Photoheterotrophic Bacteria Research Articles

Light–dark cycles improve the 3HV molar fraction in PHBV produced by photoheterotrophic bacteria from odd‐chain fatty acids and cheese whey

Light–dark cycles improve the <scp>3HV</scp> molar fraction in <scp>PHBV</scp> produced by photoheterotrophic bacteria from odd‐chain fatty acids and cheese whey

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.

A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer.

During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.

Continuous dark-photo fermentative H2 production from synthetic lignocellulose hydrolysate with different photoheterotrophic cultures: Sequential vs. co-culture processes

Integration of dark and photo-fermentation is a promising strategy to efficiently produce renewable hydrogen from different types of waste biomass. In this study, sequential and co-culture dark-photo fermentations were evaluated and compared during continuous operation using synthetic lignocellulose hydrolysate as a substrate. Mixed dark-fermentative bacterial consortium was combined with two different photo-fermentative bacterial cultures: pure culture of Rhodobacter sphaeroides (RSC) and mixed photoheterotrophic consortium (MPC). The sequential process showed higher total H2 yields compared to co-culture fermentation for both RSC and MPC. The highest yield of 4.15 mol H2/molsugar was obtained for the sequential process with RSC at an HRT of 3.5 days and pH 7.5. For the co-culture process, the yield reached 2.88 mol H2/molsugar at pH 7.0 and an HRT of 3.5 days. Complete sugar utilization was observed for dark fermentation. RSC preferred acetate as a carbon source, while MPC preferred butyrate. Photoheterotrophic bacteria, Rhodopseudomonas pseudopalustris and Rhodoplanes piscinae, present in the MPC inoculum were outcompeted by undesirable microorganisms during the continuous process, resulting in low HPR. On the other hand, in both sequential and co-culture processes, a high relative abundance of R. sphaeroides (>40%) was observed in the RSC, indicating effective cooperation between dark and photo bacteria.

Shimia ponticola sp. nov., an aerobic anoxygenic photoheterotrophic bacterium, isolated from surface seawater in the South China Sea.

A Gram-stain-negative marine bacterium, designated as WX04T, was isolated from the South China Sea. The genome of strain WX04T contained a complete photosynthetic gene cluster and is the first identified photoheterotroph of the genus Shimia with high photochemical efficiency (Fv/Fm=0.705±0.010), indicating its diverse metabolic and growth strategies, and unique evolution in the genus Shimia. The genome size of strain WX04T is 3.78 Mbp, and the G+C content is 58.8 %. Its isolate formed pink colonies and the cells were non-flagellated and rod-shaped. Growth was observed at 15-35 °C (optimum, 30 °C), at pH 5.0-11.0 (optimum, pH 7.0) and in the presence of 3-5 % (w/v) NaCl (optimum, 3 %). Both catalase activity and oxidase activity were found to be negative. The 16S rRNA gene sequence analyses revealed that this isolate represents a novel species within the genus Shimia, sharing 96.8 and 95.6% sequence identities with Shimia aestuarii DSM 15283T and Shimia marina DSM 26895T, respectively. The respiratory quinone was ubiquinone-10 (100 %). The primary cellular fatty acids (>5 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C18 : 0,C18 : 1 ω7c 11-methyl and C10 : 0 3-OH. The dominant polar lipids of strain WX04T comprised phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The combined polyphasic data shows that strain WX04T is a novel species within the genus Shimia, which is proposed as Shimia ponticola sp. nov., and the type strain is WX04T (=KCTC 62628T=MCCC 1K02295T).

Network Analysis Indicates Microbial Assemblage Differences in Life Stages of Cladophora.

Cladophora represents a microscopic forest that provides many ecological niches and fosters a diverse microbiota. However, the microbial community on Cladophora in brackish lakes is still poorly understood. In this study, the epiphytic bacterial communities of Cladophora in Qinghai Lake were investigated at three life stages (attached, floating, and decomposing). We found that in the attached stage, Cladophora was enriched with chemoheterotrophic and aerobic microorganisms, including Yoonia-Loktanella and Granulosicoccus. The proportion of phototrophic bacteria was higher in the floating stage, especially Cyanobacteria. The decomposing stage fostered an abundance of bacteria that showed vertical heterogeneity from the surface to the bottom. The surface layer of Cladophora contained mainly stress-tolerant chemoheterotrophic and photoheterotrophic bacteria, including Porphyrobacter and Nonlabens. The microbial community in the middle layer was similar to that of floating-stage Cladophora. Purple oxidizing bacteria were enriched in the bottom layer, with Candidatus Chloroploca, Allochromatium, and Thiocapsa as the dominant genera. The Shannon and Chao1 indices of epibiotic bacterial communities increased monotonically from the attached stage to the decomposing stage. Microbial community composition and functional predictions indicate that a large number of sulfur cycle-associated bacteria play an important role in the development of Cladophora. These results suggest that the microbial assemblage on Cladophora in a brackish lake is complex and contributes to the cycling of materials. IMPORTANCE Cladophora represents a microscopic forest that provides many ecological niches fostering a diverse microbiota, with a complex and intimate relationship between Cladophora and bacteria. Many studies have focused on the microbiology of freshwater Cladophora, but the composition and succession of microorganisms in different life stages of Cladophora, especially in brackish water, have not been explored. In this study, we investigated the microbial assemblages in the life stages of Cladophora in the brackish Qinghai Lake. We show that heterotrophic and photosynthetic autotrophic bacteria are enriched in attached and floating Cladophora, respectively, whereas the epiphytic bacterial community shows vertical heterogeneity in decomposing mats.

The mitigating effects of diatom-bacteria biofilm on coastal harmful algal blooms: A lab-based study concerning species-specific competition and biofilm formation

Harmful algal blooms (HABs) in coastal areas severely affected the health of ecosystem and human beings. The HABs control by biological methods, especially for biofilms, has been research hotspots in freshwater ecosystem. However, the biofilm-relating control of HABs in marine environment was very limited. In the present study, we found the population growth of two harmful algal species, Prorocentrum obtusidens Schiller (formerly P. donghaiense Lu) and Heterosigma akashiwo, were inhibited by a diatom-bacteria biofilm. The highest inhibitory rate was 79.6 ± 2.1% for P. obtusidens when co-cultured with biofilm suspension, and was 88.6 ± 5.8% for H. akashiwo when co-cultured with the biofilm filtrate without nutrient replenishment. When nitrate and phosphate were added, the inhibition rate for P. obtusidens was 72.3 ± 2.0%, but the population inhibition was not found in H. akashiwo. It suggested that P. obtusidens was mainly inhibited via interference competition, while the inhibition of H. akashiwo was resulted from exploitation competition. We further investigated the role of fatty acids for the interference competition in P. obtusidens, and found that fatty acids at their environmental-relevance concentrations can inhibit the photosynthetic capacity of P. obtusidens, but cannot inhibit the population growth. The community of biofilm shifted, and was finally dominated by the photoheterotrophic bacterium Dinoroseobacter shibae, and the diatom Fistulifera sp. with relative abundance of higher than 90%. Our study indicated that the diatom-bacteria biofilm was likely the candidate for the HABs control in marine environment. D. shibae and Fistulifera sp. were probably the effective species in the biofilm.

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.

Vulcanimicrobium alpinus gen. nov. sp. nov., the first cultivated representative of the candidate phylum “Eremiobacterota”, is a metabolically versatile aerobic anoxygenic phototroph

The previously uncultured phylum “Candidatus Eremiobacterota” is globally distributed and often abundant in oligotrophic environments. Although it includes lineages with the genetic potential for photosynthesis, one of the most important metabolic pathways on Earth, the absence of pure cultures has limited further insights into its ecological and physiological traits. We report the first successful isolation of a “Ca. Eremiobacterota” strain from a fumarolic ice cave on Mt. Erebus volcano (Antarctica). Polyphasic analysis revealed that this organism is an aerobic anoxygenic photoheterotrophic bacterium with a unique lifestyle, including bacteriochlorophyll a production, CO2 fixation, a high CO2 requirement, and phototactic motility using type IV-pili, all of which are highly adapted to polar and fumarolic environments. The cells are rods or filaments with a vesicular type intracytoplasmic membrane system. The genome encodes novel anoxygenic Type II photochemical reaction centers and bacteriochlorophyll synthesis proteins, forming a deeply branched monophyletic clade distinct from known phototrophs. The first cultured strain of the eighth phototrophic bacterial phylum which we name Vulcanimicrobium alpinus gen. nov., sp. nov. advances our understanding of ecology and evolution of photosynthesis.

Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.

Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.

Mytilus farming drives higher local bacterial diversity and facilitates the accumulation of aerobic anoxygenic photoheterotrophic related genera

Research to assess the impacts of mariculture on the microbiota of the surrounding environment is still inadequate. Here, we examined the effects of Mytilus coruscus farming on the diversity of bacterial community in surrounding seawater using field investigations and indoor simulations, focusing on the variation of members of aerobic anoxygenic photoheterotrophic (AAP) bacteria. In the field, Mytilus farming shaped bacterial community and significantly increased their diversity, including biomass, OTUs, Shannon, relative abundance, number of enriched species, as compared with the non-farming area. Higher abundance of AAP related genera was observed in the Mytilus farming seawater. Under the controlled condition, the presence of M. coruscus significantly shaped the bacterial community composition and caused species composition to become similar after 10 days. Furthermore, the presence of M. coruscus consistently strengthened local diversity in seawater bacterial community, with linkages to the recruitment of AAP members as well. In addition, the tissue-related composition of M. coruscus significantly differed from those in seawater. Our findings highlight a ecological importance of Mytilus farming, as process that shape surrounding water-cultured bacterial community and offer experimental evidence for the accumulation of AAP-related genera in aquaculture systems.

Molecular insights into the role of heme in the transcriptional regulatory system AppA/PpsR

Heme has been shown to have a crucial role in the signal transduction mechanism of the facultative photoheterotrophic bacterium Rhodobacter sphaeroides. It interacts with the transcriptional regulatory complex AppA/PpsR, in which AppA and PpsR function as the antirepressor and repressor, respectively, of photosynthesis gene expression. The mechanism, however, of this interaction remains incompletely understood. In this study, we combined electron paramagnetic resonance (EPR) spectroscopy and Förster resonance energy transfer (FRET) to demonstrate the ligation of heme in PpsR with a proposed cysteine residue. We show that heme binding in AppA affects the fluorescent properties of the dark-adapted state of the protein, suggesting a less constrained flavin environment compared with the absence of heme and the light-adapted state. We performed ultrafast transient absorption measurements in order to reveal potential differences in the dynamic processes in the full-length AppA and its heme-binding domain alone. Comparison of the CO-binding dynamics demonstrates a more open heme pocket in the holo-protein, qualitatively similar to what has been observed in the CO sensor RcoM-2, and suggests a communication path between the blue-light-using flavin (BLUF) and sensing containing heme instead of cobalamin (SCHIC) domains of AppA. We have also examined quantitatively the affinity of PpsR to bind to individual DNA fragments of the puc promoter using fluorescence anisotropy assays. We conclude that oligomerization of PpsR is initially triggered by binding of one of the two DNA fragments and observe a ∼10-fold increase in the dissociation constant Kd for DNA binding upon heme binding to PpsR. Our study provides significant new insight at the molecular level on the regulatory role of heme that modulates the complex transcriptional regulation in R. sphaeroides and supports the two levels of heme signaling, via its binding to AppA and PpsR and via the sensing of gases like oxygen.

Pulsed export of carbon in the north-western Mediterranean Sea

The short term (hourly scale) variability of heterotrophic prokaryote (HP) vertical distribution and respiratory activity, was investigated in the north-western (NW) Mediterranean Sea. HP vertical distribution was determined on board by flow cytometry analysis of seawater samples collected by series of CTD casts. Cell counts and viability were determined for all samples. HP respiratory rates were determined later in the laboratory from filtered seawater samples (23 dm3) from 300–1 150-m depth. The average cell viability was 94.8%±2.2% (n=240). There was no accumulation of dead cells, due to quick decay of damaged cells. In the epipelagic layer, three HP groups were distinguished, two (HNA1, HNA2) whose cells exhibited a high nucleic acid content and one (LNA) with low nucleic acid content cells. HNA2 was most populated at 50 m but not detected at 90 m and below, presumably aerobic anoxygenic photoheterotrophic bacteria (AAPs). The variability in HP abundance was mainly confined in the upper 80 m. A few secondary peaks of HP abundance were observed (80–150 m) in connection with abundance troughs in the surface layer. HP cells were continuously present in a wide layer around 500 m (mean 191×103 cells/cm3). Below this layer, HP abundance randomly exhibited peaks, coupled to respiratory rate peaks. The HP abundance and variability in the water column was suppressed during a strong wind event. The observed sporadic variability was tentatively interpreted through a pulsed carbon-export mechanism induced by the microorganism production of dissolved polysaccharides, followed by flocculation and rapid sinking. This mechanism would thus contribute to (i) preventing organic matter accumulation in the epipelagic layer, (ii) seeding the water column with live HP cells, and (iii) supplying the aphotic water column with fresh and labile organic matter. This important vertical flux mechanism needs further observations and modelling.

A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum.

This study isolated and characterized a new phage infecting the marine photoheterotrophic bacterium Citromicrobium bathyomarinum, which fills the gap in research on phages targeting this ecologically important species. The phage vB_CbaS-RXM (RXM) has a dsDNA genome with a length of 104,206 bp and G+C content of 61.64%. The taxonomic analysis found a close evolutionary relationship between RXM, Erythrobacter phage vB_EliS-L02, and Sphingobium phage Lacusarx, and we propose that RXM represents a new species of the Lacusarxvirus genus. A one-step growth curve revealed a burst size of 75 plaque-forming units (PFUs) per cell in a 3-hour infection cycle. The lysis profile of RXM showed an intraspecific lethal rate of 26.3% against 38 citromicrobial strains. RXM contains 15 auxiliary metabolic genes (AMGs) related to diverse cellular processes, such as putative metabolic innovation and hijacking of host nucleotide metabolism to enhance its biosynthetic capacity. An in-depth analysis showed that phage functional genes strongly rely on the host for translation, while the translation of unique phage genes with less host dependency may be complemented by phage tRNA. Overall, our study investigated the infection kinetics, genetic traits, taxonomy, and predicted roles of AMGs and tRNA genes of this new phage, which contributes to a better understanding of phage diversity and phage–bacterium interactions.

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

Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO2 to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6–23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8–28.4%), pyruvate (9.5%; 4.2–14.8%), and leucine (5.9%; 0.1–11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO2 from respiration unbalanced by net primary production was by 3.69 × 109 g CO2 lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.

Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales.

The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.

Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium.

Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic Sphingomonas strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll a quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll a and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic Sphingomonas bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation.IMPORTANCE Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium Sphingomonas sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in Sphingomonas may have other functions not linked to bioenergetics.

An Experimentally Evaluated Thermodynamic Approach to Estimate Growth of Photoheterotrophic Purple Non-sulfur Bacteria.

Distribution of energy during the growth and formation of useful chemicals by microorganisms can define the overall performance of a biotechnological system. However, to date, this distribution has not been used to reliably predict growth characteristics of phototrophic microorganisms. The presented research addresses this application by estimating the photon-associated Gibbs energy delivered for the photoheterotrophic growth of purple non-sulfur bacteria and production of dihydrogen. The approach is successfully evaluated with the data from a fed-batch growth of Rhodopseudomonas palustris nifA∗ fixing N2 gas in phototrophic conditions and a reliable prediction of growth characteristics is demonstrated. Additionally, literature-available experimental data is collected and used for evaluation of the presented thermodynamic approach to predict photoheterotrophic growth yields. A proposed thermodynamic framework with modification to account for the phototrophic growth can be used to predict growth rates in broader environmental niches and to assess the possibility for the development of novel biotechnological applications in light-induced biological systems.

Phospholipid turnover rates suggest that bacterial community growth rates in the open ocean are systematically underestimated

AbstractHeterotrophic bacteria in the surface ocean play a critical role in the global carbon cycle and the magnitude of this role depends on their growth rates. Although methods for determining bacterial community growth rates based on incorporation of radiolabeled thymidine and leucine are widely accepted, they are based on a number of assumptions and simplifications. We sought to independently assess these methods by comparing bacterial growth rates to turnover rates of bacterial membranes using previously published methods in a range of open‐ocean settings. We found that turnover rates for heterotrophic bacterial phospholipids averaged 0.80 ± 0.35 d−1. This was supported by independent measurements of turnover rates of a membrane‐bound pigment in photoheterotrophic bacteria, bacteriochlorophyll a (0.85 ± 0.09 d−1). By contrast, bacterial growth rates measured by uptake of radiolabeled thymidine and leucine were 0.12 ± 0.08 d−1, well within the range expected from the literature. We explored whether the discrepancies between phospholipid turnover rates and bacterial growth rate could be explained by membrane recycling/remodeling and other factors, but were left to conclude that the radiolabeled thymidine and leucine incorporation methods substantially underestimated actual bacterial growth rates. We use a simple model to show that the faster bacterial growth rates we observed can be accommodated within the constraints of the microbial carbon budget if bacteria are smaller than currently thought, grow with greater efficiency, or some combination of these two factors.