Microbial Bioactives
Microbial Bioactives | Online ISSN 2209-2161
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Volume 7 Number 1 2024
REVIEWS (Open Access)
Advances in Biodiversity Exploration and Bioactive Metabolite Discovery: Insights from Cyanobacteria, Microalgae, and Uncultured Microorganisms
Rizwan Rashid Bazmi1, Muhammad Asif2*, Hafiza Sidra Yaseen3 , Ashok Gnanasekaran5*
Microbial Bioactives 7 (1) 1-8 https://doi.org/10.25163/microbbioacts.7110660
Submitted: 22 September 2024 Revised: 17 November 2024 Accepted: 25 November 2024 Published: 27 November 2024
Abstract
Microorganisms, including cyanobacteria, microalgae, and uncultured bacteria, constitute a vast and largely unexplored reservoir of biodiversity and bioactive metabolites. Traditional culture-based methods have historically limited access to microbial diversity, capturing less than 1% of species, while leaving “microbial dark matter” untapped. Recent technological advancements in robotic sampling, high-resolution microscopy, high-throughput screening, and omics-based analyses have transformed our capacity to systematically explore microbial communities across diverse habitats, including deep-sea sediments, hydrothermal vents, acidic craters, and mesophotic ecosystems. These integrated approaches facilitate in situ preservation, detailed structural characterization, and functional assessment of microbial metabolites, enabling discovery of novel compounds with pharmacological and industrial potential. High-throughput extraction and screening platforms accelerate identification of bioactive molecules, while single-cell genomics and metagenomics reveal cryptic biosynthetic gene clusters in previously uncultured organisms. Cryo-electron microscopy and atomic force microscopy provide nanometer-scale visualization of cellular architectures, photosynthetic complexes, and extracellular interactions, linking morphology to ecological function. Despite these advances, challenges remain in functionally annotating novel genes, reproducing environmental conditions, and optimizing hit rates in large-scale screening. Systematic integration of robotics, imaging, genomics, and metabolomics enables a holistic understanding of microbial ecosystems, supporting meta-analytical synthesis of trends in metabolite discovery and biodiversity patterns. This review highlights the state-of-the-art methodologies that uncover microbial diversity, offering insights into sustainable bioengineering, natural product discovery, and ecological monitoring.
Keywords: microbial diversity, cyanobacteria, microalgae, uncultured bacteria, high-throughput screening, metagenomics, bioactive metabolites
References
Alam, K., Abbasi, M. N., Hao, J., Zhang, Y., & Li, A. (2021). Strategies for natural products discovery from uncultured microorganisms. Molecules, 26(10), 2977. https://doi.org/10.3390/molecules26102977
Benjin, X., & Ling, L. (2020). Developments, applications, and prospects of cryo-electron microscopy. Protein Science, 29(4), 872–882. https://doi.org/10.1002/pro.3805
Blainey, P. C. (2013). The future is now: Single-cell genomics of bacteria and archaea. FEMS Microbiology Reviews, 37, 407–427. https://doi.org/10.1111/1574-6976.12015
Crognale, S., Venturi, S., Tassi, F., Rossetti, S., Rashed, H., Cabassi, J., … Vaselli, O. (2018). Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: The case of the Solfatara Crater (Campi Flegrei, southern Italy). FEMS Microbiology Ecology, 94(6), fiy090. https://doi.org/10.1093/femsec/fiy090
Danelius, E., Patel, K., Gonzalez, B., & Gonen, T. (2023). MicroED in drug discovery. Current Opinion in Structural Biology, 79, 102549. https://doi.org/10.1016/j.sbi.2023.102549
Demir, I., Lüchtefeld, I., Lemen, C., Dague, E., Guiraud, P., Zambelli, T., & Formosa-Dague, C. (2021). Probing the interactions between air bubbles and (bio)interfaces at the nanoscale using FluidFM technology. Journal of Colloid and Interface Science, 604, 785–797. https://doi.org/10.1016/j.jcis.2021.07.035
Dextro, R. B., Delbaje, E., Cotta, S. R., Zehr, J. P., Fiore, M. F., & Mock, T. (2021). Trends in free-access genomic data accelerate advances in cyanobacteria taxonomy. Journal of Phycology, 57, 1392–1402. https://doi.org/10.1111/jpy.13204
Fernandes, T. G., Diogo, M. M., Clark, D. S., Dordick, J. S., & Cabral, J. (2009). High-throughput cellular microarray platforms: Applications in drug discovery, toxicology and stem cell research. Trends in Biotechnology, 27, 342–349. https://doi.org/10.1016/j.tibtech.2009.02.009
Garel, M., Bonin, P., Martini, S., Guasco, S., Roumagnac, M., Bhairy, N., … Tamburini, C. (2019). Pressure-retaining sampler and high-pressure systems to study deep-sea microbes under in situ conditions. Frontiers in Microbiology, 10, 453. https://doi.org/10.3389/fmicb.2019.00453
Gusmão, A. C. B., Peres, F. V., Paula, F. S., Pellizari, V. H., Kolm, H. E., & Signori, C. N. (2023). Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean. International Microbiology, 26, 1041–1051. https://doi.org/10.1007/s10123-023-00346-6
Handelsman, J. (2004). Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews, 68, 669–685. https://doi.org/10.1128/MMBR.68.4.669-685.2004
Kawakami, K., Hamaguchi, T., Hirose, Y., Kosumi, D., Miyata, M., Kamiya, N., & Yonekura, K. (2022). Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome. Nature Communications, 13, 3389. https://doi.org/10.1038/s41467-022-30962-9
Martis, E. A., Radhakrishnan, R., & Badve, R. R. (2011). High-throughput screening: The hits and leads of drug discovery — An overview. Journal of Applied Pharmaceutical Science, 1, 2–10.
McCloud, T. G. (2010). High throughput extraction of plant, marine and fungal specimens for preservation of biologically active molecules. Molecules, 15, 4526–4563. https://doi.org/10.3390/molecules15074526
Mišic Radic, T., Vukosav, P., Ackovic, A., & Dulebo, A. (2023). Insights into the morphology and surface properties of microalgae at the nanoscale by atomic force microscopy: A review. Water, 15(11), 1983. https://doi.org/10.3390/w15111983
Moore, S. K., Mickett, J. B., Doucette, G. J., Adams, N. G., Mikulski, C. M., Birch, J. M., … Newton, J. A. (2021). An autonomous platform for near real-time surveillance of harmful algae and their toxins in dynamic coastal shelf environments. Journal of Marine Science and Engineering, 9, 336. https://doi.org/10.3390/jmse9030336
Müller, D. J., & Dufrêne, Y. F. (2008). Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology. Nature Nanotechnology, 3, 261–269. https://doi.org/10.1038/nnano.2008.100
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019). New insights from uncultivated genomes of the global human gut microbiome. Nature, 568, 505–510. https://doi.org/10.1038/s41586-019-1058-x
Page, M. J., McKenzie, J. E., Bossuyt, P. M., Boutron, I., Hoffmann, T. C., Mulrow, C. D., Shamseer, L., Tetzlaff, J. M., Akl, E. A., Brennan, S. E., Chou, R., Glanville, J., Grimshaw, J. M., Hróbjartsson, A., Lalu, M. M., Li, T., Loder, E. W., Mayo-Wilson, E., McDonald, S., … Moher, D. (2021). The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. BMJ, 372, n71. https://doi.org/10.1136/bmj.n71
Park, J., Li, Y., Moon, K., Han, E. J., Lee, S. R., & Seyedsayamdost, M. R. (2022). Structural elucidation of cryptic algaecides in marine algal-bacterial symbioses by NMR spectroscopy and MicroED. Angewandte Chemie International Edition, 61(52), e202114022. https://doi.org/10.1002/anie.202114022
Pessi, I. S., Popin, R. V., Durieu, B., Lara, Y., Tytgat, B., Savaglia, V., … Verleyen, E. (2023). Novel diversity of polar cyanobacteria revealed by genome-resolved metagenomics. Microbial Genomics, 9, 001056. https://doi.org/10.1099/mgen.0.001056
Piel, J. (2002). A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proceedings of the National Academy of Sciences, 99, 14002–14007. https://doi.org/10.1073/pnas.222481399
Salman, I., Karapetyan, N., Venkatachari, A., Li, A. Q., Bourbonnais, A., & Rekleitis, I. (2022). Multi-modal lake sampling for detecting harmful algal blooms. In OCEANS 2022 (pp. 1–9).
Semchonok, D. A., Mondal, J., Cooper, C. J., Schlum, K., Li, M., & Amin, M. (2022). Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821. Plant Communications, 3, 100248. https://doi.org/10.1016/j.xplc.2021.100248
Stepanauskas, R. (2012). Single cell genomics: An individual look at microbes. Current Opinion in Microbiology, 15, 613–620. https://doi.org/10.1016/j.mib.2012.09.001
Szymanski, P., Markowicz, M., & Mikiciuk-Olasik, E. (2012). Adaptation of high-throughput screening in drug discovery — Toxicological screening tests. International Journal of Molecular Sciences, 13, 427–452. https://doi.org/10.3390/ijms13010427
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., … Nelson, W. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66–74. https://doi.org/10.1126/science.1093857
Wani, M. C., Taylor, H. L., Wall, M. E., Coggon, P., & McPhail, A. T. (1971). Plant antitumor agents VI. Isolation and structure of taxol. Journal of the American Chemical Society, 93, 2325–2327. https://doi.org/10.1021/ja00738a045
Williamson, N. R., Fineran, P. C., Leeper, F. J., & Salmond, G. P. (2005). The biosynthesis and regulation of bacterial prodiginines. Nature Reviews Microbiology, 3, 295–306. https://doi.org/10.1038/nrmicro1133
Yin, C. (2018). Structural biology revolution led by technical breakthroughs in cryo-electron microscopy. Chinese Physics B, 27(5), 58703. https://doi.org/10.1088/1674-1056/27/5/058703
Zaharia, M., Gogos, A., & Singh, G. (2023). Linking lichen metabolites to genes: Emerging concepts and lessons from molecular biology and metagenomics. Journal of Fungi, 9(2), 160. https://doi.org/10.3390/jof9020160
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