More stories

  • in

    Metadata analysis indicates biased estimation of genetic parameters and gains using conventional pedigree information instead of genomic-based approaches in tree breeding

    Beaulieu, J. et al. Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits. Evol. Appl. 13, 2704–2722 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lenz, P. et al. Multi-trait genomic selection for weevil resistance, growth and wood quality in Norway spruce. Evol. Appl. 13, 76–94 (2020).CAS 
    PubMed 

    Google Scholar 
    Lebedev, V. G., Lebedeva, T. N., Chernodubov, A. I. & Shestibratov, K. A. Genomic selection for forest tree improvement: Methods, achievements and perspectives. Forests 11, 1190 (2020).
    Google Scholar 
    Mullin, T. J. et al. Economic importance, breeding objectives and achievements. In Genetics, Genomics and Breeding of Conifers (eds Plomion, C. et al.) (Science Publishers & CRC Press, 2011).
    Google Scholar 
    Zhang, J., Peter, G. F., Powell, G. L., White, T. L. & Gezan, S. A. Comparison of breeding values estimated between single-tree and multiple-tree plots for a slash pine population. Tree Genet. Genomes 11, 48 (2015).CAS 

    Google Scholar 
    Martínez-García, P. J. et al. Predicting breeding values and genetic components using generalized linear mixed models for categorical and continuous traits in walnut (Juglans regia). Tree Genet. Genomes 13, 109 (2017).
    Google Scholar 
    Weng, Y., Ford, R., Tong, Z. & Krasowski, M. Genetic parameters for bole straightness and branch angle in Jack pine estimated using linear and generalized linear mixed models. For. Sci. 63, 111–117 (2017).
    Google Scholar 
    Mrode, R. A. Linear Models for the Prediction of Animal Breeding Values 2nd edn. (CAB International, 2005).
    Google Scholar 
    Henderson, C. R. Theoretical bias and computational methods for a number of different animal models. J. Dairy Sci. 71, 1–16 (1988).
    Google Scholar 
    Falconer, D. S. & Mackay, T. F. C. Introduction to Quantitative Genetics 4th edn. (Longman Publishing Group, 1996).
    Google Scholar 
    Henderson, C. R. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32, 69–83 (1976).MATH 

    Google Scholar 
    Wright, S. Coefficients of inbreeding and relationship. Am. Nat. 56, 330–338 (1922).
    Google Scholar 
    Hill, W. G. & Weir, B. S. Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genet. Res. 93, 47–64 (2011).CAS 

    Google Scholar 
    Doerksen, T. K. & Herbinger, C. M. Male reproductive success and pedigree error in red spruce open-pollinated and polycross mating systems. Can. J. For. Res. 38, 1742–1749 (2008).
    Google Scholar 
    Godbout, J. et al. Development of a traceability system based on SNP array for the large-scale production of high-value white spruce (Picea glauca). Front. Plant Sci. 8, 1264 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Galeano, E., Bousquet, J. & Thomas, B. R. SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program. Sci. Rep. 11, 4990 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lenz, P. et al. Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: An example from white spruce. Heredity 124, 562–578 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Askew, G. R. & El-Kassaby, Y. A. Estimation of relationship coefficients among progeny derived from wind-pollinated orchard seeds. Theor. Appl. Genet. 88, 267–272 (1994).CAS 
    PubMed 

    Google Scholar 
    Doerksen, T. K., Bousquet, J. & Beaulieu, J. Inbreeding depression in intra-provenance crosses driven by founder relatedness in white spruce. Tree Genet. Genomes 10, 203–212 (2014).
    Google Scholar 
    Meuwissen, T. H. E., Hayes, B. J. & Goddard, M. E. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 1819–1829 (2001).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Heffner, E. L., Lorenz, A. J., Jannink, J.-L. & Sorrels, M. E. Plant breeding with genomic selection: Gain per unit time and cost. Crop Sci. 50, 1681–1690 (2010).
    Google Scholar 
    Grattapaglia, D. & Resende, M. D. V. Genomic selection in forest tree breeding. Tree Genet. Genomes 7, 241–255 (2011).
    Google Scholar 
    Beaulieu, J., Doerksen, T., Clément, S., MacKay, J. & Bousquet, J. Accuracy of genomic selection models in a large population of open-pollinated families in white spruce. Heredity 113, 342–352 (2014).
    Google Scholar 
    Habier, D., Tetens, J., Seefried, F.-R., Lichtner, P. & Thaller, G. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Gen. Select. Evol. 42, 5 (2010).
    Google Scholar 
    Perkel, J. SNP genotyping: six technologies that keyed a revolution. Nat. Methods 5, 447–454 (2008).CAS 

    Google Scholar 
    Pavy, N. et al. Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Mol. Ecol. Res. 13, 324–336 (2013).CAS 

    Google Scholar 
    Thomson, M. J. High-throughput genotyping to accelerate crop improvement. Plant Breed. Biotechnol. 2, 195–212 (2014).
    Google Scholar 
    Beaulieu, J., Doerksen, T., MacKay, J., Rainville, A. & Bousquet, J. Genomic selection accuracies within and between environments and small breeding groups in white spruce. BMC Genomics 15, 1048 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Liu, L., Chen, R., Fugina, C. J., Siegel, B. & Jackson, D. High-throughput and low-cost genotyping method for plant genome editing. Curr. Prot. 1, e100 (2021).CAS 

    Google Scholar 
    Lenz, P. et al. Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana). BMC Genomics 18, 335 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    de los Campos, G., Hickey, J. M., Pong-Wong, R., Daetwyler, H. D. & Calus, M. P. L. Whole-genome regression and prediction models applied to plant and animal breeding. Genetics 193, 327–345 (2013).PubMed Central 

    Google Scholar 
    Hoerl, A. E. & Kennard, R. W. Ridge regression: biased estimation for non-orthogonal problems. Technometrics 12, 55–67 (1970).MATH 

    Google Scholar 
    Tibshirani, R. Regression shrinkage and selection via the LASSO. J. R. Stat. Soc. Series B. 58, 267–288 (1996).MathSciNet 
    MATH 

    Google Scholar 
    VanRaden, P. M. Efficient methods to compute genomic predictions. J. Dairy Sci. 91, 4414–4423 (2008).CAS 
    PubMed 

    Google Scholar 
    Legarra, A., Aguilar, I. & Misztal, I. A relationship matrix including full pedigree and genomic information. J. Dairy Sci. 92, 4656–4663 (2009).CAS 
    PubMed 

    Google Scholar 
    Zapata-Valenzuela, J., Whetten, R. W., Neale, D., McKeand, S. & Isik, F. Genomic estimated breeding values using genomic relationship matrices in a cloned population of loblolly pine. Genes Genomes Genet. 3, 909–916 (2013).
    Google Scholar 
    Muñoz, P. R. et al. Unraveling additive from non-additive effects using genomic relationship matrices. Genetics 198, 1759–1768 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Ratcliffe, B. et al. Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca. Genes Genomes Genet. 7, 935–942 (2017).
    Google Scholar 
    Gamal El-Dien, O. et al. Multienvironment genomic variance decomposition analysis of open-pollinated Interior spruce (Picea glauca x engelmannii). Mol. Breed. 38, 26 (2018).
    Google Scholar 
    Zobel, B. J. & Sprague, J. R. Juvenile Wood in Forest Trees (Springer, 1988).
    Google Scholar 
    Osorio, L. F., White, T. L. & Huber, D. A. Age trends of heritabilities and genotype-by-environment interactions for growth traits and wood density from clonal trials of Eucalyptus grandis Hill ex Maiden. Silv. Genet. 50, 108–117 (2000).
    Google Scholar 
    Baltunis, B. S., Gapare, W. J. & Wu, H. X. Genetic parameters and genotype by environment interaction in radiata pine for growth and wood quality traits in Australia. Silv. Genet. 59, 113–124 (2010).
    Google Scholar 
    Gamal El-Dien, O. et al. Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing. BMC Genomics 16, 370 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Resende, M. D. V. et al. Genomic selection for growth and wood quality in Eucalyptus: Capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol. 194, 116–128 (2012).PubMed 

    Google Scholar 
    Chen, Z.-Q. et al. Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce. BMC Genomics 19, 946 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Beaulieu, J., Perron, M. & Bousquet, J. Multivariate patterns of adaptive genetic variation and seed source transfer in Picea mariana. Can. J. For. Res. 34, 531–545 (2004).
    Google Scholar 
    Li, P., Beaulieu, J. & Bousquet, J. Genetic structure and patterns of genetic variation among populations in eastern white spruce (Picea glauca). Can. J. For. Res. 27, 189–198 (1997).
    Google Scholar 
    Namkoong, G. Inbreeding effects on estimation of genetic additive variance. For. Sci. 12, 8–13 (1966).
    Google Scholar 
    Squillace, A. E. Average genetic correlations among offspring from open-pollinated forest trees. Silv. Genet. 23, 149–156 (1974).
    Google Scholar 
    Muñoz, P. R. et al. Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy. Crop Sci. 53, 1115–1123 (2014).
    Google Scholar 
    Tan, B. et al. Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F1 hybrids. BMC Plant Biol. 17, 110 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Weigel, K. A., VanRaden, P. M., Norman, H. D. & Grosu, H. A 100-year review: Methods and impact of genetic selection in dairy cattle—From daughter-dam comparisons to deep learning algorithms. J. Dairy Sci. 100, 10234–10250 (2017).CAS 
    PubMed 

    Google Scholar 
    Grattapaglia, D. et al. Quantitative genetics and genomics converge to accelerate forest tree breeding. Front. Plant Sci. 9, 1693 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Park, Y.-S., Beaulieu, J. & Bousquet, J. Multi-varietal forestry integrating genomic selection and somatic embryogenesis. In Vegetative Propagation of Forest Trees (eds Park, Y.-S. et al.) 302–322 (National Institute of Forest Science, 2016).
    Google Scholar 
    Bousquet, J. et al. Spruce population genomics. In Population Genomics: Forest Trees (ed. Rajora, O. P.) (Springer Nature, 2021).
    Google Scholar 
    Chamberland, V. et al. Conventional versus genomic selection for white spruce improvement: A comparison of costs and benefits of plantations on Quebec public lands. Tree Genet. Genomes 16, 17 (2020).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).
    Google Scholar 
    MacFarland, T. W. & Yates, J. M. Wilcoxon matched-pairs signed-ranks test. In Introduction to Nonparametric Statistics for the Biological Sciences Using R 133–175 (Springer, 2016) https://doi.org/10.1007/978-3-319-30634-6_5.Li, Y. et al. Genomic selection for non-key traits in radiata pine when the documented pedigree is corrected using DNA marker information. BMC Genomics 20, 1026 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Calleja-Rodriguez, A. et al. Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine. BMC Genomics 21, 796 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ukrainetz, N. K. & Mansfield, S. D. Assessing the sensitivities of genomic selection for growth and wood quality traits in lodgepole pine using Bayesian models. Tree Genet. Genomes 16, 14 (2020).
    Google Scholar 
    Ukrainetz, N. K. & Mansfield, S. D. Prediction accuracy of single-step BLUP for growth and wood quality traits in the lodgepole pine breeding program in British Columbia. Tree Genet. Genomes 16, 64 (2020).
    Google Scholar 
    Thistlethwaite, F. R. et al. Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform. BMC Genomics 18, 930 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Suontama, M. et al. Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories. Heredity 122, 370–379 (2019).CAS 
    PubMed 

    Google Scholar 
    Müller, B. S. F. et al. Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. BMC Genomics 18, 524 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Thavamanikumar, S., Arnold, R. J., Luo, J. & Thumma, B. R. Genomic studies reveal substantial dominant effects and improved genomic predictions in an open-pollinated breeding population of Eucalyptus pellita. Genes Genomes Genet. 10, 3751–3763 (2020).CAS 

    Google Scholar 
    Resende, R. T. et al. Assessing the expected response to genomic selection of individuals and families in Eucalyptus breeding with an additive-dominant model. Heredity 119, 245–255 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marco de Lima, B. et al. Quantitative genetic parameters for growth and wood properties in Eucalyptus “urograndis” hybrid using near-infrared phenotyping and genome-wide SNP-based relationships. PLoS ONE 14, e0218747 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bouvet, J.-M., Makouanzi, G., Cros, D. & Vigneron, Ph. Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: Prediction accuracy implications. Heredity 116, 146–157 (2016).CAS 
    PubMed 

    Google Scholar 
    Pégard, M. et al. Favorable conditions for genomic evaluation to outperform classical pedigree evaluation highlighted by a proof-of-concept study in poplar. Front. Plant Sci. 11, 581954 (2020).PubMed 
    PubMed Central 

    Google Scholar  More

  • in

    Field experiments underestimate aboveground biomass response to drought

    Literature search and study selectionA systematic literature search was conducted in the ISI Web of Science database for observational and experimental studies published from 1975 to 13 January 2020 using the following search terms: TOPIC: (grassland* OR prairie* OR steppe* OR shrubland* OR scrubland* OR bushland*) AND TOPIC: (drought* OR ‘dry period*’ OR ‘dry condition*’ OR ‘dry year*’ OR ‘dry spell*’) AND TOPIC: (product* OR biomass OR cover OR abundance* OR phytomass). The search was refined to include the subject categories Ecology, Environmental Sciences, Plant Sciences, Biodiversity Conservation, Multidisciplinary Sciences and Biology, and the document types Article, Review and Letter. This yielded a total of 2,187 peer-reviewed papers (Supplementary Fig. 1). At first, these papers were screened by title and abstract, which resulted in 197 potentially relevant full-text articles. We then examined the full text of these papers for eligibility and selected 87 studies (43 experimental, 43 observational and 1 that included both types) on the basis of the following criteria:

    (1)

    The research was conducted in the field, in natural or semi-natural grasslands or shrublands (for example, artificially constructed (seeded or planted) plant communities or studies using monolith transplants were excluded). We used this restriction because most reports on observational droughts are from intact ecosystems, and experiments in disturbed sites or using artificial communities would thus not be comparable to observational drought studies.

    (2)

    In the case of observational studies, the drought year or a multi-year drought was clearly specified by the authors (that is, we did not arbitrarily extract dry years from a long-term dataset). Please note that some observational data points are from control plots of experiments (of any kind), where the authors reported that a drought had occurred during the study period. We did not involve gradient studies that compare sites of different climates, which are sometimes referred to as ‘observational studies’.

    (3)

    The paper reported the amount or proportion of change in annual or growing-season precipitation (GSP) compared with control conditions. We consistently use the term ‘control’ for normal precipitation (non-drought) year or years in observational studies and for ambient precipitation (no treatment) in experimental studies hereafter. Similarly, we use the term ‘drought’ for both drought year or years in observational studies and drought treatment in experimental studies. In the case of multi-factor experiments, where precipitation reduction was combined with any other treatment (for example, warming), data from the plots receiving drought only and data from the control plots were used.

    (4)

    The paper contained raw data on plant production under both control and drought conditions, expressed in any of the following variables: ANPP, aboveground plant biomass (in grassland studies only) or percentage plant cover. In 79% of the studies that used ANPP as a production variable, ANPP was estimated by harvesting peak or end-of-season AGB. We therefore did not distinguish between ANPP and AGB, which are referred to as ‘biomass’ hereafter. We included the papers that reported the production of the whole plant community, or at least that of the dominant species or functional groups approximating the abundance of the whole community.

    (5)

    When multiple papers were published on the same experiment or natural drought event at the same study site, the most long-term study including the largest number of drought years was chosen.

    In addition to the systematic literature search, we included 27 studies (9 experimental, 17 observational and 1 that included both types) meeting the above criteria from the cited references of the Web of Science records selected for our meta-analyses, and from previous meta-analyses and reviews on the topic. In total, this resulted in 114 studies (52 experimental, 60 observational and 2 that included both types; Supplementary Note 9, Supplementary Fig. 2 and ref. 25).Data compilationData were extracted from the text or tables, or were read from the figures using Web Plot Digitizer26. For each study, we collected the study site, latitude, longitude, mean annual temperature (MAT) and precipitation (MAP), study type (experimental or observational), and drought length (the number of consecutive drought years). When MAT or MAP was not documented in the paper, it was extracted from another published study conducted at the same study site (identified by site names and geographic coordinates) or from an online climate database cited in the respective paper. We also collected vegetation type—that is, grassland when it was dominated by grasses, or shrubland when the dominant species included one or more shrub species (involving communities co-dominated by grasses and shrubs). Data from the same study (that is, paper) but from different geographic locations or environmental conditions (for example, soil types, land uses or multiple levels of experimental drought) were collected as distinct data points (but see ‘Statistical analysis’ for how these points were handled). As a result, the 114 published papers provided 239 data points (112 experimental and 127 observational)25.For the observational studies, normal precipitation year or years specified by the authors was used as the control. If it was not specified in the paper, the year immediately preceding the drought year(s) was chosen as the control. When no data from the pre-drought year were available, the year immediately following the drought year(s) (14 data points) or a multi-year period given in the paper (22 data points) was used as the control. For the experimental studies, we also collected treatment size (that is, rainout shelter area or, if it was not reported in the paper, the experimental plot size).For the calculation of drought severity, we used yearly precipitation (YP), which was reported in a much higher number of studies than GSP. We extracted YP for both control (YPcontrol) and drought (YPdrought). For the observational studies, when a multi-year period was used as the control or the natural drought lasted for more than one year, precipitation values were averaged across the control or drought years, respectively. Consistently, in the case of multi-year drought experiments, YPcontrol and YPdrought were averaged across the treatment years. When only GSP was published in the paper (63 of 239 data points), we used this to obtain YP data as follows: we regarded MAP as YPcontrol, and YPdrought was calculated as YPdrought = MAP − (GSPcontrol − GSPdrought). From YPcontrol and YPdrought data, we calculated drought severity as follows: (YPdrought − YPcontrol)/YPcontrol × 100.For production, we compiled the mean, replication (N) and, if the study reported it, a variance estimate (s.d., s.e.m. or 95% CI) for both control and drought. In the case of multi-year droughts, data only from the last drought year were extracted, except in five studies (17 data points) where production data were given as an average for the drought years. When both biomass and cover data were presented in the paper, we chose biomass. For each study, we consistently considered replication as the number of the smallest independent study unit. When only the range of replications was reported in a study, we chose the smallest number.To quantify climatic aridity for each study site, we used an aridity index (AI), calculated as the ratio of MAP and mean annual PET (AI = MAP/PET). This is a frequently used index in recent climate change research27,28. AI values were extracted from the Global Aridity Index and Potential Evapotranspiration (ET0) Climate Database v.2 for the period of 1970–2000 (aggregated on annual basis)29.Because we wanted to prevent our analysis from being distorted by a strongly unequal distribution of studies between the two study types regarding some potentially important explanatory variables, we left out studies from our focal meta-analysis in three steps. First, we left out studies that were conducted at wet sites—that is, where site AI exceeded 1. The value of 1 was chosen for two reasons: above this value, the distribution of studies between the two study types was extremely uneven (22 experimental versus 2 observational data points with AI  > 1)25, and the AI value of 1 is a bioclimatically meaningful threshold, where MAP equals PET. Second, we left out shrublands, because we had only 14 shrubland studies (out of 105 studies with AI  More

  • in

    Zooplankton network conditioned by turbidity gradient in small anthropogenic reservoirs

    Lampert, W. Zooplankton research: The contribution of limnology to general ecological paradigms. Aquat. Ecol. 31, 19–27. https://doi.org/10.1023/A:1009943402621 (1997).Article 

    Google Scholar 
    Sotton, B. et al. Trophic transfer of microcystins through the lake pelagic food web: Evidence for the role of zooplankton as a vector in fish contamination. Sci. Total Environ. 466–467, 152–163. https://doi.org/10.1016/j.scitotenv.2013.07.020 (2014).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    St-Gelais, F. N., Sastri, A. R., del Giorgio, P. A. & Beisner, B. E. Magnitude and regulation of zooplankton community production across boreal lakes. Limnol. Oceanogr. Lett. 2(6), 210–217. https://doi.org/10.1002/lol2.10050 (2017).Article 

    Google Scholar 
    Dejen, E., Vijverberg, J., Nagelkerke, L. A. J. & Sibbing, F. A. Temporal and spatial distribution of microcrustacean zooplankton in relation to turbidity and other environmental factors in a large tropical lake (L. Tana, Ethiopia). Hydrobiologia 513(1), 39–49. https://doi.org/10.1023/b:hydr.0000018163.60503.b8 (2004).Article 

    Google Scholar 
    Arendt, K. E. et al. Effects of suspended sediments on copepods feeding in a glacial influenced sub-Arctic fjord. J. Plankton Res. 33, 1526–1537. https://doi.org/10.1093/plankt/fbr054 (2011).CAS 
    Article 

    Google Scholar 
    Carrasco, N. K., Perissinotto, R. & Jones, S. Turbidity effects on feeding and mortality of the copepod Acartiella natalensis (Connell and Grindley, 1974) in the St Lucia Estuary, South Africa. J. Exp. Mar. Biol. Ecol. 446, 45–51. https://doi.org/10.1016/j.jembe.2013.04.016 (2013).Article 

    Google Scholar 
    Goździejewska, A. et al. Effects of lateral connectivity on zooplankton community structure in floodplain lakes. Hydrobiologia 774, 7–21. https://doi.org/10.1007/s10750-016-2724-8 (2016).CAS 
    Article 

    Google Scholar 
    Zhou, J., Qin, B. & Han, X. The synergetic effects of turbulence and turbidity on the zooplankton community structure in large, shallow Lake Taihu. Environ. Sci. Pollut. Res. 25, 1168–1175. https://doi.org/10.1007/s11356-017-0262-1 (2018).CAS 
    Article 

    Google Scholar 
    Chou, W.-R., Fang, L.-S., Wang, W.-H. & Tew, K. S. Environmental influence on coastal phytoplankton and zooplankton diversity: A multivariate statistical model analysis. Environ. Monit. Assess. 184(9), 5679–5688. https://doi.org/10.1007/s10661-011-2373-3 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Du, X. et al. Analyzing the importance of top-down and bottom-up controls in food webs of Chinese lakes through structural equation modeling. Aquat. Ecol. 49(2), 199–210. https://doi.org/10.1007/s10452-015-9518-3 (2015).CAS 
    Article 

    Google Scholar 
    Feitosa, I. B. et al. Plankton community interactions in an Amazonian floodplain lake, from bacteria to zooplankton. Hydrobiologia 831, 55–70. https://doi.org/10.1007/s10750-018-3855-x (2019).CAS 
    Article 

    Google Scholar 
    Kruk, M. & Paturej, E. Indices of trophic and competitive relations in a planktonic network of a shallow, temperate lagoon. A graph and structural equation modeling approach. Ecol. Indic. 112, 106007. https://doi.org/10.1016/j.ecolind.2019.106007 (2020).Article 

    Google Scholar 
    Kruk, M., Paturej, E. & Artiemjew, P. From explanatory to predictive network modeling of relationships among ecological indicators in the shallow temperate lagoon. Ecol. Indic. 117, 106637. https://doi.org/10.1016/j.ecolind.2020.106637 (2020).Article 

    Google Scholar 
    Kruk, M., Paturej, E. & Obolewski, K. Zooplankton predator–prey network relationships indicates the saline gradient of coastal lakes. Machine learning and meta-network approach. Ecol. Indic. 125, 107550. https://doi.org/10.1016/j.ecolind.2021.107550 (2021).Article 

    Google Scholar 
    Oh, H.-J. et al. Comparison of taxon-based and trophi-based response patterns of rotifer community to water quality: Applicability of the rotifer functional group as an indicator of water quality. Anim. Cells Syst. 21, 133–140. https://doi.org/10.1080/19768354.2017.1292952 (2017).Article 

    Google Scholar 
    Sodré, E. D. O. & Bozelli, R. L. How planktonic microcrustaceans respond to environment and affect ecosystem: A functional trait perspective. Int. Aquat. Res. 11, 207–223. https://doi.org/10.1007/s40071-019-0233-x (2019).Article 

    Google Scholar 
    Simões, N. R. et al. Changing taxonomic and functional β-diversity of cladoceran communities in Northeastern and South Brazil. Hydrobiologia 847, 3845–3856. https://doi.org/10.1007/s10750-020-04234-w (2020).Article 

    Google Scholar 
    Goździejewska, A. M., Koszałka, J., Tandyrak, R., Grochowska, J. & Parszuto, K. Functional responses of zooplankton communities to depth, trophic status, and ion content in mine pit lakes. Hydrobiologia 848, 2699–2719. https://doi.org/10.1007/s10750-021-04590-1 (2021).CAS 
    Article 

    Google Scholar 
    Hart, R. C. Zooplankton feeding rates in relation to suspended sediment content: Potential influences on community structure in a turbid reservoir. Fresh. Biol. 19, 123–139. https://doi.org/10.1111/j.1365-2427.1988.tb00334.x (1988).Article 

    Google Scholar 
    Gliwicz, Z. M. & Pijanowska, J. The role of predation in zooplankton succession. In Plankton Ecology. Succession in Plankton Communities (ed. Sommer, U.) 253–296 (Springer Verlag, 1989).Chapter 

    Google Scholar 
    Gardner, M. B. Effects of turbidity on feeding rates and selectivity of bluegills. Trans. Am. Fish. Soc. 110(3), 446–450. https://doi.org/10.1577/1548-8659(1981)110%3c446:EOTOFR%3e2.0.CO;2 (1981).Article 

    Google Scholar 
    Zettler, E. R. & Carter, J. C. H. Zooplankton community and species responses to a natural turbidity gradient in Lake Temiskaming, Ontario-Quebec. Can. J. Fish. Aquat. Sci. 43, 665–673. https://doi.org/10.1139/f86-080 (1986).Article 

    Google Scholar 
    APHA. Standard Methods for the Examination of Water and Wastewater 20th edn. (American Public Health Association, 1999).
    Google Scholar 
    Lind, O. T., Chrzanowski, T. H. & D’avalos-Lind, L. Clay turbidity and the relative production of bacterioplankton and phytoplankton. Hydrobiologia 353, 1–18. https://doi.org/10.1023/A:1003039932699 (1997).CAS 
    Article 

    Google Scholar 
    Boenigk, J. & Novarino, G. Effect of suspended clay on the feeding and growth of bacterivorous flagellates and ciliates. Aquat. Microb. Ecol. 34, 181–192. https://doi.org/10.3354/ame034181 (2004).Article 

    Google Scholar 
    Noe, G. B., Harvey, J. W. & Saiers, J. E. Characterization of suspended particles in Everglades wetlands. Limnol. Oceanogr. 52, 1166–1178. https://doi.org/10.4319/lo.2007.52.3.1166 (2007).ADS 
    CAS 
    Article 

    Google Scholar 
    Bilotta, G. S. & Brazier, R. E. Understanding the influence of suspended solids on water quality and aquatic biota. Water Res. 42, 2849–2861. https://doi.org/10.1016/j.watres.2008.03.018 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Fernandez-Severini, M. D., Hoffmeyer, M. S. & Marcovecchio, J. E. Heavy metals concentrations in zooplankton and suspended particulate matter in a southwestern Atlantic temperate estuary (Argentina). Environ. Monit. Assess. 185, 1495–1513. https://doi.org/10.1007/s10661-012-3023-0 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Paaijmans, K. P., Takken, W., Githeko, A. K. & Jacobs, A. F. G. The effect of water turbidity on the near-surface water temperature of larval habitats of the malaria mosquito Anopheles gambiae. Int. J. Biometeorol. 52(8), 747–753. https://doi.org/10.1007/s00484-008-0167-2 (2008).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Asrafuzzaman, M., Fakhruddin, A. N. M. & Hossain, M. A. Reduction of turbidity of water using locally available natural coagulants. ISRN Microbiol. 1–6, 2011. https://doi.org/10.5402/2011/632189 (2011).Article 

    Google Scholar 
    Kirk, K. L. & Gilbert, J. J. Suspended clay and the population dynamics of planktonic rotifers and cladocerans. Ecology 71(5), 1741–1755. https://doi.org/10.2307/1937582 (1990).Article 

    Google Scholar 
    Kirk, K. L. Effects of suspended clay on Daphnia body growth and fitness. Freshwater Biol. 28, 103–109. https://doi.org/10.1111/j.1365-2427.1992.tb00566.x (1992).Article 

    Google Scholar 
    Levine, S. N., Zehrer, R. F. & Burns, C. W. Impact of resuspended sediment on zooplankton feeding in Lake Waihola, New Zealand. Freshw. Biol. 50, 1515–1536. https://doi.org/10.1111/j.1365-2427.2005.01420 (2005).Article 

    Google Scholar 
    Moreira, F. W. A. et al. Assessing the impacts of mining activities on zooplankton functional diversity. Acta Limn. Bras. 28, e7. https://doi.org/10.1590/S2179-975X0816 (2016).Article 

    Google Scholar 
    Kerfoot, W. C. & Sih, A. Predation. Direct and Indirect Impacts on Aquatic Communities Vol. 160 (University Press of New England, 1987).
    Google Scholar 
    Schou, M. O. et al. Restoring lakes by using artificial plant beds: Habitat selection of zooplankton in a clear and a turbid shallow lake. Freshw. Biol. 54(7), 1520–1531. https://doi.org/10.1111/j.1365-2427.2009.02189.x (2009).Article 

    Google Scholar 
    Goździejewska, A. M., Gwoździk, M., Kulesza, S., Bramowicz, M. & Koszałka, J. Effects of suspended micro- and nanoscale particles on zooplankton functional diversity of drainage system reservoirs at an open-pit mine. Sci. Rep. 9, 16113. https://doi.org/10.1038/s41598-019-52542-6 (2019).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ribeiro, F. et al. Silver nanoparticles and silver nitrate induce high toxicity to Pseudokirchneriella subcapitata, Daphnia magna and Danio rerio. Sci. Total Environ. 466–467, 232–241. https://doi.org/10.1016/j.scitotenv.2013.06.101 (2014).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Vallotton, P., Angel, B., Mccall, M., Osmond, M. & Kirby, J. Imaging nanoparticle-algae interactions in three dimensions using Cytoviva microscopy. J. Microsc. 257(2), 166–169. https://doi.org/10.1111/jmi.12199 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Shanthi, S. et al. Biosynthesis of silver nanoparticles using a probiotic Bacillus licheniformis Dahb1 and their antibiofilm activity and toxicity effects in Ceriodaphnia cornuta. Microb. Pathogenesis 93, 70e77. https://doi.org/10.1016/j.micpath.2016.01.014 (2016).CAS 
    Article 

    Google Scholar 
    Vijayakumar, S. et al. Ecotoxicity of Musa paradisiaca leaf extract-coated ZnO nanoparticles to the freshwater microcrustacean Ceriodaphnia cornuta. Limnologica 67, 1–6. https://doi.org/10.1016/j.limno.2017.09.004 (2017).CAS 
    Article 

    Google Scholar 
    Hart, R. C. Zooplankton distribution in relation to turbidity and related environmental gradients in a large subtropical reservoir: Patterns and implications. Freshw. Biol. 24(2), 241–263. https://doi.org/10.1111/j.1365-2427.1990.tb00706.x (1990).Article 

    Google Scholar 
    Pollard, A. I., González, M. J., Vanni, M. J. & Headworth, J. L. Effects of turbidity and biotic factors on the rotifer community in an Ohio reservoir. In Rotifera VIII: A Comparative Approach. Developments in Hydrobiology, Hydrobiologia Vol. 387388 (eds Wurdak, E. et al.) 215–223 (Springer, 1998).
    Google Scholar 
    Roman, M. R., Holliday, D. V. & Sanford, L. P. Temporal and spatial patterns of zooplankton in the Chesapeake Bay turbidity maximum. Mar. Ecol. Prog. Ser. 213, 215–227. https://doi.org/10.3354/meps213215 (2001).ADS 
    Article 

    Google Scholar 
    Young, I. R. & Ribal, A. Multiplatform evaluation of global trends in wind speed and wave height. Science 364(6440), 548–552. https://doi.org/10.1126/science.aav9527 (2019).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Goździejewska, A. M., Skrzypczak, A. R., Paturej, E. & Koszałka, J. Zooplankton diversity of drainage system reservoirs at an opencast mine. Knowl. Manag. Aquat. Ecosyst. 419, 33. https://doi.org/10.1051/kmae/2018020 (2018).Article 

    Google Scholar 
    Goździejewska, A. M., Skrzypczak, A. R., Koszałka, J. & Bowszys, M. Effects of recreational fishing on zooplankton communities of drainage system reservoirs at an open-pit mine. Fish. Manag. Ecol. 00, 1–13. https://doi.org/10.1111/fme.12411 (2020).Article 

    Google Scholar 
    Allesina, S., Bodini, A. & Bondavalli, C. Ecological subsystems via graph theory: The role of strongly connected components. Oikos 110, 164–176. https://doi.org/10.1111/j.0030-1299.2005.13082.x (2005).Article 

    Google Scholar 
    D’Alelio, D. et al. Ecological-network models link diversity, structure and function in the plankton food-web. Sci. Rep. 6, 21806. https://doi.org/10.1038/srep21806 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Krebs, C. J. Ecology: The Experimental Analysis of Distribution and Abundance 6th edn. (Benjamin Cummings, 2009).
    Google Scholar 
    Ejsmont-Karabin, J., Radwan, S. & Bielańska-Grajner, I. Rotifers. Monogononta–Atlas of Species. Polish Freshwater Fauna (Univ of Łódź, 2004).
    Google Scholar 
    Streble, H. & Krauter, D. Das Leben im Wassertropfen. Mikroflora und Mikrofauna des Süβwassers (Kosmos Gesellschaft der Naturfreunde Franckhsche Verlagshandlung Stuttgart, 1978).
    Google Scholar 
    Ejsmont-Karabin, J. The usefulness of zooplankton as lake ecosystem indicators: Rotifer trophic state index. Pol. J. Ecol. 60, 339–350 (2012).
    Google Scholar 
    Gutkowska, A., Paturej, E. & Kowalska, E. Rotifer trophic state indices as ecosystem indicators in brackish coastal waters. Oceanologia 55(4), 887–899. https://doi.org/10.5697/oc.55-4.887 (2013).Article 

    Google Scholar 
    Dembowska, E. A., Napiórkowski, P., Mieszczankin, T. & Józefowicz, S. Planktonic indices in the evaluation of the ecological status and the trophic state of the longest lake in Poland. Ecol. Indic. 56, 15–22. https://doi.org/10.1016/j.ecolind.2015.03.019 (2015).Article 

    Google Scholar 
    Sousa, W., Attayde, J. L., Rocha, E. D. S. & Eskinazi-Sant’Anna, E. M. The response of zooplankton assemblages to variations in the water quality of four man-made lakes in semi-arid northeastern Brazil. J. Plankton Res. 30(6), 699–708. https://doi.org/10.1093/plankt/fbn032 (2008).Article 

    Google Scholar 
    Kak, A. & Rao, R. Does the evasive behavior of H. exarthra influence its competition with cladocerans? In Rotifera VIII: A Comparative Approach. Developments in Hydrobiology, Hydrobiologia Vol. 387/388 (eds Wurdak, E. et al.) 409–419 (Springer, 1998).
    Google Scholar 
    Hochberg, R., Yang, H. & Moore, J. The ultrastructure of escape organs: Setose arms and crossstriated muscles in Hexarthra mira (Rotifera: Gnesiotrocha: Flosculariaceae). Zoomorphology 136, 159–173. https://doi.org/10.1007/s00435-016-0339-2 (2017).Article 

    Google Scholar 
    Brooks, J. L. & Dodson, S. I. Predation, body size, and composition of plankton. Science 150, 28–35 (1965).ADS 
    CAS 
    Article 

    Google Scholar 
    Connell, J. H. Intermediate-disturbance hypothesis. Science 204(4399), 1345 (1979).CAS 
    Article 

    Google Scholar 
    Martín González, A. M., Dalsgaard, B. & Olesen, J. M. Centrality measures and the importance of generalist species in pollination networks. Ecol. Complex. 7(1), 36–43. https://doi.org/10.1016/j.ecocom.2009.03.008 (2010).Article 

    Google Scholar 
    Paine, R. T. A note on trophic complexity and community stability. Am. Nat. 104, 91–93 (1969).Article 

    Google Scholar 
    Schmitz, O. J. & Trussell, G. C. Multiple stressors, state-dependence and predation risk—Foraging trade-offs: Toward a modern concept of trait-mediated indirect effects in communities and ecosystems. Curr. Opin. Behav. Sci. 12, 6–11. https://doi.org/10.1016/j.cobeha.2016.08.003 (2016).Article 

    Google Scholar 
    Burns, C. W. & Gilbert, J. J. Effects of daphnid size and density on interference between Daphnia and Keratella cochlearis. Limnol. Oceanogr. 31(4), 848–858. https://doi.org/10.4319/lo.1986.31.4.0848 (1986).ADS 
    Article 

    Google Scholar 
    Gilbert, J. J. Suppression of rotifer populations by Daphnia: A review of the evidence, the mechanisms, and the effects on zooplankton community structure. Limnol. Oceanogr. 33(6), 1286–1303. https://doi.org/10.4319/lo.1988.33.6.1286 (1988).ADS 
    Article 

    Google Scholar 
    Conde-Porcuna, J. M., Morales-Baquero, R. & Cruz-Pizarro, L. Effects of Daphnia longispina on rotifer populations in a natural environment: Relative importance of food limitation and interference competition. J. Plankton Res. 16(6), 691–706. https://doi.org/10.1093/plankt/16.6.691 (1994).Article 

    Google Scholar 
    Ladle, R. J. & Whittaker, R. J. (eds) Conservation Biogeography (Wiley–Blackwell, 2011).
    Google Scholar 
    Cottee-Jones, H. E. W. & Whittaker, R. J. The keystone species concept: A critical appraisal. Front. Biogeogr. 4(3), 117–127. https://doi.org/10.21425/F5FBG12533 (2012).Article 

    Google Scholar 
    Remane, A. Die Brackwasserfauna. Verhandlungen Der Deutschen Zoologischen Gesellschaft 36, 34–74 (1934).
    Google Scholar 
    Skrzypczak, A. R. & Napiórkowska-Krzebietke, A. Identification of hydrochemical and hydrobiological properties of mine waters for use in aquaculture. Aquac. Rep. 18, 100460. https://doi.org/10.1016/j.aqrep.2020.100460 (2020).Article 

    Google Scholar 
    von Flössner, D. & Krebstiere, C. Kiemen-und Blattfüsser, Branchiopoda, Fischläuse, Branchiura Vol. 382 (VEB Gustav Fischer Verlag, 1972).
    Google Scholar 
    Koste, W. Rotatoria. Die Rädertiere Mitteleuropas. Überordnung Monogononta. I Textband, II Tafelband 52–570 (Gebrüder Borntraeger, 1978).
    Google Scholar 
    Rybak, J. I. & Błędzki, L. A. Freshwater Planktonic Crustaceans (Warsaw University Press, 2010).
    Google Scholar 
    Błędzki, L. A. & Rybak, J. I. Freshwater Crustacean Zooplankton of Europe: Cladocera & Copepoda (Calanoida, Cyclopoida). Key to Species Identification with Notes on Ecology, Distribution, Methods and Introduction to Data Analysis (Springer, 2016).Book 

    Google Scholar 
    Bottrell, H. H. et al. A review of some problems in zooplankton production studies. Norw. J. Zool. 24, 419–456 (1976).
    Google Scholar 
    Ejsmont-Karabin, J. Empirical equations for biomass calculation of planktonic rotifers. Pol. Arch. Hydr. 45, 513–522 (1998).
    Google Scholar 
    Kovach, W. L. MVSP—A Multivariate Statistical Package for Windows, ver. 3.2 (Kovach Computing Services Pentraeth, 2015).
    Google Scholar 
    Borgatti, S. P. Centrality and network flow. Soc. Netw. 27, 55–71. https://doi.org/10.1016/j.socnet.2004.11.008 (2005).Article 

    Google Scholar 
    Kamada, T. & Kawai, S. An algorithm for drawing general undirected graphs—Inform. Process Lett. 31, 7–15 (1989).MathSciNet 
    Article 

    Google Scholar 
    Pavlopoulos, G. A. et al. Using graph theory to analyze biological networks. BioData Min 4, 10 (2011).Article 

    Google Scholar 
    Newman, M. E. J. A measure of betweenness centrality based on random walks. Soc. Netw. 27, 39–54. https://doi.org/10.1016/j.socnet.2004.11.009 (2005).Article 

    Google Scholar 
    Brandes, U. A. faster algorithm for betweenness centrality. J. Math. Sociol. 25, 163–177. https://doi.org/10.1080/0022250X.2001.9990249 (2001).Article 
    MATH 

    Google Scholar  More

  • in

    Physiological acclimatization in Hawaiian corals following a 22-month shift in baseline seawater temperature and pH

    Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science (80- ). 359, 80–83 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Eakin, C. M., Sweatman, H. P. A. & Brainard, R. E. The 2014–2017 global-scale coral bleaching event: Insights and impacts. Coral Reefs 38, 539–545 (2019).ADS 

    Google Scholar 
    Glynn. Coral reef bleaching: Facts, hypotheses and implications. Glob. Chang. Biol. 2, 495–509 (1996).ADS 

    Google Scholar 
    Brown, B. E. Coral bleaching: Causes and consequences. Coral Reefs 16, 129–138 (1997).
    Google Scholar 
    Maynard, J. A. et al. Projections of climate conditions that increase coral disease susceptibility and pathogen abundance and virulence. Nat. Clim. Chang. 5, 688–694 (2015).ADS 

    Google Scholar 
    Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Anthony, K. R. N., Kline, D. I., Diaz-Pulido, G., Dove, S. & Hoegh-Guldberg, O. Ocean acidification causes bleaching and productivity loss in coral reef builders. Proc. Natl. Acad. Sci. U. S. A. 105, 17442–17446 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Huang, H. et al. Positive and negative responses of coral calcification to elevated pCO2: Case studies of two coral species and the implications of their responses. Mar. Ecol. Prog. Ser. 502, 145–156 (2014).ADS 
    CAS 

    Google Scholar 
    Hoadley, K. D. et al. Physiological response to elevated temperature and pCO2 varies across four Pacific coral species: Understanding the unique host + symbiont response. Sci. Rep. 5, 1–15 (2015).
    Google Scholar 
    Schoepf, V. et al. Coral energy reserves and calcification in a high-CO2 world at two temperatures. PLoS One. 8, e75049 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    IPCC. In IPCC Special Report on the Ocean and Cryosphere in a Changing Climate, (eds. Pörtner, H.-O. et al.) 1–36 (Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA, 2019).Bahr, K. D., Jokiel, P. L. & Rodgers, K. S. Relative sensitivity of five Hawaiian coral species to high temperature under high-pCO2 conditions. Coral Reefs 35, 729–738 (2016).ADS 

    Google Scholar 
    Dove, S. G., Brown, K. T., Van Den Heuvel, A., Chai, A. & Hoegh-Guldberg, O. Ocean warming and acidification uncouple calcification from calcifier biomass which accelerates coral reef decline. Commun. Earth Environ. 1, 1–9 (2020).
    Google Scholar 
    Chow, M. H., Tsang, R. H. L., Lam, E. K. Y. & Ang, P. O. Quantifying the degree of coral bleaching using digital photographic technique. J. Exp. Mar. Bio. Ecol. 479, 60–68 (2016).
    Google Scholar 
    Amid, C. et al. Additive effects of the herbicide glyphosate and elevated temperature on the branched coral Acropora formosa in Nha Trang, Vietnam. Environ. Sci. Pollut. Res. 25, 13360–13372 (2018).CAS 

    Google Scholar 
    Anthony, K. R. N., Connolly, S. R. & Willis, B. L. Comparative analysis of energy allocation to tissue and skeletal growth in corals. Limnol. Oceanogr. 47, 1417–1429 (2002).ADS 

    Google Scholar 
    Edmunds, P. J. & Davies, P. S. An energy budget for Porites porites (Scleractinia). Mar. Biol. 92, 339–347 (1986).
    Google Scholar 
    Stimson, J. S. Location, quantity and rate of change in quantity of lipids in tissue of Hawaiian hermatypic corals. Bull. Mar. Sci. 41, 889–904 (1987).ADS 

    Google Scholar 
    Harland, A. D., Navarro, J. C., Spencer Davies, P. & Fixter, L. M. Lipids of some Caribbean and Red Sea corals: Total lipid, wax esters, triglycerides and fatty acids. Mar. Biol. 117, 113–117 (1993).CAS 

    Google Scholar 
    Grottoli, A. G., Tchernov, D. & Winters, G. Physiological and biogeochemical responses of super-corals to thermal stress from the northern gulf of Aqaba, Red Sea. Front. Mar. Sci. 4, 1–12 (2017).
    Google Scholar 
    Rodrigues, L. J. & Grottoli, A. G. Energy reserves and metabolism as indicators of coral recovery from bleaching. Limnol. Oceanogr. 52, 1874–1882 (2007).ADS 

    Google Scholar 
    Anthony, K. R. N., Hoogenboom, M. O., Maynard, J. A., Grottoli, A. G. & Middlebrook, R. Energetics approach to predicting mortality risk from environmental stress: A case study of coral bleaching. Funct. Ecol. 23, 539–550 (2009).
    Google Scholar 
    Baumann, J. H., Grottoli, A. G., Hughes, A. D. & Matsui, Y. Photoautotrophic and heterotrophic carbon in bleached and non-bleached coral lipid acquisition and storage. J. Exp. Mar. Bio. Ecol. 461, 469–478 (2014).CAS 

    Google Scholar 
    Hughes, A. D. & Grottoli, A. G. Heterotrophic compensation: A possible mechanism for resilience of coral reefs to global warming or a sign of prolonged stress?. PLoS ONE 8, 1–10 (2013).
    Google Scholar 
    Grottoli, A. G. et al. The cumulative impact of annual coral bleaching can turn some coral species winners into losers. Glob. Chang. Biol. 20, 3823–3833 (2014).ADS 
    PubMed 

    Google Scholar 
    Grottoli, A. G., Rodrigues, L. J. & Palardy, J. E. Heterotrophic plasticity and resilience in bleached corals. Nature 440, 1186–1189 (2006).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Levas, S. J. et al. Can heterotrophic uptake of dissolved organic carbon and zooplankton mitigate carbon budget deficits in annually bleached corals?. Coral Reefs 35, 495–506 (2016).ADS 

    Google Scholar 
    Jury, C. P., Delano, M. N. & Toonen, R. J. High heritability of coral calcification rates and evolutionary potential under ocean acidification. Sci. Rep. 9, 1–13 (2019).
    Google Scholar 
    Jury, C. P. & Toonen, R. J. Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans. Proc. R. Soc. B Biol. Sci. 286, 20190614 (2019).
    Google Scholar 
    Concepcion, G. T., Polato, N. R., Baums, I. B. & Toonen, R. J. Development of microsatellite markers from four Hawaiian corals: Acropora cytherea, Fungia scutaria, Montipora capitata and Porites lobata. Conserv. Genet. Resour. 2, 11–15 (2010).

    Google Scholar 
    Gorospe, K. D. & Karl, S. A. Genetic relatedness does not retain spatial pattern across multiple spatial scales: Dispersal and colonization in the coral, Pocillopora damicornis. Mol. Ecol. 22, 3721–3736 (2013).PubMed 

    Google Scholar 
    Wall, C. B., Ritson-Williams, R., Popp, B. N. & Gates, R. D. Spatial variation in the biochemical and isotopic composition of corals during bleaching and recovery. Limnol. Oceanogr. 64, 2011–2028 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bahr, K. D., Tran, T., Jury, C. P. & Toonen, R. J. Abundance, size, and survival of recruits of the reef coral Pocillopora acuta under ocean warming and acidification. PLoS ONE 15, 1–13 (2020).
    Google Scholar 
    Rogelj, J. et al. Paris agreement climate proposals need a boost to keep warming well below 2 °C. Nature 534, 631–639 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    McLachlan, R. H., Price, J. T., Solomon, S. L. & Grottoli, A. G. Thirty years of coral heat-stress experiments: A review of methods. Coral Reefs 39, 885–902 (2020).
    Google Scholar 
    Grottoli, A. G. et al. Increasing comparability among coral bleaching experiments. Ecol. Appl. 31, e02262 (2021).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grottoli, A. G. Variability of stable isotopes and maximum linear extension in reef-coral skeletons at Kaneohe Bay, Hawaii. Mar. Biol. 135, 437–449 (1999).
    Google Scholar 
    McLachlan, R. H., Dobson, K. L., Grottoli, A. G. Quantification of Total Biomass in Ground Coral Samples. Protocols.io (2020). https://doi.org/10.17504/protocols.io.bdyai7se.McLachlan, R. H., Muñoz-Garcia, A., Grottoli, A. G. Extraction of Total Soluble Lipid from Ground Coral Samples. Protocols.io (2020). https://doi.org/10.17504/protocols.io.bc4qiyvw.McLachlan, R. H., Price, J. T., Dobson, K. L., Weisleder, N. & Grottoli, A. G. Microplate Assay for Quantification of Soluble Protein in Ground Coral Samples. Protocols.io (2020). https://doi.org/10.17504/protocols.io.bdc8i2zw.McLachlan, R. H., Juracka, C. & Grottoli, A. G. Symbiodiniaceae Enumeration in Ground Coral Samples Using Countess™ II FL Automated Cell Counter. Protocols.io (2020). https://doi.org/10.17504/protocols.io.bdc5i2y6.McLachlan, R. H. & Grottoli, A. G. Geometric Method for Estimating Coral Surface Area Using Image Analysis. Protocols.io https://doi.org/10.17504/protocols.io.bdyai7se(2021).Muscatine, L., McCloskey, L. R. & Marian, R. E. Estimating the daily contribution of carbon from zooxanthellae to coral animal respiration. Limnol. Oceanogr. 26, 601–611 (1981).ADS 
    CAS 

    Google Scholar 
    Levas, S. J. et al. Organic carbon fluxes mediated by corals at elevated pCO2 and temperature. Mar. Ecol. Prog. Ser. 519, 153–164 (2015).ADS 
    CAS 

    Google Scholar 
    Perry, C. T. et al. Loss of coral reef growth capacity to track future increases in sea level. Nature 558, 396–400 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Woodley, C. M., Burnett, A. & Downs, C. A. Epidemiological Assessment of Reproductive Condition of ESA Priority Coral (2013).Logan, C. A., Dunne, J. P., Eakin, C. M. & Donner, S. D. Incorporating adaptive responses into future projections of coral bleaching. Glob. Chang. Biol. 20, 125–139 (2014).ADS 
    PubMed 

    Google Scholar 
    Rodrigues, L. J., Grottoli, A. G. & Lesser, M. P. Long-term changes in the chlorophyll fluorescence of bleached and recovering corals from Hawaii. J. Exp. Biol. 211, 2502–2509 (2008).PubMed 

    Google Scholar 
    Rowan, H. et al. Environmental gradients drive physiological variation in Hawaiian corals. Coral Reefs 40(5), 1505–1523. https://doi.org/10.1007/s00338-021-02140-8 (2021).Article 

    Google Scholar 
    Houlbrèque, F. & Ferrier-Pagès, C. Heterotrophy in tropical scleractinian corals. Biol. Rev. 84, 1–17 (2009).PubMed 

    Google Scholar 
    J. T. Price, thesis, The Ohio State University (2020). More

  • in

    Bumble bees exhibit body size clines across an urban gradient despite low genetic differentiation

    Corlett, R. T. The Anthropocene concept in ecology and conservation. Trends Ecol. Evol. 30, 36–41 (2015).PubMed 

    Google Scholar 
    IPBES. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES Secretariat, 2019).
    Google Scholar 
    Vitousek, P. M. Human domination of Earth’s ecosystems. Science 277, 494–499 (1997).CAS 

    Google Scholar 
    Wong, B. B. M. & Candolin, U. Behavioral responses to changing environments. Behav. Ecol. 26, 665–673 (2015).
    Google Scholar 
    Hale, R. & Swearer, S. E. Ecological traps: Current evidence and future directions. Proc. R. Soc. B Biol. Sci. 283, 1–8 (2016).
    Google Scholar 
    Charman, T. G., Sears, J., Green, R. E. & Bourke, A. F. G. Conservation genetics, foraging distance and nest density of the scarce Great Yellow Bumblebee (Bombus distinguendus). Mol. Ecol. 19, 2661–2674 (2010).PubMed 

    Google Scholar 
    Violle, C. et al. Let the concept of trait be functional!. Oikos 116, 882–892 (2007).
    Google Scholar 
    Husemann, M., Zachos, F. E., Paxton, R. J. & Habel, J. C. Effective population size in ecology and evolution. Heredity 117, 191–192 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wagner, D. L. Insect declines in the Anthropocene. Annu. Rev. Entomol. 65, 457–480 (2020).CAS 
    PubMed 

    Google Scholar 
    Goulson, D., Nicholls, E., Botías, C. & Rotheray, E. L. Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 347, 1255957 (2015).PubMed 

    Google Scholar 
    Thogmartin, W. E. et al. Monarch butterfly population decline in North America: Identifying the threatening processes. R. Soc. Open Sci. 4, 170760 (2017).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cameron, S. A. et al. Patterns of widespread decline in North American bumble bees. Proc. Natl. Acad. Sci. U.S.A. 108, 662–667 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Burkle, L. A., Marlin, J. C. & Knight, T. M. Plant-pollinator interactions over 120 years: Loss of species, co-occurrence, and function. Science 340, 1611–1615 (2013).ADS 

    Google Scholar 
    Grixti, J. C., Wong, L. T., Cameron, S. A. & Favret, C. Decline of bumble bees (Bombus) in the North American Midwest. Biol. Conserv. 142, 75–84 (2009).
    Google Scholar 
    Goulson, D. Bumblebees: Behaviour, Ecology, and Conservation (Oxford University Press, Oxford, 2010).
    Google Scholar 
    Colla, S. R., Gadallah, F., Richardson, L., Wagner, D. & Gall, L. Assessing declines of North American bumble bees (Bombus spp.) using museum specimens. Biodivers. Conserv. 21, 3585–3595 (2012).
    Google Scholar 
    Hatfield, R. et al. IUCN assessments of North American Bombus spp. http://www.xerces.org/ (2015).Arbetman, M. P., Gleiser, G., Morales, C. L., Williams, P. & Aizen, M. A. Global decline of bumblebees is phylogenetically structured and inversely related to species range size and pathogen incidence. Proc. R. Soc. B Biol. Sci. 284, 20170204 (2017).
    Google Scholar 
    Bommarco, R. et al. Dispersal capacity and diet breadth modify the response of wild bees to habitat loss. Proc. R. Soc. B Biol. Sci. 277, 2075–2082 (2010).
    Google Scholar 
    Hall, D. M. et al. The city as a refuge for insect pollinators. Conserv. Biol. 31, 24–29 (2017).PubMed 

    Google Scholar 
    Banaszak-Cibicka, W. & Żmihorski, M. Wild bees along an urban gradient: Winners and losers. J. Insect Conserv. 16, 331–343 (2012).
    Google Scholar 
    Wilson, C. J. & Jamieson, M. A. The effects of urbanization on bee communities depends on floral resource availability and bee functional traits. PLoS One 14, e0225852 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thompson, M.J., Capilla-Lasheras, P.C., Dominoni, D.M., Réale, D. & Charmantier, A. Phenotypic variation in urban environments: mechanisms and implications. Trends Ecol. Evol. 37, 171–182 (2022).CAS 
    PubMed 

    Google Scholar 
    Peat, J., Tucker, J. & Goulson, D. Does intraspecific size variation in bumblebees allow colonies to efficiently exploit different flowers?. Ecol. Entomol. 30, 176–181 (2005).
    Google Scholar 
    Greenleaf, S. S., Williams, N. M., Winfree, R. & Kremen, C. Bee foraging ranges and their relationship to body size. Oecologia 153, 589–596 (2007).ADS 
    PubMed 

    Google Scholar 
    Spaethe, J. & Weidenmüller, A. Size variation and foraging rate in bumblebees (Bombus terrestris). Insectes Soc. 49, 142–146 (2002).
    Google Scholar 
    Couvillon, M. J. & Dornhaus, A. Small worker bumble bees (Bombus impatiens) are hardier against starvation than their larger sisters. Insectes Soc. 57, 193–197 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pendrel, B. A. & Plowright, R. C. Larval feeding by adult bumble bee workers (Hymenoptera: Apidae). Behav. Ecol. Sociobiol. 8, 71–76 (1981).
    Google Scholar 
    Sutcliffe, G. H. & Plowright, R. C. The effects of food supply on adult size in the bumble bee Bombus terricola Kirby (Hymenoptera: Apidae). Can. Entomol. 120, 1051–1058 (1988).
    Google Scholar 
    Couvillon, M. J. & Dornhaus, A. Location, location, location: Larvae position inside the nest is correlated with adult body size in worker bumble-bees (Bombus impatiens). Proc. R. Soc. B Biol. Sci. 276, 2411–2418 (2009).
    Google Scholar 
    Bartomeus, I. et al. Historical changes in northeastern US bee pollinators related to shared ecological traits. Proc. Natl. Acad. Sci. U.S.A. 110, 4656–4660 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Austin, M. W. & Dunlap, A. S. Intraspecific variation in worker body size makes North American bumble bees (Bombus spp.) less susceptible to decline. Am. Nat. 194, 381–394 (2019).PubMed 

    Google Scholar 
    Watters, J. V., Lema, S. C. & Nevitt, G. A. Phenotype management: A new approach to habitat restoration. Biol. Conserv. 112, 435–445 (2003).
    Google Scholar 
    Haddaway, N. R., Mortimer, R. J. G., Christmas, M., Grahame, J. W. & Dunn, A. M. Morphological diversity and phenotypic plasticity in the threatened British white-clawed crayfish (Austropotamobius pallipes). Aquat. Conserv. Mar. Freshw. Ecosyst. 22, 220–231 (2012).
    Google Scholar 
    Lema, S. C. & Nevitt, G. A. Testing an ecophysiological mechanism of morphological plasticity in pupfish and its relevance to conservation efforts for endangered Devils Hole pupfish. J. Exp. Biol. 209, 3499–3509 (2006).PubMed 

    Google Scholar 
    Crispo, E. Modifying effects of phenotypic plasticity on interactions among natural selection, adaptation and gene flow. J. Evol. Biol. 21, 1460–1469 (2008).CAS 
    PubMed 

    Google Scholar 
    Fraser, D. J. & Bernatchez, L. Adaptive evolutionary conservation: Towards a unified concept for defining conservation units. Mol. Ecol. 10, 2741–2752 (2001).CAS 
    PubMed 

    Google Scholar 
    Nicotra, A. B. et al. Plant phenotypic plasticity in a changing climate. Trends Plant Sci. 15, 684–692 (2010).CAS 
    PubMed 

    Google Scholar 
    Spielman, D., Brook, B. W. & Frankham, R. Most species are not driven to extinction before genetic factors impact them. Proc. Natl. Acad. Sci. U.S.A. 101, 15261–15264 (2004).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Woodard, S. H. et al. Molecular tools and bumble bees: Revealing hidden details of ecology and evolution in a model system. Mol. Ecol. 24, 2916–2936 (2015).MathSciNet 
    PubMed 

    Google Scholar 
    Lozier, J. D., Strange, J. P., Stewart, I. J. & Cameron, S. A. Patterns of range-wide genetic variation in six North American bumble bee (Apidae: Bombus) species. Mol. Ecol. 20, 4870–4888 (2011).PubMed 

    Google Scholar 
    Williams, B. L., Brawn, J. D. & Paige, K. N. Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae). Mol. Ecol. 12, 11–20 (2003).CAS 
    PubMed 

    Google Scholar 
    IUCN. The IUCN Red List of Threatened Species. https://www.iucnredlist.org. Accessed 18 Dec 2019 (2019).MacPhail, V. J., Richardson, L. L. & Colla, S. R. Incorporating citizen science, museum specimens, and field work into the assessment of extinction risk of the American Bumble bee (Bombus pensylvanicus De Geer 1773) in Canada. J. Insect Conserv. 23, 597–611 (2019).
    Google Scholar 
    Camilo, G. R., Muñiz, P. A., Arduser, M. S. & Spevak, E. M. A checklist of the bees (Hymenoptera: Apoidea) of St. Louis, Missouri, USA. J. Kansas Entomol. Soc. 90, 175–188 (2018).
    Google Scholar 
    United States Census Bureau. Land Area and Persons Per Square Mile. https://www.census.gov/quickfacts/fact/note/US/LND110210. Accessed 26 March 2020 (2010).United States Census Bureau. City and Town Population Totals: 2010–2018. https://www.census.gov/data/tables/time-series/demo/popest/2010s-total-cities-and-towns.html. Accessed 26 March 2020 (2020).Thompson, K. & Jones, A. Human population density and prediction of local plant extinction in Britain. Conserv. Biol. 13, 185–189 (1999).
    Google Scholar 
    Fontana, C. S., Burger, M. I. & Magnusson, W. E. Bird diversity in a subtropical South-American City: Effects of noise levels, arborisation and human population density. Urban Ecosyst. 14, 341–360 (2011).
    Google Scholar 
    Lepais, O. et al. Estimation of bumblebee queen dispersal distances using sibship reconstruction method. Mol. Ecol. 19, 819–831 (2010).CAS 
    PubMed 

    Google Scholar 
    Holehouse, K. A., Hammond, R. L. & Bourke, A. F. G. Non-lethal sampling of DNA from bumble bees for conservation genetics. Insectes Soc. 50, 277–285 (2003).
    Google Scholar 
    Williams, P. H., Thorp, R., Richardson, L. & Colla, S. R. Bumble Bees of North America (Princeton University Press, 2014).
    Google Scholar 
    Cane, J. H. Estimation of bee size using intertegular span (Apoidea). J. Kansas Entomol. Soc. 60, 145–147 (1987).
    Google Scholar 
    Walsh, P. S., Metzger, D. A. & Higuchi, R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10, 506–513 (1991).CAS 
    PubMed 

    Google Scholar 
    Estoup, A., Scholl, A., Pouvreau, A. & Solignac, M. Monoandry and polyandry in bumble bees (Hymenoptera; Bombinae) as evidenced by highly variable microsatellites. Mol. Ecol. 4, 89–94 (1995).CAS 
    PubMed 

    Google Scholar 
    Estoup, A., Solignac, M., Cornuet, J. M., Goudet, J. & Scholl, A. Genetic differentiation of continental and island populations of Bombus terrestris (Hymenoptera: Apidae) in Europe. Mol. Ecol. 5, 19–31 (1996).CAS 
    PubMed 

    Google Scholar 
    Funk, C. R., Schmid-Hempel, R. & Schmid-Hempel, P. Microsatellite loci for Bombus spp. Mol. Ecol. Notes 6, 83–86 (2006).CAS 

    Google Scholar 
    Stolle, E. et al. Novel microsatellite DNA loci for Bombus terrestris (Linnaeus, 1758). Mol. Ecol. Resour. 9, 1345–1352 (2009).CAS 
    PubMed 

    Google Scholar 
    Kearse, M. et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    Chapman, R. E. & Bourke, A. F. G. The influence of sociality on the conservation biology of social insects. Ecol. Lett. 4, 650–662 (2001).
    Google Scholar 
    Geib, J. C., Strange, J. P. & Galen, A. Bumble bee nest abundance, foraging distance, and host-plant reproduction: Implications for management and conservation. Ecol. Appl. 25, 768–778 (2015).PubMed 

    Google Scholar 
    Chakraborty, R., Andrade, M. D. E., Daiger, S. P. & Budowle, B. Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications. Ann. Hum. Genet. 56, 45–57 (1992).CAS 
    PubMed 
    MATH 

    Google Scholar 
    Gruber, B. & Adamack, A. T. PopGenReport: Simplifying basic population genetic analyses in R. Methods Ecol. Evol. 5, 384–387 (2014).
    Google Scholar 
    Wang, J. Sibship reconstruction from genetic data with typing errors. Genetics 166, 1963–1979 (2004).PubMed 
    PubMed Central 

    Google Scholar 
    Crozier, R. H. Genetics of sociality. In Social Insects Vol. I (ed. Hermann, H. R.) 223–286 (Academic Press, 1979).
    Google Scholar 
    Rousset, F. genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106 (2008).PubMed 

    Google Scholar 
    Leberg, P. L. Estimating allelic richness: Effects of sample size and bottlenecks. Mol. Ecol. 11, 2445–2449 (2002).CAS 
    PubMed 

    Google Scholar 
    Goudet, J. hierfstat, a package for r to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).
    Google Scholar 
    Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).CAS 

    Google Scholar 
    Ryman, N. & Palm, S. POWSIM: A computer program for assessing statistical power when testing for genetic differentiation. Mol. Ecol. Notes 6, 600–602 (2006).
    Google Scholar 
    Zayed, A. & Packer, L. High levels of diploid male production in a primitively eusocial bee (Hymenoptera: Halictidae). Heredity 87, 631–636 (2001).CAS 
    PubMed 

    Google Scholar 
    Darvill, B., Ellis, J. S., Lye, G. C. & Goulson, D. Population structure and inbreeding in a rare and declining bumblebee, Bombus muscorum (Hymenoptera: Apidae). Mol. Ecol. 15, 601–611 (2006).CAS 
    PubMed 

    Google Scholar 
    Hale, M. L., Burg, T. M. & Steeves, T. E. Sampling for microsatellite-based population genetic studies: 25 to 30 Individuals per population is enough to accurately estimate allele frequencies. PLoS One 7, e45170 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lenth, R. V. Least-squares means: The R package lsmeans. J. Stat. Softw. 69, 1–33 (2016).
    Google Scholar 
    Fitzpatrick, S. W. et al. Gene flow constrains and facilitates genetically based divergence in quantitative traits. Copeia 105, 462–474 (2017).
    Google Scholar 
    Price, T. D., Qvarnström, A. & Irwin, D. E. The role of phenotypic plasticity in driving genetic evolution. Proc. R. Soc. B Biol. Sci. 270, 1433–1440 (2003).
    Google Scholar 
    Liu, B.-J., Zhang, B.-D., Xue, D.-X., Gao, T.-X. & Liu, J.-X. Population structure and adaptive divergence in a high gene flow marine fish: The small yellow croaker (Larimichthys polyactis). PLoS One 11, e0154020 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Vaudo, A. D., Tooker, J. F., Grozinger, C. M. & Patch, H. M. Bee nutrition and floral resource restoration. Curr. Opin. Insect Sci. 10, 133–141 (2015).PubMed 

    Google Scholar 
    Woodard, S. H. & Jha, S. Wild bee nutritional ecology: Predicting pollinator population dynamics, movement, and services from floral resources. Curr. Opin. Insect Sci. 21, 83–90 (2017).PubMed 

    Google Scholar 
    Keller, L. F. & Waller, D. M. Inbreeding effects in wild populations. Trends Ecol. Evol. 17, 230–241 (2002).
    Google Scholar 
    Sivakoff, F. S. & Gardiner, M. M. Soil lead contamination decreases bee visit duration at sunflowers. Urban Ecosyst. 20, 1221–1228 (2017).
    Google Scholar 
    Whitehorn, P. R., Norville, G., Gilburn, A. & Goulson, D. Larval exposure to neonicotinoid imidacloprid impacts adult size in the farmland butterfly Pieris brassicae. PeerJ 6, e4772 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Merckx, T., Kaiser, A. & Van Dyck, H. Increased body size along urbanization gradients at both community and intraspecific level in macro-moths. Glob. Change Biol. 24, 3837–3848 (2018).ADS 

    Google Scholar 
    Oliveira, M. O., Brito, T. F., Campbell, A. J. & Contrera, F. A. L. Body size and corbiculae area variation of the stingless bee Melipona fasciculata Smith, 1854 (Apidae, Meliponini) under different levels of habitat quality in the eastern Amazon. Entomol. Gen. 39, 45–52 (2019).
    Google Scholar 
    Warzecha, D., Diekötter, T., Wolters, V. & Jauker, F. Intraspecific body size increases with habitat fragmentation in wild bee pollinators. Landsc. Ecol. 31, 1449–1455 (2016).
    Google Scholar 
    Theodorou, P., Baltz, L. M., Paxton, R. J. & Soro, A. Urbanization is associated with shifts in bumblebee body size, with cascading effects on pollination. Evol. Appl. 14, 53–68 (2021).PubMed 

    Google Scholar 
    Strange, J. P. & Tripodi, A. D. Characterizing bumble bee (Bombus) communities in the United States and assessing a conservation monitoring method. Ecol. Evol. 9, 1061–1069 (2019).PubMed 
    PubMed Central 

    Google Scholar  More

  • in

    Effect of nest composition, experience and nest quality on nest-building behaviour in the Bonelli’s Eagle

    Collias, N.E. & Collias, E.C. Nest Building and Bird Behavior. (Princeton University Press, 1984).Hansell, M.H. Bird nests and construction behaviour. (Cambridge University Press, 2000).Deeming, D.C. & Reynolds, S.J. Nests, eggs and incubation: New ideas about avian reproduction. (Oxford University Press, 2015).Pärssinen, V., Kalb, N., Vallon, M., Anthes, N. & Heubel, K. U. Male and female preferences for nest characteristics under paternal care. Ecol. Evol. 9, 7780–7791 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Soler, J. J., Morales, J., Cuervo, J. J. & Moreno, J. Conspicuousness of passerine females is associated with the nest-building behaviour of males. Biol. J. Linn. Soc. 126, 824–835 (2019).
    Google Scholar 
    Tipton, H. C., Dreitz, V. J. & Doherty, P. F. Jr. Occupancy of Mountain Plover and Burrowing Owl in Colorado. J. Wildl. Manage. 72, 1001–1006 (2008).
    Google Scholar 
    Mukherjee, A., Kumara, H. N. & Bhupathy, S. Golden jackal’s underground shelters: Natal site selection, seasonal burrowing activity and pup rearing by a cathemeral canid. Mammal Res. 63, 325–339 (2018).
    Google Scholar 
    Berg, M. L., Beintema, N. H., Welbergen, J. A. & Komdeur, J. The functional significance of multiple nest building in the Australian Reed Warbler Acrocephalus australis. Ibis 148, 395–404 (2006).
    Google Scholar 
    Vergara, P., Gordo, O. & Aguirre, J. I. Nest size, nest building behaviour and breeding success in a species with nest reuse: the white stork Ciconia ciconia. Ann. Zool. Fennici 47, 184–194 (2010).
    Google Scholar 
    Hansell, M.H. Animal architecture. (Oxford University Press, 2005).Newton, I. Population ecology of raptors. Berkhamsted (T and AD Poyser, 1979).Ontiveros, D., Caro, J. & Pleguezuelos, J. M. Green plant material versus ectoparasites in nests of Bonelli’s Eagle. J. Zool. 274, 99–104 (2008).
    Google Scholar 
    Soler, J. J., Møller, A. P. & Soler, M. Nest building, sexual selection and parental investment. Evol. Ecol. 12, 427–441 (1998).
    Google Scholar 
    Moreno, J., Soler, M., Møller, A. P. & Linden, M. The function of stone carrying in the Black Wheatear, Oenanthe leucura. Anim. Behav. 47, 1297–1309 (1994).
    Google Scholar 
    Soler, J. J., Soler, M., Møller, A. P. & Martínez, J. G. Does the great spotted cuckoo choose magpie hosts according to their parenting ability?. Behav. Ecol. Sociobiol. 36, 201–206 (1995).
    Google Scholar 
    Soler, J. J., Cuervo, J. J., Møller, A. P. & de Lope, F. Nest building is a sexually selected behaviour in the barn swallow. Anim. Behav. 56, 1435–1442 (1998).CAS 
    PubMed 

    Google Scholar 
    Canal, D., Mulero-Pázmány, M., Negro, J. J. & Sergio, F. Decoration increases the conspicuousness of raptor nests. PLoS ONE 11, e0157440 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Biddle, L., Goodman, A. M. & Deeming, D. C. Construction patterns of birds’ nests provide insight into nest-building behaviours. PeerJ 5, e3010 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Akresh, M. E., Ardia, D. R. & King, D. I. Effect of nest characteristics on thermal properties, clutch size, and reproductive performance for an open-cup nesting songbird. Avian Biol. Res. 10, 107–118 (2017).
    Google Scholar 
    Podofillini, S. et al. Home, dirty home: Effect of old nest material on nest-site selection and breeding performance in a cavity-nesting raptor. Curr. Zool. 64, 693–702 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Ruiz-Castellano, C., Tomás, G., Ruiz-Rodríguez, M., Martín-Gálvez, D. & Soler, J. J. Nest material shapes eggs bacterial environment. PLoS ONE 11, e0148894 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Tomás, G. et al. Interacting effects of aromatic plants and female age on nest-dwelling ectoparasites and blood-sucking flies in avian nests. Behav. Proc. 90, 246–253 (2012).
    Google Scholar 
    Suárez-Rodríguez, M. & García, C. M. An experimental demonstration that house finches add cigarette butts in response to ectoparasites. J. Avian Biol. 48, 1316–1321 (2017).
    Google Scholar 
    Mennerat, A. et al. Aromatic plants in nests of the blue tit Cyanistes caeruleus protect chicks from bacteria. Oecologia 161, 849–855 (2009).ADS 
    PubMed 

    Google Scholar 
    Sanz, J. J. & García-Navas, V. Nest ornamentation in blue tits: is feather carrying ability a male status signal?. Behav. Ecol. 22, 240–247 (2011).
    Google Scholar 
    Östlund-Nilsson, S. & Holmlund, M. The artistic three-spined stickleback (Gasterosteus aculeatus). Behav. Ecol. Sociobiol. 53, 214–220 (2003).
    Google Scholar 
    Quader, S. What makes a good nest? Benefits of nest choice to female Baya Weavers (Ploceus philippinus). Auk 123, 475–486 (2006).
    Google Scholar 
    Møller, A. P. & Nielsen, J. T. Large increase in nest size linked to climate change: an indicator of life history, senescence and condition. Oecologia 179, 913–921 (2015).ADS 
    PubMed 

    Google Scholar 
    De Neve, L., Soler, J. J., Soler, M. & Pérez-Contreras, T. Nest size predicts the effect of food supplementation to magpie nestlings on their immunocompetence: An experimental test of nest size indicating parental ability. Behav. Ecol. 15, 1031–1036 (2004).
    Google Scholar 
    Szentirmai, I., Komdeur, J. & Székely, T. What makes a nest-building male successful? Male behavior and female care in penduline tits. Behav. Ecol. 16, 994–1000 (2005).
    Google Scholar 
    Tomás, G. et al. Nest size and aromatic plants in the nest as sexually selected female traits in blue tits. Behav. Ecol. 24, 926–934 (2013).
    Google Scholar 
    Jelínek, V., Požgayová, M., Honza, M. & Procházka, P. Nest as an extended phenotype signal of female quality in the great reed warbler. J. Avian Biol. 47, 428–437 (2016).
    Google Scholar 
    Muth, F. & Healy, S. D. The role of adult experience in nest building in the zebrafinch, Taeniopygia guttata. Anim. Behav. 82, 185–189 (2011).
    Google Scholar 
    Wysocki, D. et al. Factors affecting nest size in a population of Blackbirds Turdus merula. Bird Study 62, 208–216 (2015).
    Google Scholar 
    Moreno, J. Avian nests and nest-building as signals. Avian Biol. Res. 5, 238–251 (2012).
    Google Scholar 
    Bailey, I. E., Morgan, K. V., Bertin, M., Meddle, S. L. & Healy, S. D. Physical cognition: Birds learn the structural efficacy of nest material. Proc. R. Soc. B 281, 20133225 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Camacho-Alpízar, A., Eckersley, T., Lambert, C. T., Balasubramanian, G. & Guillette, L. M. If it ain’t broke don’t fix it: Breeding success affects nest-building decisions. Behav. Proc. 184, 104336 (2021).
    Google Scholar 
    Madden, J. R. Bower decorations are good predictors of mating success in the spotted bowerbird. Behav. Ecol. Sociobiol. 53, 269–277 (2003).
    Google Scholar 
    Mainwaring, M. C., Nagy, J. & Hauber, M. E. Sex-specific contributions to nest building in birds. Behav. Ecol. https://doi.org/10.1093/beheco/arab035 (2021).Article 

    Google Scholar 
    Witte, K. The differential-allocation hypothesis: Does the evidence support it?. Evolution 49, 1289–1290 (1995).PubMed 

    Google Scholar 
    Wright, J. & Cuthill, I. Monogamy in the European starling. Behaviour 120, 262–285 (1992).
    Google Scholar 
    Burley, N. Sexual selection for aesthetic traits in species with biparental care. Am. Nat. 127, 415–445 (1986).ADS 

    Google Scholar 
    Mainwaring, M. C., Hartley, I. R., Lambrechts, M. M. & Deeming, D. C. The design and function of birds’ nests. Ecol. Evol. 4, 3909–3928 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Sergio, F. et al. Raptor nest decorations are a reliable threat against conspecifics. Science 331, 327–330 (2011).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Heinrich, B. Why does a hawk build with green nesting material?. Northeast. Nat. 20, 209–218 (2013).
    Google Scholar 
    Mingju, E. et al. Old nest material functions as an informative cue in making nest-site selection decisions in the European Kestrel (Falco tinnunculus). Avian Res. 10, 43 (2019).
    Google Scholar 
    Martínez-Abraín, A. & Jiménez, J. Stick supply to nests by cliff-nesting raptors as an evolutionary load of past tree-nesting. IEE 12, 22–25. https://doi.org/10.24908/iee.2019.12.3.n (2019).Article 

    Google Scholar 
    Martínez, J. E. et al. Breeding behaviour and time-activity budgets of Bonelli’s Eagles Aquila fasciata: Marked sexual differences in parental activities. Bird Study 47, 35–44 (2020).
    Google Scholar 
    Cramp, S. & Simmons, K.E.L. Handbook of the Birds of the western Palearctic. Vol. 2. (Oxford University Press, 1980).Paillisson, J. M. & Chambon, R. Variation in male-built nest volume with nesting-support quality, colony, and egg production in whiskered terns. Ecol. Evol. 11, 15585–15600 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    Álvarez, E. & Barba, E. Nest quality in relation to adult bird condition and its impact on reproduction in Great Tits Parus major. Acta Ornithol. 43, 3–9 (2008).
    Google Scholar 
    Ferguson-Lees, J. & Christie, D. Raptors of the world. (Christopher Helm, 2001).Ontiveros, D. Águila perdicera – Aquila fasciata. In Enciclopedia Virtual de los Vertebrados Españoles. (eds. Salvador, A. & Morales, M.B.) Museo Nacional de Ciencias Naturales, Madrid; http://www.vertebradosibericos.org/ (accessed 13 September 2021) (2016).Del Hoyo, J., Elliott, A. & Sargatal, J. Handbook of the birds of the world, vol. 2. New world vultures to guineafowl. (Lynx Edicions, 1994).Ontiveros, D., Caro, J. & Pleguezuelos, J. M. Possible functions of alternative nests in raptors: the case of Bonelli’s Eagle. J. Ornithol. 149, 253–259 (2008).
    Google Scholar 
    Del Moral, J.C. & Molina, B. El águila perdicera en España, población reproductora en 2018 y método de censo. (SEO/BirdLife, 2018).BirdLife International. Aquila fasciata (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2019. https://doi.org/10.2305/IUCN.UK.2019-3.RLTS.T22696076A155464015.en. Downloaded on 26 June 2021 (2019).Balbontín, J. & Ferrer, M. Condition of large brood in Bonelli’s Eagle Hieraaetus fasciatus. Bird Study 52, 37–41 (2005).
    Google Scholar 
    Martínez, J. E. et al. Copulatory behaviour in the Bonelli’s Eagle (Aquila fasciata): assessing the paternity assurance hypothesis. PLoS ONE 14, e0217175 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Margalida, A. & Bertran, J. Nest-building behaviour of the Bearded Vulture Gypaetus barbatus. Ardea 88, 259–264 (2000).
    Google Scholar 
    Krüger, O. Dissecting common buzzard lifespan and lifetime reproductive success: the relative importance of food, competition, weather, habitat and individual attributes. Oecologia 133, 474–482 (2002).ADS 
    PubMed 

    Google Scholar 
    Morrison, T. A., Yoshizaki, J., Nichols, J. D. & Bolger, D. T. Estimating survival in photographic capture–recapture studies: overcoming misidentification error. Methods Ecol. Evol. 2, 454–463 (2011).
    Google Scholar 
    Jiménez-Franco, M. V., Martínez, J. E., Pagán, I. & Calvo, J. F. Factors determining territory fidelity in a migratory forest raptor, the Booted Eagle Hieraaetus pennatus. J. Ornithol. 154, 311–318 (2013).
    Google Scholar 
    Sreekar, R. et al. Photographic capture-recapture sampling for assessing populations of the Indian Gliding Lizard Draco dussumieri. PLoS ONE 8, e55935 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Goswami, V. R. et al. Towards a reliable assessment of Asian elephant population parameters: The application of photographic spatial capture–recapture sampling in a priority floodplain ecosystem. Sci. Rep. 9, 8578 (2019).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Méndez, D., Marsden, S. & Lloyd, H. Assessing population size and structure for Andean Condor Vultur gryphus in Bolivia using a photographic ‘capture-recapture’ method. Ibis 161, 867–877 (2019).
    Google Scholar 
    Zuberogoitia, J., Martínez, J. E. & Zabala, J. Individual recognition of territorial peregrine falcons Falco peregrinus: A key for long-term monitoring programmes. Munibe 61, 117–127 (2013).
    Google Scholar 
    Gil-Sánchez, J. M., Bautista, J., Godinho, R. & Moleón, M. Detection of individual replacements in a long-lived bird species, the Bonelli’s Eagle (Aquila fasciata), using three noninvasive methods. J. Raptor Res. https://doi.org/10.3356/JRR-20-53 (2021).Article 

    Google Scholar 
    García, V., Moreno-Opo, R. & Tintó, A. Sex differentiation of Bonelli’s Eagle Aquila fasciata in western Europe using morphometrics and plumage colour patterns. Ardeola 60, 261–277 (2013).
    Google Scholar 
    Real, J., Mañosa, S. & Codina, J. Post-nestling dependence period in the Bonelli’s Eagle Hieraaetus fasciatus. Ornis Fenn. 75, 129–137 (1998).
    Google Scholar 
    Mínguez, E., Angulo, E. & Siebering, V. Factors influencing length of the post-fledging period and timing of dispersal in Bonelli’s Eagle (Hieraaetus fasciatus) in southwestern Spain. J. Raptor Res. 35, 228–234 (2001).
    Google Scholar 
    Gil-Sánchez, J. M., Moleón, M., Otero, M. & Bautista, J. A nine-year study of successful breeding in a Bonelli’s eagle population in southeast Spain: A basis for conservation. Biol. Conserv. 118, 685–694 (2004).
    Google Scholar 
    Resano-Mayor, J. et al. Multi-scale effects of nestling diet on breeding performance in a terrestrial top predator inferred from stable isotope analysis. PLoS ONE 9, e95320 (2014).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zuberogoitia, J., Martínez, J. E., Larrea, M. & Zabala, M. Parental investment of male Peregrine Falcons during incubation: Influence of experience and weather. J. Ornithol. 159, 275–282 (2018).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing. Available at: http://www.R-project.org/ (accessed 20 March 2021) (2021).Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).
    Google Scholar 
    Fernández, C. Nest material supplies in the Marsh Harrier Circus aeruginosus: Sexual roles, daily and seasonal activity patterns and rainfall influence. Ardea 80, 281–284 (1992).
    Google Scholar 
    Margalida, A., González, L. M., Sánchez, R., Oria, J. & Prada, L. Parental behaviour of Spanish Imperial Eagles Aquila adalberti: sexual differences in a moderately dimorphic raptor. Bird Study 54, 112–119 (2007).
    Google Scholar 
    López-López, P., Perona, A. M., Egea-Casas, O., Morant, J. & Urios, V. Tri-axial accelerometry shows differences in energy expenditure and parental effort throughout the breeding season in long-lived raptors. Curr. Zool. https://doi.org/10.1093/cz/zoab010 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Morant, J., López-López, P. & Zuberogoitia, I. Parental investment asymmetries of a globally endangered scavenger: Unravelling the role of gender, weather conditions and stage of the nesting cycle. Bird Study 66, 329–341 (2019).
    Google Scholar 
    Margalida, A. & Bertran, J. Breeding biology of the Bearded Vulture Gypaetus barbatus: Minimal sexual differences in parental activities. Ibis 142, 225–234 (2000).
    Google Scholar 
    Wimberger, P. H. The use of green plant material in bird nests to avoid ectoparasites. Auk 101, 615–618 (1984).
    Google Scholar 
    Dubiec, A., Gózdz, I. & Mazgagski, T. D. Green plant material in avian nests. Avian Biol. Res. 6, 133–146 (2013).
    Google Scholar 
    Jagiello, Z. A., Dylewski, L., Winiarska, D., Zolnierowicz, K. M. & Tobolka, M. Factors determining the occurrence of anthropogenic materials in nests of the white stork Ciconia ciconia. Environ. Sci. Pollut. Res. 25, 14726–14733 (2018).
    Google Scholar 
    Fargallo, J. A., de León, A. & Potti, J. Nest maintenance effort and health status in chinstrap penguins, Pygoscelis antarctica: the functional significance of stone provisioning behaviour. Behav. Ecol. Sociobiol. 50, 141–150 (2001).
    Google Scholar  More

  • in

    Forest soil biotic communities show few responses to wood ash applications at multiple sites across Canada

    Hannam, K. D. et al. Wood ash as a soil amendment in Canadian forests: what are the barriers to utilization?. Can. J. For. Res. 48, 442–450 (2018).
    Google Scholar 
    Hope, E. S., McKenney, D. W., Allen, D. J. & Pedlar, J. H. A cost analysis of bioenergy-generated ash disposal options in Canada. Can. J. For. Res. https://doi.org/10.1139/cjfr-2016-0524 (2017).Article 

    Google Scholar 
    Bowd, E. J., Banks, S. C., Strong, C. L. & Lindenmayer, D. B. Long-term impacts of wildfire and logging on forest soils. Nat. Geosci. 12, 113–118 (2019).ADS 
    CAS 

    Google Scholar 
    Adotey, N., Harrell, D. L. & Weatherford, W. P. Characterization and liming effect of wood Ash generated from a biomass-fueled commercial power plant. Commun. Soil Sci. Plan. 49, 38–49 (2018).CAS 

    Google Scholar 
    Royer-Tardif, S., Whalen, J. & Rivest, D. Can alkaline residuals from the pulp and paper industry neutralize acidity in forest soils without increasing greenhouse gas emissions?. Sci. Total Environ. 663, 537–547 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Reid, C. & Watmough, S. A. Evaluating the effects of liming and wood-ash treatment on forest ecosystems through systematic meta-analysis. Can. J. For. Res. 44, 867–885 (2014).CAS 

    Google Scholar 
    López, R., Díaz, M. J. & González-Pérez, J. A. Extra CO2 sequestration following reutilization of biomass ash. Sci. Total Environ. 625, 1013–1020 (2018).ADS 
    PubMed 

    Google Scholar 
    Emilson, C. E. et al. Short-term growth response of jack pine and spruce spp. to wood ash amendment across Canada. GCB Bioenergy 12, 158–167 (2020).
    Google Scholar 
    Azan, S. S. E. et al. Could a residential wood ash recycling programme be part of the solution to calcium decline in lakes and forests in Muskoka (Ontario, Canada)?. FACETS 4, 69–90 (2019).
    Google Scholar 
    Gorgolewski, A. et al. Responses of eastern red-backed salamander (Plethodon cinereus) abundance 1 year after application of wood ash in a northern hardwood forest. Can. J. For. Res. 46, 402–409 (2016).
    Google Scholar 
    McTavish, M. J., Gorgolewski, A., Murphy, S. D. & Basiliko, N. Field and laboratory responses of earthworms to use of wood ash as a forest soil amendment. For. Ecol. Manag. 474, 118376 (2020).
    Google Scholar 
    Mortensen, L. H., Rønn, R. & Vestergård, M. Bioaccumulation of cadmium in soil organisms: with focus on wood ash application. Ecotox. Environ. Safe. 156, 452–462 (2018).CAS 

    Google Scholar 
    Bélanger, N., Palma Ponce, G. & Brais, S. Contrasted growth response of hybrid larch (Larix × marschlinsii), jack pine (Pinus banksiana) and white spruce (Picea glauca) to wood ash application in northwestern Quebec, Canada. iForest. 14, 155 (2021).
    Google Scholar 
    Santás-Miguel, V. et al. Use of biomass ash to reduce toxicity affecting soil bacterial community growth due to tetracycline antibiotics. J. Environ. Manage. 269, 110838 (2020).PubMed 

    Google Scholar 
    Fritze, H. et al. A microcosmos study on the effects of cd-containing wood ash on the coniferous humus fungal community and the cd bioavailability. J Soils Sediments 1, 146–150 (2001).CAS 

    Google Scholar 
    Coleman, D., Callaham, Jr., M. A. & Crossley, Jr., D. A. Fundamentals of Soil Ecology. (Elsevier, 2018). https://doi.org/10.1016/C2015-0-04083-7.Smenderovac, E. E. et al. Does intensified boreal forest harvesting impact soil microbial community structure and function?. Can. J. For. Res. 47, 916–925 (2017).CAS 

    Google Scholar 
    Joseph, R. et al. Limited effect of wood ash application on soil quality as indicated by a multisite assessment of soil organic matter attributes. GCB Bioenergy. 00, 1–22. https://doi.org/10.1111/gcbb.12928 (2022).CAS 
    Article 

    Google Scholar 
    Noyce, G. L. et al. Soil microbial responses to wood ash addition and forest fire in managed Ontario forests. Appl. Soil Ecol. 107, 368–380 (2016).
    Google Scholar 
    Liiri, M., Ilmarinen, K. & Setälä, H. Variable impacts of enchytraeid worms and ectomycorrhizal fungi on plant growth in raw humus soil treated with wood ash. Appl. Soil Ecol. 35, 174–183 (2007).
    Google Scholar 
    Brais, S., Bélanger, N. & Guillemette, T. Wood ash and N fertilization in the Canadian boreal forest: Soil properties and response of jack pine and black spruce. For. Ecol. Manag. 348, 1–14 (2015).
    Google Scholar 
    Gömöryová, E., Pichler, V., Tóthová, S. & Gömöry, D. Changes of chemical and biological properties of distinct forest floor layers after wood ash application in a Norway spruce stand. Forests 7, 108 (2016).
    Google Scholar 
    Hannam, K., Great Lakes Forestry Centre, Canada, Ressources naturelles Canada & Canadian Forest Service. Regulations and guidelines for the use of wood ash as a soil amendment in Canadian forests. (2016).Hannam, K. D. et al. AshNet: Facilitating the use of wood ash as a forest soil amendment in Canada. Forest. Chron. 93, 17–20 (2017).
    Google Scholar 
    Klavina, D. et al. The ectomycorrhizal community of conifer stands on peat soils 12 years after fertilization with wood ash. Mycorrhiza 26, 153–160 (2016).PubMed 

    Google Scholar 
    Bang-Andreasen, T. et al. Wood ash induced pH changes strongly affect soil bacterial numbers and community composition. Front. Microbiol. 8, 1400 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Vestergård, M. et al. The relative importance of the bacterial pathway and soil inorganic nitrogen increase across an extreme wood-ash application gradient. GCB Bioenergy 10, 320–334 (2018).
    Google Scholar 
    Ekenler, M. & Tabatabai, M. A. β-glucosaminidase activity as an index of nitrogen mineralization in soils. Commun. Soil Sci. Plan. 35, 1081–1094 (2004).CAS 

    Google Scholar 
    Margalef, O. et al. Global patterns of phosphatase activity in natural soils. Sci Rep 7, 1337 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vestergaard, G., Schulz, S., Schöler, A. & Schloter, M. Making big data smart—how to use metagenomics to understand soil quality. Biol. Fertil. Soils 53, 479–484 (2017).
    Google Scholar 
    Emilson, C. et al. Synthesis of current AshNet study designs and methods with recommendations towards a standardized protocol. Information Report GLC-X-22. (2018).Baldwin, K. et al. Vegetation zones of Canada: A biogeoclimatic perspective – Open Government Portal. (2019).Findlay, S. CHAPTER 11: Dissolved organic matter. In: Methods in Stream Ecology (Second Edition) (eds. Hauer, F. R. & Lamberti, G. A.) 239–248 (Academic Press, 2007). https://doi.org/10.1016/B978-012332908-0.50013-9.Saiya-Cork, K. R., Sinsabaugh, R. L. & Zak, D. R. The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biol. Biochem. 34, 1309–1315 (2002).CAS 

    Google Scholar 
    Porter, T. M. & Hajibabaei, M. METAWORKS: A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments. bioRxiv 2020.07.14.202960 (2020) https://doi.org/10.1101/2020.07.14.202960.Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Porter, T. M. & Hajibabaei, M. Automated high throughput animal CO1 metabarcode classification. Sci. Rep-UK 8, 4226 (2018).ADS 

    Google Scholar 
    Kõljalg, U., Abarenkov, K., Nilsson, R. H., Larsson, K. & Taylor, A. F. S. The UNITE Database for molecular identification and for communicating fungal species (2019). https://doi.org/10.3897/BISS.3.37402.Porter, T. M. UNITE ITS Classifier. (2020). https://github.com/terrimporter/UNITE_ITSClassifierLouca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).ADS 
    CAS 

    Google Scholar 
    Nguyen, N. H. et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
    Google Scholar 
    Hedde, M. et al. BETSI, a complete framework for studying soil invertebrate functional traits. (2012). https://doi.org/10.13140/2.1.1286.6888.McKenney, D. W. et al. Customized spatial climate models for North America. Bull. Am. Meteor. Soc. 92, 1611–1622 (2011).ADS 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2021).Fernandes, A. D., Macklaim, J. M., Linn, T. G., Reid, G. & Gloor, G. B. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLOS ONE 8, 15 (2013).
    Google Scholar 
    Wickham, H. et al. Welcome to the {tidyverse}. J. Open Source Softw. 4, 1686 (2019).ADS 

    Google Scholar 
    Oksanen, J. et al. Vegan: Community ecology package. https://CRAN.R-project.org/package=vegan (2020).Domes, K. A. et al. Short-term changes in spruce foliar nutrients and soil properties in response to wood ash application in the sub-boreal climate zone of British Columbia. Can. J. Soil. Sci. 98, 246–263 (2018).CAS 

    Google Scholar 
    Pugliese, S. et al. Wood ash as a forest soil amendment: The role of boiler and soil type on soil property response. Can. J. Soil. Sci. 94, 621–634 (2014).CAS 

    Google Scholar 
    Bang-Andreasen, T. et al. Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil. FEMS Microbiol. Ecol. 96, fiaa016 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    Haimi, J., Fritze, H. & Moilanen, P. Responses of soil decomposer animals to wood-ash fertilisation and burning in a coniferous forest stand. For. Ecol. Manag. 129, 53–61 (2000).
    Google Scholar 
    Aronsson, K. A. & Ekelund, N. G. A. Biological effects of wood ash application to forest and aquatic ecosystems. J. Environ. Qual. 33, 1595–1605 (2004).CAS 
    PubMed 

    Google Scholar 
    Omil, B., Piñeiro, V. & Merino, A. Trace elements in soils and plants in temperate forest plantations subjected to single and multiple applications of mixed wood ash. Sci. Total Environ. 381, 157–168 (2007).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Taylor, A. F. S. & Finlay, R. D. Effects of liming and ash application on below ground ectomycorrhizal community structure in two Norway spruce forests. WAFO 3, 63–76 (2003).CAS 

    Google Scholar 
    Wallander, H., Fossum, A., Rosengren, U. & Jones, H. Ectomycorrhizal fungal biomass in roots and uptake of P from apatite by Pinus sylvestris seedlings growing in forest soil with and without wood ash amendment. Mycorrhiza 15, 143–148 (2005).PubMed 

    Google Scholar 
    Kjøller, R., Cruz-Paredes, C. & Clemmensen, K. E. Ectomycorrhizal fungal responses to forest liming and wood ash addition: Review and meta-analysis. In Soil Biological Communities and Ecosystem Resilience (eds Lukac, M. et al.) 223–252 (Springer International Publishing, Berlin, 2017).
    Google Scholar 
    Peltoniemi, K., Pyrhönen, M., Laiho, R., Moilanen, M. & Fritze, H. Microbial communities after wood ash fertilization in a boreal drained peatland forest. Eur. J. Soil Biol. 76, 95–102 (2016).CAS 

    Google Scholar 
    Boisvert-Marsh, L., Great Lakes Forestry Centre, Canada & Resources naturelles Canada. The Island Lake biomass harvest experiment: early results. (2016).Couch, R. L., Luckai, N., Morris, D. & Diochon, A. Short-term effects of wood ash application on soil properties, growth, and foliar nutrition of Picea mariana and Picea glauca seedlings in a plantation trial. Can. J. Soil. Sci. 101, 203–215 (2021).CAS 

    Google Scholar 
    Perkiömäki, J. & Fritze, H. Cadmium in upland forests after vitality fertilization with wood ash—a summary of soil microbiological studies into the potential risk of cadmium release. Biol Fertil Soils 41, 75–84 (2005).
    Google Scholar 
    Paredes, C. et al. Bacteria respond stronger than fungi across a steep wood ash-driven pH gradient. Front. For. Glob. Change 4, 781884 (2021).
    Google Scholar 
    Kļaviņa, D. et al. Fungal communities in roots of scots pine and Norway spruce saplings grown for 10 years on peat soils fertilized with wood ash. Balt. For. 22, 10 (2016).
    Google Scholar 
    Hansen, M., Bang-Andreasen, T., Sørensen, H. & Ingerslev, M. Micro vertical changes in soil pH and base cations over time after application of wood ash on forest soil. For. Ecol. Manag. 406, 274–280 (2017).
    Google Scholar 
    Fu, X. et al. Understory vegetation leads to changes in soil acidity and in microbial communities 27years after reforestation. Sci. Total Environ. 502, 280–286 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Pitman, R. M. Wood ash use in forestry – a review of the environmental impacts. Forestry 79, 563–588 (2006).
    Google Scholar 
    Cruz-Paredes, C., Tájmel, D. & Rousk, J. Can moisture affect temperature dependences of microbial growth and respiration?. Soil Biol. Biochem. 156, 108223 (2021).CAS 

    Google Scholar  More

  • in

    Fast-decaying plant litter enhances soil carbon in temperate forests but not through microbial physiological traits

    Microcosm preparation and incubationLeaf litters were collected from Lilly-Dickey Woods, a mature eastern US temperate broadleaf forest located in South-Central Indiana (39°14′N, 86°13′W) using litter baskets and surveys for freshly senesced litter as described in Craig et al.52. Of the 19 species collected in Craig et al. (2018), we selected litter from 16 tree species with the goal of maximizing variation in litter chemical traits (Table S1). Litters were air-dried and then homogenized and fragmented such that all litter fragments passed a 4000 µm, but not a 250 µm mesh. Whereas leaf litters had a distinctly C3 δ13C signature of −30.1 ± 1.5 (mean, standard deviation), we used a 13C-rich (δ13C = −12.6 ± 0.4) soil obtained from the A horizon of a 35-yr continuous corn field at the Purdue University Agronomy Center for Research and Education near West Lafayette, Indiana (40°4′N, 86°56′W). The soil is classified as Chalmers silty clay loam (a fine-silty, mixed, superactive, mesic Typic Endoaquoll). Prior to use in the incubation, soils were sieved (2 mm) and remaining recognizable plant residues were thoroughly picked out. Soils were mixed with acid-washed sand—30% by mass—to facilitate litter mixing (see below) and to increase the soil volume for post-incubation processing. The resulting soil had a pH of 6.7 and a C:N ratio of 12.0.We constructed the experimental microcosms by mixing the 16 litter species with the 13C-enriched soil. Each litter treatment was replicated four times in four batches (i.e., 16 microcosms per species, 272 total microcosms including 16 soil-only controls). Two batches (C budget microcosms) were used to monitor CO2 efflux and to track litter-derived C into SOM pools, and two batches were used to quantify microbial biomass dynamics.Incubations were carried out in 50 mL centrifuge tubes modified with an O-ring to prevent leakage and a rubber septum to facilitate headspace sampling. To each microcosm, we added 5 g dry soil, adjusted moisture to 65% water-holding capacity, and pre-incubated for 24 h in the dark at 24 °C. Using a dissecting needle, 300 mg of leaf litter were carefully mixed into treatment microcosms and controls were similarly agitated. This corresponds to an average C addition rate of 27.1 ± 1.1 g C kg−1 dry soil among the 16 species. During incubation, microcosms were loosely capped to retain moisture while allowing gas exchange, and were maintained at 65% water-holding capacity by adding deionized water every week.Carbon budget in microcosmsRespiration was quantified with an infrared gas analyzer (LiCOR 6262, Lincoln, NE, USA) coupled to a sample injection system. Our first measurement was taken about 12 h after litter addition (day 1) and subsequent measurements were taken on days 2, 4, 11, 19, and 30 for both batches and on days 46, 64, 79, 92, 109, 128, 149, and 185 for the second batch. Prior to each measurement, microcosms were capped, flushed with CO2-free air, and incubated for 1–8 h depending on the expected efflux rate. Headspace was sampled with a gas-tight syringe and the CO2-C concentration was converted to a respiration rate (µg CO2-C day−1). Total cumulative CO2-C loss was derived from point measurements by numerical integration (i.e., the trapezoid method). To evaluate soil-derived CO2-C efflux, we measured δ13C in two gas samples per litter type or control on a ThermoFinnigan DELTA Plus XP isotope ratio mass spectrometer (IRMS) with a GasBench interface (Thermo Fisher Scientific, San Jose, CA). Isotopes were measured on days 1, 4, 11, 30, 64, 109, and 185. On each of these days, a two-source mixing model70 was applied to determine the fraction of total CO2-C derived from soil organic matter vs. litter:$$frac{{F}^{l}(t)}{F(t)}=frac{delta Fleft(tright)-,delta {F}^{c}(t)}{delta {C}_{l}-delta {F}^{c}(t)}$$
    (1)
    where (frac{{F}^{l}(t)}{F(t)}) is the fraction total CO2-C efflux [(F(t))] derived from litter [({F}^{l}(t))] at time (left(tright)), (delta Fleft(tright)) is the δ13C of the CO2 respired by each litter-soil combination, (delta {F}^{c}(t)) is the average δ13C of the CO2 respired by the control soil, and (delta {C}_{l}) is the δ13C of each litter type. These data were used to calculate cumulative soil-derived C efflux via numerical integration and, for each litter type, average soil-derived C efflux was subtracted from total cumulative CO2-C loss to determine cumulative litter-derived CO2-C loss.Carbon budget microcosms were harvested on days 30 and 185 to track litter-derived C into mineral-associated SOC at an early and intermediate stage of decomposition. To do this, we used a size fractionation procedure71,72 modified to minimize the recovery of soluble leaf litter compounds or dissolved organic matter in the mineral-associated SOC fraction. For each sample, we first added 30 mL deionized water, gently shook by hand to suspend all particles, and then centrifuged (2500 rpm) for 10 min. Floating leaf litter was carefully removed, dried for 48 h at 60 °C, and weighed; and the clear supernatant was discarded to remove the dissolved organic matter. The remaining sample was dispersed in 5% (w/v) sodium hexametaphosphate for 20 h on a reciprocal shaker and then washed through a 53 µm sieve. The fraction retained on the sieve was added to the floating leaf litter sample and collectively referred to as particulate SOC, while the fraction that passed through the sieve was considered the mineral-associated SOC. Both fractions were dried, ground, and weighed; and analyzed for C concentrations and δ13C values on an elemental combustion system (Costech ECS 4010, Costech Analytical Technologies, Valencia, CA, USA) as an inlet to an IRMS. As above, litter-derived C in the particulate and mineral-associated SOC was determined as follows:$$frac{{C}_{s}^{l}(t)}{{C}_{s}(t)}=frac{delta {C}_{s}left(tright)-,delta {C}_{c}(t)}{delta {C}_{l}-delta {C}_{c}(t)}$$
    (2)
    where ({C}_{s}(t)) is the total particulate or mineral-associated SOC content in the sample at time ((t)), ({C}_{s}^{l}(t)) is the litter-derived C in the soil, (delta {C}_{s}left(tright)) is the measured δ13C value for each soil fraction, (delta {C}_{c}left(tright)) is the average δ13C for each fraction in control samples, and (delta {C}_{l}) is the δ13C of each litter type. In a few cases, mineral-associated δ13C was slightly less negative in the treatment than in the control soil. In these cases, litter-derived mineral-associated SOC was considered zero.Total litter-derived SOC at each harvest date was calculated by subtracting the cumulative litter CO2-C from initial added litter C. The difference between this value and the sum of litter-derived particulate and mineral-associated SOC was considered the residual pool which we assume mostly represents water-extractable dissolved organic matter.Microbial biomass dynamics during incubationSample batches were harvested at days 15 and 100 to capture early- and intermediate-term microbial biomass responses to litter treatments. These times were selected to correspond with the middle of early and intermediate C budget microcosm incubations. We quantified microbial biomass as well as MGR, CUE, and MTR using 18O-labeled water73,74 as in Geyer et al.75.Microbial biomass C (MBC) was determined on two ~2 g subsamples using a standard chloroform fumigation extraction76. One subsample was immediately extracted in 0.5 M K2SO4 and one was fumigated for 72 h before extraction. After shaking for 1 h, extracts were gravity filtered through a Whatman No. 40 filter paper, and filtrates were analyzed for total organic C using the method of Bartlett and Ross77 as adapted by Giasson et al.78. The difference between total organic C in the fumigated and unfumigated subsamples was used to calculate MBC (extraction efficiency KEC = 0.45).To determine MGR, CUE, and MTR, we first pre-incubated two 0.5 g soil subsamples (one treatment and one control) for 2 d at 24 °C. Prior to this pre-incubation, samples were allowed to evaporate down to 53 ± 6% (mean, sd) water-holding capacity. After the pre-incubation, water was injected with a 25 µL syringe to bring each sample to 65% water-holding capacity. For one subsample, we used unlabeled deionized water. For the second subsample, enriched 18O-water (98.1 at%; ICON Isotopes) was mixed with unlabeled deionized H2O to achieve approximately 20 at% of 18O in the final soil water. Each sample was placed in a centrifuge tube (modified for gas sampling), flushed with CO2-free air, and incubated for 24 h. Headspace CO2 concentration was then measured, and samples were flash frozen in liquid N2 and stored at −80 °C until DNA extraction.DNA was extracted from each sample using a DNA extraction kit (Qiagen DNeasy PowerSoil Kit, Venlo, Netherlands) following the protocol described in Geyer et al. (2019) which sought to maximize the recovery of DNA. The DNA concentration was determined fluorometrically using a Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen). DNA extracts (80 µL) were dried at 60 °C in silver capsules spiked with 100 µL of salmon sperm DNA (42.5 ng µL−1), to reach the oxygen detection limit, and sent to the UC Davis Stable Isotope Facility for quantification of δ18O and total O content.Microbial growth rate (MGR) was calculated following Geyer et al. (2019). Specifically, atom % of soil DNA O (at% ODNA) was determined using the two-pool mixing model:$${at} % ,{O}_{{DNA}}=,frac{left[left({at} % ,{O}_{{DN}A+{ss}}times {O}_{{DNA}+{ss}}right)-left({at} % ,{O}_{{ss}}times {O}_{{ss}}right)right]}{{O}_{{DNA}}},$$
    (3)
    where at% is the atom % 18O and ODNA+ss, ODNA, and Oss are the concentration of O in the whole sample, soil DNA, and salmon sperm, respectively. Atom percent excess of soil DNA oxygen (APE Osoil) was calculated as the difference between at% ODNA in the treatment and control samples. Total microbial growth in terms of O (Total O; µg) was estimated as:$${Total},O=frac{{O}_{{soil}}times ,{{APE},O}_{{soil}}}{{at} % ,{soil},{water}}$$
    (4)
    where at% soil water is the atom % 18O in the soil water. MGR in terms of C (µg C g−1 soil d−1) was calculated by applying conversion mass ratios of oxygen:DNA (0.31) and MBC:DNA for each sample, dividing by the soil mass, and scaling by the incubation time. Assuming uptake rate (Uptake) is equal to the sum of MGR and respiration, CUE and MTR were calculated by the following equations.$${CUE}=,frac{{MGR}}{{Uptake}},$$
    (5)
    $${MTR}=,frac{{MGR}}{{MBC}}$$
    (6)
    Data analysis for microcosm experimentLitter decay constants were calculated for each species using litter-derived CO2-C values to estimate litter mass loss over time. After it was determined that a single exponential decay model provided a poor fit, we fit litter decomposition data using the double exponential decay model:$$y=s{e}^{{-k}_{1}t}+(1-s){e}^{{-k}_{2}t}$$
    (7)
    where s represents the labile or early stage decomposition fraction that decomposes at rate k1, and k2 is the decay constant for the remaining late stage decomposition fraction.To reduce the dimensionality of litter quality and microbial indicators, indices were derived by principal component analysis (PCA; Fig. S1A, B) using the ‘prcomp’ function in R. The first axis of a PCA of decomposition parameters (s, k1, and k2) and litter chemical properties (soluble and AUR contents; AUR-to-N and C-to-N ratios; and the lignocellulose index [LCI]) was taken as a litter quality index. Whereas this index highly correlated with indicators of C quality (AUR, soluble content, and LCI), the second axis of this PCA correlated with C:N and AUR:N and was therefore taken as a second litter quality index representing variation in N concentration. The first axis of a PCA of MGR, CUE, and MTR was taken as a microbial physiological trait index.Bivariate relationships were examined using simple linear regressions on average species values at each harvest (n = 16). To examine relationships between microbial physiological traits and mineral-associated SOC, data from the early-term (day 15) and intermediate-term (day 100) microbial harvest were matched with early-term (day 30) and intermediate-term (day 185) C budget microcosms, respectively. In addition to examining total mineral-associated SOC formation, we also estimated the efficiency of litter C transfer into the mineral-associated SOC pool as the fraction of lost litter C (i.e., litter C lost as CO2, recovered in the mineral-associated SOC fraction, or in the residual pool) retained in the mineral-associated SOC. Path analyses were used to evaluate the hypothesis that microbial physiological traits mediate the effect of litter quality on mineral-associated SOC formation and mineral-associated and particulate SOC decay. We hypothesized that the litter quality index would be positively associated with the microbial physiological trait index (representing faster and more efficient microbial growth) and microbial physiological traits would, in turn, be positively associated with the rate and efficiency of mineral-associated SOC formation. We expected that this mediating pathway would reduce the direct relationship between litter quality and SOC. This analysis was conducted using the LAVAAN package79 to run path analyses for total litter-derived mineral-associated SOC, mineral-associated SOC formation efficiency, and soil-derived mineral-associated and particulate SOC for both early and intermediate stage harvests. All analyses were performed using R version 3.5.2.Field study design and soil samplingWe worked in the Smithsonian’s Forest Global Earth Observatory (ForestGEO) network80 in six mature U.S. temperate forests varying in climate, soil properties, and tree community composition (Fig. 1a): Harvard forest (HF; 42°32′N, 72°11′W) in North-Central Massachusetts, Lilly-Dickey Woods (LDW; 39°14’N, 86°13’W) in South-Central Indiana, the Smithsonian Conservation Biology Institute (SCBI; 38°54′N, 78°9′W) in Northern Virginia, the Smithsonian Environmental Research Center (SERC; 38°53′N, 76°34′W) on the Chesapeake Bay in Maryland, Tyson Research Center (TRC; 38°31′N, 90°33′W) in Eastern Missouri, and Wabikon Lake Forest (WLF; 45°33′N, 88°48′W) in Northern Wisconsin, USA. Land use history across the six sites consisted mostly of timber harvesting which ceased in the early 1900s. Soils are mostly Oxyaquic Dystrudepts at HF, Typic Dystrudepts and Typic Hapludults at LDW, Typic Hapludalfs at SCBI, Typic or Aquic Hapludults at SERC, Typic Hapludalfs and Typic Paleudalfs at TRC, and Typic and Alfic Haplorthods at WLF. Further site details are reported in Table S5.Each site contains a rich assemblage of co-occurring arbuscular mycorrhizal (AM)- and ectomycorrhizal (ECM)-associated trees (Table S6), which we leveraged to generate environmental gradients in factors hypothesized to predict microbial physiological traits within each site. Specifically, the dominance of AM vs. ECM trees within a temperate forest plot has been shown to be a strong predictor of soil pH, C:N, inorganic N availability, and litter quality52,53,54. We established nine 20 × 20 m plots in each of our six sites in Fall 2016 (n = 54) distributed along a gradient of AM- to ECM-associated tree dominance. Plots were selected to avoid obvious confounding environmental factors. Where possible, we established our nine-plot gradient in three blocks (5 cm) at HF, which was removed before coring. Samples were also collected at 5–15 cm depth for soil texture analysis. We sampled from an inner 10 × 10 m square in each plot to avoid edge effects. All samples from the same plot were composited, sieved (2 mm), picked free of roots, subsampled for gravimetric moisture (105 °C), and air-dried, or refrigerated (4 °C) until analysis for microbial physiological variables and N availability.Soil propertiesWe determined several physicochemical properties known to predict mineral-associated SOC. We measured soil pH (8:1 ml 0.01 M CaCl2:g soil) and soil texture using a benchtop pH meter and a standard hydrometer procedure82, respectively. Organic matter content was high in some upper surface soils, so plot-level soil texture was determined from 5 to 15 cm depth samples. We quantified oxalate-extractable Al and Fe pools (Alox and Feox) in all soil samples as an index of poorly crystalline Al- and Fe-oxides83, which is one of the strongest predictors of SOM content in temperate forests84. Briefly, we extracted 0.40 g dried, ground soil in 40 mL 0.2 M NH4-oxalate at pH 3.0 in the dark for 4 h before gravity filtering and refrigerating until analysis (within 2 w) on an atomic-adsorption spectrometer (Aanalyst 800, Perkin Elmer, Waltham, MA, USA), using an acetylene flame and a graphite furnace for the atomization of Fe and Al, respectively.We quantified potential net N mineralization rates as an index of soil N availability. One 5 g subsample per plot was extracted immediately after processing by adding 10 mL 2 M KCl, shaking for 1 h, and filtering through a Whatman No. 1 filter paper after centrifugation at 3000 rpm. A second subsample from each plot was incubated under aerobic conditions at field moisture and 23 °C for 14 d before extraction. Extracts were frozen (−20 °C) until analysis for NH4+-N using the salicylate method and for NO3−-N plus NO2−-N after a cadmium column reduction on a Lachat QuikChem 8000 flow Injection Analyzer (Lachat Instruments, Loveland, CO, USA). Potential net N mineralization rates (mg N g dry soil−1 d−1) were calculated as the difference between pre- and post-incubation inorganic N concentrations.Microbial biomass dynamics in field plotsMicrobial biomass carbon and microbial physiological traits were quantified within 10 days of collection as described above, with four minor differences. First, 30 g soil subsamples were covered with parafilm and pre-incubated for 2 d near the field soil temperature measured at the time of sampling (16.5 °C for WLF and HF, and 21.5 °C for LDW, TRC, SCBI, and SERC). Second, for CO2 analysis, samples were placed in a 61 mL serum vial crimped with a rubber septum. Third, DNA concentrations were determined using a Qubit dsDNA BR Assay Kit (Life Technologies) and a Qubit 3.0 fluorometer (Life Technologies). Fourth, 14.5 g subsamples were used for microbial biomass analysis.Soil organic matter characterization in field plotsMineral-associated SOC was quantified as in the microcosm experiment, but without a pre-fractionation leachate removal step. We additionally measured soil amino sugar concentrations to estimate microbial necromass contributions to SOM. Amino sugars are useful microbial biomarkers because they are found in abundance in microbial cell walls, but are not produced by higher plants and soil animals19. Moreover, amino sugars can provide information on the microbial source of necromass. For example, glucosamine (Glu) is produced mostly by fungi whereas muramic acid (MurA) is produced almost exclusively by bacteria61,85. Amino sugars were extracted, purified, converted to aldononitrile acetates, and quantified with myo-inositol as in Liang et al.86. We used the concentrations of Glu and MurA to estimate total, fungal, and bacterial necromass soil C using the empirical relationships reported in Liang et al.8.$${Bacterial},{necromass},C,=,{MurA},times ,45$$
    (8)
    $${Fungal},{necromass},C,=,({mmol},{GluN},{-},2,times ,{mmol},{MurA})times ,179.17,times ,9$$
    (9)
    Leaf litter and fine roots in field plotsIn Fall 2017, we collected leaf litter on two sample dates from four baskets deployed in the inner 10 × 10 m of each plot. Litter was composited by plot, dried (60 °C), sorted by species, weighed, and ground. We performed leaf litter analyses on at least three samples of each species at each site —unless a species was only present in one or two plots— to get a site-specific mean for each species. Some non-dominant species were not included in these analyses because an insufficient amount of material was collected. Fine roots ( 0.5). Feox and Alox were correlated above this threshold and final models were selected to contain only Feox based on AIC. Residuals were screened for normality (Shapiro-Wilk), heteroscedasticity (visual assessment of residual plots), and influential observations (Cook’s D). Based on this, MGR, MTR, and mineral-associated SOC were natural log transformed. For all mixed models, we centered and standardized predictors (i.e., z-transformation) so that the slopes and significance levels of different predictors could be compared to one another on the same axis88. More