Linking microbial diversity and network complexity to soil multifunctions in Tianshan Mountains

Abstract

Understanding the relationship between soil microbial diversity and ecosystem multifunctionality is crucial for predicting ecosystem responses to environmental changes. In this study, an investigation was conducted into soil samples collected from 20 sites across five grassland types situated along an altitudinal gradient spanning 2300 m within the Tianshan Mountains, China. Microbial co-occurrence networks were constructed based on bacterial and fungal communities, with their complexity quantified using network topological features. The results revealed a significant variation in microbial diversity and network complexity across the aridity gradient. Bacterial α-diversity (Shannon index) unexpectedly showed a negative correlation with soil multifunctionality, likely reflecting intensified potential competitive associations and dominance of drought-tolerant specialists under arid conditions, whereas fungal diversity showed a weaker link. Microbial co-occurrence networks showed elevated connectivity and reduced modularity in arid regions, with potential competitive associations being dominated under water scarcity. Keystone taxa (species critical to network stability), such as Actinobacteria and Zygomycota, were identified as key players in maintaining ecosystem functions across different grassland types. Structural equation modeling (SEM) indicated that bacterial diversity and network complexity were negatively associated with soil multifunctionality. This study emphasizes the critical role of microbial networks in sustaining ecosystem functions along aridity gradients. It offers insights into management strategies towards enhancing soil multifunctionality, particularly in the context of climate change adaptation.

Graphical abstract

Keywords

soil microbial diversity / microbial networks / aridity gradient / grassland ecosystems / ecosystem multifunctionality

Highlight

	● Bacterial diversity was negatively correlated with soil multifunctionality, fungal diversity exhibited a less pronounced relationship.
	● Microbial networks show increased connectivity and competition in arid regions.
	● Keystone taxa (Actinobacteria, Zygomycota) stabilize ecosystem functions.
	● Network complexity directly and negatively affected multifunctionality.

References

[1] Abeysinghe, G., Kuchira, M., Kudo, G., Masuo, S., Ninomiya, A., Takahashi, K., Utada, A.S., Hagiwara, D., Nomura, N., Takaya, N., Obana, N., Takeshita, N., 2020. Fungal mycelia and bacterial thiamine establish a mutualistic growth mechanism. Life Science Allianc3, e202000878.

[2] Avila-Jimenez, M.L., Burns, G., He, Z.L., Zhou, J.Z., Hodson, A., Avila-Jimenez, J.L., Pearce, D., 2020. Functional associations and resilience in microbial communities. Microorganisms8, 951.

[3] 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.

[4] Banerjee, S., Walder, F., Büchi, L., Meyer, M., Held, A.Y., Gattinger, A., Keller, T., Charles, R., van der Heijden, M.G.A., 2019. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. The ISME Journal13, 1722–1736.

[5] Bardgett, R.D., Caruso, T., 2020. Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states. Philosophical Transactions of the Royal Society B: Biological Sciences375, 20190112.

[6] Bardgett, R.D., van der Putten, W.H., 2014. Belowground biodiversity and ecosystem functioning. Nature515, 505–511.

[7] Barrón-Sandoval, A., Martiny, J.B.H., Pérez-Carbajal, T., Bullock, S.H., Leija, A., Hernández, G., Escalante, A.E., 2023. Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system. FEMS Microbiology Ecology99, fiad009.

[8] Bull, A.T., 2011. Actinobacteria of the extremobiosphere. In: Horikoshi, K., ed. Extremophiles Handbook. Tokyo: Springer, 1203–1240.

[9] Byrnes, J.E.K., Gamfeldt, L., Isbell, F., Lefcheck, J.S., Griffin, J.N., Hector, A., Cardinale, B.J., Hooper, D.U., Dee, L.E., Emmett Duffy, J., 2014. Investigating the relationship between biodiversity and ecosystem multifunctionality: challenges and solutions. Methods in Ecology and Evolution5, 111–124.

[10] Cai, S.J., Wang, F.P., Laws, E. A., Liu, Y., Xu, C., Ma, L.Q., Xiao, W.P., Huang, B.Q., 2022. Linkages between bacterial community and extracellular enzyme activities crossing a coastal front. Ecological Indicators145, 109639.

[11] Cao, Q., Sun, X.X., Rajesh, K., Chalasani, N., Gelow, K., Katz, B., Shah, V.H., Sanyal, A.J., Smirnova, E., 2021. Effects of rare microbiome taxa filtering on statistical analysis. Frontiers in Microbiology11, 607325.

[12] Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., Fierer, N., Knight, R., 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America108, 4516–4522.

[13] Chen, H.H., Ma, K.Y., Huang, Y., Fu, Q., Qiu, Y.B., Lin, J.J., Schadt, C.W., Chen, H., 2022. Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics. Soil8, 297–308.

[14] Cui, S.Y., Xiao, Y.S., Zhou, Y., Wu, P.F., Cui, L.Q., Zheng, G., 2023. Variations in diversity, composition, and species interactions of soil microbial community in response to increased N deposition and precipitation intensity in a temperate grassland. Ecological Processes12, 35.

[15] DeForest, J.L., 2009. The influence of time, storage temperature, and substrate age on potential soil enzyme activity in acidic forest soils using MUB-linked substrates and L-DOPA. Soil Biology and Biochemistry41, 1180–1186.

[16] Delgado-Baquerizo, M., Maestre, F.T., Reich, P.B., Jeffries, T.C., Gaitan, J.J., Encinar, D., Berdugo, M., Campbell, C.D., Singh, B.K., 2016. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nature Communications7, 10541.

[17] 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.

[18] Dell’Olio, A., Scott, W.T.Jr., Taroncher-Ferrer, S., San Onofre, N., Soriano, J.M., Rubert, J., 2024. Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities. Microbiome12, 250.

[19] Feng, K., Peng, X., Zhang, Z., Gu, S.S., He, Q., Shen, W.L., Wang, Z.J., Wang, D.R., Hu, Q.L., Li, Y., Wang, S., Deng, Y., 2022. iNAP: an integrated network analysis pipeline for microbiome studies. iMeta1, e13.

[20] Han, M., Zhu, X.Y., Ruan, C.J., Wu, H.Q., Chen, G.W., Zhu, K., Liu, Y., Wang, G. 2024. Micro-biophysical interactions at bacterium-mineral interfaces determine potassium dissolution. Environmental Technology & Innovation33, 103524.

[21] Hernandez, D.J., David, A.S., Menges, E.S., Searcy, C.A., Afkhami, M.E., 2021. Environmental stress destabilizes microbial networks. The ISME Journal15, 1722–1734.

[22] Hou, A.M., Yang, D., Miao, J., Shi, D.Y., Yin, J., Yang, Z.W., Shen, Z.Q., Wang, H.R., Qiu, Z.G., Liu, W.L., Li, J.W., Jin, M., 2019. Chlorine injury enhances antibiotic resistance in Pseudomonas aeruginosa through over expression of drug efflux pumps. Water Research156, 366–371.

[23] Hu, W.G., Ran, J.Z., Dong, L.W., Du, Q.J., Ji, M.F., Yao, S.R., Sun, Y., Gong, C.M., Hou, Q.Q., Gong, H.Y., Chen, R.F., Lu, J.L., Xie, S.B., Wang, Z.Q., Huang, H., Li, X.W., Xiong, J.L., Xia, R., Wei, M.H., Zhao, D.M., Zhang, Y.H., Li, J.H., Yang, H.X., Wang, X.T., Deng, Y., Sun, Y., Li, H.L., Zhang, L., Chu, Q.P., Li, X.W., Aqeel, M., Manan, A., Akram, M.A., Liu, X.H., Li, R., Li, F., Hou, C., Liu, J.Q., He, J.S., An, L.Z., Bardgett, R.D., Schmid, B., Deng, J.M., 2021. Aridity-driven shift in biodiversity–soil multifunctionality relationships. Nature Communications12, 5350.

[24] Hui, C., Jiang, H., Liu, B., Wei, R., Zhang, Y.P., Zhang, Q.C., Liang, Y.C., Zhao, Y.H., 2020. Chitin degradation and the temporary response of bacterial chitinolytic communities to chitin amendment in soil under different fertilization regimes. Science of the Total Environment705, 136003.

[25] Jiao, S., Chu, H.Y., Zhang, B.G., Wei, X.R., Chen, W.M., Wei, G.H., 2022a. Linking soil fungi to bacterial community assembly in arid ecosystems. iMeta1, e2.

[26] Jiao, S., Lu, Y.H., Wei, G.H., 2022b. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems. Global Change Biology28, 140–153.

[27] Jin, X., Li, S.W., Zhang, W., Zhu, J.J., Sun, J., 2020. Prediction of soil-available potassium content with visible near-infrared ray spectroscopy of different pretreatment transformations by the boosting algorithms. Applied Sciences10, 1520.

[28] Jing, X., Sanders, N.J., Shi, Y., Chu, H.Y., Classen, A.T., Zhao, K., Chen, L.T., Shi, Y., Jiang, Y.X., He, J.S., 2015. The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate. Nature Communications6, 8159.

[29] Kakaei, E., Moradi, H.R., Moghaddam Nia, A.R., Van Lanen, H.A.J., 2018. Positive and negative human-modified droughts: a quantitative approach illustrated with two Iranian catchments. Hydrology and Earth System Sciences Discussions2018, 1–39.

[30] Kost, C., Patil, K.R., Friedman, J., Garcia, S.L., Ralser, M., 2023. Metabolic exchanges are ubiquitous in natural microbial communities. Nature Microbiology8, 2244–2252.

[31] Li, L.J., Preece, C., Lin, Q., Bréchet, L.M., Stahl, C., Courtois, E.A., Verbruggen, E., 2021. Resistance and resilience of soil prokaryotic communities in response to prolonged drought in a tropical forest. FEMS Microbiology Ecology97, fiab116.

[32] Li, W.J., Wang, J.L., Jiang, L.M., Lv, G.H., Hu, D., Wu, D.Y., Yang, X.D., 2023. Rhizosphere effect and water constraint jointly determined the roles of microorganism in soil phosphorus cycling in arid desert regions. CATENA222, 106809.

[33] Loreau, M., Hector, A. 2001. Partitioning selection and complementarity in biodiversity experiments. Nature412, 72–76.

[34] Louca, S., Polz, M.F., Mazel, F., Albright, M.B.N., Huber, J.A., O’Connor, M.I., Ackermann, M., Hahn, A.S., Srivastava, D.S., Crowe, S.A., Doebeli, M., Parfrey, L.W., 2018. Function and functional redundancy in microbial systems. Nature Ecology & Evolution2, 936–943.

[35] Luo, G.W., Rensing, C., Chen, H., Liu, M.Q., Wang, M., Guo, S.W., Ling, N., Shen, Q.R., 2018. Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long‐term fertilization management. Functional Ecology32, 1103–1116.

[36] Ma, B., Wang, Y.L., Ye, S.D., Liu, S., Stirling, E., Gilbert, J.A., Faust, K., Knight, R., Jansson, J.K., Cardona, C., Röttjers, L., Xu, J.M. 2020. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. Microbiome8, 82.

[37] Maestre, F.T., Delgado-Baquerizo, M., Jeffries, T.C., Eldridge, D.J., Ochoa, V., Gozalo, B., Quero, J.L., García-Gómez, M., Gallardo, A., Ulrich, W., Bowker, M.A., Arredondo, T., Barraza-Zepeda, C., Bran, D., Florentino, A., Gaitán, J., Gutiérrez, J.R., Huber-Sannwald, E., Jankju, M., Mau, R.L., Miriti, M., Naseri, K., Ospina, A., Stavi, I., Wang, D.L., Woods, N.N., Yuan, X., Zaady, E., Singh, B.K., 2015. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proceedings of the National Academy of Sciences of the United States of America112, 15684–15689.

[38] Manning, P., van der Plas, F., Soliveres, S., Allan, E., Maestre, F.T., Mace, G., Whittingham, M.J., Fischer, M., 2018. Redefining ecosystem multifunctionality. Nature Ecology & Evolution2, 427–436.

[39] Prieto-Rubio, J., Garrido, J.L., Alcántara, J.M., Azcón-Aguilar, C., Rincón, A., López-García, Á., 2024. Ectomycorrhizal fungal network complexity determines soil multi-enzymatic activity. Soil10, 425–439.

[40] Qu, Y.N., Yang, X.C., Zhang, M.H., Chen, J.D., Sui, Y., Zhang, X.C., Zeng, Y.Z., Huang, M.P., Gao, Y.F., Ochoa-Hueso, R., Shi, B.K., Zhao, D.Q., Yang, T.X., Sun, W., 2025. Bacterial and fungal diversity and species interactions inversely affect ecosystem functions under drought in a semi-arid grassland. Microbiological Research293, 128075.

[41] Saiya-Cork, K.R., Sinsabaugh, R.L., Zak, D.R., 2002. The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biology and Biochemistry34, 1309–1315.

[42] Schermelleh-Engel, K., Moosbrugger, H., Müller, H., 2003. Evaluating the fit of structural equation models: tests of significance and descriptive goodness-of-fit measures. Methods of Psychological Research8, 23–74.

[43] Singh, B.K., Bardgett, R.D., Smith, P., Reay, D.S., 2010. Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nature Reviews Microbiology8, 779–790.

[44] Solowiej-Wedderburn, J., Pentz, J.T., Lizana, L., Schroeder, B.O., Lind, P.A., Libby, E., 2025. Competition and cooperation: the plasticity of bacterial interactions across environments. PLoS Computational Biology21, e1013213.

[45] Tang, B., Man, J., Lehmann, A., Rillig, M.C., 2024. Arbuscular mycorrhizal fungi attenuate negative impact of drought on soil functions. Global Change Biology30, e17409.

[46] Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N.S., Wijesundera, R., Ruiz, L.V., Vasco-Palacios, A.M., Thu, P.Q., Suija, A., Smith, M.E., Sharp, C., Saluveer, E., Saitta, A., Rosas, M., Riit, T., Ratkowsky, D., Pritsch, K., Põldmaa, K., Piepenbring, M., Phosri, C., Peterson, M., Parts, K., Pärtel, K., Otsing, E., Nouhra, E., Njouonkou, A.L., Nilsson, R.H., Morgado, L.N., Mayor, J., May, T.W., Majuakim, L., Lodge, D.J., Lee, S.S., Larsson, K.H., Kohout, P., Hosaka, K., Hitisalu, I., Henkel, T.W., Harend, H., Guo, L.D., Greslebin, A., Grelet, G., Geml, J., Gates, G., Dunstan, W., Dunk, C., Drenkhan, R., Dearnaley, J., De Kesel, A., Dang, T., Chen, X., Buegger, F., Brearley, F.Q., Bonito, G., Anslan, S., Abell, S., Abarenkov, K., 2014. Global diversity and geography of soil fungi. Science346, 1256688.

[47] Wagg, C., Schlaeppi, K., Banerjee, S., Kuramae, E.E., van der Heijden, M.G.A., 2019. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nature Communications10, 4841.

[48] Wang, C.Q., Kuzyakov, Y., 2024. Mechanisms and implications of bacterial – fungal competition for soil resources. The ISME Journal18, wrae073.

[49] Wang, C.W., Pan, X., Yu, W.Y., Ye, X.H., Erdenebileg, E., Wang, C.J., Ma, L.N., Wang, R.Z., Huang, Z.Y., Indree, T., Liu, G.F., 2023a. Aridity and decreasing soil heterogeneity reduce microbial network complexity and stability in the semi-arid grasslands. Ecological Indicators151, 110342.

[50] Wang, G., Or, D., 2014. Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces. Scientific Reports4, 6757.

[51] Wang, N., Cheng, J.H., Liu, Y.H., Xu, Q.C., Zhu, C., Ling, N., Guo, J.J., Li, R., Huang, W., Guo, S.W., Wang, B.R., An, S.S., Qadir, M.F., Sheng, J.D., 2024a. Relative importance of altitude shifts with plant and microbial diversity to soil multifunctionality in grasslands of north-western China. Plant and Soil504, 545–560.

[52] Wang, T., Ren, G.Y., Chen, F., Yuan, Y.J., 2015. An analysis of precipitation variations in the west-central Tianshan Mountains over the last 300 years. Quaternary International358, 48–57.

[53] Wang, X., Zhang, Q., Zhang, Z.J., Li, W.J., Liu, W.C., Xiao, N.J., Liu, H.Y., Wang, L.Y., Li, Z.X., Ma, J., Liu, Q.Y., Ren, C.J., Yang, G.H., Zhong, Z.K., Han, X.H., 2023b. Decreased soil multifunctionality is associated with altered microbial network properties under precipitation reduction in a semiarid grassland. iMeta2, e106.

[54] Wang, Y., Zhu, K., Chen, X., Wei, K.Y., Wu, R., Wang, G., 2024b. Stochastic and deterministic assembly processes of bacterial communities in different soil aggregates. Applied Soil Ecology193, 105153.

[55] Wang, Y.T., Xie, Y.Z., Ma, H.B., Zhang, Y., Zhang, J., Zhang, H., Luo, X., Li, J.P., 2022. Responses of soil microbial communities and networks to precipitation change in a typical steppe ecosystem of the Loess Plateau. Microorganisms10, 817.

[56] Yamamoto, R., Miki, H., Itani, A., Takeshita, N., 2024. Hyphae of the fungus Aspergillus nidulans demonstrate chemotropism to nutrients and pH. PLoS Biology.22, e3002726.

[57] Yang, N., Zhang, Y., Li, J.J., Li, X.X., Ruan, H.H., Bhople, P., Keiblinger, K., Mao, L.F., Liu, D., 2022. Interaction among soil nutrients, plant diversity and hypogeal fungal trophic guild modifies root-associated fungal diversity in coniferous forests of Chinese southern Himalayas. Plant and Soil481, 395–408.

[58] Yuan, M.M., Guo, X., Wu, L.W., Zhang, Y., Xiao, N.J., Ning, D.L., Shi, Z., Zhou, X.S., Wu, L.Y., Yang, Y.F., Tiedje, J.M., Zhou, J.Z., 2021. Climate warming enhances microbial network complexity and stability. Nature Climate Change11, 343–348.

[59] Zhai, C.C., Han, L.L., Xiong, C., Ge, A.H., Yue, X.J., Li, Y., Zhou, Z.X., Feng, J.Y., Ru, J.Y., Song, J., Jiang, L., Yang, Y.F., Zhang, L.M., Wan, S.Q., 2024. Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation. Science of the Total Environment906, 167217.

[60] Zhang, B.L., Wu, X.K., Tai, X.S., Sun, L.K., Wu, M.H., Zhang, W., Chen, X.M., Zhang, G.S., Chen, T., Liu, G.X., Dyson, P., 2019. Variation in actinobacterial community composition and potential function in different soil ecosystems belonging to the arid Heihe River Basin of Northwest China. Frontiers in Microbiology10, 2209.

[61] Zhou, H., Gao, Y., Jia, X.H., Wang, M.M., Ding, J.J., Cheng, L., Bao, F., Wu, B., 2020. Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China. Soil Biology and Biochemistry144, 107782.

RIGHTS & PERMISSIONS

Higher Education Press