More stories

  • in

    Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere

    Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, et al. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res. 2015;25:534–43.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bankevich A, Pevzner PA. Joint analysis of long and short reads enables accurate estimates of microbiome complexity. Cell Syst. 2018;7:192–200.e3.CAS 
    PubMed 
    Article 

    Google Scholar 
    Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT. Individual genome assembly from complex community short-read metagenomic datasets. ISME J. 2012;6:898–901.CAS 
    PubMed 
    Article 

    Google Scholar 
    Lapidus AL, Korobeynikov AI. Metagenomic data assembly—the way of decoding unknown microorganisms. Front Microbiol. 2021;12:613791.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotech. 2014;32:822–8.CAS 
    Article 

    Google Scholar 
    Biller SJ, Berube PM, Lindell D, Chisholm SW. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol. 2015;13:13–27.CAS 
    PubMed 
    Article 

    Google Scholar 
    Crespo BG, Wallhead PJ, Logares R, Pedrós-Alió C. Probing the rare biosphere of the North-West Mediterranean Sea: an experiment with high sequencing effort. PLOS ONE. 2016;11:e0159195.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA. 2006;103:12115–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pedrós-Alió C. Dipping into the rare biosphere. Science. 2007;315:192–3.PubMed 
    Article 

    Google Scholar 
    Sauret C, Séverin T, Vétion G, Guigue C, Goutx M, Pujo-Pay M, et al. ‘Rare biosphere’ bacteria as key phenanthrene degraders in coastal seawaters. Environmental Pollution. 2014;194:246–53.CAS 
    PubMed 
    Article 

    Google Scholar 
    Kalenitchenko D, Le Bris N, Peru E, Galand PE. Ultra-rare marine microbes contribute to key sulfur related ecosystem functions. Mol Ecol. 2018;27:1494–504.PubMed 
    Article 

    Google Scholar 
    Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, et al. Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA. Mol Ecol. 2016;25:5925–43.CAS 
    PubMed 
    Article 

    Google Scholar 
    Lynch MDJ, Neufeld JD. Ecology and exploration of the rare biosphere. Nat Rev Micro. 2015;13:217–29.CAS 
    Article 

    Google Scholar 
    Debroas D, Hugoni M, Domaizon I. Evidence for an active rare biosphere within freshwater protists community. Mol Ecol. 2015;24:1236–47.CAS 
    PubMed 
    Article 

    Google Scholar 
    Banerjee S, Schlaeppi K, Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.CAS 
    PubMed 
    Article 

    Google Scholar 
    Herren CM, McMahon KD. Keystone taxa predict compositional change in microbial communities. Environ Microbiol. 2018;20:2207–17.PubMed 
    Article 

    Google Scholar 
    Hugoni M, Taib N, Debroas D, Domaizon I, Dufournel IJ, Bronner G, et al. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. PNAS. 2013;110:6004–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Debroas D, Domaizon I, Humbert J-F, Jardillier L, Lepère C, Oudart A, et al. Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data. FEMS Microbiol Ecol. 2017;93:1.Article 
    CAS 

    Google Scholar 
    Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, et al. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol. 2008;74:5422–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pascoal F, Magalhães C, Costa R. The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential. Front Microbiol. 2020;11:231.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499:431–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, et al. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front Microbiol. 2015;6:358.PubMed 
    PubMed Central 

    Google Scholar 
    Sachdeva R, Campbell BJ, Heidelberg JF Rare microbes from diverse Earth biomes dominate community activity. bioRxiv 2019; 636373. https://doi.org/10.1101/636373.Galand PE, Pereira O, Hochart C, Auguet JC, Debroas D. A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME J. 2018;12:2470–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Ulyantsev VI, Kazakov SV, Dubinkina VB, Tyakht AV, Alexeev DG. MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. Bioinformatics. 2016;32:2760–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Dixon P. VEGAN, a package of R functions for community ecology. J Vegetation Sci. 2003;14:927–30.Article 

    Google Scholar 
    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596.CAS 
    PubMed 
    Article 

    Google Scholar 
    Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nature methods. 2015;12:902–3.CAS 
    PubMed 
    Article 

    Google Scholar 
    Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biology. 2011;12:R60.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158–D169.Article 
    CAS 

    Google Scholar 
    Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44:D457–D462.CAS 
    PubMed 
    Article 

    Google Scholar 
    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Meth. 2015;12:59–60.CAS 
    Article 

    Google Scholar 
    Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB. Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome. 2014;2:15.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Front Microbiol. 2017;8:2224.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ. GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics. 2009;10:161.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 2013;29:1830–1.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rohart F, Gautier B, Singh A, Cao K-AL. mixOmics: An R package for ‘omics feature selection and multiple data integration. PLOS Computational Biology. 2017;13:e1005752.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Palarea-Albaladejo J, Martín-Fernández JA. zCompositions—R package for multivariate imputation of left-censored data under a compositional approach. Chemometrics Intell Lab Syst. 2015;143:85–96.CAS 
    Article 

    Google Scholar 
    Plaza Oñate F, Le Chatelier E, Almeida M, Cervino ACL, Gauthier F, Magoulès F, et al. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. Bioinformatics. 2019;35:1544–52.PubMed 
    Article 
    CAS 

    Google Scholar 
    Csardi G, Nepusz T. The Igraph Software Package for Complex Network Research. InterJournal 2006, Complex Systems, 1695.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Epskamp S, Cramer AOJ, Waldorp LJ, Schmittmann VD, Borsboom D. qgraph: Network Visualizations of Relationships in Psychometric Data. J Stat Softw. 2012;48:1–18.Article 

    Google Scholar 
    Lambert S, Tragin M, Lozano J-C, Ghiglione J-F, Vaulot D, Bouget F-Y, et al. Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations. ISME J. 2019;13:388–401.PubMed 
    Article 

    Google Scholar 
    Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Galand PE, Casamayor EO, Kirchman DL, Lovejoy C. Ecology of the rare microbial biosphere of the Arctic Ocean. PNAS. 2009;106:22427–32.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Campbell BJ, Yu L, Heidelberg JF, Kirchman DL. Activity of abundant and rare bacteria in a Coastal Ocean. Proc Natl Acad Sci USA. 2011;108:12776–81.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, et al. SAR11 clade dominates ocean surface bacterioplankton communities. Nature. 2002;420:806–10.CAS 
    PubMed 
    Article 

    Google Scholar 
    Bouvier T, del Giorgio PA. Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol. 2007;9:287–97.CAS 
    PubMed 
    Article 

    Google Scholar 
    Thingstad TF, Våge S, Storesund JE, Sandaa R-A, Giske J. A theoretical analysis of how strain-specific viruses can control microbial species diversity. Proc Natl Acad Sci USA. 2014;111:7813–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pedrós-Alió C. Marine microbial diversity: can it be determined? Trends Microbiol. 2006;14:257–63.PubMed 
    Article 
    CAS 

    Google Scholar 
    Gobet A, Böer SI, Huse SM, van Beusekom JEE, Quince C, Sogin ML, et al. Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J. 2012;6:542–53.PubMed 
    Article 

    Google Scholar 
    Pascoal F, Costa R, Assmy P, Duarte P, Magalhães C. Exploration of the types of rarity in the arctic ocean from the perspective of multiple methodologies. Microb Ecol. 2021;84:59–72.PubMed 
    Article 
    CAS 

    Google Scholar 
    Huete-Stauffer TM, Arandia-Gorostidi N, Díaz-Pérez L, Morán XAG. Temperature dependences of growth rates and carrying capacities of marine bacteria depart from metabolic theoretical predictions. FEMS Microbiol Ecol. 2015;91:fiv111.PubMed 
    Article 
    CAS 

    Google Scholar 
    Arandia-Gorostidi N, Huete-Stauffer TM, Alonso-Sáez L, G. Morán XA. Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom. Environ Microbiol. 2017;19:4493–505.CAS 
    PubMed 
    Article 

    Google Scholar 
    Giovannoni SJ, Bibbs L, Cho J-C, Stapels MD, Desiderio R, Vergin KL, et al. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature. 2005;438:82–85.CAS 
    PubMed 
    Article 

    Google Scholar 
    Yilmaz P, Yarza P, Rapp JZ, Glöckner FO. Expanding the world of marine bacterial and archaeal clades. Front Microbiol. 2016;6:1524.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pedler BE, Aluwihare LI, Azam F. Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc Natl Acad Sci USA. 2014;111:7202–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pereira O, Hochart C, Boeuf D, Auguet JC, Debroas D, Galand PE. Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea. ISME J. 2020;15:1302–16.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. Science. 2012;335:587–90.CAS 
    PubMed 
    Article 

    Google Scholar 
    Pereira O, Hochart C, Auguet JC, Debroas D, Galand PE. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. MicrobiologyOpen. 2019;8:e00852.PubMed 
    PubMed Central 

    Google Scholar 
    Tully BJ. Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. Nat Commun. 2019;10:271.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, et al. Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environ Microbiol. 2018;20:734–54.CAS 
    PubMed 
    Article 

    Google Scholar 
    Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, et al. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J. 2017;11:853–62.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E. Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery. Genome Biol Evol. 2018;10:707–15.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, et al. A global ocean atlas of eukaryotic genes. Nature Communications. 2018;9:373.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Thomas AM, Segata N. Multiple levels of the unknown in microbiome research. BMC Biology. 2019;17:48.PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Global soil profiles indicate depth-dependent soil carbon losses under a warmer climate

    WoSIS and permafrost-affected soil profilesThe World Soil Information Service (WoSIS) collates and manages the largest database of explicit soil profile observations across the globe29. In this study, we used the quality-assessed and standardised snapshot of 2019 (ISRIC Data Hub). We further screened the snapshot, and excluded soil profiles with obvious errors (e.g., negative depth values of mineral soil, the value of the depth for the deeper layer is smaller than that of the upper layer). Finally, there is a total of 110,695 profiles with records of SOC content (SOCc, g C kg–1 soil) in the fine earth fraction < 2 mm. The soil layer depths are inconsistent between soil profiles. We harmonised SOCc to three standard depths (i.e., 0–0.3, 0.3–1 and 1–2 m) using mass-preserving splines61,62, which makes it possible to directly compare among soil profiles. We also calculated SOC stock (SOCs, kg C m–2) in each standard depth as:$${{{{{{rm{SOC}}}}}}}_{{{{{{rm{s}}}}}}}=frac{{{{{{{rm{SOC}}}}}}}_{{{{{{rm{c}}}}}}}}{100}cdot Dcdot {{{{{rm{BD}}}}}}cdot left(1-frac{G}{100}right),$$ (1) where D is the soil depth (i.e., 0.3, 0.7, or 1 m in this study), BD is the bulk density of the fine earth fraction 2 mm) of soil. Amongst the 110,695 soil profiles, unfortunately, only 18,590 profiles have measurements of both BD and G. To utilise and take advantage of all SOCc measurements, we used generalised boosted regression modelling (GBM) to perform imputation (i.e., filling missing data). As such, SOCs can be estimated. To do so, for BD and G in each standard soil depth, GBM was developed based on all measurements of that property (e.g., BD) in the 110,695 profiles with other 32 soil properties recorded in the WoSIS database. The detailed approach for missing data imputation has been described in ref. 41.Together with the WoSIS soil profiles, a total of 2,703 soil profiles with data of SOCs from permafrost-affected regions were obtained from ref. 30. The original data used in ref. 30 have been obtained, and we used the data of SOCs in the 0–0.3, 0.3–1, and 1–2 m soil layers in this study. These permafrost-affected profiles compensate for the scarce soil profiles in high latitudinal regions in the WoSIS database. Overall, the soil profiles cover 13 major biome groups although the profile numbers vary among biome types (Supplementary Fig. 1). The profiles also cover various climate conditions across the globe with mean annual temperature (MAT) ranging from –20.0 to 30.7 °C and mean annual precipitation (MAP) ranging from 0 to 6,674 mm.Environmental covariatesMAT and MAP for each soil profile were obtained from the WorldClim version 2 (ref. 63). The WorldClim version 2 calculates biologically meaningful variables using monthly temperature and precipitation during the period 1970–2000. We obtained global spatial layers of MAT and MAP at the resolution of 30 arcsecond (i.e., 0.0083° which is equivalent to ~1 km at the equator). Soil profiles in the same 0.0083° grid (i.e., ~1 km2) share the same MAT and MAP. Besides MAT and MAP, other climatic variables for each soil profile were also obtained from the WorldClim version 2. The WWF (World Wildlife Fund) map of terrestrial ecoregions of the world (https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world) was used to extract the biome type at each soil profile. The MODIS land cover map64 at the same resolution of NPP databases was used to identify that if the land is cultivated (i.e., land cover type of croplands and cropland/natural vegetation mosaic) at the location of each soil profile.Space-for-time substitution: grouping soil profilesWe used a hybrid approach of space-for-time substitution and meta-analysis to estimate the response of SOC to warming. Traditionally, space-for-time substitution involves determining regression relationships across gradients at one time31. The regression was then used to predict future status under conditions when one or more of the covariates has changed31. However, the approach was compromised when the effects of other driving variables such as soil type and landform were not minimised. Regarding SOC dynamics, they would show non-linear relationships19 with temperature modulated by a series of other environmental covariates (e.g., precipitation, vegetation type).Based on the idea of space-for-time approach31, first, we sorted all soil profiles by MAT at the soil-profile locations and designated them into MAT classes with an increment of 1 °C (Fig. 1). Then, we derived pairs of soil profiles, with each pair including a “ambient” and “warm” class (i.e., control vs treatment in meta-analysis language) distinguished by MAT (Fig. 1). The ambient class includes soil profiles with MAT ranging from i to i + 1 degree Celsius, where i is the lowest temperature in the class. If 1 °C warming is of interest, for example, the warm class will be identified as the class with MAT ranging from i + 1 to i + 2 degree Celsius (i.e., one degree higher than that of the ambient class; Fig. 1). To control the effects of precipitation, soil type and topography, soil profiles in both ambient and warm classes were further grouped; and each group must have the same following characteristics: (1) Landform. A global landform spatial layer was obtained from Global Landform classification - ESDAC - European Commission (europa.eu), and global terrestrial lands were divided into three general landform types: plains including lowlands, plateaus, and mountains including hills. (2) Soil type. The 12 USDA soil orders were used to distinguish soil types. A global spatial layer of soil orders was obtained from The Twelve Orders of Soil Taxonomy | NRCS Soils (usda.gov). We also independently tested the sensitivity of the results to different soil classification systems by including FAO and WRB soil groups (Soil classification | FAO SOILS PORTAL|Food and Agriculture Organization of the United Nations). (3) Mean annual precipitation (MAP). MAP cannot be exactly the same between the ambient and warm groups. In practice, we considered that soils meet this criterion if the absolute difference of MAP between ambient and warm soils is less than 50 mm. We also tested the sensitivity of the results to this absolute MAP difference using another value of 25 mm, and found that this difference has negligible effect (Supplementary Fig. 11). (4) Precipitation seasonality. Precipitation seasonality indicates the temporal distribution of precipitation. In this study, we focused on warming alone, and global warming would also have less effect on this seasonal distribution of precipitation. The seasonal distribution pattern of precipitation was classified into three categories: summer-dominated precipitation, winter-dominated precipitation and uniform precipitation. Precipitation concentration index (PCI) was calculated in R precintcon package to distinguish the three patterns65: $${{{{{rm{PCI}}}}}}=frac{mathop{sum }nolimits_{{{{{{rm{i}}}}}}=1}^{12}{p}_{{{{{{rm{i}}}}}}}^{2}}{{left(mathop{sum }nolimits_{{{{{{rm{i}}}}}}=1}^{12}{p}_{{{{{{rm{i}}}}}}}right)}^{2}}cdot 100,$$ (2) where pi is the precipitation in month i in a particular year. In this study, we used the monthly precipitation from 1970 to 2000 obtained from WorldClim version 2 (ref. 63) to calculate the average (overline{{{{{{rm{PCI}}}}}}}) at the location of each profile. If (overline{{{{{{rm{PCI}}}}}}})  8.3 and total precipitation from April to September (from October to March in the Southern Hemisphere) is larger than that from October to March (from April to September in the Southern Hemisphere), precipitation mainly occurs in summer (i.e., summer precipitation); otherwise, it is winter precipitation.By applying these selection criteria to all soil profiles, we obtained pairs (i.e., an “ambient” group vs a “warm” group) of soil profiles mainly distinguished by MAT (i.e., warming). Amongst pairs, they would be different in landform, soil type, MAP and precipitation seasonality, which enables us to address their effects on the response of SOC to warming. We are interested in five warming levels including 1, 2, 3, 4, and 5 °C.Meta-analysis: estimation of the response of SOC to warmingMeta-analysis techniques were used to estimate the percentage response of SOC to warming by comparing SOC content and stock in groups in the warm group to that in the ambient group. The log response ratio of soil C (lnRR) to warming for each pair (i.e., an ambient group vs a warm group) of soil profiles was calculated as:$${{{{{rm{ln}}}}}}{{{{{rm{RR}}}}}}={{{{{rm{ln}}}}}}left(frac{bar{{{{{{{rm{SOC}}}}}}}^{*}}}{overline{{{{{{rm{SOC}}}}}}}}right),$$ (3) where (overline{{{{{{rm{SOC}}}}}}}) and (bar{{{{{{{rm{SOC}}}}}}}^{*}}) are the mean SOC (either content or stock) in groups from ambient and warm class, respectively. In order to provide a robust estimate of global mean response ratio, the individual lnRR values were weighted by the inverse of the sum of within- (v) and between-group (τ2) variances. As such, the global mean response ratio ((overline{{{{{{rm{ln}}}}}}{{{{{rm{RR}}}}}}})) could be estimated as:$$overline{{{{{{rm{ln}}}}}}{{{{{rm{RR}}}}}}}=frac{{sum }_{{{{{{rm{i}}}}}}}left({{{{{{rm{ln}}}}}}{{{{{rm{RR}}}}}}}_{{{{{{rm{i}}}}}}}times {w}_{{{{{{rm{i}}}}}}}right)}{{sum }_{{{{{{rm{i}}}}}}}{w}_{{{{{{rm{i}}}}}}}},$$ (4) where ({w}_{{{{{{rm{i}}}}}}}=frac{1}{{v}_{{{{{{rm{i}}}}}}}+{tau }^{2}}) is the weight for the ith lnRR. In addition, we estimated and compared the mean response ratios under different soil orders, landforms, and precipitation concentration patterns. These mean response rates were calculated in weighted, mixed-effects models using the rma.mv function in R package metafor. To assist interpretation, the results of (overline{{{{{{rm{ln}}}}}}{{{{{rm{RR}}}}}}}) were back-transformed and reported as percentage change under warming, i.e., (({{{{{{rm{e}}}}}}}^{{{{{{rm{RR}}}}}}}-1)times)100. These back-transformed values were also used for subsequent data analyses.An implicit assumption underlying the space-for-time substitution approach is that important events or processes which substantially change the succession direction of studied system (e.g., volcano disruption in one class but not in another class, cultivation in one class but not in another class) are independent of space and time (which includes the past and future)66. We conducted two sensitivity assessment to test this assumption. First, we repeated all above assessment by excluding soil profiles from croplands since preferential choice of land clearing for cultivation should be common. Second, we repeated all assessment by including only groups having at least 20 soil profiles. This allows the assessed pairs to cover a higher diversity of land history and future land cover/use, diluting the effect of a typical event at a specific soil profile on the estimates.Comparison with SOC turnover modelsWe compared our estimation with predictions by SOC models. A simple one-pool SOC model can be written as:$$frac{{{{{{rm{d}}}}}}C}{{{{{{rm{d}}}}}}t}=I-kcdot C,$$ (5) where I is the amount of carbon input, k is the decay rate of SOC, and C is the stock of SOC. At steady state, (C=I/k). A Q10 function can be applied to estimate k under warming (kw):$${k}_{{{{{{rm{w}}}}}}}=kcdot {{exp }}left(0.1cdot triangle Tcdot {{log }}left({Q}_{10}right)right),$$ (6) where (triangle T) is the warming level. Thus, when soil reaches a new steady state under warming, SOC stock (Cw) can be estimated as:$${C}_{{{{{{rm{w}}}}}}}=frac{{I}_{{{{{{rm{w}}}}}}}}{kcdot {{exp }}left(0.1cdot triangle Tcdot {{log }}left({Q}_{10}right)right)},$$ (7) where Iw is the carbon input amount under warming condition. Finally, the response of SOC to warming (R) can be calculated as:$$R=frac{{C}_{{{{{{rm{w}}}}}}}-C}{C}=frac{{I}_{{{{{{rm{w}}}}}}}}{I}cdot {{exp }}left(-0.1cdot triangle Tcdot {{log }}left({Q}_{10}right)right)-1.$$ (8) Using Eq. (8), we calculated R under a series of ensembles of (frac{{I}_{{{{{{rm{w}}}}}}}}{I}), (triangle T), and ({Q}_{10}), and compared R with that estimated using our space-for-time substitution approach.Comparison with field warming experimentsA number of meta-analyses based on data from field warming experiments had been performed to assess the response of SOC to warming7,26,46,47,48,49,50, which enable us to conduct comparisons with the estimates using our hybrid approach combining space-for-time substitution and meta-analysis techniques. A total of five meta-analysis papers have been found by searching the Web of Science. We retrieved the response ratios from the identified papers, and compared them to our estimations. Here, it should be noted that most field warming experiments focused on SOC changes (stock or content) in the top 0.2 m soil layer. We compared them with our estimation of the response of SOC stock in the top 0.3 m soil.Besides the published results of meta-analysis, we also conducted an independent meta-analysis using data from field warming experiments. The meta-analysis dataset was mainly from published papers on meta-analysis from 2013 to 2020 (see Supplementary Data 1). It should be noted that the field warming experiments manipulate temperature using different approaches such as open/closed-top chamber, infrared radiators and heating cables. For the comparison, we did not explicitly distinguish these approaches. The experimental duration ranged from 0.42 to 25 years with a mean of 4.7 years, and the warming magnitude ranged from 0.1 to 7°C with a mean of 1.92 °C. To ease comparison, field warming levels were classified into 0–1, 1–2, 2–3, 3–4, 4–5, and >5 °C. The same meta-analysis to that assessing soil profile data was used to predict the response ratio of SOC to the above six warming levels. In addition, we divided the data into four ecosystems (i.e., tundra, forest, shrublands and grasslands) and estimated the response ratio in each ecosystem. These estimates based on field warming experiments were compared with those estimated using our space-for-time approach.Variable importance and global mappingWe included 15 environmental predictors to derive a meta-forest model, a machine learning-based random forest model adapted for meta-analysis, to map the response of SOC stock/content to warming across the globe at the resolution of 0.0083°. The 15 environmental predictors reflect generally four broad groups of environmental conditions: baseline SOC conditions represented by current standing SOC stock or content, soil order and soil depth; current baseline climatic conditions represented by MAT, MAP, aridity index, precipitation seasonality represented by PCI, the fraction of precipitation in summer, the difference of temperature between ambient and warm groups, the difference of precipitation between ambient and warm groups; topography represented by elevation and landform; and vegetation represented by NPP and biome type.The metaforest function in the metafor package was used to derive the model. To fit the model, a fivefold cross-validation was conducted. That is, 80% of the derived response ratios was used to train the model, and the remaining 20% to validate the model. The best model hypeparameters were targeted by running the model under a series of parameter combinations, and the model performance was assessed by the rooted mean squared error (RMSE) and determination coefficient (R2). The meta-forest model allows the estimation of the relative influence of each individual variable in predicting the response, i.e. the relative contribution of variables in the model. The relative influence is calculated based on the times a variable selected for splitting when growing a tree, weighted by squared model improvement due to that splitting, and then averaged over all fitted trees which are determined by the algorithm when adding more trees cannot reduce prediction residuals. As such, the larger the relative influence of a variable, the stronger the effect of the variable on the response variable.Combining with spatial layers of predictors, the meta-forest model for SOC stock was used to predict the response of SOC to warming across the globe at the resolution of 1 km (most data layers are already at the 1 km resolution as abovementioned, for those layers that are not at the target resolution, they were resampled to the 1 km resolution). In the meta-forest model, current standing SOC stock is the most important predictor (Fig. 4). We use three global maps of SOC stocks including WISE51 (WISE Soil Property Databases | ISRIC), HWSD52 (Harmonized World Soil Database (HWSD v 1.21) – HWSD – IIASA) and SoilGrids53 (SoilGrids250m 2.0) to obtain current standing SOC stocks. These three global maps represent the major mapping products of SOC stock at the global level, and had been widely used for large scale modelling. The derived meta-forest model was applied across the globe to estimate the response ratio of SOC stock in each 1 km pixel. To do so, the same procedure to group the observed soil profiles (Fig. 1) was applied to group global land pixels (section Space-for-time substitution: grouping soil profiles). The only difference is that global mapping uses all pixels instead of the 113,013 soil profiles. In each 1 km pixel, prediction uncertainty was also quantified using estimates of randomly drawn 500 trees of the fitted meta-forest model to calcuate standard deviation of the predictions. More

  • in

    Sea turtles swim easier as poaching declines

    The shell of the endangered hawksbill sea turtle (pictured) is prized for trinkets and jewellery.Credit: Reinhard Dirscherl/SPL

    Poaching is less of a threat to the survival of sea turtles than it once was, a new analysis suggests1. Illegal sea-turtle catch has dropped sharply since 2000, with most of the current exploitation occurring in areas where turtle populations are relatively healthy.This study is the first worldwide estimate of the number of adult sea turtles moved on the black market. According to the analysis, more than one million sea turtles were illegally harvested between 1990 and 2020. But the researchers also found that the illegal catch from 2010 to 2020 was nearly 30% lower than that in the previous decade.“The silver lining is that, despite the seemingly large illegal take, exploitation is not having a negative impact on sea-turtle populations on a global scale. This is really good news,” says co-author Jesse Senko, a marine conservation scientist at Arizona State University in Tempe. The research was published 7 September in Global Change Biology.Turtles for trinketsFor millennia, humans have used both adult sea turtles and their eggs as a food source and for cultural practices. In the past 200 years, however, many sea turtle populations declined steeply as hunting rose to meet a growing demand for turtle-based goods. In Europe, North America and Asia, sea-turtle shells were used to make combs, jewelry and furniture inlays. Turtles were also hunted for meat and for use in traditional medicine.The rise in turtle hunting meant that, by 2014, an estimated 42,000 sea turtles were legally harvested every year, and an unknown number of sea turtles were sold on the black market. Today, six of the seven sea-turtle species found around the globe are endangered owing to a deadly combination of habitat destruction, poaching and accidental entanglement in fishing gear.To pin down how many sea turtles were illegally harvested, Senko and his colleagues surveyed sea-turtle specialists and sifted through 150 documents, including reports from non-governmental organizations, papers in peer-reviewed journals and news articles.

    Source: Ref. 1

    By combining this information, the researchers made a conservative estimate that around 1.1 million sea turtles were illegally caught between 1990 and 2020. Nearly 90% of these turtles were funneled into China and Japan, largely from a handful of middle- and low-income countries (see ‘Long-distance turtle transport’). Of the species that could be identified, the most frequently exploited were the endangered green turtles (Chelonia mydas), hunted for meat, and the critically endangered hawksbill turtles (Eretmochelys imbricata), prized for their beautiful shells.However, the data also showed that the number of illegally caught turtles decreased from around 61,000 each year between the start of 2000 and the end of 2009 to around 44,000 in the past decade (see ‘More sea turtles swim free’). And, although there were exceptions, most sea turtles were taken from relatively robust populations that were both large and genetically diverse.

    Source: Ref. 1

    Although sea turtles seem to be doing well globally, this doesn’t mean that threats to regional populations can be ignored, says Emily Miller, an ecologist at the Monterey Bay Aquarium Research Institute in California. The study pins down where — and for whom — sea turtles are being exploited, which could help conservationists to target communities for advocacy, she says.Overall, the numbers signal that conservation efforts could be working, says Senko. “Contrary to popular belief, most sea-turtle populations worldwide are doing quite well,” he says. “The number of turtles being exploited is a shocker, but the ocean is big, and there are a lot of turtles out there.” More

  • in

    Protect European green agricultural policies for future food security

    The European Union’s new (2023–2027) Common Agricultural Policy (CAP) aims to reverse current environmental degradation and biodiversity declines in European farmland1 through the achievement of three green objectives: contribute to climate change mitigation, support efficient natural resource management, and reverse biodiversity loss2,3. Following the outbreak of war in Ukraine, the European Commission proposed a series of short and medium-term relaxations to CAP’s environmental commitments to offset expected shortages in grain imports and enhance food security4.Here, we argue that policy changes to allow cultivation of fallow land will disproportionately impact biodiversity and support further intensification of livestock production. Thus, ultimately, these changes in policy may sacrifice long term biodiversity and agricultural sustainability in Europe, in favour of modest increases in current agricultural production and alleged improvements of food security.A catalyst for reversing green policiesRussia and Ukraine are world-leading producers and exporters of cereal and fodder production (notably, oleo-proteaginous crops)5. The Ukraine war and international sanctions on Russia are threatening the import of these products to the EU. Ukrainian winter cereal, maize and sunflower production is expected to decrease by 20–30%, at least during the 2022–2023 season, and similar reductions in Russian exports are also expected5. Therefore agro-industry lobbies and farmers’ organisations in Brussels, some political parties in the European parliament and some countries’ administrations perceive a need to increase agricultural production6 and, as a means to offset expected shortages, are pressing to relax or remove CAP’s environmental commitments. Mechanisms supporting these commitments include enhanced conditionality (compulsory for all farmers receiving subsidies), voluntary measures of Rural Development Programmes (i.e. agri-environment-climate-measures) and Greening measures (crop diversification, maintenance of permanent grasslands and promotion of Ecological Focus Areas). A call made to mobilise all relevant international groups during the informal meeting held on 2 March 2022 by Member States’ agriculture and food ministers, with the exception of Denmark, Germany and Italy, may reflect such pressure6. Indeed, the European Commission has finally proposed a series of “short- and medium-term actions to enhance global food security and to support farmers and consumers in the EU”4. In regard to land-use, actions refer to the cultivation of fallows, which are protected by green payments for keeping land in good agricultural and environmental conditions and, adequately managed (both long-term and annual), support high levels of biodiversity and ecosystem services7 (Fig. 1). More precisely, the European Commission proposes that “To enlarge the EU’s production capacity, the Commission has today adopted an implementing act to exceptionally and temporarily allow Member States to derogate from certain greening obligations. In particular, they may allow for production of any crops for food and feed on fallow land that is part of Ecological Focus Areas in 2022, while maintaining the full level of the greening payment”4. This measure was recently extended for 2023.Fig. 1: Arable field left fallow and allowed to develop a grassy vegetation cover.Under non-intensive management, fallow areas become a genuine semi-natural habitat, key for the conservation of farmland biodiversity. Credit: Jordi Bas, taken in the cereal steppes of the Lleida plain (Catalonia, Spain).Full size imageConsidering food sovereigntyHowever, the FAO does not draw the same conclusions about the possible world impacts of the conflict and recommends finding alternative suppliers, instead suggesting using existing food stocks, diversifying domestic crops and reducing fertiliser dependence and food waste as mechanisms to help guarantee Europe’s food supplies and sovereignty5. Even the European Commission, while acknowledging the vulnerability of European farmers to animal feed import shortages and increased costs, clearly stated that food supply is not at risk in the EU4. Indeed, EU-based production supplies 79% of the feed proteins consumed in European livestock farming, 90% of feed cereals and 93% of other products such as Dried Distillers’ Grains and Solubles or beet pulp8. In 2020, the EU was completely self-sufficient with respect to dairy products, pork, beef, veal, poultry, and cereals. It remained the largest global exporter of agri-food products, in spite of the COVID-19 pandemic8.Counterproductive policiesAny increase in production from cultivating fallow land will therefore likely be used to feed intensively reared livestock and sustain cattle feed exports. Supporting the increasing trend of feed exports and industrial intensive livestock farming does not align with the EU’s Green Deal due to the negative impacts on air, soil and water quality8,9,10. In addition, cultivating fallow land to support intensive livestock-based agriculture will undermine the EU’s Farm-to-Fork strategy and CAP’s ‘Food and Health’ objective of reducing meat consumption to favour a more sustainable and healthier diet among European consumers2,11. Encouraging the growth of intensive livestock farming through enabling cultivation of fallow lands will increase environmental damage, biodiversity loss and public health risks. Thus, the recent relaxations of the new CAP compromise several of its fundamental objectives, along with those of other elements of the Green Deal, such as the EU’s Nature Restoration Law2,9,12.The duration of the war in Ukraine and its effects on provision of raw materials to Europe is hard to foresee. We acknowledge the uncertainties and input costs faced by farmers but calls for further agricultural intensification may be largely unjustified at this stage. Specifically, cultivating semi-natural habitats like long-term or unploughed annual fallows will have serious environmental costs, including an increase in pesticide and fertiliser application, since fallows often occupy less productive land13. Even a moderate increase in food production at the expense of the semi-natural habitats remaining in farmland landscapes (field margins, grasslands, and fallow land), which support most of Europe’s farmland biodiversity and its associated ecosystem services14, will seriously damage farmland biodiversity and sustainability in European agricultural landscapes3,15. For example, a comprehensive study carried out on 169 farms across 10 European countries showed that semi-natural habitats, including fallows, occupied 23% of the land but hosted 49% of vascular plant, earthworm, spider, and wild bee species; a 10% decrease of these habitats if reclaimed for food production would cause exponential decreases in biodiversity, but only moderate linear increases in production15. Furthermore, the loss of semi-natural habitats in arable systems, fallows among them, would negatively affect arthropod functional diversity and the ecosystem services it supports, which may affect agriculture production14.Sustainable alternativesThere are alternatives to cultivating semi-natural habitats that may (and need to) be assessed to achieve a more strategic European agricultural policy able to meet food demands while maintaining the sustainability principles and improvements of the food-production chain sought by the Farm-to-Fork strategy. Proposals include agro-ecological approaches to increase production through the enhancement of ecosystem services such as pollination and biological control16,17,18, adjusting the amount of cultivated surface in relation to landscape structure and composition19, or relocating crops that are more in demand to areas where production is optimal without increasing the total cultivated area20.After decades of costly implementation and reforms of agricultural and conservation policies1, the EU is at risk of engaging in a hasty and misguided strategy on food production jeopardising the green transition13. As an alternative to such a ‘business as usual’ reaction, the EU has now the opportunity to consolidate the mentioned environmental and social objectives of the new CAP2,3. A more sustainable agriculture, resilient to food supply crises (present and future), should be based on ecological functionality of farmland, which ultimately depends on the conservation of its biodiversity16, along with measures to counter climate change. Responses to this and other challenges on the new CAP should be assessed with a long-term perspective and based on robust scientific evidence before undermining its environmental ambitions3,13. More

  • in

    Evaluation of ecological quality in southeast Chongqing based on modified remote sensing ecological index

    Study areaSoutheastern Chongqing, China (107° 14′–109° 19′ E, 28° 9′–30° 32′ N), has an area of about 19,800 km2 (Fig. 1). The study area has a subtropical monsoon climate. And the area has four distinct seasons, with an annual average temperature of 16.2 °C and abundant rainfall, with an average annual rainfall of 1209 mm. This region is located in the central part of the Wuling mountains, which is characterized by medium and low mountainous landforms, with an average altitude of greater than 1000 m. The water system (the Wujiang River system) in the study area is well developed, with a large drainage area and rich groundwater resources. The soil is dominated by yellow soil and limestone soil, and the sensitivity to soil erosion is high. The district exhibits the typical ecological fragility of karst areas, with barren soil, fragmented surfaces, a single community, and a low ecological carrying capacity. The area includes six counties: Qianjiang district, Shizhu Tujia Autonomous county, Xiushan Tujia and Miao Autonomous county, Youyang Tujia and Miao Autonomous county, Wulong district, and Pengshui Miao and Tujia Autonomous county. The coverage rates of the carbonatite layers in these counties are 42.11, 67.77, 25.70, 34.80, 59.70 and 88.46%, respectively38, and the average coverage of the carbonatite layers is 53.09%, making this a representative area of karst rocky desertification.Data and image pre-processingIn the study, the remote sensing data were obtained from the United States Geological Survey (USGS, https://earthexplorer.usgs.gov/), including landsat-5 thematic mapper (TM) images acquired in 2001, 2006 and 2011 and Landsat-8 operational land imager (OLI) images obtained in 2016 and 2021 (Table 1). The spatial resolution is 30 m. In order to ensure the comparability of spectral characteristics, the data collection was conducted from May to September when the vegetation grew better. In order to meet the usage requirements, the cloud cover of each image used is below 10%. For the images with poor quality, the adjacent years were selected for replacement. The difference in ecological quality between adjacent years in the same region was not particularly large. In order to represent the actual situation of the ecological environment quality in the target year as much as possible, we tried to minimize the replaced part in each target year. A total of 20 images were collected in this study. The images downloaded were all L1T products, which had undergone systematic radiometric correction and geometric correction, so precise geometric correction was no longer performed. Before the subsequent processing, all 20 images were preprocessed by radiometric calibration, atmospheric correction, image mosaicking and cropping. Then these images were calculated to obtain NDVI, WET, NDBSI, LST and RI. And based on the preprocessed Landsat images, support vector machine classification was performed to obtain the land use (LU) status.Table 1 Information of images used in this study.Full size tableThe topographical data included the elevation (EV) and slope (SP) data. Among them, the elevation data was provided by the official website of the United States Geological Survey (USGS, https://earthexplorer.usgs.gov/). And the slope data was calculated from the elevation data. The meteorological data, including the monthly average temperature (MT), monthly mean precipitation (PR), monthly even relative humidity (RH), and monthly total sunshine hours (SH) from May to September of the target year, were got from the China Meteorological Data Network (http://data.cma.cn/). In addition, socioeconomic data, including the population density (PD) and gross domestic product (GDP), were obtained from the statistical yearbooks of each district and county in the study area. The nighttime light (NTL) data were obtained from the National Oceanic and Atmospheric Administration (NOAA, https://www.noaa.gov/). The above data and LU were used as the influencing factors of ecological quality to analyze the reasons for the change of local ecological environment quality. The statistical data and monitoring data of each evaluation index used to construct the EI come from the statistical yearbooks, water resources bulletin and soil and water conservation bulletin of each district and county.MethodologyStudy frameworkA framework was developed for evaluating the ecological quality in southeastern Chongqing from 2001 to 2021 in the study. And the framework included three parts: data preparation, construction of the MRSEI, and the analysis of the ecological status in the region. Figure 2 presents the detailed information about the framework. The operations of band calculation, normalization and PCA were all carried out using the ENVI 5.3 software (https://www.harrisgeospatial.com).Figure 2The study framework.Full size imageIndicators used in MRSEIThe greenness, humidity, heat, dryness, and degree of rocky desertification were used to construct the MRSEI. The NDVI39 was chosen to characterize the greenness. The humidity component acquired from the tasseled cap transformation (WET)40 was selected to represent the humidity. The LST41 was used to represent the heat, the normalized difference build-up soil index (NDBSI)42 was used to characterize the dryness. The RI was applied to characterize the degree of rocky desertification.The NDVI is an important indicator for monitoring the physical and chemical properties of vegetation, and it can be employed to calculate the vegetation coverage, leaf area index, and so on19. In addition, it eliminates some radiation errors and has a stronger response to surface vegetation. It has been widely used in vegetation remote sensing monitoring. The equation for calculating the NDVI is as follows39:$$ {text{NDVI}} = {{(uprho }}_{{{text{NIR}}}} – {uprho }_{{{text{Red}}}} {)}/{{(uprho }}_{{{text{NIR}}}} {{ + uprho }}_{{{text{Red}}}} ), $$
    (1)
    where ({uprho }_{{{text{NIR}}}}) is the reflectance of the near-infrared band and ({uprho }_{{{text{Red}}}}) refers to the reflectance of the red band corresponding to each image.The WET can effectively reflect the humidity conditions of the surface vegetation, water, and soil, and can reveal the changes in the ecological environment, such as soil degradation. Therefore, it is commonly used in ecological environment monitoring43. The WET can be expressed as40,43:$$ {text{WET}}_{{{text{TM}}}} { = 0}{{.3102uprho }}_{{{text{Red}}}} { + 0}{{.2021uprho }}_{{{text{Green}}}} { + 0}{{.0315uprho }}_{{{text{Blue}}}} { + 0}{{.1594uprho }}_{{{text{NIR}}}} – {0}{{.6806uprho }}_{{{text{SWIR1}}}} – {0}{{.6109uprho }}_{{{text{SWIR2}}}} , $$
    (2)
    $$ {text{WET}}_{{{text{OLI}}}} { = 0}{{.3283uprho }}_{{{text{Red}}}} { + 0}{{.1972uprho }}_{{{text{Green}}}} { + 0}{{.1511uprho }}_{{{text{Blue}}}} { + 0}{{.3407uprho }}_{{{text{NIR}}}} – {0}{{.7117uprho }}_{{{text{SWIR1}}}} – {0}{{.4559uprho }}_{{{text{SWIR2}}}} , $$
    (3)
    where ({uprho }_{{text{i}}} ,) is the reflectance of band i.The NDBSI is expressed as the average of two indicators, the bare soil index (SI)44 and the index-based built-up index (IBI)45. It can be applied to characterize the dryness. The calculation formulas are44,45:$$ {text{IBI }} = {text{ }}left[ {2uprho _{{{text{SWIR1}}}} /left( {uprho _{{{text{SWIR1}}}} + {text{ }}uprho _{{{text{NIR}}}} } right) – uprho _{{{text{NIR}}}} /(uprho _{{{text{NIR}}}} + {text{ }}uprho _{{{text{Red}}}} } right) – uprho _{{{text{Green}}}} /(uprho _{{{text{Green}}}} + {text{ }}uprho _{{{text{SWIR1}}}} )]/[2uprho _{{{text{SWIR1}}}} /left( {uprho _{{{text{SWIR1}}}} + {text{ }}uprho _{{{text{NIR}}}} } right) + {text{ }}uprho _{{{text{NIR}}}} /(uprho _{{{text{NIR}}}} + {text{ }}uprho _{{{text{Red}}}} ) + {text{ }}uprho _{{{text{Green}}}} /(uprho _{{{text{Green}}}} + {text{ }}uprho _{{{text{SWIR1}}}} )], $$
    (4)
    $$ {text{SI = }}left[ {{uprho }_{{{text{SWIR1}}}} {{ + uprho }}_{{{text{red}}}} – left( {{uprho }_{{{text{Blue}}}} {{ + uprho }}_{{{text{NIR}}}} } right)} right]/left[ {{uprho }_{{{text{SWIR1}}}} {{ + uprho }}_{{{text{red}}}} { + }left( {{uprho }_{{{text{Blue}}}} {{ + uprho }}_{{{text{NIR}}}} } right)} right], $$
    (5)
    $$ {text{NDBSI = (IBI + SI)/2,}} $$
    (6)
    where ({uprho }_{{text{i}}} ,) is the reflectance of band i.The LST is closely related to natural processes and human phenomena such as crop yield, vegetation growth and distribution, surface water cycle, etc. It can well reflect the state of the surface ecological environment. The atmospheric correction method is used to invert the LST here46,47, it can be expressed as:$$ {text{L = gain}} times {text{DN + bias,}} $$
    (7)
    $$ {text{T = K}}_{{2}} /{text{ln}}left( {frac{{{text{K}}_{{1}} }}{{text{L}}}{ + 1}} right){,} $$
    (8)
    $$ {text{LST = T}}/left[ {{1 + }left( {frac{{{lambda T}}}{{upalpha }}} right){{lnvarepsilon }}} right]{,} $$
    (9)
    where L is the radiation value in the thermal infrared band, DN is the gray value, gain and bias is the gain value and offset value of the L-band, which was got from the image header file. And T is the temperature value at the sensor; K1 and K2 are calibration parameters respectively (for TM, K1 = 607.76 W/(m2 sr μm), K2 = 1260.56 K; for TIRS, K1 = 774.89 W/(m2 sr μm), K2 = 1321.08 K); λ is the central wavelength of thermal infrared band; α = 1.438 × 10−2 m K. ε is the surface emissivity and the value is estimated by the vegetation index mixture model48,49. It is calculated as follows:$$ {text{VFC = }}frac{{{text{NDVI}} – {text{NDVI}}_{{{text{Soil}}}} }}{{{text{NDVI}}_{{{text{Veg}}}} – {text{NDVI}}_{{{text{Soil}}}} }}, $$
    (10)
    $$ {text{d}}_{{upvarepsilon }} { = }left( {{1} – {upvarepsilon }_{{text{s}}} } right){{ times (1}} – {text{VFC) }}times text{F} times upvarepsilon _{{text{v}}} , $$
    (11)
    $$ {{upvarepsilon = upvarepsilon }}_{{text{v}}} times {text{ VFC}} + varepsilon _{{text{s}}} {{ times }}left( {{1} – {text{FVC}}} right){text{ + d}}_{{upvarepsilon }} , $$
    (12)
    where VFC is the vegetation fractional cover, ({text{NDVI}}_{{{text{Veg}}}}) is the NDVI of the pixel covered by full vegetation and the pixels with NDVI  > 0.72 are regarded as pure vegetation pixels; ({text{NDVI}}_{{{text{Soil}}}}) is the NDVI of the bare pixel and the pixels with NDVI  More

  • in

    Wildfire aerosol deposition likely amplified a summertime Arctic phytoplankton bloom

    Li, F. et al. Historical (1700–2012) global multi-model estimates of the fire emissions from the Fire Modeling Intercomparison Project (FireMIP). Atmos. Chem. Phys. 19, 12545–12567 (2019).CAS 
    Article 

    Google Scholar 
    Ward, D. S. et al. The changing radiative forcing of fires: Global model estimates for past, present and future. Atmos. Chem. Phys. 12, 10857–10886 (2012).CAS 
    Article 

    Google Scholar 
    Andela, N. et al. A human-driven decline in global burned area. Science 356, 1356–1362 (2017).CAS 
    Article 

    Google Scholar 
    McCarty, J. L. et al. Reviews and syntheses: Arctic fire regimes and emissions in the 21st century. Biogeosciences 18, 5053–5083 (2021).CAS 
    Article 

    Google Scholar 
    Kim, J.-S., Kug, J.-S., Jeong, S.-J., Park, H. & Schaepman-Strub, G. Extensive fires in southeastern Siberian permafrost linked to preceding Arctic Oscillation. Sci. Adv. 6, eaax3308 (2020).Article 

    Google Scholar 
    Mahowald, N. et al. Global distribution of atmospheric phosphorus sources, concentrations and deposition rates, and anthropogenic impacts. Global Biogeochem. Cy. https://doi.org/10.1029/2008gb003240 (2008).Barkley, A. E. et al. African biomass burning is a substantial source of phosphorus deposition to the Amazon, Tropical Atlantic Ocean, and Southern Ocean. Proc. Natl. Acad. Sci. USA 116, 16216–16221 (2019).CAS 
    Article 

    Google Scholar 
    Andreae, M. O. Emission of trace gases and aerosols from biomass burning—an updated assessment. Atmos. Chem. Phys. 19, 8523–8546 (2019).CAS 
    Article 

    Google Scholar 
    Guieu, C., Bonnet, S., Wagener, T. & Loÿe-Pilot, M.-D. Biomass burning as a source of dissolved iron to the open ocean? Geophys. Res. Lett. https://doi.org/10.1029/2005gl022962 (2005).Hamilton, D. S. et al. Improved methodologies for Earth system modelling of atmospheric soluble iron and observation comparisons using the Mechanism of Intermediate complexity for Modelling Iron (MIMI v1.0). Geosci. Model Dev. 12, 3835–3862 (2019).CAS 
    Article 

    Google Scholar 
    Kharol, S. K. et al. Dry deposition of reactive nitrogen from satellite observations of ammonia and nitrogen dioxide over North America. Geophys. Res. Lett. 45, 1157–1166 (2018).CAS 
    Article 

    Google Scholar 
    Wentworth, G. R. et al. Ammonia in the summertime Arctic marine boundary layer: Sources, sinks, and implications. Atmos. Chem. Phys. 16, 1937–1953 (2016).CAS 
    Article 

    Google Scholar 
    Pellegrini, A. F. A. et al. Fire frequency drives decadal changes in soil carbon and nitrogen and ecosystem productivity. Nature 553, 194–198 (2018).CAS 
    Article 

    Google Scholar 
    Mahowald, N. M. et al. Aerosol deposition impacts on land and ocean carbon cycles. Curr. Clim. Change Rep. 3, 16–31 (2017).Article 

    Google Scholar 
    van der Werf, G. R. et al. Global fire emissions estimates during 1997–2016. Earth Syst. Sci. Data 9, 697–720 (2017).Article 

    Google Scholar 
    Evangeliou, N. et al. Open fires in Greenland in summer 2017: Transport, deposition and radiative effects of BC, OC, and BrC emissions. Atmos. Chem. Phys. 19, 1393–1411 (2019).CAS 
    Article 

    Google Scholar 
    Hamilton, D. S. et al. Earth, wind, fire, and pollution: Aerosol nutrient sources and impacts on ocean biogeochemistry. Annu. Rev. Mar. Sci. 14, 303–330 (2022).Article 

    Google Scholar 
    Soja, A. J., Shugart, H. H., Sukhinin, A., Conard, S. & Stackhouse, P. W. Satellite-derived mean fire return intervals as indicators of change in Siberia (1995–2002). Mitig. Adapt. Strateg. Glob. Chang. 11, 75–96 (2006).Article 

    Google Scholar 
    Ito, A. Mega fire emissions in Siberia: Potential supply of bioavailable iron from forests to the ocean. Biogeosciences 8, 1679–1697 (2011).CAS 
    Article 

    Google Scholar 
    Myriokefalitakis, S., Gröger, M., Hieronymus, J. & Döscher, R. An explicit estimate of the atmospheric nutrient impact on global oceanic productivity. Ocean Sci. 16, 1183–1205 (2020).CAS 
    Article 

    Google Scholar 
    Harrison, W. G. & Cota, G. F. Primary production in polar waters: Relation to nutrient availability. Polar Res. 10, 87–104 (1991).Article 

    Google Scholar 
    Tremblay, J.-É. et al. Global and regional drivers of nutrient supply, primary production and CO2 drawdown in the changing Arctic Ocean. Prog. Oceanogr. 139, 171–196 (2015).Article 

    Google Scholar 
    Ardyna, M., Gosselin, M., Michel, C., Poulin, M. & Tremblay, J.-É. Environmental forcing of phytoplankton community structure and function in the Canadian High Arctic: contrasting oligotrophic and eutrophic regions. Mar. Ecol. Prog. Ser. 442, 37–57 (2011).CAS 
    Article 

    Google Scholar 
    Rainville, L. & Woodgate, R. A. Observations of internal wave generation in the seasonally ice-free Arctic. Geophys. Res. Lett. 36, L23604 (2009).Article 

    Google Scholar 
    Ardyna, M. et al. Recent Arctic Ocean sea-ice loss triggers novel fall phytoplankton blooms. Geophys. Res. Lett. 41, 6207–6212 (2014).Article 

    Google Scholar 
    Baumann, T. M. et al. On the seasonal cycles observed at the continental slope of the Eastern Eurasian Basin of the Arctic Ocean. J. Phys. Oceanogr. 48, 1451–1470 (2018).Article 

    Google Scholar 
    Bauch, D. & Cherniavskaia, E. Water mass classification on a highly variable Arctic shelf region: Origin of Laptev sea water masses and implications for the nutrient budget. J. Geophys. Res. Oceans 123, 1896–1906 (2018).Article 

    Google Scholar 
    Pnyushkov, A. V. et al. Heat, salt, and volume transports in the eastern Eurasian Basin of the Arctic Ocean from 2 years of mooring observations. Ocean Sci. 14, 1349–1371 (2018).Article 

    Google Scholar 
    Hölemann, J. A. et al. The impact of land-fast ice on the distribution of terrestrial dissolved organic matter in the Siberian Arctic shelf seas. Biogeosci. Discuss 2021, 1–30 (2021).
    Google Scholar 
    Polyakov, I. V. et al. Greater role for Atlantic inflows on sea-ice loss in the Eurasian Basin of the Arctic Ocean. Science 356, 285–291 (2017).CAS 
    Article 

    Google Scholar 
    Lutsch, E. et al. Unprecedented atmospheric ammonia concentrations detected in the high Arctic from the 2017 Canadian wildfires. J. Geophys. Res. Atmos. 124, 8178–8202 (2019).CAS 
    Article 

    Google Scholar 
    Zhang, J., Li, D., Bian, J. & Bai, Z. Deep stratospheric intrusion and Russian wildfire induce enhanced tropospheric ozone pollution over the northern Tibetan Plateau. Atmos. Res. 259, 105662 (2021).CAS 
    Article 

    Google Scholar 
    Hurrell, J. W. et al. The Community Earth System Model: A framework for collaborative research. Bull. Amer. Meteor. Soc. 94, 1339–1360 (2013).Article 

    Google Scholar 
    Clark, S. K., Ward, D. S. & Mahowald, N. M. The sensitivity of global climate to the episodicity of fire aerosol emissions. J. Geophys. Res.: Atmos. 120, 11,589–511,607 (2015).CAS 
    Article 

    Google Scholar 
    Shi, J.-H. et al. Examination of causative link between a spring bloom and dry/wet deposition of Asian dust in the Yellow Sea, China. J. Geophys. Res. Atmos. https://doi.org/10.1029/2012JD017983 (2012).Wiedinmyer, C. et al. The Fire INventory from NCAR (FINN): A high resolution global model to estimate the emissions from open burning. Geosci. Model Dev. 4, 625–641 (2011).Article 

    Google Scholar 
    Eckhardt, S. et al. Current model capabilities for simulating black carbon and sulfate concentrations in the Arctic atmosphere: a multi-model evaluation using a comprehensive measurement data set. Atmos. Chem. Phys. 15, 9413–9433 (2015).CAS 
    Article 

    Google Scholar 
    Hamilton, D. S. et al. Impact of changes to the atmospheric soluble iron deposition flux on ocean biogeochemical cycles in the anthropocene. Glob. Biogeochem. Cycle 34, e2019GB006448 (2020).CAS 
    Article 

    Google Scholar 
    Kramer, S. J., Bisson, K. M. & Fischer, A. D. Observations of phytoplankton community composition in the Santa Barbara channel during the Thomas fire. J. Geophys. Res. Oceans 125, e2020JC016851 (2020).Article 

    Google Scholar 
    Kim, Y., Hatsushika, H., Muskett, R. R. & Yamazaki, K. Possible effect of boreal wildfire soot on Arctic sea ice and Alaska glaciers. Atmos. Environ. 39, 3513–3520 (2005).CAS 
    Article 

    Google Scholar 
    Knapp, P. A. & Soulé, P. T. Spatio-temporal linkages between declining Arctic sea-ice extent and increasing wildfire activity in the Western United States. Forests 8, 313 (2017).Article 

    Google Scholar 
    Horvat, C. et al. The frequency and extent of sub-ice phytoplankton blooms in the Arctic Ocean. Sci. Adv. https://doi.org/10.1126/sciadv.1601191 (2017).Ardyna, M. et al. Under-ice phytoplankton blooms: Shedding light on the “invisible” part of arctic primary production. Front. Mar. Sci. https://doi.org/10.3389/fmars.2020.608032 (2020).Altieri, K. E., Fawcett, S. E. & Hastings, M. G. Reactive nitrogen cycling in the atmosphere and ocean. Annu. Rev. Earth Planet. Sci. https://doi.org/10.1146/annurev-earth-083120-052147 (2021).Baker, A. R. & Jickells, T. D. Atmospheric deposition of soluble trace elements along the Atlantic Meridional Transect (AMT). Prog. Oceanogr. 158, 41–51 (2017).Article 

    Google Scholar 
    Hugelius, G. et al. Large stocks of peatland carbon and nitrogen are vulnerable to permafrost thaw. Proc. Natl. Acad. Sci. USA 117, 20438–20446 (2020).CAS 
    Article 

    Google Scholar 
    Schmale, J. et al. Pan-Arctic seasonal cycles and long-term trends of aerosol properties from 10 observatories. Atmos. Chem. Phys. 22, 3067–3096 (2022).CAS 
    Article 

    Google Scholar 
    Lewis, K. M., van Dijken, G. L. & Arrigo, K. R. Changes in phytoplankton concentration now drive increased Arctic Ocean primary production. Science 369, 198–202 (2020).CAS 
    Article 

    Google Scholar 
    Ardyna, M. & Arrigo, K. R. Phytoplankton dynamics in a changing Arctic Ocean. Nat. Clim. Change 10, 892–903 (2020).CAS 
    Article 

    Google Scholar 
    Tang, W. et al. Widespread phytoplankton blooms triggered by 2019–2020 Australian wildfires. Nature 597, 370–375 (2021).CAS 
    Article 

    Google Scholar 
    Fossheim, M. et al. Recent warming leads to a rapid borealization of fish communities in the Arctic. Nat. Clim. Change 5, 673–677 (2015).Article 

    Google Scholar 
    Sathyendranath, S. et al. An ocean-colour time series for use in climate studies: The experience of the Ocean-colour Climate Change Initiative (OC-CCI). Sensors 19, 4285 (2019).CAS 
    Article 

    Google Scholar 
    Gordon, H. R. & Wang, M. Retrieval of water-leaving radiance and aerosol optical thickness over the oceans with SeaWiFS: A preliminary algorithm. Appl. Opt. 33, 443–452 (1994).CAS 
    Article 

    Google Scholar 
    Werdell, P. J. & Bailey, S. W. An improved in-situ bio-optical data set for ocean color algorithm development and satellite data product validation. Remote Sens. Environ. 98, 122–140 (2005).Article 

    Google Scholar 
    Hu, C., Lee, Z. & Franz, B. Chlorophyll a algorithms for oligotrophic oceans: A novel approach based on three-band reflectance difference. J. Geophys. Res. Oceans https://doi.org/10.1029/2011JC007395 (2012).Tilmes, S. et al. Description and evaluation of tropospheric chemistry and aerosols in the Community Earth System Model (CESM1.2). Geosci. Model Dev. 8, 1395–1426 (2015).Article 

    Google Scholar 
    Bernstein, D. et al. Short-term impacts of 2017 western North American wildfires on meteorology, the atmosphere’s energy budget, and premature mortality. Environ. Res. Lett. 16, 064065 (2021).Article 

    Google Scholar 
    Liu, X. et al. Description and evaluation of a new four-mode version of the Modal Aerosol Module (MAM4) within version 5.3 of the Community Atmosphere Model. Geosci. Model Dev. 9, 505–522 (2016).CAS 
    Article 

    Google Scholar 
    Suarez, M. J. et al. The GEOS-5 Data Assimilation System – Documentation of Versions 5.0.1, 5.1.0, and 5.2.0. No. NASA/TM-2008-104606-VOL-27 (2008).Janssens-Maenhout, G. et al. HTAP_v2.2: A mosaic of regional and global emission grid maps for 2008 and 2010 to study hemispheric transport of air pollution. Atmos. Chem. Phys. 15, 11411–11432 (2015).CAS 
    Article 

    Google Scholar 
    Dentener, F. et al. Emissions of primary aerosol and precursor gases in the years 2000 and 1750 prescribed data-sets for AeroCom. Atmos. Chem. Phys. 6, 4321–4344 (2006).CAS 
    Article 

    Google Scholar 
    Inness, A. et al. The CAMS reanalysis of atmospheric composition. Atmos. Chem. Phys. 19, 3515–3556 (2019).CAS 
    Article 

    Google Scholar 
    Stein, A. F. et al. NOAA’s HYSPLIT atmospheric transport and dispersion modeling system. Bull. Am. Meteorol. Soc. 96, 2059–2077 (2015).Article 

    Google Scholar 
    Carter, T. S. et al. How emissions uncertainty influences the distribution and radiative impacts of smoke from fires in North America. Atmos. Chem. Phys. 20, 2073–2097 (2020).CAS 
    Article 

    Google Scholar 
    Pan, X. et al. Six global biomass burning emission datasets: Intercomparison and application in one global aerosol model. Atmos. Chem. Phys. 20, 969–994 (2020).CAS 
    Article 

    Google Scholar 
    Reddington, C. L. et al. Analysis of particulate emissions from tropical biomass burning using a global aerosol model and long-term surface observations. Atmos. Chem. Phys. 16, 11083–11106 (2016).CAS 
    Article 

    Google Scholar 
    Kiely, L. et al. New estimate of particulate emissions from Indonesian peat fires in 2015. Atmos. Chem. Phys. 19, 11105–11121 (2019).CAS 
    Article 

    Google Scholar 
    Giglio, L., Boschetti, L., Roy, D. P., Humber, M. L. & Justice, C. O. The Collection 6 MODIS burned area mapping algorithm and product. Remote Sens. Environ. 217, 72–85 (2018).Arrigo, K. R. et al. Phytoplankton blooms beneath the sea ice in the Chukchi Sea. Deep Sea Res. Pt. 2 105, 1–16 (2014).Article 

    Google Scholar 
    Geider, R. J., Maclntyre, H. L. & Kana, T. M. A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature. Limnol. Oceanogr. 43, 679–694 (1998).CAS 
    Article 

    Google Scholar 
    Liefer, J. D., Garg, A., Campbell, D. A., Irwin, A. J. & Finkel, Z. V. Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes. PLoS One 13, e0195705 (2018).Article 
    CAS 

    Google Scholar  More

  • in

    Climate change increases global risk to urban forests

    Liu, Z., He, C., Zhou, Y. & Wu, J. How much of the world’s land has been urbanized, really? A hierarchical framework for avoiding confusion. Landsc. Ecol. 29, 763–771 (2014).
    Google Scholar 
    The World’s Cities in 2018: Data Booklet (UN, 2018).Miller, R. W., Hauer, R. J. & Werner, L. P. Urban Forestry: Planning and Managing Urban Greenspaces 3rd edn (Waveland Press, 2015).Escobedo, F. J., Kroeger, T. & Wagner, J. E. Urban forests and pollution mitigation: analyzing ecosystem services and disservices. Environ. Pollut. 159, 2078–2087 (2011).CAS 

    Google Scholar 
    Keeler, B. L. et al. Social-ecological and technological factors moderate the value of urban nature. Nat. Sustain. 2, 29 (2019).
    Google Scholar 
    Petri, A. C., Koeser, A. K., Lovell, S. T. & Ingram, D. How green are trees?—using life cycle assessment methods to assess net environmental benefits. J. Environ. Hortic. 34, 101–110 (2016).CAS 

    Google Scholar 
    Bastin, J.-F. et al. The global tree restoration potential. Science 365, 76–79 (2019).CAS 

    Google Scholar 
    IPCC Climate Change 2021: The Physical Science Basis (eds Masson-Delmotte, V. et al.) (Cambridge Univ. Press, 2021).Van Mantgem, P. J. et al. Widespread increase of tree mortality rates in the western United States. Science 323, 521–524 (2009).
    Google Scholar 
    Nowak, D. J. & Greenfield, E. J. Declining urban and community tree cover in the United States. Urban For. Urban Green. 32, 32–55 (2018).
    Google Scholar 
    Easterling, D. R. et al. Climate extremes: observations, modeling, and impacts. Science 289, 2068–2074 (2000).CAS 

    Google Scholar 
    Zscheischler, J. et al. Future climate risk from compound events. Nat. Clim. Change 8, 469–477 (2018).
    Google Scholar 
    Yan, P. & Yang, J. Performances of urban tree species under disturbances in 120 cities in China. Forests 9, 50 (2018).
    Google Scholar 
    Hilbert, D., Roman, L., Koeser, A. K., Vogt, J. & Van Doorn, N. S. Urban tree mortality: a literature review. Arboric. Urban For. 45, 167–200 (2019).
    Google Scholar 
    Young, R. F. & McPherson, E. G. Governing metropolitan green infrastructure in the United States. Landsc. Urban Plan. 109, 67–75 (2013).
    Google Scholar 
    Esperon-Rodriguez, M. et al. Assessing climate risk to support urban forests in a changing climate. Plants People Planet https://doi.org/10.1002/ppp3.10240 (2022).Esperon-Rodriguez, M. et al. Assessing the vulnerability of Australia’s urban forests to climate extremes. Plants People Planet 1, 387–397 (2019).Gallagher, R. V., Allen, S. & Wright, I. J. Safety margins and adaptive capacity of vegetation to climate change. Sci. Rep. 9, 8241 (2019).
    Google Scholar 
    Bertrand, R. et al. Changes in plant community composition lag behind climate warming in lowland forests. Nature 479, 517–520 (2011).CAS 

    Google Scholar 
    Bertrand, R. et al. Ecological constraints increase the climatic debt in forests. Nat. Commun. 7, 12643 (2016).Richard, B. et al. The climatic debt is growing in the understory of temperate forests: stand characteristics matter. Global Ecol. Biogeogr. 30, 1474–1487 (2021).IPCC Climate Change 2001: The Scientific Basis (eds Houghton, J. T. et al.) (Cambridge Univ. Press, 2001).Dawson, T. P., Jackson, S. T., House, J. I., Prentice, I. C. & Mace, G. M. Beyond predictions: biodiversity conservation in a changing climate. Science 332, 53–58 (2011).CAS 

    Google Scholar 
    Foden, W. B. et al. Climate change vulnerability assessment of species. WIREs Clim. Change 10, e551 (2019).
    Google Scholar 
    Pacifici, M. et al. Assessing species vulnerability to climate change. Nat. Clim. Change 5, 215–224 (2015).
    Google Scholar 
    Reisinger, A. et al. The Concept of Risk in the IPCC Sixth Assessment Report: A Summary of Cross-Working Group Discussions (IPCC, 2020).Chen, C. et al. University of Notre Dame Global Adaptation Index: Country Index Technical Report (ND-GAIN, 2015).McPherson, E. G., Berry, A. M. & van Doorn, N. S. Performance testing to identify climate-ready trees. Urban For. Urban Green. 29, 28–39 (2018).
    Google Scholar 
    Soberón, J. & Peterson, A. T. Interpretation of models of fundamental ecological niches and species’ distributional areas. Biodivers. Inform. 2 https://doi.org/10.17161/bi.v2i0.4 (2005).Pulliam, H. R. On the relationship between niche and distribution. Ecol. Lett. 3, 349–361 (2000).
    Google Scholar 
    Ordóñez, C. & Duinker, P. Assessing the vulnerability of urban forests to climate change. Environ. Rev. 22, 311–321 (2014).
    Google Scholar 
    Gallagher, R. V., Beaumont, L. J., Hughes, L. & Leishman, M. R. Evidence for climatic niche and biome shifts between native and novel ranges in plant species introduced to Australia. J. Ecol. 98, 790–799 (2010).
    Google Scholar 
    Smith, I. A., Dearborn, V. K. & Hutyra, L. R. Live fast, die young: accelerated growth, mortality, and turnover in street trees. PLoS ONE 14, e0215846 (2019).
    Google Scholar 
    Hirabayashi, Y., Kanae, S., Emori, S., Oki, T. & Kimoto, M. Global projections of changing risks of floods and droughts in a changing climate. Hydrol. Sci. J. 53, 754–772 (2008).
    Google Scholar 
    Van der Veken, S., Hermy, M., Vellend, M., Knapen, A. & Verheyen, K. Garden plants get a head start on climate change. Front. Ecol. Environ. 6, 212–216 (2008).
    Google Scholar 
    Ballinas, M. & Barradas, V. L. Transpiration and stomatal conductance as potential mechanisms to mitigate the heat load in Mexico City. Urban For. Urban Green. 20, 152–159 (2016).
    Google Scholar 
    Di Baldassarre, G. et al. Water shortages worsened by reservoir effects. Nat. Sustain. 1, 617 (2018).
    Google Scholar 
    Hoekstra, A. Y. & Mekonnen, M. M. The water footprint of humanity. Proc. Natl Acad. Sci. USA 109, 3232–3237 (2012).CAS 

    Google Scholar 
    Manoli, G. et al. Magnitude of urban heat islands largely explained by climate and population. Nature 573, 55–60 (2019).CAS 

    Google Scholar 
    Kim, D.-H., Doyle, M. R., Sung, S. & Amasino, R. M. Vernalization: winter and the timing of flowering in plants. Annu. Rev. Cell Dev. Biol. 25, 277–299 (2009).CAS 

    Google Scholar 
    Kummu, M. & Varis, O. The world by latitudes: a global analysis of human population, development level and environment across the north–south axis over the past half century. Appl. Geogr. 31, 495–507 (2011).
    Google Scholar 
    Vogt, J. et al. Citree: a database supporting tree selection for urban areas in temperate climate. Landsc. Urban Plan. 157, 14–25 (2017).
    Google Scholar 
    Paquette, A. et al. Praise for diversity: a functional approach to reduce risks in urban forests. Urban For. Urban Green. 62, 127157 (2021).
    Google Scholar 
    Esperon-Rodriguez, M. et al. Functional adaptations and trait plasticity of urban trees along a climatic gradient. Urban For. Urban Green. 54, 126771 (2020).
    Google Scholar 
    Hirons, A. D. et al. Using botanic gardens and arboreta to help identify urban trees for the future. Plants People Planet 3, 182–193 (2021).
    Google Scholar 
    Watkins, H., Hirons, A., Sjöman, H., Cameron, R. & Hitchmough, J. D. Can trait-based schemes be used to select species in urban forestry? Front. Sustain. Cities 3 https://doi.org/10.3389/frsc.2021.654618 (2021).Populated Places (Natural Earth, accessed 2018); http://www.naturalearthdata.com/downloads/Ossola, A. et al. The Global Urban Tree Inventory: a database of the diverse tree flora that inhabits the world’s cities. Glob. Ecol. Biogeogr. 29, 1907–1914 (2020).
    Google Scholar 
    Sabatini, F., Lenoir, J. & Bruelheide, H. sPlotOpen—An Environmentally-Balanced, Open-Access, Global Dataset of Vegetation Plots (iDiv, 2021); https://doi.org/10.25829/idiv.3474-40-3292Sabatini, F. M. et al. sPlotOpen—an environmentally balanced, open-access, global dataset of vegetation plots. Global Ecol. Biogeogr. 30, 1740–1764 (2021).Zizka, A. et al. CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods Ecol. Evol. 10, 744–751 (2019).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).Taxonstand: Taxonomic standardization of plant species names. R package version 2.4 https://cran.r-project.org/web/packages/Taxonstand/Taxonstand.pdf (2021).Kelso, N. & Patterson, T. World Urban Areas, LandScan, 1:10 Million (2012) (North American Cartographic Information Society, 2012).Karger, D. N. et al. Climatologies at high resolution for the earth’s land surface areas. Sci. Data 4, 170122 (2017).
    Google Scholar 
    O’Donnell, M. S. & Ignizio, D. A. Bioclimatic Predictors for Supporting Ecological Applications in the Conterminous United States (USGS, 2012).Field, C. et al. IPCC, 2014: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (Cambridge Univ. Press, 2014).Meinshausen, M. et al. The RCP greenhouse gas concentrations and their extensions from 1765 to 2300. Clim. Change 109, 213–241 (2011).CAS 

    Google Scholar 
    Zhao, L. et al. Global multi-model projections of local urban climates. Nat. Clim. Change 11, 152–157 (2021).
    Google Scholar 
    Huang, K., Li, X., Liu, X. & Seto, K. C. Projecting global urban land expansion and heat island intensification through 2050. Environ. Res. Lett. 14, 114037 (2019).
    Google Scholar 
    Alavipanah, S., Wegmann, M., Qureshi, S., Weng, Q. & Koellner, T. The role of vegetation in mitigating urban land surface temperatures: a case study of Munich, Germany during the warm season. Sustainability 7, 4689–4706 (2015).
    Google Scholar 
    Corburn, J. Cities, climate change and urban heat island mitigation: localising global environmental science. Urban Stud. 46, 413–427 (2009).
    Google Scholar 
    Baston, D., ISciences, L.L., Baston, M.D. Package ‘exactextractr’. terra. R package version 0.8.2 (2022).Hijmans, R. J. et al. raster: Geographic data analysis and modeling. R package version 2.3-33 http://cran.r-project.org/web/packages/raster/index.html (2016).Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).
    Google Scholar 
    Bivand, R. et al. maptools: Tools for handling spatial objects. R package version 08, 23 https://cran.r-project.org/web/packages/maptools/ (2013). More

  • in

    Ninety years of coastal monitoring reveals baseline and extreme ocean temperatures are increasing off the Finnish coast

    IPCC, 2014, Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change.Bindoff, N. L. et al. Changing Ocean, Marine Ecosystems, and Dependent Communities. IPCC Spec. Rep. Ocean Cryosph. a Chang. Clim. [H.-O. Pörtner, D.C. Roberts, V. Masson-Delmotte, P. Zhai, M. Tignor, E. Poloczanska, K. Mintenbeck, A. Alegría, M. Nicolai, A. Okem, J. Petzold, B. Rama, N.M. Weyer (eds.)]. Press 447–588 (2019).Cheng, L. et al. Upper Ocean Temperatures Hit Record High in 2020. Adv. Atmos. Sci. 38, 523–530 (2021).Article 

    Google Scholar 
    Smale, D. A. et al. Marine heatwaves threaten global biodiversity and the provision of ecosystem services. Nat. Clim. Chang. 9, 306–312 (2019).Article 

    Google Scholar 
    Hobday, A. J. et al. A hierarchical approach to defining marine heatwaves. Prog. Oceanogr. 141, 227–238 (2016).Article 

    Google Scholar 
    Garrabou, J. et al. Mass mortality in Northwestern Mediterranean rocky benthic communities: Effects of the 2003 heat wave. Glob. Chang. Biol. 15, 1090–1103 (2009).Article 

    Google Scholar 
    Frölicher, T. L. & Laufkötter, C. Emerging risks from marine heat waves. Nat. Commun. 9, 2015–2018 (2018).Article 

    Google Scholar 
    Oliver, E. C. J. et al. Longer and more frequent marine heatwaves over the past century. Nat. Commun. https://doi.org/10.1038/s41467-018-03732-9 (2018).Article 

    Google Scholar 
    Garcia-Herrera, R., Díaz, J., Trigo, R. M., Luterbacher, J. & Fischer, E. M. A review of the european summer heat wave of 2003. Crit. Rev. Environ. Sci. Technol. 40, 267–306 (2010).Article 

    Google Scholar 
    Marbà, N., Jordà, G., Agustí, S., Girard, C. & Duarte, C. M. Footprints of climate change on Mediterranean Sea biota. Front. Mar. Sci. 2, 56 (2015).Holbrook, N. J. et al. Keeping pace with marine heatwaves. Nat. Rev. Earth Environ. https://doi.org/10.1038/s43017-020-0068-4 (2020). in press.Article 

    Google Scholar 
    Oliver, E. C. J., Wernberg, T., Benthuysen, J., Chen, K. & Eds. Advances in Understanding Marine Heatwaves and Their Impacts. Lausanne: Frontiers Media SA. vol. 7 (2020).Smale, D. A. & Wernberg, T. Satellite-derived SST data as a proxy for water temperature in nearshore benthic ecology. Mar. Ecol. Prog. Ser. 387, 27–37 (2009).Article 

    Google Scholar 
    Schlegel, R. W., Oliver, E. C. J., Wernberg, T. & Smit, A. J. Nearshore and offshore co-occurrence of marine heatwaves and cold-spells. Prog. Oceanogr. 151, 189–205 (2017).Article 

    Google Scholar 
    Rutgersson, A., Jaagus, J., Schenk, F. & Stendel, M. Observed changes and variability of atmospheric parameters in the Baltic Sea region during the last 200 years. Clim Res. 61, 177–190 (2014).Liblik, T. & Lips, U. Stratification has strengthened in the baltic sea – an analysis of 35 years of observational data. Front. Earth Sci. 7, 1–15 (2019).Article 

    Google Scholar 
    Reusch, T. B. H. et al. The Baltic Sea as a time machine for the future coastal ocean. Sci. Adv. 4, eaar8195 (2018).Hu, S. et al. Observed strong subsurface marine heatwaves in the tropical western Pacific Ocean. Environ. Res. Lett. 16, 104024 (2021).Scannell, H. A., Johnson, G. C., Thompson, L., Lyman, J. M. & Riser, S. C. Subsurface Evolution and Persistence of Marine Heatwaves in the Northeast Pacific. Geophys. Res. Lett. 47, 1–10 (2020).Article 

    Google Scholar 
    Schaeffer, A. & Roughan, M. Subsurface intensification of marine heatwaves off southeastern Australia: The role of stratification and local winds. Geophys. Res. Lett. 44, 5025–5033 (2017).Article 

    Google Scholar 
    WMO, Guide to Climatological Practices. (2018).Hobday, A. J. et al. Categorizing and naming marine heatwaves. Oceanography 31, 162–173 (2018).Article 

    Google Scholar 
    Zanna, L., Khatiwala, S., Gregory, J. M., Ison, J. & Heimbach, P. Global reconstruction of historical ocean heat storage and transport. Proc. Natl. Acad. Sci. U. S. A. 116, 1126–1131 (2019).CAS 
    Article 

    Google Scholar 
    Reynolds, R. W. et al. Daily high-resolution-blended analyses for sea surface temperature. J. Clim. 1, 5473–5496 (2007).Veneranta, L., Vanhatalo, J. & Urho, L. Detailed temperature mapping–Warming characterizes archipelago zones. Estuar. Coast. Shelf Sci. 182, 123–135 (2016).Article 

    Google Scholar 
    Merkouriadi, I. & Leppäranta, M. Long-term analysis of hydrography and sea-ice data in Tvärminne, Gulf of Finland, Baltic Sea. Clim. Change 124, 849–859 (2014).CAS 
    Article 

    Google Scholar 
    Woolway, R. I. et al. Lake heatwaves under climate change. Nature 589, 402–407 (2021).CAS 
    Article 

    Google Scholar 
    Frölicher, T. L., Fischer, E. M. & Gruber, N. Marine heatwaves under global warming. Nature 560, 360–364 (2018).Article 

    Google Scholar 
    Rey, J., Rohat, G., Perroud, M., Goyette, S. & Kasparian, J. Shifting velocity of temperature extremes under climate change. Environ. Res. Lett. 15, 034027 (2020).Oliver, E. C. J. et al. Marine Heatwaves. Ann. Rev. Mar. Sci. 13, 313–342 (2021).Article 

    Google Scholar 
    Bennett, J. M. et al. The evolution of critical thermal limits of life on Earth. Nat. Commun. 1–9 (2021) https://doi.org/10.1038/s41467-021-21263-8.Holbrook, N. J. et al. A global assessment of marine heatwaves and their drivers. Nat. Commun. 10, 1–13 (2019).CAS 
    Article 

    Google Scholar 
    Kniebusch, M., Meier, H. E. M., Neumann, T. & Börgel, F. Temperature variability of the baltic sea since 1850 and attribution to atmospheric forcing variables. J. Geophys. Res. Ocean. 124, 4168–4187 (2019).Article 

    Google Scholar 
    Merkouriadi, I. & Leppäranta, M. Influence of sea ice on the seasonal variability of hydrography and heat content in Tvärminne, Gulf of Finland. Ann. Glaciol. 56, 274–284 (2015).Article 

    Google Scholar 
    Haapala, J. Upwelling and its influence on nutrient concentration in the coastal area of the Hanko Peninsula, entrance of the Gulf of Finland. Estuarine, Coastal and Shelf Science 38, 507–521 (1994).CAS 
    Article 

    Google Scholar 
    Sorte, C. J. B., Fuller, A. & Bracken, M. E. S. Impacts of a simulated heat wave on composition of a marine community. Oikos 119, 1909–1918 (2010).Article 

    Google Scholar 
    Pansch, C. et al. Heat waves and their significance for a temperate benthic community: A near-natural experimental approach. Glob. Chang. Biol. 24, 4357–4367 (2018).Article 

    Google Scholar 
    Morón Lugo, S. C. et al. Warming and temperature variability determine the performance of two invertebrate predators. Sci. Rep. 10, 1–14 (2020).Article 

    Google Scholar 
    Humborg, C. et al. High emissions of carbon dioxide and methane from the coastal Baltic Sea at the end of a summer heat wave. Front. Mar. Sci. 6, 1–14 (2019).Article 

    Google Scholar 
    Laakso, L. et al. 100 Years of atmospheric and marine observations at the Finnish Utö Island in the Baltic Sea. Ocean Sci. 14, 617–632 (2018).Article 

    Google Scholar 
    Høyer, J. L. & Karagali, I. Sea surface temperature climate data record for the North Sea and Baltic Sea. J. Clim. 29, 2529–2541 (2016).Article 

    Google Scholar 
    Schlegel, R. W. & Smit, A. J. heatwaveR: A central algorithm for the detection of heatwaves and cold-spells. J. Open Source Softw. 3, 821 (2018).Article 

    Google Scholar 
    Schlegel, R. W., Oliver, E. C. J., Hobday, A. J. & Smit, A. J. Detecting Marine Heatwaves With Sub-Optimal Data. Front. Mar. Sci. 6, 1–14 (2019).Article 

    Google Scholar  More