The “Dark Side” of Picocyanobacteria: Life as We Do Not Know It (Yet)

Exploring Sustainable Agriculture with Nitrogen-Fixing Cyanobacteria and Nanotechnology

The symbiotic relationship between nitrogen-fixing cyanobacteria and plants offers a promising avenue for sustainable agricultural practices and environmental remediation. This review paper explores the molecular interactions between nitrogen-fixing cyanobacteria and nanoparticles, shedding light on their potential synergies in agricultural nanotechnology. Delving into the evolutionary history and specialized adaptations of cyanobacteria, this paper highlights their pivotal role in fixing atmospheric nitrogen, which is crucial for ecosystem productivity. The review discusses the unique characteristics of metal nanoparticles and their emerging applications in agriculture, including improved nutrient delivery, stress tolerance, and disease resistance. It delves into the complex mechanisms of nanoparticle entry into plant cells, intracellular transport, and localization, uncovering the impact on root-shoot translocation and systemic distribution. Furthermore, the paper elucidates cellular responses to nanoparticle exposure, emphasizing oxidative stress, signaling pathways, and enhanced nutrient uptake. The potential of metal nanoparticles as carriers of essential nutrients and their implications for nutrient-use efficiency and crop yield are also explored. Insights into the modulation of plant stress responses, disease resistance, and phytoremediation strategies demonstrate the multifaceted benefits of nanoparticles in agriculture. Current trends, prospects, and challenges in agricultural nanotechnology are discussed, underscoring the need for responsible and safe nanoparticle utilization. By harnessing the power of nitrogen-fixing cyanobacteria and leveraging the unique attributes of nanoparticles, this review paves the way for innovative, sustainable, and efficient agricultural practices.

Mixotrophy in cyanobacteria

Cyanobacteria evolved the oxygenic photosynthesis to generate organic matter from CO2 and sunlight, and they were responsible for the production of oxygen in the Earth's atmosphere. This made them a model for photosynthetic organisms, since they are easier to study than higher plants. Early studies suggested that only a minority among cyanobacteria might assimilate organic compounds, being considered mostly autotrophic for decades. However, compelling evidence from marine and freshwater cyanobacteria, including toxic strains, in the laboratory and in the field, has been obtained in the last decades: by using physiological and omics approaches, mixotrophy has been found to be a more widespread feature than initially believed. Furthermore, dominant clades of marine cyanobacteria can take up organic compounds, and mixotrophy is critical for their survival in deep waters with very low light. Hence, mixotrophy seems to be an essential trait in the metabolism of most cyanobacteria, which can be exploited for biotechnological purposes.

Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda

Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.

Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria

Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcB and cpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10-30°C), light (10-190 μmol photons m-2  s-1 ), and salinity (2-14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

Interaction among spring phytoplankton succession, water discharge patterns, and hydrogen peroxide dynamics in the Caloosahatchee River in southwest Florida

Phytoplankton communities are major primary producers in the aquatic realm and are responsible for shaping aquatic ecosystems. The dynamics of algal blooms could be determined by a succession of variable taxonomic groups, which are altered based on complex environmental factors such as nutrient availability and hydraulic factors. In-river structures potentially increase the occurrence of harmful algal blooms (HABs) by increasing water residence time and deteriorating water quality. How flowing water stimulates cell growth and affects the population dynamics of phytoplankton communities is a prioritized question that needs to be addressed for water management tactics. The goal of this study was to determine if an interaction between water flow and water chemistry is present, furthermore, to determine the relationship among phytoplankton community successions in the Caloosahatchee River, a subtropical river strongly influenced by human-controlled water discharge patterns from Lake Okeechobee. Particularly we focused on how phytoplankton community shifts influence the natural abundance of hydrogen peroxide, the most stable reactive oxygen species and a byproduct of oxidative photosynthesis. High-throughput amplicon sequencing using universal primers amplify 23S rRNA gene in cyanobacteria and eukaryotic algal plastids revealed that Synechococcus and Cyanobium were the dominant cyanobacterial genera and their relative abundance ranged between 19.5 and 95.3% of the whole community throughout the monitoring period. Their relative abundance declined when the water discharge increased. On the contrary, the relative abundance of eukaryotic algae sharply increased after water discharge increased. As water temperature increased in May, initially dominant Dolichospermum decreased as Microcystis increased. When Microcystis declined other filamentous cyanobacteria such as Geitlerinema, Pseudanabaena, and Prochlorothreix increased in their relative abundances. Interestingly, a peak of extracellular hydrogen peroxide was observed when Dolichospermum dominance was ended, and M. aeruginosa numbers increased. Overall, phytoplankton communities were strongly impacted by human-induced water discharge patterns.

Adaptive genetic traits in pelagic freshwater microbes

Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.

Synthetic biology in marine cyanobacteria: Advances and challenges

The current economic and environmental context requests an accelerating development of sustainable alternatives for the production of various target compounds. Biological processes offer viable solutions and have gained renewed interest in the recent years. For example, photosynthetic chassis organisms are particularly promising for bioprocesses, as they do not require biomass-derived carbon sources and contribute to atmospheric CO2 fixation, therefore supporting climate change mitigation. Marine cyanobacteria are of particular interest for biotechnology applications, thanks to their rich diversity, their robustness to environmental changes, and their metabolic capabilities with potential for therapeutics and chemicals production without requiring freshwater. The additional cyanobacterial properties, such as efficient photosynthesis, are also highly beneficial for biotechnological processes. Due to their capabilities, research efforts have developed several genetic tools for direct metabolic engineering applications. While progress toward a robust genetic toolkit is continuously achieved, further work is still needed to routinely modify these species and unlock their full potential for industrial applications. In contrast to the understudied marine cyanobacteria, genetic engineering and synthetic biology in freshwater cyanobacteria are currently more advanced with a variety of tools already optimized. This mini-review will explore the opportunities provided by marine cyanobacteria for a greener future. A short discussion will cover the advances and challenges regarding genetic engineering and synthetic biology in marine cyanobacteria, followed by a parallel with freshwater cyanobacteria and their current genetic availability to guide the prospect for marine species.

Effects of light intensity, temperature, and salinity in allelopathic interactions between coexisting Synechococcus sp. phenotypes

Organisms from the Synechococcus genus constitute one of the major contributors to oceanic primary production, broadly distributed in waters with wide range of environmental conditions. This work investigated the influence of abiotic factors (temperature, irradiance, and salinity) on the strength of allelopathic interactions between different phenotypes of picoplanktonic cyanobacteria of the genus Synechococcus sp. (Type 1, Type 2, and Type 3a) employing mixed cultures and cell-free filtrate assays. The response variables studied were population growth and content of photosynthetic pigments: chlorophyll a (Chl a), carotenoids (Car), phycocyanin (PC), phycoerythrin (PE), and allophycocyanin (APC). Temperature was shown to be the most significant abiotic factor impacting the allelopathy of Synechococcus sp. phenotypes, with the Type 2 most significantly impacted. Irradiance also had a significant effect, having the largest effect on allelopathy of Type 3a phenotype. Changes in salinity had the greatest effect on allelopathy of Type 1. Our study has shown the significant influence of temperature, irradiance, and salinity on the strength of allelopathic compounds secreted by Synechococcus sp. phenotypes, with temperature the most significantly affecting allelopathic properties. Moreover, we discovered that the allelopathic response to changing environmental factors is highly phenotype-specific. This differential response of allelopathy could help different phenotypes of Synechococcus sp. to coexist in the water column.