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    Conceptual frameworks facilitate integration for transdisciplinary urban science

    1.
    Acuto, M., Parnell, S. & Seto, K. C. Building a global urban science. Nat. Sustain. 1, 2–4 (2018).
    Article  Google Scholar 
    2.
    Anderies, J. M., Folke, C., Walker, B. & Ostrom, E. Aligning key concepts for global change policy: robustness, resilience, and sustainability. Ecol. Soc. 18, 8 (2013).
    Article  Google Scholar 

    3.
    Brenner, N. & Schmid, C. Planetary urbanization. In Implosions/explosions: Towards A Study of Planetary Urbanization (ed. Brenner, N.) 142–463 (Jovis Verlag, 2014).

    4.
    Elmqvist, T. et al. Sustainability and resilience for transformation in the urban century. Nat. Sustain. 2, 267 (2019).
    Article  Google Scholar 

    5.
    McPhearson, T. Scientists must have a say in the future of cities. Nature 538, 165–166 (2016).
    CAS  Article  Google Scholar 

    6.
    Groffman, P. M. et al. Moving towards a new Urban Systems Science. Ecosystems https://doi.org/10.1007/s10021-016-0053-4 (2016).

    7.
    Pataki, D. E. Grand challenges in urban ecology. Front. Ecol. Evol. 3, 57 (2015).
    Article  Google Scholar 

    8.
    National Science Foundation. What is Convergence?|NSF-National Science Foundation. https://www.nsf.gov/od/oia/convergence/index.jsp (Accessed April 23, 2019).

    9.
    Ramaswami, A. et al. Sustainable Urban Systems: Articulating a Long-Term Convergence Research Agenda. Vol. 31 (National Science Foundation, 2018).

    10.
    Grimm, N. B., Pickett, S. T. A., Hale, R. L. & Cadenasso, M. L. Does the ecological concept of disturbance have utility in urban social-ecological-technological systems? Ecosyst. Health Sustain 3, e01255 (2017).
    Article  Google Scholar 

    11.
    McPhearson, T. et al. Advancing urban ecology towards a science of cities. BioScience 66, 198–212 (2016).
    Article  Google Scholar 

    12.
    United Nations. Transforming Our World: the 2030 Agenda for Sustainable Development. https://sustainabledevelopment.un.org/post2015/transformingourworld (Accessed March 6, 2020).

    13.
    Seto, K. C. et al. Urban land teleconnections and sustainability. Proc. Natl Acad. Sci. USA 109, 7687–7692 (2012).
    CAS  Article  Google Scholar 

    14.
    Folke, C., Biggs, R., Norstrom, A. V., Reyers, B. & Rockstrom, J. Social-ecological resilience and biosphere-based sustainability science. Ecol. Soc. 21, 41 (2016).
    Article  Google Scholar 

    15.
    Grimm, N. B., Cook, E. M., Hale, R. L. & Iwaniec, D. M. A broader framing of ecosystem services in cities: benefits and challenges of built, natural, or hybrid system function. In The Routledge Handbook of Urbanization and Global Environmental Change (eds. Seto, K. C., Solecki, W. D. & Griffith, C. A.) 203–212 (Routledge, 2016).

    16.
    Pelling, M. & Manuel-Navarrete, D. From resilience to transformation: the adaptive cycle in two Mexican urban centers. Ecol. Soc. 16, 11 (2011).
    Article  Google Scholar 

    17.
    Meerow, S., Newell, J. P. & Stults, M. Defining urban resilience: a review. Landsc. Urban Plan. 147, 38–49 (2016).
    Article  Google Scholar 

    18.
    Shane, D. G. Recombinant Urbanism: Conceptual Modeling in Architecture. (John Wiley & Sons, 2005).

    19.
    McHale, M. R. et al. The new global urban realm: complex, connected, diffuse, and diverse social-ecological systems. Sustainability 7, 5211–5240 (2015).
    Article  Google Scholar 

    20.
    Ellin, N. Integral urbanism: a context for urban design. In Resilience in ecology and urban design: linking theory and practice for sustainable cities (eds. Pickett, S. T. A., Cadenasso, M. L. & McGrath, B.) 63–78 (Springer, 2013).

    21.
    Marcotullio, P. J. & Solecki, W. What is a city? an essential definition for sustainability. In Urbanization and Sustainability: Linking Urban Ecology, Environmental Justice, and Environmental Change (eds. Boone, C. G. & Fragkias, M.) 11–25 (Springer, 2013).

    22.
    Burch, W. R., Jr., Machlis, G. E. & Force, J. E. The Structure and Dynamics of Human Ecosystems: toward A Model for Understanding and Action. (Yale University Press, 2017).

    23.
    Redman, C., Grove, J. M. & Kuby, L. Toward a Unified Understanding of Human Ecosystems: Integrating Social Sciences Into Long-term Ecological Research. Vol. 13 (LTER Network, 2000).

    24.
    Barnett, R. & Margetts, J. Disturbanism in the South Pacific: disturbance ecology as a basis for urban resilience in small island states. In Resilience in Ecology and Urban Design: Linking Theory and Practice for Sustainable Cities (eds. Pickett, S. T. A., Cadenasso, M. L. & McGrath, B.) 443–459 (Springer, 2013).

    25.
    Folke, C. et al. Resileince and Sustainable Development: Building Adaptive Capacity in A World of Transformations. (Ministry of the Environment, 2002).

    26.
    Scheffer, M., Westley, F., Brock, W. A. & Holmgren, M. Dynamic interaction of societies and ecosystems–linking theories from ecology, economy, and sociology. In Panarchy: Understanding Transformations in Human and Natural Systems (eds. Gunderson, L. H. & Holling, C. S.) 195–239 (Island Press, 2002).

    27.
    Pickett, S. T. A. et al. Dynamic heterogeneity: a framework to promote ecological integration and hypothesis generation in urban systems. Urban Ecosyst. 20, 1–14 (2017).
    Article  Google Scholar 

    28.
    Wu, J. G. & Loucks, O. L. From balance of nature to hierarchical patch dynamics: a paradigm shift in ecology. Q. Rev. Biol. 70, 439–466 (1995).
    Article  Google Scholar 

    29.
    Boone, C. G. et al. Reconceptualizing land for sustainable urbanity. In Rethinking Urban Land Use in A Global Era (eds. Seto, K. C. & Reenberg, A.) 313–330 (MIT Press, 2014).

    30.
    Machlis, G. E., Force, J. E. & Burch, W. R. The human ecosystem 1. The human ecosystem as an organizing concept in ecosystem management. Soc. Nat. Resour. 10, 347–367 (1997).
    Article  Google Scholar 

    31.
    Cadenasso, M. L. & Pickett, S. T. A. Three tides: the development and state of the art of urban ecological science. In Resilience in Ecology and Urban Design: Linking Theory and Practice for Sustainable Cities (eds. Pickett, S. T. A., Cadenasso, M. L. & McGrath, B.) 29–46 (Springer, 2013).

    32.
    Collins, S. L. et al. An integrated conceptual framework for long-term social-ecological research. Front. Ecol. Environ. 9, 351–357 (2011).
    Article  Google Scholar 

    33.
    Naveh, Z. The total human ecosystem: integrating ecology and economics. BioScience 50, 357–361 (2000).
    Article  Google Scholar 

    34.
    Pickett, S. T. A. & Cadenasso, M. L. Ecosystem as a multidimensional concept: meaning, model and metaphor. Ecosystems 5, 1–10 (2002).
    Article  Google Scholar 

    35.
    Alberti, M. Advances in Urban Ecology: Integrating Humans and Ecological Processes in Urban Ecosystems. (Springer, 2008).

    36.
    Pickett, S. T. A. & Grove, J. M. Urban ecosystems: what would Tansley do? Urban Ecosyst. 12, 1–8 (2009).
    Article  Google Scholar 

    37.
    Lachmund, J. Greening Berlin. (MIT Press, 2013).

    38.
    Rademacher, A., Cadenasso, M. L. & Pickett, S. T. A. From feedbacks to coproduction: toward an integrated conceptual framework for urban ecosystems. Urban Ecosyst. https://doi.org/10.1007/s11252-018-0751-0 (2018).

    39.
    Johnson, E. A. & Miyanishi, K. (eds.) Plant Disturbance Ecology: the Process and the Response. (Academic Press, Burlington, 2007).

    40.
    Pickett, S. T. A. & White, P. S. (eds.) The Ecology of Natural Disturbance and Patch Dynamics. (Academic Press, Orlando, 1985).

    41.
    Schumpeter, J. A. The Theory of Economic Development: an Inquiry Into Profits, Capital, Credit, Interest, and the Business Cycle. (Transaction Books, 1983).

    42.
    Peters, D. P. C. et al. Cross-system comparisons elucidate distrubance complexities and generalities. Ecosphere 2, art 81 (2011).
    Article  Google Scholar 

    43.
    Holling, C. S. Engineering resilience versus ecological resilience. In Engineering within Ecological Constraints (ed. Schulze, P. C.) 31–44 (National Academies of Engineering, 1996).

    44.
    Gunderson, L. H. & Holling, C. S. (eds.) Panarchy: understanding transformations in human and natural systems. (Island Press, Washington DC, 2002).

    45.
    Walker, B., Holling, C. S., Carpenter, S. R. & Kinzig, A. Resilience, adaptability and transformability in social-ecological systems. Ecol. Soc. 9, Article 5 (2004).
    Article  Google Scholar 

    46.
    McPhearson, T., Andersson, E., Elmqvist, T. & Frantzeskaki, N. Resilience of and through urban ecosystem services. Ecosyst. Services 12, 152–156 (2015).
    Article  Google Scholar 

    47.
    Tidball, K., Frantzeskaki, N. & Elmqvist, T. Traps! An introduction to expanding thinking on persistent maladaptive states in pursuit of resilience. Sustain. Sci. 11, 861–866 (2016).
    Article  Google Scholar 

    48.
    Biggs, R., Westley, F. R. & Carpenter, S. R. Navigating the back loop: fostering social innovation and transformation in ecosystem management. Ecol. Soc. 15, 9 (2010).
    Article  Google Scholar 

    49.
    Changnon, S. A., Kunkel, K. E. & Reinke, B. C. Impacts and responses to the 1995 heat wave: a call to action. Bullet. Am. Meteorol. Soc. 77, 1497–1506 (1996).
    Article  Google Scholar 

    50.
    Borden, K. A. & Cutter, S. L. Spatial patterns of natural hazards mortality in the United States. Int. J. Health Geogr. 7, 64 (2008).
    Article  Google Scholar 

    51.
    Park, R. E. & Burgess, E. W. The City (University of Chicago Press, 1925).

    52.
    Jacobs, J. The Death and Life of Great American Cities (Random House, 1961).

    53.
    Lynch, K. Good City Form (MIT Press, 1981).

    54.
    Shane, D. G. Urban Design Since 1945–A Global Perspective (John Wiley & Sons, Ltd, 2011).

    55.
    Hamstead, Z., Farmer, C. & McPhearson, T. Landscape-based extreme heat vulnerability assessment. J. Extreme Event. 5, 1–23 (2018).
    Google Scholar 

    56.
    Uejio, C. K. et al. Intra-urban societal vulnerability to extreme heat: the role of heat exposure and the built environment, socioeconomics and neighborhood stability. Health Place 17, 498–507 (2011).
    Article  Google Scholar 

    57.
    Rosenthal, J. K., Kinney, P. L. & Metzger, K. B. Intra-urban vulnerability to heat-related mortality in New York City. 1997–2006. Health Place 30, 45–60 (2014).
    Google Scholar 

    58.
    Madrigano, J., Ito, K., Johnson, S., Kinney, P. L. & Matte, T. A case-only study of vulnerability to heat wave–related mortality in New York City (2000–2011). Environ. Health Perspect. 123, 672–678 (2015).
    Article  Google Scholar 

    59.
    Allen, T. F. H. & Starr, T. B. Hierarchy: Perspectives for Ecological Complexity (2nd edn.) (University of Chicago Press, Chicago, 2017).

    60.
    McGrath, B. & Shane, G. Introduction: metropolis, megalopolis, and metacity. In The SAGE Handbook of Architectural Theory (eds. Crysler, C. G., Cairns, S. & Heynen, H.) (SAGE, 2012).

    61.
    Mihaljevic, J. R. (2012). Linking metacommunity theory and symbiont evolutionary ecology. Trends Ecol. Evol. 27, 323–329 (2012).
    Article  Google Scholar 

    62.
    McGrath, B., Sangawongse, S., Thaikatoo, D. & Corte, M. B. The architecture of the metacity: land use change, patch dynamics and urban form in Chiang Mai, Thailand. Urban Plan. 2, 53–71 (2017).
    Article  Google Scholar 

    63.
    Leibold, M. A. The metacommunity concept and its theoretical underpinnings. In The Theory of Ecology (eds. Scheiner, S. M. & Willig, M. R.) 163–183 (University of Chicago Press, 2011).

    64.
    McGrath, B. & Pickett, S. T. A. The metacity: a conceptual framework for integrating ecology and urban design. Challenges 2011, 55–72 (2011).
    Article  Google Scholar 

    65.
    Batty, M. The New Science of Cities. (MIT Press, 2013).

    66.
    Gandy, M. Where does the city end? In Implosions/explosions: Towards A Study of Planetary Urbanization (ed. Brenner, N.) 86–89 (jovis Verlag, 2014).

    67.
    McPhearson, T., Kremer, P. & Hamstead, Z. Mapping ecosystem services in new york city: applying a social-ecological approach in urban vacant land. Ecosyst. Service 11–26, https://doi.org/10.1016/j.ecoser.2013.06.005 (2013).

    68.
    Kremer, P., Hamstead, Z. & McPhearson, T. A social-ecological assessment of vacant lots in New York City. Landsc. Urban Plann. 218–233, https://doi.org/10.1016/j.landurbplan.2013.05.003 (2013).

    69.
    Burkholder, S. The new ecology of vacancy: rethinking land use in shrinking cities. Sustainability 4, 1154–1172 (2012).
    Article  Google Scholar 

    70.
    Bowman, A. O. M. & Pagano, M. A. Transforming America’s cities: policies and conditions of vacant land. Urban Affairs Rev. 35, 559–581 (2000).
    Article  Google Scholar 

    71.
    Kabisch N., et al. Nature-Based Solutions to Climate Change Adaptation in Urban Areas—Linkages Between Science, Policy and Practice. 91–109 (Springer, 2017).

    72.
    Schwarz, K., Berland, A. & Herrmann, D. L. Green, but not just? Rethinking environmental justice indicators in shrinking cities. Sustain. Cities Soc. 41, 816–821 (2018).
    Article  Google Scholar 

    73.
    McDonnell, M. J. & Hahs, A. K. The future of urban biodiversity research: moving beyond the ‘low-hanging fruit’. Urban Ecosyst. 16, 397–409 (2013).
    Article  Google Scholar 

    74.
    Pickett, S. T. A., Kolasa, J. & Jones, C. G. Ecological Understanding: The Nature of Theory and the Theory of Nature (Academic Press, 2007).

    75.
    Depietri Y. & McPhearson T. Integrating the grey, green, and blue in cities: Nature-based solutions for climate change adaptation and risk reduction. In Nature-based solutions to climate change adaptation in urban areas. Theory and practice of urban sustainability transitions (eds. Kabisch N., Korn H., Stadler J. & Bonn A.) (Springer, Cham, 2017). More

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    Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

    Aquarium experiment and sampling
    To examine the effect of changes in species composition on the behaviour of eDNA, we conducted aquarium experiments using two mock fish communities comprising H. neglectus, C. temminckii, O. latipes, R. flumineus, and M. anguillicaudatus. Mock community 1 (MC1) consisted of one individual of each of the five fish species, whereas mock community 2 (MC2) consisted of three H. neglectus individuals and one individual of each of the other four fish species (Fig. 2). We used two aquaria (A and B). Each aquarium was used four times, twice for each mock community, giving two replicates (R1 and R2). This resulted in eight experimental units (2 mock fish communities × 2 aquaria × 2 replicates). Figure 2 shows the experimental setup used in this study.
    Figure 2

    Experimental setup of the aquarium experiments.

    Full size image

    To set up the aquaria, 20 L of tap water was added into each aquarium (GEX Co. Ltd., Osaka, Japan) and heated with a heater (Spectrum Brands, Wisconsin, US) until the water temperature reached 25 °C. Water in the two aquaria was maintained at 25 °C and constantly circulated with an aeration device. Before adding fish to the aquaria, the water was sampled for the negative control. The first experimental samples (day 0) were taken 1 h after adding the fish and subsequent samples were taken each day until day 4. At each sampling, two 1-L samples of surface water were collected from each aquarium and then 2 L of tap water was added to each aquarium to maintain the volume of water. The weight of individual fish species was measured using an electronic balance immediately after the final sampling. After each experiment, the two aquaria were bleached before being reused.
    In Japan, experiments on fish do not require any legal procedures or permission. However, in order to avoid causing pain to the specimens, the experiments in this study were conducted in accordance with the ARRIVE guidelines, Japanese laws and guidelines for mammals, birds, and reptiles as below; Act on Welfare and Management of Animals (Notice of the Ministry of the Environment No. 105 of October 1, 1973), Standards relating to the Care and Keeping and Reducing Pain of Laboratory Animals (Notice of the Ministry of the Environment No. 88 of 2006), Fundamental Guidelines for Proper Conduct of Animal Experiment and Related Activities in Academic Research Institutions under the jurisdiction of the Ministry of Education (Notice of Ministry of Education No. 71, 2006), and Guidelines for Proper Conduct of Animal Experiments (established by the Science Council of Japan on June 1, 2006).
    DNA extraction
    Each 1-L water sample was filtered immediately through a GF/F glass fibre filter (nominal pore size = 0.7 μm, diameter = 47 mm; GE Healthcare Japan Corporation, Tokyo, Japan). Filter funnels and measuring cups were bleached after filtration to prevent cross-contamination among the water samples. All filters were stored separately at − 20 °C until DNA extraction. Total eDNA was extracted from each filter using a DNeasy Blood and Tissue Kit (QIAGEN, Hilden, Germany) and Salivette tubes (Sarstedt AG & Co. KG, Nümbrecht, Germany). Extraction methods were as previously described18 with modifications. A filter sample was placed in the upper part of the Salivette tube and 220 μL of solution containing Buffer AL (200 μL) and Proteinase K (20 μL) was added. The tube containing the filter was incubated at 56 °C for 30 min, then centrifuged at 5000 × g for 3 min, and the solution was collected in the base of the tube. To increase eDNA yield, 220 μL Tris-EDTA (TE) buffer was added to the filter sample and centrifuged at 5000 × g for 1 min. Then, ethanol (200 μL) was added to the collected solution, and the mixture was transferred to a spin column. Total eDNA was eluted in buffer AE (100 μL), following the manufacturer’s instructions. All eDNA samples were stored at − 20 °C prior to qSeq and dPCR.
    Quantitative sequencing
    Simultaneous quantification and sequencing of the extracted eDNA were performed by qSeq as previously described15,16. First, SPE was performed. The SPE reaction mixture (20 µL) consisted of 1 × PrimeSTAR Max premix (Takara Bio Inc., Kusatsu, Japan), 300 nM of the primer qSeq-MiFish-U-F (Table 1), and extracted DNA (2 µL). The SPE primer qSeq-MiFish-U-F contains an eight-base length random sequence tag, which creates 65,536 different variations, enabling the quantification of up to approximately 1.0 × 105 copies of DNA15. This amount of variation was sufficient to quantify the abundance of eDNA in this study. SPE was initiated by denaturation at 94 °C for 1 min, followed by cooling to 60 °C at 0.3 °C/s, incubation at 60 °C for 1 min, and final extension at 70 °C for 10 min. Subsequently, the excess primer was completely digested by adding exonuclease I (4 µL, 5 U/µL; Takara Bio Inc.) to the SPE mixture. The digestion was performed at 37 °C for 120 min, followed by inactivation of the exonuclease I at 80 °C for 30 min. The first-round PCR mixture (25 µL) contained PrimeSTAR Max premix (12.5 µL), primers qSeq-MiFish-U-R and F2 (300 nM each; Table 1), and the SPE product (2 µL). Following 40 cycles of amplification at 98 °C for 10 s, 55 °C for 5 s, and 72 °C for 5 s, the amplification product was subjected to agarose gel electrophoresis, and the band of the expected size was removed and purified using Nucleospin Gel and PCR Clean-up column (Takara Bio Inc.). The qSeq-MiFish-U-R primer also contains eight N bases to increase the complexity, which improves the sequencing quality, and thus PhiX was not added in this study. Finally, a 2nd-round PCR was performed to add an index for Illumina sequencing as described elsewhere15. The indexed PCR amplicon was purified using AMPure XP beads (Beckman Coulter, Indianapolis, IN) followed by sequencing using a MiSeq platform with MiSeq Reagent Kit v3 for 600 cycles (Illumina). The sequence data obtained in this study were deposited in the DDBJ database under accession numbers SAMD00219124–SAMD00219214.
    Table 1 Oligonucleotide sequences used in this study.
    Full size table

    Data analysis
    First, all sequences were assembled and screened by length and quality of reads using the mothur software package (v1.39.5)22. The processed sequence reads were classified using the MiFish pipeline (http://mitofish.aori.u-tokyo.ac.jp/mifish/), with the parameters as previously described23. Subsequently, the representative sequences of individual operational taxonomic units (OTUs) were extracted using the Usearch program (http://www.drive5.com/usearch/). The random sequence tags (RST) at the end of sequences in the OTUs were counted to quantify the environmental DNA from each fish species as described elsewhere16. For comparison, the relative proportion of eDNA from individual species in each sample was calculated from the composition of the sequences of the fish species obtained by qSeq.
    Microfluidic digital PCR
    Quantification of eDNA was also performed by microfluidic dPCR using the BioMark Real-time System and 12.765 Digital Array (Fluidigm Corporation, South San Francisco, CA, United States) as previously described13. For each sample, the PCR mixture (6 µL) contained 2 × Probe qPCR mix (3.0 µL; Takara Bio Inc.), 20 × binding dye sample loading reagent (0.6 µL; Fluidigm Corporation), forward and reverse primers (900 nM), TaqMan probe (125 nM), ROX solution (0.015 µL), and sample DNA (1.0 µL). We used three sets of primers and probes to quantify the eDNA of H. neglectus, O. latipes, and M. anguillicaudatus (Table 1). PCR was initiated at 98 °C for 2 min, followed by 50 cycles of 98 °C for 10 s and 60 °C for 1 min. The amplification curves obtained from individual reaction chambers of the microfluidic chip were analysed using Fluidigm Digital PCR analysis software (Fluidigm Corporation) to obtain abundance of DNA molecules.
    Statistical analysis
    We employed Gaussian Type II regression models with the standardised major axis method to determine the relationship between the log10 eDNA abundances obtained from qSeq and dPCR analyses with the “sma” function of the “smatr” ver. 3.4.8 package in R ver. 3.6.024. Zero values were disregarded for the modelling. We employed the Gaussian Type II model because our preliminary evaluation showed higher R2 values for Type II regression models with a Gaussian distribution than for those with a logarithmic distribution in all cases. We compared the differences in the coefficient values by overlapping the 95% confidence interval (CI) ranges. More

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    Cities should respond to the biodiversity extinction crisis

    1.
    IPBES. Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (eds. Brondizio, E.S., Settele, j., Díaz, s. & Ngo, H.T.) (IPBES Secretariat, Bonn, Germany, 2019).
    2.
    Champness, B. S., Palmer, G. C. & Fitzsimons, J. A. Bringing the city to the country: relationships between streetscape vegetation type and bird assemblages in a major regional centre. J. Urban Ecol. 5, juz018 (2019).
    Article  Google Scholar 

    3.
    Frantzeskaki, N. et al. Nature-based solutions for urban climate change adaptation: linking the science, policy and practice communities for evidence based decision-making. BioScience 69, 455–566 (2019).
    Article  Google Scholar 

    4.
    Willeme, A. Rotterdam drops €233 million on green spaces—and they look INCREDIBLE. DutchReview. https://dutchreview.com/cities/rotterdam-drops-233-million-on-green-spaces-and-they-look-incredible/ (18 June 2020).

    5.
    Díaz, S. et al. The IPBES Conceptual Framework – connecting nature and people. Curr. Opin. Environ. Sustain. 14, 1–16 (2015).
    Article  Google Scholar 

    6.
    Elmqvist, T. et al. (eds). Urbanization, Biodiversity and Ecosystem Services: Challenges and Opportunities. A Global Assessment (Springer, Dordrecht, 2013).

    7.
    Ives, C. et al. Cities are hotspots for threatened species. Glob. Ecol. Biogeograph. 25, 117–126 (2016).
    Article  Google Scholar 

    8.
    Parris, K. M. & Hazell, D. L. Biotic effects of climate change in urban environments: the case of the grey-headed flying-fox (Pteropus poliocephalus) in Melbourne, Australia. Biol. Conserv. 124, 267–276 (2005).
    Article  Google Scholar 

    9.
    Prévot, A. C., Cheval, H., Raymond, R. & Cosquer, A. Routine experiences of nature in cities can increase personal commitment toward biodiversity conservation. Biol. Conserv. 226, 1–8 (2018).
    Article  Google Scholar 

    10.
    ICLEI CBC. Edinburgh Process for Subnational and Local Governments on the Development of the Post 2020 Global Biodiversity Framework (ICLEI, 2020). https://cbc.iclei.org/edinburgh-process-for-subnational-and-local-governments-on-the-development-of-the-post-2020-global-biodiversity-framework/.

    11.
    Nilon, C. et al. Planning for the future of urban biodiversity: a global review of city-scale initiatives. BioScience 67, 332–342 (2017).
    Article  Google Scholar 

    12.
    Garrard, G. E., Williams, N. S. G., Mata, L., Thomas, J. & Bekessy, S. A. Biodiversity sensitive urban design. Conserv. Lett. 11, e12411 (2018).
    Article  Google Scholar 

    13.
    Bush, J. & Doyon, A. Building urban resilience with nature-based solutions: how can urban planning contribute? Cities 95, 102483 (2019).
    Article  Google Scholar 

    14.
    Prober, S. M., Doerr, V. A. J., Broadhurst, L. M., Williams, K. J. & Dickson, F. Shifting the conservation paradigm: a synthesis of options for renovating nature under climate change. Ecol. Monog. 89, e01333 (2019).
    Article  Google Scholar 

    15.
    Canaway, J. Unveiling the misunderstood magical mistletoes of Australia. ABC Life. https://www.abc.net.au/life/the-misunderstood-magical-mistletoes-of-australia/11505510 (20 December 2019).

    16.
    Burgin, S. What about biodiversity? Redefining urban sustainable management to incorporate endemic fauna with particular reference to Australia. Urban Ecosys. 19, 669–678 (2016).
    Article  Google Scholar 

    17.
    Rigolon, A. A complex landscape of inequity in access to urban parks: a literature review. Landsc. Urban Plann. 153, 160–169 (2016).
    Article  Google Scholar 

    18.
    Fuller, R. A. et al. Psychological benefits of greenspace increase with biodiversity. Biol. Lett. 3, 390–394 (2007).
    Article  Google Scholar 

    19.
    Sugiyama, T., Carver, A., Koohsari, M. J. & Veitch, J. Advantages of public green spaces in enhancing population health. Landsc. Urban Plann. 178, 12–17 (2018).
    Article  Google Scholar 

    20.
    Hockings, M. et al. COVID-19 and protected and conserved areas. Parks 26.1, 7–24 (2020).
    Article  Google Scholar 

    21.
    Frantzeskaki, N. Seven lessons for planning nature-based solutions in cities. Environ.Sci. Pol. 93, 101–111 (2019).
    Article  Google Scholar 

    22.
    Ahern, J. From fail-safe to safe-to-fail: sustainability and resilience in the new urban world. Landsc. Urban Plann. 100, 341–343 (2011).
    Article  Google Scholar 

    23.
    Kabisch, N., van den Bosch, M. & Lafortezza, R. The health benefits of nature-based solutions to urbanization challenges for children and the elderly—a systematic review. Environ. Res. 159, 362–373 (2017).
    CAS  Article  Google Scholar 

    24.
    Tengö, M. et al. Weaving knowledge systems in IPBES, CBD and beyond—lessons learned for sustainability. Curr. Opin. Environ. Sustain. 26–27, 17–25 (2017).
    Article  Google Scholar 

    25.
    Davies, C. & Lafortezza, R. Transitional path to the adoption of nature-based solutions. Land Use Pol. 80, 406–409 (2019).
    Article  Google Scholar 

    26.
    Mumaw, L. M. & Bekessy, S. A. Wildlife gardening for collaborative public–private biodiversity conservation. Austral. J. Environ. Manage. 24, 242–246 (2017).
    Article  Google Scholar 

    27.
    Eilam, E. & Garrard, G. E. Perception of space among children studying their local grasslands: examining attitudes and behavioural intentions. Sustainability 9, 1660 (2017).
    Article  Google Scholar 

    28.
    ICLEI. 6th Global Biodiversity Summit of Local and Subnational Governments. Event Report (2018) https://cbc.iclei.org/wp-content/uploads/2019/10/Egypt-Summit-EVENT-REPORT-FINAL-digital_compressed.pdf. More

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    Emergent vulnerability to climate-driven disturbances in European forests

    Observed forest disturbances
    We focused on the vulnerability of European forests to three major natural disturbances: forest fires, windthrows and insect outbreaks (bark beetles, defoliators and sucking insects). In order to identify/calibrate/validate vulnerability models (details on model development in the following sections) we used a large number of records of forest disturbances collected over the 2000–2017 period (Supplementary Fig. 1, step1). Fires were retrieved from the European Forest Fire Information System (EFFIS, https://effis.jrc.ec.europa.eu/) and count 15,818 records. Windthrows were acquired from the European Forest Windthrow dataset62 (FORWIND, https://doi.org/10.6084/m9.figshare.9555008) with 89,743 records. Insect outbreaks were retrieved from the National Insect and Disease Survey (IDS, http://foresthealth.fs.usda.gov) database of the United States Department of Agriculture (USDA) which includes 50,777 records. Each disturbance record is represented by a vector feature describing the spatial delineation of the damaged forest patch obtained by visual photointerpretation of aerial and satellite imagery or field surveys.
    Even if the study focuses on Europe, for insect diseases we used the IDS-USDA database due to the lack of an analogous monitoring system and related dataset for Europe. Therefore, the models of vulnerability to insect outbreaks were identified/calibrated/validated on US data and then applied in predictive mode to Europe (see following sections for details). To assure the transferability of such models, we developed models for functional groups instead of working on species-specific models. For this purpose, we classified records based on functional groups of the pest (bark beetles, defoliators and sucking insects) and on the PFT of the host tree species. Records were considered if the host plant belonged to the following PFTs: broadleaved deciduous, broadleaved evergreen, needle leaf deciduous and needle leaf evergreen.
    Reconstruction of annual biomass time series
    In order to evaluate the biomass loss expected given a disturbance event occurs, multi-temporal information of biomass is required. However, there is still no single technology for direct and continuous monitoring of such variable in time. In order to reconstruct the temporal variations in biomass over the 2000–2017 period we integrated a static 100-m above ground biomass map acquired for the year 2010 from multiple Earth Observation systems63 with forest cover changes derived from the Global Forest Change (GFC) maps recorded at 30-m spatial resolution from Landsat imagery21. The GFC maps include three major layers: “2000 Tree Cover”, “Forest Cover Loss” and “Forest Cover Gain”. “2000 Tree Cover” (TC2000) is a global map of tree canopy cover (expressed in percentage) for the year 2000. “Forest Cover Loss” is defined as the complete removal of tree-cover canopy at the Landsat pixel scale (natural or human-driven) and is reported annually. “Forest Cover Gain” reflects a non-forest to forest change and refers to the period 2000–2012 as unique feature without reporting the timing of the gain.
    The data integration approach built a on the assumption that changes in biomass are fully conditioned by the changes in tree cover. First, we quantified the percentage of tree cover in 2010 (TC2010) by masking out all pixels where forest loss occurred over the 2000–2010 period from the TC2000 map.
    Then, in order to characterize to what extent an increase or decrease in tree cover may affect biomass, we quantified the density of biomass per percentage of tree cover lost (ρloss) and gained (ρgain) as follows:

    $$rho _{mathrm{{loss}}} = frac{{B_{2010}}}{{{mathrm{{TC}}}_{2010,{mathrm{{loss}}}}}},$$
    (1)

    $$rho _{mathrm{{gain}}} = frac{{B_{2010}}}{{{mathrm{{TC}}}_{2010,{mathrm{{gain}}}}}},$$
    (2)

    where (B_{2010}) is the static biomass map available for the year 2010 (ref. 63). ({mathrm{{TC}}}_{2010,{mathrm{{loss}}}}) is the ({mathrm{{TC}}}_{2010}) masked over the pixels where there has been a forest loss during the 2011–2017 period. This filtering provides a picture of forests that were intact in 2010 but removed since then. Similarly, ({mathrm{{TC}}}_{2010,{mathrm{{gain}}}}) is the ({mathrm{{TC}}}_{2010}) masked over the pixels where there has been a forest gain and identifies the reforested and afforested areas. Since the map of forest gain is a binary map referring to the year 2012, forest gain pixels lack any information on their tree cover as their value in 2000 is zero. We therefore associated to forest gain pixels the maximum of tree cover percentage computed in a moving window with a radius of 2.5 km. This value represents the maximum potential tree cover in the local environmental conditions and refers to the whole 2000–2012 period (({mathrm{{TC}}}_{2012,{mathrm{{gain}}}})). Then, we assumed that forest gain proceeds at a constant rate over time and that the associated tree cover thus grows linearly:

    $$frac{{{mathrm{{TC}}}_{2010,{mathrm{{gain}}}}}}{{left( {2010 – 2000} right)}} = frac{{{mathrm{{TC}}}_{2012,{mathrm{{gain}}}}}}{{left( {2012 – 2000} right)}} to {mathrm{{TC}}}_{2010,{mathrm{{gain}}}} = 0.83 cdot {mathrm{{TC}}}_{2012,{mathrm{{gain}}}},$$
    (3)

    Both ({mathrm{{TC}}}_{2010,{mathrm{{loss}}}}) and ({mathrm{{TC}}}_{2010,{mathrm{{gain}}}}) were resampled to the (B_{2010}) spatial resolution (100 m). Supplementary Figure 13 shows the frequency distribution of (rho _{mathrm{{loss}}}) and (rho _{{mathrm{{gain}}}}) over a test area in Southern Finland. As expected, the density of biomass associated with forest losses is higher than that one associated to forest gain. Indeed, biomass of new forest plantations is generally lower than the biomass of an old one (e.g. a forest that is typically harvested).
    The obtained maps of (rho _{{mathrm{{loss}}}}) and (rho _{{mathrm{{gain}}}}) in Eqs. (1) and (2) refer to sparse and isolated pixels where there have been forest gain or loss. To obtain continuous fields, such density values were spatialized by computing their median over a 0.1° grid. Annual maps of biomass were finally obtained at 100 m spatial resolution as follows:

    $$B_t = B_{2010} + alpha cdot rho _{{mathrm{{loss}}}} cdot {mathrm{{TC}}}_{t,{mathrm{{loss}}}} – rho _{{mathrm{{gain}}}} cdot {mathrm{{TC}}}_{t,{mathrm{{gain}}}} cdot frac{{left( {2010 – t} right)}}{{10}},$$
    (4)

    where t is the year (over the 2000–2017 period) and α takes the value of +1 for t  5% were selected (Supplementary Fig. 1, step 3). In the case of windthrows, we noted that maximum wind speeds retrieved from 0.5° spatial resolution of reanalysis data may largely underestimate effective maximum winds. This was particularly evident for tornado events, given their limited spatial extents compared to the grid cell, and the storm event Klaus that occurred in 2009 and for which we noticed an underestimation of the effective wind speed of the 78% (retrieved ~12 ms−1 instead of observed maximum wind speed of 55 ms−1 (ref. 67)). Therefore, such events were excluded from our analysis.
    Possible missing data in the environmental variables were corrected by the median value of the variable-specific distributions (Supplementary Fig. 1, step 4). Potential effects of spatial dependence structure in the observational datasets were reduced by resampling ({mathrm{{BL}}}_{{mathrm{{rel}}}}), F, C and L along the gradients of the three principal components (PC) derived from the initial set of predictors. To this aim, we used 20 bins of equal intervals for each PC dimension spanning the full range of values. The resampling procedure was stratified by splitting the records in training and testing sets. For each year between 2000 and 2017, we randomly extracted 60% of the records. The extracted subset (({mathrm{{BL}}}_{{mathrm{{rel}}}}), F, C and L) was then binned in the PC space using the average as aggregation metric weighted by the areal extents of each disturbance record. The remaining 40% of records were similarly processed and used as a separate validation set (Supplementary Fig. 1, steps 5–7). The cover fraction of each PFT was resampled using the same approach and renormalized within each bin. Only bins with at least three records were retained for model development.
    The resampled training and testing sets were used to calibrate and validate an “approximate” RF model using the full set of variables (A) as predictors initially identified based on literature review (Supplementary Fig. 1, step 8 and Supplementary Table 1). With the RF algorithm importance scores for each environmental variable can be calculated31. These scores reflect how important each covariate is in determining the fitted values of relative biomass loss. The RF implemented here uses 500 regression trees, whose depth and number of predictors to sample at each node were identified using Bayesian optimization. To reduce potential redundancy effects across predictors and facilitate the interpretability of results, we implemented a feature selection procedure. Based on the “approximate” RF model the importance of each predictor was quantified. We then computed the Spearman correlation between each pair of predictors and when it exceeded 0.8, the predictor with the lower variable importance was excluded (Supplementary Fig. 1, step 9 and Supplementary Table 1). The remaining predictors (I) were then used for a second set of RF runs, in which we iteratively evaluated RF performance on a reduced set of predictors, excluding in each new run the less important variable computed on the new reduced set of features. The set of predictors which maximizes the R2 was finally selected (Q hereafter for short) (Supplementary Fig. 1, step 10 and Supplementary Table 1). The implemented iterative feature selection procedure identifies a reasonable compromise between computing cost and model performance. The general equation describing the vulnerability is as follows:

    $${mathrm{{BL}}}_{{mathrm{{rel}}}} = vleft( {{Q}} right),$$
    (6)

    where v is the vulnerability model implemented in the RF regression algorithm, and describes the relative biomass losses as a function of a selected Q set of environmental variables.
    Such automatic feature selection process was complemented with visual interpretation of the PDPs68 based on the RF algorithm. PDP is used to visualize the relationship between explanatory covariates (environmental predictors) and ({mathrm{{BL}}}_{{mathrm{{rel}}}}), independent of other covariates (Supplementary Figs. 2–4). PDP results were analysed in combination with a detailed study of the literature and allowed us to understand and interpret the response functions to natural disturbances (see details in the main text and Fig. 2). Consistency of PDPs at the boundaries of the observational ranges was carefully checked to reduce possible artefacts generated when the models are used to extrapolate outside the range of training conditions.
    Vulnerability models were further refined by retrieving v functions separately for each PFT. For PFT-specific vulnerability models, only resampled records in the PC space with a cover fraction >5% were retained and used for the model development (Supplementary Fig. 1, step 11). Model performances were ultimately evaluated on the testing set in terms of coefficient of determination (R2), root mean square error (RMSE), percent bias (PBIAS)69 and RE.
    Regarding the insect-related disturbance, we initially implemented specific RF models for different insect groups (bark beetles, sucking insect and defoliators). However, due to the limited sample size of the first two groups, RF was not able to represent their effects on biomass losses reliably. We therefore opted to merge all three groups in a unique insect disturbance class (hereafter referred as insect outbreaks). We recognize that different ecological processes may characterize each insect group and therefore the use of a unique insect class may potentially mask some distinctive features. The resulting vulnerability models can therefore identify only drivers and patterns common to all groups (e.g., susceptibility to temperature anomalies70,71).
    Interacting processes
    The co-occurrence of multi-dimensional environmental factors resulting from the combination of interacting physical processes (compound events) may amplify or dampen ecosystem responses29. Tree-based models consider all variables together in the model and account for nonlinear feature interactions in the final model31,68. The inherent ability of RF models to detect interacting variables allows avoiding the prescription of specific relations between variables based on “a priori” knowledge—as for instance required in parametric regression frameworks—by letting the model learn automatically these relations from data.
    In order to detect feature interactions and assess their strength in the developed RF-based vulnerability models we computed the Friedman’s H-statistic50. Here, we derived the H-statistic to assess second-order interactions by quantifying how much of the variation of the prediction depends on two-way interactions. To speed up the computation, we sampled 50 equally spaced data points over the environmental gradients.
    We complemented this analysis by estimating the amplification or dampening effect (({Delta}{{P}})) associated to each feature interaction. To this aim, we quantified the difference in the peak values between the response function which incorporates interacting processes (two-way partial dependences) and those ones decomposed without interactions (one-dimensional partial dependences) and expressed in terms of relative variations.
    The H and ({Delta}{{P}}) metrics were computed for each pair of features, and averaged for different combinations of predictor categories (forest, climate, landscape).
    Spatial and temporal patterns of vulnerability and its key drivers
    The RF models were used to evaluate the vulnerability of forests annually between 1979 and 2018 for each grid cell (0.25°) of the spatial domain covering the geographic Europe (including Turkey and European Russia). To this aim, vulnerability models were used in predictive mode using as input spatial maps of predictors, preliminary resampled to the common resolution, and with results expressed in terms of potential relative biomass loss (({mathrm{{PBL}}}_{{mathrm{{rel}}}})). Estimates of ({mathrm{{PBL}}}_{{mathrm{{rel}}}}) are obtained as the average from all trees in the RF ensemble. The ongoing changes in climate features were also accounted for in our framework. Climate predictors were kept dynamic for backward RF runs, while the remaining forest and landscape features were fixed to their current values averaged over the 2009–2018 period. Doing so, we implicitly assume that the sampling of response variables and predictors is representative for the whole temporal period. However, over longer time periods (from decades to century) additional ecosystem processes may play a role, such as adaptation phenomena driven by species change and shifting biomes, which could also affect vulnerability trends. The lack of multi-temporal monitoring of most of the forest and landscape predictors hampered the integration of their dynamics in the backward RF runs.
    Results of PFT-specific vulnerability models were averaged at grid-cell level with weighting based on the cover fractions of PFTs (Supplementary Fig. 1, steps 12–13). This resulted in annual maps of vulnerability to each natural disturbance. Spatial and temporal variations in vulnerability were both expressed in relative and absolute terms. Absolute biomass losses were retrieved by multiplying estimates of potential relative biomass loss by the available biomass. Therefore, vulnerability values in a given grid cell reflect the biomass (relative or absolute) that would be affected if exposed to a disturbance under its specific local and temporal environmental conditions.
    Grid-cell uncertainty of predicted vulnerability values were quantified in terms of standard error (SE) derived by dividing standard deviations of the computed responses over the ensemble of the grown trees of the model by the square root of the ensemble size (Supplementary Fig. 7).
    We then calculated the “current” vulnerability as the average vulnerability over the 2009–2018 period. To factor out the local dependence of the current vulnerability on each predictor we retrieved the Individual Conditional Expectation72 (ICE) for each grid cell. ICE plots show the relationship between the predicted target variable (({mathrm{{PBL}}}_{{mathrm{{rel}}}})) and one predictor variable for individual cases of the predictor dataset. In our application, an individual case is a specific combination of F, C and L data for a given grid cell. To summarize and map the ICE of each grid cell in a single number, we fitted by linear regression the partial dependence of ({mathrm{{PBL}}}_{{mathrm{{rel}}}}) versus the corresponding predictor variable and mapped the slope of this regression, hereafter referred as “local sensitivity” (Supplementary Figs. 5–7), similarly to the approach presented in ref. 30. The marginal contribution ((Z_{mathrm{{marg}}})) of each environmental category of predictors (F, C and L, hereafter referred as X for short) on the current vulnerability was derived as follows:

    $$Z_{{mathrm{{marg}}},X} = 100 times frac{{mathop {sum }nolimits_{i in X} left| {s_i} right|}}{{mathop {sum }nolimits_{j in Q} left| {s_j} right|}},$$
    (7)

    where s represents the slope of ICE, i runs over all predictors of X, whereas j runs over all available predictors Q. Therefore (Z_{mathrm{{marg}},X}) values range between 0 (no dependence of current vulnerability on X predictors) and 100% (full dependence of current vulnerability on X predictors).
    Long-term linear trends in vulnerability ((delta {mathrm{{PBL}}}_{{mathrm{{rel}}}})) were quantified over the 1979–2018 period for each grid cell and their significance evaluated by the two-sided Mann–Kendall test. In order to isolate the key determinants of the emerging trends in vulnerability, a set of factorial simulations was performed. To this aim, we estimated the vulnerability due to the temporal variations in a given k climate predictor (({mathrm{{PBL}}}_{{mathrm{{rel}}}}^k)), by applying the RF models to a data array in which the k climate variable is dynamic while all the remaining features are kept fixed to their “current” value (average value over 2009–2018). The resulting trends in vulnerability associated to the k factor (({mathrm{{PBL}}}_{{mathrm{{rel}}}}^k)) are then calculated by linear regression and subject to the Mann–Kendall test.
    Spatial and temporal patterns were visualized at grid-point scale and averaged over geographic macro-regions (Supplementary Fig. 14 and Supplementary Tables 2 and 3). Zonal statistics were obtained by averaging grid-cell results weighted by their forest areal extent. Forests with cover fraction lower than 0.1 were excluded from the analyses. Uncertainty in spatial averages were based on the 95% bootstrap confidence interval computed with 100 bootstrap samples.
    In order to derive statistics minimally affected by potential extrapolation errors of the RF models, we replicated the aforementioned analyses by excluding areas outside the observational ranges of climatological temperature and precipitation (Supplementary Fig. 8).
    Combining forest vulnerability to multiple natural disturbances
    To quantify the total vulnerability to multiple disturbances we defined the OVI, similarly to the multi-hazard index developed in ref. 73. We assumed that the considered disturbances are independent and mutually non-exclusive and the potential biomass loss of single disturbances is spread homogeneously within each grid cell. From the inclusion-exclusion principle of combinatorics the potential biomass loss associated to the OVI can be expressed for a given year as follows:

    $${mathrm{{PBL}}}_{{mathrm{{rel}}}}left( {{mathrm{{OVI}}}} right) = mathop {bigcup}nolimits_{p = 1}^D {{mathrm{{PBL}}}_{{mathrm{{rel}}},p}} = mathop {sum }limits_{q = 1}^D left( {left( { – 1} right)^{q – 1} cdot mathop {sum }limits_{{G subset left{ {1, ldots ,D} right}} atop {left| G right| = q} } {mathrm{{PBL}}}_{{mathrm{{rel}}},G}} right),$$
    (8)

    where p refers to the disturbance-specific ({mathrm{{PBL}}}_{{mathrm{{rel}}}}), D is the number of disturbances considered, the last sum runs over all subsets G of the indices {1, …, D} containing exactly q elements, and

    $${mathrm{{PBL}}}_{{mathrm{{rel}}},G}: = mathop {bigcap}nolimits_{p in I} {{mathrm{{PBL}}}_{{mathrm{{rel}}},p}} ,$$
    (9)

    expresses the intersection of all those ({mathrm{{PBL}}}_{{mathrm{{rel}}},p}) with index in G. Maps of current overall vulnerability and trends were ultimately analysed following the approach adopted for single disturbances.
    This approach does not account for the potential reduction in exposed biomass following the occurrence of a given disturbance. Furthermore, possible amplification/dampening effects due to interacting disturbances could also occur3,74. A strong interaction effect has been documented for instance between windthrows and bark beetle disturbances. Uprooted trees are virtually defenseless breeding material supporting the build-up of beetle populations and the consequent increase in vulnerability to insect outbreaks3,59. Insect outbreaks, in turn, may potentially affect the severity of subsequent forest fires by altering the abundance of available fuel60. The magnitude of these effects varies with insect type and outbreak timing. Despite the relevance of these interactions, the lack of reference observational data of compound events hampered the integration of their effects in our modelling framework. Therefore, estimates of OVI can only partially capture the overall vulnerability resulting from multiple disturbances and should be viewed in light of these limitations.
    Spatial maps of current overall vulnerability and trends in OVI were then normalized separately based on the min–max method and combined by simple multiplication into a single index, hereafter referred as space-time integrated OVI. High values of space-time integrated OVI depict forest areas that are currently susceptible to multiple disturbances and their vulnerability have experienced a substantial increase over the 1979–2018 period. The space-time integrated OVI is used to identify currently fragile ecosystems that might in the future become even more susceptible to natural disturbances.
    Reporting summary
    Further information on research design is available in the Nature Research Reporting Summary linked to this article. More

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    Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt

    1.
    Bardgett RD, Van Der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.
    CAS  PubMed  Article  Google Scholar 
    2.
    Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15:579–90.
    CAS  PubMed  Article  Google Scholar 

    3.
    De Vries FT, Shade A. Controls on soil microbial community stability under climate change. Front Microbiol. 2013;4:1–16.
    Article  Google Scholar 

    4.
    Allison SD, Martiny JBH. Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci. 2008;105:11512–9.
    CAS  PubMed  Article  Google Scholar 

    5.
    Leifeld J, Zimmermann M, Fuhrer J, Conen F. Storage and turnover of carbon in grassland soils along an elevation gradient in the Swiss Alps. Glob Chang Biol. 2009;15:668–79.
    Article  Google Scholar 

    6.
    Schirpke U, Leitinger G, Tasser E, Schermer M, Steinbacher M, Tappeiner U. Multiple ecosystem services of a changing Alpine landscape: past, present and future. Int J Biodivers Sci Ecosyst Serv Manag. 2013;9:123–35.
    PubMed  Article  Google Scholar 

    7.
    Beniston M. Is snow in the Alps receding or disappearing? Wiley Interdiscip Rev Clim Chang. 2012;3:349–58.
    Article  Google Scholar 

    8.
    Beniston M, Keller F, Koffi B, Goyette S. Estimates of snow accumulation and volume in the Swiss Alps under changing climatic conditions. Theor Appl Climatol. 2003;76:125–40.
    Article  Google Scholar 

    9.
    Monson RK, Burns SP, Williams MW, Delany AC, Weintraub M, Lipson DA. The contribution of beneath-snow soil respiration to total ecosystem respiration in a high-elevation, subalpine forest. Glob Biogeochem Cycles. 2006;20:1–13.
    Article  CAS  Google Scholar 

    10.
    Zhang Y, Wang S, Barr AG, Black TA. Impact of snow cover on soil temperature and its simulation in a boreal aspen forest. Cold Reg Sci Technol. 2008;52:355–70.
    Article  Google Scholar 

    11.
    Campbell JL, Ollinger SV, Flerchinger GN, Wicklein H, Hayhoe K, Bailey AS. Past and projected future changes in snowpack and soil frost at the Hubbard Brook Experimental Forest, New Hampshire, USA. Hydrol Process. 2010;24:2465–80.
    Google Scholar 

    12.
    Pederson GT, Gray ST, Woodhouse CA, Betancourt JL, Fagre DB, Littell JS, et al. The unusual nature of recent snowpack declines in the North American Cordillera. Science. 2011;333:332–5.
    CAS  PubMed  Article  Google Scholar 

    13.
    Gavazov K, Ingrisch J, Hasibeder R, Mills RTE, Buttler A, Gleixner G, et al. Winter ecology of a subalpine grassland: effects of snow removal on soil respiration, microbial structure and function. Sci Total Environ. 2017;590–591:316–324.
    PubMed  Article  CAS  Google Scholar 

    14.
    Buckeridge KM, Banerjee S, Siciliano SD, Grogan P. The seasonal pattern of soil microbial community structure in mesic low arctic tundra. Soil Biol Biochem. 2013;65:338–47.
    CAS  Article  Google Scholar 

    15.
    Puissant J, Cécillon L, Mills RTE, Robroek BJM, Gavazov K, De Danieli S, et al. Seasonal influence of climate manipulation on microbial community structure and function in mountain soils. Soil Biol Biochem. 2015;80:296–305.
    CAS  Article  Google Scholar 

    16.
    Bardgett RD, Bowman WD, Kaufmann R, Schmidt SK. A temporal approach to linking aboveground and belowground ecology. Trends Ecol Evol. 2005;20:634–41.
    PubMed  Article  Google Scholar 

    17.
    Schmidt SK, Costello EK, Nemergut DR, Cleveland CC, Reed SC, Weintraub MN, et al. Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil. Ecology. 2007;88:1379–85.
    CAS  PubMed  Article  Google Scholar 

    18.
    Schadt CW, Martin AP, Lipson DA, Schmidt SK. Seasonal dynamics of previously unknown fungal lineages in Tundra soils. Science. 2003;301:1359–61.
    CAS  PubMed  Article  Google Scholar 

    19.
    Jefferies RL, Walker NA, Edwards KA, Dainty J. Is the decline of soil microbial biomass in late winter coupled to changes in the physical state of cold soils? Soil Biol Biochem. 2010;42:129–35.
    CAS  Article  Google Scholar 

    20.
    Buckeridge KM, Grogan P. Deepened snow increases late thaw biogeochemical pulses in mesic low arctic tundra. Biogeochemistry. 2010;101:105–21.
    Article  Google Scholar 

    21.
    Schimel J, Balser TC, Wallenstein M. Microbial stress-response physiology and its implications for ecosystem function. Ecology. 2007;88:1386–94.
    PubMed  Article  Google Scholar 

    22.
    Buckeridge KM, Grogan P. Deepened snow alters soil microbial nutrient limitations in arctic birch hummock tundra. Appl Soil Ecol. 2008;39:210–22.
    Article  Google Scholar 

    23.
    Väisänen M, Gavazov K, Krab EJ, Dorrepaal E. The legacy effects of winter climate on microbial functioning after snowmelt in a subarctic Tundra. Micro Ecol. 2019;77:186–90.
    Article  Google Scholar 

    24.
    Darrouzet-Nardi A, Steltzer H, Sullivan PF, Segal A, Koltz AM, Livensperger C, et al. Limited effects of early snowmelt on plants, decomposers, and soil nutrients in Arctic Tundra soils. Ecol Evol. 2019;9:1820–44.
    PubMed  PubMed Central  Article  Google Scholar 

    25.
    Ernakovich JG, Hopping KA, Berdanier AB, Simpson RT, Kachergis EJ, Steltzer H, et al. Predicted responses of arctic and alpine ecosystems to altered seasonality under climate change. Glob Chang Biol. 2014;20:3256–69.
    PubMed  Article  Google Scholar 

    26.
    Li W, Wu J, Bai E, Jin C, Wang A, Yuan F, et al. Response of terrestrial carbon dynamics to snow cover change: a meta-analysis of experimental manipulation (II). Soil Biol Biochem. 2016;103:388–93.
    CAS  Article  Google Scholar 

    27.
    Neuwinger I Bodenökologische. Untersuchungen im Gebiet Obergurgler Zirbenwald—Hohe Mut. In: Patzelt G (Hrsg.. (ed). MaB-Projekt Obergurgl. 1987. Universitätsverlag Wagner, Innsbruck, Austria, pp 173-90.

    28.
    Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol. 1959;37:911–917.
    CAS  Article  Google Scholar 

    29.
    Bardgett RD, Hobbs PJ, Frostegard A. Changes in soil fungal:bacterial biomass ratios following reductions in the intensity of management of an upland grassland. Biol Fertil Soils. 1996;22:261–4.
    Article  Google Scholar 

    30.
    Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE. 2008;3:e2836.
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    31.
    Arenz BE, Schlatter DC, Bradeen JM, Kinkel LL. Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities. J Microbiol Methods. 2015;117:1–3.
    CAS  PubMed  Article  Google Scholar 

    32.
    Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, et al. New primers to amplify the fungal ITS2 region—evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol. 2012;82:666–77.
    CAS  PubMed  Article  Google Scholar 

    33.
    White TJ, Bruns T, Lee S, Taylor J. PCR protocols. 1990. Academic Press.

    34.
    Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112–20.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    35.
    Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    36.
    R Core Team. R: a language and environment for statistical computing. 2019. R Foundation for Statistical Computing.

    37.
    DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    38.
    Kõljalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, et al. UNITE: A database providing web-based methods for the molecular identification of ectomycorrhizal fungi. N. Phytol. 2005;166:1063–8.
    Article  CAS  Google Scholar 

    39.
    McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    40.
    Illumina. bcl2fastq and bcl2fastq2 Conversion software. 2020. https://support.illumina.com/sequencing/sequencing

    41.
    Sáenz JS, Marques TV, Barone RSC, Cyrino JEP, Kublik S, Nesme J, et al. Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus. Microbiome. 2019;7:1–14.
    Article  Google Scholar 

    42.
    Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016;9:1–7.
    Article  Google Scholar 

    43.
    Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE. 2011;6:e17288.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    44.
    Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7:11257.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    45.
    Tu Q, Lin L, Cheng L, Deng Y, He Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics. 2019;35:1040–8.
    CAS  PubMed  Article  Google Scholar 

    46.
    First Y, Job P. GNU parallel: the command-line power tool | USENIX. 3: 42–47.

    47.
    Jackson CR, Tyler HL, Millar JJ. Determination of microbial extracellular enzyme activity in waters, soils, and sediments using high throughput microplate assays. J Vis Exp. 2013;80:e50399.
    Google Scholar 

    48.
    De Long JR, Semchenko M, Pritchard WJ, Cordero I, Fry EL, Jackson BG, et al. Drought soil legacy overrides maternal effects on plant growth. Funct Ecol. 2019;33:1400–10.
    PubMed  PubMed Central  Article  Google Scholar 

    49.
    Kandeler E, Gerber H. Short-term assay of soil urease activity using colorimetric determination of ammonium article in biology and fertility of soils. Biol Fertil Soils. 1988;6:68–72.
    CAS  Article  Google Scholar 

    50.
    Jones DL, Willett VB. Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biol Biochem. 2006;38:991–9.
    CAS  Article  Google Scholar 

    51.
    Ross DJ. Influence of sieve mesh size on estimates of microbial carbon and nitrogen by fumigation-extraction procedures in soils under pasture. Soil Biol Biochem. 1992;24:343–50.
    Article  Google Scholar 

    52.
    De Boer W, Folman LB, Summerbell RC, Boddy L. Living in a fungal world: Impact of fungi on soil bacterial niche development. FEMS Microbiol Rev. 2005;29:795–811.
    PubMed  Article  CAS  Google Scholar 

    53.
    Moorhead DDL, Sinsabaugh RRL. A theoretical model of litter decay and microbial interaction. Ecol Monogr. 2006;76:151–74.
    Article  Google Scholar 

    54.
    Zhou Y, Pope PB, Li S, Wen B, Tan F, Cheng S, et al. Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community. Sci Rep. 2014;4:1–6.
    Google Scholar 

    55.
    Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev. 2002;66:506–77.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    56.
    Bhatnagar JM, Peay KG, Treseder KK. Litter chemistry influences decomposition through activity of specific microbial functional guilds. Ecol Monogr. 2018;88:429–44.
    Article  Google Scholar 

    57.
    Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw C, et al. Stoichiometry of soil enzyme activity at global scale. Ecol Lett. 2008;11:1252–64.
    PubMed  Article  Google Scholar 

    58.
    Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012;6:1007–17.
    CAS  PubMed  Article  Google Scholar 

    59.
    Broadbent AAD, Orwin KH, Peltzer DA, Dickie IA, Mason NWH, Ostle NJ, et al. Invasive N-fixer impacts on litter decomposition driven by changes to soil properties not litter quality. Ecosystems. 2017;20:1–13.
    Article  CAS  Google Scholar 

    60.
    Prosser JI, Nicol GW. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 2012;20:523–31.
    CAS  PubMed  Article  Google Scholar 

    61.
    Verhamme DT, Prosser JI, Nicol GW. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J. 2011;5:1067–71.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    62.
    Brooks PD, Williams MW, Schmidt SK. Inorganic nitrogen and microbial biomass dynamics before and during spring snowmelt. Biogeochemistry. 1998;43:1–15.
    Article  Google Scholar 

    63.
    Jaeger CH, Monson RK, Fisk MC, Schmidt SK. Seasonal partitioning of nitrogen by plants and soil microorganisms in an alpine ecosystem. Ecology. 1999;80:1883–91.
    Article  Google Scholar 

    64.
    Ashton IW, Miller AE, Bowman WD, Suding KN. Niche complementarity due to plasticity in resource use: plant partitioning of chemical N forms. Ecology. 2010;91:3252–60.
    PubMed  Article  Google Scholar 

    65.
    Bilbrough CJ, Welker JM, Bowman WD. Early spring nitrogen uptake by snow-covered plants: a comparison of Arctic and alpine plant function under the snowpack. Arct, Antarct Alp Res. 2000;32:404–11.
    Article  Google Scholar 

    66.
    Michelsen A, Schmidt IK, Jonasson S, Quarmby C, Sleep D. Leaf 15N abundance of subarctic plants provides field evidence that ericoid, ectomycorrhizal and non-and arbuscular mycorrhizal species access different sources of soil nitrogen. Oecologia. 1996;105:53–63.
    PubMed  Article  Google Scholar 

    67.
    Wookey PA, Aerts R, Bardgett RD, Baptist F, Bråthen K, Cornelissen JHC, et al. Ecosystem feedbacks and cascade processes: understanding their role in the responses of Arctic and alpine ecosystems to environmental change. Glob Chang Biol. 2009;15:1153–72.
    Article  Google Scholar  More

  • in

    Contribution of Vouacapoua americana fruit-fall to the release of biomass in a lowland Amazon forest

    1.
    Diaz-Martin, Z., Swamy, V., Terborgh, J., Alvarez-Loayza, P. & Cornejo, F. Identifying keystone plant resources in an Amazonian forest using a long-term fruit-fall record. J. Trop. Ecol. 30, 291–301. https://doi.org/10.1017/S0266467414000248 (2014).
    Article  Google Scholar 
    2.
    Terborgh, J. & Andresen, E. The composition of Amazonian forests: Patterns at local and regional scales. J. Trop. Ecol. 14, 645–664 (1998).
    Article  Google Scholar 

    3.
    Wright, J. S. Plant diversity in tropical forests: A review of mechanisms of species coexistence. Oecologia 130, 1–14. https://doi.org/10.1007/s004420100809 (2002).
    ADS  Article  Google Scholar 

    4.
    Bascompte, J. & Jordano, P. Plant-animal mutualistic networks: The architecture of biodiversity. Annu. Rev. Ecol. Evol. Syst. 38, 567–593. https://doi.org/10.1146/annurev.ecolsys.38.091206.095818 (2007).
    Article  MATH  Google Scholar 

    5.
    Chapman, C. A., Wrangham, R. & Chapman, L. J. Indexes of habitat-wide fruit abundance in tropical forests. Biotropica 26, 160–171. https://doi.org/10.2307/2388805 (1994).
    Article  Google Scholar 

    6.
    White, L. J. T. Patterns of fruit-fall phenology in the Lopé Reserve, Gabon. J. Trop. Ecol. 10, 289–312. https://doi.org/10.1017/S0266467400007975 (1994).
    Article  Google Scholar 

    7.
    Bello, C. et al. Defaunation affects carbon storage in tropical forests. Sci. Adv. https://doi.org/10.1126/sciadv.1501105 (2015).
    Article  PubMed  PubMed Central  Google Scholar 

    8.
    Peres, C. A., Emilio, T., Schietti, J., Desmoulière, S. J. & Levi, T. Dispersal limitation induces long-term biomass collapse in overhunted Amazonian forests. Proc. Natl. Acad. Sci. 113, 892–897 (2016).
    ADS  CAS  Article  Google Scholar 

    9.
    Dee, L. E. et al. When do ecosystem services depend on rare species?. Trends Ecol. Evol. 34, 746–758. https://doi.org/10.1016/j.tree.2019.03.010 (2019).
    Article  PubMed  Google Scholar 

    10.
    Pinho, B. X., Peres, C. A., Leal, I. R. & Tabarelli, M. In Tropical Ecosystems in the 21st Century (eds Alex, J. D., Edgar, C. T., & Tom, M. F.) Ch. 7, 253–294 (Academic Press, Cambridge, 2020).

    11.
    Bastin, J.-F. et al. Pan-tropical prediction of forest structure from the largest trees. Glob. Ecol. Biogeogr. 27, 1366–1383. https://doi.org/10.1111/geb.12803 (2018).
    Article  Google Scholar 

    12.
    Lutz, J. A. et al. Global importance of large-diameter trees. Glob. Ecol. Biogeogr. 27, 849–864. https://doi.org/10.1111/geb.12747 (2018).
    Article  Google Scholar 

    13.
    Sist, P., Mazzei, L., Blanc, L. & Rutishauser, E. Large trees as key elements of carbon storage and dynamics after selective logging in the Eastern Amazon. For. Ecol. Manag. 318, 103–109. https://doi.org/10.1016/j.foreco.2014.01.005 (2014).
    Article  Google Scholar 

    14.
    Schulze, M., Grogan, J., Landis, R. M. & Vidal, E. How rare is too rare to harvest? Management challenges posed by timber species occurring at low densities in the Brazilian Amazon. For. Ecol. Manag. 256, 1443–1457. https://doi.org/10.1016/j.foreco.2008.02.051 (2008).
    Article  Google Scholar 

    15.
    SFB. Florestas do Brasil em resumo 2013: dados de 2007–2012. (2013).

    16.
    Azevedo-Ramos, C., Silva, J. N. M. & Merry, F. The evolution of Brazilian forest concessions. Elem. Sci. Anth. https://doi.org/10.12952/journal.elementa.000048 (2015).
    Article  Google Scholar 

    17.
    Golden Kroner, R. E. et al. The uncertain future of protected lands and waters. Science 364, 881. https://doi.org/10.1126/science.aau5525 (2019).
    ADS  CAS  Article  Google Scholar 

    18.
    Degen, B. et al. Impact of selective logging on genetic composition and demographic structure of four tropical tree species. Biol. Cons. 131, 386–401. https://doi.org/10.1016/j.biocon.2006.02.014 (2006).
    Article  Google Scholar 

    19.
    Richardson, V. A. & Peres, C. A. Temporal decay in timber species composition and value in Amazonian logging concessions. PLoS ONE 11, e0159035. https://doi.org/10.1371/journal.pone.0159035 (2016).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    20.
    Aleixo, I. et al. Amazonian rainforest tree mortality driven by climate and functional traits. Nat. Clim. Change 9, 384–388. https://doi.org/10.1038/s41558-019-0458-0 (2019).
    ADS  Article  Google Scholar 

    21.
    Nepstad, D. et al. Amazon drought and its implications for forest flammability and tree growth: A basin-wide analysis. Glob. Change Biol. 10, 704–717 (2004).
    ADS  Article  Google Scholar 

    22.
    Vidal, E., West, T. A. & Putz, F. E. Recovery of biomass and merchantable timber volumes twenty years after conventional and reduced-impact logging in Amazonian Brazil. For. Ecol. Manag. 376, 1–8. https://doi.org/10.1016/j.foreco.2016.06.003 (2016).
    Article  Google Scholar 

    23.
    Varty, N. & Guadagnin, D. L. Vouacapoua americana. The IUCN Red List of Threatened Species: e.T33918A9820054, https://doi.org/10.2305/IUCN.UK.1998.RLTS.T33918A9820054.en (1998).

    24.
    Dutech, C., Maggia, L., Tardy, C., Joly, H. I. & Jarne, P. Tracking a genetic signal of extinction-recolonization events in a neotropical tree species: Vouacapoua americana aublet in french guiana. Evolution 57, 2753–2764 (2003).
    Article  Google Scholar 

    25.
    Guimarães, P. R. Jr., Galetti, M. & Jordano, P. Seed dispersal anachronisms: Rethinking the fruits extinct megafauna ate. PLoS ONE 3, e1745. https://doi.org/10.1371/journal.pone.0001745 (2008).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    26.
    Traissac, S. & Pascal, J. P. Birth and life of tree aggregates in tropical forest: Hypotheses on population dynamics of an aggregated shade-tolerant species. J. Veg. Sci. 25, 491–502. https://doi.org/10.1111/jvs.12080 (2014).
    Article  Google Scholar 

    27.
    Forget, P.-M. Seed-dispersal of Vouacapoua americana (Caesalpiniaceae) by caviomorph rodents in French Guiana. J. Trop. Ecol. 6, 459–468. https://doi.org/10.1017/S0266467400004867 (1990).
    Article  Google Scholar 

    28.
    Jansen, P. A., Bongers, F. & van der Meer, P. J. Is farther seed dispersal better? Spatial patterns of offspring mortality in three rainforest tree species with different dispersal abilities. Ecography 31, 43–52. https://doi.org/10.1111/j.2007.0906-7590.05156.x (2008).
    Article  Google Scholar 

    29.
    MMA. Vol. 18/12/2014 (ed Ministério do Meio Ambiente—MMA) 110–121 (Diário Oficial da União, Brasilia, 2014).

    30.
    Avitabile, V. et al. An integrated pan-tropical biomass map using multiple reference datasets. Glob. Change Biol. 22, 1406–1420. https://doi.org/10.1111/gcb.13139 (2016).
    ADS  Article  Google Scholar 

    31.
    Baccini, A. et al. Estimated carbon dioxide emissions from tropical deforestation improved by carbon-density maps. Nat. Clim. Change 2, 182–185. https://doi.org/10.1038/nclimate1354 (2012).
    ADS  CAS  Article  Google Scholar 

    32.
    Saatchi, S. S. et al. Benchmark map of forest carbon stocks in tropical regions across three continents. Proc. Natl. Acad. Sci. U.S.A. 108, 9899–9904. https://doi.org/10.1073/pnas.1019576108 (2011).
    ADS  Article  PubMed  PubMed Central  Google Scholar 

    33.
    Saatchi, S. S., Houghton, R. A., Dos Santos AlvalÁ, R. C., Soares, J. V. & Yu, Y. Distribution of aboveground live biomass in the Amazon basin. Glob. Change Biol. 13, 816–837. https://doi.org/10.1111/j.1365-2486.2007.01323.x (2007).
    ADS  Article  Google Scholar 

    34.
    Muller-Landau, H. C., Wright, S. J., Calderon, O., Condit, R. & Hubbell, S. P. Interspecific variation in primary seed dispersal in a tropical forest. J. Ecol. 96, 653–667. https://doi.org/10.1111/j.1365-2745.2008.01399.x (2008).
    Article  Google Scholar 

    35.
    Mendoza, I. et al. Does masting result in frugivore satiation? A test with Manilkara trees in French Guiana. J. Trop. Ecol. 31, 553–556. https://doi.org/10.1017/S0266467415000425 (2015).
    Article  Google Scholar 

    36.
    Kelly, D. The evolutionary ecology of mast seeding. Trends Ecol. Evol. 9, 465–470. https://doi.org/10.1016/0169-5347(94)90310-7 (1994).
    CAS  Article  PubMed  Google Scholar 

    37.
    Kelly, D. & Sork, V. L. Mast seeding in perennial plants: Why, how, where?. Annu. Rev. Ecol. Syst. 33, 427–447. https://doi.org/10.1146/annurev.ecolsys.33.020602.095433 (2002).
    Article  Google Scholar 

    38.
    Johnson, M. O. et al. Variation in stem mortality rates determines patterns of above-ground biomass in Amazonian forests: Implications for dynamic global vegetation models. Glob. Change Biol. 22, 3996–4013 (2016).
    ADS  Article  Google Scholar 

    39.
    Batista, A. P. B. et al. Caracterização estrutural em uma floresta de terra firme no estado do Amapá, Brasil. Pesq. flor. bras 35, 21–33 (2015).
    Article  Google Scholar 

    40.
    Charles-Dominique, P. et al. Les mammiferes frugivores arboricoles nocturnes d’une foret guyanaise: Inter-relations plantes-animaux. La Terre et la Vie: Revue d’Ecologie Appliquée 35, 341–435 (1981).
    Google Scholar 

    41.
    de Oliveira, A. N. & do Amaral, I. L. ,. Florística e fitossociologia de uma floresta de vertente na Amazônia Central, Amazonas, Brasil. Acta Amazonica 34, 21–34 (2004).
    Article  Google Scholar 

    42.
    Pereira, L. A., Pinto Sobrinho, F. D. A. & Costa Neto, S. V. D. Florística e estrutura de uma mata de terra firme na reserva de desenvolvimento sustentável rio Iratapuru, Amapá, Amazônia Oriental, Brasil. (2011).

    43.
    Pereira, L. A., Sena, K. S., dos Santos, M. R. & Neto, S. V. C. Aspectos florísticos da FLONA do Amapá e sua importância na conservação da biodiversidade. Revista Brasileira de Biociências 5, 693–695 (2007).
    Google Scholar 

    44.
    Sabatier, D. Saisonnalité et déterminisme du pic de fructification en forêt guyanaise. Revue d’Ecologie (Terrre et Vie) 40, 89–320 (1985).
    Google Scholar 

    45.
    ter Steege, H. et al. An analysis of the floristic composition and diversity of Amazonian forests including those of the Guiana Shield. J. Trop. Ecol. 16, 801–828 (2000).
    Article  Google Scholar 

    46.
    Hanya, G. et al. Seasonality in fruit availability affects frugivorous primate biomass and species richness. Ecography 34, 1009–1017. https://doi.org/10.1111/j.1600-0587.2010.06775.x (2011).
    Article  Google Scholar 

    47.
    Situmorang, J. P. & Sugianto, S. Estimation of carbon stock stands using EVI and NDVI vegetation index in production forest of Lembah Seulawah Sub-District, Aceh Indonesia. Aceh Int. J. Sci. Technol. 5 (2016).

    48.
    Asner, G. P. et al. Airborne laser-guided imaging spectroscopy to map forest trait diversity and guide conservation. Science 355, 385–389. https://doi.org/10.1126/science.aaj1987 (2017).
    ADS  CAS  Article  PubMed  Google Scholar 

    49.
    Bhardwaj, D., Banday, M., Pala, N. A. & Rajput, B. S. Variation of biomass and carbon pool with NDVI and altitude in sub-tropical forests of northwestern Himalaya. Environ. Monit. Assess. 188, 635 (2016).
    CAS  Article  Google Scholar 

    50.
    Dubayah, R. O. et al. Estimation of tropical forest height and biomass dynamics using lidar remote sensing at La Selva, Costa Rica. J. Geophys. Res. Biogeosci. https://doi.org/10.1029/2009JG000933 (2010).
    Article  Google Scholar 

    51.
    Holly, K. G., Sandra, B., John, O. N. & Jonathan, A. F. Monitoring and estimating tropical forest carbon stocks: Making REDD a reality. Environ. Res. Lett. 2, 045023 (2007).
    Article  Google Scholar 

    52.
    Asner, G. P. et al. High-resolution forest carbon stocks and emissions in the Amazon. Proc. Natl. Acad. Sci. 107, 16738–16742 (2010).
    ADS  CAS  Article  Google Scholar 

    53.
    Magnusson, W. et al. Biodiversidade e monitoramento ambiental integrado (Biodiversity and Integrated Environmental Monitoring). 335 (PPBio INPA, 2013).

    54.
    Kottek, M., Grieser, J., Beck, C., Rudolf, B. & Rubel, F. World map of the Koppen–Geiger climate classification updated. Meteorol. Z. 15, 259–263. https://doi.org/10.1127/0941-2948/2006/0130 (2006).
    Article  Google Scholar 

    55.
    ANA. Sistema de Monitoramento Hidrológico (Hydrological Monitoring System). Agência Nacional de Águas[[nl]]National Water Agency. http://www.hidroweb.ana.gov.br, 2016).

    56.
    ICMBio. Vol. I (ed MINISTÉRIO DO MEIO AMBIENTE) 222 (Instituto Chico Mendes de Conservação da Biodiversidade, Macapá, Amapá, 2014).

    57.
    Eswaran, H., Ahrens, R., Rice, T. J. & Stewart, B. A. Soil Classification: A Global Desk Reference. (CRC Press, Boca Raton, 2002).

    58.
    Dutech, C., Maggia, L. & Joly, H. I. Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest tree. Mol. Ecol. 9, 1427–1432. https://doi.org/10.1046/j.1365-294x.2000.01027.x (2000).
    CAS  Article  PubMed  Google Scholar 

    59.
    ter Steege, H. et al. Hyperdominance in the Amazonian Tree Flora. Science https://doi.org/10.1126/science.1243092 (2013).
    Article  PubMed  Google Scholar 

    60.
    Kido, T., Taniguchi, M. & Baba, K. Diterpenoids from Amazonian crude drug of Fabaceae. Chem. Pharm. Bull. 51, 207–208. https://doi.org/10.1248/cpb.51.207 (2003).
    CAS  Article  Google Scholar 

    61.
    Maurya, R., Ravi, M., Singh, S. & Yadav, P. P. A review on cassane and norcassane diterpenes and their pharmacological studies. Fitoterapia 83, 272–280. https://doi.org/10.1016/j.fitote.2011.12.007 (2012).
    CAS  Article  PubMed  Google Scholar 

    62.
    Alves, J. C. Z. O. & Miranda, I. D. S. Análise da estrutura de comunidades arbóreas de uma floresta amazônica de Terra Firme aplicada ao manejo florestal. Acta Amazonica 38, 657–666 (2008).
    Article  Google Scholar 

    63.
    Forget, P. M., Mercier, F. & Collinet, F. Spatial patterns of two rodent-dispersed rain forest trees Carapa procera (Meliaceae) and Vouacapoua americana (Caesalpiniaceae) at Paracou, French Guiana. J. Trop. Ecol. 15, 301–313. https://doi.org/10.1017/s0266467499000838 (1999).
    Article  Google Scholar 

    64.
    Forget, P.-M. Ten-year seedling dynamics in Vouacapoua americana in French Guiana: A hypothesis. Biotropica 29, 124–126 (1997).
    Article  Google Scholar 

    65.
    Forget, P. M. Recruitment pattern of Vouacapoua-Americana (Caesalpiniaceae), a rodent-dispersed tree specie in French-Guiana. Biotropica 26, 408–419. https://doi.org/10.2307/2389235 (1994).
    Article  Google Scholar 

    66.
    Forget, P. M. Effect of microhabitat on seed fate and seedling performance in two rodent-dispersed tree species in rain forest in French Guiana. J. Ecol. 85, 693–703. https://doi.org/10.2307/2960539 (1997).
    Article  Google Scholar 

    67.
    Zhang, S. Y. & Wang, L. X. Comparison of 3 fruit census methods in French-Guiana. J. Trop. Ecol. 11, 281–294 (1995).
    Article  Google Scholar 

    68.
    Stevenson, P. R. The relationship between fruit production and primate abundance in Neotropical communities. Biol. J. Lin. Soc. 72, 161–178. https://doi.org/10.1006/bijl.2000.049 (2001).
    Article  Google Scholar 

    69.
    Norris, D., Rodriguez Chuma, V. J. U., Arevalo-Sandi, A. R., Landazuri Paredes, O. S. & Peres, C. A. Too rare for non-timber resource harvest? Meso-scale composition and distribution of arborescent palms in an Amazonian sustainable-use forest. For. Ecol. Manag. 377, 182–191. https://doi.org/10.1016/j.foreco.2016.07.008 (2016).
    Article  Google Scholar 

    70.
    Paredes, O. S. L., Norris, D., Oliveira, T. G. D. & Michalski, F. Water availability not fruitfall modulates the dry season distribution of frugivorous terrestrial vertebrates in a lowland Amazon forest. PLoS ONE 12, e0174049. https://doi.org/10.1371/journal.pone.0174049 (2017).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    71.
    Magnusson, W. E. et al. RAPELD: A modification of the Gentry method for biodiversity surveys in long-term ecological research sites. Biota. Neotrop. 5, 19–24. https://doi.org/10.1590/s1676-06032005000300002 (2005).
    Article  Google Scholar 

    72.
    Norris, D., Fortin, M.-J. & Magnusson, W. E. Towards monitoring biodiversity in Amazonian forests: How regular samples capture meso-scale altitudinal variation in 25 km(2) plots. PLoS ONE https://doi.org/10.1371/journal.pone.0106150 (2014).
    Article  PubMed  PubMed Central  Google Scholar 

    73.
    The Angiosperm Phylogeny Group. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161, 105–121. https://doi.org/10.1111/j.1095-8339.2009.00996.x (2009).
    Article  Google Scholar 

    74.
    Guisan, A. & Zimmermann, N. E. Predictive habitat distribution models in ecology. Ecol. Model. 135, 147–186. https://doi.org/10.1016/S0304-3800(00)00354-9 (2000).
    Article  Google Scholar 

    75.
    Platts, P. J., McClean, C. J., Lovett, J. C. & Marchant, R. Predicting tree distributions in an East African biodiversity hotspot: Model selection, data bias and envelope uncertainty. Ecol. Model. 218, 121–134. https://doi.org/10.1016/j.ecolmodel.2008.06.028 (2008).
    Article  Google Scholar 

    76.
    Camarero, J. J., Albuixech, J., López-Lozano, R., Casterad, M. A. & Montserrat-Martí, G. An increase in canopy cover leads to masting in Quercus ilex. Trees 24, 909–918. https://doi.org/10.1007/s00468-010-0462-5 (2010).
    Article  Google Scholar 

    77.
    Fernández-Martínez, M., Garbulsky, M., Peñuelas, J., Peguero, G. & Espelta, J. M. Temporal trends in the enhanced vegetation index and spring weather predict seed production in Mediterranean oaks. Plant Ecol. 216, 1061. https://doi.org/10.1007/s11258-015-0489-1 (2015).
    Article  Google Scholar 

    78.
    Fortin, M.-J. & Dale, M. R. T. Spatial Analysis: A Guide for Ecologists. 365 (Cambridge University Press, Cambridge, 2005).

    79.
    Hastie, T. J. & Tibshirani, R. J. Generalized Additive Models. Vol. 43 (CRC Press, Boca Raton, 1990).

    80.
    Wood, S. Generalized Additive Models: An Introduction with R. (CRC Press, Boca Raton, 2006).

    81.
    Wood, S. N. & Augustin, N. H. GAMs with integrated model selection using penalized regression splines and applications to environmental modelling. Ecol. Model. 157, 157–177. https://doi.org/10.1016/S0304-3800(02)00193-X (2002).
    Article  Google Scholar 

    82.
    R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ (2016).

    83.
    Burnham, K. P. & Anderson, D. R. Model Selection and Multi-model Inference: A Practical Information-Theoretic Approach. (Springer, New York, 2002).

    84.
    Pebesma, E. J. Multivariable geostatistics in S: The gstat package. Comput. Geosci. 30, 683–691. https://doi.org/10.1016/j.cageo.2004.03.012 (2004).
    ADS  Article  Google Scholar 

    85.
    Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002).
    Google Scholar 

    86.
    e1071: Misc Functions of the Department of Statistics, Probability Theory Group v. 1.6-8 (2017). More

  • in

    Temperature thresholds of ecosystem respiration at a global scale

    1.
    Cao, M. & Woodward, F. I. Dynamic responses of terrestrial ecosystem carbon cycling to global climate change. Nature 393, 249–252 (1998).
    CAS  Article  Google Scholar 
    2.
    Heimann, M. & Reichstein, M. Terrestrial ecosystem carbon dynamics and climate feedbacks. Nature 451, 289–292 (2008).
    CAS  Article  Google Scholar 

    3.
    Allen, A. P., Gillooly, J. F. & Brown, J. H. Linking the global carbon cycle to individual metabolism. Funct. Ecol. 19, 202–213 (2005).
    Article  Google Scholar 

    4.
    Enquist, B. J. et al. Scaling metabolism from organisms to ecosystems. Nature 423, 639–642 (2003).
    CAS  Article  Google Scholar 

    5.
    Gillooly, J. F., Brown, J. H., West, G. B., Savage, V. M. & Charnov, E. L. Effects of size and temperature on metabolic rate. Science 293, 2248–2251 (2001).
    CAS  Article  Google Scholar 

    6.
    Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).
    Article  Google Scholar 

    7.
    Friedlingstein, P. et al. Uncertainties in CMIP5 climate projections due to carbon cycle feedbacks. J. Clim. 27, 511–526 (2014).
    Article  Google Scholar 

    8.
    Davidson, E. A. & Janssens, I. A. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173 (2006).
    CAS  Article  Google Scholar 

    9.
    Lenton, T. M. & Huntingford, C. Global terrestrial carbon storage and uncertainties in its temperature sensitivity examined with a simple model. Glob. Change Biol. 9, 1333–1352 (2003).
    Article  Google Scholar 

    10.
    Song, B. et al. Divergent apparent temperature sensitivity of terrestrial ecosystem respiration. J. Plant Ecol. 7, 419–428 (2014).
    Article  Google Scholar 

    11.
    Lloyd, J. & Taylor, J. A. On the temperature dependence of soil respiration. Funct. Ecol. 8, 315–323 (1994).

    12.
    Mahecha, M. D. et al. Global convergence in the temperature sensitivity of respiration at ecosystem level. Science 329, 838–840 (2010).
    CAS  Article  Google Scholar 

    13.
    Yvon-Durocher, G. et al. Reconciling the temperature dependence of respiration across timescales and ecosystem types. Nature 487, 472–476 (2012).
    CAS  Article  Google Scholar 

    14.
    Johnston, A. S. A. & Sibly, R. M. The influence of soil communities on the temperature sensitivity of soil respiration. Nat. Ecol. Evol. 2, 1597–1602 (2018).
    Article  Google Scholar 

    15.
    Dell, A. I., Pawar, S. & Savage, V. M. Systematic variation in the temperature dependence of physiological and ecological traits. Proc. Natl Acad. Sci. USA 108, 10591–10596 (2011).
    CAS  Article  Google Scholar 

    16.
    Buckley, L. B. & Huey, R. B. Temperature extremes: geographic patterns, recent changes, and implications for organismal vulnerabilities. Glob. Change Biol. 22, 3829–3842 (2016).
    Article  Google Scholar 

    17.
    Gill, A. L. & Finzi, A. C. Belowground carbon flux links biogeochemical cycles and resource-use efficiency at the global scale. Ecol. Lett. 19, 1419–1428 (2016).
    Article  Google Scholar 

    18.
    Green, J. K. et al. Large influence of soil moisture on long-term terrestrial carbon uptake. Nature 565, 476–479 (2019).
    CAS  Article  Google Scholar 

    19.
    Allison, S. D., Wallenstein, M. D. & Bradford, M. A. Soil-carbon response to warming dependent on microbial physiology. Nat. Geosci. 3, 336–340 (2010).
    CAS  Article  Google Scholar 

    20.
    Michaletz, S. T., Cheng, D., Kerkhoff, A. J. & Enquist, B. J. Convergence of terrestrial plant production across global climate gradients. Nature 512, 39–43 (2014).
    CAS  Article  Google Scholar 

    21.
    Pastorello, G. et al. The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data. Sci. Data 7, 225 (2020).
    Article  Google Scholar 

    22.
    Monson, R. K. et al. Winter forest soil respiration controlled by climate and microbial community composition. Nature 439, 711–714 (2006).
    CAS  Article  Google Scholar 

    23.
    Mauder, M. et al. A strategy for quality and uncertainty assessment of long-term eddy-covariance measurements. Agric. Meteorol. 169, 122–135 (2013).
    Article  Google Scholar 

    24.
    Kim, D.-G., Vargas, R., Bond-Lamberty, B. & Turetsky, M. R. Effects of soil rewetting and thawing on soil gas fluxes: a review of current literature and suggestions for future research. Biogeosciences 9, 2459–2483 (2012).
    CAS  Article  Google Scholar 

    25.
    Du, E. et al. Winter soil respiration during soil-freezing process in a boreal forest in Northeast China. J. Plant Ecol. 6, 349–357 (2013).
    Article  Google Scholar 

    26.
    Schuur, E. A. et al. Climate change and the permafrost carbon feedback. Nature 520, 171–179 (2015).
    CAS  Article  Google Scholar 

    27.
    Koven, C. D., Hugelius, G., Lawrence, D. M. & Wieder, W. R. Higher climatological temperature sensitivity of soil carbon in cold than warm climates. Nat. Clim. Change 7, 817–822 (2017).
    CAS  Article  Google Scholar 

    28.
    Bond-Lamberty, B. P. & Thomson, A. M. A Global Database of Soil Respiration Data Version 4.0 (ORNL DAAC, 2018); https://doi.org/10.3334/ORNLDAAC/1578

    29.
    Zhang, Z. et al. A temperature threshold to identify the driving climate forces of the respiratory process in terrestrial ecosystems. Eur. J. Soil Biol. 89, 1–8 (2018).
    Article  Google Scholar 

    30.
    Yang, Y., Donohue, R. J., McVicar, T. R., Roderick, M. L. & Beck, H. E. Long-term CO2 fertilization increases vegetation productivity and has little effect on hydrological partitioning in tropical rainforests. J. Geophys. Res. Biogeosci. 121, 2125–2140 (2016).
    Article  Google Scholar 

    31.
    Fleischer, K. et al. Amazon forest response to CO2 fertilization dependent on plant phosphorus acquisition. Nat. Geosci. 12, 736–741 (2019).
    CAS  Article  Google Scholar 

    32.
    Padfield, D. et al. Metabolic compensation constrains the temperature dependence of gross primary production. Ecol. Lett. 20, 1250–1260 (2017).
    Article  Google Scholar 

    33.
    Atkin, O. K. & Tjoelker, M. G. Thermal acclimation and the dynamic response of plant respiration to temperature. Trends Plant Sci. 8, 343–351 (2003).
    CAS  Article  Google Scholar 

    34.
    Huntingford, C. et al. Implications of improved representations of plant respiration in a changing climate. Nat. Commun. 8, 1602 (2017).
    Article  Google Scholar 

    35.
    Niu, S. et al. Thermal optimality of net ecosystem exchange of carbon dioxide and underlying mechanisms. New Phytol. 194, 775–783 (2012).
    Article  Google Scholar 

    36.
    Rind, D. The consequences of not knowing low- and high-latitude climate sensitivity. Bull. Am. Meteorol. Soc. 89, 855–864 (2008).
    Article  Google Scholar 

    37.
    Liu, Z. et al. Increased high-latitude photosynthetic carbon gain offset by respiration carbon loss during an anomalous warm winter to spring transition. Glob. Change Biol. 26, 682–696 (2020).
    Article  Google Scholar 

    38.
    Haverd, V. et al. Higher than expected CO2 fertilization inferred from leaf to global observations. Glob. Change Biol. 26, 2390–2402 (2020).
    Article  Google Scholar 

    39.
    Tagesson, T. et al. Recent divergence in the contributions of tropical and boreal forests to the terrestrial carbon sink. Nat. Ecol. Evol. 4, 202–209 (2020).
    Article  Google Scholar 

    40.
    Climate Research Unit, University of East Anglia Average Annual Temperature. Atlas Biosphere (Center for Sustainability and the Global Environment, accessed 6 February 2020); https://nelson.wisc.edu/sage/data-and-models/atlas/maps.php More

  • in

    Passive eDNA collection enhances aquatic biodiversity analysis

    1.
    Taberlet, P., Bonin, A., Zinger, L, & Coissac, E. Environmental DNA, for Biodiversity Research and Monitoring (Oxford Univ. Press, 2018).
    2.
    Jo, T., Arimoto, M., Murakami, H., Masuda, R. & Minamoto, T. Particle size distribution of environmental DNA from the nuclei of marine fish. Environ. Sci. Technol. 53, 9947–9956 (2019).
    CAS  PubMed  Article  Google Scholar 

    3.
    Wilcox, T. M., McKelvey, K. S., Young, M. K., Lowe, W. H. & Schwartz, M. K. Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis). Conserv. Genet. Resour. 7, 639–641 (2015).
    Article  Google Scholar 

    4.
    Thomsen, P. F. & Willerslev, E. Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183, 4–18 (2015).
    Article  Google Scholar 

    5.
    Seymour, M. et al. Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks. Sci. Total Environ. 729, 138801 (2020).
    CAS  PubMed  Article  Google Scholar 

    6.
    Jarman, S. N., Berry, O. & Bunce, M. The value of environmental DNA biobanking for long-term biomonitoring. Nat. Ecol. Evol. 2, 1192–1193 (2018).
    PubMed  Article  Google Scholar 

    7.
    Jeunen, G.-J. et al. Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecol. Evol. 9, 1323–1335 (2019).
    PubMed  PubMed Central  Article  Google Scholar 

    8.
    Turner, C. R. et al. Particle size distribution and optimal capture of aqueous microbial eDNA. Methods Ecol. Evol. 5, 676–684 (2014).
    Article  Google Scholar 

    9.
    Koziol, A. et al. Environmental DNA metabarcoding studies are critically affected by substrate selection. Mol. Ecol. Resour. 19, 366–376 (2019).
    CAS  PubMed  Article  Google Scholar 

    10.
    Tsuji, S., Takahara, T., Doi, H., Shibata, N. & Yamanaka, H. The detection of aquatic macroorganisms using environmental DNA analysis – a review of methods for collection, extraction, and detection. Environ. DNA 1, 99–108 (2019).
    Article  Google Scholar 

    11.
    Shu, L., Ludwig, A. & Peng, Z. Standards for methods utilizing environmental DNA for detection of fish species. Genes 11, 296 (2020).
    CAS  PubMed Central  Article  PubMed  Google Scholar 

    12.
    Deiner, K., Walser, J.-C., Mächler, E. & Altermatt, F. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol. Conserv. 183, 53–63 (2015).
    Article  Google Scholar 

    13.
    Jeunen, G.-J. et al. Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Mol. Ecol. Resour. 19, 426–438 (2019).
    CAS  PubMed  Article  Google Scholar 

    14.
    Thomas, A. C., Howard, J., Nguyen, P. L., Seimon, T. A. & Goldberg, C. S. ANDeTM: a fully integrated environmental DNA sampling system. Methods Ecol. Evol. 9, 1379–1385 (2018).
    Article  Google Scholar 

    15.
    Schumer, G. et al. Utilizing environmental DNA for fish eradication effectiveness monitoring in streams. Biol. Invasions 21, 3415–3426 (2019).
    Article  Google Scholar 

    16.
    Zinger, L. et al. DNA metabarcoding – need for robust experimental designs to draw sound ecological conclusions. Mol. Ecol. 28, 1857–1862 (2019).
    PubMed  Article  Google Scholar 

    17.
    Bessey, C. et al. Maximizing fish detection with eDNA metabarcoding. Environ. DNA 2, 493–504, https://doi.org/10.1002/edn3.74 (2020).
    Article  Google Scholar 

    18.
    Harrison, J. B., Sunday, J. M. & Rogers, S. M. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc. R. Soc. Ser. B 286, 20191409 (2019).
    CAS  Article  Google Scholar 

    19.
    Seymour, M. et al. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms. Commun. Biol. 1, https://doi.org/10.1038/s42003-017-0005-3 (2018).

    20.
    Deiner, K. & Altermatt, F. Transport distance of invertebrate environmental DNA in a natural river. PLoS ONE 9, e88786 (2014).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    21.
    Mächler, E., Deiner, K., Spahn, F. & Altermatt, F. Fishing in the water: effect of sampled water volume on environmental DNA-based detection of macroinvertebrates. Environ. Sci. Technol. 50, 305–312 (2016).
    PubMed  Article  CAS  Google Scholar 

    22.
    Hanfling, B. et al. Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol. Ecol. 25, 3101–3119 (2016).
    PubMed  Article  CAS  Google Scholar 

    23.
    Cantera, I. et al. Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers. Sci. Rep. 9, 3085 (2019).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    24.
    McQuillan, J. S. & Robidart, J. C. Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities. Curr. Opin. Biotechnol. 45, 43–50 (2017).
    CAS  PubMed  Article  Google Scholar 

    25.
    Schabacker, J. C. et al. Increased eDNA detection sensitivity using a novel high-volume water sampling method. Environ. DNA 2, 244–251 (2020).
    Article  Google Scholar 

    26.
    Mariani, S., Baillie, C., Colosimo, G. & Riesgo, A. Sponges as natural environmental DNA samples. Curr. Biol. 29, R395–R402 (2019).
    Article  CAS  Google Scholar 

    27.
    Keesing, J., Webber, B.L. & Hardiman, L. Ashmore Reef Marine Park Environmental Assessment. Final report to director of National Park (2020).

    28.
    Kirtane, A., Atkinson, J. D. & Sassoubre, L. Design and validation of passive environmental DNA samplers using granular activated carbon and montmorillonite clay. Environ. Sci. Technol. https://doi.org/10.1021/acs.est.0c01863 (2020).
    Article  PubMed  Google Scholar 

    29.
    Taberlet, P., Coissac, E., Hajibabaei, M. & Rieseberg, L. H. Environmental DNA. Mol. Ecol. Resour. 21, 1789–1793 (2012).
    CAS  Article  Google Scholar 

    30.
    Fonseca, V. G. Pitfalls in relative abundance estimation using eDNA metabarcoding. Mol. Ecol. Resour. 18, 923–926 (2018).
    CAS  Article  Google Scholar 

    31.
    Lamb, P. D. et al. How quantitative is metabarcoding: a meta-analytical approach. Mol. Ecol. 28, 420–430 (2019).
    PubMed  Article  Google Scholar 

    32.
    Derocles, S. A. P. et al. Biomonitoring for the 21st century: integrating next-generation sequencing into ecological network analysis. Adv. Ecol. Res. 58, 1–62 (2018).
    Article  Google Scholar 

    33.
    Prosser, J. I. Replicate or lie. Environ. Microbiol. 12, 1806–1810 (2010).
    CAS  PubMed  Article  Google Scholar 

    34.
    MacKenzie, D. I. What are the issues with presence-absence data for wildlife managers? J. Wildl. Manag. 69, 849–860 (2005).
    Article  Google Scholar 

    35.
    Liang, Z. & Keeley, A. Filtration recovery of extracellular DNA from environmental water samples. Environ. Sci. Technol. 47, 9324–9331 (2013).
    CAS  PubMed  Article  Google Scholar 

    36.
    Renshaw, M. A., Olds, B. P., Jerde, C. L., McVeigh, M. M. & Lodge, D. M. The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Mol. Ecol. Resour. 15, 168–176 (2015).
    CAS  PubMed  Article  Google Scholar 

    37.
    Eichmiller, J. J., Miller, L. M. & Sorensen, P. W. Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Mol. Ecol. Resour. 16, 56–68 (2016).
    CAS  PubMed  Article  Google Scholar 

    38.
    Majaneva, M. et al. Environmental DNA filtration techniques affect recovered biodiversity. Sci. Rep. 8, 4682 (2018).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    39.
    Stier, A. C., Bolker, B. M. & Osenberg, C. W. Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity. Ecosphere 7, e01612 (2016).
    Article  Google Scholar 

    40.
    Yates, M. C., Fraser, D. J. & Derry, A. M. Meta-analysis supports further refinement of eDNA for monitoring aquatic species-specific abundance in nature. Environ. DNA 1, 5–13 (2019).
    Article  Google Scholar 

    41.
    Strickland, G. J. & Roberts, J. H. Utility of eDNA and occupancy models for monitoring an endangered fish across diverse riverine habitats. Hydrobiologia 826, 129–144 (2019).
    CAS  Article  Google Scholar 

    42.
    Deagle, B. E. et al. Counting with DNA metabarcoding studies: how should we convert sequence reads to dietary data? Mol. Ecol. 28, 391–406 (2019).

    43.
    Shogren, A. J. et al. Controls on eDNA movement in streams: transport, retention, and resuspension. Sci. Rep. 7, 5065 (2017).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    44.
    Berry, T. E. et al. DNA metabarcoding for diet analysis and biodiversity: a case study using the endangered Australian sea lion (Neophoca cinerea). Ecol. Evol. 7, 5435–5453 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    45.
    Deagle, B. E. et al. Studying seabird diet through genetic analysis of faeces: a case study on Macaroni penguins (Eudyptes chrysolophus). PLoS ONE 2, e831 (2007).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    46.
    Murray, D. C., Coghlan, M. L. & Bunce, M. From benchtop to desktop: important considerations when designing amplicon sequencing workflows. PLoS ONE 10, e0124671 (2015).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    47.
    Benson, D. A. et al. GenBank. Nucleic Acids Res. 42, D32–D37 (2014).
    CAS  PubMed  Article  Google Scholar 

    48.
    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  PubMed Central  Article  Google Scholar 

    49.
    Paradis, E. APE 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
    CAS  Article  PubMed  Google Scholar 

    50.
    Baselga, A. & Orme, C. D. L. Betapart: an R package for the study of beta diversity. Methods Ecol. Evol. 3, 808–812 (2012).
    Article  Google Scholar 

    51.
    Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).
    Article  Google Scholar 

    52.
    Herve, M. RVAideMemoire, testing and plotting procedures for biostatistics. https://cran.r-project.org/web/packages/RVAideMemoire/index.html (2018). More