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.
References
Aramaki T, Blanc-Mathieu R, Endo H et al (2020) KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36:2251–2252. https://doi.org/10.1093/bioinformatics/btz859
Archibald JM (2015) Endosymbiosis and eukaryotic cell evolution. Curr Biol 25:R911–R921. https://doi.org/10.1016/j.cub.2015.07.055
Bansal MS, Kellis M, Kordi M, Kundu S (2018) RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss. Bioinformatics 34:3214–3216. https://doi.org/10.1093/bioinformatics/bty314
Bergman B, Gallon JR, Rai AN, Stal LJ (1997) N2 fixation by non-heterocystous cyanobacteria. FEMS Microbiol Rev 19:139–185. https://doi.org/10.1111/j.1574-6976.1997.tb0096.x
Blankenship RE (2010) Early Evolution of Photosynthesis. Plant Physiol 154:434–438. https://doi.org/10.1104/pp.110.161687
Blum M, Chang HY, Chuguransky S et al (2021) The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 49:D344–D354. https://doi.org/10.1093/nar/gkaa977
Bornemann TLV, Esser SP, Stach TL et al (2023) uBin: A manual refining tool for genomes from metagenomes. Environ Microbiol 25:1077–1083. https://doi.org/10.1111/1462-2920.16351
Boyd JA, Woodcroft BJ, Tyson GW (2018) GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Res 46:E59. https://doi.org/10.1093/NAR/GKY174
Bucciarelli E, Ridame C, Sunda WG et al (2013) Increased intracellular concentrations of DMSP and DMSO in iron-limited oceanic phytoplankton Thalassiosira oceanica and Trichodesmium erythraeum. Limnol Oceanogr 58:1667–1679. https://doi.org/10.4319/lo.2013.58.5.1667
Bushnell B (2014) BBTools software package. https://sourceforge.net/projects/bbmap
Carrit DE, Carpenter JH (1996) Recommendation procedure for Winkler analyses of sea water for dissolved oxygen. J Mar Res 24:313–318
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
Curson ARJ, Liu J, Bermejo Martínez A et al (2017) Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process. Nat Microbiol. https://doi.org/10.1038/nmicrobiol.2017.9
Curson ARJ, Williams BT, Pinchbeck BJ et al (2018) DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nat Microbiol 3:430–439. https://doi.org/10.1038/s41564-018-0119-5
Gage DA, Rhodes D, Nolte KD, Hicks WA, Leustek T, Cooper AJ, Hanson AD (1997) A new route for synthesis of dimethylsulphoniopropionate in marine algae. Nature 387(6636):891–894. https://doi.org/10.1038/43160
Garcia-Pichel F, Belnap J, Neuer S, Schanz F (2009) Estimates of global cyanobacterial biomass and its distribution. Arch Hydrobiol Suppl Algol Stud 109:213–227. https://doi.org/10.1127/1864-1318/2003/0109-0213
Grasshoff K, Kremling K, Ehrhardt M (1999) Methods of seawater analysis. Wiley, New York, p 600
Hatakeyama S, Okuda M, Akimoto H (1982) Formation of sulfur dioxide and methanesulfonic acid in the photooxidation of dimethyl sulfide in the air. Geophys Res Lett 9(5):583–586. https://doi.org/10.1029/GL009i005p00583
Hatton AD, Shenoy DM, Hart MC et al (2012) Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea. Biogeochemistry 110:131–146. https://doi.org/10.1007/s10533-012-9702-7
Huang X, Weisener CG, Ni J et al (2020) Nitrate assimilation, dissimilatory nitrate reduction to ammonium, and denitrification coexist in Pseudomonas putida Y-9 under aerobic conditions. Bioresour Technol 312:123597. https://doi.org/10.1016/j.biortech.2020.123597
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755. https://doi.org/10.1093/bioinformatics/17.8.754
Hug LA, Castelle CJ, Wrighton KC et al (2013) Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1:1–17. https://doi.org/10.1186/2049-2618-1-22
Hug LA, Baker BJ, Anantharaman K et al (2016) A new view of the tree of life. Nat Microbiol 1:1–6. https://doi.org/10.1038/nmicrobiol.2016.48
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Integrated nr database in protein annotation system and its localization. Nat Commun 6:1–8
Kamp A, De Beer D, Nitsch JL et al (2011) Diatoms respire nitrate to survive dark and anoxic conditions. Proc Natl Acad Sci USA 108:5649–5654. https://doi.org/10.1073/pnas.1015744108
Kang DD, Li F, Kirton E et al (2019) MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 2019:1–13. https://doi.org/10.7717/peerj.7359
Kocsis MG, Nolte KD, Rhodes D et al (1998) Dimethylsulfoniopropionate biosynthesis in Spartina alterniflora: evidence that S-methylmethionine and dimethylsulfoniopropylamine are intermediates. Plant Physiol 117:273–281. https://doi.org/10.1104/pp.117.1.273
Lam P, Kuypers (2011) Microbial nitrogen cycling processes in oxygen minimum zones. Ann Rev Mar Sci 3:317–345. https://doi.org/10.1146/annurev-marine-120709-142814
Lanfear R, Frandsen PB, Wright AM et al (2017) Partitionfinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol 34:772–773. https://doi.org/10.1093/molbev/msw260
Liang Z, Keeley A (2013) Filtration recovery of extracellular DNA from environmental water samples. Environ Sci Technol 47:9324–9331. https://doi.org/10.1021/es401342b
Lovelock JE, Maggs RJ, Rasmussen RA (1972) Atmospheric dimethyl sulphide and the natural sulphur cycle. Nature 237(5356):452–453. https://doi.org/10.1038/237452a0
Manu S, Umapathy G (2023) Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems. Ecol Indic 156:111171. https://doi.org/10.1016/j.ecolind.2023.111171
Mohapatra M, Behera P, Kim JY, Rastogi G (2020) Seasonal and spatial dynamics of bacterioplankton communities in a brackish water coastal lagoon. Sci Total Environ 705:134729. https://doi.org/10.1016/j.scitotenv.2019.134729
Mohapatra M, Manu S, Kim JY, Rastogi G (2023) Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon. Sci Total Environ 879:163109. https://doi.org/10.1016/j.scitotenv.2023.163109
Monchamp ME, Spaak P, Pomati F (2019) Long term diversity and distribution of non-photosynthetic cyanobacteria in peri-alpine lakes. Front Microbiol. https://doi.org/10.3389/fmicb.2018.03344
Moore KR, Magnabosco C, Momper L et al (2019) An expanded ribosomal phylogeny of cyanobacteria supports a deep placement of plastids. Front Microbiol 10:1–14. https://doi.org/10.3389/fmicb.2019.01612
Muduli PR, Pattnaik AK (2020) Spatio-temporal variation in physicochemical parameters of water in the Chilika Lagoon. In: Finlayson C, Rastogi G, Mishra D, Pattnaik A (eds) Ecology, conservation, and restoration of Chilika Lagoon, India. Wetlands: ecology, conservation and management, vol 6. Springer, Cham
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/molbev/msu300
Parks DH, Imelfort M, Skennerton CT et al (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114
Pessi IS, Popin RV, Durieu B et al (2023) Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics. Microb Genomics 9:1–14. https://doi.org/10.1099/mgen.0.001056
Pfreundt U, Stal LJ, Voß B, Hess WR (2012) Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium. ISME J 6:1367–1377. https://doi.org/10.1038/ismej.2011.199
Pisciotta JM, Zou Y, Baskakov IV (2010) Light-dependent electrogenic activity of cyanobacteria. PLoS ONE. https://doi.org/10.1371/journal.pone.0010821
Reji L, Francis CA (2020) Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME J 14:2105–2115. https://doi.org/10.1038/s41396-020-0675-6
Sanchez-Baracaldo P, Bianchini G, Wilson J, Knoll A (2021) Cyanobacteria and biogeochemical cycles through Earth history. Trends Microbiol. https://doi.org/10.1016/j.tim.2021.05.008
Shang H, Rothman DH, Fournier GP (2022) Oxidative metabolisms catalyzed Earth’s oxygenation. Nat Commun. https://doi.org/10.1038/s41467-022-28996-0
Shi T, Falkowski PG (2008) Genome evolution in cyanobacteria: the stable core and the variable shell. Proc Natl Acad Sci USA 105:2510–2515. https://doi.org/10.1073/pnas.0711165105
Srichandan S, Kim JY, Kumar A et al (2015) Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon. Mar Pollut Bull 101:39–52. https://doi.org/10.1016/j.marpolbul.2015.11.030
Stal LJ, Paerl HW, Bebout B, Villbrandt M (1994) Heterocystous versus non-heterocystous cyanobacteria in microbial mats. Microb Mats. https://doi.org/10.1007/978-3-642-78991-5_41
Stefels J (2000) Physiological aspects of the production and conversion of DMSP in marine algae and higher plants. J Sea Res 43:183–197. https://doi.org/10.1016/S1385-1101(00)00030-7
Sunda W, Kieber DJ, Kiene RP, Huntsman S (2002) An antioxidant function for DMSP and DMS in marine algae. Nature 418(6895):317–320. https://doi.org/10.1038/nature00851
Taberlet P, Coissac E, Pompanon F et al (2012) Towards next-generation biodiversity assessment using DNA metabarcoding-TABERLET-2012-Molecular Ecology-Wiley Online Library. Mol Ecol 21:2045–2050
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
Tarafdar L, Kim JY, Srichandan S et al (2021) Responses of phytoplankton community structure and association to variability in environmental drivers in a tropical coastal lagoon. Sci Total Environ 783:146873. https://doi.org/10.1016/j.scitotenv.2021.146873
Tee HS, Waite D, Payne L et al (2020) Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium. ISME J 14:2164–2178. https://doi.org/10.1038/s41396-020-0676-5
Teeling H, Glöckner FO (2012) Current opportunities and challenges in microbial metagenome analysis-a bioinformatic perspective. Brief Bioinform 13:728–742. https://doi.org/10.1093/bib/bbs039
Thomas AC, Howard J, Nguyen PL et al (2018) ANDeTM: a fully integrated environmental DNA sampling system. Methods Ecol Evol 9:1379–1385. https://doi.org/10.1111/2041-210X.12994
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 44:W232–W235. https://doi.org/10.1093/NAR/GKW256
Uchida A, Ooguri T, Ishida T, Kitaguchi H, Ishida Y (1996) Biosynthesis of dimethylsulfopropionate in Crypthecodinium cohnii (Dinophyceae). Biological and Environmental Chemistry of DMSP and related Sulfonium Compounds. Springer, Boston, MA, p 97–107
Vairavamurthy A, Andreae MO, Iverson RL (1985) Biosynthesis of dimethylsulfide and dimethylpropiothetin by Hymenomonas carterae in relation to sulfur source and salinity variations. Limnol Oceanogr 30:59–70. https://doi.org/10.4319/lo.1985.30.1.0059
Vargas A, Strohl WR (1985) Utilization of nitrate by Beggiatoa alba. Arch Microbiol 142:279–284. https://doi.org/10.1007/BF00693404
Waglechner N, McArthur AG, Wright GD (2019) Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance. Nat Microbiol 4:1862–1871. https://doi.org/10.1038/s41564-019-0531-5
Waterbury JB (2006) The Cyanobacteria—Isolation, purification and identification. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds), The Prokaryotes. Springer, New York. https://doi.org/10.1007/0-387-30744-3_38
Yarza P, Yilmaz P, Pruesse E et al (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645. https://doi.org/10.1038/nrmicro3330
Zehr JP (2011) Nitrogen fixation by marine cyanobacteria. Trends Microbiol 19:162–173. https://doi.org/10.1016/j.tim.2010.12.004
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