Methods in Stream Ecology

Volume 1: Ecosystem Structure

F. Richard Hauer, Gary Lamberti

• Publisher: Academic Press
• Year: 2017
• Edition: 3
• eBook ISBN:
  9780124165786
• Topic: Biological Sciences
• Subtopic: Ecology
• Index: Biological Sciences

Methods in Stream Ecology provides a complete series of field and laboratory protocols in stream ecology that are ideal for teaching or conducting research. This two part new edition is updated to reflect recent advances in the technology associated with ecological assessment of streams, including remote sensing. Volume focusses on ecosystem structure with in-depth sections on Physical Processes, Material Storage and Transport and Stream Biota. With a student-friendly price, this Third Edition is key for all students and researchers in stream and freshwater ecology, freshwater biology, marine ecology, and river ecology. This text is also supportive as a supplementary text for courses in watershed ecology/science, hydrology, fluvial geomorphology, and landscape ecology. Methods in Stream Ecology, 3rd Edition, Volume 2: Ecosystem Structure, is also available now! - Provides a variety of exercises in each chapter - Includes detailed instructions, illustrations, formulae, and data sheets for in-field research for students - Presents taxonomic keys to common stream invertebrates and algae - Includes website with tables and a link from Chapter 22: FISH COMMUNITY COMPOSITION to an interactive program for assessing and modeling fish numbers - Written by leading experts in stream ecology

Section B

Stream Biota

Outline

Introduction

Chapter 9. Heterotrophic Bacteria Production and Microbial Community Assessment

Chapter 10. Fungi: Biomass, Production, and Community Structure

Chapter 11. Benthic Stream Algae: Distribution and Structure

Chapter 12. Biomass and Pigments of Benthic Algae

Chapter 13. Macrophytes and Bryophytes

Chapter 14. Meiofauna

Chapter 15. Macroinvertebrates

Chapter 16. Fish Assemblages

Chapter 17. Amphibians and Reptiles

Introduction

F. Richard Hauer

Gary A. Lamberti

Since ecology is the study and scientific analysis of interactions among organisms and their environment, it is not surprising that early pioneers of stream ecology primarily focused on the biota found in streams. Early biologists were fascinated by the myriad of algae species and the productivity and complexity of aquatic insect life. Centuries ago, fly-fishing became as much an art centered around aquatic insect imitation and casting as it was a means of “the catch.” Early fish biologists noticed that species replacement along longitudinal gradients of streams and rivers was a common and recurring theme and referred to “trout streams” and “warm water fish streams.” The chapters in Section B address a broad range of stream organisms from microbes to large vertebrates. Chapter 9 introduces us to single-celled, nonphotosynthetic bacteria commonly referred to as heterotrophs by employing molecular techniques. Chapter 10 addresses stream fungi, an important group that plays many roles in streams and leaf litter processing. Chapter 11 provides important perspectives in the discovery of stream algae and presents the novice and the expert with an excellent identification key. Chapter 12 complements the algae chapter by focusing on the approaches to measuring stream algae biomass and pigments as fundamental measures of standing stock. Chapter 13 introduces us to the larger, more complex and evolved species of multicellular plants in streams from bryophytes to leafed macrophytes. Chapter 14 is our first introduction to the complex of stream animals by focusing on the extremely small organisms, called meiofauna, that include small worms and crustaceans generally found between the grains of stream benthic substrata. Chapter 15 opens the world of stream macroinvertebrates with an emphasis on the tremendous diversity found in the aquatic insects and includes a helpful field key to the prominent orders and families, particularly of the mayflies, stoneflies, and caddisflies. Chapter 16 introduces the myriad approaches used in the study of stream fishes and provides brilliant color plates of the most common stream fishes. Finally, Chapter 17 integrates the amphibians and reptiles that are dominant top predators in a variety of streams around the world. This collection of chapters focuses on the biological structure of plant and animal populations and communities of stream ecosystems and approaches that stream ecologists use to characterize and measure the vast array of stream organisms.

Chapter 9

Heterotrophic Bacteria Production and Microbial Community Assessment

M. Eric Benbow^1,2, Jennifer L. Pechal¹, and Amelia K. Ward^{3 1}Department of Entomology, Michigan State University ²Department of Osteopathic Medical Specialties, Michigan State University ³Center for Freshwater Studies, Department of Biological Sciences, University of Alabama

Abstract

Microbial communities in stream ecosystems are the trophic foundation for food webs and energy flow, occupying nearly all functional groups that turn over nutrients and playing a central role in recycling the detrital pool. One of the most important groups of these communities are the heterotrophic microorganisms, a suite of microscopic prokaryotes and eukaryotes that decompose organic matter and are consumed by organisms at higher trophic levels. The productivity of these microorganisms can be quantified to estimate the overall productivity of stream environments. Further, recent advances in genomic sequencing are facilitating the ability to identify the members of this functional group of microorganisms as well as many other microbes that have historically been taxonomically unknown. In this chapter, we provide state-of-the-art methodologies for quantifying heterotrophic bacteria productivity and for high-throughput DNA sequencing that allows for broader microbial community assessment through metataxonomy and high-throughput genomics. We also provide recommendations for identifying the appropriate genomic tools and computational platforms in this rapidly and constantly changing area of genomic technologies.

Keywords

Bacterial production; Community ecology; Heterotrophic microorganisms; Metagenomics; Metataxonomy; Microbial amplicon-based sequencing; Microbiome; Organic matter

9.1. Introduction

Two fundamental components of any ecosystem are community structure—the taxa in that system—and function—what those taxa do in the ecosystem. Heterotrophic microorganisms in streams, which include bacteria, protists, and fungi are important components of the microbial communities associated with the water column, submerged surfaces, such as rocks, leaves and wood, and interstitial water of benthic sediments (Aumen et al., 1983; Bott et al., 1984; Stock and Ward, 1989; Findlay et al., 1993; Stan...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• List of Contributors
• Preface
• Acknowledgments
• Section A. Physical Processes
• Section B. Stream Biota
• Section C. Community Interactions
• Glossary
• Index