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Institute of Environment, Department of Biological Sciences, Florida International University, Miami, FL, USAFrederick C. Draper & Christopher BaralotoSchool of Geography, University of Leeds, Leeds, UKFrederick C. Draper, Oliver L. Phillips, Timothy R. Baker, Roel J. W. Brienen & David R. GalbraithCenter for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USAFrederick C. Draper, Gregory P. Asner, Jason Vleminckx & Oscar J. Valverde BarrantesInstituto Nacional de Pesquisas da Amazônia (INPA), Manaus, BrazilFlavia R. C. Costa, Juliana Schietti, Fernanda Coelho de Souza, William E. Magnusson, Karina Melgaço, André B. Junqueira, Ana C. Andrade, José Luís Camargo, Flávia D. Santana, Ricardo O. Perdiz, Jessica Soares Cravo, Alberto Vicentini, Henrique Nascimento, Niro Higuchi & Thaiane Rodrigues de SousaEcology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USAGabriel Arellano & Paul E. BerryDepartamento de Ciencias Forestales, Universidad Nacional de Colombia, Medellín, ColombiaAlvaro Duque & Mauricio Sánchez SáenzDepartamento de Biología, Universidad Autónoma de Madrid, Madrid, SpainManuel J. MacíaCentro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, SpainManuel J. MacíaNaturalis Biodiversity Center, Leiden, The NetherlandsHans ter Steege & Tinde Van AndelSystems Ecology, Vrije Universiteit, Amsterdam, The NetherlandsHans ter SteegeLancaster Environment Centre, Lancaster University, Lancaster, UKErika BerenguerEnvironmental Change Institute, University of Oxford, Oxford, UKErika Berenguer & Yadvinder MalhiFaculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, NorwayJacob B. SocolarSchool of Geosciences, University of Edinburgh, Edinburgh, UKKyle G. DexterMissouri Botanical Garden, St Louis, MO, USAPeter M. Jørgensen & J. Sebastian TelloBrazilian Agricultural Research Corporation (Embrapa), Roraima, BrazilCarolina V. CastilhoUniversidad Nacional de San Antonio Abad del Cusco, Cusco, PeruAbel Monteagudo-Mendoza, Victor Chama Moscoso, Darcy Galiano Cabrera & Percy Núñez VargasDepartment of Intergrative Biology, University of California Berkeley, Berkeley, CA, USAPaul V. A. Fine & Italo MesonesDepartment of Biology, University of Turku, Turku, FinlandKalle RuokolainenInstituto de Investigaciones de la Amazonía Peruana, Iquitos, PeruEuridice N. Honorio Coronado, Nállarett Dávila, Marcos A. Rios Paredes, Jhon del Aguila Pasquel, Gerardo Flores Llampazo, Ricardo Zarate Gomez, José Reyna Huaymacari, Julio M. Grandez Rios & Cesar J. Cordova OrocheUNELLEZ-Guanare, Programa de Ciencias del Agro y el Mar, Herbario Universitario (PORT), Mesa de Cavacas, VenezuelaGerardo AymardCompensation International Progress S. A.—Ciprogress Greenlife, Bogotá, ColombiaGerardo AymardAMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceJulien Engel, Claire Fortunel, Jean-François Molino, Daniel Sabatier & Maxime Réjou-MéchainEnvironmental and Rural Science, University of New England, Armidale, New South Wales, AustraliaC. E. Timothy PaineINRA, UMR EcoFoG, AgroParisTech, CNRS, CIRAD, Université des Antilles, Université de Guyane, Kourou, French GuianaJean-Yves Goret & Elodie AllieCIRAD, UMR EcoFoG, Kourou, French GuianaAurelie Dourdain & Pascal PetronelliBIOMAS, Universidad de Las Américas, Quito, EcuadorJuan E. Guevara AndinoInstituto de Ecología, Herbario Nacional de Bolivia, La Paz, BoliviaLeslie Cayola Pérez, Narel Y. Paniagua Zambrana & Alfredo F. FuentesDepartamento de Biologia, Universidade Federal de Rondônia, Porto Velho, BrazilÂngelo G. ManzattoLaboratoire Evolution et Diversité Biologique (EDB) CNRS/UPS, Toulouse, FranceJerôme ChaveSchool of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UKSophie FausetDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USARoosevelt Garcia VillacortaDepartment of Geography, University of Exeter, Exeter, UKTed R. FeldpauschFacultad de Ciencias Biológicas, Universidad Nacional de la Amazonía Peruana, Iquito, PeruElvis Valderamma Sandoval, Gilberto E. Navarro Aguilar, Jim Vega Arenas & Manuel FloresEstación Biológica del Jardín Botánico de Missouri, Oxapampa, PeruRodolfo Vasquez Martinez, Victor Chama Moscoso & Luis Valenzuela GamarraInstitut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, Barcelona, SpainAndré B. JunqueiraSchool of Geography & Sustainable Development, University of St Andrews, St Andrews, UKKatherine H. RoucouxDepartment of Environment and Development, Federal University of Amapá, Macapa, BrazilJosé J. de Toledo & Renato R. HilárioCentre for Tropical Environmental and Sustainability Science (TESS) and College of Marine and Environmental Sciences, James Cook University, Cairns, Queensland, AustraliaWilliam F. Laurance & Susan G. LauranceDepartment of Environmental Science and Policy, George Mason University, Fairfax, VA, USAThomas E. LovejoyInventory and Monitoring Program, National Park Service, Fredericksburg, VA, USAJames A. ComiskeySmithsonian Institution, Washington DC, USAJames A. ComiskeyDepartment of Plant Sciences, University of Cambridge, Cambridge, UKMichelle KalamandeenLiving with Lakes Centre, Laurentian University, Greater Sudbury, Ontario, CanadaMichelle KalamandeenDRGB, Instituto Nacional de Innovación Agraria (INIA), Lima, PeruCarlos A. Amasifuen GuerraHerbarium Amazonense (AMAZ), Universidad Nacional de la Amazonia Peruana, Loreto, PerúLuis A. Torres MontenegroDepartment of Ecology, Universidade de São Paulo, São Paulo, BrazilMarcelo P. PansonatoInstitute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The NetherlandsJoost F. DuivenvoordenCentro de Estudos da Biodiversidade, Universidade Federal de Roraima, Boa Vista, BrazilSidney Araújo de Sousa & Marcos Salgado VitalMuseo de Historia Natural Noel Kempff Mercado, Universidad Autónoma Gabriel Rene Moreno, Santa Cruz, BoliviaLuzmila Arroyo, Alejandro Araujo-Murakami & Germaine A. Parada GutierrezFaculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidad do Estado de Mato Grosso, Nova Xavantina, BrazilBeatriz S. Marimon, Ben Hur Marimon Junior, Ricardo Keichi Umetsu & Nayane C. C. S. PrestesCentro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, BrazilFernanda Antunes CarvalhoDepartment of Ecology, Evolution and Behaviour, University of Minnesota, Minneapolis, MN, USAGabriel DamascoDepartment of Geography, University College London, London, UKMathias DisneyDepartamento de Ciencias Biológicas, Universidad de Los Andes (Colombia), Bogotá, ColombiaPablo R. Stevenson Diaz & Ana M. AldanaCentro de Ciências Biológicas e da Natureza, Universidade Federal do Acre, Rio Branco, BrazilSabina Cerruto Ribeiro, Richarlly da Costa Silva & Wenderson CastroNicholas School of the Environment, Duke University, Durham, NC, USAJohn W. TerborghIwokrama International Centre for Rainforest Conservation and Development, Georgetown, GuyanaRaquel S. ThomasSmithsonian’s National Zoo & Conservation Biology Institute, Washington DC, USAFrancisco DallmeierInstituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, ColombiaAdriana PrietoUniversidade Federal Rural da Amazônia—UFRA/CAPES, Belém, BrazilRafael P. SalomãoMuseu Paraense Emílio Goeldi, Belém, BrasilRafael P. Salomão, Ima C. Guimarães Vieira & Antonio S. LimaLaboratorio de Ecología de Bosques Tropicales y Primatología, Fundación Natura Colombia, Universidad de Los Andes, Bogotá, ColombiaLuisa F. CasasFacultad de Forestales, Universidad Nacional de la Amazonía Peruana, Iquito, PeruFredy Ramirez ArevaloInstitute of Research for Forestry Development, Universidad de los Andes, Merida, VenezuelaHirma Ramírez-Angulo, Emilio Vilanova Torre & Armando Torres-LezamaSchool of Environmental and Forest Sciences (SEFS), University of Washington, Seattle, WA, USAEmilio Vilanova TorreUniversidad Regional Amazónica Ikiam, Tena, EcuadorMaria C. PeñuelaAgteca-Amazonica, Santa Cruz, BoliviaTimothy J. KilleenUniversidad Autónoma del Beni, Riberalta, BoliviaGuido Pardo & Vincent VosInstituto Amazónico de Investigaciones (IMANI), Universidad Nacional de Colombia, Sede Amazonia, BrazilEliana Jimenez-RojasBroward County Parks and Recreation, Miami, FL, USAJohn PipolyBiological Sciences, Florida Atlantic University-Davie, Miami, FL, USAJohn PipolyMuseu Universitário, Universidade Federal do Acre, Rio Branco, BrazilMarcos SilveraFacultad de Ingeniería Ambiental, Universidad Estatal Amazónica, Puyo, EcuadorDavid NeillDepartment of Biology, Washington University in St Louis, St Louis, MO, USADilys M. VelaNational Institute for Space Research (INPE), São José dos Campos, BrazilLuiz E. O. C. AragãoGeoinformática & Sistemas (GeoIS), Quito, EcuadorRodrigo SierraSchool of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff, AZ, USAOphelia WangDepartment of Geography and the Environment, University of Texas at Austin, Austin, TX, USAKenneth R. YoungInstituto de Ciência e Tecnologia, São Paulo State University (UNESP), São José dos Campos, BrazilKlécia G. MassiSchool of Anthropology and Conservation, University of Kent, Canterbury, UKMiguel N. AlexiadesUniversidade Federal do Amazonas, Manaus, BrazilFabrício BaccaroHerbario Alfredo Paredes (QAP), Universidad Central del Ecuador, Quito, EcuadorCarlos CéronSchool of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UKAdriane Esquivel MuelbertDepartment of Life Sciences, Imperial College London, London, UKJonathan L. LloydScience and Education, The Field Museum, Chicago, IL, USANigel C. A. PitmanUniversidad Tecnica del Norte, Herbario Nacional del Ecuador, Quito, EcuadorWalter PalaciosResearch Institute Alexander von Humboldt, Bogotá, ColombiaSandra PatiñoF.C.D. and C.B. conceived the study. F.C.D., G.P.A. and C.B. designed the study with input from F.R.C.C., G. Arellano, O.L.P. and H.t.S. F.C.D. and J.B.S. performed the analysis with input from C.B., G.P.A., G. Arellano, O.L.P., A. Duque, F.C.d.S. and K.D. F.C.D. wrote the manuscript with input from C.B., F.R.C.C., G. Arellano, O.L.P., A. Duque, M.J.M., G.P.A. and H.t.S. All other coauthors contributed data and had the opportunity to comment on the manuscript. More

Experimental design and crop establishmentA microcosm experiment was conducted at Yamagata University, Tsuruoka City, Japan, from May to October 2019, with six growth containers (36 cm in height, 30 cm in width, 60 cm in length) to simulate paddy fields of 0.18 m2 in area (see Supplementary Fig. S1). The experiment was laid out in a completely randomized design with three replications of two treatments: (1) rice cropping under CSI and (2) conventional rice cultivation fertilized with mineral fertilisers and irrigated with tap water (Control).Each container was filled with 32 kg of a paddy soil collected from an experimental field in the university farm and transplanted with four hills of 30-day-old seedlings (Oryza sativa L., cv. Bekoaoba) on 27th May 2019. The experiment was performed in accordance with relevant guidelines and regulations for research involving plants. The experimental soil was classified as loamy soil (air-dried, 20% moisture) with the following basic properties: pH (H2O) of 5.78, electrical conductivity (EC) of 0.09 dS m−1, SOM of 4.9%, and a total N, P, and K of 1.46, 0.88, and 3.17 g kg−1, respectively. The TWW used in the CSI system was collected from a local WWTP and monitored weekly for its basic properties (Table 2) following our previous studies6,7. In brief, pH, EC, and DO of water samples were measured on-site using pH/conductivity and DO portable meters (D-54 and OM-51, HORIBA, Ltd., Kyoto, Japan), whereas TOC and total N were analyzed using a TOC analyzer (TOC-VCSV, Shimadzu Corp., Kyoto, Japan) attached to a total N measuring unit (TNM-1, Shimadzu Corp., Kyoto, Japan). After a standard acid-digestion of water samples6, the concentration of P was measured using a portable colorimeter (DR/890, HATCH, USA), and the concentration of K was measured using an inductively coupled plasma mass spectrometry (ICP-MS ELAN DRCII, PerkinElmer Japan Co., Ltd.). The tap water used in this study was also tested on a regular basis and found to be stable throughout the crop season, with the following properties: pH of 7.8, EC of 0.095 dS m−1, DO, TOC, N, and P of 6.85, 0.49, 0.06, and 0.07 mg L−1, respectively, with K being below the ICP-MS detection limit ( More

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Which individuals will survive?Observing and recording the devastating impacts of climate change on natural lifeforms has long been a keystone of the climate change ecology field. As a result of years of quality research, we now understand that climate change can reduce species numbers and fitness, cause local extinctions and generally alter where, when, how and with whom organisms live.From the point of view of biodiversity conservation, things look pretty bad. And modelling predictions suggest that they are likely to remain bad or worsen in the near future, even if we do manage to rapidly rein in our global emissions.For this reason — although there is still much more to understand about how the various aspects of climate change can impact different organisms and ecosystems — some of the most vital questions arising now relate to if, and how, natural species can persist.Biological persistence in a changing world relies on an ability to fit or adapt to new conditions, and/or an ability to move to ‘greener pastures’. I was pleased to see work from Andrew Gougherty and colleagues address both climate-change-induced maladaptation and the potential for migration to minimize this maladaptation, in work that focused on a wide-ranging North American tree species, balsam poplar (Populus balsamifera)9.Importantly, the authors did not assess the adaptive capacity of the species as a whole, but instead investigated vulnerability in the context of 81 balsam polar populations spanning North America, thus incorporating intraspecific (within species) variation that may play an important role in persistence potential. In the study, maladaptation was defined based on gene–environment associations, in this case centred on flowering-time genes, which are crucial in regulating plant seasonal growth, dormancy and reproduction. Understanding the genetic variations that underlie fitness under given environmental conditions may help understand and rapidly identify individuals with the best chances of survival under climate change.The Gougherty study uses modern methods to go beyond species-level modelling and, to understand population risks in the context of maladaptation and migration, under climate change. This, in turn, can be utilized to prioritize conservation efforts. Ultimately, we hope that climate change science cannot just observe and understand the human-caused alterations to our planet, but lead us to prevent, manage and save.Tegan Armarego-Marriott has been an editor at Nature Climate Change since 2019. More

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Soil propertiesStone contentThe stone content ranged from (15,pm ,8%) (w/w) at V.18 to (44,pm ,13%) (w/w) at F.3 (Fig. 1a, Table 1). These differences between sites may partly be due to different sources of the raw material used to create the SIS. Further, the stone content increased with depth within the first 15 cm (V.18) and 10 cm (W.10), but remained approximately constant over depth at F.3. Hence, the stone content in the upper layers of the older SIS (W.10 and V.18) was lower than in the lower layers. These depth-related differences at each site may be related to time-dependent developments within the SIS. In the uppermost layers of V.18 and W.10, stone content was comparatively low probably due to input of fine mineral and organic particles by storm water. For the oldest SIS (V.18), this assumption is supported by the field observation of soil material lying on a bricked stone border near the inflow within the SIS.Figure 1Depth-dependent soil properties: (a) stone content [% (w/w)], (b) bulk density ((hbox {g},hbox {cm}^{-3})), (c) pH (0.01 M (hbox {CaCl}_{2})) and (d) organic carbon content (OC) [% (w/w)] of the three sites F3, W.10, V18. The error bars are the standard deviation ((hbox {n}=4)).Full size imageTable 1 Soil properties of SIS.Full size tableBulk densityThe bulk density in the upper layers of the different SIS increased in the following order: V.18 < W.10 < F.3 (Fig. 1b, Table 1). At V.18, we observed the strongest change with depth from (1.0,pm ,0.1,hbox {g},hbox {cm}^{-3}) (0–5 cm) to (1.5,pm ,0.1,hbox {g},hbox {cm}^{-3}) (15–20 cm). In contrast, we observed almost no depth-dependent change of bulk density at the youngest site of F.3 ((1.6,pm ,0.2,hbox {g},hbox {cm}^{-3})).In samples of the older sites of V.18 and W.10, low bulk densities in the uppermost layers compared to deeper layers were probably caused by the activity of macrofauna, an intensive rooting, a higher organic carbon (OC) content and the input of strongly sorted fine material. The older the SIS, the stronger the effect of these factors.At F.3 the bulk density was relatively high. Here, we supposed an uniform compaction of the soil layer under the topsoil during construction. This assumption was supported by the observation of redox characteristics (iron-red stains next to grey iron-depleted areas) in the soil at approximately 25 cm depth caused by the lack of oxygen due to accumulating water45 in compacted soil.TextureThe mean texture of fine soil at all SIS was very similar: 57–80% (w/w) sand, 16–34% (w/w) silt and 5–9% (w/w) clay, since similar textured materials were used for construction to guarantee solute retention and sufficient hydraulic conductivity31. Average clay contents of all SIS were within acceptable ranges of Best Management Practice (BMP) claimed by ATV-DVWK A-138 (( More