Phototrophs Research Articles

Synergistic phenotypic adaptations of motile purple sulphur bacteria Chromatium okenii during lake-to-laboratory domestication.

Isolating microorganisms from natural environments for cultivation under optimized laboratory settings has markedly improved our understanding of microbial ecology. Artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into distinct selective pressures, resulting in diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms we still lack a biophysical understanding of the relevant traits emerging during domestication and their mechanistic interplay driving short-to-long-term microbial adaptation under laboratory conditions. Using microfluidics, atomic force microscopy, quantitative imaging, and mathematical modeling, we study phenotypic adaptation of Chromatium okenii, a motile phototrophic purple sulfur bacterium from meromictic Lake Cadagno, grown under laboratory conditions over multiple generations. Our results indicate that naturally planktonic C. okenii leverage shifts in cell-surface adhesive interactions, synergistically with changes in cell morphology, mass density, and distribution of intracellular sulfur globules, to suppress their swimming traits, ultimately switching to a sessile lifeform. A computational model of cell mechanics confirms the role of such phenotypic shifts in suppressing the planktonic lifeform. By investigating key phenotypic traits across different physiological stages of lab-grown C. okenii, we uncover a progressive loss of motility during the early stages of domestication, followed by concomitant deflagellation and enhanced surface attachment, ultimately driving the transition of motile sulfur bacteria to a sessile state. Our results establish a mechanistic link between suppression of motility and surface attachment via phenotypic changes, underscoring the emergence of adaptive fitness under laboratory conditions at the expense of traits tailored for natural environments.

Architectures of photosynthetic RC-LH1 supercomplexes from Rhodobacter blasticus.

The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric and dimeric RC-LH1 supercomplexes from Rhodobacter (Rba.) blasticus using cryo-electron microscopy. The RC-LH1 monomer is composed of an RC encircled by an open LH1 ring comprising 15 αβ heterodimers and a PufX transmembrane polypeptide. In the RC-LH1 dimer, two crossing PufX polypeptides mediate dimerization. Unlike Rhodabacter sphaeroides counterpart, Rba. blasticus RC-LH1 dimer has a less bent conformation, lacks the PufY subunit near the LH1 opening, and includes two extra LH1 αβ subunits, forming a more enclosed S-shaped LH1 ring. Spectroscopic assays reveal that these unique structural features are accompanied by changes in the kinetics of quinone/quinol trafficking between RC-LH1 and cytochrome bc1. Our findings reveal the assembly principles and structural variability of photosynthetic RC-LH1 supercomplexes, highlighting diverse strategies used by phototrophic bacteria to optimize light-harvesting and electron transfer in competitive environments.

Characterization of the intracellular polyphosphate granules of the phototrophic green sulfur bacterium Chlorobaculum tepidum

The ability to generate polyphosphate (polyP) granules is important for survival for bacteria during resistance to diverse environmental stresses, however the genesis of polyP granules is poorly understood. Chlorobaculum tepidum (Cba tepidum) is a thermophilic green sulfur anoxygenic phototrophic bacterium which uses reduced sulfur compounds as electron donors. The presence of electron rich granules inside the Cba tepidum was reported, but no further information was provided. In this work we used cell thin sections at three different time points of cultivation to observe the biogenesis of the inclusions over time, and the in cell total phosphate concentration was monitored over time as well. Furthermore, the elemental analysis (EDS) of the electron rich inclusions showed the presence of phosphorus and oxygen. The existence of polyphosphate was demonstrated by 31P NMR spectroscopy of cell lysates. Finally, we show that the biogenesis of the phosphorus granules correlates with an abundance of proteins that are closely related to polyphosphate metabolism.

Present Understanding of Biodiversity of Anoxygenic Phototrophic Bacteria in the Relic Lake Mogilnoe (Kildin Island, Murmansk oblast, Russia)

The relic Lake Mogilnoe, separated from the Barents Sea by a sand and pebble dam, is located in the high Arctic on the Kildin island (Murmansk region). This lake is a classic example of a meromictic basin of marine origin. The data obtained during the 2018 expedition showed changes in the hydrochemical regime of the lake that have occurred over the past 20 years. Sulfide concentration in the monimolimnion of the lake was as high as 140 mg/L. A tendency for salinization of the surface waters to 7 g/L has been noted. The Lake Mogilnoe is characterized by a discrepancy between the halocline and thermocline levels. The chemocline zone in the lake is below the halocline level. In a narrow oxygen-containing layer between 3 and 7.5 m, aerobic microflora of the marine type and marine fauna were present. The bacterial plate was formed at the boundary of the sulfide layer at ~8 m and mainly consisted of green sulfur bacteria (GSB). Brown-colored GSB species containing bacteriochlorophyll e were predominant. The previously formed concept of anaerobic phototrophic bacteria (APB) biodiversity based on morphological characteristics was modified using metagenomic data obtained by analyzing DNA from two samples of lake water in the chemocline zone, and was also supplemented by identifying new GSB species. Molecular diagnostic data confirmed the absolute dominance of the brackish species of GSB Chlorobium phaeovibrioides. This is the first on isolation and identification of brown- and green-colored Prosthecochloris aestuarii morphotypes from Lake Mogilnoe and identified, as well as of bacteriochlorophyll c-containing Prosthecochloris sp. The taxonomic position of Pelodyction phaem, which was constantly present in the Lake Mogilnoe, is discussed in detail. Despite the partial isolation of the ecosystem of Lake Mogilnoe from the Barents Sea, the main properties of the dominant GSB species of GSB and Prosthecochloris aestuarii turned out to be similar to those of the phylotypes living in lakes on the White Sea coast of the, which remained connected with the Barents Sea.

Aerobic anoxygenic phototrophic bacteria correlate with picophytoplankton across the Atlantic Ocean but show unique vertical bioenergetics

AbstractAerobic anoxygenic phototrophic (AAP) bacteria are a common part of microbial communities in the sunlit ocean. They contain bacteriochlorophyll a (BChl a)‐based photosystems that harvest solar energy for their metabolism. Across different oceanic regions, AAP bacteria seem to be more abundant in eutrophic areas, associated with high chlorophyll concentrations. While most previous studies focused on surface samplings, there is limited information regarding their vertical distribution in euphotic zones of the major ocean basins. Here, we hypothesized that AAP bacteria will follow a similar structure to the chlorophyll depth profile across areas with different degrees of stratification. To test this hypothesis, we enumerated AAP cells and determined bulk water BChl a concentrations along the photic zone of a latitudinal transect in the South and Central Atlantic Ocean. Overall, the distribution of AAP bacteria was highly correlated to that of chlorophyll a and to the abundance of picophytoplankton across both vertical and horizontal gradients. Furthermore, estimated light energy captured across the water column showed that, while AAP bacteria share a common latitudinal pattern of light absorption with picophytoplankton, they display a unique vertical arrangement with highest photoheterotrophic activity in the top 50 m of the surface ocean.

Trace metal interaction with thermophilic phototrophic anaerobic bacterium Chloroflexus aurantiacus

Towards improving the knowledge of possible paleo-microorganisms interaction with trace metals (micro-nutrients and toxicants), we studied adsorption of Mn, Zn, Sr, Cd, and Pb onto modern Chloroflexus aurantiacus, thermophilic anoxygenic phototrophic bacterium which could be highly abundant in the Precambiran aquatic environments. Acid-base surface titrations allowed quantifying the number of proton-active surface groups, whereas non-electrostatic linear programming method (LPM) was used to assess the surface site concentrations and adsorption reaction constants between divalent cations (Zn, Mb, Sr, Cd, Pb) and bacterial surface, based on results of pH-dependent adsorption edge and constant-pH ‘langmuirian’ adsorption experiments. The total proton/hydroxyl binding site number of Chl. aurantiacus surfaces was sizably lower than that of other phototrophic anaerobic bacteria studied previously using similar experimental and modeling approach. Divalent metals exhibited a decreasing order of adsorption affinity (Pb > Cd ≥ Zn ≥ Mn > Sr), which reflected the order of cation hydrolysis and was similar to adsorption order on other phototrophic bacteria. At the same time, adsorption of Zn increased with increasing of temperature, from 4 °C to 60 °C and was stronger under light compared to the darkness. This suggested some active metabolic control involved in this metal interaction with bacterial surfaces. Overall, Chl. aurantiacus exhibited trace metal adsorption parameters (site number and binding constants) which were lower compared to other anoxygenic phototrophic bacteria (Rhodopseudomonas palustris; Rhodobacter blasticus) and cyanobacteria. This may reflect different bioavailability of trace metals in the paleo-ocean, given that thermophilic Chl. aurantiacus are among the oldest phototrophs on the planet.

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

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.

The Impact of the Major Endoribonucleases RNase E and RNase III and of the sRNA StsR on Photosynthesis Gene Expression in Rhodobacter sphaeroides Is Growth-Phase-Dependent.

Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment-protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen and light has been investigated for decades, with a focus on the regulation of transcription. However, many studies have also revealed the importance of regulated mRNA processing. This study analyzes the phenotypes of wild type and mutant strains and compares global RNA-seq datasets to elucidate the impact of ribonucleases and the small non-coding RNA StsR on photosynthesis gene expression in Rhodobacter. Most importantly, the results demonstrate that, in particular, the role of ribonuclease E in photosynthesis gene expression is strongly dependent on growth phase.

The phototrophic purple non-sulfur bacteria Rhodomicrobium spp. are novel chassis for bioplastic production.

Petroleum-based plastics levy significant environmental and economic costs that can be alleviated with sustainably sourced, biodegradable, and bio-based polymers such as polyhydroxyalkanoates (PHAs). However, industrial-scale production of PHAs faces barriers stemming from insufficient product yields and high costs. To address these challenges, we must look beyond the current suite of microbes for PHA production and investigate non-model organisms with versatile metabolisms. In that vein, we assessed PHA production by the photosynthetic purple non-sulfur bacteria (PNSB) Rhodomicrobium vannielii and Rhodomicrobium udaipurense. We show that both species accumulate PHA across photo-heterotrophic, photo-hydrogenotrophic, photo-ferrotrophic, and photo-electrotrophic growth conditions, with either ammonium chloride (NH4Cl) or dinitrogen gas (N2) as nitrogen sources. Our data indicate that nitrogen source plays a significant role in dictating PHA synthesis, with N2 fixation promoting PHA production during photoheterotrophy and photoelectrotrophy but inhibiting production during photohydrogenotrophy and photoferrotrophy. We observed the highest PHA titres (up to 44.08 mg/L, or 43.61% cell dry weight) when cells were grown photoheterotrophically on sodium butyrate with N2, while production was at its lowest during photoelectrotrophy (as low as 0.04 mg/L, or 0.16% cell dry weight). We also find that photohydrogenotrophically grown cells supplemented with NH4Cl exhibit the highest electron yields - up to 58.89% - while photoheterotrophy demonstrated the lowest (0.27%-1.39%). Finally, we highlight superior electron conversion and PHA production compared to a related PNSB, Rhodopseudomonas palustris TIE-1. This study illustrates the value of studying non-model organisms like Rhodomicrobium for sustainable PHA production and indicates future directions for exploring PNSB metabolisms.

Anatomy of the late Famennian Dasberg event in a deep shelf of southern Euramerica: Oxygenation and productivity in a restricted basin during a progressive long-term cooling

The late Famennian Dasberg event is described as a series of global hypoxic and transgressive events associated with global faunal turnover. The event, recorded on a deep shelf of the Rhenohercynian basin from southern Euramerica, was investigated in the Holy Cross Mountains of Poland using integrated high-resolution geochemical, mineralogical, and palynological studies. The data revealed the progressive restriction of the intrashelf basin resulting from intense regional block tectonics likely connected with the Late Devonian Variscan tectonic activity. This led to weak chemocline ventilation, the development of anoxic conditions, and the deposition of two organic-rich Dasberg black shale (DBS) horizons. The DBS was deposited in an environment characterized by the constant contribution of detrital components from a common source area. A slight change in terrestrial input may have been driven by modest bathymetric changes associated with the tectonics and stronger winds delivering charcoal and terrestrial components (i.e., miospores and phytoclasts). A supply of nutrients from land and delivery of crucial biolimiting elements (i.e., nitrogen and phosphorus) from deeper waters stimulated primary productivity, as recorded in phytoplankton blooms. The δ13Corganic values in the DBS reflect the incorporation of primary biomass from mainly marine photoautotrophs into sedimentary organic matter. Episodic delivery of toxic sulphides to the photic zone was detected by small-sized framboids and biomarkers, which record the appearance of green sulphur bacteria that photosynthesized in euxinic water column. The activity of phototrophic sulphide-oxidizing bacteria could have led to hyper-enrichment of Zn (715–1002 ppm) in the Lower DBS. The diachronous appearance of the DBS horizons in Euramerica and Gondwana, and regionally marked extinction of benthic fauna, suggest that anoxia developed in restricted Black Sea–like basins formed by intensive tectonic activity and continental plate convergence.

Light-driven extracellular electron transfer accelerates microbiologically influenced corrosion by Rhodopseudomonas palustris TIE-1

This study investigates the microbiologically influenced corrosion (MIC) of X80 steel accelerated by the phototrophic bacterium Rhodopseudomonas palustris TIE-1. The photorespiration plays a key role in promoting extracellular electron transfer (EET)-induced MIC. In the early corrosion stage, unstable localized corrosion dominated in the dark, while intense diffusion-controlled corrosion occurs in light. Compared to the sterile anaerobic medium, R. palustris TIE-1 accelerated corrosion of X80 steel, with a significantly higher corrosion rate under light conditions, approximately three times that of dark conditions. Inhibition of photosynthetic electron transfer or cessation of photostimulation resulted in pronounced reduction in the corrosion rate.

Genes for the type-I reaction center and galactolipid synthesis are required for chlorophyll a accumulation in a purple photosynthetic bacterium.

Anoxygenic photosynthesis is diversified into two classes: chlorophototrophy based on a bacterial type-I or type-II reaction center (RC). Whereas the type-I RC contains both bacteriochlorophyll and chlorophyll, type-II RC-based phototrophy relies only on bacteriochlorophyll. However, type-II phototrophic bacteria theoretically have the potential to produce chlorophyll a by the addition of an enzyme, chlorophyll synthase, because the direct precursor for the enzyme, chlorophyllide a, is produced as an intermediate of BChl a biosynthesis. In this study, we attempted to modify the type-II proteobacterial phototroph Rhodovulum sulfidophilum to produce chlorophyll a by introducing chlorophyll synthase, which catalyzes the esterification of a diterpenoid group to chlorophyllide a thereby producing chlorophyll a. However, the resulting strain did not accumulate chlorophyll a, perhaps due to absence of endogenous chlorophyll a-binding proteins. We further heterologously incorporated genes encoding the type-I RC complex to provide a target for chlorophyll a. Heterologous expression of type-I RC subunits, chlorophyll synthase, and galactolipid synthase successfully afforded detectable accumulation of chlorophyll a in Rdv. sulfidophilum. This suggests that the type-I RC can work to accumulate chlorophyll a and that galactolipids are likely necessary for the type-I RC assembly. The evolutionary acquisition of type-I RCs could be related to prior or concomitant acquisition of galactolipids and chlorophylls.

Rapid sulfurization obscures carotenoid distributions in modern euxinic environments

Anoxygenic phototrophic bacteria (green and purple sulfur bacteria) thrive in anoxic environments where light penetrates a sulfide-containing (euxinic) water column. Genomic data and photosynthetic bacterial carotenoid pigments should provide complementary information on the spatio-temporal dynamics of anoxygenic phototrophs in modern euxinic environments. In turn, these contemporary depositional settings often serve as analogues for ancient counterparts. However, in some modern environments, DNA-informed patterns of phototrophic sulfur bacteria occurrence do not match distributions of their carotenoid inventories. One possible explanation for these seemingly incompatible observations is that the rapid sulfurization of carotenoids and incorporation into macromolecules via multiple carbon–sulfur bonds prevents or confounds their detection by conventional means. Here, to evaluate this conundrum, we revisit some representative contemporary euxinic environments where anoxygenic phototrophic bacteria have mostly been detected based on genomic analyses. Although free intact carotenoids are sporadically detected in surface sediments, their distributions do not reveal a complete picture. Exogenously sourced fossil carotenoids (e.g., paleorenieratane) is an additional complication. Carotenoid inventories obtained by desulfurization with Raney nickel, on the other hand, stand in stark contrast to those present as free lipids. In particular, sulfur-linked carotenoids present in euxinic lake sediments provide a more complete picture of compositions of anoxygenic sulfur bacterial communities and account for discrepancies reported in previous studies. We observe a closer alignment between genomic data and patterns of sulfurized carotenoids and, importantly, our results highlight how sulfurization serves as a pathway for the rapid modification of highly functionalised lipids and their sequestration into the macromolecular component of sediment extracts.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Integrating experiments with modeling to understand key bacterial taxa dynamics after episodic mixing of a stratified water column

Hydraulic mixing of stratified reservoirs homogenizes physicochemical gradients and microbial communities. This has potential repercussions for microbial metabolism and water quality, not least in dams and hydraulically controlled waters. A better understanding of how key taxa respond to mixing of such stratified water bodies is needed to understand and predict the impact of hydraulic operations on microbial communities and nutrient dynamics in reservoirs. We studied taxa transitions between cyanobacteria and sulfur-transforming bacteria following mixing of stratified water columns in bioreactors and complemented the experimental approach with a biogeochemical model. Model predictions were consistent with experimental observations, suggesting that stable stratification of DO is restored within 24 h after episodic and complete mixing, at least in the absence of other more continuous disturbances. Subsequently, the concentration of S2− gradually return to pre-mixing states, with higher concentration at the surface and lower in the bottom waters, while the opposite pattern was seen for SO42−. The total abundance of sulfate-reducing bacteria and phototrophic sulfur bacteria increased markedly after 24h of mixing. The model further predicted that the rapid re-oxygenation of the entire water column by aeration will effectively suppress the water stratification and the growth of sulfur-transforming bacteria. Based on these results, we suggest that a reduction of thermocline depth by optimal flow regulation in reservoirs may also depress sulfur transforming bacteria and thereby constrain sulfur transformation processes and pollutant accumulation. The simulation of microbial nutrient transformation processes in vertically stratified waters can provide new insights about effective environmental management measures for reservoirs.

Electricity Generation by a Phototrophic Bacterium in a Glucose−Fed Double Chambered Microbial Fuel Cell Using a Fabricated 3D Anode Electrode

Study’s Novelty/Excerpt This study presents an approach to enhancing microbial fuel cell (MFC) performance by employing phototrophic bacteria (PTB) and sustainable electrode materials, specifically a 3D anode electrode fabricated from reduced graphene oxide (rGO) and nickel (Ni) foam. By integrating morphological, biochemical, and molecular techniques to identify the electrochemically active PTB, the research achieved a significant eight-fold increase in power density using rGO-Ni electrodes compared to conventional Ni electrodes. This work underscores the potential of utilizing sustainable materials and PTB to improve MFC efficiency and economic viability, offering a promising direction for sustainable bioelectricity generation. Full Abstract Over the past years, despite intensified research on microbial fuel cells (MFC), low power densities were recorded, reducing the productivity and economic viability of the process. This necessitated testing various MFC configurations, fabricating various electrodes, and evaluating various substrate types and species of electrogenic microorganisms to improve MFC performance. Despite the dual advantage of phototrophic bacteria (PTB), metabolizing organic waste substances and generating electricity, less research was conducted on the bacterium. Although a significant amount of energy is generated using unsustainable (fossil-based) materials in electrode fabrication, this study focuses on using sustainable materials like carbon cloth and graphite to fabricate a 3D anode electrode to exploit the maximum energy generated by PTB. The PTB used in this study was identified through morphological characteristics and biochemical tests (catalase and oxidase) and confirmed using a molecular technique: 16S rRNA sequencing. Preliminary results indicated that the PTB was gram-negative, spherical in shape, non−motile, and facultatively anaerobic bacterium. Analysis of the 16S rRNA partial sequence was conducted in GenBank databases. 100 significant sequences with the lowest and highest similarities of 84.10% and 98.76% were recorded, respectively. Of these, 13 strains had the highest similarities of >90%, all belonging to the genus Dysgonomonas, with D. oryzarvi Dy73 (98.76%) as the closest. Reduced graphene oxide (rGO) used as the anode was prepared using Hummer’s method by depositing the rGO on nickel (Ni) foam which changed the colour of Ni from grey to black after depositing and annealing. In addition to the SEM images, which showed a continuous multi−layered 3D scaffold on the Ni, the cyclic voltammetry (CV) analyses indicated an increase in the electrochemical activities of the rGO−Ni electrode compared to Ni. The CV also confirmed the bacterium to be electrochemically active. The 100 mL glucose−fed two−chamber MFC were separately run with the Ni and rGO–Ni as anode electrodes in a batch mode for 11 days, while carbon cloth was used as the cathode for both runs. An approximate 0.58 W/m2 power density was recorded for Ni, but eight−fold of Ni’s, 4.9 W/m2was generated by rGO−Ni. The study demonstrated that using fabricated 3D rGO–Ni as anode electrode can increase the microbial adhesion and power density of bacterium in MFC, thereby providing a more applicable and sustainable alternative to bioelectricity generation.

Light harvesting in purple bacteria does not rely on resonance fine-tuning in peripheral antenna complexes

The ring-like peripheral light-harvesting complex 2 (LH2) expressed by many phototrophic purple bacteria is a popular model system in biological light-harvesting research due to its robustness, small size, and known crystal structure. Furthermore, the availability of structural variants with distinct electronic structures and optical properties has made this group of light harvesters an attractive testing ground for studies of structure–function relationships in biological systems. LH2 is one of several pigment-protein complexes for which a link between functionality and effects such as excitonic coherence and vibronic coupling has been proposed. While a direct connection has not yet been demonstrated, many such interactions are highly sensitive to resonance conditions, and a dependence of intra-complex dynamics on detailed electronic structure might be expected. To gauge the sensitivity of energy-level structure and relaxation dynamics to naturally occurring structural changes, we compare the photo-induced dynamics in two structurally distinct LH2 variants. Using polarization-controlled 2D electronic spectroscopy at cryogenic temperatures, we directly access information on dynamic and static disorder in the complexes. The simultaneous optimal spectral and temporal resolution of these experiments further allows us to characterize the ultrafast energy relaxation, including exciton transport within the complexes. Despite the variations in PPC molecular structure manifesting as clear differences in electronic structure and disorder, the energy-transport and—relaxation dynamics remain remarkably similar. This indicates that the light-harvesting functionality of purple bacteria within a single LH2 complex is highly robust to structural perturbations and likely does not rely on finely tuned electronic- or electron-vibrational resonance conditions.

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 > 800nm) 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.

Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation.

Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

Restoration via the aggregate spray-seeding technique affected the soil proteobacteria on an Uninhabited Island: Community structure, metabolic function, nutritional type, and life strategy

This study aimed to explore the impact of aggregate spray-seeding (ASS) restoration measures on the soil proteobacterial community. Using environmental DNA sequencing, we analyzed the proteobacterial communities in the soils of 3 natural vegetation (NV) plots, 3 traditional afforestation (TA) plots, and 12 spray-seeding restoration (SR) plots located on Triangle Island in Zhuhai city, China, during both the summer and winter seasons. We estimated the metabolic function, nutritional type, and life strategy of Proteobacteria through the FAPROTAX and rrnDB databases. Our findings demonstrated that Proteobacteria was the predominant phylum (relative abundance = 40.1–48.4%) in the soil bacterial communities across all three treatments. The relative abundance of Alphaproteobacteria ranged from 28.5% to 38.1%, which was significantly greater (2.6–10.3 times, p < 0.05) than that of Betaproteobacteria or Gammaproteobacteria. Most (90%) proteobacterial genera and all rhizobial genera found in the NV and TA soils were also present in the SR soil, but there were distinct differences in the proteobacterial community structures between the SR soil and NV/TA soil. Across all seasons and treatments, the proteobacterial communities were related to functions such as ureolysis, nitrogen fixation, nitrate reduction, and hydrocarbon degradation. The relative abundance of Proteobacteria associated with chitinolysis was greater in the SR soil than in the NV and TA soils. Among the overall proteobacterial community, the chemoheterotrophic, chemoautotrophic, and phototrophic bacteria accounted for 65–77%, 19–31%, and less than 5%, respectively. Alphaproteobacteria tended to be K strategic, while Betaproteobacteria and Gammaproteobacteria tended to be r strategic. The soil pH, organic carbon content, and nitrogen content were significantly correlated with the metabolic function and nutritional type of the soil Proteobacteria according to the Mantel test results. In conclusion, the application of the ASS technique can effectively restore the biodiversity, metabolic function, and nutritional-type structure of the soil proteobacterial community. Additionally, this study highlights that certain metabolic functions of the proteobacterial community in SR soil undergo changes in response to the use of certain restoration materials. These findings suggest that the targeted addition of specific repair materials can modulate soil microorganism functionality and provide a valuable theoretical foundation for ecological restoration engineering practices.