Chapter Outline: Restoration of Metal(loid)-Contaminated Soils

 

Proposed title:  Restoration of Metal(loid)-Contaminated Soils        Chapter no.: ____________

 

Chapter outline revised 4-27-2013 (originally posted 8-24-2012)

Authors:  Timberley Roane (PhD) and Munira Lantz (MS)

               Department of Integrative Biology
               Campus Box 171, P.O. Box 173364
               University of Colorado Denver
               Denver, CO 80217-3364
               Ph. (303) 556-6592
               E-mail  Timberley.Roane@ucdenver.edu

Proposed topics:

I.  Introduction

A.  History of the use of microorganisms in the remediation of metal-contaminated soils

II.  Metal toxicity in soils

               A.  Metal toxicity and bioavailability

               B. Environmental factors influencing metal bioavailability
                              1)  Physicochemical interactions
                              2)  Physical interactions
               C.  Microbial indicators of toxicity

III.  Remediating soils: the challenges
               A.  Metal transport
               B.  Soil heterogeneity

IV.  Microbial interactions with metals

               A.  Metal toxicity to microbial systems (cellular, population, community impacts)
                              1)  Diversity changes over time
                              2)  Free-loader populations
                              3)  Elemental cycling

               B.  Microbially facilitated metal transformations

                              1)  Single metal resistance mechanisms

                              2)  Multi-metal resistance mechanisms

               C.  Metal interactions at the population level and the community level

               D.  Prevalence of metal transforming populations

V.  Case studies: use of microorganisms in metal remediation

               A.  Volatilization

               B.  Wetland approaches

               C.  Surfactants

               D.  Manure addition

               E.  Use of microorganisms in phytoremediation

VI.  New frontiers: use of “omics” and restoration of microbial function

               A.  Bioindicators
               B.  Functional characterization and replacement

1) functional redundancy and the superorganism

 

Chapter Outline: Biodegradation of Petroleum Aromatic Compounds (Inoue, Kasuga, and Nojiri)

Proposed title:  Biodegradation of Petroleum Aromatic Compounds  

Chapter no.: _________

Authors:         Kengo Inoue (PhD)

                        Interdisciplinary Research Organization
                        University of Miyazaki
                        Miyazaki, Miyazaki 889-1692, Japan
                        Phone:             +81 (985) 85-1843
                        Fax:                 +81 (985) 85-1843
                        E-mail:            kinoue@cc.miyazaki-u.ac.jp

                        Kano Kasuga (PhD)

                        Department of Biotechnology
                        Akita Prefectural University
                        Akita city, Akita 010-0195, Japan

                        Hideaki Nojiri (PhD)

                        Biotechnology Research Center
                        The University of Tokyo
                        Bunkyo-ku, Tokyo 113-8657, Japan

Notes:

·       Biodegradation of ethylbenzene, dibenzofuran, and biphenyl (strains, pathways, genes and enzymes) will be included in other chapters?

 

Proposed topics

1) Chemistry of petroleum aromatic compounds

  1-1. Chemical structure
  1-2. Nomenclature system
  1-3. Toxicity
  1-4. Occurrence

2) Biodegradation

  2-1. Single aromatic compounds (benzene, toluene, xylene) degradation (bacterial strains, degradation pathways, genes, and enzymes)
  2-2. PAHs (naphthalene, acenaphthene, anthracene, phenanthrene, fluolene, pyrene) degradation (strains, pathways, genes and enzymes)
  2-3. Hetero-aromatic compounds (dibentothiophene, carbazole, fluorine) degradation (strains, pathways, genes, and enzymes)

3) Bioremediation: in situ petroleum aromatics degradation combined with population dynamics

4) Potential use for bioremediation

Chapter Highlights

1. Comprehensive description of chemical and biological characteristics of petroleum aromatic compounds

2. Biodegradation of petroleum aromatic compounds by specific bacteria and their biodegradative pathways, genes and enzymes involved in degradation.

3. Current and future outlook of bioremediation of petroleum aromatic compounds

 

Chapter Outline: Genomic Features of Dioxin-Like Compound Degraders (Shintani and Kimbara)

Outline of Manual of Environmental Microbiology, 4th ed., book chapter

Proposed title: Genomic Features of Dioxin-Like Compound Degraders   Chapter no.:_______

Author(s):      Masaki Shintani (PhD) and Kazuhide Kimbara (PhD)

                        Department of Applied Chemistry and Biochemical Engineering
                        Graduate School of Engineering
                        Shizuoka University
                        3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Shizuoka, Japan
                        Phone:             +81-53-478-1170
                        Fax:                +81-53-478-1170
                        E-mail:            tkkimba@ipc.shizuoka.ac.jp

Notes:

·       Agrochemicals of POPs should be described in other chapter.

            ·       Dioxin-like compounds include PCB, dioxin, and dibenzofuran.
            ·       Relationship between genomic features and physiological effects will be discussed.

Proposed topics

1)  Recent progress on genome analysis of dioxin-like compounds-degraders

2)  Multiple copies of dioxygenase in Rhodococcus jostii RHA1 and other degraders
3)  Genomic islands and other mobile genetic elements which carry degradative genes
4)  How microorganisms have acquired degradation ability
5)  Transcriptome and proteome analyses on degradation of dioxin-like compounds
6)  Physiologic features of degradation
7)  Effects on dioxin-like compounds and their metabolites on microbial population in environment
8)  Genomic and physiologic analyses for successful bioremediation
9)  New frontier: single-cell analysis on degraders in environments which include unculturable microorganisms

Chapter Highlights

The following concepts will be conveyed in this chapter:

1. Genome analysis of dioxin-like compounds-degraders

2. Mobile genetic elements for distributing degradation genes
3. Effects on dioxin-like compounds and their metabolites on microorganisms
4. Genomic and physiologic analyses for successful bioremediation

5. Future aspects of single-cell analysis on biodegradation

Chapter outline: Biodegradation of Organochlorine Pesticides (Nagata and Tsuda)

Outline of Manual of Environmental Microbiology, 4th ed., book chapter

Proposed title:  Biodegradation of organochlorine pesticides         Chapter no.: _________

Author(s):      Yuji Nagata (PhD), Yoshiyuki Ohtsubo (PhD) and Masataka Tsuda (PhD)

                        Department of Environmental Life Sciences
                        Graduate School of Life Sciences
                        Tohoku University
                        Sendai, 980-8577
                        Phone:  +81-22-217-5682
                     Fax: +81-22-217-5704  
                        E-mail: aynaga@ige.tohoku.ac.jp

Notes:

·        Biodegradation of dioxin-like compounds including PCB, dioxin, and dibenzofuran should be described in other chapter.

Proposed topics

1) Overview of organochlorine pesticides as agrochemicals: Organochlorine pesticides were widely used as agrochemicals in the past, and many of them have caused serious environmental problems and appointed in persistent organic pollutants (POPs).

2) Fate of organochlorine pesticides in the environment: degradation and contamination

3) Bacteria degrading organochlorine pesticides: pathways and genes for the degradation

a. 2,4-dichlorophenoxyacetic acid (2,4-D)

b. 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)

c. pentachlorophenol (PCP)

d. g-hexachlorocyclohexane (g-HCH or lindane) and its isomers

e. 1,1,1-trichloro-2,2-bis(p-chloro-phenyl)ethane (DDT)

f. aldrin, dieldrin, endrin, heptachlor, and chlordane.

g. Others: mirex, toxaphene, hexachlorobenzene (HCB), chlordecone, and pentachlorobenzene

4) Dehalogenases as key enzymes for the degradation of organochlorine pesticides: variation, reaction mechanisms, and protein engineering of dehalogenases

5) Factors except catalytic enzymes that are necessary for the assimilation of organochlorine pesticides in bacteria: transporters, mechanisms for the detoxification of toxic intermediates, etc.

6) Genomes and mobile genetic elements of bacteria degrading xenobiotic organochlorine pesticides: appearance and evolution of bacteria degrading xenobiotics, such as g-HCH and PCP, in sphingomonads

7) Bioremediation of organochlorine pesticides: present state, possibility, and perspectives

Chapter Highlights

The following concepts will be conveyed in this chapter:

1. Many bacterial strains have been isolated that degrade organochlorine pesticides including man-made ones.

2. Various pathways and genes for the degradation of organochlorine pesticides are known, but there still remain compounds whose biodegradation pathways are unknown.

3. Appearance and evolution of bacteria degrading man-made organochlorine pesticides can be discussed on the basis of genomic information.

4. Perspectives of bioremediation of organochlorine pesticides will be discussed.