Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica

The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64T, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m-2 s-1, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m-2 s-1) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

IMPORTANCE

Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.

Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon

Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.

Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch

The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.

Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes

BACKGROUND

During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates.

RESULTS

During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria.

CONCLUSIONS

Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.

Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network

BACKGROUND

Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of the microbial food chain. Despite their considerable contribution to the transformation of organic matter in marine environments, relatively little is still known about their community structure and ecology at fine-scale taxonomic resolution. Up to date, there is no comprehensive (i.e. qualitative and quantitative) analysis of their community composition in the Adriatic Sea.

RESULTS

Analysis was based on pufM gene metabarcoding and quantitative FISH-IR approach with the use of artificial neural network. Significant seasonality was observed with regards to absolute abundances (maximum average abundances in spring 2.136 ± 0.081 × 104 cells mL-1, minimum in summer 0.86 × 104 cells mL-1), FISH-IR groups (Roseobacter clade prevalent in autumn, other Alpha- and Gammaproteobacteria in summer) and pufM sequencing data agglomerated at genus-level. FISH-IR results revealed heterogeneity with the highest average relative contribution of AAPs assigned to Roseobacter clade (37.66%), followed by Gammaproteobacteria (35.25%) and general Alphaproteobacteria (31.15%). Community composition obtained via pufM sequencing was dominated by Gammaproteobacteria clade NOR5/OM60, specifically genus Luminiphilus, with numerous rare genera present in relative abundances below 1%. The use of artificial neural network connected this community to biotic (heterotrophic bacteria, HNA and LNA bacteria, Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic nanoflagellates, bacterial production) and abiotic environmental factors (temperature, salinity, chlorophyll a and nitrate, nitrite, ammonia, total nitrogen, silicate, and orthophosphate concentration). A type of neural network, neural gas analysis at order-, genus- and ASV-level, resulted in five distinct best matching units (representing particular environments) and revealed that high diversity was generally independent of temperature, salinity, and trophic status of the environment, indicating a potentially dissimilar behaviour of aerobic anoxygenic phototrophs compared to the general bacterioplankton.

CONCLUSION

This research represents the first comprehensive analysis of aerobic anoxygenic phototrophs in the Adriatic Sea on a trophic gradient during a year-round period. This study is also one of the first reports of their genus-level ecology linked to biotic and abiotic environmental factors revealed by unsupervised neural network algorithm, paving the way for further research of substantial contribution of this important bacterial functional group to marine ecosystems.

Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics

Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.

Urbanization influences dissolved organic matter characteristics but microbes affect greenhouse gas concentrations in lakes

Recognition and prediction of dissolved organic matter (DOM) properties and greenhouse gas (GHG) emissions is critical to understanding climate change and the fate of carbon in aquatic ecosystems, but related data is challenging to interpret due to covariance in multiple natural and anthropogenic variables with high spatial and temporal heterogeneity. Here, machine learning modeling combined with environmental analysis reveals that urbanization (e.g., population density and artificial surfaces) rather than geography determines DOM composition and properties in lakes. The structure of the bacterial community is the dominant factor determining GHG emissions from lakes. Urbanization increases DOM bioavailability and decreases the DOM degradation index (Ideg), increasing the potential for DOM conversion into inorganic carbon in lakes. The traditional fossil fuel-based path (SSP5) scenario increases carbon emission potential. Land conversion from water bodies into artificial surfaces causes organic carbon burial. It is predicted that increased urbanization will accelerate the carbon cycle in lake ecosystems in the future, which deserves attention in climate models and in the management of global warming.

Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria

Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge of the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark-light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark-light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light-induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.

Diverse aerobic anoxygenic phototrophs synthesize bacteriochlorophyll in oligotrophic rather than copiotrophic conditions, suggesting ecological niche

While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species were examined simultaneously, identifying conditions for optimal growth or pigment production to determine features that may unify this group of phototrophs. All were distributed among assorted α-Proteobacterial families including Erythrobacteraceae, Sphingomonadaceae, Sphingosinicellaceae, Acetobacteraceae, Methylobacteriaceae, and Rhodobacteraceae. Major phenotypic characteristics matched phylogenetic association, including pigmentation, morphology, metal transformations, tolerances, lipid configurations, and enzyme activities, which distinctly separated each taxonomic family. While varying pH and temperature had a limited independent impact on pigment production, bacteriochlorophyll synthesis was distinctly promoted under low nutrient conditions, whereas copiotrophy repressed its production but enhanced carotenoid yield. New AAP diversity was also reported by revealing strains related to non-phototrophic Rubellimicrobium and Sphingorhabdus, as well as spread throughout Roseomonas, Sphingomonas, and Methylobacterium/Methylorubrum, which previously only had a few known photosynthetic members. This study exemplified the overwhelming diversity of AAP in a single aquatic environment, confirming cultivation continues to be of importance in microbial ecology to discover functionality in both new and previously reported cohorts of bacteria as specific laboratory conditions were required to promote aerobic bacteriochlorophyll production.

DOM Associates with Greenhouse Gas Emissions in Chinese Rivers under Diverse Land Uses

Growing evidence indicates that rivers are hotspots of greenhouse gas (GHG) emissions and play multiple roles in the global carbon budget. However, the roles of terrestrial carbon from land use in river GHG emissions remain largely unknown. We studied the microbial composition, dissolved organic matter (DOM) properties, and GHG emission responses to different landcovers in rivers (n = 100). The bacterial community was mainly constrained by land-use intensity, whereas the fungal community was mainly controlled by DOM chemical composition (e.g., terrestrial DOM with high photoreactivity). Anthropogenic stressors (e.g., land-use intensity, gross regional domestic product, and total population) were the main factors affecting chromophoric DOM (CDOM). DOM biodegradability exhibited a positive correlation with CDOM and contributed to microbial activity for DOM transformation. Variations in CO2 and CH4 emissions were governed by the biodegradation or photomineralization of dissolved organic carbon derived from autotrophic DOM and were indirectly affected by land use via changes in DOM properties and water chemistry. Because the GHG emissions of rivers offset some of the climatic benefits of terrestrial carbon (or ocean) sinks, intensified urban land use inevitably alters carbon cycling and changes the regional microclimate.

A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs

Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.

Biosynthetic gene profiling and genomic potential of the novel photosynthetic marine bacterium Roseibaca domitiana

Shifting the bioprospecting targets toward underexplored bacterial groups combined with genome mining studies contributes to avoiding the rediscovery of known compounds by revealing novel, promising biosynthetic gene clusters (BGCs). With the aim of determining the biosynthetic potential of a novel marine bacterium, strain V10T, isolated from the Domitian littoral in Italy, a comparative phylogenomic mining study was performed across related photosynthetic bacterial groups from an evolutionary perspective. Studies on polyphasic and taxogenomics showed that this bacterium constitutes a new species, designated Roseibaca domitiana sp. nov. To date, this genus has only one other validly described species, which was isolated from a hypersaline Antarctic lake. The genomic evolutionary study linked to BGC diversity revealed that there is a close relationship between the phylogenetic distance of the members of the photosynthetic genera Roseibaca, Roseinatronobacter, and Rhodobaca and their BGC profiles, whose conservation pattern allows discriminating between these genera. On the contrary, the rest of the species related to Roseibaca domitiana exhibited an individual species pattern unrelated to genome size or source of isolation. This study showed that photosynthetic strains possess a streamlined content of BGCs, of which 94.34% of the clusters with biotechnological interest (NRPS, PKS, RRE, and RiPP) are completely new. Among these stand out T1PKS, exclusive of R. domitiana V10T, and RRE, highly conserved only in R. domitiana V10T and R. ekhonensis, both categories of BGCs involved in the synthesis of plant growth-promoting compounds and antitumoral compounds, respectively. In all cases, with very low homology with already patented molecules. Our findings reveal the high biosynthetic potential of infrequently cultured bacterial groups, suggesting the need to redirect attention to microbial minorities as a novel and vast source of bioactive compounds still to be exploited.

Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat

Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.

Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake

Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.

A bacterium from a mountain lake harvests light using both proton-pumping xanthorhodopsins and bacteriochlorophyll-based photosystems

Photoheterotrophic bacteria harvest light energy using either proton-pumping rhodopsins or bacteriochlorophyll (BChl)-based photosystems. The bacterium Sphingomonas glacialis AAP5 isolated from the alpine lake Gossenköllesee contains genes for both systems. Here, we show that BChl is expressed between 4°C and 22°C in the dark, whereas xanthorhodopsin is expressed only at temperatures below 16°C and in the presence of light. Thus, cells grown at low temperatures under a natural light-dark cycle contain both BChl-based photosystems and xanthorhodopsins with a nostoxanthin antenna. Flash photolysis measurements proved that both systems are photochemically active. The captured light energy is used for ATP synthesis and stimulates growth. Thus, S. glacialis AAP5 represents a chlorophototrophic and a retinalophototrophic organism. Our analyses suggest that simple xanthorhodopsin may be preferred by the cells under higher light and low temperatures, whereas larger BChl-based photosystems may perform better at lower light intensities. This indicates that the use of two systems for light harvesting may represent an evolutionary adaptation to the specific environmental conditions found in alpine lakes and other analogous ecosystems, allowing bacteria to alternate their light-harvesting machinery in response to large seasonal changes of irradiance and temperature.