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    Ecological niche modeling of the pantropical orchid Polystachya concreta (Orchidaceae) and its response to climate change

    1.
    Dressler, R. L. In Phylogeny and Classification of the Orchid Family (ed. Dressler, R. L.) 7–13 (Cambridge University Press, Cambridge, 1994).
    Google Scholar 
    2.
    Delforge, P. In Orchids of Europe, Nord Africa and the Middle East (ed. Delforge, P.) 67–68 (A & C Black Publishers, London, 2001).
    Google Scholar 

    3.
    Barman, D. & Devadas, R. Climate change on orchid population and conservation strategies: a review. J. Crop Weed. 9(12), 1–12 (2013).
    Google Scholar 

    4.
    Fay, M. F. Orchid conservation: how can we meet the challenges in the twenty-first century. Bot. Stud. 5, 1–6 (2018).
    Google Scholar 

    5.
    Brovkin, V. Climate–vegetation interaction. J. Phys. IV FRANCE 12, 57–72 (2002).
    Google Scholar 

    6.
    Thomas, C. D. et al. Extinction risk from climate change. Nature 427, 145–148. https://doi.org/10.1038/nature02121 (2004).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    7.
    Anderson, M. G. & Ferree, C. E. Conserving the stage: climate change and the geophysical underpinnings of species diversity. PLoS ONE 5(7), e11554 (2010).
    ADS  PubMed  PubMed Central  Google Scholar 

    8.
    Bálint, M. et al. Cryptic biodiversity loss linked to global climate change. Nat. Clim. Change. 1, 313–318. https://doi.org/10.1038/nclimate1191 (2011).
    ADS  Article  Google Scholar 

    9.
    Kolanowska, M. Niche conservatism and the future potential range of Epipactis helleborine (Orchidaceae). PLoS ONE 8(10), e77352. https://doi.org/10.1371/journal.pone.0077352 (2013).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    10.
    Kolanowska, M. The naturalization status of African Spotted Orchid (Oeceoclades maculata) in Neotropics. Plant Biosyst. 148(5), 1049–1055. https://doi.org/10.1080/11263504.2013.824042 (2014).
    Article  Google Scholar 

    11.
    Kolanowska, M. & Konowalik, K. Niche conservatism and future changes in the potential area coverage of Arundina graminifolia, an invasive orchid species from Southeast Asia. Biotropica 46(2), 157–165. https://doi.org/10.1111/btp.12089 (2014).
    Article  Google Scholar 

    12.
    Konowalik, K. & Kolanowska, M. Climatic niche shift and possible future spread of the invasive South African Orchid Disa bracteata in Australia and adjacent areas. PeerJ. 6, e6107. https://doi.org/10.7717/peerj.6107 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    13.
    Kolanowska, M. et al. Global warming not so harmful for all plants – response of holomycotrophic orchid species for the future climate change. Sci. Rep. 7, 12704. https://doi.org/10.1038/s41598-017-13088-7 (2017).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    14.
    Naczk, A. & Kolanowska, M. Glacial refugia and future habitat coverage of selected Dactylorhiza representatives (Orchidaceae). PLoS ONE 10(11), e0143478. https://doi.org/10.1371/journal.pone.0143478 (2015).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    15.
    Kolanowska, M. & Rykaczewski, M. From the past to the future – glacial refugia, current distribution patterns and future potential range changes of Diodonopsis (Orchidaceae) representatives. Lankesteriana. 17(2), 315–327 (2017).
    Google Scholar 

    16.
    Wang, H. H. et al. Species distribution modelling for conservation of an endangered endemic orchid. AoB Plants 7, plv039 (2015).
    PubMed  PubMed Central  Google Scholar 

    17.
    Tsiftsis, S., Djordjević, V. & Tsiripidis, I. Neottia cordata (Orchidaceae) at its southernmost distribution border in Europe: threat status and effectiveness of Natura 2000 Network for its conservation. J. Nat. Conserv. 48, 27–35 (2019).
    Google Scholar 

    18.
    Vollering, J., Schuiteman, A., de Vogel, E., van Vugt, R. & Raes, N. Phytogeography of New Guinean orchids: patterns of species richness and turnover. J. Biogeogr. 43(1), 204–214 (2016).
    Google Scholar 

    19.
    Reina-Rodríguez, G. A., Rubiano Mejía, J. E., Castro Llanos, F. A. & Soriano, I. Orchid distribution and bioclimatic niches as a strategy to climate change in areas of tropical dry forest in Colombia. Lankesteriana 17(1), 17–47 (2017).
    Google Scholar 

    20.
    Gogol-Prokurat, M. Predicting habitat suitability for rare plants at local spatial scales using a species distribution model. Ecol. Appl. 21, 33–47. https://doi.org/10.1890/09-1190.1 (2011).
    Article  PubMed  Google Scholar 

    21.
    Dudley, T. L. & Bean, D. W. Tamarisk biocontrol, endangered species risk and resolution of conflict through riparian restoration. Biocontrol 57, 331–347. https://doi.org/10.1007/s10526-011-9436-9 (2012).
    Article  Google Scholar 

    22.
    Antúnez, P. et al. The potential distribution of tree species in three periods of time under a climate change scenario. Forests 9(10), 628. https://doi.org/10.3390/f9100628 (2018).
    Article  Google Scholar 

    23.
    Wilson, C. D., Roberts, D. & Reid, N. Applying species distribution modeling to identify areas of high conservation value for endangered species: a case study using Margaritifera margaritifera (L.). Biol. Cons. 144, 821–829 (2011).
    Google Scholar 

    24.
    Koch, R., Almeida-Cortez, J. S. & Kleinschmit, B. Revealing areas of high nature conservation importance in a seasonally dry tropical forest in Brazil: combination of modelled plant diversity hot spots and threat patterns. J. Nat. Conserv. 35, 24–39 (2017).
    Google Scholar 

    25.
    Spiers, J. A., Oatham, M. P., Rostant, L. V. & Farrell, A. D. Applying species distribution modelling to improving conservation based decisions: a gap analysis of Trinidad and Tobago’s endemic vascular plants. Biodivers. Conserv. 27(11), 2931–2949 (2018).
    Google Scholar 

    26.
    Ramírez, S. R., Gravendeel, B., Singer, R. B., Marshall, C. R. & Pierce, N. E. Dating the origin of the Orchidaceae from a fossil orchid with its pollinator. Nature 448, 1042–1045 (2007).
    ADS  PubMed  Google Scholar 

    27.
    Conran, J. G., Bannister, J. M. & Lee, D. E. Earliest orchid macrofossils: early Miocene Dendrobium and Earina (Orchidaceae: Epidendroideae) from New Zealand. Am. J. Bot. 96(2), 466–474 (2009).
    PubMed  Google Scholar 

    28.
    Kenny, J. 2008. Orchids of Trinidad and Tobago (ed. Kenny, J.) 1–127 (Prospect Press, 2008).

    29.
    Swarts, N. D. & Dixon, K. W. Terrestrial orchid conservation in the age of extinction. Ann. Bot. 104(3), 543–556 (2009).
    PubMed  PubMed Central  Google Scholar 

    30.
    Teketay, D. History, botany and ecological requirements of coffee. Walia 20, 28–50 (1999).
    Google Scholar 

    31.
    Tupac, O. J., Ackerman, J. D. & Bayman, P. Diversity and host specificity of endophytic Rhizoctonia-like fungi from tropical orchids. Am. J. Bot. 89(11), 1852–1858 (2002).
    Google Scholar 

    32.
    Pellegrino, G., Luca, A. & Bellusci, F. Relationships between orchid and fungal biodiversity: mycorrhizal preferences in Mediterranean orchids. Plant Biosyst. 150(2), 180–189 (2016).
    Google Scholar 

    33.
    Suárez, J. P. & Kottke, I. Main fungal partners and different levels of specificity of orchid mycorrhizae in the tropical mountain forests of Ecuador. Lankesteriana 16(2), 299–305 (2016).
    Google Scholar 

    34.
    Senthilkumar, S. Mycorrhizal fungi of endangered orchid species in Kolli, a part of eastern ghats, South India. Lankesteriana 7, 15–156 (2003).
    Google Scholar 

    35.
    Pereira, O. L., Rollemberg, C. L., Borges, A. C., Matsuoka, K. & Kasuya, M. C. M. Epulorhiza epiphytica sp. nov. isolated from mycorrhizal roots of epiphytic orchids in Brazil. Mycoscience 44, 153–155 (2003).
    Google Scholar 

    36.
    Tedersoo, L. Biogeography of mycorrhizal symbiosis (Springer, Cham, 2017).
    Google Scholar 

    37.
    Waud, M., Brys, R., Van Landuyt, W., Lievens, B. & Jacquemyn, H. Mycorrhizal specificity does not limit the distribution of an endangered orchid species. Mol. Ecol. 26(6), 1687–1701 (2017).
    CAS  PubMed  Google Scholar 

    38.
    van der Cingel, N. A. An atlas of orchid pollination: America, Africa, Asia and Australia (A.A. Balkema Publishers, Rotterdam, 2001).
    Google Scholar 

    39.
    Pansarin, E. R. & Maria do Carmo, E. A. Biologia reprodutiva e polinização de duas espécies de Polystachya Hook. no Sudeste do Brasil: evidência de pseudocleistogamia em Polystachyeae (Orchidaceae). Rev. Bras. Bot. 29(3), 423–432 (2006).

    40.
    Chakraborty, D. et al. Selecting populations for non-analogous climate conditions using universal response functions: the case of Douglas-Fir in Central Europe. PLoS ONE 10(8), e0136357 (2015).
    PubMed  PubMed Central  Google Scholar 

    41.
    Broennimann, O. & Guisan, A. Predicting current and future biological invasions: both native and invaded ranges matter. Biol. Lett. 4, 585–589 (2008).
    PubMed  PubMed Central  Google Scholar 

    42.
    Abrams, M. D. Adaptations of forest ecosystems to air pollution and climate change. Tree Physiol. 31, 258–261 (2011).
    PubMed  Google Scholar 

    43.
    Atwater, D. Z., Ervine, C. & Barney, J. N. Climatic niche shifts are common in introduced plants. Nat. Ecol. Evol. 2, 34–43 (2018).
    PubMed  Google Scholar 

    44.
    Konowalik, K. & Kolanowska, M. Climatic niche shift and possible future spread of the invasive South African Orchid Disa bracteata in Australia and adjacent areas. PeerJ 6, e6107 (2018).
    PubMed  PubMed Central  Google Scholar 

    45.
    Early, R. & Sax, D. F. Climatic niche shifts between species’ native and naturalized ranges raise concern for ecological forecasts during invasions and climate change. Global Ecol. Biogeogr. 23, 1356–1365 (2014).
    Google Scholar 

    46.
    Baranow, P. & Mytnik-Ejsmont, J. Two new species of Polystachya Hook. (Orchidaceae) from Africa. Plant Syst Evol. 281, 11–16 (2009).
    Google Scholar 

    47.
    Mytnik-Ejsmont, J. & Baranow, P. Taxonomic study of Polystachya Hook. (Orchidaceae) from Asia. Plant Syst. Evol. 290, 57–63 (2010).
    Google Scholar 

    48.
    Russell, A. et al. Phylogenetics and cytology of a pantropical orchid genus Polystachya (Polystachyinae, Vandeae, Orchidaceae): Evidence from plastid DNA sequence data. Taxon 59(2), 389–404 (2010).
    Google Scholar 

    49.
    McCartney, C. African affinities, part I: the surprising relationship of some of Florida’s wild orchids. Orchids 69(2), 130–139 (2010).
    Google Scholar 

    50.
    Mytnik-Ejsmont, J. A monograph of the subtribe Polystachyinae Schltr. (Orchidaceae) (Wydawnictwo Uniwersytetu Gdańskiego, Gdańsk, 2011).
    Google Scholar 

    51.
    GBIF Occurrence Download; https://doi.org/10.15468/dl.ks410t (2018).

    52.
    Phillips, S. J., Dudík, M. & Schapire, R. E. A maximum entropy approach to species distribution modeling. In: ICML ’04. Proceedings of the Twenty-First International Conference on Machine learning. 655–662 (ACM, New York, 2004).

    53.
    Phillips, S. J., Anderson, R. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).
    Google Scholar 

    54.
    Elith, J. et al. A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17, 43–57 (2011).
    Google Scholar 

    55.
    Barve, N. et al. The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecol. Model. 222, 1810–1819 (2011).
    Google Scholar 

    56.
    Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965–1978 (2005).
    Google Scholar 

    57.
    WorldClim (version 1.4) www.worldclim.org

    58.
    Warren, D. L., Glor, R. E. & Turelli, M. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33, 607–611 (2010).
    Google Scholar 

    59.
    Chung, M. Y. et al. Comparison of genetic variation between northern and southern populations of Lilium cernuum (Liliaceae): Implications for Pleistocene refugia. PLoS ONE 13(1), e0190520. https://doi.org/10.1371/journal.pone.0190520 (2018).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    60.
    Kim, S. H. et al. Phylogeography and ecological niche modeling reveal reduced genetic diversity and colonization patterns of skunk cabbage (Symplocarpus foetidus; Araceae) from Glacial Refugia in Eastern North America. Front. Plant Sci. 9, 648. https://doi.org/10.3389/fpls.2018.00648 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    61.
    Moss, R. et al. Towards New Scenarios for Analysis of Emissions, Climate Change, Impacts, and Response Strategies. (Intergovernmental Panel on Climate Change, 2008)

    62.
    Weyant, J. et al. Report of 2.6 Versus 2.9 Watts/m2 RCPP Evaluation Panel (IPCC Secretariat, 2009).

    63.
    Sohel, S. I., Akhter, S., Ullah, H., Haque, E. & Rana, P. Predicting impacts of climate change on forest tree species of Bangladesh: evidence from threatened Dysoxylum binectariferum (Roxb.) Hook.f. ex Bedd. (Meliaceae). Forest 10(1), 154–160 (2016).
    Google Scholar 

    64.
    Sony, R. K., Sen, S., Kumar, S., Sen, M. & Jayahari, K. M. Niche models inform the effects of climate change on the endangered Nilgiri Tahr (Nilgiritragus hylocrius) populations in the southern Western Ghats, India. Ecol. Eng. 120, 355–363 (2018).
    Google Scholar 

    65.
    Mason, S. J. & Graham, N. E. Areas beneath the relative operating characteristics (ROC) and relative operating levels (ROL) curves statistical significance and interpretation. Q. J. R. Meteorol. Soc. 128, 2145–2166 (2002).
    ADS  Google Scholar 

    66.
    Evangelista, P. H. et al. Modelling invasion for a habitat generalist and a specialist plant species. Divers. Distrib. 14, 808–817 (2008).
    Google Scholar 

    67.
    Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).
    Google Scholar 

    68.
    Hijmans, R. J., Phillips, S., Leathwick, J. & Elith J. Dismo: Species Distribution Modeling. R package version 1.1-4. https://cran.r-project.org/package=dismo (2017)

    69.
    Phillips, S. B., Aneja, V. P., Kang, D. & Arya, S. P. Modelling and analysis of the atmospheric nitrogen deposition in North Carolina. Int. J. Glob. Environ. Issues 6, 231–252 (2006).
    Google Scholar 

    70.
    Warren, D. L., Glor, R. E. & Turelli, M. Environmental nicheequivalency versus conservatism: quantitative approaches toniche evolution. Evolution 62, 2868–2883. https://doi.org/10.1111/evo.2008.62.issue-11 (2008).
    Article  PubMed  Google Scholar 

    71.
    Schoener, T. W. The Anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology 49, 704–726. https://doi.org/10.2307/1935534 (1968).
    Article  Google Scholar 

    72.
    Heibl, C. & Calenge, C. Phyloclim: integrating phylogenetics and climatic Niche modeling. R package version 0.9-4 https://cran.rproject.org/web/packages/phyloclim/phyloclim.pdf (2015).

    73.
    Kremen, C. et al. Aligning conservation priorities across taxa in Madagascar with high-resolution planning tools. Science 320, 222–226 (2008).
    ADS  CAS  PubMed  Google Scholar 

    74.
    Leps, J. & Smilauer, P. Multivariate Analysis of Ecological Data Using CANOCO (Cambridge University Press, Cambridge, 2003).
    Google Scholar 

    75.
    Peterson, A. T. et al. Ecological Niches and Geographic Distributions (MPB-49) (Princeton University Press, Princeton, 2011).
    Google Scholar  More

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    Optical tracking and laser-induced mortality of insects during flight

    In-flight dosing system
    The system used in this work is detailed in Fig. 1. It can be broken down into three primary modules: (1) a “coarse tracking” system that uses a pair of stereoscopic cameras to identify the three dimensional location of a target subject, which is passed on to (2) the “fine tracking” system that uses a single higher speed camera and a fast scanning mirror (FSM) to keep the target in the middle of the field of view (FOV) of the camera using a proportional-integral-derivative (PID) control loop, and (3) the laser dosing system that fires the laser pulse, which is co-aligned with the fine tracking system to ensure the laser pulse is accurately applied to the subject even while it is moving. For both the coarse and fine tracking systems, subjects are identified by the size of their silhouettes generated from near infrared LED back-illumination or reflection. As demonstrated in Fig. 1b, the subject cages were 20 cm cubes constructed from clear acrylic, but with the side facing the tracking and dosing systems made of borosilicate glass, placed two meters away from the FSM. A high-speed video camera (Vision Research Phantom) was set up to record a small subset of experiments at 2000 frames per second as well. For all experiments, each cage contained only a single subject to be illuminated, or “dosed,” with the laser, and conditions were set such that a subject could be dosed only when it was at least 2.5 to 5 cm away from any wall of the cage to ensure the subject was flying normally, rather than taking wing or alighting.
    Figure 1

    Schematics and images of in-flight dosing setup. (a) Schematic (not to scale) of primary dosing system components and communication lines among them. Note that the mirror control and 3D position subsystems were run on separate kernels within the same PC. (b) Image of complete system setup including the test cage location, LED backlighting, and control electronics. Cameras for coarse and fine tracking, the fast scanning mirror (FSM), and dosing laser path are contained in the white circle and better seen in (c) close-up image of core tracking and dosing system components and alignment among them. Red line represents fine tracking image path, green line the dosing laser path (laser not shown), and yellow line the combined fine tracking and dosing laser path.

    Full size image

    Prior to commencing the laser dosing experiments, a number of parameters were defined to analyze the results, as detailed in Table 1 and Fig. 2. The key outcome, in line with our previous study15 and with WHO guidelines on insecticide treatments17, was whether the subjects were alive or disabled (i.e. dead or moribund) 24 h after the treatment. To characterize how well the subjects were tracked during the laser pulse, the tracking error was defined as how far the insect’s centroid was from the center of the fine tracking camera’s FOV. Other parameters defined in Table 1 relate to the “occlusion factor,” or how much of the laser beam’s energy (assuming a Gaussian profile) overlapped with the target’s outline, as demonstrated in Fig. 2. From the coarse tracking system’s output of xyz position of the target, we could also define velocity, speed, and both linear and angular acceleration of the subjects before, during, and after the laser pulse.
    Table 1 Definitions of all parameters tracked or calculated for each in-flight dosing event.
    Full size table

    Figure 2

    Representative fine tracking camera images of A. stephensi silhouettes. In each frame, the approximate outline of the thorax and abdomen is drawn (thick black lines) according to a set pixel intensity threshold. The centroid of this region is then calculated (intersection of red crosshairs) and compared with the center of the camera’s field of view (green dot) to determine the current tracking error and provide input to the fine tracking PID loop controlling the direction of the scanning mirror. The green circle around the green dot represents the spot size of the laser (2.5 mm diameter for all images shown here); occlusion factor represents how much of this laser spot (assuming a Gaussian profile) overlaps with the body of the subject. The images in (a) demonstrate a typical time course for a single subject in 1 ms intervals, and those in (b) show representative depictions of tracking errors ranging from 1 to 5 pixels for various subjects.

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    Initial results with 532 nm laser
    Initial experiments were conducted with A. stephensi subjects and a 532 nm laser (Verdi, Coherent) using parameters for power (3 W), pulse duration (25 ms), and laser spot diameter (2.5 mm) that were defined in our previous work15 as an optimal combination of potential cost and mortality performance. As seen in Supplemental Video 1, the system could be quite effective in disabling a flying mosquito with these parameters. Of note from the video, along with flight tracking data for numerous trials (not shown), the 25 ms pulse duration appeared to be short enough that the mosquitoes did not perceptibly alter their flight pattern during the pulse to throw off the tracking algorithm. From Fig. 3a,b, though, the initial system did not have consistent enough tracking performance, such that survival of the subjects was almost entirely dictated by how well the fine tracking system kept the target near the center of its FOV. From this initial experiment on a sample of 80 subjects, we set limits for mean and maximum tracking error during the laser pulse as 2 and 3 pixels, respectively, where each pixel represents ~ 250 μm. Figure 3c,d demonstrates that the system was able to achieve and maintain this performance after modifying the PID loop parameters, and that there was no longer any association between tracking performance and mortality at these conditions. These criteria were evaluated and assured for all mortality data reported in this manuscript (i.e. a Kruskal–Wallis test indicated no significant differences in tracking errors among subjects that survived or were disabled by the laser pulses). Further, Supplemental Fig. S1 shows that flight behavior, in particular speed and linear acceleration, did correlate with tracking accuracy, but that the system was able to meet the noted tracking requirements even at the extremes of flight behavior that could be observed in this study given the restricted flight volumes (though the typical values seen here largely align with available data for other Anopheles mosquitoes18,19).
    Figure 3

    Influence of mean and maximum tracking errors on mortality outcomes. Initial mortality outcomes using LD90 conditions with a 532 nm laser from previous anesthetized work showed strong correlation with (a) mean and (b) maximum tracking errors over the 25 ms pulse duration. After setting and achieving new tracking error targets of less than 2 pixels mean and 3 pixels max (see Fig. 2b for depictions of overlap between the laser spot and the subject for various error magnitudes), identical experiments no longer showed any correlation with (c) mean or (d) maximum tracking errors. Moribund and dead outcomes were grouped in (c) and (d), labeled “Disabled,” and subsequent experiments since they both represent functional kills and are grouped as such in WHO guidelines for insecticide trials.

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    Mortality results were analyzed as in Fig. 4. Each data point represents the mortality outcomes (i.e. percentage of targets that were dead or moribund at 24 h, assuming acceptable control mortality  2 × that of the other experiments at 445 or 532 nm. Note that this greater LD90 fluence value for the smaller spot still represented a lower pulse energy than required for the larger spots given the spot size differential.
    Table 2 List of in-flight dosing experimental conditions and resulting LD90 fluence values for A. stephensi subjects.
    Full size table

    Figure 5

    Dose–response curves for all experiments from Table 2, other than the two constant pulse energy tests. The x-axis is plotted on a log scale to allow clear visualization of the curves at both low and high fluence values. Individual data points and error bars not shown for the sake of clarity. The intersections of the dashed horizontal line at 90% mortality with the dose–response curves indicate the LD90 points, which are also presented in Table 2, along with pseudo R2 values for the logistic regression fits.

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    Dosing with near infrared wavelengths
    Two near infrared (NIR) laser sources were examined as well—a custom constructed 1,064 nm (1 μm) fiber laser with a maximum output of 30 W and a commercial 1,570 nm (1.5 μm) fiber laser (IPG Photonics) with a maximum deliverable output of 11 W. The right-hand side of Fig. 5 shows the dose–response curves for these laser sources in addition to those using visible wavelengths. All of the infrared experiments resulted in significantly higher LD90 fluence levels compared with the visible lasers, and given the log scale of Fig. 5, varying experimental conditions with the 1 μm source led to comparatively larger changes in LD90 compared with the visible sources. As with the blue diode, the small spot (1.5 mm) had the highest LD90 fluence, but unlike the visible lasers, the larger spot (4 mm) offered a lower LD90 fluence compared with the baseline 2.5 mm. For the 1.5 μm source, there was insufficient mortality at the maximum power available from this source with a 2.5 mm spot and 25 ms pulse duration, so Fig. 5 shows a curve using slightly longer pulse durations to make up the additional fluence required. From the available data, it appears that the LD90 fluence levels for the 1 μm and 1.5 μm sources are at least at reasonably comparable levels.
    Effects of longer pulse durations with lower power
    We then further explored the effects of increasing the pulse duration to determine whether this could relax the optical power required from the laser source, given that laser cost is correlated with output power. Figure 6a,b show the results for the 532 nm and 1,064 nm sources, respectively, with spot diameters of 2.5 mm and pulse duration set to 25, 50, or 100 ms. In all cases, the optical power was adjusted according to the pulse duration to supply a constant pulse energy, and therefore fluence at approximately the LD75 level determined from previous experiments, which was chosen to ensure a low likelihood of any data point being 100% mortality (i.e., a saturated signal). As evidenced from Fig. 6a and Table 3, at 532 nm there was a significant drop off in mortality at the longer pulse durations, although the effect is smaller going from 50 to 100 ms compared with the initial drop from 25 to 50 ms. Similar, but smaller magnitude effects were seen with the 1 μm source in Fig. 6b and Table 3. Supplemental Fig. S2 shows that the tracking accuracy for these experiments somewhat mirrors the mortality performance, with a notable decrement from 25 to 50 ms but no significant change from 50 to 100 ms.
    Figure 6

    Mortality results for experiments with constant pulse energy achieved by proportionally adjusting the power according to pulse duration (25, 50, and 100 ms). Dosing was performed with both the (a) 532 nm and (b) 1,064 nm lasers, both using a 2.5 mm spot size, and set to the approximate LD75 fluence value from the dose–response curves (solid curves with dashed line 95% confidence intervals of logistic regression fit) from the corresponding 25 ms experiments. Error bars on individual points represent 95% confidence intervals of exact binomial probabilities. Statistical differences among mortality at the various pulse durations summarized in Table 3. The slight offsets on the x axis in (a) stem from slight changes in the beam spot size as a function of power.

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    Table 3 Results of χ2 tests for mortality equivalence among experiments with constant pulse energy but varied amounts of power and pulse duration (25, 50, and 100 ms).
    Full size table

    Comparing dosing performance across other insects
    Using the same system and procedures, experiments were also run on SWD and ACP subjects as a way of cursorily exploring laser-insect interaction for species of interest besides A. stephensi. For SWD, a full dose–response curve was created for the 1 μm laser with typical exposure settings (2.5 mm spot diameter and 25 ms pulse duration). The LD90 fluence from this work was 8.6 J/cm2, compared with 12.9 J/cm2 for A. stephensi under the same conditions. Tracking performance on SWD subjects was comparable to that for A. stephensi, given that flight parameters such as speed and acceleration were comparable as well. With ACP subjects, inducing them to fly in the cages was very difficult. As such, we could not process a sufficient number of subjects to create a proper dose–response curve. Based on the limited data available, and as demonstrated in Supplemental Video 2, the system as set for the mosquito LD90 condition with the 1 μm laser, 2.5 mm spot diameter and 25 ms pulse duration was effective in tracking and disabling the ACP subjects, despite their very different flying behavior (greater speeds and accelerations, limited durations) relative to the other test species.
    Longer range dosing system demonstration
    As a final proof of principle test, a long-range version of the system from Fig. 1 was configured. This system worked at a distance of 30 m instead of 2 m, facilitated primarily by modifying the optics used for the coarse and fine tracking systems. Given the reduced flexibility of this system, it was only used with the 1 μm laser with a 2.5 mm spot diameter and 25 ms pulse duration. Rather than acquiring new dose–response curves, which was impractical given the setup’s location in a building ~ 30 km away from the insect-housing chamber, we verified the efficacy of the system using the LD90 conditions established by short-range dosing. Supplemental Video 3 shows this system dosing an A. stephensi subject from the same stock as used for short-range testing, and Supplemental Video 4 shows the same for a wild-sourced Culex pipiens mosquito obtained in a local pond. Note that the wild C. pipiens was substantially larger in size than the lab-reared A. stephensi. In all of the limited number of tests of this system for both species (10 A. stephensi and 5 C. pipiens), the mortality rate was 100%. More

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    Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits

    1.
    Yang, J., Kloepper, J. W. & Ryu, C. M. Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci. 14, 1–4 (2009).
    ADS  CAS  PubMed  Google Scholar 
    2.
    Kearl, J. et al. Salt-tolerant halophyte rhizosphere bacteria stimulate growth of alfalfa in salty soil. Front. Microbiol. 10, 1849. https://doi.org/10.3389/fmicb.2019.01849 (2019).
    Article  PubMed  PubMed Central  Google Scholar 

    3.
    Khan, N. et al. Comparative physiological and metabolic analysis reveals a complex mechanism involved in drought tolerance in Chickpea (Cicer arietinum L.) induced by PGPR and PGRs. Sci. Rep. 9, 2097. https://doi.org/10.1038/s41598-019-38702-8 (2019).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    4.
    Compant, S., Samad, A., Faist, H. & Sessitsch, A. A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. J. Adv. Res. 19, 29–37 (2019).
    CAS  PubMed  PubMed Central  Google Scholar 

    5.
    Bruto, M., Prigent-Combaret, C., Muller, D. & Moënne-Loccoz, Y. Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Sci. Rep. 4, 6261. https://doi.org/10.1038/srep06261 (2014).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    6.
    Timmusk, S. Perspectives and challenges of microbial application for crop improvement. Front. Plant Sci. 8, 49. https://doi.org/10.3389/fpls.2017.00049 (2017).
    Article  PubMed  PubMed Central  Google Scholar 

    7.
    Sessitsch, A., Pfaffenbichler, N. & Mitter, B. Microbiome applications from lab to field: facing complexity. Trends Plant Sci. 24, 194–198 (2019).
    CAS  PubMed  Google Scholar 

    8.
    Olanrewaju, O. S., Glick, B. R. & Babalola, O. O. Mechanisms of action of plant growth promoting bacteria. World J. Microb. Biot 33, 197. https://doi.org/10.1007/s11274-017-2364-9 (2017).
    CAS  Article  Google Scholar 

    9.
    Gupta, A. et al. Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PLoS ONE 9, e104259. https://doi.org/10.1371/journal.pone.0104259 (2014).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    10.
    Pérez-Jaramillo, J. E., Carrión, V. J., de Hollander, M. & Raaijmakers, J. M. The wild side of plant microbiomes. Microbiome 6, 143. https://doi.org/10.1186/s40168-018-0519-z (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    11.
    Song, J. Y. et al. Genome sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. strain JS. J. Bacteriol. 19, 14. https://doi.org/10.1128/JB.00676-12 (2012).
    CAS  Article  Google Scholar 

    12.
    Duan, J., Jiang, W., Cheng, Z., Heikkila, J. J. & Glick, B. R. The complete genome sequence of the Plant Growth-Promoting bacterium Pseudomonas sp. UW4. PLoS ONE 8, e58640. https://doi.org/10.1371/journal.pone.0058640 (2013).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    13.
    Li, S. et al. Complete genome sequence of Paenibacillus polymyxa SQR-21, a plant growth-promoting rhizobacterium with antifungal activity and rhizosphere colonization ability. Genome Announc. 2, e00281-e314. https://doi.org/10.1128/genomeA.00281-14 (2014).
    Article  PubMed  PubMed Central  Google Scholar 

    14.
    Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
    CAS  PubMed  Google Scholar 

    15.
    Penrose, D. M. & Glick, B. R. Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol. Plantarum 118, 10–15 (2003).
    CAS  Google Scholar 

    16.
    Lo, K. J., Lin, S. S., Lu, C. W., Kuo, C. H. & Liu, C. T. Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3). Sci. Rep. 8, 12769. https://doi.org/10.1038/s41598-018-31128-8 (2018).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    17.
    Liu, W. et al. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A. Sci. Rep. 6, 20–22 (2016).
    Google Scholar 

    18.
    Andrés-Barrao, C. et al. Complete genome sequence analysis of Enterobacter sp. SA187, a plant multi-stress tolerance promoting endophytic bacterium. Front. Microbiol. 8, 2023. https://doi.org/10.3389/fmicb.2017.02023 (2017).
    Article  PubMed  PubMed Central  Google Scholar 

    19.
    Esmaeel, Q. et al. Draft genome sequence of plant growth-promoting Burkholderia sp. strain BE12, isolated from the rhizosphere of maize. Genome Announc. 6, e00299-18. https://doi.org/10.1128/genomeA.00299-18 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    20.
    Wang, Z. et al. Draft genome analysis offers insights into the mechanism by which Streptomyces chartreusis WZS021 increases drought tolerance in sugarcane. Front. Microbiol. 10, 3262. https://doi.org/10.3389/fmicb.2018.03262 (2019).
    Article  Google Scholar 

    21.
    Matteoli, F. P. et al. Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost. BMC Genomics 19, 750. https://doi.org/10.1186/s12864-018-5130-y (2018).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    22.
    Yu, Z. et al. Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T. Stand. Genomic Sci. 13, 28. https://doi.org/10.1186/s40793-018-0322-2 (2018).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    23.
    Westerman, R. L. Soil Testing and Plant Analysis. SSSA Book Series 3 3rd edn. (Madison, SSSA, 1990).
    Google Scholar 

    24.
    Bharti, N., Pandey, S. S., Barnawal, D., Patel, V. K. & Kalra, A. Plant growth promoting rhizobacteria Dietzia natronolimnaea modulates the expression of stress responsive genes providing protection of wheat from salinity stress. Sci. Rep. 6, 34768. https://doi.org/10.1038/srep34768 (2016).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    25.
    Sharma, S., Kulkarni, J. & Jha, B. Halotolerant rhizobacteria promote growth and enhance salinity tolerance in peanut. Front. Microbiol. 7, 1600. https://doi.org/10.3389/fmicb.2016.01600 (2016).
    Article  PubMed  PubMed Central  Google Scholar 

    26.
    Gupta, S. & Pandey, S. ACC Deaminase producing bacteria with multifarious plant growth promoting traits alleviates salinity stress in French Bean (Phaseolus vulgaris) plants. Front. Microbiol. 10, 1506. https://doi.org/10.3389/fmicb.2019.01506 (2019).
    Article  PubMed  PubMed Central  Google Scholar 

    27.
    Pan, J. et al. The growth promotion of two salt-tolerant plant groups with PGPR inoculation: a meta-analysis. Sustainability 11, 378. https://doi.org/10.3390/su11020378 (2019).
    CAS  Article  Google Scholar 

    28.
    Vurukonda, S. S. K. P., Vardharajula, S., Shrivastava, M. & SkZ, A. Multifunctional Pseudomonas putida strain FBKV2 from arid rhizosphere soil and its growth promotional effects on maize under drought stress. Rhizosphere 1, 4–13 (2016).
    Google Scholar 

    29.
    Marasco, R. et al. Salicornia strobilacea (synonym of Halocnemum strobilaceum) grown under different tidal regimes selects rhizosphere bacteria capable of promoting plant growth. Front. Microbiol. 7, 1286. https://doi.org/10.3389/fmicb.2016.01286 (2016).
    Article  PubMed  PubMed Central  Google Scholar 

    30.
    Mukhtar, S. et al. Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome. World J. Microb. Biot. 34, 136. https://doi.org/10.1007/s11274-018-2509-5 (2018).
    CAS  Article  Google Scholar 

    31.
    Patten, C. L. & Glick, B. R. Role of Pseudomonas putida indoleacetic acid in development of the host plant root system Appl. Environ. Microbiol. 68(3795), 3801 (2002).
    Google Scholar 

    32.
    Etesami, H., Alikhani, H. A. & Hosseini, H. M. Indole-3-acetic acid (IAA) production trait, a useful screening to select endophytic and rhizosphere competent bacteria for rice growth promoting agents. MethodsX 2, 72–78 (2015).
    PubMed  PubMed Central  Google Scholar 

    33.
    Abbamondi, G. R. et al. Plant growth-promoting effects of rhizospheric and endophytic bacteria associated with different tomato cultivars and new tomato hybrids. Chem. Biol. Technol. Agric. 3, 1. https://doi.org/10.1186/s40538-015-0051-3 (2016).
    CAS  Article  Google Scholar 

    34.
    Gupta, S. & Pandey, S. Unravelling the biochemistry and genetics of ACC deaminase-An enzyme alleviating the biotic and abiotic stress in plants. Plant gene 18, 100175. https://doi.org/10.1016/j.plgene.2019.100175 (2019).
    CAS  Article  Google Scholar 

    35.
    Khamna, S., Yokota, A., Peberdy, J. F. & Lumyong, S. Indole-3-acetic acid production by Streptomyces sp. isolated from some Thai medicinal plant rhizosphere soils. EurAsian J. BioSciences 4, 23–32 (2010).
    CAS  Google Scholar 

    36.
    Spaepen, S. & Vanderleyden, J. Auxin and plant-microbe interactions. C. S. H. Perspect. Biol. 3, a001438. https://doi.org/10.1101/cshperspect.a001438 (2011).
    CAS  Article  Google Scholar 

    37.
    Patten, C. L. & Glick, B. R. Bacterial biosynthesis of indole-3-acetic acid. Can. J. Microbiol. 42, 207–220 (1996).
    CAS  PubMed  Google Scholar 

    38.
    Majeed, A., Abbasi, K. M., Hameed, S., Imran, A. & Rahim, N. Isolation and characterization of plant growth-promoting rhizobacteria from wheat rhizosphere and their effect on plant growth promotion. Front. Microbiol. 6, 198. https://doi.org/10.3389/fmicb.2015.00198 (2015).
    Article  PubMed  PubMed Central  Google Scholar 

    39.
    Apine, O. A. & Jadhav, J. P. Optimization of medium for indole-3-acetic acid production using Pantoea agglomerans strain PVM. J. Appl. Microbiol. 110, 1235–1244 (2011).
    CAS  PubMed  Google Scholar 

    40.
    Checcucci, A. et al. Role and regulation of ACC deaminase gene in Sinorhizobium melilotr: Is it a symbiotic, rhizospheric or endophytic gene?. Front. Genet. 8, 6. https://doi.org/10.3389/fgene.2017.00006 (2017).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    41.
    Belimov, A. A. et al. Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.). Soil Biol. Biochem. 37, 241–250 (2005).
    CAS  Google Scholar 

    42.
    Khan, N. A., Khan, M. I. R., Ferrante, A. & Poor, P. Editorial: ethylene: a key regulatory molecule in plants. Front. Plant Sci. 8, 1782. https://doi.org/10.3389/fpls.2017.01782 (2017).
    Article  PubMed  PubMed Central  Google Scholar 

    43.
    Glick, B. R. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol. Res. 169, 30–39 (2014).
    CAS  PubMed  Google Scholar 

    44.
    Wang, Z. et al. Isolation and characterization of a phosphorus-solubilizing bacterium from rhizosphere soils and its colonization of Chinese Cabbage (Brassica campestris ssp. chinensis). Front. Microbiol. 8, 1270. https://doi.org/10.3389/fmicb.2017.01270 (2017).
    Article  PubMed  PubMed Central  Google Scholar 

    45.
    Dinesh, R. et al. Isolation, characterization, and evaluation of multi-trait plant growth promoting rhizobacteria for their growth promoting and disease suppressing effects on ginger. Microbiol. Res. 173, 34–43 (2015).
    PubMed  Google Scholar 

    46.
    Niu, X., Song, L., Xiao, Y. & Ge, W. Drought-tolerant plant growth-promoting rhizobacteria associated with foxtail millet in a semi-arid agroecosystem and their potential in alleviating drought stress. Front. Microbiol. 8, 2580. https://doi.org/10.3389/fmicb.2017.02580 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    47.
    Singh, V. K., Singh, A. K., Singh, P. P. & Kumar, A. Interaction of plant growth promoting bacteria with tomato under abiotic stress: a review. Agricult. Ecosyst. Environ. 267, 129–140 (2018).
    CAS  Google Scholar 

    48.
    Grover, M., Bodhankar, S., Maheswari, M. & Srinivasarao, C. Actinomycetes as mitigators of climate change and abiotic stress. In Plant Growth Promoting Actinobacteria: A New Avenue for Enhancing the Productivity and Soil Fertility of Grain Legumes (eds Subramaniam, G. et al.) 203–212 (Springer, Berlin, 2016).
    Google Scholar 

    49.
    Sang, M. K., Jeong, J. J., Kim, J. & Kim, K. D. Growth promotion and root colonisation in pepper plants by phosphate-solubilising Chryseobacterium sp strain ISE14 that suppresses Phytophthora blight. Ann. Appl. Biol. 172, 208–223 (2018).
    CAS  Google Scholar 

    50.
    Xiao, X., Fan, M., Wang, E., Chen, W. & Wei, G. Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants. Appl. Microbiol. Biot. 101, 8485–8497 (2017).
    CAS  Google Scholar 

    51.
    Abdelkrim, S. et al. Effect of Pb-resistant plant growth-promoting rhizobacteria inoculation on growth and lead uptake by Lathyrus sativus. J. Basic Microb. 58, 579–589 (2018).
    CAS  Google Scholar 

    52.
    Liu, Y. et al. Characterization of Lysobacter capsici strain NF87–2 and its biocontrol activities against phytopathogens. Eur. J. Plant Pathol. 155, 859–869 (2019).
    CAS  Google Scholar 

    53.
    Edgar, R. C. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ. https://doi.org/10.7717/peerj.4652 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    54.
    Lee, Z. M., Bussema, C. III. & Schmidt, T. M. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. 37, D489–D493 (2008).
    PubMed  PubMed Central  Google Scholar 

    55.
    Shen, X., Hu, H., Peng, H., Wang, W. & Zhang, X. Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics 14, 271. https://doi.org/10.1186/1471-2164-14-271 (2013).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    56.
    Niazi, A. et al. Genome analysis of Bacillus amyloliquefaciens subsp. Plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management. PloS ONE 9, e104651. https://doi.org/10.1371/journal.pone.0104651 (2014).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    57.
    Riggs, P. J., Chelius, M. K., Leonardo, I. A., Kaeppler, S. M. & Triplett, E. W. Enhanced maize productivity by inoculation with diazotrophic bacteria. Funct. Plant Biol. 28, 829–836 (2001).
    Google Scholar 

    58.
    Saleem, M., Arshad, M., Hussain, S. & Bhatti, A. S. Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. J. Ind. Microbiol. Biot. 34, 635–648 (2007).
    CAS  Google Scholar 

    59.
    Dorjey, S., Gupta, V. & Razdan, V. K. Evaluation of Pseudomonas fluorescens isolates for the management of Fusarium oxysporum f.sp. lycopersici and Rhizoctonia solani causing wilt complex in tomato. Indian Phytopathol. 70, 127–130 (2017).
    Google Scholar 

    60.
    Dardanelli, M. S. et al. Changes in flavonoids secreted by Phaseolus vulgaris roots in the presence of salt and the plant growth-promoting rhizobacterium Chryseobacterium balustinum. Appl. Soil Ecol. 75, 31–38 (2012).
    Google Scholar 

    61.
    Ogut, M., Er, F. & Brohi, A. Excessive phosphorus fertilization does not increase cadmium concentrations in soil or carrots (Daucus carota L.) grown in Konya (Turkey). Acta Agr. Scand B-S.P. 60, 420–426 (2010).
    CAS  Google Scholar 

    62.
    Rodríguez, H., Fraga, R., Gonzalez, T. & Bashan, Y. Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil 287, 15–21 (2006).
    Google Scholar 

    63.
    Kalayu, G. Phosphate solubilizing microorganisms: Promising approach as biofertilizers. Int. J. Agron. 2019, 4917256. https://doi.org/10.1155/2019/4917256 (2019).
    CAS  Article  Google Scholar 

    64.
    Mellidou, I. et al. Silencing S-adenosyl-L-methionine decarboxylase (SAMDC) in Nicotiana tabacum points at a polyamine-dependent trade-off between growth and tolerance responses. Front. Plant Sci. 7, 379. https://doi.org/10.3389/fpls.2016.00379 (2016).
    Article  PubMed  PubMed Central  Google Scholar 

    65.
    Michael, A. J. Biosynthesis of polyamines and polyamine-containing molecules. Biochem. J. 473, 2315–2329 (2016).
    CAS  PubMed  Google Scholar 

    66.
    Nascimento, F. X., Hernández, A. G., Glick, B. R. & Rossi, M. J. Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. Biotechnol. Rep. 25, e00406. https://doi.org/10.1016/j.btre.2019.e00406 (2020).
    Article  Google Scholar 

    67.
    Goswami, R. et al. Optimization of growth determinants of a potent cellulolytic bacterium isolated from lignocellulosic biomass for enhancing biogas production. Clean Technol. Envir. 18, 1565–1583 (2016).
    CAS  Google Scholar 

    68.
    Vokou, D., Giannakou, U., Kontaxi, C. & Vareltzidou, S. Axios. Aliakmon and gallikos delta complex, Νorthern Greece. In Encyclopedia of Wetlands, Vol. 4 World Wetlands (eds Finlayson, M. et al.) (Springer, Berlin, 2016).
    Google Scholar 

    69.
    Mellidou, I., Keulemans, J., Kanellis, A. & Davey, M. W. Regulation of fruit ascorbic acid concentrations in high and low vitamin C tomato cultivars during ripening. BMC Plant Biol. 12, 239–258 (2012).
    CAS  PubMed  PubMed Central  Google Scholar 

    70.
    Bouyoucos, G. J. Hydrometer method improved for making particle size analysis of soils. Agron. J. 54, 464–465 (1962).
    Google Scholar 

    71.
    Sparks, D. L. Methods of Soil Analysis – Part 3 – Chemical Methods, SSSA Book Series 5 (ASA. Madison, WI, SSSA, 1996).
    Google Scholar 

    72.
    Karamanoli, K., Bouligaraki, P., Constantinidou, H. I. & Lindow, S. E. Polyphenolic compounds on leaves limit iron availability and affect growth of epiphytic bacteria. Ann. Appl. Biol. 159, 99–108 (2011).
    CAS  Google Scholar 

    73.
    Eevers, N. et al. Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media. Microb. Biotechnol. 8, 707–715 (2015).
    CAS  PubMed  PubMed Central  Google Scholar 

    74.
    Louden, B. C., Haarmann, D. & Lynne, A. M. Use of blue agar CAS assay for siderophore detection. J. Microbiol. Biol. Educ. 12, 51. https://doi.org/10.1128/jmbe.v12i1.249 (2011).
    Article  PubMed  PubMed Central  Google Scholar 

    75.
    García, C. A., De Rossi, B. P., Alcaraz, E., Vay, C. & Franco, M. Siderophores of Stenotrophomonas maltophilia: detection and determination of their chemical nature. Rev. Argent. Microbiol. 44, 150–154 (2012).
    PubMed  Google Scholar 

    76.
    Dworkin, M. & Foster, J. Experiments with some microorganisms which utilize ethane and hydrogen. J. Bacteriol. 75, 592–601 (1958).
    CAS  PubMed  PubMed Central  Google Scholar 

    77.
    Hontzeas, N., Zoidakis, J., Glick, B. R. & Abu-Omar, M. M. Expression and characterization of 1-aminocyclopropane-1-carboxylate deaminase from the rhizobacterium Pseudomonas putida UW4: a key enzyme in bacterial plant growth promotion. Biochim. Biophys. Acta 1703, 11–19 (2004).
    CAS  PubMed  Google Scholar 

    78.
    Bradford, M. A rapid and sensitive method for the quantitation of micro gram quantities of protein utilizing the principle of protein—dye binding. Anal. Biochem. 72, 248–258 (1976).
    CAS  Google Scholar 

    79.
    Nautiyal, C. S. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol. Lett. 170, 265–270 (1999).
    CAS  PubMed  Google Scholar 

    80.
    Luziatelli, F., Ficca, A. G., Colla, G., Švecová, E. B. & Ruzzi, M. Foliar application of vegetal-derived bioactive compounds stimulates the growth of beneficial bacteria and enhances microbiome biodiversity in lettuce. Front. Plant Sci. 10, 60. https://doi.org/10.3389/fpls.2019.00060 (2019).
    Article  PubMed  PubMed Central  Google Scholar 

    81.
    Herlemann, D. P. R. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).
    CAS  PubMed  PubMed Central  Google Scholar 

    82.
    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
    CAS  PubMed  Google Scholar 

    83.
    Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2, W537–W544 (2018).
    Google Scholar 

    84.
    Li, D. et al. MEGAHIT v.10: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 1, 3–11 (2016).
    Google Scholar 

    85.
    Seeman, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 15, 2068–2069 (2014).
    Google Scholar 

    86.
    Thompson, J. D., Gibson, T. J. & Higgins, D. G. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinform. https://doi.org/10.1002/0471250953.bi0203s00 (2002).
    Article  Google Scholar 

    87.
    Hall, T. A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acid S. 41, 95–98 (1999).
    CAS  Google Scholar 

    88.
    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
    CAS  PubMed  PubMed Central  Google Scholar 

    89.
    Felsenstein, J. Confidence limits on phylogenies: an approach using the Bootstrap. Evolution 39, 783–791 (1985).
    PubMed  PubMed Central  Google Scholar 

    90.
    Wu, S., Zhu, Z., Fu, L., Niu, B. & Li, W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12, 444. https://doi.org/10.1186/1471-2164-12-444 (2011).
    Article  PubMed  PubMed Central  Google Scholar 

    91.
    Kamou, N. N. et al. Isolation screening and characterisation of local beneficial rhizobacteria based upon their ability to suppress the growth of Fusarium oxysporum f. sp. radicis-lycopersici and tomato foot and root rot. Biocontrol Sci. Technol. 25(8), 928–949 (2015).
    Google Scholar  More

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    Long-term application of fertilizer and manures affect P fractions in Mollisol

    Total P and available P
    Fertilizer application significantly (P  0.05). The highest increase in available P concentration in NPK + S treatment observed in the 60–100 cm soil depth, with the increase of 111% and 115% in 60–80 cm and 80–100 cm soil depths, respectively, over CK treatment.
    Figure 2

    Effect of long-term application of chemical fertilizer, organic manure, and straw on total phosphorus (P) and available P concentrations. * indicates significant difference at P  3.6%) was associated with OM treatment, especially at the 0–20 and 20–40 cm soil depths (Fig. 3). The PAC values under NPK, NPK + S and OM treatments increased by 7.6%, 4.5% and 11.5% in the 0–20 cm soil depth and 4.2%, 1.3%, and 5.8% in 20–40 cm soil depth, respectively as compared to the CK treatment. However, PAC value for soil depth below 40 cm showed the trend, NPK  More

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    A recipe to reverse the loss of nature

    NEWS AND VIEWS
    09 September 2020

    How can the decline in global biodiversity be reversed, given the need to supply food? Computer modelling provides a way to assess the effectiveness of combining various conservation and food-system interventions to tackle this issue.

    Brett A. Bryan &

    Brett A. Bryan is at the Centre for Integrative Ecology, Deakin University, Melbourne, Victoria 3125, Australia.
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    Carla L. Archibald

    Carla L. Archibald is at the Centre for Integrative Ecology, Deakin University, Melbourne, Victoria 3125, Australia.

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    Nature is in trouble, and its plight will probably become even more precarious unless we do something about it1. Writing in Nature, Leclère et al.2 quantify what might be needed to reverse this deeply worrying path while also feeding people’s increasingly voracious appetites. The authors’ answer is to team ambitious conservation measures with food-system transformation in the hope of reversing the trend of global terrestrial biodiversity loss.

    By nature, we mean the diversity of life that has evolved over billions of years to exist in dynamic balance with Earth’s biophysical environment and the ecosystems present. Nature contributes to human well-being in many ways, and the services it provides, such as carbon sequestration by plants or pollination by insects, could impose a vast cost if lost3. Although the slow and long-term decline of Earth’s biodiversity4 is often overshadowed by climate change, and more recently by the COVID-19 pandemic, the loss of biodiversity is no less of a risk than those posed by the other challenges. Many would argue that the effect of biodiversity losses could surpass the combined impacts of climate change and COVID-19.
    More and more, the realization is growing that, as a planet, we are what we eat. Human demand for food is accelerating with the ever-increasing global population (projected to approach 10 billion by 2050), and each successive generation is wealthier and consumes more resource-intensive diets than did the previous one5. Trying to balance this rapidly rising demand against the limited amount of land available for crops and pasture sets agriculture and nature (Fig. 1) on a collision course6. As Leclère and colleagues show, a bold and integrated strategy is required immediately to turn this around.

    Figure 1 | A bean field bordering a rainforest reserve near Sorriso, Brazil.Credit: Florian Plaucheur/AFP/Getty

    Taking a long view out to the year 2100, Leclère et al. present a global modelling study assessing the ability of ambitious conservation and food-system intervention scenarios to reverse the decline, or, as they call it, “bending the curve”, of biodiversity losses resulting from changes in agricultural land use and management. Projections of future land use and biodiversity are uncertain, and when these models are combined, this uncertainty is compounded. One of the great innovations of Leclère and colleagues’ work is in embracing this uncertainty by combining an ensemble of four global land-use models and eight global biodiversity models and measuring the performance of future land-use scenarios in terms of higher-level model-independent metrics such as the amount of biodiversity loss avoided.
    Importantly, the study also included a baseline (termed BASE) scenario — the world expected without interventions — and Leclère et al. used this to gauge the effectiveness of the intervention scenarios. Although it is not a focus of the paper, it’s worth pausing to ponder the sobering picture painted by this business-as-usual future largely bereft of birdsong and insect chirp.
    Choosing to act now can make a difference to nature’s plight. Most (61%) of the model combinations run by the authors indicated that implementing ambitious conservation actions led to a positive uptick in the biodiversity curve by 2050. Such conservation actions included: extending the global conservation network by establishing protected nature reserves; restoring degraded land; and basing future land-use decisions on comprehensive landscape-level conservation planning. This comprehensive conservation strategy avoids more than half (an average of 58%) of the biodiversity losses expected if nothing is done, but also leads to a hike in food prices.

    When conservation actions were teamed with a range of equally ambitious food-system interventions, the prognosis for global biodiversity in the model was improved further. Including both supply- and demand-side measures, these approaches included boosting agricultural yields, having an increasingly globalized food trade, reducing food waste by half, and the global adoption of healthy diets by halving meat consumption. These combined measures of conservation and food-systems actions avoided more than two-thirds of future biodiversity losses, with the integrated action portfolio (combining all actions) avoiding an average of 90% of future biodiversity losses. Almost all models predicted a biodiversity about-face by mid-century. These food-system measures also avoided adverse outcomes for food affordability.
    Leclère and colleagues’ work complements the current global climate-change scenario framework (tools for future planning by governments and others, including scenarios called shared socio-economic pathways, which integrate future socio-economic projections with greenhouse-gas emissions), and represents the most comprehensive incorporation of biodiversity into this scenario framing7 so far. However, a major limitation of the present study is that it does not consider the potential impact of climate change on biodiversity. This raises an internal inconsistency because, on the one hand, the baseline scenario considers land-use, social and economic changes under approximately 4 °C of global heating by 21008, yet, on the other hand, it does not consider the profound effect of warming on plant and animal populations and the ecosystems they comprise9. Also absent from the models were other threats to biodiversity, including harvesting, hunting and invasive species10. Although Leclère and colleagues recognized these limitations and assigned them a high priority for future research, unfortunately for us all, omitting these key threats probably means that the authors’ estimates of biodiversity’s plight and the effectiveness of integrated global conservation and food-system action are overly optimistic. To truly bend the curve, Leclère and colleagues’ integrated portfolio will need to be substantially expanded to address the full range of threats to biodiversity.
    Although the models say that a better future is possible, is the combination of the multiple ambitious conservation and food-system interventions considered by Leclère et al. a realistic possibility? Achieving each one of the conservation and food-system actions would require a monumental coordinated effort from all nations. And even if the global community were to get its act together in prioritizing conservation and food-system transformation, would such efforts come in time and be enough to save our planet’s natural legacy? We certainly hope so.

    doi: 10.1038/d41586-020-02502-2

    References

    1.
    Díaz, S. et al. Science 366, eaax3100 (2019).

    2.
    Leclère, D. et al. Nature https://doi.org/10.1038/s41586-020-2705-y (2020).

    3.
    Costanza, R. et al. Glob. Environ. Change Hum. Policy Dimens. 26, 152–158 (2014).

    4.
    Butchart, S. H. M. et al. Science 328, 1164–1168 (2010).

    5.
    Springmann, M. et al. Nature 562, 519–525 (2018).

    6.
    Montesino Pouzols, F. et al. Nature 516, 383–386 (2014).

    7.
    Kok, M. T. J. et al. Biol. Conserv. 221, 137–150 (2018).

    8.
    Leclère, D. et al. Towards Pathways Bending the Curve of Terrestrial Biodiversity Trends Within the 21st Century https://doi.org/10.22022/ESM/04-2018.15241 (Int. Inst. Appl. Syst. Analysis, 2018).

    9.
    Warren, R., Price, J., Graham, E., Forstenhaeusler, N. & VanDerWal, J. Science 360, 791–795 (2018).

    10.
    Driscoll, D. A. et al. Nature Ecol. Evol. 2, 775–781 (2018).

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    Assessing the effect of wind farms in fauna with a mathematical model

    Multiple statistical methods have been developed to estimate the effect on birds and bats as a result of wind energy during the last 20 years26,27,28,29,30,31. Some of these studies are focused on the conservation status of the species32, the incidence factor of the wind turbines19,33, demographic parameters34,35, behavioural12 and also morphological parameters of the species36,37. In any case, it is essential to group all types of affections in order to be able to establish a global quantification that can be adapted to each species and to each specific wind farm. In other words, it can be obtained from a mathematical algorithm that allows quantifying the effect on each species, taking into account the characteristics of each wind farm3.
    Furthermore, the formula that reflects the effect on the species must consider aspects related to the wind farm itself (type and distribution of turbines, occupation of the territory, etc.) and those related to the species, both in terms of its degree of threat and social importance, as well as its special sensitivity to the presence of the wind farm. According to this, the affection to each species must respond to the following formula:

    $${text{AS}}_{{text{I}}} = {text{WF}}left( {{text{SS}}_{{text{I}}} + {text{VS}}_{{text{I}}} } right)$$

    where ASI = Affection to species i, WF = Constant derived from the characteristics of the wind farm, SSI = Sensitivity of the species i to the presence of the wind farm, VSI = Social value of species i.
    The index of affection, therefore, will be the product of multiplying the obtained values by the wind farm with those of each species that is present in the area.
    Wind farm value constant (WF)
    The impact value of the wind farm will be determined by the characteristics of the wind farm and also be influenced by both the characteristics of the wind farm (VWF) and its location (UF). At the same time, the VWF will be determined both by the affection of each wind turbine (WT) and by the distribution within the wind farm (extension and lines of turbines).

    $${text{WF}} = {text{VWF}} + {text{UF}}$$

    Value of the wind farm (VWF)
    To calculate the overall effect of the wind farm not only is necessary to know the effect of each turbine but also its distribution in space. It is relevant to assess the distances between the wind turbine and if they are or not operating because when the turbines are very close together, the risk of moving between them is greater than in wind farms with more separate wind turbines38 and to know the number of rows in which the turbine are distributed. Crossing a wind farm with a single line of wind turbines is easier than those wind farms with several consecutive rows39. For this reason, the global affection of the wind farm (VWF) is understood as:
    1.
    The individual value of each of the wind turbine (WT) multiplied by the number of existing turbines.

    2.
    The total area occupied by the wind farm (AWF); in this way, it is not only considered the whole area of affection but also is established the density of the wind turbines.

    3.
    The number of rows that are included in the wind farm.

    Based on the preceding information, the proposed formula for assessing the characteristics of the wind farm is:

    $${text{VWF}} = left( {left( {{text{Ni}}*{text{WTi}}} right)/{text{AWF}}} right)^{{{1}/{text{F}}}}$$

    where Ni: Number of wind turbines. WTi: Incidence of each wind turbines (the WT value will be the same for all unless in the same wind farm there were different types of wind turbines with different affection areas). AWF: Total surface of the area of study understood as the area formed by the vertical rectangle created between the furthest wind turbines from the same front line and the height of them. In the case of wind farms with more than one row, the total surface area is calculated as the sum of the surfaces of each row. F = Number of lines forming the wind farm.
    Of these variables considered in the previous formula, it is only necessary to develop the affection inherent to each wind turbine (WT) that has to be calculated considering both the area of the turbine’s affection and the rotation speed of the blades.

    $${text{WT}} = {text{AFM}}*{text{BRS}}$$

    where AFM: Area of affection of each wind turbines, BRS: Blade rotation speed.
    The area of affection of each turbine is the surface of the circumference formed by the blades (a), plus the surface of the triangle formed by the blades with the ground when they form an angle of 60° with the support tower (b), minus the intersection of both surfaces (c) (Fig. 3):

    $${text{AFM}} = {text{a}} + {text{b}}{-}{text{c}}$$

    Figure 3

    Scheme and values to calculate the area of affection of each wind turbine. The area of affection of each turbine is the surface of the circumference formed by the blades (a), plus the surface of the triangle formed by the blades with the ground when they form an angle of 60° with the support tower (b), minus the intersection of both surfaces (c).

    Full size image

    Figure 4

    Zoning scheme of risk areas. ZONE I: Corresponds to the free height between the ground and the blades. ZONE II: This zone corresponds to the area of the circumference formed by the blades when turning. ZONE III: Corresponds to the free height above the blades so that this interval is above the previous interval.

    Full size image

    Being: a = πr2   b = (sen60°*r)(L − cos 60° * r), where r is the length of the blades and L the height of the support tower. c = ((πr2/3) − ((sen60° * r)(cos 60° * r))).
    To calculate the affection of the rotation speed of the blades (SB) it is assumed that the greater the rotation speed, the greater the turbulence and the greater the risk for the fauna19,40. In any case, this incidence is not linear but exponential since from a certain speed the affection can be considered high. To calculate this value, we established the following formula:

    $${text{BRS}} = {1} + {text{Log}}left( {{text{SB}}} right)$$

    Given that the value of the wind Farm (VWF) is the quotient between the sum of the areas affected by each turbine and the total area occupied, the value generally will be less than 1. In cases where the value is greater (when the surface area of the turbine multiplied by the rotation speed of the turbine is greater than the total surface of the area) it will be equal to 1. i.e., the maximum surface area affected cannot be greater than the surface area occupied by the total wind farm.
    Location in the natural environment (UF)
    Many works show the importance of selecting the location of the wind farm to minimize its impact on birdlife. However, it is possible that wind farms may be authorized in sensitive areas or in areas with poor environmental conditions (predominance of fog) or that have synergistic effects with adjacent wind farms. In this sense and as indicated in the introduction, there are four factors that can influence this impact: low visibility, proximity to sensitive areas, location in migratory crossings and synergies with other wind farms. Therefore, the value of this variable should be at least the same as that established for the previous variable (VWF). In this regard, it is proposed that the maximum value of the variables used to compute this factor should also be 1.

    Visibility (VI): This variable measures the frequency of days with low visibility (fog, intense rain, etc.) compared with the total number of observation days (total number of days with low visibility/total number of observation days). The maximum value is 0.25.

    Proximity to sensitive areas (ZS): Sensitive areas are those in which occur high concentrations of individuals, either because they are breeding areas, feeding areas, resting areas or roosts. Protected areas such as IBAS or LICs may also be considered. Not all species have the same radius of action, so setting a minimum radius of affection can only be established randomly. For example, for some species a radius of influence of 10 km is small but for others can be large. In any case and for having a uniform criterion, it will be considered that a sensitive area is close to the wind farm when it is located less than 10 km4, in this case, the value of this variable will be 0.25 and if they are between 10 and 50 km the value will be 0.15 while if it is more than 50 km is considered that the location of the wind farm does not influence these areas (value 0).

    Migratory passes (MP): Migratory passes are those areas used by avian fauna for their daily or migratory movements. If the wind farm is located in one of these Migratory passes, the effect will be high so it will be valued with a maximum value (0.25) and the value will be minimal (0) if this is not the case.

    Proximity to other wind farms (PWF): It is relevant to include this variable because of the proximity of different wind farms cause negative synergistic effects on the species by limiting the length of possible free corridors of wind turbines. In this way, the location of another wind farm less than 3 km away is considered very negative (0.25), between 3 and 5 km (0.15), between 5 and 10 km (0.10) and more than 10 km (0), it does not affect. If there is more than one wind farm in the area, the value will increase 0.25 if it is between 3 and 5 km and 0.15 if it is between 5 and 10 km.

    $${text{UF}} = {text{VI}} + {text{ZS}} + {text{MP}} + {text{PWF}}$$

    where WT: Value related to the location of the wind farm. VI: Predominant visibility in the area. ZS: Presence of sensitive areas in the vicinity of the wind farm. MS = Incidence of the wind farm in migratory crossings. PWF: Proximity to wind farms.

    The possible maximum value for the wind farm location will be 1.
    Therefore, the possible maximum value inherent in the characteristics and location of the wind farm will be 2. Substituting the values in the proposed formula:

    $${text{WF}} = {text{VWF}} + {text{UF}}$$

    And considering the values obtained for each mill, the wind farm in general and its location, the result is the following formula:

    $${text{WF}} = left( {left( {{text{Ni}}*{text{IMi}}} right)/{text{AWF}}} right)^{{{1}/{text{F}}}} + left( {{text{VI}} + {text{ZS}} + {text{MP}} + {text{PWF}}} right)$$

    Affection on the species
    Not all species have the same sensitivity to the presence of the wind farm, being some of them more sensitive than others (25). On the other hand, the incidence on endangered species is not the same as that on species with stable populations in the area so, it is necessary to differentiate two types of variables related to the species: those related to the special sensitivity of each species to the presence of these infrastructures (SS) and the one inherent to its degree of threat, conservation or socioeconomic interest (VS). The affection value of each species will be the sum of the values of each type of variable. Therefore, the value of this section will be:

    $${text{Affection}};{text{to}};{text{the}};{text{species}} = left( {{text{SS }} + {text{ VS}}} right)$$

    Sensitivity of the species to the wind farm (SS)
    These variables will be considered as the impact of the wind farm on each species due to its morphological, ethological, historical and demographic characteristics, etc. It is the closest thing to what could be understood as collision risk since it assesses the different characteristics of each bird (morphological, ethological, demographic, etc.) based on the risk of colliding with wind turbines and, valuing more those characteristics that enhance the probability of collision.
    Bird size will be considered in this variable. A higher percentage of affection is detected on large birds in the majority of the recorder monitoring of the incidence of wind farms. However, this value seems to be overestimated since the detectability of carcasses of small birds and bats is lower as they remain less time on the ground30,41,42.
    On the other hand, small birds show much less resistance to wind flows generated by the blades so it seems logical to think that the affection on this group of birds and on bats is higher. For this reason, a greater impact on small species has been assessed.
    As a reference size, those birds smaller than or equal to a turtledove have been considered as small birds; medium-sized birds are those whose sizes are between a turtledove and a heron while those larger than a heron are considered as large birds. Considering these aspects:
    The behaviour of different species will influence their risk of collision increasing the possibility of being affected by wind turbines38, for example, species that tend to go in groups show a greater risk of collision. The phenological characteristics of species are also important, for example, those species that are only in passage (prenuptial and postnuptial) will be little time in the study area but as they are not accustomed to the presence of wind turbines, probability of collision is high and possibly increased by going in large groups. Breeding species in the area are more dangerous because the young ones, still inexperienced in flight, show high risks of collision1. In other words, variables reflected in this section are related to the time the species spends in the area38, its dexterity in flight and its gregariousness. Together with these variables, the type of flight carried out by each species has been also considered: direct flights avoid staying longer in the area while cycloid or indirect movements increase the possibility of collision.

    Seasonality: It considers the number of months in which the species is detected in the area. The maximum value is 1 if the species is sedentary (12 months) so each month is valued as 0.083.

    Phenology: Marks the periods in which the species is present in the area. It is considered that species present in the breeding season or in passage show a greater risk than those that are only wintering. In this sense, if the species is in the breeding season will be valued with 0.75, only in winter 0.25 and 0.5 only in passage. When it appears in all seasons or in three of them, the value will be maximum (1). The value of the station will be also maximum if appears in two periods.

    Flight height: In order to calculate flight height with risk for each species, the characteristics of each wind farm are considered. That is to say, they have to be adjusted to each wind farm since the interval of each zone will vary according to these ones. In this sense, for example, small birds that fly at lower altitudes can be located in the lower zone or not depending on the wind farm, just as large birds can be located in the area of the blades or above. In this sense, three zones have been established (Fig. 4):

    ZONE I: Corresponds to the free height between the ground and the blades so, this interval goes from 0 m to the height resulting from subtracting the size of the blade from the length of the support tower. Value 0.5

    ZONE II: This zone corresponds to the area with the greatest risk of collision since it is equivalent to the circumference formed by the blades when turning. Therefore, the interval will go from the previous height to its sum with the diameter of the circumference formed by the blades. Value: 1.

    ZONE III: Corresponds to the free height above the blades so that this interval is above the previous interval. Value: 0.

    When a species presents different flight heights, the one more frequent and that presents the greater risk will be selected.

    Type of flight: Direct flights are considered to have a lower risk of collision than those that cause a longer stay in the area. The values will be 0.25 in direct flights and 0.5 in indirect flight.

    Flock size: The risk of collision is considered higher when species show large groups so the following classification is established: One individual: 0.25; groups of 2–5 individuals: 0.5; groups of 6–10 individuals: 0.75; groups of more than 10 individuals: 1.

    Historical variables (Maximum value 2).

    A variable related to mortality detected in previous studies has also been included. Those species that are systematically detected in the mortality reviews of these infrastructures or exist high figures of mortality due to collision in specific wind farms should be considered.

    Species with previous collision data (usual 2; medium 1; scarce 0.5; no record 0). This value is established at the discretion of the technician who performs the assessment, but as a habitual criterion, it can be considered as usual when the species appears in most of the studies (more than 30% of the studies), between 15 and 30% of the studies on average; and it will be classified as scarce if it only appears between 1 and 15% of the studies.

    The last variables considered are related to the incidence on population parameters of each species. It has been considered that the species with reproductive strategy R suffer a lower incidence on the populations (although the mortality may be higher) since their reproductive efficiency partly solves this loss. However, species with K strategy suffer enormously when the mortality of young individuals is high. On the other hand, those species that frequently use the area where the wind turbines are located will show a higher probability of collision than those that are less common and those species that have high abundances in the area have also a higher probability of impact than those with few individuals16.

    Survival-Fertility (type K or R) (K = 0.5; R = 0.2).

    Frequency: This variable measures the frequency with which each species appears in the area in relation to the rest of the species present (total number of presences of the species/total number of presences detected). The maximum value is 1.

    Abundance of the species in the area (number of individuals detected of the species i/total number of individuals detected of all species) (maximum value 1).

    Species value (VS)
    This value will include the conservation and socio-economic importance of the species (including the hunting value or social interest of some species). The affections on those species that are in a situation of greater risk of extinction must be considered in a relevant way, since the loss of a few individuals can represent the unfeasibility of the population. In this respect, both the degree of threat and the legal cataloguing of the different species have been considered.
    The maximum value of this variable is much higher than the rest of variables since those species with the maximum protection value or degree of threat will have a value of 9. The cataloguing according to the Red Books will relate to the value established in Table 143. It has also been considered necessary to assess the socio-economic importance of some species. In this regard, it is taken into account not only the importance of hunting, which is relevant for some species of birds, but also its social importance, that is to say, those species which have conservation or recovery plans established in areas close to the different administrations or which are especially valued by the population, although their threat level is not very high (colonies of birds especially loved by the local population, etc.).
    Table 1 Values given to the different classifications or threat level.
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    A global-scale data set of mining areas

    1.
    Giljum, S., Dittrich, M., Lieber, M. & Lutter, S. Global patterns of material flows and their socio-economic and environmental implications: A MFA study on all countries world-wide from 1980 to 2009. Resources 3, 319–339 (2014).
    Article  Google Scholar 
    2.
    IRP, U. Global Resources Outlook 2019: Natural Resources for the Future we Want. A Report of the International Resource Panel. Report No. DTI/2226/NA (United Nations Environment Programme, 2019).

    3.
    Krausmann, F., Schandl, H., Eisenmenger, N., Giljum, S. & Jackson, T. Material flow accounting: Measuring global material use for sustainable development. Ann. Rev. Env. Resour. 42, 647–675 (2017).
    Article  Google Scholar 

    4.
    Calvo, G., Mudd, G., Valero, A. & Valero, A. Decreasing ore grades in global metallic mining: A theoretical issue or a global reality? Resources 5 (2016).

    5.
    Prior, T., Giurco, D., Mudd, G., Mason, L. & Behrisch, J. Resource depletion, peak minerals and the implications for sustainable resource management. Glob. Environ. Change 22, 577–587 (2012).
    Article  Google Scholar 

    6.
    West, J. Decreasing metal ore grades. J. Ind. Ecol. 15, 165–168 (2011).
    Article  Google Scholar 

    7.
    Mudd, G. M. Global trends in gold mining: Towards quantifying environmental and resource sustainability. Resour. Policy 32, 42–56 (2007).
    Article  Google Scholar 

    8.
    Sonter, L. J., Moran, C. J., Barrett, D. J. & Soares-Filho, B. S. Processes of land use change in mining regions. J. Clean. Prod. 84, 494–501 (2014).
    Article  Google Scholar 

    9.
    Werner, T., Bebbington, A. & Gregory, G. Assessing impacts of mining: Recent contributions from GIS and remote sensing. Extract. Indus. Soc. 6, 993–1012 (2019).
    Article  Google Scholar 

    10.
    Kobayashi, H., Watando, H. & Kakimoto, M. A global extent site-level analysis of land cover and protected area overlap with mining activities as an indicator of biodiversity pressure. J. Clean. Prod. 84, 459–468 (2014).
    Article  Google Scholar 

    11.
    Sonter, L. J., Ali, S. H. & Watson, J. E. M. Mining and biodiversity: key issues and research needs in conservation science. Proc. Biol. Sci. 285 (2018).

    12.
    Islam, K., Vilaysouk, X. & Murakami, S. Integrating remote sensing and life cycle assessment to quantify the environmental impacts of copper-silver-gold mining: A case study from laos. Resour. Conserv. Recy. 154, 104630 (2020).
    Article  Google Scholar 

    13.
    Butt, N. et al. Biodiversity risks from fossil fuel extraction. Science 342, 425–426 (2013).
    ADS  CAS  Article  Google Scholar 

    14.
    Murguía, D. I., Bringezu, S. & Schaldach, R. Global direct pressures on biodiversity by large-scale metal mining: Spatial distribution and implications for conservation. J. Eenviron. Manage. 180, 409–420 (2016).
    Google Scholar 

    15.
    Endl, A., Tost, M., Hitch, M., Moser, P. & Feiel, S. Europe’s mining innovation trends and their contribution to the sustainable development goals: Blind spots and strong points. Resour. Policy 101440 (2019).

    16.
    Bruckner, M., Fischer, G., Tramberend, S. & Giljum, S. Measuring telecouplings in the global land system: A review and comparative evaluation of land footprint accounting methods. Ecol. Econ. 114, 11–21 (2015).
    Article  Google Scholar 

    17.
    Schaffartzik, A. et al. Trading land: A review of approaches to accounting for upstream land requirements of traded products. J. Ind. Ecol. 19, 703–714 (2015).
    Article  Google Scholar 

    18.
    USGS – United States Geological Survey. Mineral resources online spatial data, https://mrdata.usgs.gov/ (2018).

    19.
    S&P Global Market Intelligence. SNL metals and mining database, https://www.spglobal.com/marketintelligence/en/campaigns/metals-mining (2018).

    20.
    Murguía, D. I. & Bringezu, S. Measuring the specific land requirements of large-scale metal mines for iron, bauxite, copper, gold and silver. Prog. Ind. Ecol. 10, 264–285 (2016).
    Article  Google Scholar 

    21.
    Werner, T. T. et al. Global-scale remote sensing of mine areas and analysis of factors explaining their extent. Glob. Environ. Change 60 (2020).

    22.
    Mountrakis, G., Im, J. & Ogole, C. Support vector machines in remote sensing: A review. ISPRS J. Photogramm. 66, 247–259 (2011).
    Article  Google Scholar 

    23.
    Belgiu, M. & Dragu, L. Random forest in remote sensing: A review of applications and future directions. ISPRS J. Photogramm. 114, 24–31 (2016).
    Article  Google Scholar 

    24.
    Zhu, X. X. et al. Deep learning in remote sensing: A comprehensive review and list of resources. IEEE Geosc. Rem. Sen. M. 5, 8–36 (2017).
    Article  Google Scholar 

    25.
    Wulder, M. A., Coops, N. C., Roy, D. P., White, J. C. & Hermosilla, T. Land cover 2.0. Int. J. Remote Sens. 39, 4254–4284 (2018).
    ADS  Article  Google Scholar 

    26.
    Zhu, Z. et al. Benefits of the free and open Landsat data policy. Remote Sens. Environ. 224, 382–385 (2019).
    ADS  Article  Google Scholar 

    27.
    Petropoulos, G. P., Partsinevelos, P. & Mitraka, Z. Change detection of surface mining activity and reclamation based on a machine learning approach of multi-temporal Landsat TM imagery. Geocarto Int. 28, 323–342 (2013).
    Article  Google Scholar 

    28.
    LaJeunesse Connette, K. J. et al. Assessment of mining extent and expansion in Myanmar based on freely-available satellite imagery. Remote Sens. 8 (2016).

    29.
    Yu, L. et al. Monitoring surface mining belts using multiple remote sensing datasets: A global perspective. Ore Geol. Rev. 101, 675–687 (2018).
    Article  Google Scholar 

    30.
    Vasuki, Y. et al. The spatial-temporal patterns of land cover changes due to mining activities in the darling range, western australia: A visual analytics approach. Ore Geol. Rev. 108, 23–32 (2019).
    Article  Google Scholar 

    31.
    Mukherjee, J., Mukherjee, J., Chakravarty, D. & Aikat, S. A novel index to detect opencast coal mine areas from Landsat 8 OLI/TIRS. IEEE J-STARS 12, 891–897 (2019).
    Google Scholar 

    32.
    Waldrop, M. M. News Feature: What are the limits of deep learning? PNAS 116, 1074–1077 (2019).
    CAS  Article  Google Scholar 

    33.
    EOX IT Services GmbH. Sentinel-2 cloudless (contains modified Copernicus sentinel data 2017 and 2018), https://s2maps.eu (2018).

    34.
    Pebesma, E. Simple Features for R: Standardized Support for Spatial Vector Data. R J. 10, 439–446 (2018).
    Article  Google Scholar 

    35.
    Gutschlhofer, J. & Maus, V. Web application for mining area polygonization version 1.2. Zenodo https://doi.org/10.5281/zenodo.3691743 (2020).

    36.
    Lesiv, M. et al. Characterizing the spatial and temporal availability of very high resolution satellite imagery in Google Earth and Microsoft Bing maps as a source of reference data. Land 7 (2018).

    37.
    Bradshaw, A. Restoration of mined lands—using natural processes. Ecol. Eng. 8, 255–269 (1997).
    Article  Google Scholar 

    38.
    EUROSTAT. Countries, 2016 – administrative units – dataset (generalised dataset derived from eurogeographics and UN-FAO GI data), https://ec.europa.eu/eurostat/cache/GISCO/distribution/v2/countries/ (2018).

    39.
    Amatulli, G. et al. A suite of global, cross-scale topographic variables for environmental and biodiversity modeling. Sci. Data 5, 180040 (2018).
    Article  Google Scholar 

    40.
    Maus, V. et al. Global-scale mining polygons (version 1). Pangaea https://doi.org/10.1594/PANGAEA.910894 (2020).

    41.
    Marazuela, M., Vázquez-Suñé, E., Ayora, C., García-Gil, A. & Palma, T. The effect of brine pumping on the natural hydrodynamics of the Salar de Atacama: The damping capacity of salt flats. Sci. Total Environ. 654, 1118–1131 (2019).
    ADS  CAS  Article  Google Scholar 

    42.
    Liu, W., Agusdinata, D. B. & Myint, S. W. Spatiotemporal patterns of lithium mining and environmental degradation in the Atacama Salt Flat, Chile. Int. J. Appl. Earth Obs. 80, 145–156 (2019).
    Article  Google Scholar 

    43.
    Hansen, K. Brazil’s Carajás mines, NASA Earth Observatory, https://earthobservatory.nasa.gov/images/144457/brazils-carajas-mines (2018).

    44.
    Mining Technology. Batu Hijau copper-gold mine, Indonesia, https://www.mining-technology.com/projects/batu/ (2020).

    45.
    Shen, L. & Gunson, A. J. The role of artisanal and small-scale mining in China’s economy. J. Clean. Prod. 14, 427–435 (2006).
    Article  Google Scholar 

    46.
    Shen, L., Dai, T. & Gunson, A. J. Small-scale mining in China: Assessing recent advances in the policy and regulatory framework. Resour. Policy 34, 150–157 (2009).
    Article  Google Scholar 

    47.
    Potere, D. Horizontal positional accuracy of Google Earth’s high-resolution imagery archive. Sensors 8, 7973–7981 (2008).
    Article  Google Scholar 

    48.
    Vajsová B & Åstrand, P. J. New sensors benchmark report on Sentinel-2A sensor over Maussane test site for CAP purposes. Report No. EUR 27674EN (Publications Office of the European Union, 2015).

    49.
    Cochran, W. G. Sampling Techniques. Series in Probability and Statistics (Wiley, 1977), 3 edn.

    50.
    Olofsson, P. et al. Good practices for estimating area and assessing accuracy of land change. Remote Sens. Environ. 148, 42–57 (2014).
    ADS  Article  Google Scholar 

    51.
    OGC – Open Geospatial Consortium. GeoPackage Encoding Standard, https://www.geopackage.org/ (2005).

    52.
    OGC – Open Geospatial Consortium. Geographic tagged image file format (GeoTIFF), https://www.ogc.org/standards/geotiff (2019).

    53.
    The Internet Society. RFC 4180: Common format and MIME type for comma-separated values (CSV). https://tools.ietf.org/html/rfc4180 (2005).

    54.
    Wang, J.-F., Zhang, T.-L. & Fu, B.-J. A measure of spatial stratified heterogeneity. Ecol. Indic. 67, 250–256 (2016).
    Article  Google Scholar 

    55.
    Brunsdon, C., Fotheringham, A. S. & Charlton, M. E. Geographically weighted regression: A method for exploring spatial nonstationarity. Geogr. Anal. 28, 281–298 (1996).
    Article  Google Scholar 

    56.
    Brunsdon, C., Fotheringham, S. & Charlton, M. Geographically weighted regression. J. R. Stat. Soc., Ser. D Stat. 47, 431–443 (1998).
    Article  Google Scholar 

    57.
    QGIS Development Team. QGIS geographic information system, version 3.12.0. Open Source Geospatial Foundation, https://www.qgis.org (2020).

    58.
    R Core Team. R: A language and environment for statistical computing, version 3.6.1. Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org (2019).

    59.
    Python Core Team. Python: A dynamic, open source programming language, version 2.7.17. Python Software Foundation, https://www.python.org (2019).

    60.
    OGC – Open Geospatial Consortium. Web map service interface standard (WMS), https://www.ogc.org/standards/wms (2020).

    61.
    GNU general public license, version 3. Free Software Foundation, https://www.gnu.org/licenses/gpl-3.0.en.html (2019).

    62.
    GDAL/OGR contributors. GDAL/OGR geospatial data abstraction software library, version 2.4.2. Open Source Geospatial Foundation, https://gdal.org (2019).

    63.
    Chang, W., Cheng, J., Allaire, J., Xie, Y. & McPherson, J. Shiny: Web Application Framework for R, version 1.3.2, https://CRAN.R-project.org/package=shiny (2019)

    64.
    The PostgreSQL Global Development Group. PostgreSQl: an open source object-relational database system, version 11.6, https://www.postgresql.org/ (2019).

    65.
    PostGIS Team. PostGIS: a spatial database extender for PostgreSQL object relational database, version 2.5.4. Open Source Geospatial Foundation, https://postgis.net (2019). More

  • in

    Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. and Gray)

    Adams HD, Collins AD, Briggs SP, Vennetier M, Dickman LT, Sevanto SA et al. (2015) Experimental drought and heat can delay phenological development and reduce foliar and shoot growth in semiarid trees. Glob Change Biol 21:4210–4220
    Google Scholar 

    Basler D, Körner C (2012) Photoperiod sensitivity of bud burst in 14 temperate forest tree species. Agric For Meteorol 165:73–81
    Google Scholar 

    Bhalerao R, Keskitalo J, Sterky F, Erlandsson R, Björkbacka H, Birve SJ et al. (2003) Gene expression in autumn leaves. Plant Physiol 131:430–442
    PubMed  PubMed Central  Google Scholar 

    Bradshaw HD, Stettler RF (1995) Molecular genetics of growth and development in populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139:963–973
    CAS  PubMed  Google Scholar 

    Brelsford CC, Nybakken L, Kotilainen TK, Robson TM (2019) The influence of spectral composition on spring and autumn phenology in trees. Tree Physiol 39:925–950
    CAS  PubMed  Google Scholar 

    Christensen K, Frederiksen H, Vaupel JW, McGue M (2003) Age trajectories of genetic variance in physical functioning: a longitudinal study of Danish twins aged 70 years and older. Behav Genet 33:125–136
    PubMed  Google Scholar 

    Chuine I (2010) Why does phenology drive species distribution? Philos Trans R Soc B 365:3149–3160
    Google Scholar 

    Class B, Brommer JE (2020) Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations? Evolution 74:1540–1550
    PubMed  Google Scholar 

    Cong N, Shen M, Piao S (2016) Spatial variations in responses of vegetation autumn phenology to climate change on the Tibetan Plateau. J Plant Ecol 10:744–752.
    Google Scholar 

    Costa e Silva J, Borralho NMG, Potts BM (2004) Additive and non-additive genetic parameters from clonally replicated and seedling progenies of Eucalyptus globulus. Theor Appl Genet 108:1113–1119
    PubMed  Google Scholar 

    Cronk QCB (2005) Plant eco‐devo: the potential of poplar as a model organism. N Phytologist 166:39–48
    CAS  Google Scholar 

    Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W et al. (2014) Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 46:1089
    CAS  PubMed  Google Scholar 

    Fabbrini F, Gaudet M, Bastien C, Zaina G, Harfouche A, Beritognolo I et al. (2012) Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar. BMC Plant Biol 12:47
    CAS  PubMed  PubMed Central  Google Scholar 

    Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics. 4th edn. Longman

    Fracheboud Y, Luquez V, Björkén L, Sjödin A, Tuominen H, Jansson S (2009) The control of autumn senescence in European Aspen. Plant Physiol 149:1982–1991
    CAS  PubMed  PubMed Central  Google Scholar 

    Hadfield JD (2010) MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J Stat Softw 33:1–22.
    Google Scholar 

    Horvath DP, Anderson JV, Chao WS, Foley ME (2003) Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci 8:534–540
    CAS  PubMed  Google Scholar 

    Howe GT, Aitken SN, Neale DB, Jermstad KD, Wheeler NC, Chen THH (2003) From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees. Can J Bot 81:1247–1266
    CAS  Google Scholar 

    Howe GT, Saruul P, Davis J, Chen THH (2000) Quantitative genetics of bud phenology, frost damage, and winter survival in an F2 family of hybrid poplars. Theor Appl Genet 101:632–642
    Google Scholar 

    Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S (2008) Nucleotide polymorphism and phenotypic associations Within and Around the phytochrome B2 Locus in European Aspen (Populus tremula, Salicaceae). Genetics 178:2217
    CAS  PubMed  PubMed Central  Google Scholar 

    Jansson S, Douglas CJ (2007) Populus: a model system for plant biology. Annu Rev Plant Biol 58:435–458
    CAS  PubMed  Google Scholar 

    Karacic A, Verwijst T, Weih M (2003) Above-ground woody biomass production of short-rotation populus plantations on agricultural land in Sweden. Scand J For Res 18:427–437
    Google Scholar 

    Kennedy BW, Schaeffer LR (1989) Genetic evaluation under an animal model when identical genotypes are represented in the population. J Anim Sci 67:1946–1955
    Google Scholar 

    Keskitalo J, Bergquist G, Gardeström P, Jansson S (2005) A cellular timetable of autumn senescence. Plant Physiol 139:1635–1648
    CAS  PubMed  PubMed Central  Google Scholar 

    Lagercrantz ULF (2009) At the end of the day: a common molecular mechanism for photoperiod responses in plants? J Exp Bot 60:2501–2515
    CAS  PubMed  Google Scholar 

    Leuchner M, Menzel A, Werner H (2007) Quantifying the relationship between light quality and light availability at different phenological stages within a mature mixed forest. Agric For Meteorol 142:35–44
    Google Scholar 

    Luquez V, Hall D, Albrectsen BR, Karlsson J, Ingvarsson P, Jansson S (2008) Natural phenological variation in aspen (Populus tremula): the SwAsp collection. Tree Genet Genomes 4:279–292
    Google Scholar 

    Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Sunderland

    MacKenzie CM, Primack RB, Miller-Rushing AJ (2018) Local environment, not local adaptation, drives leaf-out phenology in common gardens along an elevational gradient in Acadia National Park, Maine. Am J Bot 105:986–995
    Google Scholar 

    Marron N, Storme V, Dillen SY, Bastien C, Ricciotti L, Salani F et al. (2010) Genomic regions involved in productivity of two interspecific poplar families in Europe. 2. Biomass production and its relationships with tree architecture and phenology. Tree Genet Genomes 6:533–554
    Google Scholar 

    McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, Cronk QC et al. (2014a) Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. N. Phytologist 201:1263–1276
    CAS  Google Scholar 

    McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J et al. (2014b) Genome‐wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. N. Phytologist 203:535–553
    CAS  Google Scholar 

    McKown AD, Klápště J, Guy RD, El-Kassaby YA, Mansfield SD (2018) Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa. N. Phytologist 220:300–316
    CAS  Google Scholar 

    Michelson I, Ingvarsson Pär K, Robinson Kathryn M, Edlund E, Eriksson Maria E, Nilsson O et al. (2017) Autumn senescence in aspen is not triggered by day length. Physiol Plant 162:123–134
    PubMed  Google Scholar 

    Olson M, Levsen N, Soolanayakanahally Raju Y, Guy Robert D, Schroeder William R, Keller Stephen R et al. (2013) The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate. Mol Ecol 22:1214–1230
    CAS  PubMed  Google Scholar 

    Pliura A, Suchockas V, Sarsekova D, Gudynaitė V (2014) Genotypic variation and heritability of growth and adaptive traits, and adaptation of young poplar hybrids at northern margins of natural distribution of Populus nigra in Europe. Biomass Bioenergy 70:513–529
    Google Scholar 

    Polgar CA, Primack RB (2011) Leaf‐out phenology of temperate woody plants: from trees to ecosystems. N Phytologist 191:926–941
    Google Scholar 

    Porth I, El‐Kassaby YA (2015) Using Populus as a lignocellulosic feedstock for bioethanol. Biotechnol J 10:510–524
    CAS  PubMed  Google Scholar 

    Porth I, Klápště J, McKown AD, La Mantia J, Guy RD, Ingvarsson PK et al. (2015) Evolutionary quantitative genomics of Populus trichocarpa. PLoS ONE 10:e0142864
    PubMed  PubMed Central  Google Scholar 

    Porth I, Klápště J, McKown AD, La Mantia J, Hamelin RC, Skyba O et al. (2014) Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics. Plant Physiol 164:548–554
    CAS  PubMed  Google Scholar 

    Rohde A, Bastien C, Boerjan W (2011b) Temperature signals contribute to the timing of photoperiodic growth cessation and bud set in poplar. Tree Physiol 31:472–482
    PubMed  Google Scholar 

    Rohde A, Storme V, Jorge V, Gaudet M, Vitacolonna N, Fabbrini F et al. (2011a) Bud set in poplar – genetic dissection of a complex trait in natural and hybrid populations. N Phytologist 189:106–121
    CAS  Google Scholar 

    Sannigrahi P, Ragauskas AJ, Tuskan GA (2010) Poplar as a feedstock for biofuels: a review of compositional characteristics. Biofuels Bioprod Bioref 4:209–226
    CAS  Google Scholar 

    Singh RK, Svystun T, AlDahmash B, Jönsson AM, Bhalerao RP (2017) Photoperiod- and temperature-mediated control of phenology in trees—a molecular perspective. N Phytologist 213:511–524
    CAS  Google Scholar 

    Slavov GT, Leonardi S, Burczyk J, Adams WT, Strauss Sh, DiFazio SP (2009) Extensive pollen flow in two ecologically contrasting populations of Populus trichocarpa. Mol Ecol 18:357–373

    Triozzi PM, Ramos-Sánchez JM, Hernández-Verdeja T, Moreno-Cortés A, Allona I, Perales M (2018) Photoperiodic regulation of shoot apical growth in poplar. Front Plant Sci 9:1030–1030
    PubMed  PubMed Central  Google Scholar 

    Vitasse Y, Delzon S, Dufrêne E, Pontailler J-Y, Louvet J-M, Kremer A et al. (2009) Leaf phenology sensitivity to temperature in European trees: Do within-species populations exhibit similar responses? Agric For Meteorol 149:735–744
    Google Scholar 

    Walsh B, Lynch M (2018) Evolution and selection of quantitative traits. Oxford University Press

    Weih M (2004) Intensive short rotation forestry in boreal climates: present and future perspectives. Can J For Res 34:1369–1378
    Google Scholar 

    Wilson AJ, Kruuk LEB, Coltman DW (2005) Ontogenetic patterns in heritable variation for body size: using random regression models in a wild ungulate population. Am Naturalist 166:E177–E192
    Google Scholar 

    Yu Q, Tigerstedt PMA, Haapanen M (2001) Growth and phenology of hybrid aspen clones (Populus tremula L. x Populus tremuloides Michx.)

    Zanewich KP, Pearce DW, Rood SB (2018) Heterosis in poplar involves phenotypic stability: cottonwood hybrids outperform their parental species at suboptimal temperatures. Tree Physiol 38:789–800
    CAS  PubMed  Google Scholar 

    Zhou L, Bawa R, Holliday JA (2014) Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa). Mol Ecol 23:2486–2499
    CAS  PubMed  Google Scholar  More