Winkler, K., Fuchs, R., Rounsevell, M. & Herold, M. Global land use changes are four times greater than previously estimated. Nat. Commun. 12, 2501 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Newbold, T. et al. Global effects of land use on local terrestrial biodiversity. Nature 520, 45–50 (2015).

Article 
PubMed 

Google Scholar
 

Campbell, J. E., Lobell, D. B., Genova, R. C. & Field, C. B. The global potential of bioenergy on abandoned agriculture lands. Environ. Sci. Technol. 42, 5791–5794 (2008).

Article 
PubMed 

Google Scholar
 

Walker, L. R. & Moral, R. del. Primary Succession and Ecosystem Rehabilitation. (Cambridge University Press, 2003).

Horn, H. S. The ecology of secondary succession. Annu. Rev. Ecol. Syst. 5, 25–37 (1974).

Article 

Google Scholar
 

Clements, F. E. Nature and structure of the climax. J. Ecol. 24, 252–284 (1936).

Article 

Google Scholar
 

Simberloff, D. A succession of paradigms in ecology: essentialism to materialism and probabilism. Synthese 43, 3–39 (1980).

Article 

Google Scholar
 

Vera, F. W. M. et al. Grazing Ecology and Forest History. (CABI, Oxford, 2000).

Johnson, E. A. & Miyanishi, K. Testing the assumptions of chronosequences in succession. Ecol. Lett. 11, 419–431 (2008).

Article 
PubMed 

Google Scholar
 

Arias-Navarro, C., Baritz, R. & Jones, A. The State of Soils in Europe. https://doi.org/10.2760/7007291 (2024).

Eriksson, O., Cousins, S. A. O. & Bruun, H. H. Land-use history and fragmentation of traditionally managed grasslands in Scandinavia. J. Veg. Sci. 13, 743–748 (2002).

Article 

Google Scholar
 

Gustavsson, E., Lennartsson, T. & Emanuelsson, M. Land use more than 200 years ago explains current grassland plant diversity in a Swedish agricultural landscape. Biol. Conserv. 138, 47–59 (2007).

Article 

Google Scholar
 

Auffret, A. G., Kimberley, A., Plue, J. & Waldén, E. Super-regional land-use change and effects on the grassland specialist flora. Nat. Commun. 9, 3464 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Bremer, L. L. & Farley, K. A. Does plantation forestry restore biodiversity or create green deserts? A synthesis of the effects of land-use transitions on plant species richness. Biodivers. Conserv. 19, 3893–3915 (2010).

Article 

Google Scholar
 

Prangel, E. et al. Afforestation and abandonment of semi-natural grasslands lead to biodiversity loss and a decline in ecosystem services and functions. J. Appl. Ecol. 60, 825–836 (2023).

Article 

Google Scholar
 

Kindermann, E. et al. Resurveying inner-alpine dry grasslands after 70 years calls for integrative conservation efforts. Biol. Conserv. 289, 110393 (2024).

Article 

Google Scholar
 

Öckinger, E., Eriksson, A. K. & Smith, H. G. Effects of grassland abandonment, restoration and management on butterflies and vascular plants. Biol. Conserv. 133, 291–300 (2006).

Article 

Google Scholar
 

Moyano, J. et al. Unintended consequences of planting native and non-native trees in treeless ecosystems to mitigate climate change. J. Ecol. 112, 2480–2491 (2024).

Article 

Google Scholar
 

Quested, H., Eriksson, O., Fortunel, C. & Garnier, E. Plant traits relate to whole-community litter quality and decomposition following land use change. Funct. Ecol. 21, 1016–1026 (2007).

Article 

Google Scholar
 

Zhou, Z., Wang, C., Jiang, L. & Luo, Y. Trends in soil microbial communities during secondary succession. Soil Biol. Biochem. 115, 92–99 (2017).

Article 

Google Scholar
 

Tian, J. et al. Ecological succession pattern of fungal community in soil along a retreating glacier. Front. Microbiol. 8, 1028 (2017).

Cline, L. C. & Zak, D. R. Soil microbial communities are shaped by plant-driven changes in resource availability during secondary succession. Ecology 96, 3374–3385 (2015).

Article 
PubMed 

Google Scholar
 

Egidi, E., Coleine, C., Delgado-Baquerizo, M. & Singh, B. K. Assessing critical thresholds in terrestrial microbiomes. Nat. Microbiol. 8, 2230–2233 (2023).

Article 
PubMed 

Google Scholar
 

Allison, S. D. A trait-based approach for modelling microbial litter decomposition. Ecol. Lett. 15, 1058–1070 (2012).

Article 
PubMed 

Google Scholar
 

Cortez, J., Garnier, E., Pérez-Harguindeguy, N., Debussche, M. & Gillon, D. Plant traits, litter quality and decomposition in a Mediterranean old-field succession. Plant Soil 296, 19–34 (2007).

Article 

Google Scholar
 

Hernandez, D. J., Kiesewetter, K. N., Almeida, B. K., Revillini, D. & Afkhami, M. E. Multidimensional specialization and generalization are pervasive in soil prokaryotes. Nat. Ecol. Evol. 7, 1408–1418 (2023).

Article 
PubMed 

Google Scholar
 

Hättenschwiler, S., Tiunov, A. V. & Scheu, S. Biodiversity and litter decomposition in terrestrial ecosystems. Annu. Rev. Ecol. Evol. Syst. 36, 191–218 (2005).

Article 

Google Scholar
 

Hannula, S. E. & van Veen, J. A. Primer sets developed for functional genes reveal shifts in functionality of fungal community in soils. Front. Microbiol. 7, 1897 (2016).

Louca, S. et al. Function and functional redundancy in microbial systems. Nat. Ecol. Evol. 2, 936–943 (2018).

Article 
PubMed 

Google Scholar
 

Walker, L. R., Wardle, D. A., Bardgett, R. D. & Clarkson, B. D. The use of chronosequences in studies of ecological succession and soil development. J. Ecol. 98, 725–736 (2010).

Article 

Google Scholar
 

Cousins, S. A. O. & Eriksson, O. After the hotspots are gone: Land use history and grassland plant species diversity in a strongly transformed agricultural landscape. Appl. Veg. Sci. 11, 365–374 (2008).

Article 

Google Scholar
 

Mason, W. L. Changes in the management of British forests between 1945 and 2000 and possible future trends. Ibis 149, 41–52 (2007).

Article 

Google Scholar
 

Hooftman, D. A. P. & Bullock, J. M. Mapping to inform conservation: a case study of changes in semi-natural habitats and their connectivity over 70 years. Biol. Conserv. 145, 30–38 (2012).

Article 

Google Scholar
 

Mietkiewicz, N., Kulakowski, D., Rogan, J. & Bebi, P. Long-term change in sub-alpine forest cover, tree line and species composition in the Swiss Alps. J. Veg. Sci. 28, 951–964 (2017).

Article 

Google Scholar
 

da Silva Camilo, G., de Freitas Terra, B. & Araújo, F. G. Using the relationship between taxonomic and functional diversity to assess functional redundancy in streams of an altered tropical watershed. Environ. Biol. Fishes 101, 1395–1405 (2018).

Article 

Google Scholar
 

Chen, H. et al. Functional redundancy in soil microbial community based on metagenomics across the globe. Front. Microbiol. 13, 878978 (2022).

Bobay, L.-M. & Ochman, H. The evolution of bacterial genome architecture. Front. Genet. 8, 72 (2017).

Ricotta, C. et al. Measuring the functional redundancy of biological communities: a quantitative guide. Methods Ecol. Evol. 7, 1386–1395 (2016).

Article 

Google Scholar
 

Ricotta, C. et al. The ternary diagram of functional diversity. Methods Ecol. Evol. 14, 1168–1174 (2023).

Article 

Google Scholar
 

Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 685–688 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Sun, S., Jones, R. B. & Fodor, A. A. Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories. Microbiome 8, 46 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Malard, L. A. & Guisan, A. Into the microbial niche. Trends Ecol. Evol. 38, 936–945 (2023).

Article 
PubMed 

Google Scholar
 

Gubry-Rangin, C., Aigle, A., Herrera-Alsina, L., Lancaster, L. T. & Prosser, J. I. Niche breadth specialization impacts ecological and evolutionary adaptation following environmental change. ISME J. 18, wrae183 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Fang, J. et al. Threshold effects of soil pH regulate the biogeography of bacterial communities in inland wetlands across eastern China. Soil Ecol. Lett. 7, 240274 (2024).

Article 

Google Scholar
 

Garnier, E. et al. Plant functional markers capture ecosystem properties during secondary succession. Ecology 85, 2630–2637 (2004).

Article 

Google Scholar
 

Berthrong, S. T., Jobbágy, E. G. & Jackson, R. B. A global meta-analysis of soil exchangeable cations, pH, carbon, and nitrogen with afforestation. Ecol. Appl. 19, 2228–2241 (2009).

Article 
PubMed 

Google Scholar
 

Tscherko, D., Hammesfahr, U., Marx, M.-C. & Kandeler, E. Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence. Soil Biol. Biochem. 36, 1685–1698 (2004).

Article 

Google Scholar
 

Jobbágy, E. G. & Jackson, R. B. Patterns and mechanisms of soil acidification in the conversion of grasslands to forests. Biogeochemistry 64, 205–229 (2003).

Article 

Google Scholar
 

Fierer, N. et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342, 621–624 (2013).

Article 
PubMed 

Google Scholar
 

Inkpen, S. A. et al. The coupling of taxonomy and function in microbiomes. Biol. Philos. 32, 1225–1243 (2017).

Article 

Google Scholar
 

Wang, C. et al. Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient. Nat. Commun. 14, 7437 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, H.-Y., Bissett, A., Aguilar-Trigueros, C. A., Liu, H.-W. & Powell, J. R. Fungal genome size and composition reflect ecological strategies along soil fertility gradients. Ecol. Lett. 26, 1108–1118 (2023).

Article 
PubMed 

Google Scholar
 

Bhatnagar, J. M., Peay, K. G. & Treseder, K. K. Litter chemistry influences decomposition through activity of specific microbial functional guilds. Ecol. Monogr. 88, 429–444 (2018).

Article 

Google Scholar
 

Berg, B. Litter decomposition and organic matter turnover in northern forest soils. Ecol. Manag. 133, 13–22 (2000).

Article 

Google Scholar
 

Silverstein, M. R., Bhatnagar, J. M. & Segrè, D. Metabolic complexity drives divergence in microbial communities. Nat. Ecol. Evol. 8, 1493–1504 (2024).

Article 
PubMed 

Google Scholar
 

Hernández, D. L. & Hobbie, S. E. The effects of substrate composition, quantity, and diversity on microbial activity. Plant Soil 335, 397–411 (2010).

Article 

Google Scholar
 

Dal Bello, M., Lee, H., Goyal, A. & Gore, J. Resource–diversity relationships in bacterial communities reflect the network structure of microbial metabolism. Nat. Ecol. Evol. 5, 1424–1434 (2021).

Article 
PubMed 

Google Scholar
 

Foote, R. L. & Grogan, P. Soil carbon accumulation during temperate forest succession on abandoned low productivity agricultural lands. Ecosystems 13, 795–812 (2010).

Article 

Google Scholar
 

Bongers, F. J. et al. Functional diversity effects on productivity increase with age in a forest biodiversity experiment. Nat. Ecol. Evol. 5, 1594–1603 (2021).

Article 
PubMed 

Google Scholar
 

Biggs, C. R. et al. Does functional redundancy affect ecological stability and resilience? a review and meta-analysis. Ecosphere 11, e03184 (2020).

Article 

Google Scholar
 

Auber, A. et al. A functional vulnerability framework for biodiversity conservation. Nat. Commun. 13, 4774 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rocca, J. D. et al. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed. ISME J. 9, 1693–1699 (2015).

Article 
PubMed 

Google Scholar
 

Chen, J. & Sinsabaugh, R. L. Linking microbial functional gene abundance and soil extracellular enzyme activity: Implications for soil carbon dynamics. Glob. Change Biol. 27, 1322–1325 (2021).

Article 

Google Scholar
 

Cooke, R. S. C., Bates, A. E. & Eigenbrod, F. Global trade-offs of functional redundancy and functional dispersion for birds and mammals. Glob. Ecol. Biogeogr. 28, 484–495 (2019).

Article 

Google Scholar
 

Kerfahi, D. et al. Elevation trend in bacterial functional gene diversity decouples from taxonomic diversity. CATENA 199, 105099 (2021).

Article 

Google Scholar
 

Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).

Article 
PubMed 

Google Scholar
 

Ricotta, C., Pavoine, S., Cerabolini, B. E. L. & Pillar, V. D. A new method for indicator species analysis in the framework of multivariate analysis of variance. J. Veg. Sci. 32, e13013 (2021).

Article 

Google Scholar
 

Cousins, S. A. O. Analysis of land-cover transitions based on 17th and 18th century cadastral maps and aerial photographs. Landsc. Ecol. 16, 41–54 (2001).

Article 

Google Scholar
 

Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).

Article 
PubMed 

Google Scholar
 

Egnér, H., Riehm, H. & Domingo, W. R. Untersuchungen uber die chemische Bodenanalyse als Grundlage fur die Beurteilung des Nährstoffzustandes der Böden. II. Chemische Extraktionsmethoden zur Phosphor- und Kaliumbestimmung. K. Lantbrukshögskolans Ann. 26, 199–215 (1960).


Google Scholar
 

Kattge, J. et al. TRY – a global database of plant traits. Glob. Change Biol. 17, 2905–2935 (2011).

Article 

Google Scholar
 

Roscher, C. et al. Interspecific trait differences rather than intraspecific trait variation increase the extent and filling of community trait space with increasing plant diversity in experimental grasslands. Perspect. Plant Ecol. Evol. Syst. 33, 42–50 (2018).

Article 

Google Scholar
 

Manrubia, M. et al. Soil functional responses to drought under range-expanding and native plant communities. Funct. Ecol. 33, 2402–2416 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Bradford, M. A. et al. Thermal adaptation of soil microbial respiration to elevated temperature. Ecol. Lett. 11, 1316–1327 (2008).

Article 
PubMed 

Google Scholar
 

Birch, H. F. The effect of soil drying on humus decomposition and nitrogen availability. Plant Soil 10, 9–31 (1958).

Article 

Google Scholar
 

Bongiorno, G. et al. Soil management intensity shifts microbial catabolic profiles across a range of European long-term field experiments. Appl. Soil Ecol. 154, 103596 (2020).

Article 

Google Scholar
 

Walters, W. et al. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems https://doi.org/10.1128/msystems.00009-15 (2015).

Tedersoo, L. & Lindahl, B. Fungal identification biases in microbiome projects. Environ. Microbiol. Rep. 8, 774–779 (2016).

Article 
PubMed 

Google Scholar
 

Tedersoo, L. et al. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Divers. 111, 573–588 (2021).

Article 

Google Scholar
 

Özkurt, E. et al. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. Microbiome 10, 176 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 4, 914–919 (2013).

Article 

Google Scholar
 

Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).

Article 
PubMed 

Google Scholar
 

Hildebrand, F. et al. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe 29, 1167–1176.e9 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Bahram, M. et al. Metagenomic assessment of the global diversity and distribution of bacteria and fungi. Environ. Microbiol. 23, 316–326 (2021).

Article 
PubMed 

Google Scholar
 

Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

Article 
PubMed 

Google Scholar
 

Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).

Article 
PubMed 

Google Scholar
 

Nayfach, S. & Pollard, K. S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 16, 51 (2015).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Levasseur, A., Drula, E., Lombard, V., Coutinho, P. M. & Henrissat, B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol. Biofuels 6, 41 (2013).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Piton, G. et al. Life history strategies of soil bacterial communities across global terrestrial biomes. Nat. Microbiol. 8, 2093–2102 (2023).

Article 
PubMed 

Google Scholar
 

Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353–D361 (2017).

Article 
PubMed 

Google Scholar
 

Zeng, J. et al. PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. Microbiome 10, 101 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Tu, Q., Lin, L., Cheng, L., Deng, Y. & He, Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 35, 1040–1048 (2019).

Article 
PubMed 

Google Scholar
 

Ben-Shachar, M., Lüdecke, D. & Makowski, D. effectsize: estimation of effect size indices and standardized parameters. J. Open Source Softw. 5, 2815 (2020).

Article 

Google Scholar
 

Oksanen, J. et al. vegan: Community Ecology Package. Package version: 2.7-2. https://doi.org/10.32614/CRAN.package.vegan (2025).

Pavoine, S. adiv: An r package to analyse biodiversity in ecology. Methods Ecol. Evol. 11, 1106–1112 (2020).

Article 

Google Scholar
 

Bates, D. et al. Fitting Linear Mixed-Effect Models Using lme4. J. Stat. Softw. 67, 1–48 (2015)

Finn, D. R. et al. MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data. FEMS Microbiol. Ecol. 96, fiaa131 (2020).

Article 
PubMed 

Google Scholar
 

Archer, E. rfPermute: estimate permutation p-values for random forest importance metrics. Package version: 2.5-.5 https://doi.org/10.32614/CRAN.package.rfPermute (2025).

Beule, L. & Karlovsky, P. Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities. PeerJ 8, e9593 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Lai, J., Zhu, W., Cui, D. & Mao, L. Extension of the glmm.hp package to zero-inflated generalized linear mixed models and multiple regression. J. Plant Ecol. 16, rtad038 (2023).

Article 

Google Scholar
 

Ramond, P., Galand, P. E. & Logares, R. Microbial functional diversity and redundancy: moving forward. FEMS Microbiol. Rev. 49, fuae031 (2025).

Article 
PubMed 

Google Scholar
 

Hurlbert, S. H. The measurement of niche overlap and some relatives. Ecology 59, 67–77 (1978).

Article 

Google Scholar