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Chapter 15 : Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems

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Abstract:

Long-term study sites for ecological research exist in a variety of habitats, including forests, deserts, streams, and oceans, providing the observational framework for studying microbial ecological processes over time and space. In this chapter, the authors describe the advantages for microbial ecologists of studies at long-term ecological research sites, the opportunities of various types of research sites and locations available for microbial research and the integration of microbial and ecosystem ecology. The chapter is written from the point of view that studies of the ecology of microbes are a necessary part of gaining a predictive knowledge of ecosystems. There are three types of studies illustrated: correlation between microbial ecology and environmental factors, correlation studies with added data on measurements of a microbial process, and correlation studies that make use of a large-scale and long-term experimental manipulation. Multivariate analysis indicated strong functional differences between meadow and forest soils. Levels of both potential denitrifying enzyme activity (DEA) and potential nitrification were substantially higher in the meadow soils. Denitrifier communities formed distinct groups according to vegetation type and site as evidenced by terminal restriction fragment length polymorphism (TRFLP) data. Nonmetric multidimensional scaling (NMS) analysis of the binary coded TRFLP data was used to assess the effects of fertilization on the composition of the microbial communities.

Citation: Hobbie J, Bahr M, Reysenbach A. 2007. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, p 182-189. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch15

Key Concept Ranking

Microbial Ecology
0.66370314
Restriction Fragment Length Polymorphism
0.43069208
Microbial Communities in Environment
0.42907557
Denaturing Gradient Gel Electrophoresis
0.41802466
Ecological Processes
0.40070823
0.66370314
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Figures

Image of FIGURE 1
FIGURE 1

Ordination (NMS) of denitrifying community composition along a meadow-to-forest transect at the H. J. Andrews LTER site in Oregon ( ). Community composition was measured with TRFLP profiles of , a key gene in the denitrification pathway. The percentage of variation represented by each axis is indicated (in parentheses). Vectors show the directions and relative magnitudes of correlation coefficients ( ) between NMS axes and functional variables; values for the correlation between the functional variable and axis 1 or 2 (in that order) are shown in parentheses. Nitrification is the log of nitrification potential, denitrification is the log of denitrifying enzyme activity, C:N is of the soil, and NH is ammonification. (Reprinted from reference with permission.)

Citation: Hobbie J, Bahr M, Reysenbach A. 2007. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, p 182-189. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch15
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Image of FIGURE 2
FIGURE 2

Physical (temperature), chemical (chlorophyll [Chl a], DOC, pH, pCO), and biological (bacterial production [BP]) changes in the control Tuesday Lake and the fertilized experimental Peter Lake. (Reprinted from reference with permission.)

Citation: Hobbie J, Bahr M, Reysenbach A. 2007. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, p 182-189. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch15
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Image of FIGURE 3
FIGURE 3

NMS of matrix calculated from binary-coded TRFLP patterns in Tuesday Lake (squares) and Peter Lake (diamonds) during the summer. Open symbols represent the results from the first sampling date. (Reprinted from reference with permission.)

Citation: Hobbie J, Bahr M, Reysenbach A. 2007. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, p 182-189. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch15
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Image of FIGURE 4
FIGURE 4

The effects of increased snow cover, caused by a snow fence, on net N mineralization at the Arctic LTER site in Alaska. The values were calculated as the changes in average soil N contents over a season; the units are milligrams of N per square meter per season. Thus, for the control (ambient), the seasons are fall (September to November), winter (November to March), spring (March to May), and summer (May to August). Results for two types of soils are illustrated, moist tundra (tussock, intertus-sock) and dry heath ( and ) soils. (Reprinted from reference with permission.)

Citation: Hobbie J, Bahr M, Reysenbach A. 2007. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, p 182-189. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch15
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Image of FIGURE 5
FIGURE 5

The snow-shrub-soil-microbe feedback loop. Soil temperatures in and around shrubs are higher than in shrub-poor locations, resulting in enhanced winter microbial activity throughout more of the winter. As a result, there is more net nitrogen mineralization during the winter and higher shrub leaf nitrogen content and plant growth in the summer. Larger and more abundant shrubs trap more snow and reduce winter sublimation losses, leading to deeper snow cover and still higher soil temperatures. (Reprinted from reference with permission.)

Citation: Hobbie J, Bahr M, Reysenbach A. 2007. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, p 182-189. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch15
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References

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1. Adamczyk, J.,, M. Hesselsoe,, N. Iversen,, M. Horn,, A. Lehner,, P. Halkjaer Nielsen,, M. Schloter,, P. Roslev, and, M. Wagner. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69:68756887.
2. Buckley, D. H.,, and T. M. Schmidt. 2001. The structure of microbial communities in soils and the lasting impact of cultivation. Microb. Ecol. 42:1121.
3. Buckley, D. H.,, and T. M. Schmidt. 2003. Diversity and dynamics of microbial communities in soils from agroecosystems. Environ. Microbiol. 5:441452.
4. Caffrey, J. M.,, N. Harrington,, I. Solem, and, B. B. Ward. 2003. Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets. Mar. Ecol. Prog. Ser. 248:2740.
5. Hobbie, J. E. 2003. Scientific accomplishments of the Long Term Ecological Research program: an introduction. BioScience 53:1720.
6. Hobbie, J. E.,, S. R. Carpenter,, N. B. Grimm,, J. R. Gosz, and, T. T. Seastedt. 2003. The US Long Term Ecological Research program. BioScience 53:2132.
7. Kent, A. D.,, S. E. Jones,, A. C. Yannarell,, J. M. Graham,, G. H. Lauster,, T. K. Kratz, and, E. W. Triplett. 2004. Annual patterns in bacterioplankton community variability in a humic lake. Microb. Ecol. 48:550560.
8. Kratz, T. K.,, L. A. Deegan,, M. E. Harmon, and, W. K. Lauenroth. 2003. Ecological variability in space and time: insights gained from the US LTER program. BioScience 53:5767.
9. Kritzberg, E. S.,, J. J. Cole,, M. L. Pace,, W. Granéli, and, D. R. Bade. 2004. Autochthonous versus allochthonous carbon sources of bacteria: results from whole-lake 13C addition experiments. Limnol. Oceanogr. 49:588596.
10. Kritzberg, E. S.,, S. Langenheder, and, E. S. Lindström. 2006. Influence of dissolved organic matter source on lake bacterioplankton community structure and function—implications for seasonal dynamics. FEMS Microbiol. Ecol. 56:406417.
11. Loy, A.,, K. Kusel,, A. Lehner,, H. L. Drake, and, M. Wagner. 2004. Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages. Appl. Environ. Microbiol. 70:69987009.
12. McKane, R.,, E. Rastetter,, G. Shaver,, K. Nadelhoffer,, A. Giblin,, J. Laundre, and, F. Chapin. 1997. Climatic effects on tundra carbon storage inferred from experimental data and a model. Ecology 78:11701187.
13. Mintie, A. T.,, R. S. Heichen,, K. Cromack, Jr.,, D. D. Myrold, and, P. T. Bottomley. 2003. Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon Cascade Mountains. Appl. Environ. Microbiol. 69:31293136.
14. O’Mullan, G. D.,, and B. B. Ward. 2005. Comparison of temporal and spatial variability of ammonia-oxidizing bacteria to nitrification rates in Monterey Bay, California. Appl. Environ. Microbiol. 71:697705.
15. Rhee, S.-K.,, X. Liu,, L. Wu,, S. C. Chong,, X. Wan, and, J. Zhou. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:43034317.
16. Rich, J. J.,, R. S. Heichen,, P. T. Bottomley,, K. Cromack, Jr., and, D. D. Myrold. 2003. Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl. Environ. Microbiol. 69:59745982.
17. Schimel, J.,, C. Bilbrough, and, J. M. Welker. 2004. Increased snow depth affects microbial activity and nitrogen mineralization in two Arctic tundra communities. Soil Biol. Biochem. 36:217227.
18. Sturm, M.,, J. Schimel,, G. Michaelson,, J. M. Welker,, S. F. Oberbauer,, G. E. Liston,, J. Fahnestock, and, V. E. Romanovsky. 2005. Winter biological processes could help convert arctic tundra to shrubland. BioScience 55:1726.
19. Tringe, S. G.,, C. von Mering,, A. Kobayashi,, A. A. Salamov,, K. Chen,, H. W. Chang,, M. Podar,, J. M. Short,, E. J. Mathur,, J. C. Detter,, P. Bork,, P. Hugenholtz, and, E. M. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308:554557.
20. Ward, B. B. 2005. Temporal variability in nitrification rates and related biogeochemical factors in Monterey Bay, California, USA. Mar. Ecol. Prog. Ser. 292:97109.
21. Yannarell, A. C.,, A. D. Kent,, G. H. Lauster,, T. K. Kratz, and, E. W. Triplett. 2003. Temporal patterns in bacterial communities in three temperate lakes of different trophic status. Microb. Ecol. 46:391405.

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