IJLTEMAS International Journal of Latest Technology in Engineering, Management & Applied Science (IJLTEMAS) IJLTEMAS 2278-2540 IJLTEMAS 357 10.51583/IJLTEMAS.2026.150900006 Mycology Metagenomic Characterization of Fungal Diversity in Lotic and Lentic Freshwater Ecosystems of Palghar District, India Vijay Patil Swati Department of Botany, M.V. P’s KTHM College, Nashik, affiliated to Savitribai Phule Pune University, Pune, Maharashtra India S. Borade Dnyaneshwar Department of Botany, M. V. P's Arts, Commerce and Science College, Ozar Mig, Nashik, Maharashtra India Shankarrao Antapurkar Durgesh Department of Botany, M.V. P’s KTHM College, Nashik, affiliated to Savitribai Phule Pune University, Pune, Maharashtra India 15 9 74 86 14 09 2026 19 09 2026 29 09 2026 Aquatic fungi Chytridiomycota Lotic and lentic habitats Metagenomics Shotgun Sequencing Abstract

Freshwater fungal communities remain poorly characterized in many tropical regions, particularly through culture-independent approaches. The present study employed shotgun metagenomic sequencing to characterize fungal diversity in selected lotic and lentic freshwater habitats of Palghar District, Maharashtra, India. Four environmental samples representing two lotic and two lentic habitats were sequenced on an Illumina NovaSeq X Plus platform, generating approximately 25 Gb of paired-end data per sample. Fungal taxa were identified using Kaiju, and community diversity was evaluated using species richness, Shannon diversity, Simpson diversity, Pielou evenness and Bray–Curtis dissimilarity. Estimated fungal relative abundance ranged from 0.98% to 2.82%, with the highest abundance observed in Lentic 1. Basidiomycota and Chytridiomycota were prominent among the resolved fungal groups. Chytridiomycota occurred in all four samples and showed comparatively greater representation in the lotic habitats, while Lentic 1 was characterized by a strong contribution of Agaricales, particularly Coprinopsis cinerea. Lentic 1 showed the highest resolved species richness but the lowest diversity and evenness, whereas the lotic samples exhibited higher Shannon and Simpson diversity and greater evenness. Bray–Curtis analysis showed the greatest similarity between Lotic 1 and Lotic 2, while Lentic 1 was compositionally distinct. The findings demonstrate that Palghar freshwater habitats support heterogeneous fungal assemblages comprising both aquatic-associated and terrestrially derived fungal signatures and highlight the value of shotgun metagenomics for assessing understudied freshwater mycobiomes.

 References Bai, Y., Wang, Q., Liao, K., Jian, Z., Zhao, C., & Qu, J. (2018). Fungal community as a bioindicator to reflect anthropogenic activities in a river ecosystem. Frontiers in microbiology, 9, 3152. Barros, J., Ben Tanfous, S., & Seena, S. (2024). Aquatic fungi as bioindicators of freshwater ecosystems. Water, 16(23), 3404. Comeau, A. M., Vincent, W. F., Bernier, L., & Lovejoy, C. (2016). Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats. Scientific Reports, 6(1), 30120. D’Silva, S., Mathew, B. P., VK, V., Bhadran, A., Girishbai, D., & Gopinath, G. (2025). Geomorphic evolution of a tropical river basin in the Deccan Volcanic Province: a critical water supply source to Mumbai metropolitan region (MMR), India. Geology, Ecology, and Landscapes, 9(3), 988-999. da Silva, G. V. R., Castañeda-Ruiz, R. F., & Malosso, E. (2019). Comparison of aquatic hyphomycetes communities between lotic and lentic environments in the Atlantic rain forest of Pernambuco, Northeast Brazil. Fungal biology, 123(9), 660-668. Deiner, K., Fronhofer, E. A., Mächler, E., Walser, J.-C., & Altermatt, F. (2016). Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nature communications, 7(1), 12544. Frenken, T., Alacid, E., Berger, S. A., Bourne, E. C., Gerphagnon, M., Grossart, H. P., Gsell, A. S., Ibelings, B. W., Kagami, M., & Küpper, F. C. (2017). Integrating chytrid fungal parasites into plankton ecology: research gaps and needs. Environmental Microbiology, 19(10), 3802-3822. Grossart, H.-P., Van den Wyngaert, S., Kagami, M., Wurzbacher, C., Cunliffe, M., & Rojas-Jimenez, K. (2019). Fungi in aquatic ecosystems. Nature Reviews Microbiology, 17(6), 339-354. Ingold, C. (1942). Aquatic hyphomycetes of decaying alder leaves. Transactions of the British Mycological Society, 25(4), 339-IN336. Jobard, M., Rasconi, S., Solinhac, L., Cauchie, H. M., & Sime‐Ngando, T. (2012). Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes. Environmental Microbiology, 14(9), 2480-2494. Khomich, M., Davey, M. L., Kauserud, H., Rasconi, S., & Andersen, T. (2017). Fungal communities in Scandinavian lakes along a longitudinal gradient. Fungal Ecology, 27, 36-46. Koivusaari, P., Tejesvi, M. V., Tolkkinen, M., Markkola, A., Mykrä, H., & Pirttilä, A. M. (2019). Fungi originating from tree leaves contribute to fungal diversity of litter in streams. Frontiers in microbiology, 10, 651. Lepère, C., Domaizon, I., Humbert, J.-F., Jardillier, L., Hugoni, M., & Debroas, D. (2019). Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ, 7, e6247. Matsuoka, S., Sugiyama, Y., Sato, H., Katano, I., Harada, K., & Doi, H. (2019). Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan. bioRxiv, 637686. Monchy, S., Sanciu, G., Jobard, M., Rasconi, S., Gerphagnon, M., Chabé, M., Cian, A., Meloni, D., Niquil, N., & Christaki, U. (2011). Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environmental Microbiology, 13(6), 1433-1453. Naik, P. K., Dehury, B. N., & Tiwari, A. N. (2007). Groundwater pollution around an industrial area in the coastal stretch of Maharashtra state, India. Environmental monitoring and assessment, 132(1), 207-233. Ortiz-Vera, M. P., Olchanheski, L. R., da Silva, E. G., de Lima, F. R., Martinez, L. R. d. P. R., Sato, M. I. Z., Jaffé, R., Alves, R., Ichiwaki, S., & Padilla, G. (2018). Influence of water quality on diversity and composition of fungal communities in a tropical river. Scientific Reports, 8(1), 14799. Pham, P., Shi, Y., Khan, I., Sumarah, M., Renaud, J., Sunohara, M., Craiovan, E., Lapen, D., Aris-Brosou, S., & Chen, W. (2024). The functions and factors governing fungal communities and diversity in agricultural waters: Insights into the ecosystem services aquatic mycobiota provide. Frontiers in microbiology, 15, 1460330. Porter, K. L., Schinteie, R., Mariani, C., Greenfield, P., Gong, S., Sestak, S., Tran‐Dinh, N., & Midgley, D. J. (2026). Pilliga Ghosts: The Novel Fungi of the Rivers, Creeks, Lakes, and Dams of the Narrabri Region, Australia. Environmental Microbiology Reports, 18(3), e70348. Rajashekhar, M., & Kaveriappa, K. (1996). Studies on the aquatic hyphomycetes of a sulfur spring in the Western Ghats, India. Microbial ecology, 32(1), 73-80. Rajashekhar, M., & Kaveriappa, K. (2003). Diversity of aquatic hyphomycetes in the aquatic ecosystems of the Western Ghats of India. Hydrobiologia, 501(1), 167-177. Raviraja, N., Sridhar, K., & Bärlocher, F. (1998). Fungal species richness in Western Ghat streams (southern India): is it related to pH, temperature or altitude. Fungal Diversity, 1, 179-191. Rojas-Jimenez, K., Wurzbacher, C., Bourne, E. C., Chiuchiolo, A., Priscu, J. C., & Grossart, H.-P. (2017). Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Scientific Reports, 7(1), 15348. Sanyal, A., Kluge, M., Redondo, M. A., Buck, M., Mehrshad, M., Garcia, S. L., Bertilsson, S., & Peura, S. (2025). Aquatic fungal diversity assessment through metagenomics is still limited to current databases. Limnology and Oceanography, 70(11), 3249-3260. Sugiyama, Y., Matsuoka, S., Shimono, Y., Ushio, M., & Doi, H. (2024). Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities? Fungal Ecology, 67, 101311. Wurzbacher, C. M., Bärlocher, F., & Grossart, H.-P. (2010). Fungi in lake ecosystems. Aquatic Microbial Ecology, 59, 125-149. Zhang, T., Wang, N.-F., Zhang, Y.-Q., Liu, H.-Y., & Yu, L.-Y. (2016). Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic) T. Zhang et al. Microbial ecology, 71(3), 543-554.