Sunlight-Harvesting Ocean Bacteria Turn Out Far More Diverse Than DNA Surveys Suggested

In the shallow, sunlit waters of Kaštela Bay on the Croatian coast, an extraordinary group of bacteria has been quietly rewriting what scientists thought they knew about life in the sea. Aerobic anoxygenic phototrophic, or AAP, bacteria are microorganisms that breathe oxygen and consume organic matter like ordinary heterotrophs, yet they also carry a molecular light-harvesting engine borrowed from the photosynthetic world. Using a pigment called bacteriochlorophyll a packed into type-II reaction centres, these cells supplement their metabolism with energy harvested from sunlight without ever splitting water or releasing oxygen. A new study of the central Adriatic Sea now reveals that the way these bacteria deploy their phototrophic machinery is far more lineage-specific, seasonal and lifestyle-dependent than standard DNA surveys have ever captured, with important consequences for how scientists model carbon cycling in coastal waters.

The research, led by Cristian Villena-Alemany of the Institute of Microbiology of the Czech Academy of Sciences together with colleagues in Croatia and the Czech Republic, was published in the journal Ocean Microbiology. The team sampled seawater from Kaštela Bay in February, May and July of 2023, separating the bacterial community into a free-living fraction and a total fraction that included bacteria attached to particles. For each sample they measured AAP abundance under the epifluorescence microscope, quantified bacteriochlorophyll a by high-performance liquid chromatography, and built both DNA and RNA amplicon libraries of the pufM gene, which encodes the M subunit of the anoxygenic reaction centre and serves as the standard taxonomic marker for this group. Sequencing hundreds of thousands of reads per sample on an Illumina MiSeq platform yielded more than a thousand distinct pufM sequence variants for analysis.

The seasonal signal was unmistakable. AAP abundance climbed from roughly 1.27 × 10⁴ cells per millilitre in winter to 8.30 × 10⁴ cells per millilitre in summer, peaking at 13.8 percent of the total bacterial community, a figure well above the 0.1 to 11 percent typically reported for the open ocean, the Baltic Sea, the Arctic and the Mediterranean. Bacteriochlorophyll a concentrations followed the same trajectory, reaching maxima of 4.23 and 3.76 nanograms per litre in summer and spring respectively. Critically, cell counts and pigment concentrations correlated strongly, allowing the authors to calculate that each AAP cell carries between roughly 1,600 and 11,200 reaction centres, corresponding to 2.14 × 10¹⁰ to 8.51 × 10¹¹ photosynthetic units per litre of seawater. This near-constant complement of reaction centres per cell across seasons and fractions suggests that changes in community phototrophic capacity are driven primarily by shifts in cell numbers rather than by cells tinkering with their pigment investment.

The more surprising findings emerged when the team compared the total community, read from DNA, against the phototrophically active community, read from RNA transcripts of pufM. The two libraries told strikingly different stories. In winter, DNA amplicons suggested a community dominated by the genus Luminiphilus, but the RNA library revealed a much more diverse active assemblage in which several genera of Burkholderiales, along with Rhizobiales, Limnohabitans and Rhodoferax, were punching far above their genetic weight. In spring, Luminiphilus dominated both libraries, yet the transcript data showed that genera such as UBA9115, Limnohabitans and Rhodoferax were expressing their phototrophy genes at levels their DNA abundance never predicted. In summer, the season of peak photoheterotrophy, the gap widened further: Arenicellales UBA868 drastically overexpressed its phototrophy genes in the free-living fraction relative to its DNA signal, while the coastal lineage Rhodobacterales HIMB11 was underrepresented in DNA libraries from the particle-attached fraction despite its activity.

These discrepancies mean that the conventional practice of estimating phototrophic potential from DNA-based pufM amplicons can seriously distort the picture of which bacteria are actually harvesting light. Some abundant lineages, notably Luminiphilus, appear to coast along with their phototrophy genes largely switched down, inflating their apparent importance in gene surveys. Meanwhile, rarer lineages that barely register in DNA libraries are working overtime at the transcript level, quietly contributing to the community’s light-driven metabolism. The pattern echoes earlier observations from freshwater lakes, where gene presence likewise failed to guarantee gene expression, but this is among the clearest demonstrations that the same principle holds in the sea. For modellers of marine carbon fluxes, the implication is sobering: knowing which phototrophs are present is not the same as knowing which ones are plugged into the sun.

Lifestyle added a second, equally consequential layer of structure. Bacteriochlorophyll a concentrations were consistently higher in the particle-attached fraction than in the free-living fraction during winter and spring, and the active community compositions of the two fractions diverged markedly. Luminiphilus tended to express its phototrophy genes more when living freely, whereas Rhizobiales, Limnohabitans, Rhodoferax and other Burkholderiales preferred to switch on their light-harvesting machinery while clinging to particles. In summer, free-living Arenicellales UBA868 was highly active, while particle-attached communities saw a dramatic surge in pufM expression from Rhodobacterales HIMB11, which at its peak accounted for more than 66 percent of the active AAP assemblage when both AAP abundance and phototrophy were at their annual maximum. Because the total fraction also contains free-living cells, the authors note that these fraction differences are likely conservative estimates, and the true contrast between attached and free lifestyles may be even sharper.

The study also captured a fingerprint of the bay’s transitional character. Kaštela Bay receives freshwater from the nearby Jadro River and from rain runoff, and in winter and spring the team detected phototrophic lineages classically associated with freshwaters, including Rhodoferax, Limnohabitans and certain Rhizobiales. Remarkably, these were not merely passive immigrants swept in by currents; they were transcriptionally active, particularly in the particle-attached fraction, indicating that allochthonous phototrophs can participate meaningfully in coastal photoheterotrophy. Together with the estuary-derived Arenicellales UBA868 and the coastal HIMB11 lineage, the picture is one of a dynamic mixing zone where freshwater, estuarine and fully marine phototrophic strategies overlap and trade dominance across the seasons.

Why should a ship’s worth of seawater genetics matter to anyone beyond microbial ecologists? AAP bacteria are believed to play a significant role in the microbial loop, the pathway by which dissolved organic carbon is recycled into the food web rather than exported to the deep ocean. Culture experiments have shown that light-exposed AAP cells respire less and accumulate more biomass, and field studies have demonstrated that infrared illumination, which selectively feeds AAP phototrophy, reduces community respiration and boosts uptake of labelled organic substrates. If particular lineages perform disproportionate amounts of photoheterotrophy, and if that performance depends on whether cells are attached to particles or drifting free, then carbon models built on averages will systematically misjudge how much solar energy flows through these bacteria and where in the water column that flow occurs. The pronounced partitioning of AAP diversity and activity between fractions documented here suggests that particles may function as hotspots of light-driven organic matter consumption, especially in winter and spring.

The authors are careful about the limits of their snapshot. All samples were collected in the morning, and previous work has shown that phototrophy gene expression can vary across the day-night cycle, so lineages appearing transcriptionally silent at dawn may simply operate on a different schedule, as has been observed in the phylum Gemmatimonadota. The chemical composition of the particles themselves, which likely shapes the attached lifestyle’s appeal, was not characterised. High-resolution diel transcriptomics, the authors suggest, would clarify how daily light cycles regulate marine AAP gene expression. Even so, the central conclusion stands firmly: the marine AAP community is a heterogeneous federation of lineages, each with its own niche preferences for where to live and when to harvest light, and only transcript-based approaches can reveal which members are truly earning their living from the sun at any given moment.

For a group of bacteria first recognised in the late 1970s as curiosities of aerobic heterotrophy, AAP organisms have come a long way toward centre stage in marine biogeochemistry. This Adriatic study adds a crucial nuance: their ecological role is written not in the inventory of genes floating in the water, but in the shifting transcriptomes of cells negotiating season, substrate and lifestyle. As sequencing technologies mature and RNA-based monitoring becomes routine, coastal carbon budgets may need recalibration to account for the hidden phototrophs that DNA surveys have been overcounting and undercounting all at once. In the sunlit waters of the world’s coastal seas, the business of harvesting light, it turns out, is conducted by a rotating cast of specialists whose identities change with the calendar, and whose work only becomes visible when scientists listen for the transcripts rather than tally the genes.

Subject of Research: Lineage-specific phototrophy and lifestyle strategies of aerobic anoxygenic phototrophic bacteria in coastal marine waters

Article Title: Lineage-specific phototrophy and lifestyle of coastal marine aerobic anoxygenic phototrophs

Article References: Villena-Alemany, C., Tomaš, A. V., Mujakić, I., Kopejtka, K., Šantić, D., & Koblížek, M. (2025). Lineage-specific phototrophy and lifestyle of coastal marine aerobic anoxygenic phototrophs. Ocean Microbiology, 1(1), Article 5. https://doi.org/10.1186/s44375-025-00005-x

Image Credits: AI Generated

DOI: 10.1186/s44375-025-00005-x

Keywords: aerobic anoxygenic phototrophs, photoheterotrophy, pufM gene expression, Adriatic Sea, marine microbiology, particle-attached bacteria, free-living bacteria, bacteriochlorophyll a, carbon cycling, RNA transcripts, Luminiphilus, coastal waters