![Loading full text...](/images/jp/spinner.gif)
Full text loading...
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.
Article metrics loading...
Full text loading...
Literature Cited
Data & Media loading...
Download Supplemental Table 1 (XLSX) Download Supplemental Table 2 (XLSX) Download Supplemental Table 3 (XLSX) Download Supplemental Figure 1: Phylogenetic tree of Prokaryota based on 16S rRNA gene sequences from type strain species. The tree is based on the tree implemented in the SSURefNR99_1200_slv_128 tree in the SILVA release 128 SSU Ref NR 99 database, released September 2016 (https://www.arb-silva.de/). Only selected sequences are shown. Groups containing chlorophototrophic members with homodimeric type-1 RCs are indicated in green; groups containing pufLM genes encoding type-2 RCs are marked in purple; and cyanobacteria containing Photosystem I and Photosystem II are indicated in blue. The numbers indicate the total number of sequences for each group. (PDF) Download Supplemental Figure 2: Phylogenetic tree of Cyanobacteria and additional major lines of descent based on 12599 16S rRNA gene sequences. The tree is based on the tree implemented in the SSURefNR99_1200_slv_128 tree in the SILVA release 128 SSU Ref NR 99 database, released September 2016 (https://www.arb-silva.de/). Groups containing Photosystem I and Photosystem II are indicated in blue. The numbers indicate the total number of sequences for each group. (PDF) Download Supplemental Figure 3: Phylogenetic overview tree of the phylum Proteobacteria based on 4797 16S rRNA gene sequences from type strain species. Tree is based on the SILVA Living Tree Project, LTP128_SSU, released February 2017 (s2,s3). Only selected proteobacterial sequences are shown. Groups containing chlorophototrophic members and/or genomes containing pufLM genes are marked in purple. (PDF) Download Supplemental Figure 4A and Supplemental Figure 4B : Phylogenetic tree of the phylum Proteobacteria based on 4797 16S rRNA gene sequences. The tree is showing detailed positions of chlorophototrohic members in the Alpha- (A) and the Beta/Gamma- (B) classes. The trees are based on the Living Tree Project (LTP) release 128 tree (s2,s3) with some additional sequences added. Sequences displayed in green represent species type strain sequence, while purple denotes the type species of a genus. Pink denotes short (<1300bp) sequences, and red color is indicating species with the presence of pufLM genes in the genome and/or verified BChl a production. (PDF) Download Supplemental Figure 5: Phylogenetic tree of the phylum Chlorobi based on 55 16S rRNA gene sequences. The tree was generated using the Maximum Likelihood method and the GTR model in the software package ARB (s1). Chlorophototrophic members (containing type-1 RCs) are marked in green. (PDF) Download Supplemental Figure 6: Phylogenetic tree of the phylum Chloroflexi based on 57 16S rRNA gene sequences. The tree was generated using the Maximum Likelihood method and the GTR model in the software package ARB (s1). Chlorophototrophic members (containing type-2 RCs) are marked in purple. (PDF) Download Supplemental Figure 7: Phylogenetic tree of selected members of the phyla Acidobacteria, Firmicutes and Gemmatimonadetes based on 82 16S rRNA gene sequences. The tree was generated using the Maximum Likelihood method and the GTR model in the software package ARB (s1). Chlorophototrophic members (containing type-1 RCs) are marked in green. (PDF) References for Supplemental Figures 1–7.
s1 Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. 2004. ARB: a software environment for sequence data. Nucl. Acids Res. 32:1363–71. doi: 10.1093/nar/gkh293.
s2 Munoz R, Yarza P, Ludwig W, Euzeby J, Amann R et al. 2011. Release LTPs104 of the All-Species Living Tree. Syst. Appl. Microbiol. 34:169–70. doi: 10.1016/j.syapm.2011.03.001.
s3 Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. 2008. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst. Appl. Microbiol. 31:241–50. doi: 10.1016/j.syapm.2008.07.001.