Microbial transformation of organic and inorganic halogen compounds

Peng Peng

Research output: Thesisinternal PhD, WU

Abstract

Halogenated organic compounds, organohalogens, and inorganic chlorate are largely produced and used for a wide range of applications in industry and agriculture. Besides their anthropogenic origin, these compounds are also naturally produced in various environments including, for example, forest soils, deserts, marine environments and hypersaline lakes. Halogen compounds are often toxic and have adverse effects on human, animal and environmental health, and hence microbes capable of their transformation are important for bioremediation of polluted sites and for natural halogen cycling. Research described in this thesis set out to characterize ecophysiology, genetics and potential applications of microbes obtained from pristine and polluted environments that can (co)metabolically transform organohalogens and chlorate.

Many contaminated sites contain mixtures of organic and/or inorganic halogen compounds. Microbes that can concurrently degrade different halogen compounds are of particular interest. P. chloritidismutans AW-1T is a facultative anaerobic chlorate-reducing bacterium isolated from an anaerobic chlorate-reducing bioreactor. Analysis of the genome of strain AW-1T showed co-existence of chlorate reduction genes (clrABDC, cld) and D/L-2-haloacid dehalogenase genes (dehI and L-DEX gene). This study, for the first time, verified concurrent transformation of haloalkanoates and chlorate by a single bacterium using combined physiological, biochemical and molecular techniques.

Organohalogens have a long history on earth e.g. in marine environments where dehalogenating microbes could evolve, most probably triggered by the natural production of organohalogens. Desulfoluna spongiiphila strain DBB is a newly isolated sulfate-reducing and organohalide-respiring bacterium from pristine marine intertidal sediment samples. Comparative genomics of strain DBB and two other marine isolated Desulfoluna species revealed similar potential of the three Desulfoluna strains for organohalide respiration, corrinoid biosynthesis, and resistance to oxygen. Physiological experiments confirmed the observed genomic potentials and showed specific preference of the Desulfoluna strains for brominated/iodinated compounds rather than chlorinated compounds, and stimulation of organohalide respiration during concurrent sulfate reduction.

Hypersaline lake Strawbridge in Western Australia is a natural source of chloroform (CF). Microbial CF transformation in sediment samples obtained from this lake was observed. In the sediment- and sediment-free enrichment cultures, CF was transformed to dichloromethane and CO2. Known organohalide-respiring bacteria (OHRB) and corresponding reductive dehalogenase encoding rdhA genes were not present in the sediment-free enrichment cultures. Rather, Clostridium spp. carrying genes involved in acetogenesis were enriched that likely mediated fortuitous transformation of CF to CO2. This study indicated that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere.

The co-existence of different organohalogens such as multiple chlorinated solvents in contaminated sites often hampers reductive dechlorination due to inhibitory effects of one or more organohalogens on dehalogenation of another organohalogen. We investigated kinetics of 1,2-dichloroethane (1,2-DCA) reductive dechlorination in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants as well as the population dynamics of known OHRB. Dechlorination rates of 1,2-DCA were strongly decreased in the presence of a single chlorinated co-contaminant in enrichment cultures, and the type of chlorinated substrate drove the selection of specific OHRB. This study contributed to a better understanding of the mechanisms underlying the often observed 1,2-DCA persistence in environments in relation to specific 1,2-DCA dechlorinating microbial populations. 

In conclusion, this thesis contributes to extend our understanding of physiology, genomics and ecology of different dehalogenating microbes in contaminated as well as pristine environments.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Smidt, Hauke, Promotor
  • Atashgahi, Siavash, Co-promotor
Award date6 Sep 2019
Place of PublicationWageningen
Publisher
Print ISBNs9789463950190
DOIs
Publication statusPublished - 2019

Fingerprint

organohalogen
halogen
chloroform
bacterium
dechlorination
gene
genomics
sediment
lake
coexistence
marine environment
respiration
pristine environment
sulfate
ecophysiology
pollutant
bioremediation
bioreactor
forest soil
physiology

Cite this

Peng, Peng. / Microbial transformation of organic and inorganic halogen compounds. Wageningen : Wageningen University, 2019. 182 p.
@phdthesis{800b9eec2d534eae9cd3788aa88a163b,
title = "Microbial transformation of organic and inorganic halogen compounds",
abstract = "Halogenated organic compounds, organohalogens, and inorganic chlorate are largely produced and used for a wide range of applications in industry and agriculture. Besides their anthropogenic origin, these compounds are also naturally produced in various environments including, for example, forest soils, deserts, marine environments and hypersaline lakes. Halogen compounds are often toxic and have adverse effects on human, animal and environmental health, and hence microbes capable of their transformation are important for bioremediation of polluted sites and for natural halogen cycling. Research described in this thesis set out to characterize ecophysiology, genetics and potential applications of microbes obtained from pristine and polluted environments that can (co)metabolically transform organohalogens and chlorate. Many contaminated sites contain mixtures of organic and/or inorganic halogen compounds. Microbes that can concurrently degrade different halogen compounds are of particular interest. P. chloritidismutans AW-1T is a facultative anaerobic chlorate-reducing bacterium isolated from an anaerobic chlorate-reducing bioreactor. Analysis of the genome of strain AW-1T showed co-existence of chlorate reduction genes (clrABDC, cld) and D/L-2-haloacid dehalogenase genes (dehI and L-DEX gene). This study, for the first time, verified concurrent transformation of haloalkanoates and chlorate by a single bacterium using combined physiological, biochemical and molecular techniques. Organohalogens have a long history on earth e.g. in marine environments where dehalogenating microbes could evolve, most probably triggered by the natural production of organohalogens. Desulfoluna spongiiphila strain DBB is a newly isolated sulfate-reducing and organohalide-respiring bacterium from pristine marine intertidal sediment samples. Comparative genomics of strain DBB and two other marine isolated Desulfoluna species revealed similar potential of the three Desulfoluna strains for organohalide respiration, corrinoid biosynthesis, and resistance to oxygen. Physiological experiments confirmed the observed genomic potentials and showed specific preference of the Desulfoluna strains for brominated/iodinated compounds rather than chlorinated compounds, and stimulation of organohalide respiration during concurrent sulfate reduction. Hypersaline lake Strawbridge in Western Australia is a natural source of chloroform (CF). Microbial CF transformation in sediment samples obtained from this lake was observed. In the sediment- and sediment-free enrichment cultures, CF was transformed to dichloromethane and CO2. Known organohalide-respiring bacteria (OHRB) and corresponding reductive dehalogenase encoding rdhA genes were not present in the sediment-free enrichment cultures. Rather, Clostridium spp. carrying genes involved in acetogenesis were enriched that likely mediated fortuitous transformation of CF to CO2. This study indicated that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere. The co-existence of different organohalogens such as multiple chlorinated solvents in contaminated sites often hampers reductive dechlorination due to inhibitory effects of one or more organohalogens on dehalogenation of another organohalogen. We investigated kinetics of 1,2-dichloroethane (1,2-DCA) reductive dechlorination in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants as well as the population dynamics of known OHRB. Dechlorination rates of 1,2-DCA were strongly decreased in the presence of a single chlorinated co-contaminant in enrichment cultures, and the type of chlorinated substrate drove the selection of specific OHRB. This study contributed to a better understanding of the mechanisms underlying the often observed 1,2-DCA persistence in environments in relation to specific 1,2-DCA dechlorinating microbial populations.  In conclusion, this thesis contributes to extend our understanding of physiology, genomics and ecology of different dehalogenating microbes in contaminated as well as pristine environments.",
author = "Peng Peng",
note = "WU thesis 7297 Includes bibliographical references. - With summary in English",
year = "2019",
doi = "10.18174/494863",
language = "English",
isbn = "9789463950190",
publisher = "Wageningen University",
school = "Wageningen University",

}

Peng, P 2019, 'Microbial transformation of organic and inorganic halogen compounds', Doctor of Philosophy, Wageningen University, Wageningen. https://doi.org/10.18174/494863

Microbial transformation of organic and inorganic halogen compounds. / Peng, Peng.

Wageningen : Wageningen University, 2019. 182 p.

Research output: Thesisinternal PhD, WU

TY - THES

T1 - Microbial transformation of organic and inorganic halogen compounds

AU - Peng, Peng

N1 - WU thesis 7297 Includes bibliographical references. - With summary in English

PY - 2019

Y1 - 2019

N2 - Halogenated organic compounds, organohalogens, and inorganic chlorate are largely produced and used for a wide range of applications in industry and agriculture. Besides their anthropogenic origin, these compounds are also naturally produced in various environments including, for example, forest soils, deserts, marine environments and hypersaline lakes. Halogen compounds are often toxic and have adverse effects on human, animal and environmental health, and hence microbes capable of their transformation are important for bioremediation of polluted sites and for natural halogen cycling. Research described in this thesis set out to characterize ecophysiology, genetics and potential applications of microbes obtained from pristine and polluted environments that can (co)metabolically transform organohalogens and chlorate. Many contaminated sites contain mixtures of organic and/or inorganic halogen compounds. Microbes that can concurrently degrade different halogen compounds are of particular interest. P. chloritidismutans AW-1T is a facultative anaerobic chlorate-reducing bacterium isolated from an anaerobic chlorate-reducing bioreactor. Analysis of the genome of strain AW-1T showed co-existence of chlorate reduction genes (clrABDC, cld) and D/L-2-haloacid dehalogenase genes (dehI and L-DEX gene). This study, for the first time, verified concurrent transformation of haloalkanoates and chlorate by a single bacterium using combined physiological, biochemical and molecular techniques. Organohalogens have a long history on earth e.g. in marine environments where dehalogenating microbes could evolve, most probably triggered by the natural production of organohalogens. Desulfoluna spongiiphila strain DBB is a newly isolated sulfate-reducing and organohalide-respiring bacterium from pristine marine intertidal sediment samples. Comparative genomics of strain DBB and two other marine isolated Desulfoluna species revealed similar potential of the three Desulfoluna strains for organohalide respiration, corrinoid biosynthesis, and resistance to oxygen. Physiological experiments confirmed the observed genomic potentials and showed specific preference of the Desulfoluna strains for brominated/iodinated compounds rather than chlorinated compounds, and stimulation of organohalide respiration during concurrent sulfate reduction. Hypersaline lake Strawbridge in Western Australia is a natural source of chloroform (CF). Microbial CF transformation in sediment samples obtained from this lake was observed. In the sediment- and sediment-free enrichment cultures, CF was transformed to dichloromethane and CO2. Known organohalide-respiring bacteria (OHRB) and corresponding reductive dehalogenase encoding rdhA genes were not present in the sediment-free enrichment cultures. Rather, Clostridium spp. carrying genes involved in acetogenesis were enriched that likely mediated fortuitous transformation of CF to CO2. This study indicated that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere. The co-existence of different organohalogens such as multiple chlorinated solvents in contaminated sites often hampers reductive dechlorination due to inhibitory effects of one or more organohalogens on dehalogenation of another organohalogen. We investigated kinetics of 1,2-dichloroethane (1,2-DCA) reductive dechlorination in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants as well as the population dynamics of known OHRB. Dechlorination rates of 1,2-DCA were strongly decreased in the presence of a single chlorinated co-contaminant in enrichment cultures, and the type of chlorinated substrate drove the selection of specific OHRB. This study contributed to a better understanding of the mechanisms underlying the often observed 1,2-DCA persistence in environments in relation to specific 1,2-DCA dechlorinating microbial populations.  In conclusion, this thesis contributes to extend our understanding of physiology, genomics and ecology of different dehalogenating microbes in contaminated as well as pristine environments.

AB - Halogenated organic compounds, organohalogens, and inorganic chlorate are largely produced and used for a wide range of applications in industry and agriculture. Besides their anthropogenic origin, these compounds are also naturally produced in various environments including, for example, forest soils, deserts, marine environments and hypersaline lakes. Halogen compounds are often toxic and have adverse effects on human, animal and environmental health, and hence microbes capable of their transformation are important for bioremediation of polluted sites and for natural halogen cycling. Research described in this thesis set out to characterize ecophysiology, genetics and potential applications of microbes obtained from pristine and polluted environments that can (co)metabolically transform organohalogens and chlorate. Many contaminated sites contain mixtures of organic and/or inorganic halogen compounds. Microbes that can concurrently degrade different halogen compounds are of particular interest. P. chloritidismutans AW-1T is a facultative anaerobic chlorate-reducing bacterium isolated from an anaerobic chlorate-reducing bioreactor. Analysis of the genome of strain AW-1T showed co-existence of chlorate reduction genes (clrABDC, cld) and D/L-2-haloacid dehalogenase genes (dehI and L-DEX gene). This study, for the first time, verified concurrent transformation of haloalkanoates and chlorate by a single bacterium using combined physiological, biochemical and molecular techniques. Organohalogens have a long history on earth e.g. in marine environments where dehalogenating microbes could evolve, most probably triggered by the natural production of organohalogens. Desulfoluna spongiiphila strain DBB is a newly isolated sulfate-reducing and organohalide-respiring bacterium from pristine marine intertidal sediment samples. Comparative genomics of strain DBB and two other marine isolated Desulfoluna species revealed similar potential of the three Desulfoluna strains for organohalide respiration, corrinoid biosynthesis, and resistance to oxygen. Physiological experiments confirmed the observed genomic potentials and showed specific preference of the Desulfoluna strains for brominated/iodinated compounds rather than chlorinated compounds, and stimulation of organohalide respiration during concurrent sulfate reduction. Hypersaline lake Strawbridge in Western Australia is a natural source of chloroform (CF). Microbial CF transformation in sediment samples obtained from this lake was observed. In the sediment- and sediment-free enrichment cultures, CF was transformed to dichloromethane and CO2. Known organohalide-respiring bacteria (OHRB) and corresponding reductive dehalogenase encoding rdhA genes were not present in the sediment-free enrichment cultures. Rather, Clostridium spp. carrying genes involved in acetogenesis were enriched that likely mediated fortuitous transformation of CF to CO2. This study indicated that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere. The co-existence of different organohalogens such as multiple chlorinated solvents in contaminated sites often hampers reductive dechlorination due to inhibitory effects of one or more organohalogens on dehalogenation of another organohalogen. We investigated kinetics of 1,2-dichloroethane (1,2-DCA) reductive dechlorination in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants as well as the population dynamics of known OHRB. Dechlorination rates of 1,2-DCA were strongly decreased in the presence of a single chlorinated co-contaminant in enrichment cultures, and the type of chlorinated substrate drove the selection of specific OHRB. This study contributed to a better understanding of the mechanisms underlying the often observed 1,2-DCA persistence in environments in relation to specific 1,2-DCA dechlorinating microbial populations.  In conclusion, this thesis contributes to extend our understanding of physiology, genomics and ecology of different dehalogenating microbes in contaminated as well as pristine environments.

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DO - 10.18174/494863

M3 - internal PhD, WU

SN - 9789463950190

PB - Wageningen University

CY - Wageningen

ER -