Comparative analysis of Nitrosococcus genomes; isolation, physiological and genomic characterization of the new ammonia-oxidizing species Nitrosococcus wardiae, strain D1FHST; and molecular studies towards a better understanding of ammonia-dependent chemo

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Wang, L. (2016). Comparative analysis of Nitrosococcus genomes; isolation, physiological and genomic characterization of the new ammonia-oxidizing species Nitrosococcus wardiae, strain D1FHST; and molecular studies towards a better understanding of ammonia-dependent chemolithotrophy. Unc Charlotte Electronic Theses And Dissertations.
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Abstract

Obligate aerobic chemolithoautotrophic ammonia-oxidzing bacteria (AOB) derive energy and reductant needed for growth solely from the oxidation of ammonia to nitrite thereby facilitating the process of nitritation. A strain of an ammonia-oxidizing Gammaproteobacterium, D1FHS, was isolated into pure culture from an enrichment of sediment sampled from Jiaozhou Bay, China. Critical bioinformatics analyses of the whole genome sequence assigned D1FHST as the type-strain to a new Nitrosococcus species, named Nitrosococcus wardiae, and revealed unique genetic features and its archetypal metabolic capacity in the ammonia-oxidizing gammaproteobacterial genus Nitrosococcus. Growth-physiological studies of its salt, ammonium and thermal tolerance confirmed that N. wardiae represented by strain D1FHST is distinct from other known Nitrosococcus species, including N. oceani, N. halophilus and N. watsonii. Presently, only Nitrosococcus oceani is represented by multiple strains isolated into pure culture from different oceanic gyres, several of which have been genome-sequenced. Comparative analysis of genome-sequenced strains of Nitrosococcus oceani from four different oceanic locations suggests that they have evolved by genome economization while maintaining a high level of identity in sequence and synteny, which correlates with their molecular defense capacity. Chemolithoautotrophic ammonia-oxidizing bacteria facilitate the process of nitritation as their sole catabolic activity. The Gammaproteobacterium Methylococcus capsulatus Bath (MCB) is also capable of oxidizing ammonia and hydroxylamine to nitrite but cannot support growth on this nitritation process. MCB, a nitrifying and denitrifying obligate methanotroph, is thus the best thinkable host for investigating the molecular basis of ammonia-dependent chemolithotrophy. Quantitative real-time PCR studies of steady-state mRNA levels revealed that genes involved in nitrification (haoA, haoB, cytL), denitrification (norC, norB, cytS) and ammonification (nirB, nasA) were differentially expressed with in the presence of ammonium, which is consistent with physiological observations. It is known that the Epsilonmicrobium Nautilia profundicola is able to use nitrate as a terminal electron acceptor and as a source of nitrogen in the absence of ammonium; however, it lacks any known ammonium-forming nitrite reductase. Because involvement of reversely operating nitritation inventory, the reverse "hydroxylamine ubiquinone redox module" (HURM), has been demonstrated to contribute to ammonification and respiration in Nautilia and other bacteria, expression constructs were designed to assess the function of the reverse-HURM pathway with further investigations ongoing.

Details
Author

Wang, Lin

Title

Comparative analysis of Nitrosococcus genomes; isolation, physiological and genomic characterization of the new ammonia-oxidizing species Nitrosococcus wardiae, strain D1FHST; and molecular studies towards a better understanding of ammonia-dependent chemolithotrophy

Physical Description

1 online resource (224 pages) : PDF

Date

2016

Degree Granting Institution

University of North Carolina at Charlotte

Abstract

Obligate aerobic chemolithoautotrophic ammonia-oxidzing bacteria (AOB) derive energy and reductant needed for growth solely from the oxidation of ammonia to nitrite thereby facilitating the process of nitritation. A strain of an ammonia-oxidizing Gammaproteobacterium, D1FHS, was isolated into pure culture from an enrichment of sediment sampled from Jiaozhou Bay, China. Critical bioinformatics analyses of the whole genome sequence assigned D1FHST as the type-strain to a new Nitrosococcus species, named Nitrosococcus wardiae, and revealed unique genetic features and its archetypal metabolic capacity in the ammonia-oxidizing gammaproteobacterial genus Nitrosococcus. Growth-physiological studies of its salt, ammonium and thermal tolerance confirmed that N. wardiae represented by strain D1FHST is distinct from other known Nitrosococcus species, including N. oceani, N. halophilus and N. watsonii. Presently, only Nitrosococcus oceani is represented by multiple strains isolated into pure culture from different oceanic gyres, several of which have been genome-sequenced. Comparative analysis of genome-sequenced strains of Nitrosococcus oceani from four different oceanic locations suggests that they have evolved by genome economization while maintaining a high level of identity in sequence and synteny, which correlates with their molecular defense capacity. Chemolithoautotrophic ammonia-oxidizing bacteria facilitate the process of nitritation as their sole catabolic activity. The Gammaproteobacterium Methylococcus capsulatus Bath (MCB) is also capable of oxidizing ammonia and hydroxylamine to nitrite but cannot support growth on this nitritation process. MCB, a nitrifying and denitrifying obligate methanotroph, is thus the best thinkable host for investigating the molecular basis of ammonia-dependent chemolithotrophy. Quantitative real-time PCR studies of steady-state mRNA levels revealed that genes involved in nitrification (haoA, haoB, cytL), denitrification (norC, norB, cytS) and ammonification (nirB, nasA) were differentially expressed with in the presence of ammonium, which is consistent with physiological observations. It is known that the Epsilonmicrobium Nautilia profundicola is able to use nitrate as a terminal electron acceptor and as a source of nitrogen in the absence of ammonium; however, it lacks any known ammonium-forming nitrite reductase. Because involvement of reversely operating nitritation inventory, the reverse "hydroxylamine ubiquinone redox module" (HURM), has been demonstrated to contribute to ammonification and respiration in Nautilia and other bacteria, expression constructs were designed to assess the function of the reverse-HURM pathway with further investigations ongoing.

Genre

doctoral dissertations

Subjects--Topics

Molecular biology
Biology
Genetics

Degree

Ph.D.

Keywords

Ammonia-Oxidizing Bacteria
Chemolithotrophy
Genomics
Nitrogen Cycle
Nitrosococcus Wardiae D1fhs

Subject Area

Biology

Advisor(s)

Klotz, Martin
Redmond, Molly

Committee Members

Steck, Todd
Parrow, Matthew
Fodor, Anthony

Degree Note

Thesis (Ph.D.)--University of North Carolina at Charlotte, 2016.

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Identifier

Wang_uncc_0694D_11226

Permalink

http://hdl.handle.net/20.500.13093/etd:264