Post A Reply
my profile
login
|
register
|
search
|
faq
|
forum home
»
Allstocks.com's Bulletin Board
»
Micro Penny Stocks, Penny Stocks $0.10 & Under
»
BUGS --HUGE play!!!
» Post A Reply
Post A Reply
Login Name:
Password:
Message Icon:
Message:
HTML is not enabled.
UBB Code™ is enabled.
[QUOTE]Originally posted by Dustoff101: [QB] Kellogg Biological Station, Hickory Corners, Michigan Michael J. Klug (klug*kbs.msu.edu) James M. Tiedje (tiedjej*pilot.msu.edu) Eldor A. Paul (paulea*pilot.msu.edu) Katherine L. Gross (kgross*kbs.msu.edu) G. Philip Robertson (robertson*kbs.msu.edu) Thomas M. Schmidt (tschmidt*pilot.msu.edu) -------------------------------------------------------------------------------- Soil microbial ecology is a central part of KBS LTER research. Understanding the ecological interactions underlying the productivity of field crop agriculture is the central focus of LTER research at KBS, and microbes comprise one of our most intensively studied taxa, together with vascular plants and insects. Microbial studies at KBS take a variety of forms, with most studies directed towards questions about the patterns, causes, and consequences of microbial diversity and microbial biomass for ecosystem processes in intensively managed ecosystems. Our studies to date have centered on examinations of microbial growth rates, biomass, and fungal: bacterial ratios. We have also focused on population-level questions using direct microscopy, classical pure-culture techniques, and, for the multitude of unculturable microbes in soil, molecular analyses of phenotypes and genomes. Many of these latter techniques provide whole-soil signatures of community composition, and have been particularly useful for examaning community-level differences among sites and experimental treatments. For questions related to specific populations we have focused our efforts on examinations of specific functional groups such as denitrifiers, nitrifiers, lignin and 2,4-D degraders, and the rhizobacteria, linking these groups to specific microbial processes. Much of this research has been collaborative with the NSF Center for Microbial Ecology (www.cme.msu.edu) at Michigan State; a number of KBS LTER co-PI's are also co-investigators in the CME. We provide below background information on our current studies of microbial community structure. Other microbial work is also underway at KBS but not described here due to space limitations – including detailed biogeochemical and population-level investigations of microbial processes such as denitrification, trace gas fluxes, and soil organic matter turnover and DOC and DON fluxes. Following this section we highlight specific analytical procedures now in use at KBS. Microbial Community Structure The diversity and complexity of soil microbial communities present a major challenge to our efforts to understand how biological processes can be managed in agricultural systems. Soil microbial communities are arguably the most diverse communities on earth, and the factors that determine this extraordinarily high diversity are not well understood (Caldwell et al. 1997). Torsvick et al. (1994) have provided evidence that in one gram of soil there are billions of individual organisms and thousands of species. What are the ecological consequences of such high diversity at such a small spatial scale? And how does this change across the range of scales that we consider to be important for other organisms (e.g. plants and consumers) and biogeochemical processes? To determine how to manage the biological processes controlled by soil microbes, it is important to understand the patterns, causes, and consequences of microbial diversity and the scale at which microbial communities are structured. Understanding the link between the scale at which the microbial community is structured and the scale at which ecosystem processes occur may itself tell us a great deal about the role of microbial diversity in ecosystem functioning. The high spatial heterogeneity of soil in an ecological context is well documented (Robertson and Gross 1994, Paul and Clark 1996). Differences among habitats in the degree of soil heterogeneity may influence the diversity of microbes that occur there and their function (Gross et al. 1995). For example, our results with nitrifiers and soil C dynamics are best interpreted in relation to differences among treatments in soil heterogeneity (reflecting the availability of microhabitats) and soil organic fractions (reflecting resource heterogeneity; Paul et al. 1998a). Spatial heterogeneity in soil microbial communities occurs at a broad range of scales, from soil particles (e.g. soil macroaggregates), to plant rhizospheres, to field plots, and to the ecosystem and global levels (Tiedje 1994). At KBS we have documented that there is spatially-structured dependence in microbial processes at both a macro- (e.g 10's of meters, Robertson et al.1997) and micro- (cm, Cavigelli et al. 1995) scale. We have shown that microbial activity (measured by short-term microbial respiration) varies among and within plant communities; in some sites samples taken only centimeters apart vary by a factor of >2. The among-community scale component of this nested variation may be attributable to differences in primary productivity and soil physical properties (e.g. depth to the Bt horizon). At the within-community scales, the doubling of microbial activity may be attributable to the distance to the nearest plant. However, we suspect that these differences may also be due to heterogeneity in soil structure, leading to discontinuous resource availability at the millimeter-scale. This small-scale heterogeneity may be driven by the interaction of plant-derived substrates, such as roots and decaying plant particles, and within-aggregate habitats differences due to clay content, pore sizes, and aeration. To date, our investigations of soil microbial communities have primarily concentrated on the level and pattern of microbial diversity among the different plant communities that occur on the KBS LTER site. These communities range from the intensively managed row crops under different input intensities to native communities at different successional stages. Our results, generated by a variety of phenotypic and genetic approaches, have documented differences in the apparent diversity of whole-soil microbial communities (patterns of bacterial fatty acids, FAMEs), as well as differences in the diversity of key functional groups, notably denitrifiers (Cavigelli 1998) and nitrifiers (Bruns et al. 1998). In the past decade we have concentrated on documenting the level and patterns of microbial diversity among ecosystems using strategies such as those outlined in the figure at right. We have now begun more intense investigations of the regulation, maintenance, and consequences of microbial community structure. We hypothesize that the majority of soil microbial diversity is driven by the heterogeneous distribution of resources and habitats in soil. For example, we have found a variety of autotrophic nitrifier genera in our never-tilled successional plots (Bruns et al. 1998), all of which grow in the laboratory only at low NH4+ concentrations. In contrast, in our agronomic plots there is a single dominant genus (Nitrosomonas) that is able to grow across a wider range of NH4+ concentrations. These differences in nitrifier diversity could be due to differences in resource availability, and therefore competitive interactions. However, this pattern may also be due to greater diversity of protective soil habitats in the never-tilled community. Heterogeneity in soil structure, which may lead to higher levels of microbial diversity, is affected not only by cultivation regime but also by the presence and activity of plants that create biopores and habitat for the mesofauna that are directly responsible for much of the soil structure (Oades 1993). To improve our knowledge of how microbial community structure interacts with the functioning of ecosystems we must obtain a more quantitative knowledge of the interaction between microbes, plant residues and disturbance, at a variety of spatial scales. This will require examining the availability of specific resources (at the substrate level) across multiple spatial scales. We are currently concentrating our research on soil microbial communities at the KBS LTER in four areas: Investigations of the availability of microbial resources (especially substrates) through continued studies on the pools and fluxes of soil organic matter; Examination of the scales at which carbon turns over in soils from the microaggregate (mm) to the landscape (km); Investigations of the diversity and structure of specific groups of soil microbes across the 11 different communities on the KBS LTER, with an initial emphasis on Basidiomycete fungi, a microbial group that is responsible for significant carbon turnover in soil; and Investigations of the linkage between plant diversity, disturbance, soil structure, microbial diversity, and key ecosystem functions such as primary productivity, nitrogen cycling, and nutrient retention in general. -------------------------------------------------------------------------------- Analytical Procedures Used for Microbial Ecology at KBS Microbial Biomass Microbial biomass is enumerated at KBS using the chloroform incubation technique calibrated with direct microscopy. Specific techniques are documented in Howarth et al. (1994, 1996) and Paul et al. (1998). Results are available on the KBS LTER web site. Fungal Biomass and Fungal: Bacterial Ratios Ergosterol is a steroid found in most fungi, but absent in other microorganisms. We have found that the concentration of ergosterol in soils (Stahl and Parkin 1996) is directly related to the growth rate of fungi and provides an estimate of the fungal biomass in soil. Comparisons of fungal and bacterial ratios, and the size of bacterial biomass are also useful for documenting changes within soil microbial communities. Computerized fluorescence microscopy has greatly aided our ability to examine these characteristics. Culturable Microorganisms During the establishment of our main cropping systems site a culture collection of bacteria was established to provide a benchmark collection. From over 1000 isolates a 100-isolate subset was selected for intensive study ("the KBS 100"). These isolates have been characterized using a variety of polyphasic taxonomic tools (see figure above) and are maintained as a long-term reference collection. Additional collections include lignin decomposing Basidiomycetes from the site (molecular techniques show that many have previously not been described; Thorn et al. 1996) as well as collections of denitrifiers (Cavigelli 1998) and nitrifiers (Bruns 1996). Non-Culturable Microbes: Community-Level Signatures We have used a variety of phenotypic tools to characterize soil microbial community composition as related to ecological change (Klug and Tiedje 1993, Sinsabaugh et al. 1998). These include fatty acid methyl ester (FAME) and phospholipid fatty acid (PLFA) analyses (Peterson and Klug 1994, Haack et al. 1994, Cavigelli et al. 1995, Corlew-Newman and Klug 1998), as well as Biolog™ carbon utilization signatures. We are also using G+C analysis to examine the distributions of low G+C populations (e.g. Pseudomonas) vs. high G+C populations (e.g. Arthrobacter), and L-asparaginase activity to resolve differences in rhizosphere populations. Population-Level Signatures: Gene Probes We have collaborated with the NSF Center for Microbial Ecology (CME) at MSU in the development and testing of several gene probes for assaying specific soil populations at KBS. Particularly successful has been the deployment of probes for 2,4-D metabolism (Holben et al. 1992, Ka et al. 1994a,b,c,d, 1995), and for nitrifying bacteria (Zhou et al. 1995, Bruns 1996, Bruns et al. 1998). We are beginning to design population-specific rRNA oligonucleotide probes to determine the contribution of these various fractions of rRNA to total prokaryotic community rRNA. The advantage of working with RNA is that it allows detection of the most active (highest ribosome content) populations, which are also probably the most dominant populations. Population-Level Signatures: Phenotypic Techniques We have used lipid analysis (fatty acid markers) to track changes in fungal communities in different soils (Stahl and Klug 1996, 1998, Stahl et al. 1998), changes in mycorrhizal associations (Calderon 1997), and differences in denitrifier community composition (Cavigelli 1998). These techniques have been combined with techniques for culturable microbes and community-level signatures (above). Bacterial Growth Rates Microbial biomass provides an estimate of the pool size of microorganisms, but not of biomass turnover. We have examined bacterial turnover dynamics using 3H, thymidine, and 14C-leucine incorporation kinetics (Harris 1994, Harris and Paul 1994). Microbial Process Measurements Measurements of key microbial processes such as nitrification, carbon mineralization, and carbon and nitrogen gas fluxes are coupled to those of microbial and plant community structure to provide insight into the functional significance of microbial diversity at KBS. Processes examined include CH4 oxidation and N2O production (Robertson 1993, Paustian et al. 1995, Ambus and Robertson 1998a,b), carbon oxidation (Paul et al. 1994, 1998a,b, Paustian et al. 1995), denitrification (Cavigelli 1998), and nitrification (Bruns 1996, Knoke 1997). Microbial Predators Nematodes are important fungal and bacterial consumers that can affect the distribution and abundance of microbial populations. We have examined changes in nematode groups among cropping system treatments (Freckman and Ettema 1993) as well as the distribution of various nematode trophic groups (Robertson and Freckman 1995). These studies, in combination with our data on biomass and biomass turnover measurements, provide evidence on the controls in the distribution of key microbial groups in soils. -------------------------------------------------------------------------------- References Ambus, P., and G.P. Robertson. 1998. Automated near-continuous measurement of CO2 and N2O fluxes with a photoacoustic infra-red spectrometer and flow-through soil cover boxes. Soil Science Society of America Journal 62:394-400. Ambus, P., and G.P. Robertson. 1999. Fluxes of CH4 and N2O from Poplar stands grown under ambient and twice-ambient CO2. Plant and Soil (submitted). Bruns, M. 1996. Nucleic acid probe analysis of autotrophic ammonia-oxidizer populations in soils. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan. Bruns, M.A., J.A. Fries, J.M. Tiedje, and E.A. Paul. 1998. Functional gene hybridization patterns of terrestrial ammonia-oxidizing bacteria. Microbial Ecology 36:293-302. Calderon, F. 1997. Lipids: Their value as molecular markers and their role in the carbon cycle of arbuscular mycorrihizae. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan. Caldwell, D.E., G.M. Wolfaardt, D.R. Korber, and J.R. Lawrence. 1997. Do bacterial communities transcend Darwinism? Advances in Microbial Ecology 15: 105-191 Cavigelli, M.A., G.P. Robertson, and M.J. Klug. 1995. Fatty acid methyl ester (FAME) profiles as measures of soil microbial community structure. Pages 99-113 in H.P. Collins, G.P. Robertson, and M.J. Klug, eds. The Significance and Regulation of Soil Biodiversity. Plant and Soil 170. Kluwer Academic Publishing, Dordrecht, Netherlands. Cavigelli, M. 1998. Ecosystem consequences and spatial variability of microbial soil community structure. Ph.D. Thesis, Michigan State University, East Lansing, Michigan. Cavigelli, M. A., G. P. Robertson, and M. J. Klug. 1995. Fatty acid methyl ester (FAME) profiles as measures of soil microbial community structure. Pages 99-113 in H. P. Collins, G. P. Robertson, and M. J. Klug, eds. The Significance and Regulation of Soil Biodiversity. Plant and Soil 170. Kluwer Academic Publishers, Dordrecht, Netherlands. Cavigelli, M. A., and G. P. Robertson. 1999. The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology (in press). Collins, H. P., G. P. Robertson, and M. J. Klug, eds. 1995. The Significance and Regulation of Soil Biodiversity. Kluwer Academic Publishers, Dordrecht, The Netherlands. Also published as Plant and Soil 170:1-241. Freckman, D.W. and C.H. Ettema. 1993. Assessing nematode communities in agroecosystems of varying human intervention. Agriculture, Ecosystems and Envrionment 45:239-261. Haack, S.K., H. Garchow, D.A. Odelson, L.J. Forney and M.J. Klug. 1994. Microbial community analysis: accuracy, reproducibility and interpretation of fatty acid methyl ester profiles from model bacterial communities. Applied and Environmental Microbiology 60:2483-2493. Harris, D. 1994. Analyses of DNA extracted from microbial communities. Pages 111-118 in K. Ritz, J. Dighton, and K. Giller, eds. Beyond the Biomass. John Wiley & Sons, Chichester, England. Harris, D., and E.A. Paul. 1994. Measurement of microbial growth rates in soil. Applied Soil Ecology 1:277-290. Holben, W.E., B.M. Schroeder, V.G.M. Calabrese, R.H. Olsen, J.K. Kukor, V.O. Biederbeck, A.E. Smith, and J.M. Tiedje. 1992. Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid (2,4-D). Applied Environment Microbiology 58:3941-3948. Horwath, W.R., and E.A. Paul. 1994. Microbial biomass. Pages 753-774 in R.W. Weaver, J.S. Angle, P.J. Bottomley, D.F. Bezdicek, M.S. Smith, M.A. Tabatabai, and A.G. Wollum, eds. Methods of Soil Analysis Part 2-Microbiological and Biochemical Properties. Soil Science Society of America, Madison, Wisconsin, USA. Horwath, W.R., E.A. Paul, D. Harris, J. Norton, L. Jagger, and K.A. Horton. 1996. Defining a realistic control for the chloroform-fumigation incubation method using microscopic counting and 14C-substrates. Can. J. Soil Sci. 96:459-467. Ka, J.O., P. Burauel, J.A. Bronson, W.E. Holben, and J.M. Tiedje. 1995. DNA probe analysis of microbial community selected in field by long-term 2,4-D application. Soil Science Society of America Journal 59:1581-1587. Ka, J.O., W.E. Holben, and J.M. Tiedje. 1994. Analysis of competition in soil among 2,4-D degrading bacteria. Applied and Environmental Microbiology 60:1121-1128. Ka, J.O., W.E. Holben, and J.M. Tiedje. 1994. Genetic and phenotypic diversity of 2,4-D degrading bacteria isolated from 2,4-D treated field soils. Applied and Environmental Microbiology 60:1106-1115. Ka, J.O., W.E. Holben, and J.M. Tiedje. 1994. Integration and excision of a 2,4-dichlorophenoxyacetate acid-degradative plasmid in alcaligenes paradoxus and evidence of its natural intergeneric transfer. Journal Bacteriology 176:5284-5289. Ka, J.O., W.E. Holben, and J.M. Tiedje. 1994. Use of gene probes to aid recovery and identification of functionally dominant 2,4-D degrading populations in soil. Applied and Environmental Microbiology 60:1116-1120. Klug, M.J. and J.M. Tiedje. 1993. Response of microbial communities to changing environmental conditions: chemical and physiological approaches. Pages 371-374 in R. Guerrero and C. Pedros-Alio, eds. Trends in Microbial Ecology, Spanish Society for Microbiology, Barcelona, Spain. Knoke, K.E. 1997. Assessment of the origin and fate of nitrate from soil lysimeters using stable nitrogen isotopes. M.Sc. Thesis, Michigan State University, East Lansing, Michigan. Oades, J. M. 1993. The role of biology in the formation, stabilization and degradation of soil structure. Geoderma 56: 377-400. Paul, E.A. and F.E. Clark. 1996. Soil Microbiology and Biochemistry. 2nd edition. Academic Press, Inc., San Diego, CA. 340 pp Paul, E.A., D. Harris, M. Klug, and R. Ruess. 1999. The determination of microbial biomass. In G.P. Robertson, D.C. Coleman, C.S. Bledsoe, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research, Oxford University Press, New York (In press). Paul, E.A., H.P. Collins, D. Harris, U. Schulthess, and G.P. Robertson. 1998. The influence of biological management inputs on carbon mineralization in ecosystems. Applied Soil Ecology 327: 1-13. Paul, E.A., E.T. Elliott, C.V. Cole and K. Paustian (eds.). 1994. Soil Organic Matter Dynamics in Agroecosystems. Lewis CRC Publishers, Boca Raton, Florida. 500 pp. Paustian, K., G.P. Robertson, and E.T. Elliott. 1995. Management impacts on carbon storage and gas fluxes (CO2, CH4) in mid-latitude cropland ecosystems. Pages 69-84 in R. Lal, J. Kimble, E. Levine, and B.A. Stewart, eds. Soil Management and the Greenhouse Effect, Advances in Soil Science. CRC Press, Boca Raton, Florida. Paustian, K., H.P. Collins, and E.A. Paul. 1997. Management controls on soil carbon. Pages 15-49 in E.A. Paul, K. Paustian, E.T. Elliot and C.V. Cole, eds. Soil Organic Matter in Temperate Agroecosystems: Long-Term Experiments in North America. CRC Press, Boca Raton, Florida, USA. Peterson, S.O. and M.J. Klug. 1994. Effects of sieving, storage and incubation temperature on the phospholipid fatty acid profile of a soil microbial community. Applied and Environmental Microbiology 60:2421-2430. Robertson, G.P. 1993. Fluxes of nitrous oxide and other nitrogen trace gases from intensively managed landscapes: a global perspective. Pages 95-108 in L.A. Harper, A.R. Mosier, J.M. Duxbury, and D.E. Rolston, eds. Agricultural Ecosystem Effects on Trace Gases and Global Climate Change. American Society of Agronomy, Madison, Wisconsin, USA. Robertson, G.P., and D.W. Freckman. 1995. The spatial distribution of nematode trophic groups across a cultivated ecosystem. Ecology 76:1425-1432. Robertson, G. P. and E.A. Paul. 1998. Ecological research in agricultural ecosystems: contributions to ecosystem science and to the management of agronomic resources. Pages 142-164 in M. L. Pace and P. M. Groffman, eds. Successes, Limitations and Frontiers in Ecosystem Science. Cary Conference VII, Springer-Verlag, New York. Robertson, G. P., K. M. Klingensmith, M. J. Klug, E. A. Paul, J. C. Crum, and B. G. Ellis. 1997. Soil resources, microbial activity, and primary production across an agricultural ecosystem. Ecological Applications 7: 158-170. Sinsabaugh, R.L., M.J. Klug, H.P. Collins, P.E. Yeager, and S. O. Peterson. 1999. Characterizing soil microbial communities. In G.P. Robertson, C.S. Bledsoe, D.C. Coleman, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research, Oxford University Press, New York (In press). Stahl, P.D., and T.B. Parkin. 1996. Relationship of soil ergosterol content and fungal biomass. Soil Biology and Biochemistry 28:847-855. Stahl, P.D., and M.J. Klug. 1999. Lipid comparisons of microfungal communities from soils and on different agricultural management practices. Plant and Soil (In press). Stahl, P.D., and M.J. Klug. 1996. Characterization and differentiation of filamentous fungi based on fatty acid composition. Applied and Environmental Microbiology 62:4136-4146. Tiedje, J.M. 1994. Approaches to the comprehensive evaluation of procaryote diversity of a habitat. In: D.Allsopp, R.R. Colwell, and D.L. Hawksworth (eds) Microbial Diversity and Ecosystem Function, CAB International,Wallingford, U.K. Torsvik, V., J. Goksoyr, F.L. Daae, R. Sorheim, J. Michelsen, and K. Salte. 1994. Use of DNA analysis to determine the diversity of microbial communities. In: Beyond the Biomass. K. Ritz, J. Dighton, and K.E. Diller (eds.) Wiley Sayce, London, England. pp. 39-48 Zhou, J., M.A. Bruns, and J.M. Tiedje. 1995. Rapid method for recovery of DNA from soils of diverse composition. Applied and Environmental Microbiology 62:316-322. -------------------------------------------------------------------------------- http://lter.kbs.msu.edu/ Copyright 2004 Michigan State University Board of Trustees [Legal Disclaimer] [/QB][/QUOTE]
Instant Graemlins
Instant UBB Code™
What is UBB Code™?
Options
Disable Graemlins in this post.
*** Click here to review this topic. ***
Contact Us
|
Allstocks.com Message Board Home
© 1997 - 2021 Allstocks.com. All rights reserved.
Powered by
Infopop Corporation
UBB.classic™ 6.7.2