hyphae and glomalin in a western Montana grassland. Plant Soil 257:71–83.
  • Lynch JM, Whipps JM. 1990. Substrate flow in the rhizosphere. Plant Soil 129:1–10.
  • Maddison DR, Maddison WP. 2001. MacClade 4: Analysis of phylogeny and character evolution. Version 4.06. Sunderland, Massachusetts: Sinauer Associates.
  • Maddison WP, Slatkin M. 1991. Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution 45:1184–1197.
  • Maidak BL, Cole JR, Parker CT, Jr., Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR. 1999. A new version of the RDP (Ribosomal Database Project). Nucl Acids Res 27:171–173.
  • Martin AP. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68:3673–3682.
  • McCulley RL, Burke IC. 2004. Microbial community composition across the great Plains: landscape versus regional variability. Soil Science Society of America Journal 68:106–115.
  • McKune B. 1991. Multivariate analysis on the PC-ORD system. Corvallis, Oregon: Oregon State University.
  • Mearns LO, Rosenzweig C, Goldberg R. 1997. Mean and variance change in climate scenarios: Methods, agricultural applications, and measures of uncertainty. Climatic Change 35:367–396.
  • Mullins TD, Britschgl TB, Krest RL, Giovannoni SJ. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bactetioplankton communities. Limnology and Oceanography 40:148–158.
  • Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734–740.
  • Palmer MW. 1990. The estimation of species richness by extrapolation. Ecology 71:1195–1198.
  • Peter M, Ayer F, Egli S. 2001. Nitrogen addition in a Norway spruce stand altered macromycete sporocarp production and below-ground ectomycorrhizal species composition. New Phytol 149:311–325.
  • Rambelli A, Persiani AM, Maggi O, Lunghini D, Onofri S, Riess S, Dowgiallo G, Puppi G. 1983. Comparative studies on microfungi in tropical ecosystems. Rome: UNESCO. p.
  • Reysenbach A, Giver LJ, Wickham GS, Pace NR. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417–3418.
  • Saiya-Cork KR, Sinabaugh RL, Zak DR. 2002. The effects of long term nitrogen deposition on extracelular enzyme activity in an Acer saccharum forest soil. Soil Biol Biochem 34:1309–1315.
  • Sambrook J. 1989. Molecular cloning—a laboratory manual. 2nd ed. New York: Cold Spring Laboratory Press. 999 p.
  • Sanders IR, Fitter AH. 1992. The ecology and functioning of vesicular-arbuscular mycorrhizas in co-existing grassland species. I. Seasonal patterns of mycorrhizal occurrence and morphology. New Phytol 120:525–533.
  • SAS. 1989. SAS/STAT User’s Guide, Version 6. 4th ed. Vol. 1. Cary, North Carolina: SAS Institute Inc. 943 p.
  • Schadt CW, Martin AW, Lipson DA, Schmidt SK. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359–1361.
  • Shannon CE, Weaver W. 1949. The mathematical theory of communication. Urbana, Illinois: University of Illinois Press. 116 p.
  • Sinabaugh RL, Carreiro MM, Repert DA. 2002. Allocation of extracellular enzymatic activity in relation to litter composition, N deposition, and mass loss. Biogeochemistry 60:1–24.
  • Smit E, Leeflang P, Glandorf B, van Elsas JD, Wernars K. 1999. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621.
  • Smith SE, Read DJ. 1997. Mycorrhizal symbiosis. London: Academic Press. 605 p.
  • Sneh B, Burpee L, Ogoshi A. 1991. Identification of Rhizoctonia species. St. Paul, Minnesota: APS Press. 133 p.
  • Suzuki MT, Giovannoni SJ. 1996. Bias caused by template annealing in the amplification mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630.
  • Swofford DL. 2001. PAUP*, phylogenetic analysis using parsimony (and other methods). Version 4. Sunderland, Massachusetts: Sinauer Associates.
  • Söderberg KH, Probanza A, Jumpponen A, Bååth E. 2004. The microbial community in the rhizosphere determined by community-level physiological profiles (CLPP) and direct soil- and cfu-PLFA techniques. Applied Soil Ecology 25:135–145.
  • Trevors JT. 1998. Bacterial biodiversity in soil with an emphasis on chemically contaminated soil. Water, Air and Soil Pollution 101:45–67.
  • Trudell S, Rygiewicz PT, Edmunds RL. 2003. Nitrogen and carbon stable isotope abundances support the myco-heterotrophic nature and host specificity of certain achlorophyllous plants. New Phytol 160:391–401.
  • van Elsas JD, Duarte GF, Keijzer-Wolters A, Smit E. 2000. Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Meth 43:133–151.
  • Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW. 2002a. Extensive fungal diversity in plant roots. Science 295:2051.
  • ———, Husband R, Daniell TJ, Watson IJ, Duck JM, Fitter AH, Young JPW. 2002b. Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Mol Ecol 11:1555–1564.
  • Vitousek P, Aber J, Howart R, Likens G, Matson P, Schindler D, Schlesinger W, Tilman D. 1997a. Human alteration of the global nitrogen cycle: sources and consequences. Ecol Appl 7:737–750.
  • Vitousek PM, Mooney HA, Lubchenco J, Melillo JM. 1997b. Human domination of earth’s ecosystems. Science 277:494–499.
  • von Wintzingerode F, Göbel UB, Stackebrandt E. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 21:213–229.
  • Wallenda T, Kottke I. 1998. Nitrogen deposition and ectomycorrhizas. New Phytol 139:169–187.
  • Ward DM, Bateson MM, Weller R, Ruff-Roberts AL. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Advences in Microbial Ecology 12:219–286.
  • Wiklund K, Nilsson L-O, Jacobsson S. 1995. Effect of irrigation, fertilization, and artificial drought on basidioma production in a Norway spruce stand. Can J Bot 73:200–208.
  • Wilkinson SC, Anderson JM, Scardelis SP, Tisiafouli M, Taylor A, Wolters V. 2002. PLFA profiles of microbial communities in decomposing litters subjected to moisture stress. Soil Biol Biochem 34:189–200.
  • Wilson GWT, Hartnett DC. 1998. Interspecific variation in plant responses to mycorrhizal colonization in tallgrass prairie. Am J Bot 85:1732–1738.
  • Zheng D, Alm EW, Stahl DA, Raskin L. 1996. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62:4504–4513.

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