Research on nitrification and related processes: A
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, AP
2011
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
486 |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XLIX, 548 S. Ill., graph. Darst. |
| ISBN: | 9780123812940 |
Internformat
MARC
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| 020 | |a 9780123812940 |9 978-0-12-381294-0 | ||
| 035 | |a (OCoLC)890760741 | ||
| 035 | |a (DE-599)BVBBV037292974 | ||
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| 041 | 0 | |a eng | |
| 049 | |a DE-91G |a DE-19 |a DE-12 |a DE-355 | ||
| 245 | 1 | 0 | |a Research on nitrification and related processes |n A |c ed. by Martin G. Klotz |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, AP |c 2011 | |
| 300 | |a XLIX, 548 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods in enzymology |v 486 | |
| 490 | 0 | |a Methods in enzymology |v ... | |
| 700 | 1 | |a Klotz, Martin G. |e Sonstige |4 oth | |
| 773 | 0 | 8 | |w (DE-604)BV037292921 |g 1 |
| 830 | 0 | |a Methods in enzymology |v 486 |w (DE-604)BV000000938 |9 486 | |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-021205510 | ||
Datensatz im Suchindex
| _version_ | 1804143927874289664 |
|---|---|
| adam_text | Contents
Contributors
xlii
Preface
xix
Volumes in Series
xxi
Section i. Modeling
1
1. Modeling the Role of Nitrification in Open Ocean Productivity
and the Nitrogen Cycle
3
Andrew Yool
1.
Introduction
4
2.
Ocean Carbon Cycle
4
3.
Export Production and the /-Ratio
7
4.
Plankton Ecosystem Models
12
5.
Modeling Nitrification
15
6.
Operational Considerations
22
7.
Future Modeling
24
8.
Summary
27
Acknowledgments
28
References
28
2.
Continuous Cultivation and Thermodynamic Aspects of Niche
Definition in the Nitrogen Cycle
33
Stefanie
Muller
and Marc Strous
1.
Introduction
33
2.
A Minimal Model for Microbial Behavior
35
3.
Continuous Cultivation—Background and Experimental Approach
43
4.
Conclusion
50
Acknowledgments
50
References
50
vi
Contents
Section
2.
Cultivation and Cell Physiology
53
3.
Isolation, Cultivation, and Characterization of Ammonia-Oxidizing
Bacteria and Archaea Adapted to Low Ammonium Concentrations
55
Annette Bollmann, Elizabeth French, and
Hendrikus J.
Laanbroek
1.
Introduction
56
2.
General Description of Cultivation Methods for Ammonia-Oxidizing
Microorganisms
57
3.
Enrichment of Ammonia Oxidizers
63
4.
Isolation of Ammonia Oxidizers
68
5.
Characterization of Ammonia-Oxidizing Prokaryotes
72
References
84
4.
Cultivation, Detection, and Ecophysiology of Anaerobic
Ammonium-Oxidizing Bacteria
89
Boran
Kartal, Wim
Geerts, and Mike S. M.
Jetten
1.
Introduction
90
2.
Enrichment of Anammox Bacteria as
Planktonic
Cell Suspensions
93
3.
Molecular Detection of Anammox Bacteria
97
4.
Conclusions
104
Acknowledgments
104
References
105
5.
Cultivation, Growth Physiology, and Chemotaxonomy
of Nitrite-Oxidizing Bacteria
109
Eva Spieck and
André
Lipski
1.
Introduction
110
2.
Recipes for the Culture of NOB
112
3.
Cultivation Procedure
114
4.
Isolation
116
5.
Physiological Investigations
118
6.
Chemical Analyses
121
7.
Monitoring the Cultures
121
8.
Fatty Acid Analyses
124
Acknowledgments
127
References
127
6.
Surveying ^O-Producing Pathways in Bacteria
131
Lisa Y. Stein
1.
introduction
132
2.
Bioinformatics 135
Contents
vii
3.
Surveying Function
143
4.
Concluding Remarks
147
References
148
Section
3.
Molecular Microbial Ecology and
Processes Measurements
153
7.
Stable Isotope Probing with 180-Water to Investigate Growth and
Mortality of Ammonia Oxidizing Bacteria and Archaea in Soil
155
Karen Adair and Egbert Schwartz
1.
Introduction
156
2.
Materials and Methods
158
3.
Calculation of Growth and Mortality Indices
160
4.
Results
161
5.
Discussion
165
6.
Conclusions
167
Acknowledgments
167
References
168
8.
Measuring Nitrification, Den it
rif
¡cation, and Related
Biomarkers
in Terrestrial Geothermal Ecosystems
171
Jeremy A. Dodsworth, Bruce Hungate,
José
R.
de la Torre, Hongchen
Jiang,
and Brian P.
Hedlund
1.
Introduction
172
2.
General Considerations for Measurement of N-Cycle Activities in
Terrestrial Geothermal Habitats
177
3.
Methods for Measuring Nitrification in Terrestrial Geothermal Habitats
179
4.
Methods for Measuring Denitrification in Terrestrial
Geothermal Habitats
187
5.
Detection and Quantification of Potential
Biomarkers
for
Thermophilic AOA and Denitrifying Thermus thermophilus
193
6.
Closing Remarks
198
Acknowledgments
198
References
198
9.
Determining the Distribution of Marine and Coastal
Ammonia-Oxidizing Archaea and Bacteria Using
a Quantitative Approach
205
Annika C.
Mosier
and Christopher A. Francis
1.
Introduction
206
2.
Methods for Measuring the Abundance of AOA and AOB Within
Marine and Coastal Systems
209
viii Contents
3.
Methodological Considerations
213
4.
Targeting Specific Ecotypes: Quantifying Shallow and Deep Clades
of Marine Water Column AOA
214
Acknowledgments
217
References
218
io.
15N-Labeling
Experiments to Dissect the Contributions of
Heterotrophic Denitrification and Anammox to Nitrogen
Removal in the OMZ Waters of the Ocean
223
Moritz
Holtappels,
Gaute Lavik,
Marlene
M.
Jensen,
and Marcel
M. M.
Kuypers
1.
Introduction
224
2.
Theoretical Description of 15N-lncubation Experiments
227
3.
In the Field: Supplementary Measurements
233
4.
In the Field: Incubation Experiments
237
5.
In the Lab: Mass Spectrometry Measurements
240
6.
Data Processing and Interpretation
243
7.
Common Pitfalls
248
8.
Concluding Remarks
249
Acknowledgments
249
References
250
її.
Assessment of Nitrogen and Oxygen
Isotopie Fractionation
During
Nitrification and Its Expression in the Marine Environment
253
Karen L. Casciotti, Carolyn
Buchwald,
Alyson E. Santoro, and Caitlin Frame
1.
Introduction
254
2.
Methods
259
3.
Analytical Techniques
262
4.
Data Analysis
264
5.
Discussion
272
References
275
12.
Identification of Diazotrophic Microorganisms in Marine
Sediment via Fluorescence In Situ Hybridization Coupled to
Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS)
281
Anne E. Dekas and Victoria J. Orphan
1.
Introduction
282
2.
Methods
285
3.
Concluding Remarks
300
Acknowledgments
301
References
301
Contents ix
13.
Measurement and Distribution of Nitrification Rates in
the Oceans
307
В. В.
Ward
1.
Introduction
308
2.
Nitrification Rate Measurements in Seawater (Table
13.1) 310
3.
Nitrification Rate Measurements in Sediments
318
4.
Distribution of Nitrification
319
References
320
14.
Construction of STOX Oxygen Sensors and Their Application for
Determination of 02 Concentrations in Oxygen Minimum Zones
325
Niels Peter Revsbech, Bo Thamdrup,
Tage Dalsgaard,
and Donald Eugene Canfield
1.
Introduction
326
2.
STOX Sensor Principle
327
3.
Sensor Construction
328
4.
Electronics for STOX Sensors
332
5.
STOX Sensor Calibration and Performance
333
6.
Calculation of Oxygen Concentrations from STOX Data
335
7.
In Situ Deployment of STOX Sensors in OMZs
337
8.
Future Fast Response STOX Sensors
339
9.
Using STOX Sensors to Recalibrate Conventional Oxygen Sensors
339
Acknowledgments
340
References
340
15.
Regulation and Measurement of Nitrification in
Terrestrial Systems
343
Jeanette
M.
Norton and John M. Stark
1.
Introduction
344
2.
Diversity of the Nitrification Process in Terrestrial Environments
345
3.
Substrates and Products of Nitrification Reactions
346
4.
Controls on Nitrification Rates in Soil Environments
347
5.
Measurements of Nitrification in Terrestrial Environments
350
6.
Measurement of Nitrification Rates in Terrestrial Ecosystems
351
7.
Measurement of Nitrification Kinetics
357
8.
Nitrifier
Population Size
361
9.
Modeling Approaches
361
10.
Future Advancements in Nitrification Rate Research in
Terrestrial Environments
362
References
362
x
Contents
16.
Protocol
for the Measurement of Nitrous Oxide Fluxes from
Biological Wastewater Treatment Plants
369
Kartik Chandran
1.
Introduction
370
2.
Sampling Design for Full-Scale Monitoring
370
3.
Sampling Procedures: Headspace Gas Measurement
373
4.
Sampling Procedures: Measurement of Aqueous N20 Concentrations
376
5.
Sampling Procedures: Measurement of Advective Gas Flow Rate
from Bioreactor Headspace
376
6.
Principles of
Real-Time
N2O Measurement
377
7.
Data Analysis: Determination of Fluxes
377
8.
Data Analysis: Determination of Emission Fractions
378
9.
Data Analysis: Calculation of N2O Emission Factors
378
10.
Standardization of Protocol and Comparison with Established
Emissions Flux Measurement Methods
379
11.
N2O Emission Fluxes from Activated Sludge Processes
381
12.
Triggers for N2O Emission from Wastewater Treatment Operations
382
13.
Lab-Scale and Field-Scale Adaptation of Protocol N2O Emission
Measurements
383
14.
Concluding Remarks
383
Acknowledgment
383
References
384
Section
4.
Genetics, Biochemistry and Biogeochemistry
387
17.
Genetic Transformation of Ammonia-Oxidizing Bacteria
389
Luis A. Sayavedra-Soto and Lisa Y. Stein
1.
Introduction
390
2.
Transformation of AOB 391
3.
Gene Inactivation in AOB
393
4.
Use of Broad-Host Range Plashnids
398
5.
Strain Stability and Maintenance
399
6.
Conclusions
399
References
400
18.
Dissecting Iron Uptake and Homeostasis in
Nitrosomonas europaea
40З
Luis A. Sayavedra-Soto, Neeraja Vajrala, and Daniel J. Arp
1.
Introduction
404
2.
Use of Bioinformatics to Plan Fe-Related Studies
406
Contents xi
3.
Methods to Learn About the Physiological Responses
to Fe Limitation
407
4.
Methods to Study Siderophore Uptake
418
5.
Genetic Complementation to Study fur Homologs
421
6.
Methods for Gene Inactivation of Fe Uptake Systems
422
7.
Lingering Questions that can be Answered by the Above Protocols
423
8.
Conclusion
425
References
425
19.
Production of
Recombinant
Multiheme Cytochromes
с
in
Wolinella succinogenes
429
Melanie Kern
and
Jörg
Simon
1.
Introduction
430
2.
Bacterial Cytochrome
с
Biogenesis Systems
433
3.
Recombinant
Cytochrome
с
Production
435
4.
Cytochromes
c
in the Epsilonproteobacterium W. succinogenes
435
5.
Three Cytochrome
с
Heme
Lyase
Isoenzymes in
W. succinogenes
439
6.
Heterologous
Production of
Cytochromes
с
ín
W. succinogenes
439
7.
Conclusions and Perspectives
442
Acknowledgments
443
References
443
20.
Techniques for Investigating Hydroxylamine Disproportionation
by Hydroxylamine Oxidoreductases
447
A. Andrew
Pacheco,
Jennifer McGarry, Joshua Kostera, and Angel Corona
1.
Introduction
448
2.
General Considerations
450
3.
Ammonia Concentration Determination
454
4.
Nitric Oxide Concentration Determination
457
5.
Nitrite Concentration Determination
458
6.
Nitrous Oxide and Dinitrogen Concentration Determination
460
References
462
21.
Liquid Chromatography—Mass Spectrometry-Based Proteomics
of Nftrosomonas
465
Hans j. C. T. Wessels, Jolein Gloerich,
Erwin
van
der Biezen,
Mike
S. M.
Jetten,
and
Boran
Kartal
1.
Introduction
466
2.
LC-MS/MS Instrument Setup
468
3.
Growth of
N.
eutropha
€91
Pure Culture
469
4.
Sample Preparation
470
xii
Contents
5.
C18 Reversed Phase LC-MS/MS Analysis
471
6.
Database Searches and Validation of Results
472
7.
Dataset
Description and Protein Identification Example
476
8.
Conclusions
479
References
479
22.The Geochemical Record of the Ancient Nitrogen Cycle, Nitrogen
Isotopes, and Metal Cofactors
483
Linda V. Godfrey and Jennifer B. Glass
1.
Introduction
484
2.
Reconstructing the Nitrogen Cycle and Associated Trace Metal
Abundances through Time
489
3.
Determining Changes in the N-Cycle from the Geological Record
of
N
Isotopes and Metal Availability
492
4.
Measurement
497
5.
Concluding Remarks
499
Acknowledgments
499
References
499
Author Index
507
Subject Index
533
|
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| indexdate | 2024-07-09T22:55:27Z |
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| isbn | 9780123812940 |
| language | English |
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Research on nitrification and related processes A ed. by Martin G. Klotz 1. ed. Amsterdam [u.a.] Elsevier, AP 2011 XLIX, 548 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 486 Methods in enzymology ... Klotz, Martin G. Sonstige oth (DE-604)BV037292921 1 Methods in enzymology 486 (DE-604)BV000000938 486 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021205510&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Research on nitrification and related processes Methods in enzymology |
| title | Research on nitrification and related processes |
| title_auth | Research on nitrification and related processes |
| title_exact_search | Research on nitrification and related processes |
| title_full | Research on nitrification and related processes A ed. by Martin G. Klotz |
| title_fullStr | Research on nitrification and related processes A ed. by Martin G. Klotz |
| title_full_unstemmed | Research on nitrification and related processes A ed. by Martin G. Klotz |
| title_short | Research on nitrification and related processes |
| title_sort | research on nitrification and related processes |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021205510&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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| work_keys_str_mv | AT klotzmarting researchonnitrificationandrelatedprocessesa |