Ecophysiology and Metabolism of Green Bacteria Inferred from -omics Studies
Open Access
- Author:
- Liu, Zhenfeng
- Graduate Program:
- Biochemistry, Microbiology, and Molecular Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- February 07, 2012
- Committee Members:
- Donald Bryant, Dissertation Advisor/Co-Advisor
Sarah Ellen Ades, Committee Member
Stephan Schuster, Committee Member
Christopher Howard House, Committee Member - Keywords:
- Green Bacteria
Chlorobi
Genomics
Metagenomics
Metatranscriptomics
Bacteriochlorophyll - Abstract:
- Green bacteria are a subset of chlorophototrophic bacteria that use a specialized light-harvesting structure, the chlorosome, which enables them to grow under low-light conditions. Green bacteria, which consist of members of three phyla, Chlorobi, Chloroflexi, and Acidobacteria, are widely spread and ecologically important. Green bacteria are physiologically diverse as a group, but their members from the phylum Chlorobi, known as green sulfur bacteria (GSB), are strikingly uniform in their physiology—nearly all are anaerobic photoautotrophs that oxidize sulfide. This work takes advantage of DNA sequencing technologies that have experienced dramatic advances recently to investigate different aspects of physiology and metabolism, on multiple levels from genes to single organisms and beyond to bacterial communities. Genome data for fifteen GSB strains revealed the genomic basis of the physiological congruence among them. Comparisons among genomes of different strains also provided information on the phylogeny, genome structure, and genes specific to each lineage. Sequence data suggested dramatically different physiologies for two members of the Chlorobi, Ignavibacterium album (I. album) and “Candidatus Thermochlorobacter aerophilum” (“Ca. T. aerophilum”). The complete genome sequence of I. album indicated that it is a versatile, facultative anaerobic organoheterotroph. A combination of metagenomic and metatranscriptomic studies suggested that the uncultured “Ca. T. aerophilum” is an aerobic photoheterotroph that cannot oxidize sulfide. These data suggested that there is much more physiological diversity within the phylum Chlorobi than generally assumed. Comparisons of these two organisms with GSB implied that ancestors of the phylum Chlorobi might be very different from extant GSB. Metatranscriptomic analyses of the photosynthetic microbial community that harbors “Ca. T. aerophilum” showed that the community included seven populations of chlorophototrophs with very different life styles, which exhibit patterns of expression of their photosynthesis genes. Complete genome sequences of the two partners of the phototrophic consortium “Chlorochromatium aggregatum,” one of which is a GSB, provided insights into the physiological and metabolic basis for the symbiotic relationship between the two. These data suggested that the two organisms have specialized roles in the consortium: the GSB partner is the primary producer and provider of nutrients while the betaproteobacterial partner is responsible for sensing the environment and motility of the consortium. Schemes for potential interspecies electron transfer were proposed. Last but not least, one of the many hypotheses generated from sequence analyses was tested and verified by experimental studies. A gene involved in the biosynthesis of bacteriochlorphylls c, d, and e, which are main components of the chlorosome, was identified by comparative genomics and characterized by genetic and biochemical approaches. Results showed that the gene is essential for the first committed step in the biosynthetic pathway leading from chlorophyllide a to the three bacteriochlorophylls. Overall, this work offered answers to several high-interest research questions concerning green bacteria and provided invaluable resources for future research.