Chapter outline, Benthic Environments

Proposed title:  The Microbial Ecology of Benthic Environments    Chapter no.: _____

Author(s):       Robert H. Findlay (PhD)

                        Department of Biological Sciences

                        2105 Bevill Building, Box 870206

                        University of Alabama

                        Tuscaloosa, AL USA 35487

                        Phone:  (205) 348-4167

                        Fax:      (205) 348-1403

                        E-mail: rfindlay@as.ua.edu

and

                        Tom J. Battin (PhD)

                        Department of Limnology

                        University of Vienna

                        Vienna, Austria

                        Phone:  +43-1-4277-57200

                        Fax:

                        E-mail: tom.battin@univie.ac.at

 

Notes:  Questions to section and volume editors

Subjects included in other chapters?

 

1) Benthic sampling/need for undisturbed sediment – sampling chapter

2) PLFA (as opposed to whole cell FAME) – Target-Specific Detection section

3) PLFA-SIP – SIP chapter

4) biofilms present on rock in streams and rivers – biofilms chapter

5) Possible advantages of attached (in our case, benthic) life - biofilms chapter

6) Deep Marine/hydrothermal vents – extreme environments section

7) Exclude “deep/dark” marine as extreme environment and subject to recent review (Orcutt et al. 2011) – Bob Miller

Proposed topics

1.0 Introduction

2.0 Major questions in the microbial ecology of benthic environments.

      2.1 Possible advantages of benthic life

      2.2 Factors controlling the distribution and abundance of microorganisms

            2.2.1 Classic ten

            2.2.2 Focus

            2.2.2.1 Disturbance

            2.2.2.2 Starvation and resource pulses

            2.2.2.3 season

            2.2.2.4 flow

            2.2.2.5 UV-radiation

            2.2.2.6 DOM

            2.2.2.7 net heterotrophic /phototrophic but also autotrophic (to be linked with the cycling below)

            2.2.3    Biotic interactions

            2.2.3.1 predation (viruses?)

            2.2.3.2 priming/phycosphere

      2.3 Elemental cycling

      2.4 Biogeography

3.0 Analyses of Benthic Microbial communities

      3.1 Sampling

      3.1.1 Sediments

      3.1.2 Hard surfaces

      3.2 Measurement of activity

      3.2.1 Classical

      3.2.2 Biochemical

      3.2.3 Molecular

      3.3 Measurement of abundance and biomass

      3.3.1 Classical

      3.3.2 Biochemical

      3.3.3 Molecular

      3.4 Measurement of diversity and community structure

      3.4.1 Biochemical

      3.4.1 Molecular

      3.5 Methods specific to topics within 2.0

      3.5.1 Methods for characterizing DOM

      3.5.2 Methods for foodweb analysis

      3.5.3 To be expanded as necessary

4.0 Interplay among methods: classical, biochemical, molecular

Chapter Highlights

The following concepts will be conveyed in this chapter:

1) A series of abiotic/biotic interactions control the distribution of microbes in sediments

2) sediments (and hard surfaces in streams) are currently a focus of microbial ecologist interested in the application of macro ecological theory to microbial ecology

perhaps also: benthic environment as a “microbial skin” of the landscape that regulates fluxes across adjacent systems (subseafloor and pelagic/ groundwater and surface water ect)

3) Application of quantitative and descriptive methodologies strengthen experimental approaches