Comparative genomic insights into culturable symbiotic cyanobacteria from the water fern Azolla

Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals

Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.

Symbiosis between cyanobacteria and plants: from molecular studies to agronomic applications

Nitrogen-fixing cyanobacteria from the order Nostocales are able to establish symbiotic relationships with diverse plant species. They are promiscuous symbionts, as the same strain of cyanobacterium is able to form symbiotic biological nitrogen-fixing relationships with different plants species. This review will focus on the different types of cyanobacterial-plant associations, both endophytic and epiphytic, and provide insights from a structural viewpoint, as well as our current understanding of the mechanisms involved in the symbiotic crosstalk. In all these symbioses, the benefit for the plant is clear; it obtains from the cyanobacterium fixed nitrogen and other bioactive compounds, such as phytohormones, polysaccharides, siderophores, or vitamins, leading to enhanced plant growth and productivity. Additionally, there is increasing use of different cyanobacterial species as bio-inoculants for biological nitrogen fixation to improve soil fertility and crop production, thus providing an eco-friendly, alternative, and sustainable approach to reduce the over-reliance on synthetic chemical fertilizers.

Hormogonium Development and Motility in Filamentous Cyanobacteria

Filamentous cyanobacteria exhibit some of the greatest developmental complexity observed in the prokaryotic domain. This includes the ability to differentiate nitrogen-fixing cells known as heterocysts, spore-like akinetes, and hormogonia, which are specialized motile filaments capable of gliding on solid surfaces. Hormogonia and motility play critical roles in several aspects of the biology of filamentous cyanobacteria, including dispersal, phototaxis, the formation of supracellular structures, and the establishment of nitrogen-fixing symbioses with plants. While heterocyst development has been investigated extensively at the molecular level, much less is known about akinete or hormogonium development and motility. This is due, in part, to the loss of developmental complexity during prolonged laboratory culture in commonly employed model filamentous cyanobacteria. In this review, recent progress in understanding the molecular level regulation of hormogonium development and motility in filamentous cyanobacteria is discussed, with a focus on experiments performed using the genetically tractable model filamentous cyanobacterium Nostoc punctiforme, which retains the developmental complexity of field isolates.

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.

Evolutionary genomic insights into cyanobacterial symbioses in plants

Photosynthesis, the ability to fix atmospheric carbon dioxide, was acquired by eukaryotes through symbiosis: the plastids of plants and algae resulted from a cyanobacterial symbiosis that commenced more than 1.5 billion years ago and has chartered a unique evolutionary path. This resulted in the evolutionary origin of plants and algae. Some extant land plants have recruited additional biochemical aid from symbiotic cyanobacteria; these plants associate with filamentous cyanobacteria that fix atmospheric nitrogen. Examples of such interactions can be found in select species from across all major lineages of land plants. The recent rise in genomic and transcriptomic data has provided new insights into the molecular foundation of these interactions. Furthermore, the hornwort Anthoceros has emerged as a model system for the molecular biology of cyanobacteria-plant interactions. Here, we review these developments driven by high-throughput data and pinpoint their power to yield general patterns across these diverse symbioses.

The primary transcriptome of hormogonia from a filamentous cyanobacterium defined by cappable-seq

Hormogonia are motile filaments produced by many filamentous cyanobacteria that function in dispersal, phototaxis and the establishment of nitrogen-fixing symbioses. The gene regulatory network promoting hormogonium development is initiated by the hybrid histidine kinase HrmK, which in turn activates a sigma factor cascade consisting of SigJ, SigC and SigF. In this study, cappable-seq was employed to define the primary transcriptome of developing hormogonia in the model filamentous cyanobacterium Nostoc punctiforme ATCC 29133 in both the wild-type, and sigJ, sigC and sigF mutant strains 6 h post-hormogonium induction. A total of 1544 transcriptional start sites (TSSs) were identified that are associated with protein-coding genes and are expressed at levels likely to lead to biologically relevant transcripts in developing hormogonia. TSS expression among the sigma-factor deletion strains was highly consistent with previously reported gene expression levels from RNAseq experiments, and support the current working model for the role of these genes in hormogonium development. Analysis of SigJ-dependent TSSs corroborated the presence of the previously identified J-Box in the -10 region of SigJ-dependent promoters. Additionally, the data presented provides new insights on sequence conservation within the -10 regions of both SigC- and SigF-dependent promoters, and demonstrates that SigJ and SigC coordinate complex co-regulation not only of hormogonium-specific genes at different loci, but within an individual operon. As progress continues on defining the hormogonium gene regulatory network, this data set will serve as a valuable resource.