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    Past climate conditions predict the influence of nitrogen enrichment on the temperature sensitivity of soil respiration

    1.Bond-Lamberty, B. & Thomson, A. Temperature-associated increases in the global soil respiration record. Nature 464, 579–582 (2010).CAS 

    Google Scholar 
    2.Raich, J. W., Potter, C. S. & Bhagawati, D. Interannual variability in global soil respiration, 1980–94. Glob. Change Biol. 8, 800–812 (2002).
    Google Scholar 
    3.Davidson, E. A. & Janssens, I. A. Temperature sensitivity of soil carbon decomposition feedbacks to climate change. Nature 440, 165–173 (2006).CAS 

    Google Scholar 
    4.Feng, X., Simpson, A. J., Wilson, K. P., Williams, D. D. & Simpson, M. J. Increased cuticular carbon sequestration and lignin oxidation in response to soil warming. Nat. Geosci. 1, 836–839 (2008).CAS 

    Google Scholar 
    5.Heimann, H. & Reichstein, R. Terrestrial ecosystem carbon dynamics and climate feedbacks. Nature 451, 289–292 (2008).CAS 

    Google Scholar 
    6.Fang, C. et al. Impacts of warming and nitrogen addition on soil autotrophic and heterotrophic respiration in a semi-arid environment. Agr. Forest Meteorol. 248, 449–457 (2018).
    Google Scholar 
    7.Wang, Q., Liu, S., Wang, Y., Tian, P. & Sun, T. Influences of N deposition on soil microbial respiration and its temperature sensitivity depend on N type in a temperate forest. Agr. Forest Meteorol. 260–261, 240–246 (2018).
    Google Scholar 
    8.Zhong, Y. Q. W., Yan, W. M., Zong, Y. Z. & Shangguan, Z. P. The effects of nitrogen enrichment on soil CO2 fluxes depending on temperature and soil properties. Global Ecol. Biogeogr. 25, 475–488 (2016).
    Google Scholar 
    9.Yu, G. R. et al. Stabilization of atmospheric nitrogen deposition in China over the past decade. Nat. Geosci. 12, 424–429 (2019).CAS 

    Google Scholar 
    10.Coucheney, E., Strömgren, M., Lerch, T. Z. & Herrmann, A. M. Long-term fertilization of a boreal Norway spruce forest increases the temperature sensitivity of soil organic carbon mineralization. Ecol. Evol. 3, 5177–5188 (2013).
    Google Scholar 
    11.Jiang, J. S., Guo, S. L., Wang, R., Liu, Q. F. & Sun, Q. Q. Effects of nitrogen fertilization on soil respiration and temperature sensitivity in spring maize field in semi-arid regions on loess plateau. Environ. Sci. 36, 1802–1809 (2015).
    Google Scholar 
    12.Wang, Q., Zhao, X., Tian, P., Liu, S. & Sun, Z. Bioclimate and arbuscular mycorrhizal fungi regulate continental biogeographic variations in effect of nitrogen deposition on the temperature sensitivity of soil organic carbon decomposition. Land Degrad. Dev. 32, 936–945 (2021).
    Google Scholar 
    13.Schindlbacher, A., Zechmeister-Boltenstern, S. & Jandl, R. Carbon losses due to soil warming: do autotrophic and heterotrophic soil respiration respond equally? Glob. Change Biol. 15, 901–903 (2009).
    Google Scholar 
    14.Carey, J. C. et al. Temperature response of soil respiration largely unaltered with experimental warming. Proc. Natl Acad. Sci. 113, 13797–13802 (2016).CAS 

    Google Scholar 
    15.Lyu, M., Giardina, C. P. & Litton, C. M. Interannual variation in rainfall modulates temperature sensitivity of carbon allocation and flux in a tropical montane wet forest. Glob. Change Biol. 27, 3824–3836 (2021).
    Google Scholar 
    16.Wang, Q. et al. Global synthesis of temperature sensitivity of soil organic carbon decomposition: latitudinal patterns and mechanisms. Funct. Ecol. 33, 514–523 (2019).
    Google Scholar 
    17.Li, J. et al. Biogeographic variation in temperature sensitivity of decomposition in forest soils. Glob. Change Biol. 26, 1873–1885 (2020).
    Google Scholar 
    18.Delgado-Baquerizo, M. et al. Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities. Nat. Ecol. Evol. 1, 1339–1347 (2017).
    Google Scholar 
    19.Delgado-Baquerizo, M. et al. Climate legacies drive global soil carbon stocks in terrestrial ecosystems. Sci. Adv. 3, e1602008 (2017).
    Google Scholar 
    20.Delgado-Baquerizo, M. et al. Ecological drivers of soil microbial diversity and soil biological networks in the southern hemisphere. Ecology 99, 583–596 (2018).
    Google Scholar 
    21.Ding, J. Y. & Eldridge, D. J. Contrasting global effects of woody plant removal on ecosystem structure, function and composition. Perspect. Plant Ecol. 39, 125460 (2019).
    Google Scholar 
    22.Eldridge, D. J. & Delgado-Baquerizo, M. The influence of climatic legacies on the distribution of dryland biocrust communities. Glob. Change Biol. 25, 327–336 (2019).
    Google Scholar 
    23.Pärtel, M., Chiarucci, A., Chytrý, M. & Pillar, V. D. Mapping plant community ecology. J. Veg. Sci. 26, 1–3 (2017).
    Google Scholar 
    24.Richter, D. D. & Yaalon, D. H. “The changing model of soil” revisited. Soil Sci. Soc. Am. J. 76, 766–778 (2012).CAS 

    Google Scholar 
    25.Lyons, S. K. et al. Holocene shifts in the assembly of plant and animal communities implicate human impacts. Nature 529, 80–83 (2016).
    Google Scholar 
    26.Schmidt, M. W. I. et al. Persistence of soil organic matter as an ecosystem property. Nature 478, 49–56 (2011).CAS 

    Google Scholar 
    27.Delgado-Baquerizo, M. et al. Carbon content and climate variability drive global soil bacterial diversity patterns. Ecol. Monogr. 86, 373–390 (2016).
    Google Scholar 
    28.Maestre, F. T., Delgado-Baquerizo, M., Jeffries, T. C., Eldridge, D. J. & Singh, B. K. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc. Natl Acad. Sci. 112, 15684–15689 (2015).CAS 

    Google Scholar 
    29.Monger, C. et al. Legacy effects in linked ecological–soil–geomorphic systems of drylands. Front. Ecol. Environ. 13, 13–19 (2016).
    Google Scholar 
    30.Cox, P. M., Betts, R. A., Jones, C. D., Spall, S. A. & Totterdell, I. J. Acceleration of global warming due to carbon-cycle feedbacks in a coupled climate model. Nature 408, 184–187 (2000).CAS 

    Google Scholar 
    31.Fierer, N., Colman, B. P., Schimel, J. P. & Jackson, R. B. Predicting the temperature dependence of microbial respiration in soil: a continental-scale analysis. Glob. Biogeochem. Cy. 20, GB3026 (2006).
    Google Scholar 
    32.Peng, S., Piao, S., Wang, T., Sun, J. & Shen, Z. Temperature sensitivity of soil respiration in different ecosystems in China. Soil Biol. Biochem. 41, 1008–1014 (2009).CAS 

    Google Scholar 
    33.Xu, Z. et al. Temperature sensitivity of soil respiration in China’s forest ecosystems: patterns and controls. Appl. Soil Ecol. 93, 105–110 (2015).
    Google Scholar 
    34.Niu, B. et al. Warming homogenizes apparent temperature sensitivity of ecosystem respiration. Sci. Adv. 7, eabc7358 (2021).
    Google Scholar 
    35.Janssens, I. A. et al. Reduction of forest soil respiration in response to nitrogen deposition. Nat. Geosci. 3, 315–322 (2010).CAS 

    Google Scholar 
    36.Yan, G. Y. et al. Sequestration of atmospheric CO2 in boreal forest carbon pools in northeastern China: Effects of nitrogen deposition. Agr. Forest Meteorol. 248, 70–81 (2018).
    Google Scholar 
    37.Du, E. Z. et al. Global patterns of terrestrial nitrogen and phosphorus limitation. Nat. Geosci. 13, 221–226 (2020).CAS 

    Google Scholar 
    38.Chen, Z. M. et al. Nitrogen fertilization stimulated soil heterotrophic but not autotrophic respiration in cropland soils: A greater role of organic over inorganic fertilizer. Soil Biol. Biochem. 116, 253–264 (2018).CAS 

    Google Scholar 
    39.Chen, F. et al. Effects of N addition and precipitation reduction on soil respiration and its components in a temperate forest. Agr. Forest Meteorol. 271, 336–345 (2019).
    Google Scholar 
    40.Zhang, C. et al. Effects of simulated nitrogen deposition on soil respiration components and their temperature sensitivities in a semiarid grassland. Soil Biol. Biochem. 75, 113–123 (2014).CAS 

    Google Scholar 
    41.Moinet, G. Y. K. et al. The temperature sensitivity of soil organic matter decomposition is constrained by microbial access to substrates. Soil Biol. Biochem. 116, 333–339 (2018).CAS 

    Google Scholar 
    42.Li, Y. et al. Soil acid cations induced reduction in soil respiration under nitrogen enrichment and soil acidification. Sci. Total Environ. 615, 1535–1546 (2018).CAS 

    Google Scholar 
    43.Sanderman, J. Comment on “Climate legacies drive global soil carbon stocks in terrestrial ecosystems”. Sci. Adv. 4, e1701482 (2018).
    Google Scholar 
    44.Ding, J. et al. The paleoclimatic footprint in the soil carbon stock of the Tibetan permafrost region. Nat. Commun. 10, 4195 (2019).
    Google Scholar 
    45.Gershenson, A., Bader, N. E. & Cheng, W. X. Effects of substrate availability on the temperature sensitivity of soil organic matter decomposition. Glob. Change Biol. 15, 176–183 (2009).
    Google Scholar 
    46.Doetterl, S. et al. Soil carbon storage controlled by interactions between geochemistry and climate. Nat. Geosci. 8, 780–783 (2015).CAS 

    Google Scholar 
    47.Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W. & Courchamp, F. Impacts of climate change on the future of biodiversity. Ecol. Lett. 15, 365–377 (2012).
    Google Scholar 
    48.Li, J., Ziegler, S. E., Lane, C. S. & Billings, S. A. Legacies of native climate regime govern responses of boreal soil microbes to litter stoichiometry and temperature. Soil Biol. Biochem. 66, 204–213 (2013).CAS 

    Google Scholar 
    49.Xu, M. et al. High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau. Glob. Chang. Biol. 27, 2061–2075 (2021).
    Google Scholar 
    50.Du, Y. et al. The response of soil respiration to precipitation change is asymmetric and differs between grasslands and forests. Glob. Chang. Biol. 26, 6015–6024 (2020).
    Google Scholar 
    51.Meier, I. C. & Leuschner, C. Leaf size and leaf area index in Fagus sylvatica forests: competing effects of precipitation, temperature, and nitrogen availability. Ecosystems 11, 655–669 (2008).CAS 

    Google Scholar 
    52.Li, J., Pei, J., Pendall, E., Fang, C. & Nie, M. Spatial heterogeneity of temperature sensitivity of soil respiration: A global analysis of field observations. Soil Biol. Biochem. 141, 107675 (2020).CAS 

    Google Scholar 
    53.Katz, M. H. Multivariable Analysis: A Practical Guide for Clinicians and Public Health Researchers (Cambridge Univ. Press, Cambridge, 2006).54.Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl Acad. Sci. 112, 10967–10972 (2015).CAS 

    Google Scholar 
    55.Grace, J. B. Structural Equation Modeling Natural Systems (Cambridge Univ. Press, Cambridge, 2006).56.Lefcheck, J. S. PiecewiseSEM: piecewise structural equation modelling in r for ecology, evolution, and systematics. Methods Ecol. Evol 7, 573–579 (2016).
    Google Scholar 
    57.Bates, D. et al. lme4: Linear mixed-effects models using Eigen and S4. R package version 1, 1–13 (2017).
    Google Scholar  More

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    Large diatom bloom off the Antarctic Peninsula during cool conditions associated with the 2015/2016 El Niño

    Due to contrasts in oceanographic properties along the NAP24, the sampling grid was split in two subregions: north and south (Fig. 1; see “Methods”). The north and south subregions showed from the satellite data a much higher spring/summer (November–February) mean chlorophyll-a (Chl-a) in 2015/2016 than the decadal average time series (2010–2019; Table 1). In agreement with the El Niño effects10,16, the sea surface temperature (SST) and the air temperature showed substantially lower mean values during the spring/summer of 2015/2016 along the subregions (Table 1). However, there was an evident spatial/temporal variability in sea ice concentration/duration between the subregions, with a northward (southward) lower (higher) mean value during 2015/2016 in relation to the decadal average (Table 1). Along the south subregion during the spring/summer of 2015/2016, the increased Chl-a during January followed the decline in the sea ice concentration over the spring and early summer, concurrent with increased SST, which was markedly colder throughout the seasonal phytoplankton succession (Fig. 2a). These results to the south subregion are consistent with previous studies along the WAP, in which years characterized by longer sea ice cover in winter have led to higher phytoplankton biomass in the following summer associated with a more stable water column11,16,26. To the north subregion, however, although there was a similar pattern between Chl-a and SST, the increased Chl-a during January was not related with the sea ice retreat (Fig. 2b). Moreover, there was a clear difference between the Chl-a peaks (the highest Chl-a value reached) along the subregions from the satellite data. The Chl-a peak in the south subregion occurred in early January (10 January 2016, reaching 1.73 mg m–3), whereas in the north subregion the Chl-a peak was observed in late January (29 January 2016, reaching 2.23 mg m–3).Fig. 1: Study area.Location of hydrographic stations is marked by open circles (November), stars (January), and blue circles (February). The black dashed lines indicate the subregions (north and south) along the NAP and delimit the areas used to estimate average remote sensing measurements. The decadal-mean (2010–2019) remote sensing chlorophyll-a (Chl-a) is exhibited in the background, indicating the biomass (Chl-a) distribution of phytoplankton along the NAP in the last decade. An inset map in the lower right corner shows the location of the NAP within the Atlantic sector of the Southern Ocean.Full size imageTable 1 Biological production and ocean/atmosphere parameters by measurements of remote sensing and local meteorological stations during spring/summer in the NAP subregions.Full size tableFig. 2: Biological production and sea ice dynamics in the NAP seasonal phytoplankton succession of 2015/2016.Continuum remote sensing measurements of chlorophyll-a (Chl-a; solid green line), sea surface temperature (SST; solid blue line), and sea ice concentration (gray area) along the NAP, in south (a) and north (b) subregions during spring/summer of 2015/2016. The dashed green, blue and gray lines indicate the decadal average (2010–2019) of Chl-a, SST, and sea ice concentration, respectively. The solid light green lines represent the Chl-a interpolated values. The background shades show the in situ data sampling periods. It is important to note that Chl-a remote sensing data in Antarctic coastal waters are typically underestimated in respect to in situ Chl-a data (see Supplementary Fig. 1)12,29.Full size imageIt has been estimated that drifters entrained in the Gerlache Strait Current and the Bransfield Strait Current exit the Bransfield Strait in 10–20 days17, which is consistent with the interval of 19 days between both Chl-a peaks when considering the extreme distance between the subregions (see Fig. 1). These authors also estimated that drifters deployed in the Gerlache Strait Current were quickly advected out of the Gerlache Strait in less than 1 week (i.e., low residence time)17, which supports the similar diatom species assemblages identified in our microscopic analysis between stations of the Gerlache Strait and southwestern Bransfield Strait24. Therefore, it is plausible that phytoplankton growth in the north of the Gerlache Strait may be laterally advected northward into the Bransfield Strait, explaining the observed concomitant increase of satellite Chl-a data in both subregions from spring, associated with sea ice retreat southward (Fig. 2). In addition, as phytoplankton biomass tends to accumulate northward17,27,28, the advection processes could also explain the temporal and intensity differences of the Chl-a peaks along the subregions (see Fig. 2). This suggests that there was a link between the sea ice dynamics, phytoplankton biomass (Chl-a) and advection processes along the NAP during the spring/summer of 2015/2016, in which the sea ice melting first triggered an increase in phytoplankton biomass through water column stratification along the south subregion, and the advection processes led to a subsequent increase northward.The satellite Chl-a data require extensive validation with in situ data, especially in polar regions, where cloud cover is ubiquitous and performance is typically poor, due to not properly accurate Chl-a algorithms12,29. For that, although the mean Chl-a in 2015/2016 from the satellite data was approximately twice as large as the decadal average, there was a severe discrepancy in the mean Chl-a values observed between the in situ and remote sensing data (see Table 1 and Supplementary Table 1). This highlights the importance of the in situ dataset reported here, especially evident during February 2016, when the signal of an intense diatom bloom ( > 40 mg m–3 Chl-a)24 was not captured in the satellite data (Supplementary Fig. 1), supporting that phytoplankton biomass accumulation during this summer was much higher than recorded by remote sensing observations (see Table 1). In general, the in situ Chl-a achieved its maximum (40 mg m–3) and higher mean value (17.4 mg m–3) during February comparing to November and January (Supplementary Table 1).Phytoplankton community structure during the spring/summer of 2015/2016 was assessed through Chemical taxonomy (CHEMTAX) software, using accessory pigments versus in situ Chl-a concentrations measured via high-performance liquid chromatography (HPLC; see “Methods”). The main phytoplankton group over the season were diatoms, followed by haptophytes (Phaeocystis antarctica), cryptophytes, and dinoflagellates, according to the succession stage (Fig. 3a). Diatoms dominated the phytoplankton community composition in relation to the other groups along the whole in situ sampling period, although their relative biomass (to the total in situ Chl-a) was lower in some stations compared to others in different moments during spring/summer (Fig. 3a). To assess the degree to which the water column structure was a primary driver for development and intensity of diatom growth3,24, the mixed layer depth (MLD) and water column stability were calculated as a function of seawater potential density (see “Methods”). There was an inverse polynomial relationship between MLD and mean upper ocean stability (averaged over 5−150 m depth; hereafter referred to as upper ocean stability) (Fig. 3b). The significant positive exponential relationship between the upper ocean stability and diatom absolute concentrations (in situ Chl-a) demonstrates that stability, associated with MLD, was an important driver of diatom dynamics (Fig. 3b). This elucidates the increase in biological production during summer months of 2016, when upper ocean physical structures (MLD and stability) were sufficiently shallow and stable to produce the high phytoplankton biomass (in situ Chl-a) registered here. However, as MLD and stability showed similar values between summer months (Supplementary Table 1), only the upper ocean physical structures cannot be accounted for the high differences of in situ Chl-a values observed between diatom blooms in January (maximum of 12 mg m–3) and February (maximum of 40 mg m–3). Likewise, also not explaining these differences of in situ Chl-a values between summer months, macronutrients were highly abundant throughout the seasonal phytoplankton succession (Supplementary Table 1). Furthermore, although no measurements of dissolved iron, which can be considered as a limiting factor to primary productivity30, were carried out here, the Antarctic Peninsula continental shelves have been depicted as a substantial source of this micronutrient to the upper ocean, not limiting phytoplankton growth even during intense blooms31,32.Fig. 3: Phytoplankton community composition and upper ocean physical structures along the NAP seasonal phytoplankton succession of 2015/2016.a Relative biomass (to the total in situ chlorophyll-a; Chl-a) distribution of phytoplankton groups on surface, via HPLC/CHEMTAX analysis, during spring/summer of 2015/2016 along the NAP subregions. The black open circles indicate diatoms, the blue squares indicate Phaeocystis antarctica, the gray diamonds with crosses indicate cryptophytes, the green triangles indicate dinoflagellates, and the light gray open circles indicate green flagellates. b Exponential curve (R2 = 0.57; p 40% the community composition proportion in respect to the total Chl-a (considering the three fractionated size classes). Symbol color indicates the sampling month in respect to November (brown), January (gray), and February (black). The inset shows the polynomial inverse relationship (R2 = 0.51; p  70 µm in length; ref. 24), during January a large number ( > 2.5 × 106 cells L–1) of small ( More

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    Sustainable intensification for a larger global rice bowl

    Data sourcesEighteen rice-producing countries were selected for our analysis (Supplementary Table 1). Those countries account for 88 and 86% of global rice production and harvested rice area2, respectively (FAOSTAT, 2015–2017). We followed two steps to select the dominant cropping systems in each country. Within each country, our study focused on the main rice-producing area(s) (Supplementary Tables 2 and 3). For example, in the case of Brazil, we selected the southern and northern regions, which together account for nearly all rice production in this country. In the case of Vietnam, we selected the Mekong Delta region, which accounts for nearly 60% of national rice production57. While we tried to cover all major rice cropping systems in each country, this was not possible in the case of rainfed lowland rice cropping systems in northeastern Thailand and eastern India because of lack of reliable estimates of yield potential and access to farmer yield and management data. Once the main rice-producing region(s) in each country was (were) identified, we then determined the dominant rice cropping system(s) for each of them (Supplementary Table 3). We note that “cropping system” refers to a unique combination of a number of rice crops planted on the same piece of land within a 12-month period (and their temporal arrangement), water regime (rainfed or irrigated), and ecosystem (upland or lowland) (Supplementary Fig. 1 and Supplementary Table 2). In our study, rice cropping systems are single-, double-, or triple-season rice; none of the cropping systems are ratoon rice. Following the previous examples, two cropping systems were selected for Brazil (rainfed upland single rice and lowland irrigated single rice in the northern and southern regions, respectively) and two systems (double and triple) were selected for the Mekong Delta region in Vietnam. These systems account for nearly all rice harvested areas in these regions. We distinguished between rice-based cropping systems sowing hybrid versus inbred cultivars in the southern USA. Across the 18 countries, this study included a total of 32 rice cropping systems, which, in turn, covered 51% of the global rice harvested area (Supplementary Tables 1 and 3). Note that the area coverage reported here corresponds to that accounted by 32 cropping systems (and not by the countries where the cropping systems were located). These systems portrayed a wide range of biophysical and socio-economic backgrounds (Supplementary Figs. 1 and 2 and Supplementary Tables 1 and 2), leading to average rice yields ranging from 2–10.4 Mg ha−1 (Supplementary Fig. 3). For data analysis purposes, rice cropping systems were classified into tropical and non-tropical9,58,59 and also based upon water regime and crop season.Agronomic information was collected via structure questionnaires completed by agricultural specialists in each country or region (Supplementary Table 6). The collected data included field size, tillage method, crop establishment method, degree of mechanization for each field operation, seeding rate, crop establishment, and harvest dates, nutrient fertilizer rates, manure type, and rate, pesticides (number of applications, products, and rates), irrigation amount (in irrigated systems), energy source for irrigation pumping, labor input, and straw management (Supplementary Tables 4 and 5). Average values for each cropping system reported by country experts were retrieved from survey data available from previous projects (Supplementary Table 7). Rice grain yield was reported at a standard moisture content of 140 g H2O kg−1 grain, separately for each crop cycle, using data from, at least, three recent cropping seasons in each cropping system. In the case of irrigated rice cropping system in Nigeria and Mali, data were only available for one crop cycle in double-season rice. In this case, we assumed management and actual yield to be identical in the two crop cycles.In all cases, and wherever possible, data were cross-validated with other independent datasets (e.g., FAOSTAT, World Bank, IFA, and published journal papers), which gives confidence about the representativeness and accuracy of the survey data. For example, we estimated area-weighted national yield according to actual yield provided for each cropping system and annual rice harvested area in each system for each of the 18 countries. Comparison of these yields against those reported by FAOSTAT2 showed a strong association and agreement between data sources (Supplementary Fig. 10). We also cross-validated actual yield, N fertilizer, labor, and irrigation from our database with those reported by previous studies (published after the year 2000) based on on-farm data collected in ten selected countries. Due to the lack of on-farm data on irrigation, we used published data collected from experiments that follow typical farmer irrigation practices. In the case of irrigation, our cross-validation differentiated between crop seasons (wet versus dry) in the case of irrigated double-season rice cropping systems. In all cases, average yield, N fertilizer, labor, and irrigation from our database fell within (or very close) the range of values reported in previously published studies for those same cropping systems (Supplementary Table 8). Measured daily weather data, including daily solar radiation, minimum and maximum temperatures, and precipitation, were derived from representative weather stations in each region (Supplementary Fig. 2 and Supplementary Table 9). Data on per-capita gross domestic product (GDP) during 2015–2017 were retrieved for each country to explore relationships between yield gap and economic development60 (Supplementary Fig. 9 and Supplementary Table 1).Estimation of yield gapsThe yield gap is defined as the difference between yield potential and average farmer yield. Estimates of yield potential for irrigated rice or water-limited yield potential for rainfed rice were adopted from Global Yield Gap Atlas (GYGA)61 (Supplementary Table 7). Yield potential simulation in GYGA was performed using crop growth and development model ORYZA2000 or ORYZA (v3) (except for APSIM in the case of India) and based on actual data on crop management, soil data, measured daily weather data, and representative rice varieties planted in each region (see details for yield potential simulation in Supplementary Information Text Section 1). Data on yield potential were not available for Australia (AUIS) in GYGA; hence, we used estimates of yield potential from Lacy et al.62. Yield potential (or water-limited yield potential for rainfed rice) and average yields were computed separately for each rice crop in each rice cropping system (Supplementary Fig. 3). The coefficient of variation (CV) of yield potential (or water-limited yield potential) was estimated for each cropping system (Supplementary Fig. 4). In this study, average rice yield was expressed as percentage of the yield potential (or water-limited yield potential for rainfed rice) for each cropping system (Fig. 1 and Supplementary Fig. 5). In those cropping systems where more than one rice crop is grown within a 12-month period, we estimated yield potential and average yield on both per-crop and annual basis by averaging and summing up the estimates for each rice crop, respectively. In the case of per-crop averages, for those cropping systems in which the harvested rice area changed between crop cycles, we weighted the values for each cycles based on the associated harvested rice area. However, for simplicity, the main text reports only the values on a per-crop basis; annual estimates are provided in the Supplementary Information. Normalizing average yield by the yield potential at each site provides a direct comparison of yield gap closure across systems with diverse biophysical backgrounds (e.g., variation in solar radiation, temperature, and water supply). Without this normalization, one might make biased assessment in relation to the available room for improving yield. For example, an actual yield of 8 Mg ha−1 is equivalent to 80% of yield potential in the cropping system of central China, whereas a yield of 8 Mg ha−1 achieved by irrigated rice farmers in Brazil only represents 55% of yield potential (Supplementary Fig. 3).Quantifying resource-use efficiencyWe assessed the performance of rice production by calculating the following metrics: global warming potential (GWP), fossil-fuel energy inputs, water supply (irrigation plus in-season precipitation), number of pesticide applications, nitrogen (N) balance, and labor input, each expressed on an area and yield-scaled basis (Figs. 2, 3 and 4 and Supplementary Figs. 6, 7 and 11). We estimated metrics on both per-crop and annual basis and report the values on a per-crop basis in the main text while the annual estimates are provided in the Supplementary Information. In the case of GWP, it includes CO2, CH4, and N2O emissions (expressed as CO2-eq) from (i) production, packaging, and transportation of agricultural inputs (seed, fertilizer, pesticides, machinery, etc.), (ii) fossil-fuel energy directly used for farm operations (including irrigation pumping), and (iii) CH4 and N2O emission during rice cultivation63. Emissions from agricultural inputs were calculated on application rates and associated GHG emissions factors (see details in Supplementary Information Text Section 2, Supplementary Table 10). In the case of fossil fuel used for field operations, it was calculated based on the number and type of farm operations and associated fuel requirements (Supplementary Table 11). Total N2O emissions were calculated as the sum of direct and indirect N2O emissions. A previous meta-analysis including rice showed that direct soil N2O emissions can be estimated from the magnitude of N-surplus, which was calculated as applied N inputs minus accumulated N in aboveground biomass at physiological maturity21. Therefore, direct soil N2O emissions for a given rice crop cycle were estimated following van Groenigen et al. N-balance approach21. Indirect N2O emissions were estimated based on the Intergovernmental Panel on Climate Change (IPCC) methodology64, assuming indirect N2O emissions represent 20% of direct N2O emissions. The CH4 emissions from rice paddy field were calculated following IPCC65. Following this approach, CH4 emissions are estimated considering the duration of the rice cultivation period, water regime during the cultivation period and during the pre-season before the cultivation period, and type and amount of organic amendment applied (e.g., straw, manure, compost) based on a baseline emission factor. We assumed no net change in soil carbon stocks as soil organic matter is typically at steady state in lowland rice66. We did not attempt to estimate changes on soil C in the upland rice system in Brazil. All emissions were converted to CO2-eq, with GWP for CH4 set at 25 relatives to CO2 and 298 for N2O on a per mass basis over a 100-year time horizon67. For each rice crop cycle in each of the 32 rice systems, GWP was calculated as the sum of CO2, CH4, and N2O emissions expressed as CO2-eq. (Details on N2O and CH4 emissions estimates and GWP calculations are provided in Supplementary Information Text Section 2).Calculation of energy inputs was similar to that of GWP and was based on the reported rates of agricultural inputs and field operations and associated embodied energy (see details for energy input estimates in Supplementary Information Text Section 2, Supplementary Table 12). Human labor was also included in the calculation of energy inputs. There was a strong positive relationship between energy input and GWP on both per-crop (r = 0.81; p  More

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    Human skin triglycerides prevent bed bug (Cimex lectularius L.) arrestment

    Bed bugsFour bed bug populations (one laboratory strain and three collected from infested homes) were used in this study (Table 1). All populations were reared in the laboratory as described by DeVries et al.28. Briefly, bed bugs were maintained in 168 cm3 plastic containers on paper substrate at 25 °C, 50% relative humidity, and a photoperiod of 12 h:12 h (Light:Dark). Bed bugs were fed defibrinated rabbit blood (Hemostat Laboratories, Dixon, CA, USA) weekly using an artificial feeding system. This system maintained blood at 35 °C by circulating water through custom-made water-jacketed glass feeders. An artificial membrane (plant budding tape, A.M. Leonared, Piqua, OH, USA) was stretched over the bottom of each glass feeder, containing the blood while simultaneously allowing bed bugs to feed through it. In all experiments, adult males starved for 7–10 days were used. All populations were used for documenting responses to human skin swabs. The WS population was used for bioassays with various human volunteers and hexane extracted swabs, and the JC population was used for testing various lipids.Table 1 Bed bug populations used in this study.Full size tableSkin swab collectionThe North Carolina State University Institutional Review Board approved this study (IRB #14173). Informed consent was obtained from all human participants, and all the methods were performed according to the relevant guidelines and regulations. Six human volunteers (3 males, 3 females) ranging from 25 to 50 years old representing several ethnicities (white/Caucasian, Hispanic, Asian) provided samples for this project. Skin swabs were collected following the exact methods outlined by DeVries et al.16. In our 2019 study, these swabs were reported to attract bed bugs independent of other cues in Y-tube olfactometer assays. Briefly, participants were asked to follow a standard operating procedure, which was reviewed with them prior to sample collection. Before collecting skin swabs, participants were asked to not to eat ‘spicy’ food for at least 24 h, take a morning shower, avoid the use of deodorant and cosmetics after showering, and avoid strenuous physical activity. Skin swabs were collected 4–8 h after showering. Hands were washed with water only before lifting filter paper. Swabs were collected using 4.5 cm diameter filter paper discs (#1; Whatman plc, Madistone, United Kingdom). Both sides of a single filter paper disc were rubbed over the left arm from hand to armpit for 12 s, left leg from lower thigh to ankle for 12 s, and left armpit for 6 s. This procedure was repeated on the right side using a new filter paper disc, so that two samples were collected during each swabbing session. The skin swab samples were then stored in glass vials at − 20 °C, and used within one month of collection. The swabs from all human volunteers were used to compare participants and establish that bed bugs responded similarly to all, and participant A’s skin swabs were used for all subsequent bioassays.Two-choice arrestment bioassaysTwo-choice bioassays were conducted in plastic Petri dishes of 6 cm diameter (Corning Life Sciences, Durham, NC, USA) (Fig. 1). The bottom surface of each Petri dish was roughened so that bed bugs could freely move about the arena. Two tents (3 × 1.5 cm) were created using filter paper (Whatman #1). One tent served as the control tent, and the other served as the treatment tent. Control tents were either untreated (nothing added) or treated with hexane only. Treatment tents were either made directly from human odor swabs, treated with human odor extract (in hexane), or treated with a specific compound (in hexane). Tents were allowed 60 min to acclimate to room conditions and allow for the solvent to evaporate prior to initiating bioassays. The positions of tents (treatment and control) were alternated to account for any side-bias.Figure 1Two-choice behavioral assay (top-view) consisting of two equal size paper shelter tents. A clean filter paper (control) was always paired with a treated filter paper that either represented a human skin swab, hexane extract of swabbed paper, SPE fraction of human skin swab extract, or authentic TAGs. A single male bed bug was introduced into the center of each arena and allowed to select a tent to arrest under.Full size imageAdult male bed bugs were housed in individual vials for 24 h prior to each experiment. A single adult male bed bug was released in the middle of the arena 5 h into the scotophase, by transferring it on its harborage. The harborage material was removed immediately after the bed bug moved off of it (the harborage). Bed bugs were allowed the remaining 7 h of the scotophase to freely move around the arena, with their final position reported 3 h into the photophase. Bed bugs that were in contact with the filter paper with any part of their body were recorded as making a choice (i.e. arrestment state); others not in contact with either filter paper tent were recorded as non-responders, reported in the figures, but not used in data analysis. It should be noted that momentary pauses in movement (feeding or other behaviors) are not referred to as arrestment in this study. In total, 15–39 replicates were performed for each experiment (reported for each bioassay).Bioassays with human skin swabsBioassays with human skin swabs were performed to understand if bed bug arrestment behavior (1) differed among different bed bug populations, and (2) influenced by different host odors. Skin swabs were removed from the freezer, equilibrated to room temperature, divided into three equal parts and trimmed to a rectangular shape corresponding to the size of a shelter tent (Fig. 1). Skin swabs from participant A were used to evaluate the responses of four bed bug populations (Table 1). Skin swabs from all participants A–F were used to evaluate the robustness of our findings across multiple human hosts.Skin swab extraction and fractionationSkin swabs collected from volunteer A were pooled and extracted in hexane. Extraction procedures were carried out sequentially by placing a single skin swab into a 20 ml glass vial containing 5 ml of hexane, vortexing for 30 s, then moving the filter paper to a new 20 ml vial containing 5 ml of hexane and repeating the process. Three sequential extractions were performed for each skin swab, and a minimum of 10 skin swabs (collected over several days) were used for each extraction. After all skin swabs were extracted, all sequential hexane extracts were combined and concentrated to a final concentration of one skin swab equivalent per 300 µl, or one bioassay equivalent (BE) per 100 µl (since each swab was used for 3 bioassays; see “Bioassays with human skin swabs” for more information on the size used for each bioassay). Control swabs were also extracted. These swabs were treated identically to the skin swabs, except they did not contact human skin.To determine what compound classes were responsible for the observed behavior, hexane extracts were fractionated using solid phase extraction (SPE). Extracted samples were concentrated to 1 BE/10 µl hexane, then loaded onto a 1 g silica SPE column (6 ml total volume; J.T. Baker, Phillipsburg, NJ, USA). The column was eluted with the following solvents (4 ml of each, each repeated twice sequentially): hexane, 2% ether (in hexane), 5% ether (in hexane), 10% ether (in hexane), 20% ether (in hexane), 50% ether (in hexane), 100% ether, ethyl acetate, and methanol (all solvents acquired from Sigma Aldrich, St. Louis, MO, USA). Each solvent fraction was then concentrated to a final concentration of 1 BE/100 µl and stored at − 20 °C.Bioassays with extracted and fractionated human skin swabsFor all extraction and fractionation bioassays, filter paper tents were cut to a size of 3 cm × 1.5 cm (Fig. 1) and treated with 100 µl (1 BE) of extracted or fractionated human skin swabs (50 µl on each side). A dose–response bioassay was run first to determine if the compounds responsible for bed bug arrestment responses could be extracted and at what concentration (BE) they were behaviorally active. Dilutions were made in hexane, with control tents receiving extracts of control filter paper. At least 20 replicates were conducted for each concentration. After validating an appropriate BE that could be used in future experiments, SPE fractions were diluted in hexane to 0.1 BE and applied to filter paper tents as previously described (50 µl per side). A minimum of 15 replicates were conducted for each fraction to identify behaviorally active fractions.Compound identificationTo better understand what classes of compounds were present in behaviorally active fractions, we conducted thin layer chromatography (TLC) with known standards. A flexible, silica (250 µm) TLC plate (Whatman) was placed into a glass chamber containing a solvent layer of 1.5 cm. The plate was cleaned twice with acetone, then standards (triglyceride [TAG], wax ester, squalene) and samples (fractions) were each loaded into separate lanes. The plate was developed twice in 10% ether (in hexane), then visualized non-destructively with iodine.In addition, behaviorally active fractions were further evaluated for their composition with GC–MS and LC–MS. GC–MS was employed to analyze free fatty acids, squalene, and cholesterol29, whereas LC–MS was employed to characterize the intact skin lipids as previously described30. Samples were analyzed with a GC 7890A coupled to the MS 5975 VL analyzer (Agilent Technologies, CA, USA) following derivatization. Briefly, 50 µL of the extract dissolved in isopropanol were dried under nitrogen and derivatized with 100 µL BSTFA containing 1% trimethylchlorosilane (TCMS) in pyridine to generate the trimethylsilyl (TMS) derivatives at 60 °C for 60 min. GC separation was performed with a 30 m × 0.250 mm (i.d.) × 0.25 µm film thickness DB-5MS fused silica column (Agilent). Helium was used as the carrier gas. Samples were acquired in scan mode by means of electron impact (EI) MS.Liquid-chromatography coupled to the MS analyzer by means of an electrospray interface (ESI) was used to determine abundance and ESI tandem MS of non-volatile lipids as previously described29,30. LC separation was performed with a reverse phase Zorbax SB-C8 column (2.1 × 100 mm, 1.8 μm particle size, Agilent). Data were acquired in the positive ion mode at unit mass resolving power by scanning ions between m/z 100 and 1000 with G6410A series triple quadrupole (QqQ) (Agilent). LC runs and MS spectra were processed with the Mass Hunter software (B.09.00 version).Bioassays with triglyceridesAfter determining that TAGs were prominent compounds in bioactive skin swab fractions, commercially available TAGs were evaluated for behavioral activity. Filter paper tents were treated with 100 µl of hexane (50 µl to each side) containing TAG standards. First, tripalmitin (16:0/16:0/16:0) (Sigma-Aldrich) was evaluated in a dose–response fashion (60 µg to 0.6 µg) to determine what level of TAG was appropriate for bioassays. The upper level of testing was set at 60 µg as a conservative estimate of the amount of TAGs bed bugs may be exposed to, based on calculations of our arena size and previous reports of TAGs on human skin and sebum. Specifically, previous reports documented that 1.5 mg of sebum could be passively collected using Sebutape from an area of 4.7 cm230,31. Because TAGs typically constitute 60% of human sebum32, it is reasonable to assume that passive collection of sebum can result in  > 190 µg/cm2 of TAGs in a short amount of time (30 min). Our sampling methods involved swabbing rather than passive collection, but our use of 60 µg over a 9 cm2 (two sides of 4.5 cm2) shelter tent (6.67 µg/cm2) is a low-estimate of the amount of TAGs collected (although this was not directly measured in the current study). Other TAGs that we tested at a concentration of 60 µg per 9 cm2 included the saturated TAGs trimyristin (14:0/14:0/14:0) and tristearin (18:0/18:0/18:0) and the unsaturated TAGs triolein (18:1/18:1/18:1), trilinolein (18:2/18:2/18:2), and trilinolenin (18:3/18:3/18:3) (all from Sigma-Aldrich). A minimum of 30 replicates were conducted with each TAG.Statistical analysisA Chi-square goodness of fit test was used to compare the responses of bed bugs to control versus treated tents in all two-choice bioassays, with the null hypothesis that if bed bugs do not respond differentially to treated tents they should display a 1:1 preference ratio for both sides of the assay. All tests were conducted in SPSS Version 26 (IBM Corp., Armonk, NY). More

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    Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA

    1.Dirzo, R. et al. Defaunation in the Anthropocene. Science 345, 401–406 (2014).ADS 
    CAS 
    PubMed 

    Google Scholar 
    2.Pimm, S. L. et al. The biodiversity of species and their rates of extinction, distribution, and protection. Science 344, 1246752 (2014).CAS 
    PubMed 

    Google Scholar 
    3.Boivin, N. L. et al. Ecological consequences of human niche construction: examining long-term anthropogenic shaping of global species distributions. Proc. Natl Acad. Sci. USA 113, 6388–6396 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    4.Asner, G. P., Vaughn, N., Smit, I. P. J. & Levick, S. Ecosystem-scale effects of megafauna in African savannas. Ecography (Cop.). 39, 240–252 (2016).
    Google Scholar 
    5.Bakker, E. S. et al. Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation. Proc. Natl Acad. Sci. USA 113, 847–855 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    6.Bakker, E. S., Pagès, J. F., Arthur, R. & Alcoverro, T. Assessing the role of large herbivores in the structuring and functioning of freshwater and marine angiosperm ecosystems. Ecography (Cop.). 39, 162–179 (2016).
    Google Scholar 
    7.Brault, M. O., Mysak, L. A., Matthews, H. D. & Simmons, C. T. Assessing the impact of late Pleistocene megafaunal extinctions on global vegetation and climate. Clim 9, 1761–1771 (2013).ADS 

    Google Scholar 
    8.Doughty, C. E., Faurby, S. & Svenning, J. C. The impact of the megafauna extinctions on savanna woody cover in South America. Ecography (Cop.). 39, 213–222 (2016).
    Google Scholar 
    9.Doughty, C. E., Wolf, A. & Malhi, Y. The legacy of the Pleistocene megafauna extinctions on nutrient availability in Amazonia. Nat. Geosci. 6, 761–764 (2013).ADS 
    CAS 

    Google Scholar 
    10.Doughty, C. E. et al. Global nutrient transport in a world of giants. Proc. Natl Acad. Sci. USA 113, 1–6 (2015).
    Google Scholar 
    11.Malhi, Y. et al. Megafauna and ecosystem function from the Pleistocene to the Anthropocene. Proc. Natl Acad. Sci. USA 113, 838–846 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    12.Smith, F. A. et al. Exploring the influence of ancient and historic megaherbivore extirpations on the global methane budget. Proc. Natl Acad. Sci. USA 113, 201502547 (2015).
    Google Scholar 
    13.le Roux, E., Kerley, G. I. H. & Cromsigt, J. P. G. M. Megaherbivores modify trophic cascades triggered by fear of predation in an African Savanna Ecosystem. Curr. Biol. 28, 2493–2499.e3 (2018).PubMed 

    Google Scholar 
    14.Boulanger, M. T. & Lyman, R. L. Northeastern North American Pleistocene megafauna chronologically overlapped minimally with Paleoindians. Quat. Sci. Rev. 85, 35–46 (2013).ADS 

    Google Scholar 
    15.Rozas-Dávila, A., Valencia, B. G. & Bush, M. B. The functional extinction of Andean megafauna. Ecology 97, 2533–2539 (2016).PubMed 

    Google Scholar 
    16.Guthrie, R. D. New Carbon Dates Link Climatic Change with Human Colonization and Pleistocene Extinctions. Nature 441, 207–209 (2006).ADS 
    CAS 
    PubMed 

    Google Scholar 
    17.Meltzer, D. J. Overkill, glacial history, and the extinction of North America’s Ice Age megafauna. Proc. Natl. Acad. Sci. USA https://doi.org/10.1073/pnas.2015032117 (2020).18.Sandom, C., Faurby, S., Sandel, B. & Svenning, J.-C. Global late Quaternary megafauna extinctions linked to humans, not climate change. Proc. R. Soc. Lond. B Biol. Sci. 281, 20133254 (2014).
    Google Scholar 
    19.Martin, P. S. in Quaternary Extinctions: A Prehistoric Revolution (eds. Martin, P. S. & Klein, R. G.) 354–403 (University of Arizona Press, 1984).20.Braje, T. J. & Erlandson, J. M. Human acceleration of animal and plant extinctions: a late Pleistocene, Holocene, and Anthropocene continuum. Anthropocene 4, 14–23 (2013).
    Google Scholar 
    21.Smith, F. A., Smith, R. E. E. E., Lyons, S. K. & Payne, J. L. Body size downgrading of mammals over the late Quaternary. Science. 360, 310–313 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    22.Barnosky, A. D., Koch, P. L., Feranec, R. S., Wing, S. L. & Shabel, A. B. Assessing the causes of late pleistocene extinctions on the continents. Science 306, 70–75 (2004).ADS 
    CAS 
    PubMed 

    Google Scholar 
    23.Zimov, S. A. et al. Steppe-Tundra Transition: A Herbivore-Driven Biome Shift at the End of the Pleistocene. Am. Nat. 146, 765–794 (1995).
    Google Scholar 
    24.Lorenzen, E. D. et al. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479, 359–364 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    25.Mann, D. H., Groves, P., Gaglioti, B. V. & Shapiro, B. A. Climate-driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis. Biol. Rev. 94, 328–352 (2019).
    Google Scholar 
    26.Zazula, G. D. et al. American mastodon extirpation in the Arctic and Subarctic predates human colonization and terminal Pleistocene climate change. Proc. Natl Acad. Sci. USA 111, 18460–18465 (2014).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    27.Stuart, A. J. Late Quaternary megafaunal extinctions on the continents: a short review. Geol. J. 50, 414–433 (2015).
    Google Scholar 
    28.Mann, D. H., Groves, P., Kunz, M. L., Reanier, R. E. & Gaglioti, B. V. Ice-age megafauna in Arctic Alaska: extinction, invasion, survival. Quat. Sci. Rev. 70, 91–108 (2013).ADS 

    Google Scholar 
    29.Mann, D. H. et al. Life and extinction of megafauna in the ice-age Arctic. Proc. Natl Acad. Sci. USA 112, 14301–14306 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Rabanus-Wallace, M. T. et al. Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions. Nat. Ecol. Evol. 1, 1–5 (2017).
    Google Scholar 
    31.Zimov, S. A., Zimov, N. S., Tikhonov, A. N. & Chapin, I. S. Mammoth steppe: a high-productivity phenomenon. Quat. Sci. Rev. 57, 26–45 (2012).ADS 

    Google Scholar 
    32.Owen-Smith, N. Pleistocene extinctions: the pivotal role of megaherbivores. Paleobiology 13, 351–362 (1987).
    Google Scholar 
    33.Willerslev, E. et al. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506, 47–51 (2014).ADS 
    CAS 
    PubMed 

    Google Scholar 
    34.Jackson, S. T. Representation of flora and vegetation in Quaternary fossil assemblages: known and unknown knowns and unknowns. Quat. Sci. Rev. 49, 1–15 (2012).ADS 

    Google Scholar 
    35.Froese, D. G. et al. The Klondike goldfields and Pleistocene environments of Beringia. GSA Today 19, 4–10 (2009).
    Google Scholar 
    36.Murchie, T. J. et al. Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set. Quat. Res. 99, 305–328 (2021).CAS 

    Google Scholar 
    37.Haile, J. et al. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc. Natl Acad. Sci. USA 106, 22352–22357 (2009).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    38.Clark, P. U. The last glacial maximum. Science 325, 710–714 (2009).ADS 
    CAS 
    PubMed 

    Google Scholar 
    39.Zazula, G. D. et al. A middle Holocene steppe bison and paleoenvironments from the versleuce meadows, Whitehorse, Yukon, Canada. Can. J. Earth Sci. 54, 1138–1152 (2017).ADS 

    Google Scholar 
    40.Heintzman, P. D. et al. Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada. Proc. Natl Acad. Sci. USA 113, 8057–8063 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    41.Graham, R. W. et al. Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska. Proc. Natl Acad. Sci. USA 113, 9310–9314 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Vartanyan, S. L., Arslanov, K. A., Karhu, J. A., Possnert, G. & Sulerzhitsky, L. D. Collection of radiocarbon dates on the mammoths (Mammuthus primigenius) and other genera of Wrangel Island, northeast Siberia, Russia. Quat. Res. 70, 51–59 (2008).CAS 

    Google Scholar 
    43.Faith, J. T. & Surovell, T. A. Synchronous extinction of North America’s Pleistocene mammals. Proc. Natl Acad. Sci. USA 106, 20641–20645 (2009).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    44.Signor, P. W. & Lipps, J. H. Sampling bias, gradual extinction patterns and catastrophes in the fossil record. GSA Spec. Pap. 190, 291–296 (1982).
    Google Scholar 
    45.Fiedel, S. in American Megafaunal Extinctions at the End of the Pleistocene (ed. Haynes, G.) 21–37 (Springer Netherlands, 2009).46.Graf, K. E. Uncharted Territory: Late Pleistocene Hunter-Gatherer Dispersals in the Siberian Mammoth-Steppe (University of Nevada, 2008).47.Kuzmina, S. A. et al. The late Pleistocene environment of the Eastern West Beringia based on the principal section at the Main River, Chukotka. Quat. Sci. Rev. 30, 2091–2106 (2011).ADS 

    Google Scholar 
    48.Hoffecker, J. F., Elias, S. A. & Rourke, D. H. O. Out of Beringia? Science 343, 979–980 (2014).ADS 
    CAS 
    PubMed 

    Google Scholar 
    49.Zazula, G. D. et al. Ice-age steppe vegetation in East Beringia. Nature 423, 603 (2003).ADS 
    CAS 
    PubMed 

    Google Scholar 
    50.Guthrie, R. D. Origin and causes of the mammoth steppe: a story of cloud cover, woolly mammal tooth pits, buckles, and inside-out Beringia. Quat. Sci. Rev. 20, 549–574 (2001).ADS 

    Google Scholar 
    51.Pavelková Řičánková, V., Robovský, J. & Riegert, J. Ecological structure of recent and last glacial mammalian faunas in northern Eurasia: the case of Altai-Sayan refugium. PLoS ONE 9, e85056 (2014).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    52.Bocherens, H. Isotopic tracking of large carnivore palaeoecology in the mammoth steppe. Quat. Sci. Rev. 117, 42–71 (2015).ADS 

    Google Scholar 
    53.Ritchie, J. C. & Cwynar, L. C. in Paleoecology of Beringia (eds. Hopkins, D. M. et al.) 113–126 (Academic Press, 1982).54.Zhu, D. et al. The large mean body size of mammalian herbivores explains the productivity paradox during the Last Glacial Maximum. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-018-0481-y (2018).55.Hopkins, D. M., Matthews, J. V., and Schweger, C. E. eds. Paleoecology of Beringia. (Academic Press, 1982).56.Stivrins, N. et al. Biotic turnover rates during the Pleistocene-Holocene transition. Quat. Sci. Rev. 151, 100–110 (2016).ADS 

    Google Scholar 
    57.Bakker, E. S., Ritchie, M. E., Olff, H., Milchunas, D. G. & Knops, J. M. H. Herbivore impact on grassland plant diversity depends on habitat productivity and herbivore size. Ecol. Lett. 9, 780–788 (2006).PubMed 

    Google Scholar 
    58.Bradshaw, R. H. W., Hannon, G. E. & Lister, A. M. A long-term perspective on ungulate-vegetation interactions. Ecol. Manag. 181, 267–280 (2003).
    Google Scholar 
    59.Gill, J. L. Ecological impacts of the late Quaternary megaherbivore extinctions. N. Phytologist 201, 1163–1169 (2014).
    Google Scholar 
    60.Gill, J. L., Williams, J. W., Jackson, S. T., Donnelly, J. P. & Schellinger, G. C. Climatic and megaherbivory controls on late-glacial vegetation dynamics: a new, high-resolution, multi-proxy record from Silver Lake, Ohio. Quat. Sci. Rev. 34, 66–80 (2012).ADS 

    Google Scholar 
    61.Gill, J. L., Williams, J. W., Jackson, S. T., Lininger, K. B. & Robinson, G. S. Pleistocene megafaunal collapse, novel plant communities, and enhanced fire regimes in North America. Science 326, 1100–1103 (2009).ADS 
    CAS 
    PubMed 

    Google Scholar 
    62.Johnson, C. N. Ecological consequences of Late Quaternary extinctions of megafauna. Proc. Biol. Sci. 276, 2509–2519 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    63.Owen-Smith, N. Megaherbivores: The Influence of Very Large Body Size on Ecology (Cambridge University Press, 1992).64.Wright, J. P. & Jones, C. G. The concept of organisms as ecosystem engineers ten years on: progress, limitations, and challenges. Bioscience 56, 203 (2006).
    Google Scholar 
    65.Gutierrez, J. L. & Jones, C. G. Physical ecosystem engineers as agents of biogeochemical heterogeneity. Bioscience 56, 227 (2006).
    Google Scholar 
    66.Berke, S. K. Functional groups of ecosystem engineers: a proposed classification with comments on current issues. Integr. Comp. Biol. 50, 147–157 (2010).PubMed 

    Google Scholar 
    67.Ries, L., Fletcher, R. J. J., Battin, J. & Sisk, T. D. Ecological responses to habitat edges: Mechanisms, models, and variability explained. Annu. Rev. Ecol., Evolution, Syst. 35, 491–522 (2004).
    Google Scholar 
    68.Rasmussen, S. O. et al. A new Greenland ice core chronology for the last glacial termination. J. Geophys. Res. Atmos. 111, 1–16 (2006).
    Google Scholar 
    69.Swift, J. A. et al. Micro methods for Megafauna: novel approaches to late quaternary extinctions and their contributions to faunal conservation in the Anthropocene. Bioscience 69, 877–887 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    70.Andersen, K. et al. Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Mol. Ecol. 21, 1966–1979 (2012).CAS 
    PubMed 

    Google Scholar 
    71.Comandini, O. & Rinaldi, A. C. Tracing megafaunal extinctions with dung fungal spores. Mycologist 18, 140–142 (2004).
    Google Scholar 
    72.Säterberg, T., Sellman, S. & Ebenman, B. High frequency of functional extinctions in ecological networks. Nature 499, 468–470 (2013).ADS 
    PubMed 

    Google Scholar 
    73.Courchamp, F., Berec, L. & Gascoigne, J. Allee Effects in Ecology and Conservation. Allee Effects in Ecology and Conservation (Oxford University Press, 2008).74.Allee, W. C. Animal aggregations. Q. Rev. Biol. 2, 367–398 (1927).
    Google Scholar 
    75.Allee, W. C. & Bowen, E. S. Studies in animal aggregations: mass protection against colloidal silver among goldfishes. J. Exp. Zool. 61, 185–207 (1932).CAS 

    Google Scholar 
    76.Taberlet, P., Bonin, A., Zinger, L. & Coissac, E. Environmental DNA: For Biodiversity Research and Monitoring. (Oxford University Press, 2018).77.Edwards, M. E. et al. Metabarcoding of modern soil DNA gives a highly local vegetation signal in Svalbard tundra. Holocene 28, 2006–2016 (2018).ADS 

    Google Scholar 
    78.Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017).ADS 
    CAS 
    PubMed 

    Google Scholar 
    79.Anderson-Carpenter, L. L. et al. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evol. Biol. 11, 1–15 (2011).
    Google Scholar 
    80.Bellemain, E. et al. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environ. Microbiol. 15, 1176–1189 (2013).CAS 
    PubMed 

    Google Scholar 
    81.Ahmed, E. et al. Archaeal community changes in Lateglacial lake sediments: evidence from ancient DNA. Quat. Sci. Rev. 181, 19–29 (2018).ADS 

    Google Scholar 
    82.Niemeyer, B., Epp, L. S., Stoof-Leichsenring, K. R., Pestryakova, L. A. & Herzschuh, U. A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline. Mol. Ecol. Resour. 17, e46–e62 (2017).CAS 
    PubMed 

    Google Scholar 
    83.Rawlence, N. J. et al. Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects. J. Quat. Sci. 29, 610–626 (2014).
    Google Scholar 
    84.Blum, S. A. E., Lorenz, M. G. & Wackernagel, W. Mechanism of retarded DNA degradation and prokaryotic origin of DNases in nonsterile soils. Syst. Appl. Microbiol. 20, 513–521 (1997).CAS 

    Google Scholar 
    85.Greaves, M. P. & Wilson, M. J. The degradation of nucleic acids and montmorillonite-nucleic-acid complexes by soil microorganisms. Soil Biol. Biochem. 2, 257–268 (1970).CAS 

    Google Scholar 
    86.Gardner, C. M. & Gunsch, C. K. Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated. Chemosphere 175, 45–51 (2017).ADS 
    CAS 
    PubMed 

    Google Scholar 
    87.Lorenz, M. G. & Wackernagel, W. Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53, 2948–2952 (1987).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    88.Ogram, A., Sayler, G., Gustin, D. & Lewis, R. DNA adsorption to soils and sediments. Environ. Sci. Technol. 22, 982–984 (1988).ADS 
    CAS 
    PubMed 

    Google Scholar 
    89.Lorenz, M. G. & Wackernagel, W. Adsorption of DNA to sand and variable degradation of adsorbed DNA. Appl. Environ. Microbiol. 53, 2948–2952 (1987).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    90.Morrissey, E. M. et al. Dynamics of extracellular DNA decomposition and bacterial community composition in soil. Soil Biol. Biochem. 86, 42–49 (2015).CAS 

    Google Scholar 
    91.Arnold, L. J. et al. Paper II – Dirt, dates and DNA: OSL and radiocarbon chronologies of perennially frozen sediments in Siberia, and their implications for sedimentary ancient DNA studies. Boreas 40, 417–445 (2011).
    Google Scholar 
    92.Allentoft, M. E. et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B Biol. Sci. https://doi.org/10.1098/rspb.2012.1745 (2012).93.Kistler, L., Ware, R., Smith, O., Collins, M. & Allaby, R. G. A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res. 45, 6310–6320 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    94.Cribdon, B., Ware, R., Smith, O., Gaffney, V. & Allaby, R. G. PIA: more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North Sea. Front. Ecol. Evol. 8, 1–12 (2020).
    Google Scholar 
    95.Yoccoz, N. G. et al. DNA from soil mirrors plant taxonomic and growth form diversity. Mol. Ecol. 21, 3647–3655 (2012).CAS 
    PubMed 

    Google Scholar 
    96.Doi, H. et al. Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshw. Biol. 62, 30–39 (2017).CAS 

    Google Scholar 
    97.Burn, C. R., Michel, F. A. & Smith, M. W. Stratigraphic, isotopic, and mineralogical evidence for an early Holocene thaw unconformity at Mayo, Yukon Territory. Can. J. Earth Sci. 23, 794–803 (1986).ADS 
    CAS 

    Google Scholar 
    98.Kotler, E. & Burn, C. R. Cryostratigraphy of the Klondike ‘muck’ deposits, west-central Yukon Territory. Can. J. Earth Sci. 37, 849–861 (2000).ADS 
    CAS 

    Google Scholar 
    99.Fraser, T. A. & Burn, C. R. On the nature and origin of ‘muck’ deposits in the Klondike area, Yukon Territory. Can. J. Earth Sci. 34, 1333–1344 (1997).ADS 

    Google Scholar 
    100.Mahony, M. E. 50,000 years of paleoenvironmental change recorded in meteoric waters and coeval paleoecological and cryostratigraphic indicators from the Klondike goldfields, Yukon, Canada. (University of Alberta, 2015). https://doi.org/10.7939/R34T6FF58.101.Lydolph, M. C. et al. Beringian paleoecology inferred from permafrost-preserved fungal DNA. Appl. Environ. Microbiol. 71, 1012–1017 (2005).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    102.Willerslev, E. et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300, 791–795 (2003).ADS 
    CAS 
    PubMed 

    Google Scholar 
    103.Haile, J. et al. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol. Biol. Evol. 24, 982–989 (2007).CAS 
    PubMed 

    Google Scholar 
    104.Willerslev, E., Hansen, A. J. & Poinar, H. N. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol. Evol. 19, 141–147 (2004).PubMed 

    Google Scholar 
    105.Hansen, A. J. et al. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173, 1175–1179 (2006).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    106.D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011).ADS 
    PubMed 

    Google Scholar 
    107.Johnson, S. S. et al. Ancient bacteria show evidence of DNA repair. Proc. Natl Acad. Sci. USA 104, 14401–14405 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    108.Hebsgaard, M. B. et al. ‘The Farm Beneath the Sand’- an archaeological case study on ancient ‘dirt’ DNA. Antiquity 83, 430–444 (2009).
    Google Scholar 
    109.Sadoway, T. R. A Metagenomic Analysis of Ancient Sedimentary DNA Across the Pleistocene-Holocene Transition (McMaster University, 2014).110.Bronk Ramsey, C. Deposition models for chronological records. Quat. Sci. Rev. 27, 42–60 (2008).ADS 

    Google Scholar 
    111.Reimer, P. J. et al. The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0-55 cal kBP). Radiocarbon 62, 725–757 (2020).CAS 

    Google Scholar 
    112.Nichols, R. V. et al. Minimizing polymerase biases in metabarcoding. Mol. Ecol. Resour. 18, 927–939 (2018).CAS 

    Google Scholar 
    113.Wei, N., Nakajima, F. & Tobino, T. A microcosm study of surface sediment environmental DNA: decay observation, abundance estimation, and fragment length comparison. Environ. Sci. Technol. 52, 12428–12435 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    114.Matesanz, S. et al. Estimating belowground plant abundance with DNA metabarcoding. Mol. Ecol. Resour. 19, 1265–1277 (2019).CAS 
    PubMed 

    Google Scholar 
    115.Takahara, T., Minamoto, T., Yamanaka, H., Doi, H. & Kawabata, Z. Estimation of fish biomass using environmental DNA. PLoS ONE 7, 3–10 (2012).
    Google Scholar 
    116.Doi, H. et al. Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLoS ONE 10, 1–11 (2015).
    Google Scholar 
    117.Debruyne, R. et al. Out of America: ancient DNA evidence for a new world origin of late Quaternary Woolly Mammoths. Curr. Biol. 18, 1320–1326 (2008).CAS 
    PubMed 

    Google Scholar 
    118.Metcalfe, J. Z., Longstaffe, F. J. & Zazula, G. D. Nursing, weaning, and tooth development in woolly mammoths from Old Crow, Yukon, Canada: Implications for Pleistocene extinctions. Palaeogeogr. Palaeoclimatol. Palaeoecol. 298, 257–270 (2010).
    Google Scholar 
    119.Shapiro, B. et al. Rise and fall of the Beringian steppe bison. Science 306, 1561–1565 (2004).ADS 
    CAS 
    PubMed 

    Google Scholar 
    120.Sinclair, P. H., Nixon, W. A., Eckert C. D. & Hughes, N. L.Hughes, eds. Birds of the Yukon Territory. (UBC Press, 2003).121.Keesing, F. & Young, T. P. Cascading consequences of the loss of large mammals in an African Savanna. Bioscience 64, 487–495 (2014).
    Google Scholar 
    122.Taberlet, P. et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35, e14 (2007).PubMed 

    Google Scholar 
    123.Chevalier, M. et al. Pollen-based climate reconstruction techniques for late Quaternary studies. Earth-Sci. Rev. 210, 103384 (2020).
    Google Scholar 
    124.Wang, X.-C. & Geurts, M.-A. Post-glacial vegetation history of the Ittlemit Lake basin, southwest Yukon Territory. Arctic 44, 23–30 (1991).
    Google Scholar 
    125.Wang, X.-C. & Geurts, M.-A. Late Quaternary pollen records and vegetation history of the southwest Yukon Territory: a review. Geogr. Phys. Quat. 45, 175–193 (1991).
    Google Scholar 
    126.Rainville, R. A. & Gajewski, K. Holocene environmental history of the Aishihik region, Yukon, Canada. Can. J. Earth Sci. 50, 397–405 (2013).ADS 
    CAS 

    Google Scholar 
    127.Lacourse, T. & Gajewski, K. Late Quaternary vegetation history of Sulphur Lake, southwest Yukon Territory, Canada. Arctic 53, 27–35 (2000).
    Google Scholar 
    128.Bunbury, J. & Gajewski, K. Postglacial climates inferred from a lake at treeline, southwest Yukon Territory, Canada. Quat. Sci. Rev. 28, 354–369 (2009).ADS 

    Google Scholar 
    129.Gajewski, K., Bunbury, J., Vetter, M., Kroeker, N. & Khan, A. H. Paleoenvironmental studies in Southwestern Yukon. Arctic 67, 58–70 (2014).
    Google Scholar 
    130.Schofield, E. J., Edwards, K. J. & McMullen, A. J. Modern Pollen-Vegetation Relationships in Subarctic Southern Greenland and the Interpretation of Fossil Pollen Data from the Norse landnám. J. Biogeogr. 34, 473–488 (2007).
    Google Scholar 
    131.Pennington, W. & Tutin, T. G. Modern pollen samples from west greenland and the interpretation of pollen data from the british late-glacial (late Devesian). N. Phytol. 84, 171–201 (1980).
    Google Scholar 
    132.Bradshaw, R. H. W. Modern pollen-representation factors for Woods in South-East England. J. Ecol. 69, 45 (1981).
    Google Scholar 
    133.Roy, I. et al. Over-representation of some taxa in surface pollen analysis misleads the interpretation of fossil pollen spectra in terms of extant vegetation. Trop. Ecol. 59, 339–350 (2018).
    Google Scholar 
    134.Bryant, J. P. et al. Biogeographic evidence for the evolution of chemical defense by boreal birch and willow against mammalian browsing. Am. Nat. 134, 20–34 (1979).
    Google Scholar 
    135.Christie, K. S. et al. The role of vertebrate herbivores in regulating shrub expansion in the Arctic: a synthesis. Bioscience 65, 1123 (2015).
    Google Scholar 
    136.Bryant, J. P. et al. Can antibrowsing defense regulate the spread of woody vegetation in arctic tundra? Ecography (Cop.). 37, 204–211 (2014).137.Bryant, J. P. & Kuropat, P. J. Selection of winter forage by subarctic browsing vertebrates: the role of plant chemistry. Annu. Rev. Ecol. Syst. 11, 261–285 (1980).CAS 

    Google Scholar 
    138.Fox-Dobbs, K., Leonard, J. A. & Koch, P. L. Pleistocene megafauna from eastern Beringia: Paleoecological and paleoenvironmental interpretations of stable carbon and nitrogen isotope and radiocarbon records. Palaeogeogr. Palaeoclimatol. Palaeoecol. 261, 30–46 (2008).
    Google Scholar 
    139.Gardner, C., Berger, M. & Taras, M. Habitat assessment of potential wood bison relocation sites in Alaska. Arctic 1–30 (2007).140.Jiménez-Hidalgo, E. et al. Species diversity and paleoecology of late pleistocene horses from Southern Mexico. Front. Ecol. Evol. 7, 1–18 (2019).
    Google Scholar 
    141.van Geel, B. et al. The ecological implications of a Yakutian mammoth’s last meal. Quat. Res. 69, 361–376 (2008).
    Google Scholar 
    142.van Geel, B. et al. Palaeo-environmental and dietary analysis of intestinal contents of a mammoth calf (Yamal Peninsula, northwest Siberia). Quat. Sci. Rev. 30, 3935–3946 (2011).ADS 

    Google Scholar 
    143.Guthrie, R. D. Rapid body size decline in Alaskan Pleistocene horses before extinction. Nature 426, 169–171 (2003).ADS 
    PubMed 

    Google Scholar 
    144.Bourgeon, L. Bluefish Cave II (Yukon Territory, Canada): Taphonomic Study of a Bone Assemblage. PaleoAmerica 1, 105–108 (2015).
    Google Scholar 
    145.Bourgeon, L., Burke, A. & Higham, T. Earliest human presence in North America dated to the last glacial maximum: new radiocarbon dates from Bluefish Caves, Canada. PLoS ONE 12, e0169486 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    146.Bourgeon, L. Revisiting the mammoth bone modifications from Bluefish Caves (YT, Canada). J. Archaeol. Sci. Rep. 37, 102969 (2021).147.Bourgeon, L. & Burke, A. Horse exploitation by Beringian hunters during the Last Glacial Maximum. Quat. Sci. Rev. 261, (2021).148.Vachula, R. S., Sae-Lim, J. & Russell, J. M. Sedimentary charcoal proxy records of fire in Alaskan tundra ecosystems. Palaeogeogr. Palaeoclimatol. Palaeoecol. 541, 109564 (2020).149.Vachula, R. S. Alaskan lake sediment records and their implications for the Beringian standstill hypothesis. PaleoAmerica 6, 303–307 (2020).
    Google Scholar 
    150.Vachula, R. S. et al. Evidence of Ice Age humans in eastern Beringia suggests early migration to North America. Quat. Sci. Rev. 205, 35–44 (2019).ADS 

    Google Scholar 
    151.Vachula, R. S. et al. Sedimentary biomarkers reaffirm human impacts on northern Beringian ecosystems during the Last Glacial period. Boreas 49, 514–525 (2020).
    Google Scholar 
    152.Abramova, Z. A. in Paleolit Kavkaza i Severnoi Azii (ed. Boriskovskii, P. I.) 145–243 (Nauka, 1989).153.Abramova, Z. A., Astakhov, S. N., Vasil’ev, S. A., Ermolva, N. M. & Lisitsyn, N. F. Paleolit Eniseya. (Nauka, 1991).154.Goebel, T. in Encyclopedia of prehistory. Vol 2: Arctic and Subarctic (eds. Peregrine, P. N. & Ember, M.) 192–196 (Kluwer Academic Publishers, 2002).155.Ermolova, N. M. Teriofauna doliny Angary v pozdem antropogene. (Nauka, 1978).156.Hoffecker, J. F. & Elias, S. A. Human Ecology of Beringia. (Columbia University Press, 2007).157.Johnson, C. N. Determinants of loss of mammal species during the Late Quaternary ‘megafauna’ extinctions: life history and ecology, but not body size. Proc. Biol. Sci. 269, 2221–2227 (2002).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    158.Laland, K. N. & O’Brien, M. J. Niche Construction Theory and Archaeology. J. Archaeol. Method Theory 17, 303–322 (2010).
    Google Scholar 
    159.Riede, F. Adaptation and niche construction in human prehistory: a case study from the southern Scandinavian Late Glacial. Philos. Trans. R. Soc. Lond. 366, 793–808 (2011).
    Google Scholar 
    160.Roos, C. I., Zedeño, M. N., Hollenback, K. L. & Erlick, M. M. H. Indigenous impacts on North American Great Plains fire regimes of the past millennium. Proc. Natl. Acad. Sci. USA https://doi.org/10.1073/pnas.1805259115 (2018).161.Pinter, N., Fiedel, S. & Keeley, J. E. Fire and vegetation shifts in the Americas at the vanguard of Paleoindian migration. Quat. Sci. Rev. 30, 269–272 (2011).ADS 

    Google Scholar 
    162.Haynes, G. Extinctions in North America’s Late Glacial landscapes. Quat. Int. 285, 89–98 (2013).
    Google Scholar 
    163.Graf, K. E. in Paleoamerican Odyssey (eds. Graf, K. E., Ketron, C. V. & Waters, M. R.) 65–80 (Texas A&M University Press, 2014).164.Pečnerová, P. et al. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size. Evol. Lett. 1, 292–303 (2017).165.Conroy, K. J. et al. Tracking late-Quaternary extinctions in interior Alaska using megaherbivore bone remains and dung fungal spores. Quat. Res. https://doi.org/10.1017/qua.2020.19 (2020).166.Bakker, E. S. et al. Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation. Proc. Natl Acad. Sci. USA 113, 847–855 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    167.Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    168.Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5, pdb.prot5448 (2010).169.Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, 1–8 (2012).
    Google Scholar 
    170.Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).CAS 
    PubMed 

    Google Scholar 
    171.Agarwala, R. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 44, D7–D19 (2016).CAS 

    Google Scholar 
    172.Benson, D. A. et al. GenBank. Nucleic Acids Res. 41, D36–D42 (2013).173.Huson, D. H. et al. MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput. Biol. 12, e1004957 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    174.Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res. 17, 377–386 (2007).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    175.Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. MapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    176.Bronk Ramsey, C. & Lee, S. Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013).
    Google Scholar 
    177.Bronk Ramsey, C. Dealing with outliers and offsets in radiocarbon dating. Radiocarbon 51, 1023–1045 (2009).
    Google Scholar 
    178.Davies, L. J., Jensen, B. J. L., Froese, D. G. & Wallace, K. L. Late Pleistocene and Holocene tephrostratigraphy of interior Alaska and Yukon: key beds and chronologies over the past 30,000 years. Quat. Sci. Rev. 146, 28–53 (2016).ADS 

    Google Scholar 
    179.Westgate, J. A., Preece, S. J., Kotler, E. & Hall, S. Dawson tephra: a prominent stratigraphic marker of Late Wisconsinan age in west-central Yukon, Canada. Can. J. Earth Sci. 37, 621–627 (2000).ADS 
    CAS 

    Google Scholar 
    180.Froese, D., Westgate, J., Preece, S. & Storer, J. Age and significance of the Late Pleistocene Dawson tephra in eastern Beringia. Quat. Sci. Rev. 21, 2137–2142 (2002).ADS 

    Google Scholar 
    181.Zazula, G. D. et al. Vegetation buried under Dawson tephra (25,300 14C years BP) and locally diverse late Pleistocene paleoenvironments of Goldbottom Creek, Yukon, Canada. Palaeogeogr. Palaeoclimatol. Palaeoecol. 242, 253–286 (2006).
    Google Scholar 
    182.Froese, D. G., Zazula, G. D. & Reyes, A. V. Seasonality of the late Pleistocene Dawson tephra and exceptional preservation of a buried riparian surface in central Yukon Territory, Canada. Quat. Sci. Rev. 25, 1542–1551 (2006).ADS 

    Google Scholar 
    183.Klunk, J. et al. Genetic resiliency and the Black Death: no apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark. Am. J. Phys. Anthropol. 169, 240–252 (2019).PubMed 

    Google Scholar 
    184.Renaud, G., Stenzel, U. & Kelso, J. LeeHom: Adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res 42, e141 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    185.Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    186.Adobe Inc. Adobe Illustrator. (2020). https://adobe.com/products/illustrator.187.Lebart, L., Morineau, A. & Tabard, N. Techniques De La Description Statistique Méthodes Et Logiciels Pour L’analyse Des Grands Tableaux. (Dunod, 1977).188.Potter, B. A. et al. Current evidence allows multiple models for the peopling of the Americas. Sci. Adv. 4, 1–9 (2018).
    Google Scholar 
    189.Grootes, P. M. & Stuiver, M. Oxygen 18/16 variability in Greenland snow and ice with 10-3- to 105-year time resolution. J. Geophys. Res. Ocean. 102, 26455–26470 (1997).ADS 
    CAS 

    Google Scholar 
    190.Wolbach, W. S. et al. Extraordinary Biomass-Burning Episode and Impact Winter Triggered by the Younger Dryas Cosmic Impact ∼12,800 Years Ago. 2. Lake, Marine, and Terrestrial Sediments. J. Geol. 126, 185–205 (2018).ADS 
    CAS 

    Google Scholar  More

  • in

    Disturbance and distribution gradients influence resource availability and feeding behaviours in corallivore fishes following a warm-water anomaly

    1.Jentsch, A. & White, P. A theory of pulse dynamics and disturbance in ecology. Ecology 100, e02734 (2019).PubMed 

    Google Scholar 
    2.Stuart-Smith, R. D., Brown, C. J., Ceccarelli, D. M. & Edgar, G. J. Ecosystem restructuring along the Great Barrier Reef following mass coral bleaching. Nature 560, 92–96 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    3.Trisos, C. H., Merow, C. & Pigot, A. L. The projected timing of abrupt ecological disruption from climate change. Nature 580, 496–501 (2020).ADS 
    CAS 
    PubMed 

    Google Scholar 
    4.Blowes, S. A. et al. The geography of biodiversity change in marine and terrestrial assemblages. Science 366, 339–345 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    5.Schwartz, M. W. et al. Increasing elevation of fire in the Sierra Nevada and implications for forest change. Ecosphere 6, art121 (2015).
    Google Scholar 
    6.Sommerfeld, A. et al. Patterns and drivers of recent disturbances across the temperate forest biome. Nat. Commun. 9, 4355 (2018).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    7.Giraldo-Ospina, A., Kendrick, G. A. & Hovey, R. K. Depth moderates loss of marine foundation species after an extreme marine heatwave: Could deep temperate reefs act as a refuge?. Proc. R. Soc. B Biol. Sci. 287, 20200709 (2020).
    Google Scholar 
    8.Fahrig, L. Ecological responses to habitat fragmentation per se. Annu. Rev. Ecol. Evol. Syst. 48, 1–23 (2017).
    Google Scholar 
    9.Stephens, S. L. et al. Wildfire impacts on California spotted owl nesting habitat in the Sierra Nevada. Ecosphere 7, e01478 (2016).
    Google Scholar 
    10.Sih, A., Ferrari, M. C. O. & Harris, D. J. Evolution and behavioural responses to human-induced rapid environmental change. Evol. Appl. 4, 367–387 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    11.Duckworth, R. A. The role of behavior in evolution: a search for mechanism. Evol. Ecol. 23, 513–531 (2009).
    Google Scholar 
    12.Snell-Rood, E. C. An overview of the evolutionary causes and consequences of behavioural plasticity. Anim. Behav. 85, 1004–1011 (2013).
    Google Scholar 
    13.Schluter, D. Distributions of Galapagos ground finches along an altitudinal gradient: The importance of food supply. Ecology 63, 1504–1517 (1982).
    Google Scholar 
    14.Fryxell, J. M. & Sinclair, A. R. E. Causes and consequences of migration by large herbivores. Trends Ecol. Evol. 3, 237–234 (1988).CAS 
    PubMed 

    Google Scholar 
    15.Abraham, J. O., Hempson, G. P. & Staver, A. C. Drought-response strategies of savanna herbivores. Ecol. Evol. 9, 7047–7056 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    16.Fryxell, J. M. & Lundberg, P. Diet choice and predator-prey dynamics. Evol. Ecol. 8, 407–421 (1994).
    Google Scholar 
    17.Heron, S. et al. Impacts of climate change on world heritage coral reefs: Update to the first global scientific assessment. https://apo.org.au/node/193206 (2018).18.Jones, G. P., McCormick, M. I., Srinivasan, M. & Eagle, J. V. Coral decline threatens fish biodiversity in marine reserves. Proc. Natl. Acad. Sci. 101, 8251–8253 (2004).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    19.Bellwood, D. R., Hoey, A. S., Ackerman, J. L. & Depczynski, M. Coral bleaching, reef fish community phase shifts and the resilience of coral reefs. Glob. Change Biol. 12, 1587–1594 (2006).ADS 

    Google Scholar 
    20.Graham, N. A. J., Jennings, S., MacNeil, M. A., Mouillot, D. & Wilson, S. K. Predicting climate-driven regime shifts versus rebound potential in coral reefs. Nature 518, 94–97 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    21.Pratchett, M. S., Thompson, C. A., Hoey, A. S., Cowman, P. F. & Wilson, S. K. Effects of coral bleaching and coral loss on the structure and function of reef fish assemblages. In Coral Bleaching: Patterns, Processes, Causes and Consequences (eds van Oppen, M. J. H. & Lough, J. M.) 265–293 (Springer International Publishing, 2018). https://doi.org/10.1007/978-3-319-75393-5_11.Chapter 

    Google Scholar 
    22.Baird, A. H. & Marshall, P. A. Mortality, growth and reproduction in scleractinian corals following bleaching on the Great Barrier Reef. Mar. Ecol. Prog. Ser. 237, 133–141 (2002).ADS 

    Google Scholar 
    23.Gintert, B. E. et al. Marked annual coral bleaching resilience of an inshore patch reef in the Florida Keys: A nugget of hope, aberrance, or last man standing?. Coral Reefs 37, 533–547 (2018).ADS 

    Google Scholar 
    24.Gold, Z. & Palumbi, S. R. Long-term growth rates and effects of bleaching in Acropora hyacinthus. Coral Reefs 37, 267–277 (2018).ADS 

    Google Scholar 
    25.Fox, M. D. et al. Limited coral mortality following acute thermal stress and widespread bleaching on Palmyra Atoll, central Pacific. Coral Reefs 38, 701–712 (2019).ADS 

    Google Scholar 
    26.Thinesh, T., Meenatchi, R., Jose, P. A., Kiran, G. S. & Selvin, J. Differential bleaching and recovery pattern of southeast Indian coral reef to 2016 global mass bleaching event: Occurrence of stress-tolerant symbiont Durusdinium (Clade D) in corals of Palk Bay. Mar. Pollut. Bull. 145, 287–294 (2019).CAS 
    PubMed 

    Google Scholar 
    27.Ritson-Williams, R. & Gates, R. D. Coral community resilience to successive years of bleaching in Kāne‘ohe Bay, Hawai‘i. Coral Reefs 39, 757–769 (2020).
    Google Scholar 
    28.Sakai, K., Singh, T. & Iguchi, A. Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016. PeerJ 7, e8138 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    29.Muir, P. R., Marshall, P. A., Abdulla, A. & Aguirre, J. D. Species identity and depth predict bleaching severity in reef-building corals: shall the deep inherit the reef?. Proc. R. Soc. B Biol. Sci. 284, 20171551 (2017).
    Google Scholar 
    30.Baird, A. H. et al. A decline in bleaching suggests that depth can provide a refuge from global warming in most coral taxa. Mar. Ecol. Prog. Ser. 603, 257–264 (2018).ADS 

    Google Scholar 
    31.Frade, P. R. et al. Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching. Nat. Commun. 9, 3447 (2018).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    32.Crosbie, A., Bridge, T., Jones, G. & Baird, A. Response of reef corals and fish at Osprey Reef to a thermal anomaly across a 30 m depth gradient. Mar. Ecol. Prog. Ser. 622, 93–102 (2019).ADS 

    Google Scholar 
    33.Harrison, H. B. et al. Back-to-back coral bleaching events on isolated atolls in the Coral Sea. Coral Reefs 38, 713–719 (2019).ADS 

    Google Scholar 
    34.Sheppard, C., Sheppard, A. & Fenner, D. Coral mass mortalities in the Chagos Archipelago over 40 years: Regional species and assemblage extinctions and indications of positive feedbacks. Mar. Pollut. Bull. 154, 111075 (2020).CAS 
    PubMed 

    Google Scholar 
    35.Berumen, M. L., Pratchett, M. S. & McCormick, M. I. Within-reef differences in diet and body condition of coral-feeding butterflyfishes (Chaetodontidae). Mar. Ecol. Prog. Ser. 287, 217–227 (2005).ADS 

    Google Scholar 
    36.Coker, D. J., Pratchett, M. S. & Munday, P. L. Coral bleaching and habitat degradation increase susceptibility to predation for coral-dwelling fishes. Behav. Ecol. 20, 1204–1210 (2009).
    Google Scholar 
    37.Glynn, P. W. Corallivore population sizes and feeding effects following El Niño (1982–1983) associated coral mortality in Panama. in Proceedings of the 5th International Coral Reef Congress Symposium vol. 4, 183–188 (1985).38.Gates, R. D. Seawater temperature and sublethal coral bleaching in Jamaica. Coral Reefs 8, 193–197 (1990).ADS 

    Google Scholar 
    39.Cole, A. J., Pratchett, M. S. & Jones, G. P. Effects of coral bleaching on the feeding response of two species of coral-feeding fish. J. Exp. Mar. Biol. Ecol. 373, 11–15 (2009).
    Google Scholar 
    40.Pisapia, C., Cole, A. J. & Pratchett, M. S. Changing feeding preferences of butterflyfishes following coral bleaching. in Proceedings of the 12th International Coral Reef Symposium 5 (2012).41.Brooker, R. M., Munday, P. L., Brandl, S. J. & Jones, G. P. Local extinction of a coral reef fish explained by inflexible prey choice. Coral Reefs 33, 891–896 (2014).ADS 

    Google Scholar 
    42.Rocha, L. A. et al. Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361, 281–284 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    43.Loya, Y., Puglise, K. A. & Bridge, T. C. L. Mesophotic Coral Ecosystems (Springer, 2019).
    Google Scholar 
    44.Goldstein, E. D., D’Alessandro, E. K. & Sponaugle, S. Fitness consequences of habitat variability, trophic position, and energy allocation across the depth distribution of a coral-reef fish. Coral Reefs 36, 957–968 (2017).ADS 

    Google Scholar 
    45.MacDonald, C., Jones, G. P. & Bridge, T. Marginal sinks or potential refuges? Costs and benefits for coral-obligate reef fishes at deep range margins. Proc. R. Soc. B Biol. Sci. 285, 20181545 (2018).
    Google Scholar 
    46.MacDonald, C., Bridge, T. C. L., McMahon, K. W. & Jones, G. P. Alternative functional strategies and altered carbon pathways facilitate broad depth ranges in coral-obligate reef fishes. Funct. Ecol. 33, 1962–1972 (2019).
    Google Scholar 
    47.MacDonald, C. Depth as Refuge: Depth Gradients in Ecological Pattern, Process, and Risk Mitigation Among Coral Reef Fishes (James Cook University, 2018).
    Google Scholar 
    48.MacDonald, C., Tauati, M. I. & Jones, G. P. Depth patterns in microhabitat versatility and selectivity in coral reef damselfishes. Mar. Biol. 165, 138 (2018).
    Google Scholar 
    49.MacDonald, C., Bridge, T. & Jones, G. Depth, bay position and habitat structure as determinants of coral reef fish distributions: Are deep reefs a potential refuge?. Mar. Ecol. Prog. Ser. 561, 217–231 (2016).ADS 

    Google Scholar 
    50.Keith, S. A. et al. Synchronous behavioural shifts in reef fishes linked to mass coral bleaching. Nat. Clim. Change 8, 986–991 (2018).ADS 

    Google Scholar 
    51.Tricas, T. C. Determinants of feeding territory size in the corallivorous butterflyfish, Chaetodon multicinctus. Anim. Behav. 37, 830–841 (1989).
    Google Scholar 
    52.Coker, D. J., Pratchett, M. S. & Munday, P. L. Influence of coral bleaching, coral mortality and conspecific aggression on movement and distribution of coral-dwelling fish. J. Exp. Mar. Biol. Ecol. 414–415, 62–68 (2012).
    Google Scholar 
    53.Wismer, S., Tebbett, S. B., Streit, R. P. & Bellwood, D. R. Spatial mismatch in fish and coral loss following 2016 mass coral bleaching. Sci. Total Environ. 650, 1487–1498 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    54.Berumen, M. L. & Pratchett, M. S. Trade-offs associated with dietary specialization in corallivorous butterflyfishes (Chaetodontidae: Chaetodon). Behav. Ecol. Sociobiol. 62, 989–994 (2008).
    Google Scholar 
    55.Brooker, R. M., Jones, G. P. & Munday, P. L. Prey selectivity affects reproductive success of a corallivorous reef fish. Oecologia 172, 409–416 (2013).ADS 
    PubMed 

    Google Scholar 
    56.Burns, C. E. Behavioral ecology of disturbed landscapes: the response of territorial animals to relocation. Behav. Ecol. 16, 898–905 (2005).
    Google Scholar 
    57.Blowes, S. A., Pratchett, M. S. & Connolly, S. R. Heterospecific aggression and dominance in a guild of coral-feeding fishes: the roles of dietary ecology and phylogeny. Am. Nat. 182, 157–168 (2013).PubMed 

    Google Scholar 
    58.Pratchett, M. S. Feeding preferences and dietary specialization among obligate coral-feeding butterflyfishes. Biol. Butterflyfishes CRC Press Boca Raton USA 140–179 (2013).59.Penin, L., Vidal-Dupiol, J. & Adjeroud, M. Response of coral assemblages to thermal stress: Are bleaching intensity and spatial patterns consistent between events?. Environ. Monit. Assess. 185, 5031–5042 (2013).
    Google Scholar 
    60.Wyatt, A. S. J. et al. Heat accumulation on coral reefs mitigated by internal waves. Nat. Geosci. 13, 28–34 (2020).ADS 
    CAS 

    Google Scholar 
    61.Bloomberg, J. & Holstein, D. M. Mesophotic coral refuges following multiple disturbances. Coral Reefs 40, 821–834 (2021).
    Google Scholar 
    62.Bridge, T. C. L. et al. Variable responses of benthic communities to anomalously warm sea temperatures on a high-latitude coral reef. PLoS One 9, e113079 (2014).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    63.Grottoli, A. G. et al. The cumulative impact of annual coral bleaching can turn some coral species winners into losers. Glob. Change Biol. 20, 3823–3833 (2014).ADS 

    Google Scholar 
    64.Hoogenboom, M. O. et al. Environmental drivers of variation in bleaching severity of Acropora species during an extreme thermal anomaly. Front. Mar. Sci. 4, 376 (2017).
    Google Scholar 
    65.Suggett, D. J. & Smith, D. J. Coral bleaching patterns are the outcome of complex biological and environmental networking. Glob. Change Biol. 26, 68–79 (2020).ADS 

    Google Scholar 
    66.Starbuck, C. A., Considine, E. S. & Chambers, C. L. Water and elevation are more important than burn severity in predicting bat activity at multiple scales in a post-wildfire landscape. PLoS One 15, e0231170 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    67.Bond, M. L., Bradley, C. & Lee, D. E. Foraging habitat selection by California spotted owls after fire: Spotted Owls and Fire. J. Wildl. Manag. 80, 1290–1300 (2016).
    Google Scholar 
    68.NOAA. Kaplan SST V2 data provided by the NOAA/OAR/ESRL PSL. https://psl.noaa.gov/ (2020).69.Pinheiro, H. T. et al. Upper and lower mesophotic coral reef fish communities evaluated by underwater visual censuses in two Caribbean locations. Coral Reefs 35, 139–151 (2016).ADS 

    Google Scholar 
    70.Yabuta, S. & Berumen, M. L. Social structure and spawning behavior of Chaetodon butterflyfishes. in The Biology of Butterflyfishes (CRC Press, 2013).71.Pearl, J., Glymour, M. & Jewell, N. P. Causal Inference in Statistics: A Primer (Wiley, 2016).MATH 

    Google Scholar 
    72.McElreath, R. Statistical Rethinking: A Bayesian Course with Examples in R and Stan (Chapman and Hall/CRC, 2020). https://doi.org/10.1201/9780429029608.Book 

    Google Scholar 
    73.Manly, B. F., McDonald, L., Thomas, D. L., McDonald, T. L. & Erickson, W. P. Resource Selection by Animals: Statistical Design and Analysis for Field Studies (Springer Science & Business Media, 2007).
    Google Scholar  More

  • in

    Closely related gull species show contrasting foraging strategies in an urban environment

    1.Ditchkoff, S. S., Saalfeld, S. T. & Gibson, C. J. Animal behavior in urban ecosystems: Modifications due to human-induced stress. Urban Ecosyst. 9, 5–12 (2006).
    Google Scholar 
    2.Shochat, E., Warren, P. S., Faeth, S. H., McIntyre, N. E. & Hope, D. From patterns to emerging processes in mechanistic urban ecology. Trends Ecol. Evol. 21, 186–191 (2006).PubMed 

    Google Scholar 
    3.Witherington, B. E. Behavioral responses of nesting sea turtles to artificial lighting. Herpetologica 48, 31–39 (1992).
    Google Scholar 
    4.Markovchick-Nicholls, L. et al. Relationships between human disturbance and wildlife land use in urban habitat fragments. Conserv. Biol. 22, 99–109 (2008).PubMed 

    Google Scholar 
    5.Dunagan, S. P., Karels, T. J., Moriarty, J. G., Brown, J. L. & Riley, S. P. D. Bobcat and rabbit habitat use in an urban landscape. J. Mammal. 100, 401–409 (2019).
    Google Scholar 
    6.Prange, S., Gehrt, S. D. & Wiggers, E. P. Influences of anthropogenic resources on raccoon (Procyon lotor) movements and spatial distribution. J. Mammal. 85, 483–490 (2004).
    Google Scholar 
    7.Cooper, D. S., Yeh, P. J. & Blumstein, D. T. Tolerance and avoidance of urban cover in a southern California suburban raptor community over five decades. Urban Ecosyst. https://doi.org/10.1007/s11252-020-01035-w (2020).Article 

    Google Scholar 
    8.Auman, H. J., Bond, A. L., Meathrel, C. E. & Richardson, A. Urbanization of the silver gull: Evidence of anthropogenic feeding regimes from stable isotope analyses. Waterbirds 34, 70–76 (2011).
    Google Scholar 
    9.McKinney, M. L. Effects of urbanization on species richness: A review of plants and animals. Urban Ecosyst. 11, 161–176 (2008).
    Google Scholar 
    10.Faeth, S. H., Warren, P. S., Shochat, E. & Marussich, W. A. Trophic dynamics in urban communities. Bioscience 55, 399–407 (2005).
    Google Scholar 
    11.Rodewald, A. D., Kearns, L. J. & Shustack, D. P. Anthropogenic resource subsidies decouple predator–prey relationships. Ecol. Appl. 21, 936–943 (2011).PubMed 

    Google Scholar 
    12.Shochat, E., Lerman, S. B., Katti, M. & Lewis, D. B. Linking optimal foraging behavior to bird community structure in an urban-desert landscape: Field experiments with artificial food patches. Am. Nat. 164, 232–243 (2004).PubMed 

    Google Scholar 
    13.Baruch-Mordo, S., Breck, S. W., Wilson, K. R. & Theobald, D. M. Spatiotemporal distribution of black bear–human conflicts in Colorado, USA. J. Wildl. Manag. 72, 1853–1862 (2005).
    Google Scholar 
    14.Bateman, P. W. & Fleming, P. A. Big city life: Carnivores in urban environments. J. Zool. 287, 1–23 (2012).
    Google Scholar 
    15.Nisbet, I., Veit, R. R., Auer, S. & White, T. Marine Birds of the Eastern United States and the Bay of Fundy: Distribution, Numbers, Trends, Threats, and Management (Nuttall Ornithological Club, 2013).
    Google Scholar 
    16.Washburn, B. E., Bernhardt, G. E., Kutschbach-Brohl, L., Chipman, R. B. & Francoeur, L. C. Foraging ecology of four gull species at a coastal–urban interface. Condor 115, 67–76 (2013).
    Google Scholar 
    17.Fuirst, M., Veit, R. R., Hahn, M., Dheilly, N. & Thorne, L. H. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS One 13, 1–22 (2018).
    Google Scholar 
    18.Shaffer, S. A. et al. Population-level plasticity in foraging behavior of western gulls (Larus occidentalis). Mov. Ecol. 5, 1–13 (2017).
    Google Scholar 
    19.Rock, P. et al. Results from the first GPS tracking of roof-nesting Herring Gulls Larus argentatus in the UK. Ring. Migr. 31(1), 47–62 (2016).
    Google Scholar 
    20.Spelt, A. et al. Urban gulls adapt foraging schedule to human-activity patterns. Ibis (Lond. 1859) 163, 274–282 (2021).
    Google Scholar 
    21.Belant, J. L. Gulls in urban environments: Landscape-level reduce conflict. Landsc. Urban Plan. 38, 245–258 (1997).
    Google Scholar 
    22.Steenweg, R. J., Ronconi, R. A. & Leonard, M. L. Seasonal and age-dependent dietary partitioning between the great black-backed and herring gulls. Condor 113, 795–805 (2011).
    Google Scholar 
    23.Maynard, L. D. & Ronconi, R. A. Foraging behaviour of great black-backed gulls Larus marinus near an urban centre in atlantic Canada: Evidence of individual specialization from GPS tracking. Mar. Ornithol. 46, 27–32 (2018).
    Google Scholar 
    24.Borrmann, R. M., Phillips, R. A., Clay, T. A. & Garthe, S. High foraging site fidelity and spatial segregation among individual great black-backed gulls. J. Avian Biol. 50, 1–10 (2019).
    Google Scholar 
    25.Smith, J. A., Mazumder, D., Suthers, I. M. & Taylor, M. D. To fit or not to fit: Evaluating stable isotope mixing models using simulated mixing polygons. Methods Ecol. Evol. 4, 612–618 (2013).
    Google Scholar 
    26.Stock, B. C. et al. Analyzing mixing systems using a new generation of Bayesian tracer mixing models. PeerJ 6, 1–27 (2018).
    Google Scholar 
    27.Shochat, E. Credit or debit? Resource input changes population dynamics of city-slicker birds. Oikos 106, 622–626 (2004).
    Google Scholar 
    28.Seress, G. & Liker, A. Habitat urbanization and its effects on birds. Acta Zool. Acad. Sci. Hungar. 61, 373–408 (2015).
    Google Scholar 
    29.Annett, C. A. & Pierotti, R. Long-term reproductive output in western gulls: Consequences of alternate tactics in diet choice. Ecology 80, 288–297 (1999).
    Google Scholar 
    30.Anderson, J. G. T., Shlepr, K. R., Bond, A. L. & Ronconi, R. A. Introduction: A historical perspective on trends in some gulls in eastern North America, with reference to other regions. Waterbirds 39, 1–9 (2016).
    Google Scholar 
    31.Washburn, B. E., Elbin, S. B. & Davis, C. Historical and current population trends of herring gulls (Larus argentatus) and Great Black-Backed Gulls (Larus marinus) in the New York Bight, USA. Waterbirds 39, 74–86 (2016).
    Google Scholar 
    32.Duhem, C., Roche, P., Vidal, E. & Tatoni, T. Effects of anthropogenic food resources on yellow-legged gull colony size on Mediterranean islands. Popul. Ecol. 50, 91–100 (2008).
    Google Scholar 
    33.Zorrozua, N. et al. Breeding yellow-legged Gulls increase consumption of terrestrial prey after landfill closure. Ibis (Lond. 1859) 162, 50–62 (2020).
    Google Scholar 
    34.Pons, J. Effects of changes in the availability of human refuse on breeding parameters in a herring gull. Ardea 1983, 143–150 (1992).
    Google Scholar 
    35.Ordeñana, M. A. et al. Effects of urbanization on carnivore species distribution and richness. J. Mammal. 91, 1322–1331 (2010).
    Google Scholar 
    36.Duchamp, J. E., Sparks, D. W. & Whitaker, J. O. Foraging-habitat selection by bats at an urban-rural interface: Comparison between a successful and a less successful species. Can. J. Zool. 82, 1157–1164 (2004).
    Google Scholar 
    37.USDA. Feedgrains sector at a glance (2021). https://www.ers.usda.gov/topics/crops/corn-and-other-feedgrains/feedgrains-sector-at-a-glance/ (Accessed 10th July 2021).38.Jahren, A. H. & Schubert, B. A. Corn content of French fry oil from national chain vs. small business restaurants. Proc. Natl. Acad. Sci. U.S.A. 107, 2099–2101 (2010).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Hebert, C. E., Shutt, J. L., Hobson, K. A. & Weseloh, D. V. C. Spatial and temporal differences in the diet of Great Lakes herring gulls (Larus argentatus): Evidence from stable isotope analysis. Can. J. Fish. Aquat. Sci. 56, 323–338 (1999).
    Google Scholar 
    40.Moreno, R., Jover, L., Munilla, I., Velando, A. & Sanpera, C. A three-isotope approach to disentangling the diet of a generalist consumer: The yellow-legged gull in northwest Spain. Mar. Biol. 157, 545–553 (2010).
    Google Scholar 
    41.Coulson, J. C. Re-evaluation of the role of landfills and culling in the historic changes in the herring gull (Larus argentatus) population in Great Britain. Waterbirds 38, 339–354 (2015).
    Google Scholar 
    42.Shlepr, K. R., Ronconi, R. A., Hayden, B., Allard, K. A. & Diamond, A. W. Estimating the relative use of anthropogenic resources by herring gull (Larus argentatus) in the Bay of Fundy, Canada. Avian Conserv. Ecol. 16, 1–18 (2021).
    Google Scholar 
    43.Orians, G. & Pearson, N. On the theory of central place foraging. In Analysis of Ecological Communities (eds Horn, D. et al.) 154–177 (Ohio State University Press, 1979).
    Google Scholar 
    44.Walter, G. H. What is resource partitioning?. J. Theor. Biol. 150, 137–143 (1991).ADS 
    CAS 
    PubMed 

    Google Scholar 
    45.Schoener, T. Resource Partitioning. In Community Ecology: Pattern and Process (eds Kikkawa, J. & Anderson, D.) 91–126 (Blackwell Science Inc, 1986).
    Google Scholar 
    46.Rome, M. S. & Ellis, J. C. Foraging Ecology and Interactions between Herring Gulls and Great Black-Backed Gulls in New England rocky intertidal. Waterbirds 27, 200–210 (2017). http://www.jstor.org/stable/152243547.Weimerskirch, H., Bartle, J. A., Jouventin, P. & Claude, J. Foraging ranges and partitioning of feeding zones in three species of southern Albatrosses. Condor 90, 214–219 (1998). http://www.jstor.org/stable/136845048.Barger, C. P., Young, R. C., Will, A., Ito, M. & Kitaysky, A. S. Resource partitioning between sympatric seabird species increases during chick-rearing. Ecosphere 7, 1–15 (2016).
    Google Scholar 
    49.Ronconi, R. A., Steenweg, R. J., Taylor, P. D. & Mallory, M. L. Gull diets reveal dietary partitioning, influences of isotopic signatures on body condition, and ecosystem changes at a remote colony. Mar. Ecol. Prog. Ser. 514, 247–261 (2014).ADS 

    Google Scholar 
    50.Knoff, A., Macko, S. A., Erwin, R. M. & Brown, K. M. Stable isotope analysis of temporal variation in the diets of pre-fledged laughing gulls. Waterbirds 25, 142–148 (2017).
    Google Scholar 
    51.Clewley, G. D. et al. Foraging habitat selection by breeding Herring Gulls (Larus argentatus) from a declining coastal colony in the United Kingdom. Estuar. Coast. Shelf Sci. 261, 107564 (2021).
    Google Scholar 
    52.Evans, B. A. & Gawlik, D. E. Urban food subsidies reduce natural food limitations and reproductive costs for a wetland bird. Sci. Rep. 10, 1–12 (2020).
    Google Scholar 
    53.Auman, H. J., Meathrel, C. E. & Richardson, A. Supersize me: Does anthropogenic food change the body condition of silver gulls? A comparison between urbanized and remote, non-urbanized areas. Waterbirds 31, 122–126 (2008).
    Google Scholar 
    54.Pierotti, R. & Annett, C. The ecology of Western Gulls in habitats varying in degree of urban influence. in Avian Ecology and Conservation in an Urbanizing World 307–329 (2001).55.Belant, J. L., Ickes, S. K. & Seamans, T. W. Importance of landfills to urban-nesting herring and ring-billed gulls. Landsc. Urban Plan. 43, 11–19 (1998).
    Google Scholar 
    56.Murray, M. H., Hill, J., Whyte, P. & St. Clair, C. C. Urban compost attracts coyotes, contains toxins, and may promote disease in urban-adapted wildlife. EcoHealth 13, 285–292 (2016).PubMed 

    Google Scholar 
    57.Sapolsky, R. & Else, J. Bovine tuberculosis in a wild baboon population: Epidemiological aspects. J. Med. Primatol. 16, 229–235 (1987).CAS 
    PubMed 

    Google Scholar 
    58.Thorne, L. H., Fuirst, M., Veit, R. & Baumann, Z. Mercury concentrations provide an indicator of marine foraging in coastal birds. Ecol. Indic. 121, 106922 (2021).CAS 

    Google Scholar 
    59.Fauchald, P. & Tveraa, T. Using first-passage time in the analysis of area-restricted reports. Ecology 84, 282–288 (2003).
    Google Scholar 
    60.Suryan, R. M. et al. Foraging destinations and marine habitat use of short-tailed albatrosses: A multi-scale approach using first-passage time analysis. Deep. Res. Part II Top. Stud. Oceanogr. 53, 370–386 (2006).ADS 

    Google Scholar 
    61.McCune, B. & Grace, J. B. Nonmetric multidimensional scaling. in Analysis of Ecological Communities 125–142 (2002).62.Hobson, K. A. & Clark, R. G. Assessing avian diets using stable isotopes I: Turnover of 13C in tissues. Condor 94, 181–188 (1992). http://www.jstor.com/stable/136880763.Post, D. M. et al. Getting to the fat of the matter: Models, methods and assumptions for dealing with lipids in stable isotope analyses. Oecologia 152, 179–189 (2007).ADS 
    PubMed 

    Google Scholar 
    64.Sweeting, C. J., Polunin, N. V. C. & Jennings, S. Effects of chemical lipid extraction and arithmetic lipid correction on stable isotope ratios of fish tissues. Rapid Commun. Mass Spectrom. 20, 595–601 (2006).ADS 
    CAS 
    PubMed 

    Google Scholar 
    65.Caut, S., Angulo, E. & Courchamp, F. Variation in discrimination factors (Δ15N and Δ13C): The effect of diet isotopic values and applications for diet reconstruction. J. Appl. Ecol. 46, 443–453 (2009).CAS 

    Google Scholar 
    66.Hobson, K. A. & Clark, R. G. Assessing avian diets using stable isotopes II: Factors influencing diet-tissue fractionation. Condor 94, 189–197 (1992).
    Google Scholar 
    67.EvansOgden, L. J., Hobson, K. A. & Lank, D. B. Blood isotopic (δ13C and δ15N) turnover and diet-tissue fractionation factors in captive dunlin (Calidris alpina pacifica). Auk 121, 170–177 (2004).
    Google Scholar  More

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    High stability and metabolic capacity of bacterial community promote the rapid reduction of easily decomposing carbon in soil

    Site characteristics and experimental designIn this study, agricultural soils with five SOM contents were collected in 2015 from the following three different locations with the same climate type (the moderate temperate continental climate) in Northeast China (Table S3 and Fig. 1): Bei’an (BA), Hailun (HL), and Dehui (DH). Their MAT and MAP range from 1.0 to 4.4 and 520 to 550, respectively. After collection, the samples were transported to the Hailun Agricultural Ecological Experimental Station (HL), where the samples were packed into the same PVC tubes. Moving the soil from these three initial sampling points to the HL may have had some influence on the microbes, but compared with longer-distance soil translocation across different climatic zones, the HL site can be regarded as an in situ site that reflects the original climatic conditions. The SOM contents were 2%, 3%, 5%, 7%, and 9% (equivalent to 10, 18, 28, 36, and 56 g C kg−1 soil−1, respectively), and all the soils were classified as Mollisols according to the FAO classification. Here, we designed a unique latitudinal soil translocation experiment to investigate the relationship between the bacterial and fungal community stability and the responses of soil C molecular structure to climate warming. The detailed protocol for the experiment was the following: (1) Forty kilograms of topsoil (0–25 cm) was collected for each SOM. The latitude and longitude of the sampling sites and soil geochemical characteristics are shown in Tables S3 and S4. Detailed data can be found in Supplementary Data 1. (2) The soil was homogenized using a 2 mm sieve and filled with sterilized PVC tubes. The PVC tube was 5 cm in diameter at the bottom and 31 cm in height. Each tube was filled with a 25 cm-high soil column, which corresponded to approximately 1 kg of soil. The bottom of the pipe was filled with 1 cm quartz sand, and a 5 cm space was left at the top. (3) From October to November 2015, 90 PVC pipes containing soil (5 SOM gradients × 3 replicates × 6 climatic conditions) were transported to six ecological research stations with different geoclimatic conditions and SOM contents, and 15 PVC pipes were placed in each station. Once the experiment was set up, the weeds growing in each PVC pipe were manually removed every 2–3 weeks to avoid the impact of plants.The six ecological research stations were the Hailun Agricultural Ecological Experimental Station (HL, N 47°27′, E 126°55′) in Heilongjiang Province, Shenyang Agriculture Ecological Experimental Station (SY, N 41°49′, E 123°33′) in Liaoning Province, Fengqiu Agricultural Ecological Experimental Station (FQ, N 35°03′, E 114°23′) in Henan Province, Changshu Agricultural Ecological Experimental Station (CS, N 31°41′, E 120°41′) in Jiangsu Province, Yingtan Red Soil Ecological Experiment Station (YT, N 28°12′, E 116°55′) in Jiangxi Province and Guangzhou National Agricultural Science and Technology Park (GZ, N 23°23′, E 113°27′) in Guangdong Province. The MAT and MAP at the six ecological research stations ranged from 1.5 to 21.9 °C and from 550 to 1750 mm from north to south, respectively. Details of their climatic conditions (e.g., climatic types) are shown in Table S5. All tubes were removed from each station after 1 year.The soil samples were stored on dry ice and rapidly transported back to the laboratory. The soil pH was measured by the potentiometric method. Nitrate (NO3−-N) and ammonium nitrogen (NH4+-N) were measured by the Kjeldahl method. DOC was measured using a total organic carbon analyzer (Shimadzu Corporation, Kyoto, Japan). SOC was determined by wet digestion using the potassium dichromate method53. Microbial biomass C (MBC) was measured by the chloroform fumigation-incubation method54. All geochemical attributes are shown in Table S4.Solid-state 13C NMR analysis of soil C molecular groupsSolid-state 13C NMR spectroscopy analysis was performed to determine the molecular structure of SOC. A Bruker-Avance-iii-300 spectrometer was used at a frequency of 75 MHz (300 MHz 1H). Before the examination, the soil samples were pretreated with hydrofluoric acid to eliminate the interference of Fe3+ and Mn2+ ions in the soil. Specifically, 5 g of air-dried soil was weighed in a 100 ml centrifuge tube with 50 ml of hydrofluoric acid solution (10% v/v) and shaken for 1 h. The supernatant was then removed by centrifugation at 3000 rpm for 10 min. The residues were washed eight times with a hydrofluoric acid solution (10%) with ultrasonication. The oscillation program consisted of the following: four × 1 h, three × 12 h, and one × 24 h. The soil samples were washed with distilled water four times to remove the residual hydrofluoric acid. The above-mentioned treated soil samples were dried in an oven at 40 °C, ground and passed through a 60-mesh sieve for NMR measurements.The soil samples were then subjected to solid-state magic-angle rotation-NMR measurements (AVANCE II 300 MH) using a 7 mm CPMAS probe with an observed frequency of 100.5 MHz, an MAS rotation frequency of 5000 Hz, a contact time of 2 s, and a cycle delay time of 2.5 s. The external standard material for the chemical shift was hexamethyl benzene (HMB, methyl 17.33 mg kg−1). The spectra were quantified by subdividing them into the following chemical shift regions55: 0–45 ppm (alkyl), 45–60 ppm (N-alkyl and methoxyl), 60–110 ppm (O-alkyl), 110–140 ppm (aryl), 140–160 ppm (O-aryl), 160–185 ppm (carboxy), and 185–230 ppm (carbonyl) (Fig. 3a). We classified O-alkyl, O-aryl, and carboxy C as labile C and alkyl, N-alkyl/methoxyl, and aryl C were classified as recalcitrant C.Soil microbial C metabolic profilesThe soil microbial C metabolic capacities were measured with BIOLOG 96-well Eco-Microplates (Biolog Inc., USA) using 31 different C sources and three replicates in each microplate. These C sources included carbohydrates, carboxylic acids, polymers, amino acids, amines, and phenolic acids (Table S2). Carbohydrates, amino acids, and carboxylic acids are generally considered labile C sources, amines and phenolic acid compounds are relatively resistant C sources, and polymers are recalcitrant C. The diverse nature of these C sources allowed us to identify differences in the capacity of microbes to degrade different C sources56. Soil microbes were extracted as follows: (1) Five grams of soil (dry weight equivalent) was incubated at 25 °C for 24 h, and 45 ml of sterile 0.85% (w/v) sodium chloride solution was added57. (2) At room temperature (25 °C), the mixture was shaken at 200 rpm for 30 min and allowed to stand for 15 min. (3) Subsequently, 0.1 ml of the supernatant was collected and diluted to 100 ml with sterile sodium chloride solution. (4) Soil suspensions were dispensed into each of the 93 wells (150 μl per well), and the plates were then incubated at 25 °C in the dark for 14 days. The optical density (OD, reflecting C utilization) of each well was read at 590 nm (color development) every 12 h. The normalized OD of different C sources was calculated as the OD of the well that contained the C source minus the OD of the well that contained sterile sodium chloride solution (control well). The normalized OD at a single time point (228 h) was used for the posterior analysis when it reached the asymptote.DNA extraction, PCR amplification, and sequencingDNA was extracted from all 90 soil samples. Briefly, well-mixed soil samples (0.6 g) were analyzed using the Power Soil DNA Isolation Kit (MoBio Laboratories, Inc., Carlsbad, CA, USA) following the manufacturer’s instructions. The quality of the DNA extracts was determined by spectrophotometry (OD-1000+, OneDrop Technologies, China). The DNA extracts were considered of sufficient quality if the ratio of OD260 to OD280 (optical density, OD) and the ratio of OD260 to OD230 were approximately 1.8. All eligible DNA samples were stored at −80 °C.Taxonomic profiling of the soil bacterial and fungal communities was performed using an Illumina® HiSeq Benchtop Sequencer. PCR amplification was performed using an ABI GeneAmp® 9700 (ABI, Foster City, CA, USA) with a 20 μl reaction system containing 4 μl of 5× FastPfu Buffer, 0.8 μl of each primer (5 μM), 2 μl of 2.5 mM dNTPs, 2 μl of template DNA, and 0.4 μl of FastPfu Polymerase. For bacterial analysis, the forward the primer 515F (GTGCCAGCMGCCGCGG) and the reverse primer 907R (CCGTCAATTCMTTTRAGTTT) were used to amplify the bacteria-specific V4-V5 hypervariable region of the 16S rRNA gene58. For fungal analysis, the internal transcribed spacer 1 (ITS1) region of the ribosomal RNA gene was amplified with primers ITS1-1737F (GGAAGTAAAAGTCGTAACAAGG) and ITS2-2043R (GCTGCGTTCTTCATCGATGC)59. The PCR protocol for bacteria consisted of an initial predenaturation step of 95 °C for 2 min, 35 cycles of 20 s at 94 °C, 40 s at 55 °C and 1 min at 72 °C, and a final 10 min extension at 72 °C. The PCR protocol for fungi consisted of an initial predenaturation step of 95 °C for 3 min, 35 cycles of 30 s at 95 °C, 30 s at 59.3 °C, and 45 s at 72 °C and a final 10 min extension at 72 °C.Each sample was independently amplified three times. Following amplification, 2 μl of each of the PCR products was checked by agarose gel (2.0%) electrophoresis, and all the PCR products from the same sample were then pooled together. The pooled mixture was purified using the Agencourt AMPure XP Kit (Beckman Coulter, CA, USA). The purified products were indexed in the 16S and ITS libraries. The quality of these libraries was assessed using Qubit@2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 systems. These pooled libraries (16S and ITS) were subsequently sequenced with an Illumina HiSeq 2500 Sequencer to generate 2 × 250 bp paired-end reads at the Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc., Shanghai, China.The raw reads were quality filtered and merged as follows: (1) TrimGalore was used for truncation of the raw reads at any site with an average quality score  5%) soils, changes in the C metabolic capacity of microbes under elevated temperatures were characterized using the ratio of the OD of microbes measured in the translocated soils to the OD of microbes in the in situ HL soil. A ratio greater than 1 indicates that translocation warming increases the C metabolism of microbes.Mantel and partial Mantel analysisA previous study showed that partial Mantel analysis is a robust method for evaluating the relationship among three variables65. This approach can control the z-axis and assess only the relationship between the x- and y-axes, avoiding the interaction between the z- and x-axes on the y-axis. In this study, Mantel analysis was employed to assess the relationships between the stability of the bacterial and fungal communities and C metabolic capacity. Stability refers primarily to the ability of the microbial community to resist translocation warming66. A higher similarity between the microbial communities in translocated soil compared with that in the in situ HL area indicates that the community is more resistant to translocation-related warming and that the microbial community is more stable.Calculation of the microbial β-diversityBray-Curtis and Euclidean dissimilarity metrics were calculated to estimate the bacterial and fungal taxonomic dissimilarity (β-diversity) and environmental dissimilarity (e.g., latitude, MAT, and MAP), respectively, using the vegan package (version 2.5–6) in the R statistical program (version 4.0.2, https://www.r-project.org/)67. Corresponding to the 45 C metabolism ratios in soils with the same OM content, the β-diversity values of bacteria and fungi were selected to analyze the relationship between the community similarity (1-β-diversity) of bacteria and fungi and changes in microbial C metabolism.Impact of the SOM content and climate change on changes in microbial communitiesThe distribution patterns of the bacterial and fungal communities under different SOM gradients and climatic regimes were determined through nonmetric multidimensional scaling (NMDS)68. To quantitatively compare the effects of the SOM gradient and climatic regimes on the bacterial and fungal community composition, three nonparametric multivariate statistical analyses were used in this study: nonparametric multivariate analysis of variance (Adonis), analysis of similarity (ANOSIM), and multiple response permutation procedure (MRPP)69. The linear fit between environmental dissimilarity and microbial β-diversity was analyzed using the lm function in R. A significant difference in the bacterial and fungal β-diversity among different SOM contents was evaluated by Student’s paired t-test using the ggpubr (version 0.4.0) package70. RDA was performed to analyze the relationships of bacterial and fungal communities with various environmental factors (soil geochemical attributes and climatic conditions, such as MAP and MAT). In parallel, the Monte Carlo permutation test (999 permutations) was employed to determine whether the explanation of the microbial distribution by individual factors (e.g., pH, SOC, and TN) was significant71.Construction of the structural equation model and random forest modelA SEM was fitted to illustrate the direct or indirect effects of soil properties (e.g., pH, moisture, ammonia, and nitrate nitrogen), climate change (e.g., MAT and MAP), and bacterial and fungal β-diversity on soil C metabolic capacity72. Based on the Euclidean method, the changes in soil properties and climatic conditions of five translocated sites compared with those in the in situ HL site were calculated. A total of 45 ratios were obtained for each OM content. Corresponding to the 45 ratios in soils with the same OM content, the β-diversity values of bacteria and fungi were selected. The model construction process was mainly divided into three steps. In brief, these steps include the establishment of an a priori model, data normality detection, and an overall goodness-of-fit test. The prior model was constructed based on a literature review and our knowledge. For the variables that did not conform to the normal distribution, we performed logarithmic transformation. Here, we used the χ2 test (the model was assumed to exhibit a good fit if p  > 0.05), the goodness-of-fit index (GFI; the model was assumed to show a good fit if GFI  > 0.9), the root mean square error of approximation (RMSEA; the model was assumed to exhibit a good fit if RMSEA  0.05)73 and the Bollen-Stine bootstrap test (the model was assumed to show a good fit if the bootstrap p  > 0.10) to test the overall goodness of fit of the SEM. All SEM analyses were conducted using IBM® SPSS® Amos 21.0 (AMOS, IBM, USA). Additionally, the importance of the metabolic capacity of different types of C on labile and recalcitrant C was assessed by random forest models using the randomForest package (version 4.6-14) in R74, and the model significance and amount of interpretation were evaluated using the rfUtilities package (version 2.1–5)75.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More