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Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl⁻, were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlatedwith chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl⁻. Chlorophyceae and Bacillariophyceae were positively correlated with CO₃2−. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.

Ultraviolet (UV) radiation directly affects plants and microorganisms, but also alters the species-specific interactions between them. The distinct bands of UV radiation, UV-A, UV-B, and UV-C have different effects on plants and their associated microorganisms. While UV-A and UV-B mainly affect morphogenesis and phototropism, UV-B and UV-C strongly trigger secondary metabolite production. Short wave (<350 nm) UV radiation negatively affects plant pathogens in direct and indirect ways. Direct effects can be ascribed to DNA damage, protein polymerization, enzyme inactivation and increased cell membrane permeability. UV-C is the most energetic radiation and is thus more effective at lower doses to kill microorganisms, but by consequence also often causes plant damage. Indirect effects can be ascribed to UV-B specific pathways such as the UVR8-dependent upregulated defense responses in plants, UV-B and UV-C upregulated ROS accumulation, and secondary metabolite production such as phenolic compounds. In this review, we summarize the physiological and molecular effects of UV radiation on plants, microorganisms and their interactions. Considerations for the use of UV radiation to control microorganisms, pathogenic as well as non-pathogenic, are listed. Effects can be indirect by increasing specialized metabolites with plant pre-treatment, or by directly affecting microorganisms.

Phototrophic microorganisms that convert carbon dioxide are being explored for their capacity to solve different environmental issues and produce bioactive compounds for human therapeutics and as food additives. Full-scale phototrophic cultivation of microalgae and cyanobacteria can be done in open ponds or closed photobioreactor systems, which have a broad range of volumes. This review focuses on laboratory-scale photobioreactors and their different designs. Illuminated microtiter plates and microfluidic devices offer an option for automated high-throughput studies with microalgae. Illuminated shake flasks are used for simple uncontrolled batch studies. The application of illuminated bubble column reactors strongly emphasizes homogenous gas distribution, while illuminated flat plate bioreactors offer high and uniform light input. Illuminated stirred-tank bioreactors facilitate the application of very well-defined reaction conditions. Closed tubular photobioreactors as well as open photobioreactors like small-scale raceway ponds and thin-layer cascades are applied as scale-down models of the respective large-scale bioreactors. A few other less common designs such as illuminated plastic bags or aquarium tanks are also used mainly because of their relatively low cost, but up-scaling of these designs is challenging with additional light-driven issues. Finally, this review covers recommendations on the criteria for photobioreactor selection and operation while up-scaling of phototrophic bioprocesses with microalgae or cyanobacteria.

Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

Abstract Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae–bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae–bacteria consortia, by drawing out knowledge from natural periphyton. This review considers the ecological diversity and functional drivers of periphyton, highlighting the role of microalgae and bacteria. It explores published concepts in greater detail, and distils knowledge draw knowledge from natural periphyton for that may be applied in biotechnology.

One-carbon (C1) biotechnology offers a promising approach for mitigating climate change via the rapid development of new C1 assimilation pathways. However, their integration into naturally photosynthetic organisms remains limited, and this constrains the full impact of these advances.Natural photosynthetic organisms are inefficient at carbon fixation owing to the energy-intensive Calvin cycle that relies on the slow and unspecific catalyst, ribulose 1,5-bisphosphate carboxylase oxygenase (rubisco). Exploring alternative and more efficient C1 fixation pathways is essential for improving photosynthetic efficiency.Photochemotrophic metabolism presents a promising solution by utilizing electrons from natural photosystems to fix more reduced C1 compounds. This approach could minimize energy losses in carbon assimilation by decoupling carbon and electron metabolism, thereby enabling enhanced photosynthetic carbon fixation. Excessive CO2 emissions, caused by an imbalance between carbon oxidation and reduction, drive climate change. To address this, we propose photochemotrophic metabolism as an alternative to both canonical photosynthesis and synthetic one-carbon (C1) metabolism in heterotrophs. In photochemotrophy, naturally phototrophic microorganisms such as cyanobacteria serve as the chassis to assimilate chemically reduced and soluble C1 compounds such as formate or methanol by using carbon fixation cycles that are more efficient than the native Calvin cycle. Key potential advantages of photochemotrophy include enhanced carbon fixation efficiency, utilization of storable carbon compounds, retention of energy from the original CO2 reduction, and decoupling of carbon delivery and electron source. This proposed strategy positions photochemotrophic cyanobacteria as a promising tool for advancing the bioeconomy. Excessive CO2 emissions, caused by an imbalance between carbon oxidation and reduction, drive climate change. To address this, we propose photochemotrophic metabolism as an alternative to both canonical photosynthesis and synthetic one-carbon (C1) metabolism in heterotrophs. In photochemotrophy, naturally phototrophic microorganisms such as cyanobacteria serve as the chassis to assimilate chemically reduced and soluble C1 compounds such as formate or methanol by using carbon fixation cycles that are more efficient than the native Calvin cycle. Key potential advantages of photochemotrophy include enhanced carbon fixation efficiency, utilization of storable carbon compounds, retention of energy from the original CO2 reduction, and decoupling of carbon delivery and electron source. This proposed strategy positions photochemotrophic cyanobacteria as a promising tool for advancing the bioeconomy.

Anoxygenic phototrophic bacteria have recently been recognized as a ubiquitous component of microbial communities in lakes and marine environments, but studies of the ecological factors that control their significance are scarce. We conducted a manipulative field experiment using natural freshwater microcosms, the tank bromeliad ecosystem, to test the response of anoxygenic and oxygenic phototrophic microorganisms to an environmental gradient across the forest edge. We assessed the biomass of these photosynthetic communities by their pigment content and used structural equation modeling to evaluate the importance of different habitat variables as ecological drivers. We show that anoxygenic phototrophic bacteria are primarily driven by small detrital organic particles rather than directly by light. In contrast, light and habitat size were the main factors controlling the biomass of oxygenic phototrophic microorganisms. Anoxygenic phototrophic bacteria inhabiting the bromeliad ecosystem represent huge concentrations of bacteriochlorophyll a relative to large pelagic environments and form an essential and dominant part of photosynthetic biomass across a wide range of ecological conditions. These freshwater photoheterotrophs are likely to play a pivotal and unsuspected role in energy flow and nutrient cycling in neotropical forests.

The societal importance of renewable carbon-based commodities and energy carriers has elicited a particular interest for high performance phototrophic microorganisms. Selection of optimal strains is often based on direct comparison under laboratory conditions of maximal growth rate or additional valued features such as lipid content. Instead of reporting growth rate in culture, estimation of photosynthetic efficiency (quantum yield of PSII) by pulse-amplitude modulated (PAM) fluorimetry is an often applied alternative method. Here we compared the quantum yield of PSII and the photonic yield on biomass for the green alga Chlorella sorokiniana 211-8K and the cyanobacterium Synechocystis sp. PCC 6803. Our data demonstrate that the PAM technique inherently underestimates the photosynthetic efficiency of cyanobacteria by rendering a high F0 and a low FM, specifically after the commonly practiced dark pre-incubation before a yield measurement. Yet when comparing the calculated biomass yield on light in continuous culture experiments, we obtained nearly equal values for both species. Using mutants of Synechocystis sp. PCC 6803, we analyzed the factors that compromise its PAM-based quantum yield measurements. We will discuss the role of dark respiratory activity, fluorescence emission from the phycobilisomes, and the Mehler-like reaction. Based on the above observations we recommend that PAM measurements in cyanobacteria are interpreted only qualitatively.

Irrigated and rain-fed rice fields are unique agroecosystems and anthropogenic wetlands whose main feature is seasonal flooding. Flooded soils are characterized by spatiotemporal shifts and oscillation of the oxygen status and redox potential, sustaining varieties of microbial metabolisms, where bacteria and methanogenic archaea play principal roles and thus have been the major research targets. In this review, we focus on the diversity and ecology of protists—often overlooked biological entities—in wetland rice field soils. Protists with different ecological functions, i.e., phagotrophs, phototrophs, saprotrophs, and parasites, inhabit a rice field soil with a community- and individual-level adaptation to the wide range of oxygen tensions and redox potential. Other agricultural managements like fertilization and char application also influence the protist community. They link to the material cycling in rice soil and affect the activities and community composition of the microorganisms involved in the biogeochemical cycles. Rice roots are the hot spot for protists, which control the rhizospheric bacterial community and could increase the plant productivity through enhancing nutrient release and altering bacterial activities. This review highlights the essential roles of protists in a wetland rice field soil and needs for further research to fill the gaps in knowledge regarding the diversity and functions of the protists in this unique agroecosystem.

Summary Purple non‐sulphur bacteria (PNSB) are phototrophic microorganisms, which increasingly gain attention in plant production due to their ability to produce and accumulate high‐value compounds that are beneficial for plant growth. Remarkable features of PNSB include the accumulation of polyphosphate, the production of pigments and vitamins and the production of plant growth‐promoting substances (PGPSs). Scattered case studies on the application of PNSB for plant cultivation have been reported for decades, yet a comprehensive overview is lacking. This review highlights the potential of using PNSB in plant production, with emphasis on three key performance indicators (KPIs): fertilization, resistance to stress (biotic and abiotic) and environmental benefits. PNSB have the potential to enhance plant growth performance, increase the yield and quality of edible plant biomass, boost the resistance to environmental stresses, bioremediate heavy metals and mitigate greenhouse gas emissions. Here, the mechanisms responsible for these attributes are discussed. A distinction is made between the use of living and dead PNSB cells, where critical interpretation of existing literature revealed the better performance of living cells. Finally, this review presents research gaps that remain yet to be elucidated and proposes a roadmap for future research and implementation paving the way for a more sustainable crop production. Purple non‐sulfur bacteria (PNSB) are beneficial for plant growth, due to their ability to produce and accumulate high‐value compounds. These phototrophs have the potential to enhance plant growth performance, increase the yield and quality of edible plant biomass, boost the resistance to environmental stresses, bioremediate heavy metals and mitigate greenhouse gas emissions. Therefore, the use of PNSB in agricultural applications can pave the way for a more sustainable crop production.