All Manual of Environmental Microbiology 4th edition authors and editors are cordially invited to network on Monday, May 20, 5:30 to 6:30 pm over drinks and hors d'oeurves. See you at Peak's Lounge at the top of the Hyatt Regency Denver!
Christine Charlip
Director, ASM Press
Monday, April 8, 2013
Thursday, March 28, 2013
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
- 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
- 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
- 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
- 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
- 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:
- 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
- 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
- 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)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
Tuesday, March 26, 2013
*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
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.
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
Monday, February 4, 2013
Chapter outline: Life at High Temperature
Proposed title: Life at High Temperature Chapter no.: _______
Author(s): Brian P. Hedlund
Greg
Fullmer Associate Professor of Life Sciences
School
of Life Sciences, University of Nevada Las Vegas
89154 Las Vegas, NV, USA
Phone:
702-895-0809
Fax:
702-895-3956
E-mail: brian.hedlund@unlv.edu
Jeremy A.
Dodsworth
School
of Life Sciences, University of Nevada Las Vegas
89154 Las Vegas, NV, USA
Phone:
702-895-0809
Fax:
702-895-3956
E-mail:
jeremy.dodsworth@unlv.edu
Chuanlun
Zhang
Department
of Marine Sciences, University of Georgia
166
Marine Sciences Building
Athens,
GA 30602-3636
Phone: (706) 542-3034
FAX Number:
(706) 542-5888
archaea.zhang@gmail.com
Proposed topics
1)
Diversity of high temperature environments.
-
Continental (liquid water and vapor-condensation systems; volcanically active
areas, tectonically driven systems, influence of climate and hydrologic setting,
deep subsurface).
-
Marine (on-axis, off-axis systems). - Other systems (briefly: coal piles,
compost, industrial cooling and heating, subsurface).
2) Definitions,
upper temperature limits of domains, and polyextremophiles.
-
Hyperthermophiles and thermophiles - distinguishing growth from survival. - Upper temperature limits of domains.
-
Polyextremophiles and their habitats - thermoacidophiles, thermophilic
piezophiles.
3)
Diversity of extremely and moderately thermophilic microorganisms: Archaea,
Bacteria, and Eukarya.
- Phylogenetic diversity - transition to
specific thermophilic lineages around 80°C.
- Physiological diversity.
4) Modes
of adaptation of microorganisms to life at high temperature.
- Nucleic acids (positive supercoiling, GC
content in nontranscribed RNAs)
-
Lipids (membrane-spanning lipids, cyclization, ether and ester linkages)
- Proteins
- Adaptations to instability of small
molecules
- Cytoplasm (compatible solutes)
5) Effect
of high temperature on microbial community diversity and structure.
- Increase in temperature leads to loss of
diversity, simplification of communities.
- Quantitative relationships between high
temperature and microbial diversity.
- Loss of diversity translates into loss
of ecosystem functions.
6) Effect
of temperature on ecosystem functioning and biogeochemical cycles.
- Photosynthetic/chemosynthetic transition.
- Carbon cycle. Distinguishing features of
the high temperature cycle.
- Nitrogen cycle. Distinguishing features
of the high temperature cycle.
7) Recent
developments and future directions.
- Impact of genomics approaches (e.g.
“dark matter” lineages)
- Need for more in situ measurements (from
biomarkers to activities)
- Need for more dynamic studies (from
snapshots to movies)
Chapter
Highlights
The
following concepts will be conveyed in this chapter:
1. The
high temperature biome is extensive and diverse. It is inhabited by a
physiologically and phylogenetically diverse group of microorganisms. Above ~80°C the microbial community
is composed entirely of thermophilic phylum- and class-level lineages.
2. A
variety of molecular adaptations to high temperature exist, including
adaptations to protect macromolecules (nucleic acids, lipids, and proteins), to
decrease molecular motion in the cytoplasm, and to address the instability of
small molecules at high temperature.
3. High
temperature leads to a loss of diversity, which leads to loss of ecosystem
function, including a key transition from photosynthetic communities to
chemosynthetic communities. Temperature impacts all biogeochemical cycles in
ways that are currently poorly understood.
4. Current
and future advancements include the discovery of the function of major,
uncultivated lineages, so-called “biological dark matter,” and an increased
focus on the effect of high temperature on ecosystem function.
Chapter outline: Microbial life in extreme low-biomass environments–a genetic approach
Proposed title: Microbial life in
extreme low-biomass environments – a genetic approach
Chapter no.: _________
Author(s): Venkateswaran,
K., M.T. La Duc, P. Vaishampayan, and J.A. Spry
Jet
Propulsion Lab, California Institute of Technology
M/S:
89-2; Biotechnology and Planetary Protection
4800,
Oakgrove Dr., Pasadena, CA 91109
Proposed topics
1.
ATP as a biomarker of
viable microorganisms in clean-room facilities.
2. Evaluation of Procedures for the
Collection, Processing, and Analysis of Biomolecules from Low-Biomass Surfaces.
3.
Comparative analysis
of methods for the purification of DNA from low-biomass samples based on total
yield and conserved microbial diversity.
4. Differential recovery of phylogenetically
disparate microbes from spacecraft-qualified metal surfaces.
B. Cultivable and problematic microbes of spacecraft and associated surfaces
7.
Recurrent isolation of
extremotolerant bacteria from the clean room where Phoenix spacecraft
components were assembled.
8.
Extreme spore UV
resistance of Bacillus pumilus
isolates obtained from an ultraclean spacecraft assembly facility.
9.
Recurrent isolation of
hydrogen peroxide-resistant spores of Bacillus
pumilus from a spacecraft assembly facility.
12. Effect of Shadowing on Survival of Bacteria
under Conditions Simulating the Martian Atmosphere and UV Radiation.
15.
Molecular microbial
community structure of the Regenerative Enclosed Life Support Module Simulator
air system.
16.
Impact of assembly,
testing, and launch operations on the airborne bacterial diversity within a
spacecraft assembly facility clean-room.
19.
Diversity of anaerobic
microbes in spacecraft assembly clean rooms.
21.
Comprehensive Census
of Bacteria in Clean Rooms by Using DNA Microarray and Cloning Methods.
22.
Comparison of
Innovative Molecular Approaches and Standard Spore Assays for Assessment of
Surface Cleanliness.
23.
High-density 16S
microarray and clone library-based microbial community composition of the
Phoenix spacecraft assembly clean room.
24.
Pyrosequencing-derived
bacterial, archaeal, and fungal diversity of spacecraft hardware destined for
Mars.
Chapter Highlights
The
following concepts will be conveyed in this chapter:
I.
Effectiveness of sample collection
methods and efficacy of sample processing in measuring molecular microbial
community of low biomass surfaces
II.
Are molecular methods comprehensive
enough to measure microbial diversity?
III.
Are clean surfaces selectively
enriching subset of microbial population?
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