Campbell, J. E. et al. Large historical growth in global terrestrial gross primary production. Nature 544, 84–87 (2017).
Google Scholar
Schwalm, C. R. et al. Modeling suggests fossil fuel emissions have been driving increased land carbon uptake since the turn of the 20th Century. Sci. Rep. 10, 9059 (2020).
Google Scholar
Wenzel, S., Cox, P. M., Eyring, V. & Friedlingstein, P. Projected land photosynthesis constrained by changes in the seasonal cycle of atmospheric CO2. Nature 538, 499–501 (2016).
Google Scholar
Piao, S. et al. Characteristics, drivers and feedbacks of global greening. Nat. Rev. Earth Environ. 1, 14–27 (2020).
Google Scholar
Ellsworth, D. S. et al. Elevated CO2 does not increase eucalypt forest productivity on a low-phosphorus soil. Nat. Clim. Change 7, 279–282 (2017).
Google Scholar
Hararuk, O., Campbell, E. M., Antos, J. A. & Parish, R. Tree rings provide no evidence of a CO2 fertilization effect in old-growth subalpine forests of western Canada. Glob. Change Biol. 25, 1222–1234 (2019).
Google Scholar
Jiang, M. et al. The fate of carbon in a mature forest under carbon dioxide enrichment. Nature 580, 227–231 (2020).
Google Scholar
Friedlingstein, P. et al. Uncertainties in CMIP5 climate projections due to carbon cycle feedbacks. J. Clim. 27, 511–526 (2014).
Google Scholar
Koven, C. D. et al. Controls on terrestrial carbon feedbacks by productivity versus turnover in the CMIP5 earth system models. Biogeosciences 12, 5211–5228 (2015).
Google Scholar
Norby, R. J. & Zak, D. R. Ecological lessons from free-air CO2 enrichment (FACE) experiments. Annu. Rev. Ecol. Evol. Syst. 42, 181–203 (2011).
Google Scholar
Sigurdsson, B. D., Medhurst, J. L., Wallin, G., Eggertsson, O. & Linder, S. Growth of mature boreal Norway spruce was not affected by elevated [CO2] and/or air temperature unless nutrient availability was improved. Tree Physiol. 33, 1192–1205 (2013).
Google Scholar
Walker, A. P. et al. Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO2. N. Phytol. 229, 2413–2445 (2021).
Google Scholar
Gedalof, Z. & Berg, A. A. Tree ring evidence for limited direct CO2 fertilization of forests over the 20th century. Glob. Biogeochem. Cycles 24, (2010).
van der Sleen, P. et al. No growth stimulation of tropical trees by 150 years of CO2 fertilization but water-use efficiency increased. Nat. Geosci. 8, 24–28 (2015).
Google Scholar
Girardin, M. P. et al. No growth stimulation of Canada’s boreal forest under half-century of combined warming and CO2 fertilization. Proc. Natl Acad. Sci. USA 113, E8406–E8414 (2016).
Google Scholar
Giguère-Croteau, C. et al. North America’s oldest boreal trees are more efficient water users due to increased [CO2], but do not grow faster. Proc. Natl Acad. Sci. USA 116, 2749–2754 (2019).
Google Scholar
Walker, A. P. et al. Decadal biomass increment in early secondary succession woody ecosystems is increased by CO2 enrichment. Nat. Commun. 10, 454 (2019).
Google Scholar
Du, E. et al. Global patterns of terrestrial nitrogen and phosphorus limitation. Nat. Geosci. https://doi.org/10.1038/s41561-019-0530-4 (2020).
Schimel, J. P. & Bennett, J. Nitrogen mineralization: challenges of a changing paradigm. Ecology 85, 591–602 (2004).
Google Scholar
Vitousek, P. M. & Howarth, R. W. Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13, 87–115 (1991).
Google Scholar
Taylor, K. E., Stouffer, R. J. & Meehl, G. A. An overview of CMIP5 and the experiment design. Bull. Am. Meteorol. Soc. 93, 485–498 (2012).
Google Scholar
Näsholm, T., Kielland, K. & Ganeteg, U. Uptake of organic nitrogen by plants. N. Phytol. 182, 31–48 (2009).
Google Scholar
Lindahl, B. D. & Tunlid, A. Ectomycorrhizal fungi – potential organic matter decomposers, yet not saprotrophs. N. Phytol. 205, 1443–1447 (2015).
Google Scholar
Terrer, C., Vicca, S., Hungate, B. A., Phillips, R. P. & Prentice, I. C. Mycorrhizal association as a primary control of the CO2 fertilization effect. Science 353, 72–74 (2016).
Google Scholar
Terrer, C. et al. Ecosystem responses to elevated CO2 governed by plant–soil interactions and the cost of nitrogen acquisition. N. Phytol. 217, 507–522 (2018).
Google Scholar
Sulman, B. N. et al. Diverse Mycorrhizal associations enhance terrestrial C storage in a global model. Glob. Biogeochem. Cycles 33, 501–523 (2019).
Google Scholar
Terrer, C. et al. A trade-off between plant and soil carbon storage under elevated CO2. Nature 591, 599–603 (2021).
Google Scholar
Wieder, W. R., Cleveland, C. C., Smith, W. K. & Todd-Brown, K. Future productivity and carbon storage limited by terrestrial nutrient availability. Nat. Geosci. 8, 441–444 (2015).
Google Scholar
Smith, S. E. & Read, D. J. Mycorrhizal symbiosis. (Academic Press, 2010).
Pellitier, P. T. & Zak, D. R. Ectomycorrhizal fungi and the enzymatic liberation of nitrogen from soil organic matter: why evolutionary history matters. N. Phytol. 217, 68–73 (2018).
Google Scholar
Phillips, R. P. et al. Roots and fungi accelerate carbon and nitrogen cycling in forests exposed to elevated CO2. Ecol. Lett. 15, 1042–1049 (2012).
Google Scholar
Terrer, C. et al. Nitrogen and phosphorus constrain the CO2 fertilization of global plant biomass. Nat. Clim. Change 9, 684–689 (2019).
Google Scholar
Christian, N. & Bever, J. D. Carbon allocation and competition maintain variation in plant root mutualisms. Ecol. Evol. 8, 5792–5800 (2018).
Google Scholar
Hortal, S. et al. Role of plant–fungal nutrient trading and host control in determining the competitive success of ectomycorrhizal fungi. ISME J. 11, 2666–2676 (2017).
Google Scholar
Bogar, L. et al. Plant-mediated partner discrimination in ectomycorrhizal mutualisms. Mycorrhiza 29, 97–111 (2019).
Google Scholar
Bödeker, I. T. M., Nygren, C. M. R., Taylor, A. F. S., Olson, Å. & Lindahl, B. D. ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi. ISME J. 3, 1387–1395 (2009).
Google Scholar
Hobbie, E. A. & Agerer, R. Nitrogen isotopes in ectomycorrhizal sporocarps correspond to belowground exploration types. Plant Soil 327, 71–83 (2010).
Google Scholar
Koide, R. T., Fernandez, C. & Malcolm, G. Determining place and process: functional traits of ectomycorrhizal fungi that affect both community structure and ecosystem function. N. Phytol. 201, 433–439 (2014).
Google Scholar
Lindahl, B. D. et al. A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest. Ecol. Lett. 24, 1341–1351 (2021).
Google Scholar
van der Linde, S. et al. Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 558, 243–248 (2018).
Google Scholar
Read, D. J. & Perez-Moreno, J. Mycorrhizas and nutrient cycling in ecosystems: a journey towards relevance? N. Phytol. 157, 475–492 (2003).
Google Scholar
Bödeker, I. T. M. et al. Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems. N. Phytol. 203, 245–256 (2014).
Google Scholar
Bogar, L. & Peay, K. Processes maintaining the coexistence of ectomycorrhizal fungi at a fine spatial scale. in Biogeography of Mycorrhizal Symbiosis (ed. Tedersoo, L.) vol. 230 79–105 (Springer, 2017).
Xu, K. et al. Tree-ring widths are good proxies of annual variation in forest productivity in temperate forests. Sci. Rep. 7, 1945 (2017).
Google Scholar
Nehrbass‐Ahles, C. et al. The influence of sampling design on tree-ring-based quantification of forest growth. Glob. Change Biol. 20, 2867–2885 (2014).
Google Scholar
Mathias, J. M. & Thomas, R. B. Disentangling the effects of acidic air pollution, atmospheric CO2, and climate change on recent growth of red spruce trees in the Central Appalachian Mountains. Glob. Change Biol. 24, 3938–3953 (2018).
Google Scholar
Fierer, N., Barberán, A. & Laughlin, D. C. Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Front. Microbiol. 5, 614 (2014).
Zak, D. R. & Pregitzer, K. S. Spatial and temporal variability of nitrogen cycling in northern lower Michigan. Science 36, 367–380 (1990).
Zak, D. R., Pregitzer, K. S. & Host, G. E. Landscape variation in nitrogen mineralization and nitrification. Can. J. Res. 16, 1258–1263 (1986).
Google Scholar
Chen, J. & Gupta, A. K. Parametric Statistical Change Point Analysis: With Applications to Genetics, Medicine, and Finance. (Springer Science & Business Media, 2011).
Thomas, R. Q., Canham, C. D., Weathers, K. C. & Goodale, C. L. Increased tree carbon storage in response to nitrogen deposition in the US. Nat. Geosci. 3, 13–17 (2010).
Google Scholar
Pellitier, P. T., Zak, D. R., Argiroff, W. A. & Upchurch, R. A. Coupled shifts in ectomycorrhizal communities and plant uptake of organic nitrogen along a soil gradient: an isotopic perspective. Ecosystems (2021).
Sterkenburg, E., Clemmensen, K. E., Ekblad, A., Finlay, R. D. & Lindahl, B. D. Contrasting effects of ectomycorrhizal fungi on early and late stage decomposition in a boreal forest. ISME J. 12, 2187–2197 (2018).
Google Scholar
Lilleskov, E. A., Hobbie, E. A. & Fahey, T. J. Ectomycorrhizal fungal taxa differing in response to nitrogen deposition also differ in pure culture organic nitrogen use and natural abundance of nitrogen isotopes. N. Phytol. 154, 219–231 (2002).
Google Scholar
Kohler, A. et al. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat. Genet. 47, 410–415 (2015).
Google Scholar
Moeller, H. V., Peay, K. G. & Fukami, T. Ectomycorrhizal fungal traits reflect environmental conditions along a coastal California edaphic gradient. FEMS Microbiol. Ecol. 87, 797–806 (2014).
Google Scholar
Defrenne, C. E. et al. Shifts in Ectomycorrhizal fungal communities and exploration types relate to the environment and fine-root traits across interior douglas-fir forests of Western Canada. Front. Plant Sci. 10, 643 (2019).
Google Scholar
Fawal, N. et al. PeroxiBase: a database for large-scale evolutionary analysis of peroxidases. Nucleic Acids Res. 41, D441–D444 (2013).
Google Scholar
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014).
Google Scholar
Garajova, S. et al. Single-domain flavoenzymes trigger lytic polysaccharide monooxygenases for oxidative degradation of cellulose. Sci. Rep. 6, 28276 (2016).
Google Scholar
Janusz, G. et al. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol. Rev. 41, 941–962 (2017).
Google Scholar
Shah, F. et al. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. N. Phytol. 209, 1705–1719 (2016).
Google Scholar
Baldrian, P. Fungal laccases – occurrence and properties. FEMS Microbiol. Rev. 30, 215–242 (2006).
Google Scholar
Fernandez, C. W. & Kennedy, P. G. Revisiting the ‘Gadgil effect’: do interguild fungal interactions control carbon cycling in forest soils? N. Phytol. 209, 1382–1394 (2016).
Google Scholar
Reich, P. B. et al. Nitrogen limitation constrains sustainability of ecosystem response to CO2. Nature 440, 922–925 (2006).
Google Scholar
Oren, R. et al. Soil fertility limits carbon sequestration by forest ecosystems in a CO2-enriched atmosphere. Nature 411, 469–472 (2001).
Google Scholar
Norby, R. J., Warren, J. M., Iversen, C. M., Medlyn, B. E. & McMurtrie, R. E. CO2 enhancement of forest productivity constrained by limited nitrogen availability. Proc. Natl Acad. Sci. USA 107, 19368–19373 (2010).
Google Scholar
Andrew, C. & Lilleskov, E. A. Productivity and community structure of ectomycorrhizal fungal sporocarps under increased atmospheric CO2 and O3. Ecol. Lett. 12, 813–822 (2009).
Google Scholar
Näsholm, T. et al. Are ectomycorrhizal fungi alleviating or aggravating nitrogen limitation of tree growth in boreal forests? N. Phytol. 198, 214–221 (2013).
Google Scholar
Finzi, A. C. et al. Increases in nitrogen uptake rather than nitrogen-use efficiency support higher rates of temperate forest productivity under elevated CO2. Proc. Natl Acad. Sci. USA 104, 14014–14019 (2007).
Google Scholar
Merkel, D. Soil Nutrients in Glaciated Michigan Landscapes: Distribution of Nutrients and Relationships with Stand Productivity. (Doctoral Thesis Submitted to Michigan State University, 1988).
Host, G. E. & Pregitzer, K. S. Geomorphic influences on ground-flora and overstory composition in upland forests of northwestern lower Michigan. Can. J. Res. 22, 1547–1555 (1992).
Google Scholar
Edwards, I. P. & Zak, D. R. Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape. Mol. Ecol. 19, 1469–1482 (2010).
Google Scholar
Schimel, D., Stephens, B. B. & Fisher, J. B. Effect of increasing CO2 on the terrestrial carbon cycle. Proc. Natl Acad. Sci. USA 112, 436–441 (2015).
Google Scholar
Medlyn, B. E. et al. Using ecosystem experiments to improve vegetation models. Nat. Clim. Change 5, 528–534 (2015).
Google Scholar
Peñuelas, J. et al. Shifting from a fertilization-dominated to a warming-dominated period. Nat. Ecol. Evol. 1, 1438–1445 (2017).
Google Scholar
McClaugherty, C. A., Pastor, J., Aber, J. D. & Melillo, J. M. Forest litter decomposition in relation to soil nitrogen dynamics and litter quality. Ecology 66, 266–275 (1985).
Google Scholar
Pastor, J., Aber, J. D., McClaugherty, C. A. & Melillo, J. M. Aboveground production and N and P cycling along a nitrogen mineralization gradient on Blackhawk Island, Wisconsin. Ecology 65, 256–268 (1984).
Google Scholar
Serra-Maluquer, X., Mencuccini, M. & Martínez-Vilalta, J. Changes in tree resistance, recovery and resilience across three successive extreme droughts in the northeast Iberian Peninsula. Oecologia 187, 343–354 (2018).
Google Scholar
Vitousek, P. Nutrient cycling and nutrient use efficiency. Am. Nat. 119, 553–572 (1982).
Google Scholar
Darrouzet-Nardi, A., Ladd, M. P. & Weintraub, M. N. Fluorescent microplate analysis of amino acids and other primary amines in soils. Soil Biol. Biochem. 57, 78–82 (2013).
Google Scholar
Ibáñez, I., Zak, D. R., Burton, A. J. & Pregitzer, K. S. Anthropogenic nitrogen deposition ameliorates the decline in tree growth caused by a drier climate. Ecology 99, 411–420 (2018).
Google Scholar
Lines, E. R., Zavala, M. A., Purves, D. W. & Coomes, D. A. Predictable changes in aboveground allometry of trees along gradients of temperature, aridity and competition. Glob. Ecol. Biogeogr. 21, 1017–1028 (2012).
Google Scholar
Taylor, D. L. et al. Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for illumina amplicon sequencing. Appl. Environ. Microbiol. 82, 7217–7226 (2016).
Google Scholar
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).
Google Scholar
Konar, A. et al. High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra. BMC Genomics 18, 417 (2017).
Google Scholar
Sork, V. L. et al. First draft assembly and annotation of the genome of a California Endemic oak. Genes|Genomes|Genet. 6, 3485–3495 (2016).
Google Scholar
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Treiber, M. L., Taft, D. H., Korf, I., Mills, D. A. & Lemay, D. G. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. BMC Bioinforma. 21, 74 (2020).
Google Scholar
Peng, M. et al. Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes. Fungal Genet. Biol. 112, 40–46 (2018).
Google Scholar
Floudas, D. et al. Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi. ISME J. https://doi.org/10.1038/s41396-020-0667-6 (2020).
Kriventseva, E. V. et al. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res. 47, D807–D811 (2019).
Google Scholar
Quinn, T. P., Erb, I., Richardson, M. F. & Crowley, T. M. Understanding sequencing data as compositions: an outlook and review. Bioinformatics 34, 2870–2878 (2018).
Google Scholar
Ferrier, S., Manion, G., Elith, J. & Richardson, K. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers. Distrib. 13, 252–264 (2007).
Google Scholar
Duhamel, M. et al. Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance. Ecol. Monogr. 89, e01367 (2019).
Google Scholar
Qin, C., Zhu, K., Chiariello, N. R., Field, C. B. & Peay, K. G. Fire history and plant community composition outweigh decadal multi-factor global change as drivers of microbial composition in an annual grassland. J. Ecol. 108, 611–625 (2020).
Google Scholar
Oksanen, J., et al. Package vegan.
Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).
Google Scholar
Spiegelhalter, D. J., Best, N. G., Carlin, B. P. & Linde, A. V. D. Bayesian measures of model complexity and fit. J. R. Stat. Soc. Ser. B Stat. Methodol. 64, 583–639 (2002).
Google Scholar
Source: Ecology - nature.com
