Methods in Enzymology - Environmenral Microbiology (AP).pdf - Biochemia - rpf123

METHODS IN ENZYMOLOGY

EDITORS-IN-CHIEF

John N. Abelson Melvin I. Simon

DIVISION OF BIOLOGY

CALIFORNIA INSTITUTE OF TECHNOLOGY

PASADENA, CALIFORNIA

FOUNDING EDITORS

Sidney P. Colowick and Nathan O. Kaplan

Preface

Environmental Microbiology per se has not previously been the dedicated

subject of its own volume in this long running series. The desire to understand

the activities of microbes in natural environmental settings and samples has

longstanding roots. Take, for example, van Leeuwenhoek’s ﬁrst observations of

the microbial communities of the human mouth. Or take the ‘‘crude analytical

technique’’ employed by Alessandro Volta during his investigations of the

biogenesis of methane in sediments. Environmental Microbiology has a rich

history that not only has continued up through the present, but that has

markedly accelerated in pace in recent years.

The last 30 year period has witnessed incredible advances in the study

of microbes in the environment. From the brilliant, ﬁrst isolation of many

diverse microbes having novel forms, functions, and phylogenies. To the

continued development of techniques used to image cells and the physical,

chemical, and biological gradients within which they reside. To the large-scale

sequencing efforts that are now beginning to characterize the gene contents

of literally hundreds of microbes in one fell swoop. Environmental Micro-

biology remains in a golden age of discovery and of methods development.

Because of the current maturity of, and methodological richness in the study

of microbes in the environment, no single volume on the subject could be

complete. In choosing the topics covered in this volume, I have attempted to

cover a broad swath of methods that I feel represent, and thus serve to expose

ﬁeld- and bench-enthusiasts to a reasonable diversity of approaches that are

currently being used to tackle a great variety of issues of interest. The overall

aim of this volume is to continue to encourage the development of methods

and investigations encompassing a great variety of experimental ﬂavors and

colors. I wish to thank all of the authors as well as Cindy Minor, whose

experience in and guidance of such endeavors proved so invaluable.

I dedicate this volume to my parents, Gloria Ann and Edward Renton

Leadbetter. Their 50 year partnership has not only served to mentor the

development their own four children, but also (during the course of their

travels in life from Austin to Amherst to Storrs to Woods Hole and to

the many other hot spots of microbiology they have visited in between)

served to foster the development of countless other early-career environmental

microbiologists of this nation and from abroad. Thank You.

ared

R. L

eadbetter

xiii

Table of Contents

ontributors to

olume

397................. ix

reface

. . . . . . . . . . . . . . . . . . . . . . . .

xiii

olumes in

eries

..................... xv

Section I. Cultivation

1. Anoxic Media Design, Preparation, and

Considerations

aroline

M. P

lugge

2. Enrichment and Isolation of Anaerobic

Hydrocarbon-Degrading Bacteria

rene

A. D

avidova and

oseph

M. S

uﬂita

3. Anammox Organisms: Enrichment,

Cultivation, and Environmental Analysis

ike

etten

arkus

chmid

atinka van de

-S

choonen

aap

inninghe

amst ´ , and

arc

trous

4. Enrichment and Isolation of Ferric-Iron- and

Humic-Acid-Reducing Bacteria

ristina

L. S

traub

ndreas

appler

and

ernhard

chink

5. Enrichment, Cultivation, and Detection of

Reductively Dechlorinating Bacteria

rank

E. L

¨ fﬂer

obert

A. S

anford

and

irsti

M. R

italahti

6. Enrichment and Isolation of Iron-oxidizing

Bacteria at Neutral pH

avid

merson and

elissa

errill

loyd

112

7. High-Throughput Cultivation of

Microorganisms Using Microcapsules

arsten

engler

arion

alcher

reg

lark

mke

aller

erardo

oledo

revin

olland

ric

J. M

athur

ary

oodnutt

M. S

hort

and

artin

eller

124

table of contents

Section II. Physiological Ecology

8. Chemotaxis and Behavioral Physiology of

Not-yet-cultivated Microbes

¨ rg

vermann

133

9. Analysis of Microbial Communities with

Electrochemical Microsensors and

Microscale Biosensors

iels

eter

evsbech

147

10. Optical Microsensors for Analysis of Microbial

Communities

ichael

¨ hl

166

11.

Measurements of Metabolite Fluxes:

Microinjection of Radiotracers into Insect

Guts and Other Small Compartments

ndreas

rune and

ichael

ester

200

12. Assaying for the 3-Hydroxypropionate Cycle

of Carbon Fixation

ichael

¨ gler and

eorg

uchs

212

13. Analysis of Trace Hydrogen Metabolism F

rank

E. L

¨ fﬂer and

obert

A. S

anford

222

14. Advances in Microscopy:

Microautoradiography of Single Cells

eppe

und

ielsen and

alkj Æ r

ielsen

237

15. Atomic Force Microscopy of Bacterial

Communities

egan

E. N

´ ˜ ez

ark

O. M

artin

hyllis

H. C

han

K. D

uong

nil

R. S

indhurakar

and

ileen

M. S

pain

256

Section III. Nucleic Acid Techniques

16. Nucleic Acid Recovery from Complex

Environmental Samples

evin

J. P

urdy

271

17. The Application of Rarefaction Techniques

to Molecular Inventories of Microbial

Diversity

ennifer

B. H

ughes and

essica

J. H

ellmann

292

18. Culture-Independent Microbial Community

Analysis with Terminal Restriction

Fragment Length Polymorphism

erence

L. M

arsh

308

19. Quantitative Community Analysis: Capillary

Electrophoresis Techniques

eremy

D. S

emrau and

ong

-I

329

20.

Functional Gene Analysis: Recognition

of Individual Genes by Fluorescence

atrin

wirglmaier

In Situ

atrin

ichtl

and

Hybridization

olfgang

udwig

338

In Situ

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