Environmental Microbiology: Methods and Protocols

241 Pages·2014·3.475 MB·English

by  Ian T. Paulsen, Andrew J. Holmes (eds.)

Methods in
Molecular Biology 1096
Ian T. Paulsen
Andrew J. Holmes Editors
Environmental
Microbiology
Methods and Protocols
Second Edition
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Environmental Microbiology
Methods and Protocols
Second Edition
Edited by
Ian T. Paulsen
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
Andrew J. Holmes
School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
Editors
Ian T. P aulsen Andrew J. H olmes
Department of Chemistry School of Molecular Bioscience
and Biomolecular Sciences University of Sydney
Macquarie University Sydney, NSW, Australia
Sydney, NSW, Australia
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-711-2 ISBN 978-1-62703-712-9 (eBook)
DOI 10.1007/978-1-62703-712-9
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Prefa ce
This new volume on Environmental Microbiology provides an up-to-date view of molecular
mechanisms for investigating microbial communities and their biological activities. In par-
ticular, it looks at recent advances that have a big impact on the fi eld such as metagenomics
and other “omics” technologies, NanoSIMS, and stable isotope probing. As such, this
volume should be of broad general interest not only to scientists working directly in envi-
ronmental microbiology, molecular microbiology, and genomics but also to industrial sci-
entists and educators in molecular microbiology.
This volume is organized into four sections: the fi rst looks at methods involved in sam-
pling environmental microorganisms, the second profi les different methods for investigat-
ing the diversity and composition of microbial communities, the third focuses on techniques
for analyzing biological activities in situ, and the fi nal section examines high-throughput
“omics” approaches for the characterization of environmental microbial communities.
It is an exciting time for environmental microbiologists, and some of the technical advances
outlined in this volume should provide an unprecedented glimpse into the structure, composi-
tion, and activity of microbial communities across diverse environments and illuminate their
impact on global ecological processes. We sincerely thank all of the contributors for sharing
their technical knowledge with the wider environmental microbiology community.
Sydney , N SW , A ustralia Ian T. Paulsen
Andrew J. Holmes
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
PART I RECOVERY AND INVESTIGATION OF BIOLOGICAL SAMPLES
1 Methods for Isolation and Cultivation of Filamentous Fungi. . . . . . . . . . . . . . 3
Helena Nevalainen, Liisa Kautto, and Junior Te’o
2 Rapid Extraction of PCR-Competent DNA
from Recalcitrant Environmental Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Michael R. Gillings
3 Quantitative PCR for Detection of mRNA
and gDNA in Environmental Isolates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Anthony J. Brzoska and Karl A. Hassan
PART II DESCRIBING MICROBIAL COMMUNITIES
4 Analysis of Community Dynamics in Environmental Samples
Using Denaturing Gradient Gel Electrophoresis . . . . . . . . . . . . . . . . . . . . . . . 45
Claire L. Thompson
5 Terminal Restriction Fragment Length Polymorphism (T-RFLP)
Profiling of Bacterial 16S rRNA Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Catherine A. Osborne
6 Profiling the Diversity of Microbial Communities with Single-Strand
Conformation Polymorphism (SSCP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Achim Schmalenberger and Christoph C. Tebbe
7 Human Fecal Source Identification with Real-Time Quantitative PCR . . . . . . 85
Orin C. Shanks, Lindsay Peed, Mano Sivaganesan,
Richard A. Haugland, and Eunice C. Chern
8 Next Generation Barcode Tagged Sequencing
for Monitoring Microbial Community Dynamics. . . . . . . . . . . . . . . . . . . . . . . 101
Katy Breakwell, Sasha G. Tetu, and Liam D.H. Elbourne
9 Analysis of Methanotroph Community Structure
Using a pmoA-Based Microarray. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Guy C.J. Abell, Nancy Stralis-Pavese, Yao Pan, and Levente Bodrossy
10 Biolog Phenotype MicroArrays for Phenotypic Characterization
of Microbial Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Amanda M. Mackie, Karl A. Hassan, Ian T. Paulsen,
and Sasha G. Tetu
vii
viii Contents
PART III INVESTIGATION OF BIOLOGICAL ACTIVITIES IN SITU
11 Visualization of Metabolic Properties of Bacterial Cells
Using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS). . . . . . . . . . 133
Yi Vee Chew, Andrew J. Holmes, and John B. Cliff
12 Single-Cell Raman Sorting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Mengqiu Li, Dan G. Boardman, Andrew Ward, and Wei E. Huang
13 Bacterial Whole-Cell Biosensors for the Detection
of Contaminants in Water and Soils. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Yun Wang, Dayi Zhang, Paul A. Davison, and Wei E. Huang
14 Stable Isotope Probing to Study Functional Components
of Complex Microbial Ecosystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Sophie Mazard and Hendrik Schäfer
PART IV HIGH THROUGHPUT GENOMIC APPROACHES
FOR ENVIRONMENTAL MICROBIOLOGY
15 Metagenomics Using Next-Generation Sequencing. . . . . . . . . . . . . . . . . . . . . 183
Lauren Bragg and Gene W. Tyson
16 Targeted Genomics of Flow Cytometrically Sorted
Cultured and Uncultured Microbial Groups . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Sophie Mazard, Martin Ostrowski, Ross Holland,
Mikhail V. Zubkov, and David J. Scanlan
17 Quantitative Microbial Metatranscriptomics . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Scott Gifford, Brandon Satinsky, and Mary Ann Moran
18 Quantitative Metaproteomics: Functional Insights
into Microbial Communities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Chongle Pan and Jillian F. Banfield
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
Contributors
GUY C. J . ABELL • CSIRO Marine and Atmospheric Research and Wealth from Ocean
Flagship , H obart , T AS , A ustralia
JILLIAN F. BANFIELD • Department of Earth and Planetary Science, Policy, and Management,
University of California , Berkeley , CA , USA ; Department of Environmental Science,
Policy, and Management, University of California , Berkeley , CA , USA
DAN G. BOARDMAN • Kroto Research Institute, Sheffi eld University , S heffi eld , U K
LEVENTE BODROSSY • CSIRO Marine and Atmospheric Research and Wealth from Ocean
Flagship , H obart , T AS , A ustralia ; D epartment of Bioresources, A ustrian Institute of
Technology , S eibersdorf, A ustria
LAUREN BRAGG • Advanced Water Management Centre , T he University of Queensland ,
St. Lucia, Q LD , A ustralia ; A ustralian Centre for Ecogenomics, T he University of
Queensland , S t. Lucia, Q LD , A ustralia ; C SIRO Mathematics, Informatics and
Statistics , S t. Lucia, Q LD , A ustralia
KATY BREAKWELL • Department of Chemistry and Biomolecular Sciences, M acquarie
University , S ydney, N SW , A ustralia
ANTHONY J. BRZOSKA • School of Biological Sciences, U niversity of Sydney , S ydney,
NSW , A ustralia
EUNICE C. CHERN • National Risk Management Research Laboratory, Offi ce of Research
and Development, U .S. Environmental Protection Agency , C incinnati, O H , U SA
YI VEE CHEW • School of Molecular Bioscience, U niversity of Sydney , S ydney,
NSW , A ustralia
JOHN B. CLIFF • The Centre for Microscopy, Characterisation, and Analysis, T he University
of Western Australia , C rawley , W A, A ustralia
PAUL A. DAVISON • Kroto Research Institute, Sheffi eld University , S heffi eld , U K
LIAM D. H. ELBOURNE • Department of Chemistry and Biomolecular Sciences, M acquarie
University , S ydney, N SW , A ustralia
SCOTT GIFFORD • Department of Marine Sciences, U niversity of Georgia , A thens, G A , U SA
MICHAEL R. GILLINGS • Department of Biological Sciences, M acquarie University , S ydney,
NSW , A ustralia
KARL A. HASSAN • Department of Chemistry and Biomolecular Sciences, M acquarie
University , S ydney, N SW , A ustralia
RICHARD A. HAUGLAND • National Risk Management Research Laboratory, Offi ce of
Research and Development, U.S. Environmental Protection Agency , Cincinnati, OH , USA
ROSS HOLLAND • National Oceanography Centre , S outhampton, U K
ANDREW J. HOLMES • School of Molecular Bioscience, University of Sydney , S ydney, N SW ,
Australia
WEI E. HUANG • Kroto Research Institute, Sheffi eld University , S heffi eld , U K
LIISA KAUTTO • Department of Chemistry and Biomolecular Sciences, M acquarie
University , S ydney, N SW , A ustralia
MENGQIU LI • Kroto Research Institute, Sheffi eld University , S heffi eld , U K
ix