Environmental Microbiology (2000) 2(6), 632±643 Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes Cherie J. Ziemer, 1 * ² Richard Sharp, 2³ Marshall D. Stern, 1 Michael A. Cotta, 3 Terence R. Whitehead 3 and David A. Stahl 2 1 Department of Animal Science, University of Minnesota, St. Paul, Minnesota 55108, USA. 2 Department of Civil Engineering, North-western University, Evanston, Illinois 60208, USA. 3 Fermentation Biochemistry, National Center for Agricultural Utilization Research, USDA, § Agricultural Research Service, Peoria, Illinois 61604, USA. Summary A model rumen system, dual-flow continuous culture fermenters, was evaluated by two comparative cri- teria in two experiments using ribosomal (r)RNA- targeted DNA probes to compare key microbial groups in samples. The initial experiment measured temporal changes in population structure during adaptation of ruminal microbial populations in fer- menters over 240 h. The fermenter inoculum con- tained 34.9% Bacteria, 60.1% Eukarya and 6.8% Archaea measured as a fraction of total small subunit (SSU) rRNA quantified using a universal probe. The cellulolytic bacterial genus Fibrobacter comprised 9.5% of total SSU rRNA in the inoculum. After 240 h of fermenter operation, the average abundance was 80.9% Bacteria, 6.1% Eukarya, 5.1% Archaea and Fibrobacter genus accounted for 6.6% of the total SSU rRNA. Divergence between ruminal and fermen- ter population structure was evaluated in the second experiment and samples were classified as ruminal, inoculum or fermenter (96, 120, 144 and 168 h of fermenter operation). Fermenter samples had higher relative abundances of Bacteria (84.5%) and Archaea (2.1%) and lower relative abundances of Eukarya (1.8%) than ruminal samples (average 48.0% Bacteria, 1.3% Archaea and 61.5% Eukarya). The relative abundance of Fibrobacter was similar in all samples, averaging 2.5%. The ruminal and fermenter samples had similar proportions of F. succinogenes and F. succinogenes subgroup 3 (as a percentage of Fibrobacter SSU rRNA). Fibrobacter succinogenes subgroup 1 and F. intestinalis proportions of Fibro- bacter were lower in fermenter samples (8.2% and 0.7% respectively) than in ruminal samples (28.4% and 2.2% respectively). Fermenters were able to maintain a core prokaryotic community structure similar to the native microbial community in the rumen. Although protozoa populations were lost, maintenance of Fibrobacter and archaeal populations indicated that the model system supported a func- tional community structure similar to the rumen. This model rumen system may serve as a suitable tool for studying aspects of ruminal microbial ecology and may resolve some of the relationships between microbial community structure and function by providing control of experimental conditions. Introduction A natural history of microoganisms, an essential prelude to more refined ecological studies, does not exist in a form recognizable to macroecologists. The limited ability of the microbial ecologist to directly observe specific organisms in their environment is a major constraint to the study of microbial ecology (Atlas, 1986). As a result, the study of microbial ecology is one of the least developed and quantified areas of research in microbiology (Karl, 1986). Pure culture studies may bias understanding of microbial ecology because characteristics and activities measured in microbial monoculture are not necessarily representative of in situ responses (Karl, 1986). Furthermore, organisms isolated and raised in culture do not necessarily represent predominant populations. Although the rumen is among the better-characterized microbial habitats in terms of identification of species present, substrate utilization and metabolism (Hungate, 1966; Russell, 1983), little is known about the ruminal microbial population and trophic structure (Stewart and Bryant, 1988; Dehority, 1993). The study of ruminal Q 2000 Blackwell Science Ltd Received 15 June, 2000; accepted 15 August, 2000. Present addresses: ² National Center for Agricultural Utilization Research, Pretoria, IL 61604, USA. ³ School of Applied Sciences, South Bank University, London SE1 0AA, UK. *For correspondence. E-mail cziemer@nadc.ars.usda.gov; Tel. (11) 309 681 6281; Fax (11) 309 681 6427. §Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.