Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions

Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms

BACKGROUND

Diazotrophs carry out biological nitrogen fixation (BNF) using the nitrogenase enzyme complex (NEC), which relies on nitrogenase encoded by nif genes. Horizontal gene transfer (HGT) and gene duplications have created significant diversity among these genes, making it challenging to identify potential diazotrophs. Previous studies have established a minimal set of Nif proteins, known as the Nif core, which includes NifH, NifD, NifK, NifE, NifN, and NifB. This study aimed to identify potential diazotroph groups based on the Nif core and to analyze the inheritance patterns of accessory Nif proteins related to Mo-nitrogenase, along with their impact on N2 fixation maintenance.

RESULTS

In a systematic study, 118 diazotrophs were identified, resulting in a database of 2,156 Nif protein sequences obtained with RAFTS³G. Using this Nif database and a data mining strategy, we extended our analysis to 711 species and found that 544 contain the Nif core. A partial Nif core set was observed in eight species in this study. Finally, we cataloged 662 species with Nif core, of which 52 were novel. Our analysis generated 10,076 Nif proteins from these species and revealed some Nif core duplications. Additionally, we determined the optimal cluster value (k = 10) for analyzing diazotrophic diversity. Combining synteny and phylogenetic analyses revealed distinct syntenies in the nif gene composition across ten groups.

CONCLUSIONS

This study advances our understanding of the distribution of nif genes, aiding in the prediction and classification of N₂-fixing organisms. Furthermore, we present a comprehensive overview of the diversity, distribution, and evolutionary relationships among diazotrophic organisms associated with the Nif core. The analysis revealed the phylogenetic and functional organization of different groups, identifying synteny patterns and new nif gene arrangements across various bacterial and archaeal species.The identified groups serve as a valuable framework for further exploration of the molecular mechanisms underlying biological nitrogen fixation and its evolutionary significance across different bacterial lineages.

Bacterial Isolation from Natural Grassland on Nitrogen-Free Agar Yields Many Strains Without Nitrogenase

Nitrogen inputs for sustainable crop production for a growing population require the enhancement of biological nitrogen fixation. Efforts to increase biological nitrogen fixation include bioprospecting for more effective nitrogen-fixing bacteria. As bacterial nitrogenases are extremely sensitive to oxygen, most primary isolation methods rely on the use of semisolid agar or broth to limit oxygen exposure. Without physical separation, only the most competitive strains are obtained. The distance between strains provided by plating on solid media in reduced oxygen environments has been found to increase the diversity of culturable potential diazotrophic bacteria. To obtain diverse nitrogen-fixing isolates from natural grasslands, we plated soil suspensions from 27 samples onto solid nitrogen-free agar and incubated them under atmospheric and oxygen-reducing conditions. Putative nitrogen fixers were confirmed by subculturing in liquid nitrogen-free media and PCR amplification of the nifH genes. Streaking of the 432 isolates on nitrogen-rich R2A revealed many cocultures. In most cases, only one community member then grew on NFA, indicating the coexistence of nonfixers in coculture with fixers when growing under nitrogen-limited conditions. To exclude isolates able to scavenge residual nitrogen, such as that from vitamins, we used a stringent nitrogen-free medium containing only 6.42 μmol/L total nitrogen and recultured them in a nitrogen-depleted atmosphere. Surprisingly, PCR amplification of nifH using various primer pairs yielded amplicons from only 17% of the 442 isolates. The majority of the nifH PCR-negative isolates were Bacillus and Streptomyces. It is unclear whether these isolates have highly effective uptake systems or nitrogen reduction systems that are not closely aligned with known nitrogenase families. We advise caution in determining the nitrogen fixation ability of plants from growth on nitrogen-free media, even where the total nitrogen is very limited.

Cyanobacteria's power trio: auxin, siderophores, and nitrogen fixation to foster thriving agriculture

Cyanobacteria, often overlooked in traditional agriculture, are gaining recognition for their roles in enhancing plant growth and soil health through diverse mechanisms. This review examines their multifaceted contributions to agricultural systems, highlighting their proficiency in auxin production, which promotes plant growth and development. Additionally, we examined cyanobacteria's ability to produce siderophores that enhance iron absorption and address micronutrient deficiencies, as well as their capacity for nitrogen fixation, which converts atmospheric nitrogen into a form that plants can utilize, all with the goal of reducing reliance on synthetic fertilizers. A meta-analysis of existing studies indicates significant positive effects of cyanobacteria on crop yield, although variability exists. While some research shows considerable yield increases, other studies report non-significant changes, suggesting benefits may depend on specific conditions and crop types. The overall random-effects model estimate indicates a significant aggregate effect, with a few exceptions, emphasizing the need for further research to optimize the use of cyanobacteria as biofertilizers. Although cyanobacteria-based products are limited in comparison to seaweed-derived alternatives, for instance, ongoing challenges include regulatory issues and production costs. Integrating cultivation with wastewater treatment could enhance competitiveness and viability in the agricultural market.

Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins

Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, emphasizing their genomic resources and their potential in the genomic mining of toxin-related genes.

Investigate Freshwater Algae Extract's Efficacy in Treating Diabetes Ulcers and Its Anti-Staphylococcal Properties

Background

Infection of diabetic foot ulcer is very common and leads in 20% of cases to amputation. Antibiotic-resistant Staphylococcus aureus is the main cause of severe infection. Antibiotic resistance is a major challenge to the global health system. This work aimed to investigate the antibacterial efficacy of some algae extracts against Staphylococcus aureus isolated from diabetic foot ulcers.

Methods

freshwater river samples were collected to isolate the algae, and PCR was used for identification. The ethanol, water, and ethyl acetate extract of these algae were prepared and analyzed using high-performance liquid chromatography-mass spectrometry to determine the key components that have antibacterial properties. The antibacterial activity of these extracts against S. aureus was determined by broth dilution and well diffusion methods.

Results

Chlorella vulgaris and Anabaena flos-aquae were isolated from freshwater river and identified by PCR. Anabaena flos-aquae has a greater antibacterial efficacy against Staphylococcus aureus in comparison to Chlorella vulgaris, and the ethanolic extract demonstrated superior outcomes compared to the aqueous and ethyl acetate extracts. The MS spectrum of both algae had a very similar pattern, but the frequency of detected peaks was different.

Conclusions

Ethanolic extract of A. flos-aquae and Chlorella vulgaris can be suggested to treat and control diabetic foot ulcer infection caused by S. aureus. Further studies are required to explore the full potential of these algae safely and extensively.

Arginine inhibits the arginine biosynthesis rate-limiting enzyme and leads to the accumulation of intracellular aspartate in Synechocystis sp. PCC 6803

Cyanobacteria are oxygen-evolving photosynthetic prokaryotes that affect the global carbon and nitrogen turnover. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a model cyanobacterium that has been widely studied and can utilize and uptake various nitrogen sources and amino acids from the outer environment and media. l-arginine is a nitrogen-rich amino acid used as a nitrogen reservoir in Synechocystis 6803, and its biosynthesis is strictly regulated by feedback inhibition. Argininosuccinate synthetase (ArgG; EC 6.3.4.5) is the rate-limiting enzyme in arginine biosynthesis and catalyzes the condensation of citrulline and aspartate using ATP to produce argininosuccinate, which is converted to l-arginine and fumarate through argininosuccinate lyase (ArgH). We performed a biochemical analysis of Synechocystis 6803 ArgG (SyArgG) and obtained a Synechocystis 6803 mutant overexpressing SyArgG and ArgH of Synechocystis 6803 (SyArgH). The specific activity of SyArgG was lower than that of other arginine biosynthesis enzymes and SyArgG was inhibited by arginine, especially among amino acids and organic acids. Both arginine biosynthesis enzyme-overexpressing strains grew faster than the wild-type Synechocystis 6803. Based on previous reports and our results, we suggest that SyArgG is the rate-limiting enzyme in the arginine biosynthesis pathway in cyanobacteria and that arginine biosynthesis enzymes are similarly regulated by arginine in this cyanobacterium. Our results contribute to elucidating the regulation of arginine biosynthesis during nitrogen metabolism.

Phylogenetic analysis of Nostocales (Cyanobacteria) based on two novel molecular markers, implicated in the nitrogenase biosynthesis

The characterization of cyanobacteria communities remains challenging, as taxonomy of several cyanobacterial genera is still unresolved, especially within Nostocales taxa. Nostocales cyanobacteria are capable of nitrogen fixation; nitrogenase genes are grouped into operons and are located in the same genetic locus. Structural nitrogenase genes (nifH, nifK and nifD) as well as 16S rRNA have been shown to be adequate genetic markers for distinguishing cyanobacterial genera. However, there is no available information regarding the phylogeny of regulatory genes of the nitrogenase cluster. Aiming to provide a more accurate overview of the evolution of nitrogen fixation, this study analyzed for the first time nifE and nifN genes, which regulate the production of nitrogenase, alongside nifH. Specific primers were designed to amplify nifE and nifN genes, previously not available in literature and phylogenetic analysis was carried out in 13 and 14 TAU-MAC culture collection strains, respectively, of ten Nostocales genera along with other sequences retrieved from cyanobacteria genomes. Phylogenetic analysis showed that these genes seem to follow a common evolutionary pattern with nitrogenase structural genes and 16S rRNA. The classification of cyanobacteria based on these molecular markers seems to distinguish Nostocales strains with common morphological, ecological, and physiological characteristics.

Co-cultures from Plants and Cyanobacteria: A New Way for Production Systems in Agriculture and Bioprocess Engineering

Due to the global increase in the world population, it is not possible to ensure a sufficient food supply without additional nitrogen input into the soil. About 30-50% of agricultural yields are due to the use of chemical fertilizers in modern times. However, overfertilization threatens biodiversity, such as nitrogen-loving, fast-growing species overgrow others. The production of artificial fertilizers produces nitrogen oxides, which act as greenhouse gases. In addition, overfertilization of fields also releases ammonia, which damages surface waters through acidification and eutrophication. Diazotrophic cyanobacteria, which usually form a natural, stable biofilm, can fix nitrogen from the atmosphere and release it into the environment. Thus, they could provide an alternative to artificial fertilizers. In addition to this, biofilms stabilize soils and thus protect against soil erosion and desiccation. This chapter deals with the potential of cyanobacteria as the use of natural fertilizer is described. Possible partners such as plants and callus cells and the advantages of artificial co-cultivation will be discussed later. In addition, different cultivation systems for studying artificial co-cultures will be presented. Finally, the potential of artificial co-cultures in the agar industry will be discussed.

How diverse a genus can be: An integrated multi-layered analysis into Desmonostoc (Nostocaceae, Cyanobacteriota)

Cyanobacteria (Phylum Cyanobacteriota) are Gram-negative bacteria capable of performing oxygenic photosynthesis. Although the taxonomic classification of cyanobacteria was for a long time based primarily on morphological characters, the application of other techniques (e.g. molecular phylogeny), especially in recent decades, has contributed to a better resolution of cyanobacteria systematics, leading to a revision of the phylum. Although Desmonostoc occurs as a new genus/cluster and some species have been described recently, relatively few studies have been carried out to elucidate its diversity, which encompasses strains from different ecological origins, or examine the application of new characterization tools. In this context, the present study investigated the diversity within Desmonostoc, based on morphological, molecular, metabolic, and physiological characteristics. Although the usage of physiological parameters is unusual for a polyphasic approach, they were efficient in the characterization performed here. The phylogenetic analysis based on 16S rRNA gene sequences put all studied strains (25) into the D1 cluster and indicated the emergence of novel sub-clusters. It was also possible to observe that nifD and nifH exhibited different evolutionary histories within the Desmonostoc strains. Collectively, metabolic and physiological data, coupled with the morphometric data, were in general, in good agreement with the separation based on the phylogeny of the 16S rRNA gene. Furthermore, the study provided important information on the diversity of Desmonostoc strains collected from different Brazilian biomes by revealing that they were cosmopolitan strains, acclimatized to low luminous intensities, with a large metabolic diversity and great biotechnological potential.

Arginine inhibition of the argininosuccinate lyases is conserved among three orders in cyanobacteria

This study revealed different catalytic efficiencies of cyanobacterial argininosuccinate lyases in non-nitrogen-fixing and nitrogen-fixing cyanobacteria, demonstrating that L-arginine inhibition of L-argininosuccinate lyase is conserved among enzymes of three cyanobacterial orders. Arginine is a nitrogen-rich amino acid that uses a nitrogen reservoir, and its biosynthesis is strictly controlled by feedback inhibition. Argininosuccinate lyase (EC 4.3.2.1) is the final enzyme in arginine biosynthesis that catalyzes the conversion of argininosuccinate to L-arginine and fumarate. Cyanobacteria synthesize intracellular cyanophycin, which is a nitrogen reservoir composed of aspartate and arginine. Arginine is an important source of nitrogen for cyanobacteria. We expressed and purified argininosuccinate lyases, ArgHs, from Synechocystis sp. PCC 6803, Nostoc sp. PCC 7120, and Arthrospira platensis NIES-39. The catalytic efficiency of the Nostoc sp. PCC 7120 ArgH was 2.8-fold higher than those of Synechocystis sp. PCC 6803 and Arthrospira platensis NIES-39. All three ArgHs were inhibited in the presence of arginine, and their inhibitory effects were lowered at pH 7.0, compared to those at pH 8.0. These results indicate that arginine inhibition of ArgH is widely conserved among the three cyanobacterial orders. The current results demonstrate the conserved regulation of enzymes in the cyanobacterial aspartase/fumarase superfamily.

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

Phylogenomics uncovers evolutionary trajectory of nitrogen fixation in Cyanobacteria

Biological nitrogen fixation (BNF) by cyanobacteria is of significant importance for the Earth’s biogeochemical nitrogen cycle but is restricted to a few genera that do not form monophyletic group. To explore the evolutionary trajectory of BNF and investigate the driving forces of its evolution, we analyze 650 cyanobacterial genomes and compile the database of diazotrophic cyanobacteria based on the presence of nitrogen fixation gene clusters (NFGCs). We report that 266 of 650 examined genomes are NFGC-carrying members, and these potentially diazotrophic cyanobacteria are unevenly distributed across the phylogeny of Cyanobacteria, that multiple independent losses shaped the scattered distribution. Among the diazotrophic cyanobacteria, two types of NFGC exist, with one being ancestral and abundant, which have descended from diazotrophic ancestors, and the other being anaerobe-like and sparse, possibly being acquired from anaerobic microbes through horizontal gene transfer. Interestingly, we illustrate that the origin of BNF in Cyanobacteria coincide with two major evolutionary events. One is the origin of multicellularity of cyanobacteria, and the other is concurrent genetic innovations with massive gene gains and expansions, implicating their key roles in triggering the evolutionary transition from nondiazotrophic to diazotrophic cyanobacteria. Additionally, we reveal that genes involved in accelerating respiratory electron transport (coxABC), anoxygenic photosynthetic electron transport (sqr), as well as anaerobic metabolisms (pfor, hemN, nrdG, adhE) are enriched in diazotrophic cyanobacteria, representing adaptive genetic signatures that underpin the diazotrophic lifestyle. Collectively, our study suggests that multicellularity, together with concurrent genetic adaptations contribute to the evolution of diazotrophic cyanobacteria.

Sustainable production of algae-bacteria granular consortia based biological hydrogen: New insights

Microbes recycling nutrient and detoxifying ecosystems are capable to fulfil the future energy need by producing biohydrogen by due to the coupling of autotrophic and heterotrophic microbes. In granules microbes mutualy exchanging nutrients and electrons for hydrogen production. The consortial biohydrogen production depend upon constituent microbes, their interdependence, competition for resources, and other operating parameters while remediating a waste material in nature or bioreactor. The present review deals with development of granular algae-bacteria consortia, hydrogen yield in coculture, important enzymes and possible engineering for improved hydrogen production.

Influence of Mo and Fe on Photosynthetic and Nitrogenase Activities of Nitrogen-Fixing Cyanobacteria under Nitrogen Starvation

The potential of cyanobacteria to perform a variety of distinct roles vital for the biosphere, including nutrient cycling and environmental detoxification, drives interest in studying their biodiversity. Increasing soil erosion and the overuse of chemical fertilizers are global problems in developed countries. The option might be to switch to organic farming, which entails largely the use of biofertilisers. Cyanobacteria are prokaryotic, photosynthetic organisms with considerable potential, within agrobiotechnology, to produce biofertilisers. They contribute significantly to plant drought resistance and nitrogen enrichment in the soil. This study sought, isolated, and investigated nitrogen-fixing cyanobacterial strains in rice fields, and evaluated the effect of Mo and Fe on photosynthetic and nitrogenase activities under nitrogen starvation. Cyanobacterial isolates, isolated from rice paddies in Kazakhstan, were identified as Trichormus variabilis K-31 (MZ079356), Cylindrospermum badium J-8 (MZ079357), Nostoc sp. J-14 (MZ079360), Oscillatoria brevis SH-12 (MZ090011), and Tolypothrix tenuis J-1 (MZ079361). The study of the influence of various concentrations of Mo and Fe on photosynthetic and nitrogenase activities under conditions of nitrogen starvation revealed the optimal concentrations of metals that have a stimulating effect on the studied parameters.

The Beneficial Effects of Cyanobacterial Co-Culture on Plant Growth

Cyanobacteria are ubiquitous phototrophic prokaryotes that find a wide range of applications in industry due to their broad product spectrum. In this context, the application of cyanobacteria as biofertilizers and thus as an alternative to artificial fertilizers has emerged in recent decades. The benefit is mostly based on the ability of cyanobacteria to fix elemental nitrogen and make it available to the plants in a usable form. However, the positive effects of co-cultivating plants with cyanobacteria are not limited to the provision of nitrogen. Cyanobacteria produce numerous secondary metabolites that can be useful for plants, for example, they can have growth-promoting effects or increase resistance to plant diseases. The effects of biotic and abiotic stress can as well be reduced by many secondary metabolites. Furthermore, the biofilms formed by the cyanobacteria can lead to improved soil conditions, such as increased water retention capacity. To exchange the substances mentioned, cyanobacteria form symbioses with plants, whereby the strength of the symbiosis depends on both partners, and not every plant can form symbiosis with every cyanobacterium. Not only the plants in symbiosis benefit from the cyanobacteria, but also vice versa. This review summarizes the beneficial effects of cyanobacterial co-cultivation on plants, highlighting the substances exchanged and the strength of cyanobacterial symbioses with plants. A detailed explanation of the mechanism of nitrogen fixation in cyanobacterial heterocysts is given. Finally, a summary of possible applications of co-cultivation in the (agrar-)industry is given.

Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea

The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.

Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01

Microalgae and cyanobacteria are good sources for prospecting metabolites of biotechnological interest, including glucosidase inhibitors. These inhibitors act on enzymes related to various biochemical processes; they are involved in metabolic diseases, such as diabetes and Gaucher disease, tumors and viral infections, thus, they are interesting hubs for the development of new drugs and therapies. In this work, the screening of 63 environmental samples collected in the Brazilian Amazon found activity against β-glucosidase, of at least 60 min, in 13.85% of the tested extracts, with Synechococcus sp. GFB01 showing inhibitory activity of 90.2% for α-glucosidase and 96.9% against β-glucosidase. It was found that the nutritional limitation due to a reduction in the concentration of sodium nitrate, despite not being sufficient to cause changes in cell growth and photosynthetic apparatus, resulted in reduced production of α and β-glucosidase inhibitors and differential protein expression. The proteomic analysis of cyanobacteria isolated from the Amazon is unprecedented, with this being the first work to evaluate the protein expression of Synechococcus sp. GFB01 subjected to nutritional stress. This evaluation helps to better understand the metabolic responses of this organism, especially related to the production of inhibitors, adding knowledge to the industrial potential of these cyanobacterial compounds.

Molecular Components of Nitrogen Fixation Gene Cluster and Associated Enzymatic Activities of Non-Heterocystous Thermophilic Cyanobacterium Thermoleptolyngbya sp

Thermoleptolyngbya is a genus of non-heterocystous cyanobacteria that are typical inhabitants of hot spring microbial mats. These filamentous cyanobacteria are capable of nitrogen fixation. In this study, we examined the genome sequences of five publicly available Thermoleptolyngbya strains to explore their nitrogen fixation gene cluster. Analysis of the nitrogen-fixation clusters in these extremophilic strains revealed that the cluster is located in a single locus in Thermoleptolyngbyace. The average nucleotide and amino acid identities of the nitrogen-fixation cluster combined with phylogenetic reconstructions support that nitrogen fixation genes in Thermoleptolyngbyaceae are closely related to one another but also heterogeneous within the genus. The strains from Asia, and China more specifically, generate a separate clade within the genus. Among these strains Thermoleptolyngbya sp. PKUAC-SCTB121 has been selected for experimental validation of clade's nitrogen fixation capacity. The acetylene reduction experiments of that strain shown that the strain can reduce acetylene to ethylene, indicating a fully functional nitrogenase. The activity of nitrogenase has been tested using different gas compositions across 72 h and exhibited a two-phase trend, high nitrogenase activity at the beginning of the assay that slowed down in the second phase of the analysis.

Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives

Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.

The Evolution of Molybdenum Dependent Nitrogenase in Cyanobacteria

Simple Summary

Nitrogen fixation is the process by which nitrogen in the atmosphere is converted into ammonia and other nitrogen-containing organic compounds. It is carried out by a variety of bacteria, including Cyanobacteria. Previous studies have shown that several groups of Cyanobacteria have the ability to fix nitrogen; however, because these groups are scattered throughout the Cyanobacterial lineage, the evolutionary history of nitrogen fixation in these bacteria has not been clarified. In this study, we attempted to identify the origin of nitrogen fixation development in Cyanobacterium by focusing on molybdenum dependent nitrogenase, a major nitrogen fixing enzyme. We compared a phylogenetic tree from 179 species of Cyanobacteria to one generated from nitrogen fixation-related genes. We also compared the genomic locations of those genes. As a result, we found that nitrogen fixing genes were acquired in the Cyanobacterium common ancestor and subsequently lost in some lineages. The results demonstrate that inconsistencies between species phylogeny and organism characteristics can occur and be caused not only by horizontal gene transfer, but also by gene deletion.

Abstract

Nitrogen fixation plays a crucial role in the nitrogen cycle by helping to convert nitrogen into a form usable by other organisms. Bacteria capable of fixing nitrogen are found in six phyla including Cyanobacteria. Molybdenum dependent nitrogenase (nif) genes are thought to share a single origin as they have homologs in various phyla. However, diazotrophic bacteria have a mosaic distribution within the cyanobacterial lineage. Therefore, the aim of this study was to determine the cause of this mosaic distribution. We identified nif gene operon structures in the genomes of 85 of the 179 cyanobacterial strains for which whole genome sequences were available. Four nif operons were conserved in each diazotroph Cyanobacterium, although there were some gene translocations and insertions. Phylogenetic inference of these genes did not reveal horizontal gene transfer from outside the phylum Cyanobacteria. These results support the hypothesis that the mosaic distribution of diazotrophic bacteria in the cyanobacterial lineage is the result of the independent loss of nif genes inherited from common cyanobacterial ancestors in each lineage.

Small but Smart: On the Diverse Role of Small Proteins in the Regulation of Cyanobacterial Metabolism

Over the past few decades, bioengineered cyanobacteria have become a major focus of research for the production of energy carriers and high value chemical compounds. Besides improvements in cultivation routines and reactor technology, the integral understanding of the regulation of metabolic fluxes is the key to designing production strains that are able to compete with established industrial processes. In cyanobacteria, many enzymes and metabolic pathways are regulated differently compared to other bacteria. For instance, while glutamine synthetase in proteobacteria is mainly regulated by covalent enzyme modifications, the same enzyme in cyanobacteria is controlled by the interaction with unique small proteins. Other prominent examples, such as the small protein CP12 which controls the Calvin-Benson cycle, indicate that the regulation of enzymes and/or pathways via the attachment of small proteins might be a widespread mechanism in cyanobacteria. Accordingly, this review highlights the diverse role of small proteins in the control of cyanobacterial metabolism, focusing on well-studied examples as well as those most recently described. Moreover, it will discuss their potential to implement metabolic engineering strategies in order to make cyanobacteria more definable for biotechnological applications.

Nitrogenase Inhibition Limited Oxygenation of Earth's Proterozoic Atmosphere

Cyanobacteria produced the oxygen that began to accumulate on Earth 2.5 billion years ago, at the dawn of the Proterozoic Eon. By 2.4 billion years ago, the Great Oxidation Event (GOE) marked the onset of an atmosphere containing oxygen. The oxygen content of the atmosphere then remained low for almost 2 billion years. Why? Nitrogenase, the sole nitrogen-fixing enzyme on Earth, controls the entry of molecular nitrogen into the biosphere. Nitrogenase is inhibited in air containing more than 2% oxygen: the concentration of oxygen in the Proterozoic atmosphere. We propose that oxygen inhibition of nitrogenase limited Proterozoic global primary production. Oxygen levels increased when upright terrestrial plants isolated nitrogen fixation in soil from photosynthetic oxygen production in shoots and leaves.

Disruption of the Gene trx-m1 Impedes the Growth of Anabaena sp. PCC 7120 under Nitrogen Starvation

Cyanobacteria possess a sophisticated photosynthesis-based metabolism with admirable plasticity. This plasticity is possible via the deep regulation network, the thiol-redox regulations operated by thioredoxin (hereafter, Trx). In this context, we characterized the Trx-m1-deficient mutant strain of Anabaena sp., PCC 7120 (shortly named A.7120), cultivated under nitrogen limitation. Trx-m1 appears to coordinate the nitrogen response and its absence induces large changes in the proteome. Our data clearly indicate that Trx-m1 is crucial for the diazotrophic growth of A.7120. The lack of Trx-m1 resulted in a large differentiation of heterocysts (>20% of total cells), which were barely functional probably due to a weak expression of nitrogenase. In addition, heterocysts of the mutant strain did not display the usual cellular structure of nitrogen-fixative cells. This unveiled why the mutant strain was not able to grow under nitrogen starvation.

An investigation into the effects of increasing salinity on photosynthesis in freshwater unicellular cyanobacteria during the late Archaean

The oldest species of bacteria capable of oxygenic photosynthesis today are the freshwater Cyanobacteria Gloeobacter spp., belonging to the class Oxyphotobacteria. Several modern molecular evolutionary studies support the freshwater origin of cyanobacteria during the Archaean and their subsequent acquisition of salt tolerance mechanisms necessary for their expansion into the marine environment. This study investigated the effect of a sudden washout event from a freshwater location into either a brackish or marine environment on the photosynthetic efficiency of two unicellular freshwater cyanobacteria: the salt-tolerant Chroococcidiopsis thermalis PCC7203 and the cyanobacterial phylogenetic root species, Gloeobacter violaceus PCC7421. Strains were cultured under present atmospheric levels (PAL) of CO₂ or an atmosphere containing elevated levels of CO₂ and reduced O₂ (eCO₂ rO₂ ) in simulated shallow water or terrestrial environmental conditions. Both strains exhibited a reduction in growth rates and gross photosynthesis, accompanied by significant reductions in chlorophyll a content, in brackish water, with only C. thermalis able to grow at marine salinity levels. While the experimental atmosphere caused a significant increase in gross photosynthesis rates in both strains, it did not increase their growth rates, nor the amount of O₂ released. The differences in growth responses to increasing salinities could be attributed to genetic differences, with C. thermalis carrying additional genes for trehalose synthesis. This study demonstrates that, if cyanobacteria did evolve in a freshwater environment, they would have been capable of withstanding a sudden washout into increasingly saline environments. Both C. thermalis and G. violaceus continued to grow and photosynthesise, albeit at diminished rates, in brackish water, thereby providing a route for the evolution of open ocean-dwelling strains, necessary for the oxygenation of the Earth's atmosphere.

Role of cyanobacteria in agricultural and industrial sectors: an outlook on economically important byproducts

Cyanobacteria are potential organisms, which are used as food, feed and fuel. The unique characters of cyanobacteria include short generation times, their ubiquitous presence and efficient nitrogen fixing potential. Cyanobacteria are unique organisms performing photosynthesis, bioremediation of wastewater, high biomass and biofuel productions etc. They are also used in the treatment of industrial and domestic wastewaters for the utilization or removal of ammonia, phosphates and other heavy metals (Cr, Pb, Co, Cu, Zn). Biomasses of cyanobacteria are used as biofertilizers for the improvement of nutrient or mineral status and water-holding capacity of the soil. The secondary metabolites of cyanobacteria are used in pharmaceuticals, nutraceutical and chemical industries. In the industrial sector, value-added products from cyanobacteria such as pigments, enzymes and exopolysaccharides are being produced in large scales for biomedical and health applications. Age-old applications of cyanobacteria in agroecosystems as biofertilizers (Anabaena sp; Nostoc sp.) and in industrial sectors as food products (Spirulina) have motivated the researchers to come up with much more specific applications of cyanobacteria both in agricultural and in industrial sectors. Therefore, considering the effectiveness and efficiency of cyanobacteria, the present review has enlisted the standout qualities of cyanobacteria and their potential applications in agricultural and industrial sectors for the benefit of human beings and environment.

Evolution of light-independent protochlorophyllide oxidoreductase

The nonhomologous enzymes, the light-independent protochlorophyllide reductase (DPOR) and the light-dependent protochlorophyllide oxidoreductase (LPOR), catalyze the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) in the penultimate step of biosynthesis of chlorophyll (Chl) required for photosynthetic light absorption and energy conversion. The two enzymes differ with respect to the requirement of light for catalysis and oxygen sensitivity. DPOR and LPOR initially evolved in the ancestral prokaryotic genome perhaps at different times. DPOR originated in the anoxygenic environment of the Earth from nitrogenase-like enzyme of methanogenic archaea. Due to the transition from anoxygenic to oxygenic photosynthesis in the prokaryote, the DPOR was mostly inactivated in the daytime by photosynthetic O₂ leading to the evolution of oxygen-insensitive LPOR that could function in the light. The primary endosymbiotic event transferred the DPOR and LPOR genes to the eukaryotic phototroph; the DPOR remained in the genome of the ancestor that turned into the plastid, whereas LPOR was transferred to the host nuclear genome. From an evolutionary point of view, several compelling theories that explain the disappearance of DPOR from several species cutting across different phyla are as follows: (i) pressure of the oxygenic environment; (ii) change in the light conditions and temperature; and (iii) lineage-specific gene losses, RNA editing, and nonsynonymous substitution. Certain primary amino acid sequence and the physiochemical properties of the ChlL subunit of DPOR have similarity with that of LPOR suggesting a convergence of these two enzymes in certain evolutionary event. The newly obtained sequence data from different phototrophs will further enhance the width of the phylogenetic information on DPOR.

CO-dependent hydrogen production by the facultative anaerobe Parageobacillus thermoglucosidasius

Background

The overreliance on dwindling fossil fuel reserves and the negative climatic effects of using such fuels are driving the development of new clean energy sources. One such alternative source is hydrogen (H₂), which can be generated from renewable sources. Parageobacillus thermoglucosidasius is a facultative anaerobic thermophilic bacterium which is frequently isolated from high temperature environments including hot springs and compost.

Results

Comparative genomics performed in the present study showed that P. thermoglucosidasius encodes two evolutionary distinct H₂-uptake [Ni-Fe]-hydrogenases and one H₂-evolving hydrogenases. In addition, genes encoding an anaerobic CO dehydrogenase (CODH) are co-localized with genes encoding a putative H₂-evolving hydrogenase. The co-localized of CODH and uptake hydrogenase form an enzyme complex that might potentially be involved in catalyzing the water-gas shift reaction (CO + H₂O → CO₂ + H₂) in P. thermoglucosidasius. Cultivation of P. thermoglucosidasius DSM 2542^T with an initial gas atmosphere of 50% CO and 50% air showed it to be capable of growth at elevated CO concentrations (50%). Furthermore, GC analyses showed that it was capable of producing hydrogen at an equimolar conversion with a final yield of 1.08 H₂/CO.

Conclusions

This study highlights the potential of the facultative anaerobic P. thermoglucosidasius DSM 2542^T for developing new strategies for the biohydrogen production.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0954-3) contains supplementary material, which is available to authorized users.

Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization

BACKGROUND

Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus. sp. nov., isolated from the volcanic Lake Albano (Central Italy).

RESULTS

The novel species Vulcanococcus limneticus sp. nov. falls inside the sub-cluster 5.2, close to the estuarine/marine strains in a maximum-likelihood phylogenetic tree generated with 259 marker genes with representatives from marine, brackish, euryhaline and freshwater habitats. V.limneticus sp. nov. possesses a complete nitrogenase and nif operon. In an experimental setup under nitrogen limiting and non-limiting conditions, growth was observed in both cases. However, the nitrogenase genes (nifHDK) were not transcribed, i.e., V.limneticus sp. nov. did not fix nitrogen, but instead degraded the phycobilisomes to produce sufficient amounts of ammonia. Moreover, the strain encoded many other pathways to incorporate ammonia, nitrate and sulphate, which are energetically less expensive for the cell than fixing nitrogen. The association of the nif operon to a genomic island, the relatively high amount of mobile genetic elements (52 transposases) and the lower observed GC content of V.limneticus sp. nov. nif operon (60.54%) compared to the average of the strain (68.35%) support the theory that this planktonic strain may have obtained, at some point of its evolution, the nif operon by horizontal gene transfer (HGT) from a filamentous or heterocystous cyanobacterium.

CONCLUSIONS

In this study, we describe the novel species Vulcanococcus limneticus sp. nov., which possesses a complete nif operon for nitrogen fixation. The finding that in our experimental conditions V.limneticus sp. nov. did not express the nifHDK genes led us to reconsider the actual ecological meaning of these accessory genes located in genomic island that have possibly been acquired via HGT.

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.