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Genome Announc. 2017 March; 5(13): e01584-16.
Published online 2017 March 30. doi:  10.1128/genomeA.01584-16
PMCID: PMC5374249

Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans

ABSTRACT

Here, we report the draft genome sequence of Chlorobium phaeoferrooxidans, a photoferrotrophic member of the genus Chlorobium in the phylum Chlorobi. This genome sequence provides insight into the metabolic capacity that underpins photoferrotrophy within low-light-adapted pelagic Chlorobi.

GENOME ANNOUNCEMENT

Members of the bacterial phylum Chlorobi are best known for growth through anoxygenic photosynthesis, oxidizing reduced sulfur to replace electrons lost from the photosystem during fixation of CO2 into biomass (1). One previously cultured Chlorobi member, Chlorobium ferrooxidans strain KoFox, however, grows by oxidizing ferrous iron [Fe(II)] instead of reduced sulfur (2). Over long stretches of Earth’s history during the Precambrian eons, the oceans were anoxic and Fe(II) rich (ferruginous) (3), making photoferrotrophy the most likely mode of primary production (4, 5). Photoferrotrophs are also implicated in the deposition of the world’s largest iron ore deposits, banded iron formations (BIFs), which deposited from ferruginous oceans (6, 7). C. ferrooxidans strain KoFox and all other photoferrotrophs in previous culture collections were isolated from benthic habitats, making them imperfect analogues of the pelagic photoferrotrophs that likely deposited BIFs and supported early Earth primary production. Chlorobium phaeoferrooxidans was isolated from the water column of a ferruginous subbasin of Lake Kivu (East Africa), bringing the first known pelagic photoferrotroph into culture (8).

The 16S rRNA gene of C. phaeoferrooxidans is 99% similar to that of C. ferrooxidans strain KoFox (8), but the two organisms have distinct physiological characteristics (8). C. phaeoferrooxidans grows in axenia, whereas KoFox grows in coculture with Geospirillum sp. strain KoFum. C. phaeoferrooxidans is adapted to low light, using bacteriochlorophyll (BChl) e as its light-harnessing pigment, rather than the BChl c used in KoFox. The genome of C. phaeoferrooxidans was sequenced to determine the metabolic capacity of pelagic photoferrotrophic organisms and inform models for photoferrotrophy during the Precambrian eons.

C. phaeoferrooxidans was grown and its DNA extracted and purified as previously described (8, 9). Genomic DNA was subjected to Illumina paired-end library construction and sequenced (MiSeq platform, version 3 chemistry) to generate 16,133,652 paired 250-nucleotide (nt) reads. Quality-filtered reads were assembled into 116 contigs, with an N50 of 44,807 bp, using ABySS 1.3.5 (10), with default settings. The genome was screened for contaminants based on coverage, G+C composition (49.72%), and conserved single-copy genes. Open reading frame (ORF) prediction and annotation were conducted using MetaPathways (11).

The draft genome is 2.573 Mb, with 2,403 predicted ORFs, one 16S rRNA gene, 51 tRNA genes, and two clustered regularly interspaced short palindromic repeat (CRISPR) arrays. It is 99.45% complete based on 272 conserved single-copy genes (12) and only 71% identical to strain KoFox at the nucleotide level. This genome-level diversity is the basis for defining the two organisms as different species. The C. phaeoferrooxidans genome encodes an assimilatory sulfur metabolism but not the canonical oxidative sulfur metabolisms found in most other Chlorobi. C. phaeoferrooxidans has the genomic capacity to fix carbon using the reverse tricarboxylic acid (TCA) cycle, key genes for the type 1 photosynthetic reaction center, and the Fenna-Matthews-Olson complex characteristic of the Chlorobi (13). The genome also encodes an outer membrane cytochrome (cyc2PV-1) implicated in Fe(II) oxidation in the microaeorphillic Fe(II)-oxidizing zetaproteobacterium Mariprofundus ferrooxidans strain PV1 (14). These data expand the metabolic blueprint for photoferrotrophy in the Chlorobi and provide an opportunity to define the physiological basis for BIF deposition and primary production in the Precambrian oceans.

Accession number(s).

This whole-genome shotgun project has been deposited in GenBank under the accession no. MPJE00000000. The version described in this paper is the first version.

Footnotes

Citation Crowe SA, Hahn AS, Morgan-Lang C, Thompson KJ, Simister RL, Llirós M, Hirst M, Hallam SJ. 2017. Draft genome sequence of the pelagic photoferrotroph Chlorobium phaeoferrooxidans. Genome Announc 5:e01584-16. https://doi.org/10.1128/genomeA.01584-16.

REFERENCES

1. Overmann J. 2006. The family Chlorobiaceae, p 359–378. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (ed), The prokaryotes. Vol 7: proteobacteria: delta and epsilon subclasses. Springer, New York, NY.
2. Heising S, Richter L, Ludwig W, Schink B 1999. Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with a ‘Geospirillum’ sp. strain. Arch Microbiol 172:116–124. [PubMed]
3. Poulton SW, Canfield DE 2011. Ferruginous conditions: a dominant feature of the ocean through Earth’s history. Elements 7:107–112.
4. Canfield DE, Rosing MT, Bjerrum C 2006. Early anaerobic metabolisms. Philos Trans R Soc Lond B Biol Sci 361:1819–1836. doi:.10.1098/rstb.2006.1906 [PMC free article] [PubMed] [Cross Ref]
5. Jones C, Nomosatryo S, Crowe SA, Bjerrum CJ, Canfield DE 2015. Iron oxides, divalent cations, silica, and the early earth phosphorus crisis. Geology 43:135–138.
6. Kappler A, Pasquero C, Konhauser KO, Newman DK 2005. Deposition of banded iron formations by anoxygenic phototrophic Fe(II)-oxidizing bacteria. Geology 33:865–868.
7. Konhauser KO, Hamade T, Raiswell R, Morris RC, Ferris FG, Southam G, Canfield DE 2002. Could bacteria have formed the Precambrian banded iron formations? Geology 30:1079–1082.
8. Llirós M, García-Armisen T, Darchambeau F, Morana C, Triadó-Margarit X, Inceoğlu Ö, Borrego CM, Bouillon S, Servais P, Borges AV, Descy JP 2015. Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin. Sci Rep 5:13803. [PMC free article] [PubMed]
9. Lee S, Hallam SJ 2009. Extraction of high molecular weight genomic DNA from soils and sediments. J Vis Exp 33:e1569. doi:.10.3791/1569 [PubMed] [Cross Ref]
10. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123. doi:.10.1101/gr.089532.108 [PubMed] [Cross Ref]
11. Konwar KM, Hanson NW, Pagé AP, Hallam SJ 2013. MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. BMC Bioinformatics 14:202. doi:.10.1186/1471-2105-14-202 [PMC free article] [PubMed] [Cross Ref]
12. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi:.10.1101/gr.186072.114 [PubMed] [Cross Ref]
13. Frigaard NU, Bryant DA 2008. Genomic and evolutionary perspectives on sulfur metabolism in green sulfur bacteria, p 60–76. In Dahl C, Friedrich CG (ed), Microbial sulfur metabolism. Springer Berlin Heidelberg, Heidelberg, Germany.
14. Barco RA, Emerson D, Sylvan JB, Orcutt BN, Jacobson Meyers MEJ, Ramírez GA, Zhong JD, Edwards KJ 2015. New insight into microbial iron oxidation as revealed by the proteomic profile of an obligate iron-oxidizing chemolithoautotroph. Appl Environ Microbiol 81:5927–5937. doi:.10.1128/AEM.01374-15 [PMC free article] [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)