Salinity gradients drive bacterial–fungal divergence through diversity variation, network fragility, and stochastic assembly in saline-alkali soils

Abstract

Soil salinization, an accelerating form of land degradation, is reshaping terrestrial ecosystems worldwide. Although salinity is recognized as a strong environmental filter, its influence on bacterial and fungal communities remains insufficiently understood beyond taxonomic shifts. Here, we conducted a controlled irrigation experiment simulating salinity gradients to disentangle how diversity, network interactions, and assembly processes of bacteria and fungi respond to increasing salt stress. Results showed that high salinity significantly suppressed microbial richness, while mild salinity enhanced diversity, indicating a dual role of salinity as both stressor and structuring factor. Bacterial communities underwent pronounced taxonomic shifts, with halotolerant taxa dominating under high salinity, whereas fungal taxonomic composition remained relatively stable. Network analyses revealed that low salinity supported complex and resilient microbial networks, but high salinity simplified structures, reduced stability, and shifted keystone taxa toward tolerant groups. Fungal networks declined more sharply in connectivity than bacterial ones, reflecting higher vulnerability. Assembly process analyses demonstrated that bacteria, flexibly shifting under stress, while fungi were consistently governed by stochastic processes dominated by drift and dispersal limitation. These findings identify salinity thresholds as critical drivers of microbial ecological strategies and provide a mechanistic framework linking diversity loss, network fragility, and assembly shifts. Overall, our results reveals the differences of soil bacterial and fungal community construction under saline-alkali stress, providing an important theoretical basis for understanding the response of microorganisms to environmental changes and the ecological restoration of saline-alkali soils.

Graphical abstract

Keywords

salinization / microbial diversity / bacterial–fungal interactions / co-occurrence networks / community assembly

Highlight

	● Reduced microbial diversity and network complexity―High salinity treatments corresponded to lower microbial diversity and a simpler network structure, indicating reduced community complexity under elevated salt stress.
	● Divergent bacterial–fungal strategies―Bacteria maintained a balance between deterministic selection and stochastic drift, with a shift toward mixed processes under extreme salinity, whereas fungal communities were consistently dominated by stochastic processes, primarily driven by dispersal limitation and ecological drift.
	● Network shifts to keystone halotolerants―Halotolerant taxa become keystone nodes in simplified co-occurrence networks, sustaining partial ecosystem functions despite reduced connectivity.

References

[1] Albert, R., Jeong, H., Barabási, A.L., 2000. Error and attack tolerance of complex networks. Nature406, 378–382.

[2] Banerjee, S., Schlaeppi, K., van der Heijden, M.G.A., 2018. Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews Microbiology16, 567–576.

[3] Benlloch, S., López-López, A., Casamayor, E.O., Øvreås, L., Goddard, V., Daae, F.L., Smerdon, G., Massana, R., Joint, I., Thingstad, F., Pedrós-alió, C., Rodríguez-Valera, F., 2002. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environmental Microbiology4, 349–360.

[4] Berendsen, R.L., Pieterse, C.M.J., Bakker, P.A.H.M., 2012. The rhizosphere microbiome and plant health. Trends in Plant Science17, 478–486.

[5] Berry, D., Widder, S., 2014. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Frontiers in Microbiology5, 219.

[6] Blaalid, R., Kumar, S., Nilsson, R.H., Abarenkov, K., Kirk, P.M., Kauserud, H., 2013. ITS1 versus ITS2 as DNA metabarcodes for fungi. Molecular Ecology Resources13, 218–224.

[7] Blomberg, A., Adler, L., 1992. Physiology of osmotolerance in fungi. Advances in Microbial Physiology33, 145–212.

[8] Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., Mills, D.A., Caporaso, J.G., 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods10, 57–59.

[9] Canfora, L., Bacci, G., Pinzari, F., Lo Papa, G., Dazzi, C., Benedetti, A., 2014. Salinity and bacterial diversity: to what extent does the concentration of salt affect the bacterial community in a saline soil?. PLoS One9, e106662.

[10] Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R., 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods7, 335–336.

[11] Chase, J.M., 2007. Drought mediates the importance of stochastic community assembly. Proceedings of the National Academy of Sciences of the United States of America104, 17430–17434.

[12] Chen, Z., Tang, S., Zhu, X., Zhu, G., Luo, X., Wang, X., 2025.. Environmental Stress and the Deterministic Assembly of Bacterial Communities in Daqu: The Role of Amino Acid Content Fluctuations.. .

[13] Cui, F.Y., Yao, X.W., Xu, H.L., Zhong, X.L., Yu, H.D., Jin, S.S., Liu, Z.S., Zhu, W.L., Wang, J.H., Zhang, M., Hu, B.L., 2025. Negative microbial interactions enhance network complexity and stability under increasing salinity stress in electroplating wastewater treatment systems. Journal of Water Process Engineering74, 107764.

[14] Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., Fierer, N., 2018. A global atlas of the dominant bacteria found in soil. Science359, 320–325.

[15] Deng, Y., Jiang, Y.H., Yang, Y.F., He, Z.L., Luo, F., Zhou, J.Z., 2012. Molecular ecological network analyses. BMC Bioinformatics13, 113.

[16] DeVilbiss, S.E., Steele, M.K., Brown, B.L., Badgley, B.D., 2022. Stream bacterial diversity peaks at intermediate freshwater salinity and varies by salt type. Science of the Total Environment840, 156690.

[17] Dini-Andreote, F., Stegen, J.C., van Elsas, J.D., Salles, J.F., 2015. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proceedings of the National Academy of Sciences of the United States of America112, E1326–E1332.

[18] Drenovsky, R. E., Vo, D., Graham, K. J., Scow, K. M., 2010. Land use and climatic factors structure regional patterns in soil microbial communities. Global Ecology and Biogeography 19, 27–39.

[19] Edgar, R.C., 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods10, 996–998.

[20] Eichorst, S.A., Strasser, F., Woyke, T., Schintlmeister, A., Wagner, M., Woebken, D., 2015. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiology Ecology91, fiv106.

[21] FAO, 2024a. Global Status of Salt-Affected Soils – Main Report. Rome: Food and Agriculture Organization of the United Nations.

[22] FAO, 2024b. The State of Food and Agriculture 2024 – Value-Driven Transformation of Agrifood Systems. Rome: Food and Agriculture Organization of the United Nations.

[23] Faust, K., Raes, J., 2012. Microbial interactions: from networks to models. Nature Reviews Microbiology10, 538–550.

[24] Fierer, N., 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology15, 579–590.

[25] Friedman, J., Alm, E.J., 2012. Inferring correlation networks from genomic survey data. PLoS Computational Biology8, e1002687.

[26] Gadd, G.M., 2010. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 156, 609–643.

[27] Gotelli, N.J., McGill, B.J., 2006. Null versus neutral models: what’s the difference? Ecography 29, 793–800.

[28] Gu, Z.G., Gu, L., Eils, R., Schlesner, M., Brors, B., 2014. circlize implements and enhances circular visualization in R. Bioinformatics30, 2811–2812.

[29] Haj-Amor, Z., Araya, T., Kim, D.G., Bouri, S., Lee, J., Ghiloufi, W., Yang, Y.R., Kang, H., Jhariya, M.K., Banerjee, A., Lal, R., 2022. Soil salinity and its associated effects on soil microorganisms, greenhouse gas emissions, crop yield, biodiversity and desertification: a review. Science of the Total Environment843, 156946.

[30] Hanson, C.A., Fuhrman, J.A., Horner-Devine, M.C., Martiny, J.B.H., 2012. Beyond biogeographic patterns: processes shaping the microbial landscape. Nature Reviews Microbiology10, 497–506.

[31] Hohmann, S., 2002. Osmotic stress signaling and osmoadaptation in yeasts. Microbiology and Molecular Biology Reviews66, 300–372.

[32] Ji, M.Z., Zhou, J.Y., Li, Y., Ma, K., Song, W., Li, Y.Y., Zhou, J.Z., Tu, Q.C., 2024. Biodiversity of mudflat intertidal viromes along the Chinese coasts. Nature Communications15, 8611.

[33] Kaushal, S.S., Likens, G.E., Pace, M.L., Utz, R.M., Haq, S., Gorman, J., Grese, M., 2018. Freshwater salinization syndrome on a continental scale. Proceedings of the National Academy of Sciences of the United States of America115, E574–E583.

[34] Kembel, S.W., Cowan, P.D., Helmus, M.R., Cornwell, W.K., Morlon, H., Ackerly, D.D., Blomberg, S.P., Webb, C.O., 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics26, 1463–1464.

[35] Kurtz, Z.D., Müller, C.L., Miraldi, E.R., Littman, D.R., Blaser, M.J., Bonneau, R.A., 2015. Sparse and compositionally robust inference of microbial ecological networks. PLoS Computational Biology11, e1004226.

[36] Lauber, C. L., Hamady, M., Knight, R., Fierer, N., 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75, 5111–5120.

[37] Li, X., Wang, Y., Zhang, Q., 2020. Climatic characteristics and water balance in the Minqin Oasis, Northwest China. Journal of Arid Land12, 456–468.

[38] Li, Y., Wang, J., Li, E.Y., Yang, X.D., Yang, J.J., 2024. Shifts in microbial community structure and co-occurrence network along a wide soil salinity gradient. Microorganisms12, 1268.

[39] Liu, J., Zhu, S., Liu, X., 2023. Deterministic processes dominate in low salinity soils. Microbial Ecology85, 345–356.

[40] Ma, Y., Dias, M.C., Freitas, H., 2020. Drought and salinity stress responses and microbe-induced tolerance in plants. Frontiers in Plant Science11, 591911.

[41] Ma, Y., Vosátka, M., Freitas, H., 2019. Arbuscular mycorrhizal fungi in saline soils: occurrence, adaptation, and potential for bioremediation. Soil Biology and Biochemistry135, 426–436.

[42] Maslov, S., Sneppen, K., 2002. Specificity and stability in topology of protein networks. Science296, 910–913.

[43] Mo, Y., Zhang, W., Yang, J., 2021. Assembly processes of microbial communities in saline soils. ISME Journal15, 1425–1437.

[44] Mukhtar, S., Mirza, B.S., Mehnaz, S., 2019. Halotolerant rhizobacteria from saline soils enhance plant growth under salt stress. Plant and Soil445, 383–397.

[45] Newman, M., 2018. Networks. 2nd ed. Oxford: Oxford University Press.

[46] Nielsen, S.R., Oksanen, J., Blanchet, F.G., 2021. MicEco: Microbial Ecology Tools for R (R Package Version 0.9.1) [Online]. .

[47] Ning, D.L., Yuan, M.T., Wu, L.W., Zhang, Y., Guo, X., Zhou, X.S., Yang, Y.F., Arkin, A.P., Firestone, M.K., Zhou, J.Z., 2020. A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nature Communications11, 4717.

[48] Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H., Szöcs, E., Wagner, H.H., 2020. vegan: Community Ecology Package (R Package Version 2.5-7) [Online]. .

[49] Oren, A., 2015. Halophilic microbial communities and their environments. .

[50] Parsek, M.R., Singh, P.K., 2003. Bacterial biofilms: an emerging link to disease pathogenesis. Annual Review of Microbiology57, 677–701.

[51] Rath, K.M., Fierer, N., Murphy, D.V., Rousk, J., 2019a. Linking bacterial community composition to soil salinity along environmental gradients. The ISME Journal13, 836–846.

[52] Rath, K.M., Maheshwari, A., Rousk, J., 2019b. Salt effects on the soil microbial decomposer community. Soil Biology and Biochemistry135, 193–203.

[53] Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., Fierer, N., 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal4, 1340–1351.

[54] Sloan, W.T., Lunn, M., Woodcock, S., Head, I.M., Nee, S., Curtis, T.P., 2006. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environmental Microbiology8, 732–740.

[55] Stegen, J.C., Lin, X.J., Konopka, A.E., Fredrickson, J.K., 2012. Stochastic and deterministic assembly processes in subsurface microbial communities. The ISME Journal6, 1653–1664.

[56] Stegen, J. C., Lin, X., Konopka, A., Fredrickson, J. K., 2013. Quantifying community assembly processes and their implications for microbial management. The ISME Journal 7, 2069–2079.

[57] Summerell, B.A., Leslie, J.F., Backhouse, D., Bryden, W.L., Burgess, L.W., 2001. Fusarium: Paul E. Nelson Memorial Symposium. St. Paul: APS Press.

[58] Tedersoo, L., Bahram, M., Zobel, M., 2020. How mycorrhizal associations drive plant population and community biology. Science367, eaba1223.

[59] Tharanath, A.C., Upendra, R.S., Rajendra, K., 2024. Soil symphony: a comprehensive overview of plant–microbe interactions in agricultural systems. Applied Microbiology4, 1549–1567.

[60] Thouin, H., Battaglia-Brunet, F., Norini, M.P., Joulian, C., Hellal, J., Le Forestier, L., Dupraz, S., Gautret, P., 2019. Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions. Science of the Total Environment697, 134108.

[61] Wang, J., Zhang, Q., Li, Y., 2019a. Microbial inoculation enhances soil health and crop productivity in saline-alkaline soils. Soil Biology and Biochemistry138, 107583.

[62] Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., 2018. Soil microbial community changes associated with reclamation of desertified land in the Mu Us Desert, China. Land Degradation & Development29, 2356–2367.

[63] Wang, R.H., Qin, H., Shi, Z.J., Wang, M.B., Li, J.J., 2025. Enhanced microbial network stability and biogeochemical cycles in saline-alkali soil through simplified prokaryotes and complex fungal networks. Applied Soil Ecology213, 106245.

[64] Wang, Y.L., Niu, Q.G., Zhang, X., Liu, L., Wang, Y.B., Chen, Y.Q., Negi, M., Figeys, D., Li, Y.Y., Zhang, T., 2019b. Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics. Microbiome7, 122.

[65] Wang, Z., Zhang, H., Li, J., 2022. Soil salinization and groundwater dynamics in the Minqin Oasis: implications for ecological restoration. CATENA211, 105987.

[66] Wang, Z.G., Bi, Y.L., Jiang, B., Zhakypbek, Y., Peng, S.P., Liu, W.W., Liu, H., 2016. Arbuscular mycorrhizal fungi enhance soil carbon sequestration in the coalfields, northwest China. Scientific Reports6, 34336.

[67] Weiss, S., Van Treuren, W., Lozupone, C., Faust, K., Friedman, J., Deng, Y., Xia, L.C., Xu, Z.Z., Ursell, L., Alm, E.J., Birmingham, A., Cram, J.A., Fuhrman, J.A., Raes, J., Sun, F.Z., Zhou, J.Z., Knight, R., 2016. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The ISME Journal10, 1669–1681.

[68] Yang, W., Zhao, H., Chen, X., 2023. Fungal community responses to salinity in arid soils. Soil Ecology Letters5, 45–56.

[69] Zhang, K.Y., Chang, L., Li, G.H., Li, Y.F., 2023. Advances and future research in ecological stoichiometry under saline-alkali stress. Environmental Science and Pollution Research30, 5475–5486.

[70] . .

[71] Zhou, J.Z., Ning, D.L., 2017. Stochastic community assembly: does it matter in microbial ecology?. Microbiology and Molecular Biology Reviews81( e00002-17), .

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