Using Microbial Ecology to Teach Experimental Design and Sampling Methods Mary Allen, Hartwick College Ruth A. Gyure, Western CT State University SEM of Bacteria in Mouse Ileum. Source: Ken Rozee et al., Microbe Library, ASM

INTRODUCTION

Learning Objectives 1.Understand challenges that microbial ecologists face in measuring and sampling these variables in the natural environment. ( Introduction) 2.Differentiate between species diversity and community structure as applied to microbial ecology. (Activity 1) 3.Design appropriate sampling scheme that takes into account scaling issues as well as temporal and spatial variability. (Activity 2) 4.Recognize and avoid some common pitfalls when sampling and measuring microbial systems. (Activity 3).

USING MICROBIAL ECOLOGY SAMPLING EXPERIMENTS IN TEACHING -- ADVANTAGES? Relevant: Examples are relevant in many classes, including traditional ecology, microbiology, health, statistics, etc.) Hands-on: Students can learn about and explore ecological principles in just about any available environment. Unifying concepts: Examples unite traditional ecology with biochemistry and molecular biology (“molecules to ecosystems approach”) Quantitative skills addressed: Examples illustrate basic principles of hypothesis testing, experimental design, and data analysis.

CONSIDERATIONS WHEN SAMPLING MICROBES IN THE NATURAL ENVIRONMENT: 1. Detection and visualization 2. Definition and differentiation of taxa 3. Cultivation issues and ecological relevance 4. Interdependence (consortia) 5. Adherence (biofilms)

MICROBIAL VIEW OF THE RHIZOSPHERE Back to list

Current, genetic view of species-level difference: DNA-DNA hybridization rate of about 70% 16s rDNA similarity of >98% Figures from Ogunseitan, Microbial Diversity WHAT IS A PROKARYOTIC SPECIES???

In the literature: Trichococcus flocculiformis Lactosphaera pasteurii Ruminococcus palustris Carnococcus allantoicus Nostocoida limicola How many genera, actually? How many species? Actually, they are all in 1 genus, Trichococcus, and: DNA-DNA hybridization studies separate them into 4 species. Ralph Tanner, University of Oklahoma EXAMPLE: IDENTIFICATION, SPECIES-LEVEL IDENTIFICATION

These isolates are all in the same genus. Why so different????? THEY CHANGE MORPHOLOGY DEPENDING ON THE CULTURE MEDIUM! Back to list

CAN I ISOLATE? IS THE ISOLATE ECOLOGICALY RELEVANT? Photo credit: D. J. Patterson, L. Amaral-Zettler and V. Edgcomb. Courtesy of micro*scope. Back to list

This pictures was made using "Fluorescent in Situ Hybridization" (FISH). The organisms in red represent the anaerobic methanotrophic Archaea (ANME) and the green organisms are sulfate reducing bacteria (SRB). Picture made by C. Jagersma at the Max Planck Institute Bremen. MICROBIAL CONSORTIA Example: AMETHOX Back to list

BIOFILMS S. Lowry—University of Ulster—Stone/Getty Images Elude traditional sampling and visualization methods Cells tightly clumped and difficult to separate, isolate, identify Phenotypic variation difficult to assess after sampling

ON TO ACTIVITIES!