Working Outline of MEM4

Here are the working section titles and section editors, and if available, chapter titles and authors (NOTE: subject to change):

General Methodology  

1. Culture-Based and Physiological Detection: Yoichi Kamagata
• General Introduction: Yoichi Kamagata
• Improved Solid (Media) Cultivation: Peter H. Janssen, Belinda C. Ferrari
• Dilution-to-Extinction Cultivation: Stephen J. Giovannoni, Jan-Cheon Cho
• Anerobic Cultivation: Kohei Nakamura, Yoichi Kamagata
• Detection of Specific Bacteria Based on Chromogenic Media: Mohammed Manafi
• In Situ Cultivation: Slava Epstein, Yoshiteru Aoi
2. Microscopic Methods: Cleber Ouverney
• Introduction: Cleber Ouverney
• NANO-SIMS: Peter Weber, Jennifer Pett-Ridge
• Gold-FISH: Thilo Eickhost
• Autoradiography with FISH to Study Microbial Ecophysiology in Situ: Cleber Ouverney
3. Target-Specific Detection: Doug Call
• Antibody-Based Biosensors and Immune-Microarray Technology: Cheryl Baird, Susan Varnum, Timothy Straub, Doug Call
• PCR, qPCR, Digital PCR, and Isothermal Amplification: Rachel Bartholomew
• Microarray and Bead-Coupled Detectors: Darrell Chandler
• Field Application of Detection Techologies: H. Nakaido
4. The Microbiotas of Environments: Next-Generation Techniques: Stefan Green
• Next-Generation Sequencing Technologies: M.L. Metzker
• Metagenome and High-Throughput Sequencing for Microbial Detection: James Versalovic
• Linking Metagenome Data with Bioinformatics: Phillip Hugenholtz
• Large-Scale Feature Prediction and Feature Annotation and Comparison in Metagenomes: E. Glass, F. Meyer
• Evolving Standards in Metagenomics: D. Field, J. Gilbert, F. Meyer, N. Kyrpides
5. Statistical Tools and Analysis for Environmental Studies: J. Vaun McArthur
• Statistical Thinking: J. Vaun McArthur
• Statistical Analysis: R. Cary Tuckfield
• Ecological Modeling:
• Modeling the Fate and Transport of Human Pathogens:
6. QA/QC in Environmental Microbiology: Yildiz T. Chambers
• Introduction: Kevin Connell
• Bacteria: Ellen Braun-Howland
• Viruses: Rick Danielson
• Protozoa: Greg Sturbaum, George DiGiovanni
• Molecular Assays: Greg Sturbaum, George DiGiovanni
• Study Design: Robin K. Oshiro, Yildiz Chambers
7. Sampling Methods: John Scott Meschke
• Air Sampling: Gedi Mainelis
• Water Sampling: Vince Hill
• Surface Sampling: Laura Rose, Matthew Arduino
• Soils Sampling: John Brooks
• Wastewater and Biosolids Sampling: John Scott Meschke

Environmental Public Health Microbiology                           

1. Water: Gary Toranzos
• Waterborne Transmission of Infectious Agents: Sam Dorevitch (tentative)
• Microorganisms in Freshwaters: Julie Kinzelman (tentative)
• Microorganisms in Marine Waters: John Griffith (tentative)
• Detection of Pathogens in Sludges, etc.: Judy Blackbeard (tentative)
• Pathogens in Shellfish: Angelo de Paola (tentative)
• Control of Microorganisms in Source Waters: Christobel Ferguson (tentative)
• Assessing the Efficiency of Wastewater Treatment: Wesley Pipes (tentative)
• Toxic Photosynthetic Prokaryotes and Eukaryotes: Wesley Pipes (tentative)
2. Air: Mark Buttner
• Introduction to Aerobiology: Paula Krauter
• Sampling for Airborne Microorganisms: Sergey A. Grinshpun, Mark P. Buttner, Klaus Willeke
• Analysis of Bioaerosol Samples: Patricia Cruz, Mark P. Buttner
• Fate and Transport of Microorganisms in Air: Gary S. Brown, Alan Jeff Mohr
• Airborne Fungi and Mycotoxins: Chin S. Yang, Eckardt Johanning, DeWei Li, Peter S. Thorne, Caroline Duchaine
• Legionellae and Legionnaires' Disease: Claressa Lucas, Barry S. Fields
• Airborne Viruses: Syed A. Satter, M. Khalid Ijaz
• Aerobiology of Agricultural Pathoges: Estelle Levetin
3. Soil: Ed Topp
• Fate of Enteric Bacteria in Soils: Population Biology, Genetic Stability, and Exchange
• Fate of Pathogenic Microorganisms in Soils
• Natural Solid Reservoirs and Hosts for Human Pathogens; Distinguishing Soil-Adapted from Allochthonous Bacterial Populations
4. Microbial Source Tracking: Valerie J(ody) Harwood
• MST: An Evolving Science: V.J. Harwood, Chick Hagedorn, Michael Sadowsky
• Validating MST Methods: Don Stoeckel, John Griffith
• Overview of Existing MST Methods Targeting Human Sources: Orin Shanks, Kate Field, Anicet Blanch, Jennifer Weidhaas, Jorge Santo Domingo
• Field Study Planning and Implementation: Julie Kinzelman, Warish Ahmed
5. Microbial Risk Assessment: Nicholas Ashbolt
• Problem Formulation and the Risk Management Context: Nicholas Ashbolt (tentative)
• Exposure Characterization: Schoen & Ashbolt (tentative)
• Dose-Response Characterization: Haas (tentative)
• Risk Characterization, Interpretation, and Uncertainties: Rose (tentative)

Microbial Ecology                            

1. Theory: Larry Forney
• Genome Evolution (Phylogenomics): Tal Dagan
• Evolutionary Ecology of Microbial Populations: Jay Lennon
• Biodiversity and Ecosystem Functioning in Bacterial Communities: Thomas Bell
• Theoretical Community Ecology: Zhansham (Sam) Ma
2. Aquatic Environments: Bob Findlay
• The Microbial Ecology of Benthic Environments: Bob Findlay, Tom Battin
• Planktonic--Lakes, Oceans: J. Fuhrman
• Acquatic Biofilms: Development, Cultivation, Sampling, Analyses, and Applications: G. Wolfaardt, John Lawrence
3. Soils, Phytosphere and Subsurface: G. Kowalchuk
• Phyllosphere: Julia Verholt
• Rhizosphere: Noel Frierer
• Soil Microbial Diversity and Function with Respect to Biogeography: Rob Griffiths
• Microbial Succession, Colonization, and Activity in the Phytosphere: G. Kowalchuk
4. Extreme Environments: Brian Hedlund
• Life at High Temperature: Brian Hedlund
• Arctic/Antarctic Systems: Alisaon Murray, Henry Sun (tentative)
• Extremely Acidic Systems: Barrie Johnson
• Life in High-Salinity Environments: Aharon Oren
• Deep Subsurface: Mark Schrenck
• Ultraclean Rooms for Planetary Protection: Kasthuri Venkateswaran
• Extreme Aridity/Exobiology: Chris McKay
5. Animal-Gut Microbiomes: J.R. Marchesi
• Invertebrate-Gut Associations: Daniele Daffonchio
• Human: Hauke Smidt, Paul W. O'Toole, J.R. Marchesi
• Animal Guts: Mark Morrison, Christ McSweeney, Richard Ellis, Liljana Petrovska

Bioremediation, Biotransformation, and Biofuels                             

1. Biodegradation:
• Aromatic organics: Aerobic Biodegredation:
• Halogenated Organics: Anaerobic Biodegradation: Max Haggblom
• Microbial Electrochemical Technologies: Producing Electricity and Valuable Chemicals from Biodegredation of Waste Organic Matters: Tae-Ho Lee, Akihiro Okamoto, Sokhee Jung, Ryuhei Nakamura, Jung Rae Kim, Kazuya Watanabe, Kazuhito Hashimoto
• Biofuels from Algae:
• Appliation of Emerging Technologies in Biodegredation (Metagenomics, Proteomics, Stable Isotope Probing):
• Natural Polymers: Lignin, Cellulose, Keratin, Chitosan:
• Synthetic Polymers and Industrial Wastes: Dyes, Detergents, Plastics
• Pharmaceuticals: Biodegradation in Aquatic Systems 
2. Biotransformation: Chris Rensing
• Metal Transformation: Mercury: Tamar Barkay
• Metal Transformations Linked to Resistance Processes: Barry Rosen
• Breathing Metals and Use as Terminal Electron Acceptor: Tom DiChristina
• Metals for Energy Production: Derek Lovely
• Metals and Geochemical Cycling: Tim McDermott
• Metal Transformation at the Organic/Inorganic Interface: Jon Chorover
• Iron and Microbial Life--From the Beginning to the Present Day: Timothy Magnuson
• Restoration fo Metal(loid) Contaminated Soil: Timberley M. Roane

                               

*Revised schedule for MEM4*

                                         SCHEDULE FOR MEM4  revised March 2013

Publication date: March 2015

Volume Editors (VEs) and Section Editors (SEs) in place:              30 April 2012

Authors chosen by:                                                                             1 June 2012

Page limits and schedule to authors by:                                            8 June 2012

Editors meeting at ASM 2012                                                         16 June 2012

TOC final:                                                                                          1 April 2013

Deadline for authors to send chapter outlines to SEs:                      29 April 2013

SEs touch base with authors about deadline for submission of

            manuscripts:                                                                           6 May 2013

VEs hold conference calls with SEs to assess status of chapters:    May/June 2013

 Online system begins accepting manuscript submissions                1 September 2012

Conference call among Editor in Chief, VEs, and ASM Press:        early July 2013

 

Deadline for submission of manuscripts to online system for review:        29 July 2013

 

Turnaround time for revision and return of final manuscripts to SEs

(once author receives reviews from SE):                              2-4 weeks*

SEs send their reviews to authors:                                                     by 26 August 2013

Authors get their revised mss. back to SEs by:                                 30 September 2013

 

LAST of the final accepted manuscripts to ASM:                           4 November 2013

 

*Can be extended for chapters where major revisions are needed.

Significant benchmark dates are highlighted.

Notes on the production schedule:

·       These are the general time frames for tasks after manuscripts are accepted.

·       Tasks are coordinated by Production Editor (PE) John Bell, who will be working on multiple books in addition to MEM4.

·       Chapters will be processed on a continuous basis; some chapters will be in proof while others are being copyedited or aren’t even final.

·       Chapters will not be typeset in numerical order.

Chapter outline: Iron and Microbial Life—from the Beginning to the Present Day

Proposed title: Iron and Microbial Life—from the Beginning to the Present Day

 

Chapter no.:                 _____________

 

Author:                            TS Magnuson

 

1.     Introduction

1.1.  An earth history of microbial life with metals

1.2.  Overall biogeochemical significance

1.3.  Importance of Fe transformation on early and present earth

1.4.  Evolution of mechanisms of microbial iron respiration

1.5.  Link to present day processes

2.     The present state of knowledge

2.1.1.     Geobacter and Shewanella

2.2.  Other microbial systems

2.2.1.     Desulfovibrio, thermophilic, extremophilic microbes studied thus far

2.3.  Methods for cultivation and study of Fe transforming microbes

2.3.1.     Use of proper substrates-solid vs. soluble Fe

2.3.2.     Biofilm physiology studies

2.4.  Genomics of Fe-transformation

2.4.1.     Methods used in genomic and proteomic studies

2.4.2.     Common genome features among Fe transforming microbes

2.5.  Biochemistry and physiology of Fe transformation

2.5.1.     Methods applied in the study of biochemistry/physiology

2.5.2.     The biofilm matrix—a redox active interface between cells and the mineral substrate

2.5.3.     Redox proteins involved in Fe transformation

2.5.4.     Other potential mechanisms

2.5.4.1.          Shuttles and redox partner bacteria

2.5.5.     Common themes among Fe transforming bacteria

2.6.  Areas of controversy

2.6.1.     Nanowires, membrane vesicles, and the biofilm matrix

2.6.2.     Gram positive and archaeal systems

3.     The happy consequences of microbial Fe transformation

3.1.  Transformation and bioremediation of toxic metals

3.2.  Cr and U transformation mechanisms

3.3.  Mechanisms and relatedness to Fe transformation activity

4.     The great beyond—Future directions for research

4.1.  Exploration of extremophilic microbial Fe transformation systems

4.2.  Bioremediation

4.3.  A common theme for microbial Fe transformation?

5.     Acknowledgments

6.     References

 

 

Chapter outline: Breathing Metals: Molecular Mechanism of Microbial Metal Respiration

Proposed title: Breathing Metals: Molecular Mechanism of Microbial Metal Respiration

Chapter no.:   ____________

Author:           Thomas DiChristina

A. Direct enzymatic pathway

 

1. Genetic and biochemical studies of Shewanella oneidensis genes and proteins

required for direct enzymatic metal reduction

2. Evidence of cytochrome localization on S. oneidensis outer membrane

3. Predicted structure and proposed mechanism of external electron transfer via

outer membrane metal-reducing, porin-cytochrome complex

4. Functions of porin-cytochrome complex in other bacterial species

5. Gaps in knowledge and future research directions

 

B. Electron-shuttling pathway

 

1. Discovery of electron shuttling compounds

2. Endogenous and exogenous electron shuttling compounds

3. Soluble and solid electron shuttling compounds

4. Electron shuttling mechanism and rate limiting step in microbial metal respiration

5. Gaps in knowledge and future research directions

C. Metal solubilization pathway

 

1. Introduction to metal-ligand chemistry

2. Chemical basis of metal solubilization by organic ligands

3. Metal solubilization by siderophores produced by aerobic microorganisms

4. Metal solubilization by organic ligands produced by S. oneidensis under

anaerobic, metal-reducing conditions

5. Gaps in knowledge and future research directions

D. Nanowire pathway

 

1. Overall strategy for electron transfer via nanowires produced by S. oneidensis

2. Nanowire structure and proposed mechanism of electron transfer via nanowires

3. Nanowire networks between bacteria

4. Nanotechnological applications of nanowires

5. Gaps in knowledge and future research directions