Soil bacteria exhibit short-term variations in community structure, providing an indication of anthropogenic disturbances. In this study, microbial biomass carbon (MBC), potentially mineralizable nitrogen (PMN), community level physiological profiling (CLPP), and culture-dependent DGGE (CD DGGE) fingerprinting of the 16S rRNA gene were used to compare microbial communities in organic farm and pasture soils subjected to differing agronomic treatments. Correlation analyses revealed significant relationships between MBC, PMN, and data derived from microbial community analyses. All measures separated soil types but varied in their ability to distinguish among treatments within a soil type. Overall, MBC, PMN, and CLPP were most responsive to compost and manure amendments, while CD DGGE resolved differences in legume cropping and inorganic fertilization. The results support the hypothesis that culturable soil bacteria are a responsive fraction of the total microbial community, sensitive to agronomic perturbations and amenable to further studies aimed at linking community structure with soil functions. 1. Introduction Microorganisms play essential roles in organic matter decomposition, nutrient cycling, and plant productivity [1, 2]. Parameters that integrate diverse microbial populations into a single measure, such as microbial biomass carbon (MBC) and potentially mineralizable nitrogen (PMN), historically have proven to be useful and are widely employed measures of soil quality [3, 4]. Microbial biomass C encompasses a small labile fraction of total soil organic carbon that responds actively to changes in soil fertility, supports soil aggregation, and can be related to environmental factors such as climate, soil moisture, texture, and organic matter quality [5]. Potentially mineralizable nitrogen provides an index of a soil’s nitrogen-supplying capacity and has been positively correlated with other chemical and physical indicators of soil quality [4]. Various measures of functional and structural diversity in microbial communities have been proposed as appropriate indicators of changing soil quality [3, 6]. Community-level physiological profiling (CLPP) measures soil functional diversity by characterizing the relative utilization of a suite of carbon substrates. Community-level physiological profiling is a culture-based enrichment method that primarily characterizes and selects for fast-growing organisms that may be distinct from dominant bacteria in soil inocula [7, 8]; therefore, the ecological significance of CLPP data sometimes is questioned [9, 10].
References
[1]
A. C. Kennedy and R. I. Papendick, “Microbial characteristics of soil quality,” Journal of Soil & Water Conservation, vol. 50, no. 3, pp. 243–248, 1995.
[2]
H. Y. Sun, S. P. Deng, and W. R. Raun, “Bacterial community structure and diversity in a century-old manure-treated agroecosystem,” Applied and Environmental Microbiology, vol. 70, no. 10, pp. 5868–5874, 2004.
[3]
B. Stenberg, “Monitoring soil quality of arable land: microbiological indicators,” Acta Agriculturae Scandinavica, vol. 49, no. 1, pp. 1–24, 1999.
[4]
A. M. Ibekwe, A. C. Kennedy, P. S. Frohne, S. K. Papiernik, C. H. Yang, and D. E. Crowley, “Microbial diversity along a transect of agronomic zones,” FEMS Microbiology Ecology, vol. 39, no. 3, pp. 183–191, 2002.
[5]
P. Templer, S. Findlay, and G. Lovett, “Soil microbial biomass and nitrogen transformations among five tree species of the Catskill Mountains, New York, USA,” Soil Biology and Biochemistry, vol. 35, no. 4, pp. 607–613, 2003.
[6]
M. Schloter, O. Dilly, and J. C. Munch, “Indicators for evaluating soil quality,” Agriculture, Ecosystems and Environment, vol. 98, no. 1–3, pp. 255–262, 2003.
[7]
K. Smalla, U. Wachtendorf, H. Heuer, W. T. Liu, and L. Forney, “Analysis of BIOLOG GN substrate utilization patterns by microbial communities,” Applied and Environmental Microbiology, vol. 64, no. 4, pp. 1220–1225, 1998.
[8]
J. L. Garland, “Potential and limitations of BIOLOG for microbial community analysis,” in Proceedings of the 8th International Symposium on Microbial Ecology Atlantic Canada Society for Microbial Ecology, C. R. Bell, M. Brylinsky, and P. Johnson-Green , Eds., pp. 1–7, Society for Microbial Ecology, Halifax, NS, Canada, 1999.
[9]
A. Konopka, L. Oliver, and R. F. Turco, “The use of carbon substrate utilization patterns in environmental and ecological microbiology,” Microbial Ecology, vol. 35, no. 2, pp. 103–115, 1998.
[10]
J. Preston-Mafham, L. Boddy, and P. F. Randerson, “Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles—a critique,” FEMS Microbiology Ecology, vol. 42, no. 1, pp. 1–14, 2002.
[11]
S. Sharma, A. Rangger, and H. Insam, “Effects of decomposing maize litter on community level physiological profiles of soil bacteria,” Microbial Ecology, vol. 35, no. 3, pp. 301–310, 1998.
[12]
G. D. Bending, C. Putland, and F. Rayns, “Changes in microbial community metabolism and labile organic matter fractions as early indicators of the impact of management on soil biological quality,” Biology and Fertility of Soils, vol. 31, no. 1, pp. 78–84, 2000.
[13]
B. Williams, S. Grayston, and E. Reid, “Influence of synthetic sheep urine on the microbial biomass, activity and community structure in two pastures in the Scottish uplands,” Plant and Soil, vol. 225, no. 1-2, pp. 175–185, 2000.
[14]
R. Miethling, G. Wieland, H. Backhaus, and C. C. Tebbe, “Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33,” Microbial Ecology, vol. 40, no. 1, pp. 43–56, 2000.
[15]
F. Widmer, A. Flie？bach, E. Laczkó, J. Schulze-Aurich, and J. Zeyer, “Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and biolog analyses,” Soil Biology and Biochemistry, vol. 33, no. 7-8, pp. 1029–1036, 2001.
[16]
G. D. Bending, M. K. Turner, and J. E. Jones, “Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities,” Soil Biology and Biochemistry, vol. 34, no. 8, pp. 1073–1082, 2002.
[17]
M. S. Girvan, J. Bullimore, J. N. Pretty, A. M. Osborn, and A. S. Ball, “Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils,” Applied and Environmental Microbiology, vol. 69, no. 3, pp. 1800–1809, 2003.
[18]
E. Malosso, L. English, D. W. Hopkins, and A. G. O'Donnell, “Community level physiological profile response to plant residue additions in Antarctic soils,” Biology and Fertility of Soils, vol. 42, no. 1, pp. 60–65, 2005.
[19]
C. H. Nakatsu, “Soil microbial community analysis using denaturing gradient gel electrophoresis,” Soil Science Society of America Journal, vol. 71, no. 2, pp. 562–571, 2007.
[20]
J. E. Thies, “Soil microbial community analysis using terminal restriction fragment length polymorphisms,” Soil Science Society of America Journal, vol. 71, no. 2, pp. 579–591, 2007.
[21]
G. Muyzer and K. Smalla, “Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology,” Antonie van Leeuwenhoek, vol. 73, no. 1, pp. 127–141, 1998.
[22]
S. J. Bent, J. D. Pierson, L. J. Forney, et al., “Measuring species richness based on microbial community fingerprints: the emperor has no clothes,” Applied and Environmental Microbiology, vol. 73, no. 7, pp. 2399–2401, 2007.
[23]
R. I. Amann, “Fluorescently labeled, ribosomal RNA-targeted oligonucleotide probes in the study of microbial ecology,” Molecular Ecology, vol. 4, pp. 543–553, 1995.
[24]
P. Hugenholtz, B. M. Goebel, and N. R. Pace, “Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity,” Journal of Bacteriology, vol. 180, no. 18, pp. 4765–4774, 1998.
[25]
L. ？vre？s and V. Torsvik, “Microbial diversity and community structure in two different agricultural soil communities,” Microbial Ecology, vol. 36, no. 3, pp. 303–315, 1998.
[26]
S. M. Barns, S. L. Takala, and C. R. Kuske, “Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment,” Applied and Environmental Microbiology, vol. 65, no. 4, pp. 1731–1737, 1999.
[27]
R. J. Ellis, P. Morgan, A. J. Weightman, and J. C. Fry, “Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil,” Applied and Environmental Microbiology, vol. 69, no. 6, pp. 3223–3230, 2003.
[28]
S. L. Edenborn and A. J. Sexstone, “DGGE fingerprinting of culturable soil bacterial communities complements culture-independent analyses,” Soil Biology and Biochemistry, vol. 39, no. 7, pp. 1570–1579, 2007.
[29]
Soil Survey Staff, Soil Taxonomy, A Basic System of Soil Classification for Making and Interpreting Soil Surveys, Agricultural Handbook Number 436, Natural Resources Conservation Service, Washington, DC, USA, 2nd edition, 1999.
[30]
T. B. Childers, The effects of low and high fertility treatments on soil quality, yields, pest incidence and labor requirements of a post-translational organic market garden system, M.S. thesis, West Virginia University, Morgantown, WVa, USA, 2005.
[31]
Y. Sutanto, Manure from grazing cattle: effects on soil microbial communities and soil quality in northern West Virginia pastures, M.S. thesis, West Virginia University, Morgantown, WVa, USA, 2005.
[32]
K. R. Islam and R. R. Weil, “Microwave irradiation of soil for routine measurement of microbial biomass carbon,” Biology and Fertility of Soils, vol. 27, no. 4, pp. 408–416, 1998.
[33]
D. Keeney, “Nitrogen—availability indices,” in Methods of Soil Analysis, Part 2—Chemical and Microbiological Properties, A. L. Page, R. H. Miller, and D. R. Keeney, Eds., pp. 711–733, American Society of Agronomy, Madison, Wis, USA, 2nd edition, 1982.
[34]
J. L. Garland and A. L. Mills, “Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization,” Applied and Environmental Microbiology, vol. 57, no. 8, pp. 2351–2359, 1991.
[35]
D. A. Zuberer, “Recovery and enumeration of viable bacteria,” in Methods of Soil Analysis, Part 2. Microbiological and Biochemical Properties, R.W. Weaver, Ed., pp. 119–144, Soil Science Society of America, Madison, Wis, USA, 1994.
[36]
G. Caetano-Anolles and P. M. Gresshoff, “Staining nucleic acids with silver: an alternative to radioisotopic and fluorescent labeling,” Promega Notes Magazine, vol. 45, pp. 13–18, 1994.
[37]
G. Rees, D. Baldwin, B. Watson, S. Perryman, and D. Nielsen, “Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics,” Antonie van Leeuwenhoek, vol. 86, no. 4, pp. 339–347, 2004.
[38]
N. Fromin, J. Hamelin, S. Tarnawski et al., “Statistical analysis of denaturing gel electrophoresis (DGGE) fingerprinting patterns,” Environmental Microbiology, vol. 4, no. 11, pp. 634–643, 2002.
[39]
J. D. Knoepp, D. C. Coleman, D. A. Crossley Jr., and J. S. Clark, “Biological indices of soil quality: an ecosystem case study of their use,” Forest Ecology and Management, vol. 138, no. 1–3, pp. 357–368, 2000.
[40]
J. Oksanen, R. Kindt, P. Legendre, and B. O'Hara, “Vegan: community ecology package,” R package version 1.8-5, 2007 http://cran.r-project.org/.
[41]
F. B. Bryant and P. R. Yarnold, “Principal-components analysis and exploratory and confirmatory factor analysis,” in Reading and Understanding Multivariate Statistics, L. G. Grimm and P. R. Yarnold, Eds., pp. 99–136, American Psychological Association, Washington, DC, USA, 1995.
[42]
J. W. Doran and T. B. Parkin, “Quantitative indicators of soil quality: a minimum data set,” in Methods for Assessing Soil Quality, J. W. Doran and A. J. Jones, Eds., pp. 25–37, Soil Science Society of America, Madison, Wis, USA, 1996.
[43]
S. D. Allison and J. B. H. Martiny, “Resistance, resilience, and redundancy in microbial communities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 1, pp. 11512–11519, 2008.
[44]
E. C. Prigge, W. B. Bryan, and E. S. Goldman-Innis, “Early- and late-season grazing of orchardgrass and fescue hayfields overseeded with red clover,” Agronomy Journal, vol. 91, no. 4, pp. 690–696, 1999.
[45]
C. B. Zhang, L. N. Huang, W. S. Shu, J. W. Qiu, J. T. Zhang, and C. Y. Lan, “Structural and functional diversity of a culturable bacterial community during the early stages of revegetation near a Pb/Zn smelter in Guangdong, PR China,” Ecological Engineering, vol. 30, no. 1, pp. 16–26, 2007.
[46]
W. B. Bryan, T. A. Mills, and F. X. Rosica, “Effects of grazing management and soil amendments on hill land pasture botanical composition,” Applied Agricultural Research, vol. 1, pp. 279–302, 1987.
[47]
N. Kennedy, E. Brodie, J. Connolly, and N. Clipson, “Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms,” Environmental Microbiology, vol. 6, no. 10, pp. 1070–1080, 2004.
[48]
H. Chu, T. Fujii, T. Morimoto et al., “Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil,” Applied and Environmental Microbiology, vol. 73, no. 2, pp. 485–491, 2007.
[49]
C. H. Orr, A. James, C. Leifert, J. M. Cooper, and S. P. Cummings, “Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils,” Applied and Environmental Microbiology, vol. 77, no. 3, pp. 911–919, 2011.
[50]
W. R. Cookson, M. Osman, P. Marschner et al., “Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature,” Soil Biology and Biochemistry, vol. 39, no. 3, pp. 744–756, 2007.
[51]
L. Kerkhof, M. Santoro, and J. Garland, “Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis,” FEMS Microbiology Letters, vol. 184, no. 1, pp. 95–101, 2000.
[52]
E. Brodie, S. Edwards, and N. Clipson, “Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem,” Microbial Ecology, vol. 44, no. 3, pp. 260–270, 2002.
[53]
S. J. Grayston, C. D. Campbell, R. D. Bardgett et al., “Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques,” Applied Soil Ecology, vol. 25, no. 1, pp. 63–84, 2004.
[54]
S. Langenheder, E. S. Lindstrom, and L. J. Tranvik, “Structure and function of bacterial communities emerging from different sources under identical conditions,” Applied and Environmental Microbiology, vol. 72, no. 1, pp. 212–220, 2006.
[55]
K. Ritz, “The plate debate: cultivable communities have no utility in contemporary environmental microbial ecology,” FEMS Microbiology Ecology, vol. 60, no. 3, pp. 358–362, 2007.
[56]
D. Nichols, “Cultivation gives context to the microbial ecologist,” FEMS Microbiology Ecology, vol. 60, no. 3, pp. 351–357, 2007.
