Abstract
The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.
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Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Atlas RM, Horowitz A, Krichevsky M, Bej AK (1991) Response of microbial populations to environmental disturbance. Microb Ecol 22:249–256
Baath E, Frostegard A, Pennanen T, Fritze H (1995) Microbial community structure and pH response in relation to soil organic-matter quality in wood-ash fertilized, clear-cut or burned coniferous forest soils. Soil Biol Biochem 27:229–240
Bloem J, Ruiter PCd, Koopman GJ, Lebbink G, Brussard L (1992) Microbial numbers and activity in dried and rewetted arable soil under integrated and conventional management. Soil Biol Biochem 24:655–665
Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Neinhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1943
Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual micro-organisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653
Bossio DA, Scow KM (1995) Impact of carbon and flooding on the metabolic diversity of microbial communities in soils. Appl Environ Microbiol 61:4043–4050
Bossio DA, Scow KM, Gunapala N, Graham KJ (1998) Determinants of soil microbial communities: Effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb Ecol 36:1–12
Broughton LC, Gross KL (2000) Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field. Oecologia 125:420–427
Bruns MA, Stephen JR, Kowalchuk GA, Prosser JI, Paul EA (1999) Comparitive diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Appl Environ Microbiol 65:2994–3000
Buckley DH, Graber JR, Schmidt TM (1998) Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl Environ Microbiol 64:4333–4339
Cavigelli MA, Robertson GP, Klug MJ (1995) Fatty acid methyl ester (FAME) profiles as measures of soil microbial comunity structure. In: Collins HP, Robertson GP, Klug MJ (eds) The Significance and Regulation of Soil Biodiversity. Kluwer Academic Publishers, Boston, pp 99–113
Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81:1402–1414
Chatzinotas A, Sandaa RA, Schonhuber W, Amann R, Daae FL, Torsvik V, Zeyer J, Hahn D (1998) Analysis of broad-scale differences in microbial community composition of two pristine forest soils. System Appl Microbiol 21:579–587
Clegg CD, Ritz K, Griffiths BS (1998) Broad-scale analysis of soil microbial community DNA from upland grasslands. Antonie Leeuwenhoek 73:9–14
Daims H, Bruhl A, Amann R, Schleifer K, Wagner M (1999) The domain-specific probe Eub338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. System Appl Microbiol 22:434–444
Daniels L, Hanson RS, Phillips JA (1994) Chemical analysis. In: Gerhardt P (ed) Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, DC, pp 536
Drinkwater LE, Wagoner P, Sarrantonio M (1998) Legume-based cropping systems have reduced carbon and nitrogen losses. Nature 396:262–265
Duarte GF, Rosado AS, Seldin L, Keijzer-Wolters AC, van Elsas JD (1998) Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community. J Microbiol Methods 32:21–29
Duineveld BM, Rosado AS, van Elsas JD, van Veen JA (1998) Analysis of the dynamics of bacterial communities in the rhizosphere of the Chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol 64:4950–4957
Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669
Felske A, Akkermans ADL (1998) Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. Microb Ecol 36:31–36
Gunapala N, Scow KM (1998) Dynamics of soil microbial biomass and activity in conventional and organic farming systems. Soil Biol Biochem 30:805–816
Hassink J, Lebbink G, van Veen JA (1991) Microbial biomass and activity of a reclaimed-polder soil under a conventional or a reduced-input farming system. Soil Biol Biochem 23:507–513
Huberty LE, Gross KL, Miller CJ (1998) Effects of nitrogen addition on successional dynamics and species diversity in Michigan old-fields. J Ecol 86:794–803
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
Ibekwe AM, Kennedy AC (1998) Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils. Plant Soil 206:151–161
Klug MJ, Tiedje JM (1993) Response of microbial communities to changing environmental conditions: chemical and physiological approaches. In: Guerrero R, Pedros-Alio C (eds) Trends in Microbial Ecology. Spanish Society for Microbiology, Barcelona, pp 371–374
Knops JMH, Tilman D (2000) Dynamics of soil nitrogen and carbon accumulation for 61 years after agricultural abandonment. Ecology 81:88–98
Kuske CR, Barns SM, Busch JD (1997) Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl Environ Microbiol 63:3614–3621
Lee S-Y, Bollinger J, Bezdicek D, Ogram A (1996) Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl Environ Microbiol 62:3787–3793
Liesack W, Stackebrandt E (1992) Occurence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078
Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522
Magurran AE (1988) Ecological Diversity and Its Measurement. Princeton University Press, Princeton, NJ, pp
McCaig AE, Glover LA, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65:1721–1730
Neidhart FC, Magasanik B (1960) Studies on the role of ribonucleic acid in the growth of bacteria. Biochim Biophys Acta 42:99–116
Ohtonen R, Fritze H, Pennanen T, Jumpponen A, Trappe J (1999) Ecosystem properties and microbial community changes in primary succession on a glacier forefront Oecologia 119:239–246
Ovreas L, Torsvik V (1998) Microbial diversity and community structure in two different agricultural soil communities. Microb Ecol 36:303–315
Paul EA, Harris D, Collins HP, Schulthess U, Robertson GP (1999) Evolution of CO2 and soil carbon dynamics in biologically managed, row-crop agroecosystems. Appl Soil Ecol 11:53–65
Pennanen T, Liski J, Baath E, Kitunen V, Uotila J, Westman CJ, Fritze H (1999) Structure of the microbial communities in coniferous forest soils in relation to the site fertility and strand development stage. Microb Ecol 38:168–179
Purdy KJ, Embley TM, Takii S, Nedwell DB (1996) Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl Environ Microbiol 62:3905–3907
Robertson GP, Crum JR, Ellis BG (1993) The spatial variability of soil resources following long-term disturbance. Oecologia 96:451–456
Robertson GP, Huston MA, Evans FC, Tiedje JM (1988) Spatial variability in a successional plant community: patterns of nitrogen availability. Ecology 69:1517–1524
Robertson GP, Klingensmith KM, Klug MJ, Paul EA, Crum JR, Ellis BG (1997) Soil resources, microbial activity, and primary production across an agricultural ecosystem. Ecol Appl 7:158–170
Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236
Stahl DA, Flesher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically based probes for studies of ruminal microbial ecology. Appl Environ Microbiol 54:1079–1084
Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787
Ueda T, Suga Y, Matsuguchi T (1995) Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur J Soil Science 46:415–421
Wander MM, Hedrick DS, Kaufman D, Traina SJ, Stinner BR, Kehrmeyer SR, White DC (1995) The functional significance of the microbial biomass in organic and conventionally managed soils. In: Collins HP, Robertson GP, Klug MJ (eds) The Significance and Regulation of Soil Biodiversity. Kluwer Academic Publishers, Boston, pp 87–97
Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv Microb Ecol 12:219–268
Yang C, Crowley DE (2000) Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol 66:345–351
Zarda B, Hahn D, Chatzinotas A, Schonhuber W, Neef A, Amann RI, Zeyer J (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168:185–192
Zhou JZ, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913–3919
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Buckley, D.H., Schmidt, T.M. The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42, 11–21 (2001). https://doi.org/10.1007/s002480000108
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DOI: https://doi.org/10.1007/s002480000108