Abstract
Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
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Chlorophyll-based phototrophy sustains life on Earth through the conversion of light into biologically usable energy5,6. Diverse microorganisms affiliated with at least eight bacterial phyla, discovered over nearly 200 years of scientific exploration7,8,9,10,11,12,13,14,15, perform this key process. Although these bacteria share common phototrophic ancestry1,16, many steps in their diversification remain unclear. Substantial gaps in the evolutionary record of phototrophy, apparent through inconsistent topology of photosynthesis gene phylogenies2,17 and a lack of transition forms between anoxygenic and oxygenic phototrophs16, have hindered our ability to answer fundamental questions about the order and timing of phototrophic evolution17,18. Discovery of evolutionary intermediates between known radiations of phototrophic life can help to resolve how phototrophs gained their modern functional characteristics.
Anoxygenic phototrophs belonging to the Chloroflexota (formerly Chloroflexi) phylum were first cultivated nearly 50 years ago11 and have since been characterized from diverse aquatic ecosystems19,20,21,22, but the evolution of phototrophy in this group has remained unclear. All known phototrophic Chloroflexota members use a RCII for light energy conversion7,23,24, yet several phototrophs within the Chloroflexota also contain chlorosomes, which are bacteriochlorophyll c-containing protein–pigment complexes, involved in light harvesting3,25, that are otherwise associated with RCI13. Although structurally homologous, RCI and RCII are functionally distinct and are well separated in the modern tree of life1,16,26. With the exception of oxygenic phototrophs, the only known lineage where RCI and RCII are used in tandem for electron flow16, each major lineage of phototrophic life is associated with only one of these two reaction centre classes7,27, and no examples of gene exchange between RCI-utilizing and RCII-utilizing phototroph groups have been reported in nature. How RCI-associated genes came to be encoded by RCII-utilizing Chloroflexota members thus represents an enigma linked to fundamental knowledge gaps in how the major modes of phototrophy diversified16,17,18.
Here we report the cultivation of a highly novel phototrophic bacterium that is phylogenetically related to known RCII-utilizing Chloroflexota members but uses chlorosomes and RCI, not RCII, for conversion of light energy. Discovery of the novel bacterium clarifies how chlorosomes came to be used by modern Chloroflexota members and substantially revises our view of the diversity of phototrophy. In this work, we demonstrate active usage of RCI by the novel strain and discuss the implications of our findings for the evolution of photosynthesis.
Enrichment cultivation
With the original intention of cultivating anoxygenic phototrophs from the Chlorobiales order (phylum Bacteroidota), we sampled the anoxic water column of an iron-rich Boreal Shield lake (Extended Data Fig. 1a–c) and gradually amended lake water, incubated under light, with a previously published freshwater medium28 and ferrous chloride, using Diuron as an inhibitor of oxygenic phototrophs (Extended Data Fig. 1d). On the basis of 16S rRNA gene profiles, some of the incubated batch cultures developed high relative abundances of novel microbial populations that were only distantly associated with known Chloroflexota members (Supplementary Data 1). We used agar-containing medium to further enrich a novel strain, named L227-S17, from one batch culture that represented one of the sequence variants from earlier culture profiles (Extended Data Fig. 1e). In addition, via metagenome sequencing of a separate batch culture, we recovered a metagenome-assembled genome (MAG) corresponding to a second novel sequence variant, named strain L227-5C (Extended Data Fig. 1e and Supplementary Note 1).
After 19 subcultures over 4 years, strain L227-S17 was brought into a stable enrichment culture that included a putative iron-reducing bacterium, associated with the Geothrix genus29, named strain L227-G1 (Extended Data Fig. 1f and Supplementary Note 1). Under phototrophic growth conditions, only strains L227-S17 and L227-G1 were detectable in the culture, using 16S rRNA gene amplicon sequencing, to a detection limit of 0.004% (Extended Data Fig. 1f), allowing us to characterize the physiology of strain L227-S17 within a two-member culture system. On the basis of the RCI-utilizing phototrophic metabolism of L227-S17, we provisionally name the strain ‘Candidatus Chlorohelix allophototropha’ (a green spiral, phototrophic in a different way; the full etymology is provided in the ‘Species description’ section).
Phototrophic physiology
We compared the phototrophic properties of the L227-S17 enrichment culture to properties of known bacterial phototrophs (Fig. 1 and Extended Data Fig. 2). The in vivo absorption spectrum of the culture included a strong absorbance peak at 749 nm, which is characteristic of chlorosome-containing phototrophic bacteria13 (Fig. 1a and Extended Data Fig. 2a; see Extended Data Table 1 for microbial community data associated with spectroscopy and microscopy analyses). Using high-performance liquid chromatography, we confirmed that the L227-S17 culture contained multiple bacteriochlorophyll c species that had absorbance peaks at 435 nm and 667 nm (ref. 13) (Fig. 1b,c), as well as bacteriochlorophyll a that can serve as a core reaction centre pigment30 (Supplementary Fig. 1). Large spiralling filaments composed of cells 0.5–0.6 µm wide and 2–10 µm long were visible in the culture (Fig. 1d,e) and were accompanied by smaller rod-shaped cells. The rod-shaped cells corresponded to the Geothrix L227-G1 strain based on enrichment of L227-G1 under dark conditions and subsequent microscopy (Extended Data Fig. 2b). Thus, we could establish that strain L227-S17 corresponded to the filamentous cells. The inner membranes of the filamentous cells contained electron-transparent and spherical structures, which matched the expected appearance of chlorosomes after fixation with osmium tetroxide31 (Fig. 1e and Extended Data Fig. 2c). Furthermore, strain L227-S17 and the 749-nm absorbance peak were consistently absent when the culture was incubated in the dark (Fig. 1f,g and Extended Data Fig. 2d). Although the culture was typically grown photoheterotrophically to stabilize growth, we could also grow the culture photoautotrophically and reproduce the loss of strain L227-S17 in the dark (Extended Data Fig. 2e,f). These data demonstrate that strain L227-S17 is the phototrophic and chlorosome-containing member of the enrichment culture.
a, In vivo absorption spectrum of the L227-S17 culture compared with reference cultures. The inset shows the 760–925-nm region with spectra separated on the y axis. a.u., arbitrary units. b,c, Bacteriochlorophyll c species in the cultures. High-performance liquid chromatography (HPLC) profiles (b) and the in vitro absorption spectra associated with the largest HPLC peaks in the profiles (c) are shown. The largest HPLC peaks are marked with an asterisk in b. d, Scanning electron microscopy image of L227-S17 colony material from an early enrichment culture. e, Transmission electron microscopy image showing a longitudinal section of cells from an early L227-S17 enrichment culture. An example chlorosome-like structure is marked with an arrow. Scale bars, 3 μm (d) and 0.3 μm (e). Panels d and e are representative of imaging repeated more than five times on different regions of the same or related sample preparations. f,g, Light versus dark growth test of the L227-S17 culture amended with iron(II) and acetate. In vivo absorption spectra (f) and a heatmap of relative abundances (%) of 16S rRNA gene operational taxonomic units (g) are shown for the culture after two subcultures in the light or dark. Standard deviations (n = 3; biological replicate cultures) of the mean are shown as shaded areas in f. bdl, below detection limit.
Our spectroscopic data indicate that strain L227-S17 uses a related but novel phototrophic pathway compared with the RCII-utilizing Chloroflexus aurantiacus, a chlorosome-containing and phototrophic Chloroflexota member11. Although both strains shared the major chlorosome-associated peak at 740–750 nm in their in vivo absorption spectra, the spectrum of C. aurantiacus had additional absorbance peaks at 798 nm and 867 nm (Fig. 1a, inset). These peaks, as observed previously1e), we obtained a closed genome bin for the Geothrix L227-G1 partner strain that consisted of a single circular chromosome (3.73 Mb) and encoded no phototrophic marker genes.
We found no evidence of the RCII-associated pufLM genes, used by all known phototrophic Chloroflexota members, in the strain L227-S17 genome. Instead, we identified a remote homologue of known RCI genes, analogous to pscAMethods) of each MAG, and MAGs with greater than 1% relative expression are shown. Standard deviations were 7.0% of the mean on average; see Supplementary Data 5 for exact values. All MAGs had greater than 90% estimated completion unless indicated beside the MAG ID. RPP, reductive pentose phosphate. e, Gene expression of bin ELA319 in the Lake 221 (5 m) dataset. Mean normalized gene expression values are shown for the top 30 highest expressed protein-coding genes; the error bars show the standard deviation of metatranscriptomes derived from biological replicate filters (n = 3). Additional gene expression data are presented in Extended Data Fig. 7 and Supplementary Data 6.
We probed the in situ gene expression of the two RCI-encoding Chloroflexota MAGs using metatranscriptomes associated with the illuminated and anoxic water columns of lakes 221 and 304. Light penetration into the anoxic zones of lakes 221 and 304 (Fig. 4c) was roughly an order of magnitude higher than Lake 227 (Extended Data Fig. 1c), where a surface cyanobacterial bloom blocks light penetration in the summer42,43. The two RCI-encoding Chloroflexota MAGs were highly active compared with other bacterial populations based on RNA data, recruiting as much as 1.8% of mappable metatranscriptome reads from the Lake 221 and Lake 304 samples (Fig. 4d and Supplementary Data 5). Both MAGs had upregulated expression of the pscA-like RCI gene, the fmoA gene and the rbcLS genes encoding RuBisCO (Fig. 4e; the full dataset is available in Extended Data Fig. 7 and Supplementary Data 6). The MAGs also had high expression levels of homologues of gvpA, involved in the formation of gas vesicles that may function in buoyancy regulation44. Moreover, the MAGs co-occurred with RCII-encoding Chloroflexota and RCI-encoding Chlorobiales-associated MAGs, which were among the highest RNA read-recruiting MAGs in the dataset (Fig. 4d). Our data thus demonstrate that RCI-based phototrophy is actively used by Chloroflexota members in natural environments. These RCI-utilizing Chloroflexota members potentially form part of a more complex phototrophic microbial consortium in Boreal Shield lake anoxic waters. Given that Boreal Shield lakes number in the millions globally42 and might commonly develop iron-rich and anoxic bottom waters, as observed in Fennoscandian lakes geographically distant from the lakes presented in this study45, phototrophic consortia including RCI-utilizing Chloroflexota members could be relevant to widespread northern ecosystems.