Abstract
Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.
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Data Availability
The raw reads from the metagenomic sequencing are available in NCBI SRA under the BioProject accession PRJNA691704. The NCBI accession numbers for the cyanobacterial MAGs generated as a part of this study can be found in supplementary material S5.
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Acknowledgements
We acknowledge the support received by G.U. from the Department of Biotechnology (DBT), Govt. of India, vide Grant No. BT/PR29032/FCB/125/4/2018 for this study which also included funding of PhD fellowship for M.R. S.M. was supported by a BINC fellowship from DBT, Govt. of India. We thank Chilika Development Authority, Balugaon, Odisha for providing logistics for sample collection and laboratory facility for initial processing of sample. We also acknowledge Dr. Mihir Trivedi for his constructive suggestions during phylogenetic analysis.
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Funding was provided by Department of Biotechnology, Ministry of Science and Technology, India (Grant No. BT/PR29032/FCB/125/4/2018).
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Ray, M., Manu, S., Rastogi, G. et al. Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution. J Mol Evol 92, 121–137 (2024). https://doi.org/10.1007/s00239-024-10159-y
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DOI: https://doi.org/10.1007/s00239-024-10159-y