This research uncovers a groundbreaking link between electron spin and proton transport in biological environment, using lysozyme as a model system. Proton transfer, vital in many life processes, is shown to couple with electron spin polarization, a discovery aligned with the Chiral Induced Spin Selectivity (CISS) effect. Specifically, we show that proton conduction through the lysozyme crystal is selective to the polarization of injected electrons, highlighting a synergy between spin polarization and information transfer in life. This mechanism provides insights into proton-coupled electron transfer (PCET) processes, emphasizing the role of chirality in biological processes. These findings bridge quantum physics with biochemistry enabling better understanding and opening the possibility of controlled information transfer in biological environments. Proton transport plays a fundamental role in many biological and chemical systems. In life, proton transport is crucial for biochemical and physiological functions. It is usually accepted that the main mechanism of proton transfer is a result of hopping between neighboring water molecules and amino acid side chains. It was recently suggested that the proton transfer can be simultaneously coupled with electron transfer. As life is homochiral, proton transfer in biology is occurring in a chiral environment. In this environment, the chiral-induced spin selectivity effect relating to electron transfer and chirality is expected to occur. The present work establishes that the proton transfer is coupled to a specific electron spin polarization in lysozyme crystals, associating proton transfer to electron movement and polarization. To preserve total angular momentum, this motion may be coupled to chiral phonons that propagate in the crystal. Our work shows that the interaction of the electrons' spin and phonons is very significant in proton transfer through lysosome crystals. Injecting the opposite electron spin into the lysosome crystal results in a significant change in proton transfer impedance. This study presents the support for the proton-coupled electron transfer mechanism and indicates the importance of spin polarization in the process.This research uncovers a groundbreaking link between electron spin and proton transport in biological environment, using lysozyme as a model system. Proton transfer, vital in many life processes, is shown to couple with electron spin polarization, a discovery aligned with the Chiral Induced Spin Selectivity (CISS) effect. Specifically, we show that proton conduction through the lysozyme crystal is selective to the polarization of injected electrons, highlighting a synergy between spin polarization and information transfer in life. This mechanism provides insights into proton-coupled electron transfer (PCET) processes, emphasizing the role of chirality in biological processes. These findings bridge quantum physics with biochemistry enabling better understanding and opening the possibility of controlled information transfer in biological environments. Proton transport plays a fundamental role in many biological and chemical systems. In life, proton transport is crucial for biochemical and physiological functions. It is usually accepted that the main mechanism of proton transfer is a result of hopping between neighboring water molecules and amino acid side chains. It was recently suggested that the proton transfer can be simultaneously coupled with electron transfer. As life is homochiral, proton transfer in biology is occurring in a chiral environment. In this environment, the chiral-induced spin selectivity effect relating to electron transfer and chirality is expected to occur. The present work establishes that the proton transfer is coupled to a specific electron spin polarization in lysozyme crystals, associating proton transfer to electron movement and polarization. To preserve total angular momentum, this motion may be coupled to chiral phonons that propagate in the crystal. Our work shows that the interaction of the electrons' spin and phonons is very significant in proton transfer through lysosome crystals. Injecting the opposite electron spin into the lysosome crystal results in a significant change in proton transfer impedance. This study presents the support for the proton-coupled electron transfer mechanism and indicates the importance of spin polarization in the process.

In an era of interdisciplinary scientific research, new methodologies are necessary to simultaneously advance several fields of study. One such case involves the measurement of electron spin effects on biological systems. While magnetic effects are well known in biology, recent years have shown a surge in published evidence isolating the dependence on spin, rather than magnetic field, in biological contexts. Herein we present a simple method for the distinction between the two effects in solution-based samples. The induction of a single uniform spin upon molecules can be achieved by interacting them with a magnetized surface, thereby exposing them to controlled electron spin orientations. With many live biological systems, adsorption to a single surface severely limits the experimental output. A low signal to noise ratio from monolayers interacting with a relatively small surface area, and conformational restrictions due to immobilization, are common challenges when performing biological measurements on macroscopic magnetized surfaces. Here we demonstrate the use of Janus-like ferromagnetic microparticles, originally developed for a spin-based enantiomer separation procedure, as a platform for the spin-controlled measurement of biological molecules in solution. We find new evidence for electron spin involvement in biological systems, with influence observed on the kinetics, and to a lesser degree on the spectrum, of phycocyanin fluorescence. Our results provide both new scientific findings and proof of concept for the use of these unique magnetic particles as a flexible, soluble, high surface area, spin-controlled tool for scientific research.

Abstract Under natural conditions, plants face the need to acclimate to widely varying light intensities to optimize photosynthetic efficiency and minimize photodamage. Studying the mechanisms underlying these acclimation processes is essential for understanding plant productivity and resilience under fluctuating environmental conditions. This study aimed to investigate static and dynamic acclimation mechanisms in Hedera helix (Ivy) plants under two extreme light conditions spanning the range of their adaptive abilities, deep shade (LL, ~5??mol photons m?2?s?1) to full sunlight (HL, ~2000??mol photons m?2?s?1), focusing on their structural and functional acclimation. LL and HL plants were examined for their leaf structure, chlorophyll and carotenoid contents, and photosynthetic protein levels. Dynamic responses were evaluated through chlorophyll fluorescence spectroscopy, measuring the effective photosynthetic unit size (σ) and the capacity for non-photochemical quenching (NPQ). HL plants exhibited a?~?78% lower chlorophyll contents as compared to LL and increased chlorophyll a/b ratios. The carotenoid content of HL plants was ~94% lower, while the PsbS content increased fivefold. These results may indicate a smaller HL effective antenna size. However, σ fast fluorescence kinetics analysis indicated the opposite. NPQ analysis demonstrated that both compositions of the photosynthetic systems supported the ability to quench access energy. HL plants had a large dynamic range for NPQ and faster on/off kinetics. Our finding suggests massive changes in the organization of the photosynthetic apparatus. These modifications preserve a large dynamic range for reacting to light intensity under both conditions.

Elucidating the energetic processes which govern photosynthesis, the engine of life on earth, are
an essential goal both for fundamental research and for cutting‑edge biotechnological applications.
Fluorescent signal of photosynthetic markers has long been utilised in this endeavour. In this
research we demonstrate the use of fluorescent noise analysis to reveal further layers of intricacy
in photosynthetic energy transfer. While noise is a common tool analysing dynamics in physics
and engineering, its application in biology has thus far been limited. Here, a distinct behaviour
in photosynthetic pigments across various chemical and biological environments is measured.
These changes seem to elucidate quantum effects governing the generation of oxidative radicals.
Although our method offers insights, it is important to note that the interpretation should be further
validated expertly to support as conclusive theory. This innovative method is simple, non‑invasive,
and immediate, making it a promising tool to uncover further, more complex energetic events in
photosynthesis, with potential uses in environmental monitoring, agriculture, and food‑tech.

Phytoplankton are a major source of primary productivity. Their photosynthetic fluorescence are unique measures of their type, physiological state, and response to environmental conditions. Changes in phytoplankton photophysiology are commonly monitored by bulk fluorescence spectroscopy, where gradual changes are reported in response to different perturbations, such as light intensity changes. What is the meaning of such trends in bulk parameters if their values report ensemble averages of multiple unsynchronized cells? To answer this, we developed an experimental scheme that enables tracking fluorescence intensities, brightnesses, and their ratios, as well as mean photon nanotimes equivalent to mean fluorescence lifetimes, one cell at a time. We monitored three different phytoplankton species during diurnal cycles and in response to an abrupt increase in light intensity. Our results show that we can define specific subpopulations of cells by their fluorescence parameters for each of the phytoplankton species, and in response to varying light conditions. Importantly, we identify the cells undergo well-defined transitions between these subpopulations. The approach shown in this work will be useful in the exact characterization of phytoplankton cell states and parameter signatures in response to different changes these cells experience in marine environments, which will be applicable for monitoring marine-related environmental effects.

The oxygen isotopes ratio (δ¹⁸O) of microbial cell water strongly controls the δ¹⁸O of cell phosphate and of other oxygen-carrying moieties. Recently it was suggested that the isotopic ratio in cell water is controlled by metabolic water, which is the water produced by cellular respiration. This potentially has important implications for paleoclimate reconstruction, and for measuring microbial carbon use efficiency with the ¹⁸O-water method. Carbon use efficiency strongly controls soil organic matter preservation. Here, we directly tested the effect of metabolic water on microbial cells, by conducting experiments with varying the δ¹⁸O of headspace O₂ and the medium water, and by measuring the δ¹⁸O of cell phosphate. The latter is usually assumed to be in isotopic equilibrium with the cell’s water. Our results showed no correlation between the δ¹⁸O of O₂ and that of the cell phosphate, contradicting the hypothesis that metabolic water is an important driver of δ¹⁸O of microbial cell water. However, our labeled ¹⁸O water experiments indicated that only 43% of the oxygen in the cell’s phosphate is derived from equilibration with the medium water, during late-log to early-stationary growing phase. This could be explained by the isotopic effects of intra-and extra-cellular hydrolysis of organic compounds containing phosphate.

Cyanobacteria inhabiting desert biological soil crusts face the harsh conditions of the desert. They evolved a suite of strategies toward desiccation-hydration cycles mixed with high light irradiations, etc. In this study we purified and characterized the structure and function of Photosystem I (PSI) from Leptolyngbya ohadii, a desiccation-tolerant desert cyanobacterium. We discovered that PSI forms tetrameric (PSI-Tet) aggregate. We investigated it by using sucrose density gradient centrifugation, clear native PAGE, high performance liquid chromatography, mass spectrometry (MS), time-resolved fluorescence (TRF) and time-resolved transient absorption (TA) spectroscopy. MS analysis identified the presence of two PsaB and two PsaL proteins in PSI-Tet and uniquely revealed that PsaLs are N-terminally acetylated in contrast to non-modified PsaL in the trimeric PSI from Synechocystis sp. PCC 6803. Chlorophyll (Chl) a fluorescence decay profiles of the PSI-Tet performed at 77 K revealed two emission bands at  690 nm and 725 nm with the former appearing only at early delay time. The main fluorescence emission peak, associated with emission from the low energy Chls a, decays within a few nanoseconds. TA studies demonstrated that the 725 nm emission band is associated with low energy Chls a with absorption band clearly resolved at  710 nm at 77 K. In summary, our work suggests that the heterogenous composition of PsaBs and PsaL in PSI-Tet is related with the adaptation mechanisms needed to cope with stressful conditions under which this bacterium naturally grows.

Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions.

Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene-expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function, and hence in plant physiology. Proteins that harbor the Plant Organelle RNA Recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene-locus encodes an essential PORR-protein in Arabidopsis, termed as ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e., nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.

Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function and hence in plant physiology. Proteins that harbor the plant organelle RNA recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene locus encodes an essential PORR protein in Arabidopsis, termed ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e. nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.

The light environment in a mixing water column is arguably the most erratic condition under which photosynthesis functions. Shifts in light intensity, by an order of magnitude, can occur over the time scale of hours. In marine Synechococcus, light is harvested by massive, membrane attached, phycobilisome chromophore-protein complexes (PBS). We examined the ability of a phycobilisome-containing marine Synechococcus strain (WH8102) to acclimate to illumination perturbations on this scale. Although changes in pigment composition occurred gradually over the course of days, we did observe significant and reversible changes in the pigment's fluorescence emission spectra on a time scale of hours. Upon transition to ten-fold higher intensities, we observed a decrease in the energy transferred to Photosystem II. At the same time, the spectral composition of PBS fluorescence emission shifted. Unlike fluorescence quenching mechanisms, this phenomenon resulted in increased fluorescence intensities. These data suggest a mechanism by which marine Synechococcus WH8102 detaches hexamers from the phycobilisome structure. The fluorescence yield of these uncoupled hexamers is high. The detachment process does not require protein synthesis as opposed to reattachment. Hence, the most likely process would be the degradation and resynthesis of labile PBS linker proteins. Experiments with additional species yielded similar results, suggesting that this novel mechanism might be broadly used among PBS-containing organisms.

Photosynthetic organisms adapt to changing light conditions by manipulating their light harvesting complexes. Biophysical, biochemical, physiological and genetic aspects of these processes are studied extensively. The structural basis for these studies is lacking. In this study we address this gap in knowledge by focusing on phycobilisomes (PBS), which are large structures found in cyanobacteria and red algae. In this study we focus on the phycobilisomes (PBS), which are large structures found in cyanobacteria and red algae. Specifically, we examine red algae (Porphyridium purpureum) grown under a low light intensity (LL) and a medium light intensity (ML). Using cryo-electron microscopy, we resolve the structure of ML-PBS and compare it to the LL-PBS structure. The ML-PBS is 13.6 MDa, while the LL-PBS is larger (14.7 MDa). The LL-PBS structure have a higher number of closely coupled chromophore pairs, potentially the source of the red shifted fluorescence emission from LL-PBS. Interestingly, these differences do not significantly affect fluorescence kinetics parameters. This indicates that PBS systems can maintain similar fluorescence quantum yields despite an increase in LL-PBS chromophore numbers. These findings provide a structural basis to the processes by which photosynthetic organisms adapt to changing light conditions.

Abstract Control phenomena in biology usually refer to changes in gene expression and protein translation and modification. In this paper, another mode of regulation is highlighted; we propose that photosynthetic organisms can harness the interplay between localization and delocalization of energy transfer by utilizing small conformational changes in the structure of light-harvesting complexes. We examine the mechanism of energy transfer in photosynthetic pigment-protein complexes, first through the scope of theoretical work and then by in vitro studies of these complexes. Next, the biological relevance to evolutionary fitness of this localization-delocalization switch is explored by in vivo experiments on desert crust and marine cyanobacteria, which are both exposed to rapidly changing environmental conditions. These examples demonstrate the flexibility and low energy cost of this mechanism, making it a competitive survival strategy.

Partially charged chiral molecules act as spin filters, with preference for electron transport toward one type of spin (“up” or “down”), depending on their handedness. This effect is named the chiral induced spin selectivity (CISS) effect. A consequence of this phenomenon is spin polarization concomitant with electric polarization in chiral molecules. These findings were shown by adsorbing chiral molecules on magnetic surfaces and investigating the spin-exchange interaction between the surface and the chiral molecule. This field of study was developed using artificial chiral molecules. Here we used such magnetic surfaces to explore the importance of the intrinsic chiral properties of proteins in determining their stability. First, proteins were adsorbed on paramagnetic and ferromagnetic nanoparticles in a solution, and subsequently urea was gradually added to induce unfolding. The structural stability of proteins was assessed using two methods: bioluminescence measurements used to monitor the activity of the Luciferase enzyme, and fast spectroscopy detecting the distance between two chromophores implanted at the termini of a Barnase core. We found that interactions with magnetic materials altered the structural and functional resilience of the natively folded proteins, affecting their behavior under varying mild denaturing conditions. Minor structural disturbances at low urea concentrations were impeded in association with paramagnetic nanoparticles, whereas at higher urea concentrations, major structural deformation was hindered in association with ferromagnetic nanoparticles. These effects were attributed to spin exchange interactions due to differences in the magnetic imprinting properties of each type of nanoparticle. Additional measurements of proteins on macroscopic magnetic surfaces support this conclusion. The results imply a link between internal spin exchange interactions in a folded protein and its structural and functional integrity on magnetic surfaces. Together with the accumulating knowledge on CISS, our findings suggest that chirality and spin exchange interactions should be considered as additional factors governing protein structures.

Iron is an essential micronutrient for the ecologically important photoautotrophic cyanobacteria which are found across diverse aquatic environments. Low concentrations and poor bioavailability of certain iron species exert a strong control on cyanobacterial growth, affecting ecosystem structure and biogeochemical cycling. Here, we review the iron-acquisition pathways cyanobacteria utilize for overcoming these challenges. As the molecular details of cyanobacterial iron transport are being uncovered, an overall scheme of how cyanobacteria handle and exploit this scarce and redox-active micronutrient is emerging. Importantly, the range of biological solutions used by cyanobacteria to increase iron fluxes goes beyond transport and includes behavioral traits of colonial cyanobacteria and intricate cyanobacteria–bacteria interactions.

Phycobilisomes (PBS) are massive structures that absorb and transfer light energy to photochemical reaction centres. Among the range of light harvesting systems, PBS are considered to be excellent solutions for absorption cross-sections but relatively inefficient energy transferring systems. This is due to the combination of a large number of chromophores with intermediate coupling distances. Nevertheless, PBS systems persisted from the origin of oxygenic photosynthesis to present-day cyanobacteria and red algae, organisms that account for approximately half of the primary productivity in the ocean. In this study, we modelled energy transfer through subsets of PBS structures, using a comprehensive dynamic Hamiltonian model. Our approach was applied, initially, to pairs of phycobilin hexamers and then extended to short rods. By manipulating the distances and angles between the structures, we could probe the dynamics of exciton transfer. These simulations suggest that the PBS chromophore network enhances energy distribution over the entire PBS structure—both horizontally and vertically to the rod axis. Furthermore, energy transfer was found to be relatively immune to the effects of distances or rotations, within the range of intermediate coupling distances. Therefore, we suggest that the PBS provides unique advantages and flexibility to aquatic photosynthesis.

Cyanobacteria of the genus Synechococcus play a key role as primary producers and drivers of the global carbon cycle in temperate and tropical oceans. Synechococcus use phycobilisomes as photosynthetic light-harvesting antennas. These contain phycoerythrin, a pigment-protein complex specialized for absorption of blue light, which penetrates deep into open ocean water. As light declines with depth, Synechococcus photo-acclimate by increasing both the density of photosynthetic membranes and the size of the phycobilisomes. This is achieved with the addition of phycoerythrin units, as demonstrated in laboratory studies. In this study, we probed Synechococcus populations in an oligotrophic water column habitat at increasing depths. We observed morphological changes and indications for an increase in phycobilin content with increasing depth, in summer stratified Synechococcus populations. Such an increase in antenna size is expected to come at the expense of decreased energy transfer efficiency through the antenna, since energy has a longer distance to travel. However, using fluorescence lifetime depth profile measurement approach, which is applied here for the first time, we found that light-harvesting quantum efficiency increased with depth in stratified water column. Calculated phycobilisome fluorescence quantum yields were 3.5% at 70 m and 0.7% at 130 m. Under these conditions, where heat dissipation is expected to be constant, lower fluorescence yields correspond to higher photochemical yields. During winter-mixing conditions, Synechococcus present an intermediate state of light harvesting, suggesting an acclimation of cells to the average light regime through the mixing depth (quantum yield of ~2%). Given this photo-acclimation strategy, the primary productivity attributed to marine Synechococcus should be reconsidered.

Summary Cyanobacteria are globally important primary producers and nitrogen fixers. They are frequently limited by iron bioavailability in natural environments that often fluctuate due to rapid consumption and irregular influx of external Fe. Here we identify a succession of physiological changes in Synechocystis sp. PCC 6803 occurring over 14–16 days of iron deprivation and subsequent recovery. We observe several adaptive strategies that allow cells to push their metabolic limits under the restriction of declining intracellular Fe quotas. Interestingly, cyanobacterial populations exposed to prolonged iron deprivation showed discernible heterogeneity in cellular auto-fluorescence during the recovery process. Using FACS and microscopy techniques we revealed that only cells with high auto-fluorescence were able to grow and reconstitute thylakoid membranes. We propose that ROS-mediated damage is likely to be associated with the emergence of the two subpopulations, and, indeed, a rapid increase in intracellular ROS content was observed during the first hours following iron addition to Fe-starved cultures. These results suggest that an increasing iron supply is a double-edged sword - posing both an opportunity and a risk. Therefore, phenotypic heterogeneity within populations is crucial for the survival and proliferation of organisms facing iron fluctuations within natural environments.

Photosynthetic light harvesting is the first step in harnessing sunlight toward biological productivity. To operate efficiently under a broad and dynamic range of environmental conditions, organisms must tune the harvesting process according to the available irradiance. The marine cyanobacteria Synechococcus WH8102 species is well-adapted to vertical mixing of the water column. By studying its responses to different light regimes, we identify a new photo-acclimation strategy. Under low light, the phycobilisome (PBS) is bigger, with extended rods, increasing the absorption cross-section. In contrast to what was reported in vascular plants and predicted by Forster resonance energy transfer (FRET) calculations, these longer rods transfer energy faster than in the phycobilisomes of cells acclimated to a higher light intensity. Comparison of cultures grown under different blue light intensities, using fluorescence lifetime and emission spectra dependence on temperature at the range of 4–200 K in vivo, indicates that the improved transfer arises from enhanced energetic coupling between the antenna rods' pigments. We suggest two physical models according to which the enhanced coupling strength results either from additional coupled pathways formed by rearranging rod packing or from the coupling becoming non-classical. In both cases, the energy transfer would be more efficient than standard one-dimensional FRET process. These findings suggest that coupling control can be a major factor in photosynthetic antenna acclimation to different light conditions.

Cyanobacteria are key photosynthetic organisms in many aquatic ecosystems and hold great potential for sustainable green biotechnology. Growth of cyanobacteria in batch cultures is expected to be part of future biotechnological practices. However, the issue of correlating the dynamics of metabolic and photosynthetic parameters with the culture fitness during batch cultivation is still outstanding. In this paper we take advantage of a photobioreactor system to continuously track growth parameters of Synechocystis sp. PCC 6803, and to couple online culture monitoring with offline measurements of photosynthetic efficiency and biochemical and elemental cell composition under several light intensity and CO2 regimes. Light intensity determines the flux of energy into the photosynthetic system while CO2 concentrations determines the ability to capture this energy in chemical form. From this perspective, four distinct source-sink regimes were established and compared, which allowed us to reveal specific strategies to acclimate to both carbon and light limitation. As part of the measurements, room temperature excitation-emission spectra and elemental composition of Synechocystis cells were, for the first time, compared throughout the exponential and linear growth phases. In total, 39 parameters (out of 170 measured) were identified as highly correlating (R2 > 0.9) with growth rate or productivity under at least one tested cultivation condition, including concentrations and ratios of pigments or particular elements. For online fitness and productivity monitoring in cyanobacteria batch cultures, parameters such as photosynthesis and respiration rates and ratios, energy-dependent non-photochemical quenching (qE) or Zn and Mo concentration in the cultivation medium can be of interest.