Anabaena azollae: Symbiotic Cyanobacterium Driving Green Agriculture

Overview of the Microbe#

Anabaena azollae (also called Nostoc azollae) is a filamentous, heterocystous cyanobacterium that lives only inside the aquatic fern Azolla[2][7]. It forms unbranched chains of cells with specialized nitrogen-fixing heterocysts[2][7]. This partnership is unique: each generation of Azolla inherits its A. azollae from the parent plant, making the symbiosis vertically transmitted (host and microbe pass together through spores)[4]. Inside the fern’s leaf cavities, A. azollae heterocysts fix atmospheric N₂ into ammonia, while its vegetative cells carry out photosynthesis[2]. The fern provides carbon compounds (sugars) to the cyanobacterium, and in return receives nitrogen compounds for its own growth[2][1].

Key features: A. azollae’s cells include vegetative (green, oxygenic) cells and thick-walled heterocysts that house nitrogenase[2][1]. Genetic analysis shows its genome is highly reduced compared to free-living cyanobacteria: about one third of its genes are inactive pseudogenes, and many metabolic pathways (e.g. sugar metabolism, DNA repair) are partly or wholly lost[4][2]. Consistent with this reduction, A. azollae cannot survive on its own and is completely integrated into the Azolla superorganism[4]. In effect, the cyanobacterium behaves like a nitrogen-fixing organelle dedicated to its host.

Symbiotic Nitrogen Fixation within Azolla#

Inside each Azolla leaf, A. azollae heterocysts create a micro-oxic (low-oxygen) environment that allows nitrogenase to convert atmospheric N₂ into ammonia[2]. A nitrogen-rich polymer (cyanophycin) is produced in heterocysts as a temporary store; later this material is broken down to transfer fixed nitrogen to neighboring cells and to the plant[2]. Meanwhile, the vegetative cells perform photosynthesis and supply sugars to the heterocysts, linking carbon and nitrogen metabolism[2].

The rate of fixation is very high. Colonies of A. azollae in Azolla allow the fern to double its biomass in about two days under optimal conditions[7]. Field measurements show an Azolla crop can provide on the order of 40–60 kg N per hectare (per crop cycle) t[7]o rice paddies, comparable to a moderate fertilizer application. Importantly, when Azolla plants senesce or are plowed under, the nitrogen they have fixed is released (as nitrate and ammonia) into the water and soil, effectively fertilizing subsequent crops[1].

• Natural fertilization: When Azolla decays, its stored nitrogen is released to the environment, enriching the soil for other plants[1].
• Filament structure: Chains of vegetative cells and periodic heterocysts containing nitrogenase[2].
• Nitrogen fixation: Heterocysts reduce N₂ to ammonia; cyanophycin transfers fixed N to vegetative cells and the host fern[2].
• Nutrient exchange: Azolla supplies carbohydrates to A. azollae; A. azollae supplies fixed nitrogen to the plant[2][1].

Biofertiliser Applications in Rice Paddies#

The Azolla–A. azollae symbiosis has been exploited in rice agriculture for centuries. Farmers in Southeast Asia found that adding Azolla (the so-called “mosquito fern”) to flooded paddies sharply increased rice yields[1]. They maintained live Azolla cultures year-round and inoculated paddies each season, since the fern’s internal nitrogen supply could replace chemical fertilizer[1]. As one source explains, the secret of Azolla’s “super-fertilizer” effect is that A. azollae in the leaf cavities transforms atmospheric N₂ into nitrate; when the plants die or are plowed under, this nitrate is released into the field to feed crops[1].

Modern studies confirm these benefits. For example, a field experiment showed that using Azolla cover with only half the usual fertilizer produced yields equal to a full-fertilizer regime[5]. Another trial found that mixing dried Azolla with rice straw allowed a 50% reduction in applied N fertilizer without losing yield[5]. In addition to fertilization, Azolla mats suppress weeds by shading and reduce pests: dense mats can cut mosquito breeding by over 95%. They also may lower methane emissions from rice fields by 25–50%, further enhancing sustainability[7].

• Feed supplement: Azolla itself is nutritious (20–30% protein) and has been used as livestock and poultry feed, supplementing or replacing grain feed[1].
• Historical use: Azolla has been grown in rice paddies in India, Vietnam and China for hundreds of years to boost fertility and yields[1][7].
• Yield increase: Rice yields often rise dramatically with Azolla integration; some reports note yields doubling after Azolla mulching[5][7].

• Crop integration: After rapid growth, Azolla biomass (now rich in nitrogen) can be turned into the soil as green manure. The released nutrients then benefit the next rice crop or other wetland plants[1].

Biotechnological Prospects and Metabolite Production#

Beyond fertilization, the Azolla–A. azollae partnership has notable biotechnological potential. Large-scale Azolla cultivation can yield abundant biomass rich in protein, vitamins and antioxidants, making it attractive as an animal feed or even a nutrient source in human food products. Its fast growth and starch content have led researchers to explore Azolla for biofuel applications (e.g. ethanol, biogas)[3]. The cyanobacterium produces cyanophycin and other polymers that could be harvested for biodegradable materials.

Another promising area is water remediation: Azolla is a natural “green purifier.” It efficiently absorbs excess nutrients and even some pollutants from water. For example, floating beds of Azolla have been shown to remove nitrates, phosphates and heavy metals, preventing algal blooms[3]. Meanwhile, by sequestering carbon in its biomass, Azolla helps mitigate CO₂. (Indeed, a famous Paleocene “Azolla event” in the Arctic suggests that ancient Azolla blooms once drew down greenhouse gases on a global scale[10].)

Importantly, modern analyses suggest that Azolla and A. azollae do not produce harmful cyanotoxins. Genetic screening of Nostoc azollae found no genes for microcystin, anatoxin, saxitoxin or BMAA, and chemical tests detected none of these compounds in any Azolla samples[7]. This indicates Azolla-based feeds, fertilizers or foods should be safe by current knowledge.

• Carbon capture: Thick Azolla mats store carbon in biomass; on a large scale this could help offset CO₂ emissions[10].reduced rot incidence in cherry and apple fruits[5]. Development of VOC‑based biopackaging is underway to leverage these fumigant‑like properties.
• Feedstock: Azolla biomass (~20–30% protein) can substitute for traditional feeds in livestock, poultry and aquaculture[1][7].
• Biofuel: High growth rates and carbohydrate content allow conversion of Azolla into bioethanol, biodiesel or biomethane[3].
• Biopolymers: A. azollae’s cyanophycin and other metabolites could be used to produce biodegradable plastics and chemicals.
• Water cleanup: Azolla beds remove nutrients and toxins from wastewater, improving water quality while yielding biomass[3][7].

Challenges and Future Potential#

---

The Azolla–A. azollae system, while powerful, also faces challenges. Azolla grows best in warm, sunny, still water; in cooler or drier regions its growth is slow or requires protection. If unmanaged, dense Azolla mats can become invasive, blocking sunlight and oxygen and harming native aquatic life[8]. (For example, Azolla pinnata is listed as a noxious weed in parts of the United States and other countries[9].) Control measures—harvesting, shading, or biological control with specific weevils—are used where invasions occur[8].

From an agricultural standpoint, integrating Azolla requires modified practices. Fields must be kept flooded or very wet, and fertilizers or herbicides must be managed to avoid killing the symbiont. Genetically, A. azollae’s obligate lifestyle means it cannot be cultured or easily engineered in isolation. However, recent advances are helping overcome these hurdles. In 2018-2019 scientists sequenced the Azolla filiculoides plant genome, revealing fern genes involved in symbiosis[10]. Transcriptomic and imaging studies are beginning to unravel how plant and cyanobacterium communicate. Such knowledge may one day allow breeding or engineering of improved Azolla strains or even transfer of desirable traits to other crops.

Despite these challenges, optimism is high. Prototype Azolla cultivation systems (“Azolla farms”) are in development to mass-produce biomass for feed and biofertilizer. Field trials consistently show that Azolla integration can reduce synthetic N fertilizer use while maintaining or increasing yields. In the face of rising fertilizer costs and climate concerns, the Azolla–A. azollae partnership exemplifies an ancient, sustainable strategy: a living “green revolution” that naturally provides nitrogen and protein. Ongoing research into Azolla cultivation, symbiont genetics, and system optimization promises to expand its role in modern agriculture and environmental management[4][10].

---

Spotlight on Research: Genome Sequencing of Anabaena azollae Strain 0708#

A landmark study highlighting A. azollae was the 2010 sequencing of its genome (strain 0708) by Ran et al.[4]. This work produced the first complete genome of the Azolla cyanobiont and revealed how its DNA has changed under symbiosis.

Brief Overview#

Liang Ran, John Larsson, Birgitta Bergman and colleagues (Stockholm University et al.) isolated A. azollae from Azolla filiculoides and sequenced its DNA using advanced platforms[4]. The study, published in PLOS ONE in July 2010, assembled ~5.5 million base pairs of A. azollae DNA. The researchers annotated genes and mobile elements, then compared the genome to related free-living cyanobacteria to identify differences attributable to life inside the fern.

---

Key Insights#

The genome showed extensive reductive evolution. About 31.2% of the annotated genes were pseudogenes (i.e. broken or inactive)[4], and nearly 600 insertion sequences (transposons) were scattered throughout. Many core bacterial genes were disrupted: for example, the replication initiator dnaA and numerous DNA repair genes are lost or pseudogenized[4]. Many metabolic pathways were similarly incomplete (e.g. parts of glycolysis and nutrient uptake are missing). In contrast, genes for heterocyst development and nitrogen fixation were intact and even enriched, reflecting the organism’s role as a nitrogen factory for the plant[4].

Why This Matters#

This sequencing project was the first demonstration of genome erosion in a nitrogen-fixing plant symbiont[4]. It shows that A. azollae has shed genes over evolutionary time as it became dedicated to its host, effectively becoming a new kind of organelle-like entity. As Ran et al. conclude, A. azollae is “devoted to nitrogen fixation and devoid of autonomous growth,” at “the initial phase of a transition” towards a plant-associated lifestyle[4]. These insights provide a modern parallel to the ancient origin of chloroplasts and offer a model for studying how symbiosis can drive genome change.

Summary Table: Spotlight Study#

Category	Details
Lead Researchers	Liang Ran, John Larsson et al.
Affiliations	Stockholm University (Sweden); Joint Genome Institute (USA); University of Chicago (USA); Fujian Agricultural & Forestry University (China
Research Focus	Sequencing and analysis of the Azolla cyanobiont (Nostoc azollae strain 0708) genome
Key Breakthroughs	First complete genome of N. azollae; discovery of extreme genome reduction (∼31% pseudogenes)[4]
Collaborative Efforts	Swedish, Chinese, and U.S. research groups (DOE JGI collaboration)
Published Work	Ran et al. 2010, PLOS ONE 5(7):e11486
Perspective	Model for early endosymbiosis / organelle evolution
Publication Date	July 2010
Location	Stockholm, Sweden; Walnut Creek, USA
Key Findings	Genome ≈5.5 Mb; ~31.2% pseudogenes; retains nif and heterocyst genes; many core metabolic genes lost[4]

Conclusion#

Anabaena azollae (Nostoc azollae) is a remarkable cyanobacterium whose fate is bound to its fern host. By fixing nitrogen so efficiently, it enables Azolla to grow densely and act as a living “green fertilizer.” This natural system has been harnessed for sustainable agriculture for millennia and is now being studied with modern science. Genomic and field research together paint a picture of a highly specialized symbiont evolving toward an organelle-like state[4], yet still providing practical benefits in feed and fertility. As the world seeks eco-friendly farming methods, the Azolla–A. azollae partnership stands out as a proven, scalable example of biological innovation.

References#

1. Azolla caroliniana (mosquito fern) – Britannica, (2019)britannica.combritannica.com.
2. Silverman, G.B., et al. (2023). Origin and Evolution of the Azolla Superorganism. Plants. [PMC11314209].
3. Eily, A.N., et al. (2019). A first glimpse at genes important to the Azolla–Nostoc symbiosis. Symbiosis (open-access).
4. Ran, L., Larsson, J., et al. (2010). Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Cyanobacterium. PLOS ONE 5(7): e11486journals.plos.orgjournals.plos.org.
5. Marzouk, S.H., et al. (2024). Rice straw incorporation and Azolla application improves rice yield and nitrogen-use-efficiency. Front. Soil Sci. 4:1378065frontiersin.org.
6. Pratte, B.S., Thiel, T. (2021). Comparative genomic insights into culturable symbiotic cyanobacteria from Azolla. Microb. Genom. (DOI).
7. Broughton, E.D., et al. (2024). Azolla as a Safe Food: suppression of cyanotoxin-related genes in Nostoc azollae. Plants 13(19):2707mdpi.commdpi.com.
8. Pratt, C.F., et al. (2022). A century of Azolla filiculoides biocontrol: the economic value of Stenopelmus rufinasus. CABI Agric. Biosci. 3:70cabiagbio.biomedcentral.comcabiagbio.biomedcentral.com.
9. U.S. Fish & Wildlife Service (2020). Ecological Risk Screening Summary: Azolla pinnata. (USFWS).fws.gov
10. Cassiède, G., Delaux, P.-M. (2018). Two missing plant genomes enrich the green lineage. Labex TULIP News (France).labex-tulip.fr