Abstract
Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.
Similar content being viewed by others
References
RD Bardgett PJ Hobbs A Frostegård (1996) ArticleTitleChanges in soil fungal:bacterial biomass ratios following reductions in the intensity of management of an upland grassland Biol Fertil Soils 22 261–264
RD Bardgett RD Lovell PJ Hobbs SC Jarvis (1999) ArticleTitleSeasonal changes in soil microbial communities along a fertility gradient of temperate grasslands Soil Biol Biochem 31 1021–1030 Occurrence Handle1:CAS:528:DyaK1MXjsFCnu7w%3D
RD Bardgett JL Mawdsley S Edwards PJ Hobbs JS Rodwell WJ Davies (1999) ArticleTitlePlant species and nitrogen effects on soil biological properties of temperate upland grasslands Funct Ecol 13 650–660 Occurrence Handle10.1046/j.1365-2435.1999.00362.x
RD Bardgett E McAlister (1999) ArticleTitleThe measurement of soil fungal:bacterial biomass ratios as an indicator of ecosystem self-regulation in temperate meadow grasslands Biol Fertil Soils 29 282–290 Occurrence Handle10.1007/s003740050554
DA Bossio KM Scow N Gunapala KJ Graham (1998) ArticleTitleDeterminants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles Microb Ecol 36 1–12 Occurrence Handle10.1007/s002489900087 Occurrence Handle1:CAS:528:DyaK1cXksVOrt78%3D Occurrence Handle9622559
NC Brady RR Weil (2002) The Nature and Properties of Soils Prentice-Hall Upper Saddle River, NJ, USA 592–637
JM Bremner (1996) Nitrogen—total DL Sparks AL Page PA Helmke RH Loeppert PN Soltanpour MA Tabatabai CT Johnston ME Sumner (Eds) Methods of Soil Analysis: Part 3, Chemical Methods Soil Science Society of America Madison, WI 1085–1121
E Brodie S Edwards N Clipson (2002) ArticleTitleBacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem Microb Ecol 44 260–270 Occurrence Handle10.1007/s00248-002-2012-1 Occurrence Handle1:CAS:528:DC%2BD38XovFyrtro%3D Occurrence Handle12209255
E Brodie S Edwards N Clipson (2003) ArticleTitleSoil fungal community structure in a temperate upland grassland soil FEMS Microbiol Ecol 45 105–114 Occurrence Handle1:CAS:528:DC%2BD3sXlsVaju78%3D
DH Buckley TM Schmidt (2003) ArticleTitleDiversity and dynamics of microbial communities in soils from agro-ecosystems Environ Microbiol 5 441–452 Occurrence Handle10.1046/j.1462-2920.2003.00404.x Occurrence Handle12755711
CD Clegg K Ritz BS Griffiths (1998) ArticleTitleBroad-scale analysis of soil microbial community DNA from upland grasslands Antonie van Leeuwenhoek 73 9–14 Occurrence Handle10.1023/A:1000545804190 Occurrence Handle1:CAS:528:DyaK1cXjsVaqtLY%3D Occurrence Handle9602274
CD Clegg K Ritz BS Griffiths (2000) ArticleTitle%G + C profiling and cross-hybridisation of microbial DNA reveals great variation in below-ground community structure in UK upland grasslands Appl Soil Ecol 14 125–134 Occurrence Handle10.1016/S0929-1393(00)00045-7
LD Crosby CS Criddle (2003) ArticleTitleUnderstanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity BioTechniques 34 790–802 Occurrence Handle1:CAS:528:DC%2BD3sXivFajsr8%3D Occurrence Handle12703304
M Egert MW Friedrich (2003) ArticleTitleFormation of pseudo-terminal restriction ribotypes, a PCR-related bias affecting terminal restriction length polymorphism analysis of microbial community structure Appl Environ Microbiol 69 2555–2562 Occurrence Handle1:CAS:528:DC%2BD3sXjslOls78%3D Occurrence Handle12732521
GB Fogel CR Collins J Li CF Brunk (1999) ArticleTitleProkaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population Microb Ecol 38 93–113 Occurrence Handle10.1007/s002489900162 Occurrence Handle1:CAS:528:DyaK1MXltF2qu7c%3D Occurrence Handle10441703
M Gardes TD Bruns (1993) ArticleTitleITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts Mol Ecol 2 113–118 Occurrence Handle1:CAS:528:DyaK3sXlslOmsro%3D Occurrence Handle8180733
Gardiner, MJ, Radford, T (1980) Soil survey bulletin number 36: Soil associations of Ireland and their land use potential. National Soil Survey of Ireland, An Foras Talúntais (The Agricultural Institute), Dublin, Ireland
A Gastine M Scherer-Lorenzen PW Leadley (2003) ArticleTitleNo consistent effects of plant biodiversity on root biomass, soil biota and soil abiotic conditions in temperate grassland communities Appl Soil Ecol 24 101–111 Occurrence Handle10.1016/S0929-1393(02)00137-3
A Gelsomino AC Keijzer-Wolters G Cacco JD Elsas Particlevan (1999) ArticleTitleAssessment of bacterial community structure in soil by polymer-ase chain reaction and denaturing gradient gel electrophoresis J Microbiol Methods 38 1–15 Occurrence Handle10.1016/S0167-7012(99)00054-8 Occurrence Handle1:CAS:528:DyaK1MXmtVGmsLs%3D Occurrence Handle10520580
InstitutionalAuthorNameGeological Survey of Ireland (2000) Geology of Kildare–Wicklow (Sheet 16) 1:100,000 Geological Survey of Ireland Ballsbridge, Dublin, Ireland
A Gollotte D Tuinen Particlevan D Atkinson (2004) ArticleTitleDiversity of arbuscular mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and Lolium perenne in a field experiment Mycorrhiza 14 111–117 Occurrence Handle10.1007/s00572-003-0244-7 Occurrence Handle12768382
SJ Grayston S Wang CD Campbell AC Edwards (1998) ArticleTitleSelective influence of plant species on microbial diversity in the rhizosphere Soil Biol Biochem 30 369–378 Occurrence Handle10.1016/S0038-0717(97)00124-7 Occurrence Handle1:CAS:528:DyaK1cXhvFWrsro%3D
SJ Grayston GS Griffith JL Mawdsley CD Campbell RD Bardgett (2001) ArticleTitleAccounting for variability in soil microbial communities of temperate upland grassland ecosystems Soil Biol Biochem 33 533–551 Occurrence Handle10.1016/S0038-0717(00)00194-2 Occurrence Handle1:CAS:528:DC%2BD3MXis1aks70%3D
SJ Grayston CD Campbell RD Bardgett JL Mawdsley CD Clegg K Ritz BS Griffiths JS Rodwell SJ Edwards WJ Davies DJ Elston P Millard (2004) ArticleTitleAssessing 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 Occurrence Handle10.1016/S0929-1393(03)00098-2
PM Groffman P Eagan WM Sullivan JL Lemunyon (1996) ArticleTitleGrass species and soil type effects on microbial biomass and activity Plant Soil 183 61–67 Occurrence Handle10.1007/BF02185565 Occurrence Handle1:CAS:528:DyaK28Xnt1aksL0%3D
K Hedlund I Santa Regina WH Putten ParticleVan der J Lepš T Díaz GW Korthals S Lavorel VK Brown D Gormsen SR Mortimer C Rodríguez Barrueco J Roy P Smilauer M Smilauerová C Dijk ParticleVan (2003) ArticleTitlePlant species diversity, plant biomass and responses of the soil community on abandoned land across Europe: idiosyncrasy or above–belowground time lags Oikos 103 45–58 Occurrence Handle10.1034/j.1600-0706.2003.12511.x
PA Helmke DL Sparks (1996) Lithium, sodium, potassium, rubidium, and cesium DL Sparks AL Page PA Helmke RH Loeppert PN Soltanpour MA Tabatabai CT Johnston ME Sumner (Eds) Methods of Soil Analysis: Part 3, Chemical Methods Soil Science Society of America Madison, WI 551–574
GT Hill NA Mitkowski L Aldrich-Wolfe LR Emele DD Jurkonie A Ficke S Maldonado-Ramirez ST Lynch EB Nelson (2000) ArticleTitleMethods for assessing the composition and diversity of soil microbial communities Appl Soil Ecol 15 25–36 Occurrence Handle10.1016/S0929-1393(00)00069-X
DU Hooper PM Vitousek (1997) ArticleTitleThe effects of plant composition and diversity on ecosystem processes Science 277 1302–1305 Occurrence Handle10.1126/science.277.5330.1302 Occurrence Handle1:CAS:528:DyaK2sXlslans7c%3D
L Innes PJ Hobbs RD Bardgett (2004) ArticleTitleThe impacts of individual plant species on rhizosphere microbial communities in soils of different fertility Biol Fertil Soils 40 7–13 Occurrence Handle10.1007/s00374-004-0748-0
D Johnson RE Booth AS Whiteley MJ Bailey DJ Read JP Grime JR Leake (2003) ArticleTitlePlant community composition affects the biomass, activity and diversity of microorganisms in limestone grassland soil Eur J Soil Biol 54 671–677
MJ Johnson KY Lee KM Scow (2003) ArticleTitleDNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities Geoderma 114 279–303 Occurrence Handle10.1016/S0016-7061(03)00045-4
RHG Jongman CJF Braak Particleter OFR Tongeren Particlevan (1995) Data Analysis in Community and Landscape Ecology Cambridge University Press Cambridge 91–173
A Jumpponen (2003) ArticleTitleSoil fungal community assembly in a primary successional glacier forefront ecosystem as inferred from rDNA sequence analysis New Phytol 158 569–578 Occurrence Handle10.1046/j.1469-8137.2003.00767.x
N Kennedy E Brodie J Connolly N Clipson (2004) ArticleTitleImpact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms Environ Microbiol 6 1070–1080 Occurrence Handle10.1111/j.1462-2920.2004.00638.x Occurrence Handle1:CAS:528:DC%2BD2cXptVemtr8%3D Occurrence Handle15344932
D Knudsen D Beegle (1988) Recommended phosphorus tests WC Dahnke (Eds) Recommended Soil Tests Procedures for the North Central Region: Bulletin Number 499 (revised) North Dakota Agricultural Experiment Station Fargo, ND 12–15
DJ Lane (1991) 16S/23S rRNA sequencing E Stackebrandt M Goodfellow (Eds) Nucleic Acid Techniques in Bacterial Systematics John Wiley & Sons Chichester 115–175
W-T Liu TL Marsh H Cheng LJ Forney (1997) ArticleTitleCharacterization of microbial diversity by determining terminal restriction ribotype length polymorphisms of genes encoding 16S rRNA Appl Environ Microbiol 63 4516–4522 Occurrence Handle1:CAS:528:DyaK2sXnt12ntbs%3D Occurrence Handle9361437
T Lueders MW Friedrich (2003) ArticleTitleEvaluation of PCR amplification bias by terminal restriction ribotype length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts Appl Environ Microbiol 69 320–326 Occurrence Handle10.1128/AEM.69.1.320-326.2003 Occurrence Handle1:CAS:528:DC%2BD3sXkvValsw%3D%3D Occurrence Handle12514011
JM Lynch JM Whipps (1990) ArticleTitleSubstrate flow in the rhizosphere Plant Soil 129 1–10 Occurrence Handle10.1007/BF00011685 Occurrence Handle1:CAS:528:DyaK3MXotVCjtQ%3D%3D
L Marilley M Aragno (1999) ArticleTitlePhylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots Appl Soil Ecol 13 127–136 Occurrence Handle10.1016/S0929-1393(99)00028-1
P Marschner CH Yang R Lieberei DE Crowley (2001) ArticleTitleSoil and plant specific effects on bacterial community composition in the rhizosphere Soil Biol Biochem 33 1437–1445 Occurrence Handle10.1016/S0038-0717(01)00052-9 Occurrence Handle1:CAS:528:DC%2BD3MXmtFSlsrk%3D
AE McCaig LA Glover JI Prosser (2001) ArticleTitleNumerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns Appl Environ Microbiol 67 4554–4559 Occurrence Handle10.1128/AEM.67.10.4554-4559.2001 Occurrence Handle1:CAS:528:DC%2BD3MXns1WisLs%3D Occurrence Handle11571155
TP McGonigle AH Fitter (1990) ArticleTitleEcological specificity of vesicular arbuscular mycorrhizal associations Mycol Res 94 120–122 Occurrence Handle10.1016/S0953-7562(09)81272-0
Morgan, MF (1941) Chemical soil diagnosis by the universal soil testing system. In: Connecticut Agricultural Experimental Station Bulletin Number 450
AM O'Sullivan (1982) The lowland grasslands of Ireland J White (Eds) Studies on Irish Vegetation Royal Dublin Society Dublin
MF Polz CM Cavanaugh (1998) ArticleTitleBias in template-to-product ratios in multitemplate PCR Appl Environ Microbiol 64 3724–3730 Occurrence Handle1:CAS:528:DyaK1cXms1entrc%3D Occurrence Handle9758791
K Ritz JW McNicol N Nunan S Grayston P Millard D Atkinson A Gollotte D Habeshaw B Boag CD Clegg BS Griffiths RE Wheatley LA Glover AE McCaig JI Prosser (2004) ArticleTitleSpatial structure in soil chemical and microbiological properties in an upland grassland FEMS Microbiol Ecol 49 191–205 Occurrence Handle1:CAS:528:DC%2BD2cXlsl2iur0%3D
JS Rodwell (1992) British Plant Communities: Grasslands and Montane Communities Cambridge University Press Cambridge
AD Rovira (1969) ArticleTitlePlant root exudates Bot Rev 35 35–37 Occurrence Handle1:CAS:528:DyaF1MXltFWksL8%3D
ME Schutter JM Sandeno RP Dick (2001) ArticleTitleSeasonal, soil type, and alternative management influences on microbial communities of vegetable cropping systems Biol Fertil Soils 34 397–410 Occurrence Handle1:CAS:528:DC%2BD3MXosFGntrg%3D
GP Sparling PB Tinker (1978) ArticleTitleMycorrhizal infection in pennine grassland. I. Levels of infection in the field J Appl Ecol 15 943–950
J Steer JA Harris (2000) ArticleTitleShifts in the microbial community in rhizosphere and non-rhizosphere soils during the growth of Agrostis stolonifera Soil Biol Biochem 32 869–878 Occurrence Handle10.1016/S0038-0717(99)00219-9 Occurrence Handle1:CAS:528:DC%2BD3cXktFWjt74%3D
A Thalmann (1968) ArticleTitleZur methodik ber Bestimmung der dehydrogenaseaktivität im Boden mittels triphenyltetrazoliumchlorid (TTC) Landwirtsch Forsch 21 249–258 Occurrence Handle1:CAS:528:DyaF1MXksVyksrw%3D
GW Thomas (1996) Soil pH and soil acidity DL Sparks AL Page PA Helmke RH Loeppert PN Soltanpour MA Tabatabai CT Johnston ME Sumner (Eds) Methods of Soil Analysis: Part 3, Chemical Methods Soil Science Society of America Madison, WI 475–490
F Wintzingerode Particlevan UB Gobel E Stackebrandt (1997) ArticleTitleDetermination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol Rev 21 213–229
P Vandenkoornhuyse KP Ridgway IJ Watson AH Fitter JPW Young (2003) ArticleTitleCo-existing grass species have distinctive arbuscular mycorrhizal communities Mol Ecol 12 3085–3095 Occurrence Handle10.1046/j.1365-294X.2003.01967.x Occurrence Handle1:STN:280:DC%2BD3srltFChtw%3D%3D Occurrence Handle14629388
DA Wardle (1992) ArticleTitleA comparative assessment of factors which influence microbial biomass carbon and nitrogen levels in soil Biol Rev 67 321–358
DA Wardle KI Bonner KS Nicholson (1997) ArticleTitleBiodiversity and plant litter: experimental evidence which does not support the view that enhanced species richness improves ecosystem function Oikos 79 247–258
G Webster TM Embley JI Prosser (2002) ArticleTitleGrassland management regimens reduce small-scale heterogeneity and species diversity of β-proteobacterial ammonia oxidizer populations Appl Environ Microbiol 68 20–30 Occurrence Handle10.1128/AEM.68.1.20-30.2002 Occurrence Handle1:CAS:528:DC%2BD38Xjt1Wiuw%3D%3D Occurrence Handle11772604
KM Westover AC Kennedy SE Kelley (1997) ArticleTitlePatterns of rhizosphere microbial community structure associated with co-occurring plant species J Ecol 85 863–873
TJ White T Bruns S Lee J Taylor (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics MA Innis DH Gelfand JJ Sninsky TJ White (Eds) PCR Protocols: A Guide to Methods and Applications Academic Press New York 315–322
BL Williams SJ Grayston EJ Reid (2000) ArticleTitleInfluence of synthetic sheep urine on the microbial biomass, activity and community structure in two pastures in the Scottish uplands Plant Soil 225 175–185 Occurrence Handle10.1023/A:1026595309349 Occurrence Handle1:CAS:528:DC%2BD3MXotVGitA%3D%3D
YG Zhu AS Laidlaw P Christie MER Hammond (2000) ArticleTitleThe specificity of arbuscular mycorrhizal fungi in perennial ryegrass–white clover pasture Agric Ecosyst Environ 77 211–218
Acknowledgments
Part of this work was supported by an Environmental Protection Agency contributory scholarship under the Environmental Research Technological Development and Innovation (ERTDI) program. We thank Dr. John Connolly of Statistics Department, UCD for statistical advice and guidance, and John Flynn for technical assistance.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kennedy, N., Edwards, S. & Clipson, N. Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands. Microb Ecol 50, 463–473 (2005). https://doi.org/10.1007/s00248-005-0256-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-005-0256-2