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

Correspondence:         kjvenkat@jpl.nasa.gov; Tel: (818) 393-1481; Fax: (818) 393-4176

 

Proposed topics


1.      ATP as a biomarker of viable microorganisms in clean-room facilities.



4.      Differential recovery of phylogenetically disparate microbes from spacecraft-qualified metal surfaces.

B.     Cultivable and problematic microbes of spacecraft and associated surfaces

5.      Microbial characterization of the Mars Odyssey spacecraft and its encapsulation facility.


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.


10.   Survival of spacecraft-associated microorganisms under simulated martian UV irradiation.



13.   Rapid inactivation of seven Bacillus spp. under simulated Mars UV irradiation.

14.   Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032.


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.

20.   Archaeal diversity analysis of 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?

 

Tuesday, January 8, 2013

Chapter outline: Life in High-Salinity Environments


Proposed title:  Life in High-Salinity Environments                       Chapter no.: ____

 
Author(s):       Aharon Oren (PhD)
                        Department of Plant and Environmental Sciences
                        Institute of Life Sciences
                        The Hebrew University of Jerusalem
                        91904 Jerusalem, Israel
                        Phone:            972 (2) 6584951
                        Fax:                972 (2) 6584425        
                        E-mail:            aharon.oren@mail.huji.ac.il

Proposed topics

1) Diversity of hypersaline environments; thalassohaline and athalassohaline brines.

2) Diversity of extremely and moderately halophilic microorganisms: Archaea, Bacteria, and Eukarya.

3) Polyextremophilic halophiles, combining life at high salt concentrations with life at high or low pH and high or low temperatures.

4) Modes of adaptation of microorganisms to life at high salt concentrations: intracellular concentrations of inorganic ions and organic solutes and adaptation of cellular macromolecules to high intracellular solute concentrations.

5) Functional diversity of microorganisms in high-salt environments: the upper salt concentration at which different physiological processes occur.

6) Assessment of the contribution of archaeal and bacterial halophiles to the microbial activities in hypersaline environments.

7) Culture-dependent studies of the microbial communities inhabiting high-salinity environments: growth media and incubation conditions to optimize recovery of culturable microorganisms.

8) Polar lipids and carotenoid pigments of extremely halophilic Archaea (family Halobacteriaceae) and Bacteria (Salinibacter) and their use as biomarkers.

9) Culture-independent, DNA-based analyses of microbial communities in hypersaline environments.

Chapter Highlights

The following concepts will be conveyed in this chapter:

1. Hypersaline environments are inhabited by diverse communities of halophilic and halophilic microorganisms belonging to all thee domains of life: Archaea, Bacteria, and Eukarya.

2. Adaptation of halophilic microorganisms to life at high salt is based either on the biosynthesis and/or accumulation of organic osmotic solutes, or on the maintenance of high intracellular KCl concentrations.

3. Not all physiological types of microorganisms known from low-salt ecosystems are known to function at the highest salt concentrations.

4. Culture-dependent and culture-independent methods developed for conventional ecosystems can be adapted for use in high salinity environments.

5. Specific pigments and lipids produced by different groups of halophilic microorganisms can be used as biomarkers for the characterization of high-salt ecosystems.

Wednesday, December 12, 2012

Chapter Outline: Assessment of prokaryotic biological activity, at the single cell level, by combining microautoradiography with fluorescence in situ hybridization (FISH)


Chapter Outline: Assessment of prokaryotic biological activity, at the single cell level, by combining microautoradiography with fluorescence in situ hybridization (FISH)

Proposed title: Assessment of prokaryotic biological activity, at the single cell level, by combining microautoradiography and fluorescence in situ hybridization (FISH) 

Chapter no.: _________

Author(s):      Cleber C. Ouverney (PhD)
                        Department of Biological Sciences
                        San Jose State University
                        San Jose, CA 95192-0100
                        Phone:             +1(408) 924-4806
Fax:                 +1(408) 924-4840
                        E-mail:             cleber.ouverney@sjsu.edu

Notes:
·       Some materials in this chapter may overlay with those covered in the Molecular Detection of Target Organisms and Sequences as well as chapters covering Physiological Detection of microorganisms.


Proposed topics
1)    A culture-independent method to render function of the 99% microbes in most environmental sites.
2)    A brief overview of in situ detection of biological activity by environmental microbes.
3)    How do MAR-FISH, STARFISH, Micro-FISH methods work to assess microbial metabolic activity in situ at the single cell level.
4)    Advantages to the approach, specifically the ability to simultaneously detect specific microbes using fluorescently labeled oligonucleotide probes and detect the capacity of microbes to uptake specific dissolved nutrient.
5)    What are the pros and contras of such approach?
6)    How do the microautoradiography-FISH methods compare to similar approaches?
7)    What substrates are used to render what type of metabolic activity?
8)    Suggestions on how to increase fluorescence signal to detect slow growing organisms.
9)    Will such laborious methods withstand the era of fast genomic sequencing?
10) Broad implications from studies applying such methods in the understanding of biogeochemical cycling of dissolved organic and inorganic nutrients in aquatic systems.
11) What other discoveries in the microbial world have been made from these techniques?


Chapter Highlights
The following concepts will be conveyed in this chapter:
1. How metabolic activity can be assessed from uncultured microbes in natural microbial communities.
2. Is Autoradiography-FISH technique right for my application? What do I need to know to make an intelligent decision?
3. Can genomic sequence data be tested/validated using this approach? How?

Chapter Outline: Gold-tagged in situ hybridization for whole cell detection in environmental samples


Chapter Outline: Gold-tagged in situ hybridization for whole cell detection in environmental samples


Proposed title: Gold-tagged in situ hybridization for whole cell detection in environmental samples                                                                      

Chapter no.: _________

Authors:         Hannes Schmidt (MS) and Thilo Eickhorst (PhD)
                        University of Bremen
                        Leobener Str., UFT
                        28359 Bremen, Germany
                        Phone:             +49(421) 218-63446
Fax:                 +49(421) 218-9863446
                        E-mail: eickh@uni-bremen.de


Notes:
·      TBD


Proposed chapters

In situ detection of microbes in environmental microbiology
Aim
Methods available and their limitations
-       Detection of single microbial cells
-       Identification and visualization in situ
-       Quantification of absolute and relative abundances
-       Top-to-bottom approach

Need for combinative approaches and higher resolution
-       Correlative in situ detection of microbes and living conditions
-       Surface structure and substrate conditions
-       Combination with high resolution microscopy techniques
-       Quantification and localization on different microscopic scales


NanoGold as a marker for in situ detection of microbes
State of the art
-       Nanogold-labeled substrates
-       Immunological approaches
-       ISH-approaches (Table)
-       Autometallography (Silver/Gold)

Problems/drawbacks
-       Review of previously documented problems for ISH techniques
-       General problems in environmental samples
-       Need for increased specificity and signal intensity


Gold-FISH – microscopy/detection of fluorescent and gold signals
Development of the new Gold-FISH protocol
-       Goal: simultaneous application/deposition of fluorescent and gold markers
-       Signal amplification for both markers
-       Enhancement of nanogold particles for EM applications

Results/Applications so far
-       pure and mixed bacterial cultures
-       soil and sediment
-       plant roots

Technical aspects/hints /troubleshooting for the application of Gold-FISH to environmental samples
-       Cell wall permeabilization
-       Autometallography
-       Surface charge
-       Computer-aided analysis


Potential for gold-based detection techniques in Environmental microbiology

-       Correlative microcopy of Gold-FISH (e.g. FM and SEM-EDS)
-       Combination with nanoSIMS
-       Potential for non-invasive microscopy (e.g. X-ray CT)


Chapter Highlights
The following concepts will be conveyed in this chapter:
  1. Novel approach for a simultaneous labeling of microorganisms with a fluorescent dye and nanogold
  2. Optimization of specific nanogold deposition by tyramide signal amplification
  3. Possible application of different microscopy techniques for the analysis of gold-FISH labeled single cells
  4. Microorganism interactions on different surface morphologies and microenvironments in terms of structure and biogeochemical conditions
  5. Element-microorganism interactions