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    A robust multiple-objective decision-making paradigm based on the water–energy–food security nexus under changing climate uncertainties

    As stated, the primary goal of this study is to promote an objective decision support framework for water resource planning and management purposes within the context of the WEF security nexus, which takes into account the uncertainties imposed by the climate change phenomenon. Such a framework is “robust” since it takes the multi-dimensionality of water-related problems into account while addressing the uncertainties imposed by climate change projections. The basic components of this decision-making paradigm are depicted in Fig. 1. In principle, while this framework is sensitive to the uncertainties associated with the climate change projections, it can provide a dynamic water resources planning and management scheme promoted within the WEF security network. Thus, in addition to the status quo, a series of climate change projections (i.e., RCP 2.6, RCP 4.5, and RCP 8.5) are also integrated into the proposed decision support framework. In essence, the main components of the proposed framework are simulation and operation of the water resources system based on the standard operation policy (SOP), evaluating the system’s efficiency through a series of quantitative performance criteria, and finally, applying the MADM-based framework to opt for a robust system renovation setting.Figure 1Basic components of the robust decision-making paradigm for water resources planning and management.Full size imageSimulating the water resources systemSOP is a primitive, and perhaps the most-well-known real-time operation policy in water resources planning and management14. The core principle here is to minimize the prioritized water shortage at the current time step with no conservation policy (e.g., hedging rules) in place. SOP, as a standard rule curve (RC), determines how the operator should behave at any given state of a reservoir15,16. This rule curve is established as an attempt to balance various water demands including but not limited to flood control, hydropower, water supply, and recreation17. A SOP operating system attempts to release water to meet a water demand at the current time, with no regard to the future.In general, SOP can be mathematically expressed as18:$$R_{t} = left{ {begin{array}{*{20}c} {D_{t} } \ {AW_{t} } \ 0 \ end{array} – S_{min } } right.begin{array}{*{20}c} {} & {if} & {AW_{t} > S_{min } } \ {} & {if} & {AW_{t} > S_{min } } \ {} & {if} & {AW_{t} le S_{min } } \ end{array} begin{array}{*{20}c} {} & {and} & {AW_{t} – S_{min } ge D_{t} } \ {} & {and} & {AW_{t} – S_{min } < D_{t} } \ {} & {} & {} \ end{array} quad t = { 1},{ 2},{ 3}, , ... , ,T$$ (1a) where$$AW_{t} = S_{t} + Q_{t} - Loss_{t}$$ (1b) in which Rt = amount of water supplied during the tth time step; Dt = consumers’ water demand during the tth time step; AWt = amount of available water during the tth time step; St = amount of stored water during the tth time step; Smin = dead storage of the reservoir; Qt = inflow during the tth time step; Losst = net water loss (i.e., precipitation minus evaporation) of the reservoir during the tth time step; and T = total number of time steps in the operational horizon.In practice, however, a different type of water demand leads to a different interpretation of water shortage. There are cases in which the stakeholders’ needs are represented by a set of volumetric demand targets, and the decision-makers’ objective would be to minimize the water deficit based on a set of priorities for these demands. This is a typical case for agricultural, domestic, industrial, and environmental demands. For hydropower generation, however, a conventional interpretation of SOP would be to generate maximum electricity permitted by the power plant capacity (PPC) at each given time step19. For a hydropower system, the amount of water needed to reach a power plant capacity is given by19:$$R_{t} = frac{{86400 times PF times Countday_{t} times PPC}}{{gamma_{w} times g times eta times Delta H_{t} }}$$ (2) in which, γw = water specific weight; g = gravitational acceleration; η = efficiency of the hydropower system; ΔHt = height difference between the reservoir water level and the tailwater level at time step t; Countdayt = number of days within time step t; and PF = plant factor of the hydropower system.As stated earlier, applying an SOP-based plan requires a set of pre-defined priorities to advise decision-makers concerning the order, in which each of these demands is to be met. The major water demands include drinking, industry, environment, agriculture, and hydropower. Thus, according to the SOP’s principle, the decision-makers, first, allocate the available water to meet the demand of the stakeholder with the highest priority (i.e., the domestic and industrial demand). After this first water demand is fully satisfied, the available water can be used for the next demand. Such an allocation process continues until no water is available. It should be noted, however, that if the released water in each stage passes through the penstock equipped with the turbines, electricity can be generated. The amount of energy generated in previous stages must be accounted for before computing the amount of water released for hydropower purposes.Performance criteriaPerformance criteria are, in essence, quantitative measures that can provide a practical insight for the decision-makers regarding the status of a system. This definition covers a broad spectrum of mathematical representations, which can range from simple mathematical formulas such as the average of a specific output to more complex and probability-based entities20,21. The most fundamental and universal probability-based performance criteria are reliability, resiliency, and vulnerability22,23,24. In essence, reliability is the probability of successful function of a system; resiliency measures the probability of successful functioning following a system failure; and vulnerability quantifies the severity of failure during an operation horizon25. It should be noted that these three criteria assess different aspects of a water resources system, and as such, they complement one another26. For more information regarding these probabilistic performance criteria, the readers can refer to Sandoval-Solis et al.27 and Zolghadr-Asli et al.20.In this study, the concept of levelized cost of energy (LCOE) is utilized for economic evaluation. The LCOE of a given hydropower system is the ratio of lifetime costs to lifetime electricity generation, both of which are discounted back to a common year using a discount rate that reflects the average cost of capital28. The LCOE of renewable energy systems depends on the technology, geographic criteria, capital and operating costs, and the efficiency of the system. The LCOE can be mathematically expressed as follows29:$$LCOE = frac{{sumnolimits_{t = 1}^{n} {frac{{I_{t} + M_{t} + F_{t} }}{{left( {1 + r} right)^{t} }}} }}{{sumnolimits_{t = 1}^{n} {frac{{E_{t} }}{{left( {1 + r} right)^{t} }}} }}$$ (3) in which It = investment expenditures in year t; Mt = operation and maintenance expenditures in year t; Ft = fuel expenditures in year t; Et = electricity generation in year t; r = discount rate; and n = economic life expectancy of the system.MADMMADM is an umbrella term to describe a series of frameworks, which aim to help individuals or a group of individuals to prioritize a series of discretely defined alternatives with regard to a set of evaluation attributes30,31. MADM can provide the necessary means to conduct planning and management under changing circumstances such as those under climate change conditions10,32. According to one of the basic principles of MADM, the decision-maker can use the similarity of the feasible alternatives and the preferential result and/or incongruity of the undesirable alternatives. The notion mentioned above is, chiefly, the core principle of the reference-dependent theory33. Accordingly, the reference-based branch of the MADM methods can, itself, be classified into two major groups: screening methods and ranking methods. Screening methods eliminate alternatives that cannot satisfy the pre-determined conditions for the desirable solution, while ranking methods order all the alternatives from the best to the worst34.Pioneered by Hwang and Yoon35, the technique for order references by similarity to an ideal solution (TOPSIS) is a compensatory, objective MADM solving method rooted from the basic principles of the reference-dependent theory. The core idea is that the chosen alternative should have the shortest distance from the ideal solution and the farthest distance from the negative-ideal solution36. The basic computation algorithm of TOPSIS can be summarized as follows37,38:Step I: Construct the original decision matrix (X), where m feasible alternatives are to be evaluated based on n evaluation criteria:$$X = left[ {begin{array}{*{20}c} {x_{11} } & {x_{12} } & cdots & {x_{1n} } \ {x_{21} } & {x_{22} } & cdots & {x_{2n} } \ vdots & vdots & ddots & vdots \ {x_{m1} } & {x_{m2} } & cdots & {x_{mn} } \ end{array} } right]$$ (4) in which xij = the element of the ith alternative concerning the jth criterion.Step II: Defining the reference alternatives [i.e., the ideal solution (s+) and the negative-ideal solution (s−)]. To do so, first, the elements of the decision matrix that are associated with negative criteria must be redefined by using the following equation:$$x_{ij}^{ * } = frac{1}{{x_{ij} }}$$ (5a) The elements of the decision matrix that are associated with positive criteria would remain the same:$$x_{ij}^{ * } = x_{ij}$$ (5b) The ideal alternative is an arbitrarily defined vector, which describes the aspired solution to the given problem, while the inferior alternative is an arbitrarily defined solution that represents the most undesirable option for the given MADM problem. Here, the ideal and negative-ideal solutions would be represented with two separate vectors where each pair of the corresponding elements in these vectors is, respectively, the maximum and minimum values of (x_{ij}^{ * }) with regard to each of the evaluation criteria.Step III: Each element of the decision matrix should be normalized by using the following equation:$$p_{ij} = frac{{x_{ij}^{ * } }}{{sqrt {sumnolimits_{i = 1}^{m} {x_{ij}^{ * 2} } } }}$$ (6) in which pij = the normalized performance value for the ith alternative with respect to the jth criterion.Step IV: The weighted normalized preference value (zij) can be computed as follows:$$z_{ij} = p_{ij} times w_{j} quad forall i,j$$ (7) in which wj = the weight (i.e., the importance value) of the jth criterion. The weights assigned to the evolution criteria reflect their relative importance to the decision-makers. The higher the weights are, the more crucial their roles would be in the selection process. Chiefly, these weighting mechanisms are either subjective in nature or follow an objective procedure. In the subjective approaches, the weights of the attributes are assigned based on the performance information given by the decision-maker, whereas in the objective approaches, the weights of the evaluation attributes would be obtained by using the objective information extracted from the decision matrix39. Shannon’s Entropy method, used in this study as the weight assignment mechanism, is a well-known objective weighting technique40. This method tends to assign the highest weight to an evaluation attribute with the highest dispersity in its values. For more information on the computational framework of this method, the readers can refer to Lotfi and Fallahnejad41.Step V: In this step, every given alternative is compared to the reference points, namely, the ideal and inferior alternatives. The described procedure, which is known as the separation measurement in TOPSIS, can be mathematically expressed as follows35:$$D_{i}^{ + } = sqrt {sumlimits_{j = 1}^{n} {left( {z_{ij} - z_{j}^{ + } } right)^{2} } }$$ (8) And$$D_{i}^{ - } = sqrt {sumlimits_{j = 1}^{n} {left( {z_{ij} - z_{j}^{ - } } right)^{2} } }$$ (9) in which (D_{j}^{ + }) and (D_{j}^{ - }) = separation measurements of the jth criterion with respect to the ideal and inferior alternatives, respectively.Step VI: The relative closeness to the ideal solution (χi), which can be used to rank the desirability of the feasible alternative, can be computed as follows35:$$chi_{i} = frac{{D_{i}^{ - } }}{{D_{i}^{ + } + D_{i}^{ - } }}quad forall i$$ (10) The further this distance (i.e., larger values of χi), the more desirable the alternative would be.Robust multi-attribute frameworkAs stated, each climate change scenario depicts a unique future with regard to the changing climate, which in turn introduces an element of uncertainty to the projected performance of water resources systems during their operation horizon. Furthermore, downscaling methods, which link these projected changes in the global climatic pattern to a local or regional scale, can be another source of uncertainty. Naturally, for long-lasting water infrastructure such as a hydropower system, addressing these uncertainties in a proper and timely manner can be one of the key components of a robust project. Thus, this study aims to not only evaluate the system’s performance under the status quo but also assess the credibility of the system under the projected climate change conditions.The other characteristic one might expect from a robust project is its ability to take into account the multi-dimensionality nature of water-related infrastructure. Most notably, addressing the WEF security nexus must be a priority in water resources planning and management. Resultantly, any robust decision-making paradigm for water resources planning and management purposes should also account for the other pillars of the WEF nexus (i.e., energy and food sectors), as they would be consequentially affected by such decisions. It is also important to note that these sectors could be affected by the climate change phenomenon. The other crucial feature of a robust decision-making paradigm is that it should be able to account for the socio-economic, environmental, and technical factors that determine the overall quality of the project. Such a decision-making paradigm is depicted in Fig. 2. This notion in practice, however, can typically lead to a mega decision matrix composed of numerous criteria and alternatives that can be overwhelming if the subjective MADM methods are to be employed. This study, thus, employs an objective MADM framework (i.e., TOPSIS/Entropy) to help overcome the above-described problem. The basic idea is to promote a universal and practical decision support framework that enables the water resources planners and managers to account for the intricacies of the WEF security nexus while simultaneously taking the uncertainties of climate change projections into account. Figure 3 illustrates the flowchart of the proposed decision support framework.Figure 2Schematic diagram of the MADM problem.Full size imageFigure 3Flowchart of the proposed framework.Full size image More

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    Oceanographic anomalies coinciding with humpback whale super-group occurrences in the Southern Benguela

    1.Dawbin, W. H. The migrations of humpback whales which pass the New Zealand coast. Trans. R. Soc. New Zeal. 84, 147–196 (1956).
    Google Scholar 
    2.Chittleborough, R. Dynamics of two populations of the humpback whale, Megaptera novaeangliae (Borowski). Mar. Freshw. Res. 16, 33–128. https://doi.org/10.1071/mf9650033 (1965).Article 

    Google Scholar 
    3.Rasmussen, K. et al. Southern Hemisphere humpback whales wintering off Central America: Insights from water temperature into the longest mammalian migration. Biol. Let. 3, 302–305. https://doi.org/10.1098/rsbl.2007.0067 (2007).Article 

    Google Scholar 
    4.Friedlaender, A. S. et al. Whale distribution in relation to prey abundance and oceanographic processes in shelf waters of the Western Antarctic Peninsula. Mar. Ecol. Prog. Ser. 317, 297–310. https://doi.org/10.3354/meps317297 (2006).ADS 
    Article 

    Google Scholar 
    5.Nowacek, D. P. et al. Super-aggregations of krill and humpback whales in Wilhelmina Bay Antarctic Peninsula. PLoS ONE 6, e19173. https://doi.org/10.1371/journal.pone.0019173 (2011).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    6.Barendse, J. et al. Transit station or destination? Attendance patterns, movements and abundance estimate of humpback whales off west South Africa from photographic and genotypic matching. Afr. J. Mar. Sci. 33, 353–373. https://doi.org/10.2989/1814232X.2011.637343 (2011).Article 

    Google Scholar 
    7.Best, P. B., Sekiguchi, K. & Findlay, K. P. A suspended migration of humpback whales Megaptera novaeangliae on the west coast of South Africa. Marine Ecol. Progr. Ser. Oldendorf 118, 1–12. https://doi.org/10.3354/meps118001 (1995).ADS 
    Article 

    Google Scholar 
    8.Findlay, K. & Best, P. Summer incidence of humpback whales on the west coast of South Africa. S. Afr. J. Mar. Sci. 15, 279–282. https://doi.org/10.2989/02577619509504851 (1995).Article 

    Google Scholar 
    9.Findlay, K. P. et al. Humpback whale “super-groups”–A novel low-latitude feeding behaviour of Southern Hemisphere humpback whales (Megaptera novaeangliae) in the Benguela Upwelling System. PLoS ONE 12, e0172002. https://doi.org/10.1371/journal.pone.0172002 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    10.Pirotta, V., Owen, K., Donnelly, D., Brasier, M. J. & Harcourt, R. First evidence of bubble‐net feeding and the formation of ‘super‐groups’ by the east Australian population of humpback whales during their southward migration. Aquat. Conserv. (2021).11.Veitch, J., Penven, P. & Shillington, F. The Benguela: A laboratory for comparative modeling studies. Prog. Oceanogr. 83, 296–302. https://doi.org/10.1016/j.pocean.2009.07.008 (2009).ADS 
    Article 

    Google Scholar 
    12.Preston-Whyte, R. A. & Tyson, P. D. Atmosphere and weather of southern Africa (Oxford University Press, 1988).
    Google Scholar 
    13.Nemoto, T., Best, P., Ishimaru, K. & Takano, H. Diatom films on whales [minke whales and 4 species of toothed whales] in South African waters. Scientific Reports of the Whales Research Institute (1980).14.Hutchings, L., Pitcher, G., Probyn, T. & Bailey, G. in Upwelling in the ocean: modern processes and ancient records Vol. 18 (eds CP Summerhayes et al.) Ch. 3, 65–81 (Wiley & Sons, 1995).15.Clapham, P. J. in Encyclopedia of marine mammals (eds B Würsig, JGM Thewissen, & KM Kovacs) 489–492 (Academic Press, 2018).16.Bakun, A. et al. Anticipated effects of climate change on coastal upwelling ecosystems. Curr. Clim. Change Rep. 1, 85–93. https://doi.org/10.1007/s40641-015-0008-4 (2015).Article 

    Google Scholar 
    17.Mackas, D. L. & Beaugrand, G. Comparisons of zooplankton time series. J. Mar. Syst. 79, 286–304. https://doi.org/10.1016/j.jmarsys.2008.11.030 (2010).Article 

    Google Scholar 
    18.Mackas, D. et al. Changing zooplankton seasonality in a changing ocean: Comparing time series of zooplankton phenology. Prog. Oceanogr. 97, 31–62. https://doi.org/10.1016/j.pocean.2011.11.005 (2012).ADS 
    Article 

    Google Scholar 
    19.Huggett, J., Verheye, H., Escribano, R. & Fairweather, T. Copepod biomass, size composition and production in the Southern Benguela: Spatio–temporal patterns of variation, and comparison with other eastern boundary upwelling systems. Prog. Oceanogr. 83, 197–207. https://doi.org/10.1016/j.pocean.2009.07.048 (2009).ADS 
    Article 

    Google Scholar 
    20.Verheye, H. M., Lamont, T., Huggett, J. A., Kreiner, A. & Hampton, I. Plankton productivity of the Benguela current large marine ecosystem (BCLME). Environ. Dev. 17, 75–92. https://doi.org/10.1016/j.envdev.2015.07.011 (2016).Article 

    Google Scholar 
    21.Shannon, L. J. et al. Exploring temporal variability in the Southern Benguela ecosystem over the past four decades using a time-dynamic ecosystem model. Front. Mar. Sci. 7, 540 (2020).ADS 
    Article 

    Google Scholar 
    22.Jarre, A. et al. Synthesis: climate effects on biodiversity, abundance and distribution of marine organisms in the Benguela. Fish. Oceanogr. 24, 122–149. https://doi.org/10.1111/fog.12086 (2015).Article 

    Google Scholar 
    23.Lamont, T., García-Reyes, M., Bograd, S., Van Der Lingen, C. & Sydeman, W. Upwelling indices for comparative ecosystem studies: Variability in the Benguela Upwelling System. J. Mar. Syst. 188, 3–16. https://doi.org/10.1016/j.jmarsys.2017.05.007 (2018).Article 

    Google Scholar 
    24.Tim, N., Zorita, E. & Hünicke, B. Decadal variability and trends of the Benguela upwelling system as simulated in a high-resolution ocean simulation. Ocean Sci. 11, 483–502. https://doi.org/10.5194/os-11-483-2015 (2015).ADS 
    Article 

    Google Scholar 
    25.Lamont, T., Barlow, R. & Brewin, R. Long-term trends in phytoplankton chlorophyll a and size structure in the Benguela Upwelling System. J. Geophys. Res. Oceans 124, 1170–1195. https://doi.org/10.1029/2018JC014334 (2019).ADS 
    Article 

    Google Scholar 
    26.Ragoasha, N. et al. Lagrangian pathways in the southern Benguela upwelling system. J. Mar. Syst. 195, 50–66. https://doi.org/10.1016/j.jmarsys.2019.03.008 (2019).Article 

    Google Scholar 
    27.Shannon, V., Hempel, G., Moloney, C., Woods, J. D. & Malanotte-Rizzoli, P. Benguela: Predicting a Large Marine Ecosystem (Elsevier, 2006).
    Google Scholar 
    28.Veitch, J., Penven, P. & Shillington, F. Modeling equilibrium dynamics of the Benguela current system. J. Phys. Oceanogr. 40, 1942–1964. https://doi.org/10.1175/2010jpo4382.1 (2010).ADS 
    Article 

    Google Scholar 
    29.Lachkar, Z. & Gruber, N. A comparative study of biological production in eastern boundary upwelling systems using an artificial neural network. Biogeosciences 9, 293–308. https://doi.org/10.5194/bg-9-293-2012 (2012).ADS 
    Article 

    Google Scholar 
    30.Gruber, N. et al. Eddy-induced reduction of biological production in eastern boundary upwelling systems. Nat. Geosci. 4, 787–792. https://doi.org/10.1038/ngeo1273 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    31.Hutchings, L. et al. Multiple factors affecting South African anchovy recruitment in the spawning, transport and nursery areas. S. Afr. J. Mar. Sci. 19, 211–225. https://doi.org/10.2989/025776198784126908 (1998).Article 

    Google Scholar 
    32.Rossi, V., López, C., Sudre, J., Hernández-García, E. & Garçon, V. Comparative study of mixing and biological activity of the Benguela and Canary upwelling systems. Geophys. Res. Lett. https://doi.org/10.1029/2008gl033610 (2008).Article 

    Google Scholar 
    33.Barendse, J. & Best, P. B. Shore-based observations of seasonality, movements, and group behavior of southern right whales in a nonnursery area on the South African west coast. Mar. Mamm. Sci. 30, 1358–1382 (2014).Article 

    Google Scholar 
    34.Barendse, J. et al. Migration redefined? Seasonality, movements and group composition of humpback whales Megaptera novaeangliae off the west coast of South Africa. Afr. J. Mar. Sci. 32, 1–22 (2010).Article 

    Google Scholar 
    35.Gibbons, M. J. An introduction to the Zooplankton of the Benguella current Region. (1997).36.Olsen, Ø. Hvaler og hvalfangst i Sydafrika. 1–56 (Bergens Museums Arbok 1914–1915, 1914).37.Meynecke, J. O. et al. Responses of humpback whales to a changing climate in the Southern Hemisphere: Priorities for research efforts. Mar. Ecol. 41, e12616 (2020).Article 

    Google Scholar 
    38.Stockin, K. A. & Burgess, E. A. Opportunistic Feeding of an Adult Humpback Whale (Megaptera novaeangliae) Migrating Along the Coast of Southeastern Queensland, Australia. Aquat. Mamm. 31, 120. https://doi.org/10.1578/AM.31.1.2005.120 (2005).Article 

    Google Scholar 
    39.Visser, F., Hartman, K. L., Pierce, G. J., Valavanis, V. D. & Huisman, J. Timing of migratory baleen whales at the Azores in relation to the North Atlantic spring bloom. Mar. Ecol. Prog. Ser. 440, 267–279. https://doi.org/10.3354/meps09349 (2011).ADS 
    Article 

    Google Scholar 
    40.Trudelle, L. et al. Influence of environmental parameters on movements and habitat utilization of humpback whales (Megaptera novaeangliae) in the Madagascar breeding ground. R. Soc. Open Sci. 3, 160616. https://doi.org/10.1098/rsos.160616 (2016).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    41.Veitch, J., Hermes, J., Lamont, T., Penven, P. & Dufois, F. Shelf-edge jet currents in the southern Benguela: A modelling approach. J. Mar. Syst. 188, 27–38 (2018).Article 

    Google Scholar 
    42.Hutchings, L. et al. The Benguela current: An ecosystem of four components. Prog. Oceanogr. 83, 15–32. https://doi.org/10.1016/j.pocean.2009.07.046 (2009).ADS 
    Article 

    Google Scholar 
    43.Rockwood, R. C., Elliott, M. L., Saenz, B., Nur, N. & Jahncke, J. Modeling predator and prey hotspots: Management implications of baleen whale co-occurrence with krill in Central California. PLoS ONE 15, e0235603 (2020).CAS 
    Article 

    Google Scholar 
    44.Hayward, T. L. & Venrick, E. L. Nearsurface pattern in the California Current: Coupling between physical and biological structure. Deep Sea Res. Part II 45, 1617–1638 (1998).ADS 
    Article 

    Google Scholar 
    45.Croll, D. A. et al. From wind to whales: trophic links in a coastal upwelling system. Mar. Ecol. Prog. Ser. 289, 117–130 (2005).ADS 
    Article 

    Google Scholar 
    46.Walker, D. & Peterson, W. Relationships between hydrography, phytoplankton production, biomass, cell size and species composition, and copepod production in the southern Benguela upwelling system in April 1988. S. Afr. J. Mar. Sci. 11, 289–305 (1991).Article 

    Google Scholar 
    47.Stuart, V. & Pillar, S. Diel grazing patterns of all ontogenetic stages of Euphausia lucens and in situ predation rates on copepods in the southern Benguela upwelling region. Mar. Ecol. Progr. Ser. 2, 227–241 (1990).ADS 
    Article 

    Google Scholar 
    48.Clapham, P. & Baker, C. (Academic, New York, 2002).49.Shannon, L. J., Field, J. G. & Moloney, C. L. Simulating anchovy–sardine regime shifts in the southern Benguela ecosystem. Ecol. Model. 172, 269–281 (2004).Article 

    Google Scholar 
    50.Lett, C., Roy, C., Levasseur, A., Van Der Lingen, C. D. & Mullon, C. Simulation and quantification of enrichment and retention processes in the southern Benguela upwelling ecosystem. Fish. Oceanogr. 15, 363–372. https://doi.org/10.1111/j.1365-2419.2005.00392.x (2006).Article 

    Google Scholar 
    51.Branch, T. A. Humpback whale abundance south of 60°S from three complete circumpolar sets of surveys. J. Cetacean Res. Manage. https://doi.org/10.47536/jcrm.vi.305 (2011).Article 

    Google Scholar 
    52.Findlay, K., Best, P. & Meÿer, M. Migrations of humpback whales past Cape Vidal, South Africa, and an estimate of the population increase rate (1988–2002). Afr. J. Mar. Sci. 33, 375–392. https://doi.org/10.2989/1814232x.2011.637345 (2011).Article 

    Google Scholar 
    53.Henson, S. A., Cole, H. S., Hopkins, J., Martin, A. P. & Yool, A. Detection of climate change-driven trends in phytoplankton phenology. Glob. Change Biol. 24, e101–e111 (2018).ADS 
    Article 

    Google Scholar 
    54.Carvalho, I. et al. Does temporal and spatial segregation explain the complex population structure of humpback whales on the coast of West Africa?. Mar. Biol. 161, 805–819 (2014).Article 

    Google Scholar 
    55.Kershaw, F. et al. Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales. Mol. Ecol. 26, 977–994 (2017).Article 

    Google Scholar 
    56.Korrûbel, J. An age-structured simulation model to investigate species replacement between pilchard and anchovy populations in the southern Benguela. S. Afr. J. Mar. Sci. 12, 375–391 (1992).Article 

    Google Scholar 
    57.Shannon, L. et al. The 1980s–a decade of change in the Benguela ecosystem. S. Afr. J. Mar. Sci. 12, 271–296 (1992).Article 

    Google Scholar 
    58.Verheye, H., Richardson, A., Hutchings, L., Marska, G. & Gianakouras, D. Long-term trends in the abundance and community structure of coastal zooplankton in the southern Benguela system, 1951–1996. Afr. J. Mar. Sci. 19, 2 (1998).
    Google Scholar 
    59.Bakun, A. Global climate change and intensification of coastal ocean upwelling. Science 247, 198–201 (1990).ADS 
    CAS 
    Article 

    Google Scholar 
    60.Sydeman, W. et al. Climate change and wind intensification in coastal upwelling ecosystems. Science 345, 77–80 (2014).ADS 
    CAS 
    Article 

    Google Scholar 
    61.Bonino, G., Di Lorenzo, E., Masina, S. & Iovino, D. Interannual to decadal variability within and across the major eastern boundary upwelling systems. Sci. Rep. 9, 1–14 (2019).Article 

    Google Scholar 
    62.Fearon, G. et al. Enhanced vertical mixing in coastal upwelling systems driven by diurnal-inertial resonance: Numerical experiments. J. Geophys. Res. Oceans https://doi.org/10.1002/essoar.10502743.1 (2020).Article 

    Google Scholar 
    63.Xiu, P., Chai, F., Curchitser, E. N. & Castruccio, F. S. Future changes in coastal upwelling ecosystems with global warming: The case of the California Current System. Sci. Rep. 8, 1–9 (2018).
    Google Scholar 
    64.Roxy, M. K. et al. A reduction in marine primary productivity driven by rapid warming over the tropical Indian Ocean. Geophys. Res. Lett. 43, 826–833 (2016).ADS 
    Article 

    Google Scholar 
    65.Lockerbie, E. M. & Shannon, L. Toward exploring possible future states of the southern Benguela. Front. Mar. Sci. 6, 380 (2019).Article 

    Google Scholar 
    66.Ortega-Cisneros, K., Cochrane, K. L., Fulton, E. A., Gorton, R. & Popova, E. Evaluating the effects of climate change in the southern Benguela upwelling system using the Atlantis modelling framework. Fish. Oceanogr. 27, 489–503 (2018).Article 

    Google Scholar 
    67.Rykaczewski, R. R. & Checkley, D. M. Influence of ocean winds on the pelagic ecosystem in upwelling regions. Proc. Natl. Acad. Sci. 105, 1965–1970 (2008).ADS 
    CAS 
    Article 

    Google Scholar 
    68.Veitch, J. A. & Penven, P. The role of the A gulhas in the B enguela current system: A numerical modeling approach. J. Geophys. Res. Oceans 122, 3375–3393 (2017).ADS 
    Article 

    Google Scholar 
    69.Beal, L. M., De Ruijter, W. P., Biastoch, A. & Zahn, R. On the role of the Agulhas system in ocean circulation and climate. Nature 472, 429–436 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    70.Beal, L. M. & Elipot, S. Broadening not strengthening of the Agulhas current since the early 1990s. Nature 540, 570–573 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    71.Lilliefors, H. W. On the Kolmogorov-Smirnov test for the exponential distribution with mean unknown. J. Am. Stat. Assoc. 64, 387–389. https://doi.org/10.1080/01621459.1969.10500983 (1969).Article 

    Google Scholar 
    72.Shchepetkin, A. F. & McWilliams, J. C. The regional oceanic modeling system (ROMS): A split-explicit, free-surface, topography-following-coordinate oceanic model. Ocean Model 9, 347–404. https://doi.org/10.1016/j.ocemod.2004.08.002 (2005).ADS 
    Article 

    Google Scholar 
    73.Debreu, L., Marchesiello, P., Penven, P. & Cambon, G. Two-way nesting in split-explicit ocean models: Algorithms, implementation and validation. Ocean Model 49, 1–21. https://doi.org/10.1016/j.ocemod.2012.03.003 (2012).ADS 
    Article 

    Google Scholar 
    74.Shchepetkin, A. F. & McWilliams, J. C. Quasi-monotone advection schemes based on explicit locally adaptive dissipation. Mon. Weather Rev. 126, 1541–1580. https://doi.org/10.1175/1520-0493(1998)126%3C1541:qmasbo%3E2.0.co;2 (1998).ADS 
    Article 

    Google Scholar 
    75.Warner, J. C., Sherwood, C. R., Arango, H. G. & Signell, R. P. Performance of four turbulence closure models implemented using a generic length scale method. Ocean Model 8, 81–113. https://doi.org/10.1016/j.ocemod.2003.12.003 (2005).ADS 
    Article 

    Google Scholar 
    76.Saha, S. et al. NCEP Climate Forecast System Reanalysis (CFSR) 6-Hourly Products, January 1979 to December 2010 (Boulder, 2010).
    Google Scholar 
    77.Saha, S. et al. NCEP Climate Forecast System Version 2 (CFSv2) 6-hourly Products. D61C61TXF (Boulder, 2011).
    Google Scholar 
    78.Burchard, H. & Hofmeister, R. A dynamic equation for the potential energy anomaly for analysing mixing and stratification in estuaries and coastal seas. Estuar. Coast. Shelf Sci. 77, 679–687. https://doi.org/10.1016/j.ecss.2007.10.025 (2008).ADS 
    Article 

    Google Scholar 
    79.Yamaguchi, R., Suga, T., Richards, K. J. & Qiu, B. Diagnosing the development of seasonal stratification using the potential energy anomaly in the North Pacific. Clim. Dyn. 53, 4667–4681. https://doi.org/10.1007/s00382-019-04816-y (2019).Article 

    Google Scholar 
    80.Lennard, C., Hahmann, A. N., Badger, J., Mortensen, N. G. & Argent, B. Development of a numerical wind atlas for South Africa. Energy Proc. 76, 128–137. https://doi.org/10.1016/j.egypro.2015.07.873 (2015).Article 

    Google Scholar 
    81.Thomson, R. E. & Emery, W. J. Data Analysis Methods in Physical Oceanography 3rd edn. (Elsevier, 2014).
    Google Scholar  More

  • in

    Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters

    1.Collins, M. et al. SPM6 Extremes, abrupt changes and managing risks. In: IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (eds. Pörtner, H.-O. et al.) 589-655 (In press, 2019).2.Hegerl, G. C., Hanlon, H. & Beierkuhnlein, C. Elusive extremes. Nat. Geosci. 4, 142–143 (2011).CAS 
    Article 

    Google Scholar 
    3.Bérard, A., Ben Sassi, M., Renault, P. & Gros, R. Severe drought-induced community tolerance to heat wave. An experimental study on soil microbial processes. J. Soils Sediment. 12, 513–518 (2012).Article 

    Google Scholar 
    4.Schimel, J., Balser, T. C. & Wallenstein, M. Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386–1394 (2007).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    5.Acosta-Martínez, V. et al. Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling. Appl. Soil Ecol. 84, 69–82 (2014).Article 

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

    Google Scholar 
    7.Frölicher, T. L. & Laufkötter, C. Emerging risks from marine heat waves. Nat. Commun. 9, 650 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

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

    Google Scholar 
    9.Wernberg, T. et al. An extreme climatic event alters marine ecosystem structure in a global biodiversity hotspot. Nat. Clim. Change 3, 78–82 (2013).Article 

    Google Scholar 
    10.Bond, N. A., Cronin, M. F., Freeland, H. & Mantua, N. Causes and impacts of the 2014 warm anomaly in the NE Pacific. Geophys. Res. Lett. 9, 3414–3420 (2015).11.Freeland, H. & Ross, T. ‘The Blob’—or, how unusual were ocean temperatures in the Northeast Pacific during 2014-2018? Deep Sea Res. Part I: Oceanographic Res. Pap. 150, 103061 (2019).Article 

    Google Scholar 
    12.Lorenzo, E. D. & Mantua, N. Multi-year persistence of the 2014/15 North Pacific marine heatwave. Nat. Clim. Change 6, 1042–1047 (2016).Article 

    Google Scholar 
    13.Peña, M. A., Nemcek, N. & Robert, M. Phytoplankton responses to the 2014–2016 warming anomaly in the northeast subarctic Pacific Ocean. Limnol. Oceanogr. 64, 515–525 (2019).Article 

    Google Scholar 
    14.Yang, B., Emerson, S. R. & Peña, M. A. The effect of the 2013–2016 high temperature anomaly in the subarctic Northeast Pacific (the “Blob”) on net community production. Biogeosciences 15, 6747–6759 (2018).CAS 
    Article 

    Google Scholar 
    15.Cavole, L. et al. Biological impacts of the 2013–2015 warm-water anomaly in the Northeast Pacific: winners, losers, and the future. Oceanography 29, 273–285 (2016).16.Azam, F. et al. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10, 257–263 (1983).Article 

    Google Scholar 
    17.Sarmento, Hugo, Montoya, JoséM., Vázquez-Domínguez, Evaristo, Vaqué, Dolors & Gasol, JosepM. Warming effects on marine microbial food web processes: how far can we go when it comes to predictions? Philos. Trans. R. Soc. B: Biol. Sci. 365, 2137–2149 (2010).Article 

    Google Scholar 
    18.Joint, I. & Smale, D. A. Marine heatwaves and optimal temperatures for microbial assemblage activity. FEMS Microbiol Ecol 93, fiw243 (2017).19.Deschaseaux, E. O., Brien, J., Siboni, N., Petrou, K. & Seymour, J. R. Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate Alexandrium minutum during a simulated marine heatwave. Biogeosciences 16, 4377–4391 (2019).CAS 
    Article 

    Google Scholar 
    20.Hawley, A. K. et al. Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat. Commun. 8, 1507 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    21.Allers, E. et al. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISME J. 7, 256–268 (2013).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Roux, S. et al. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife 3, e03125 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Wright, J. J. et al. Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. ISME J. 8, 455–468 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    24.Sherry, N. D., Boyd, P. W., Sugimoto, K. & Harrison, P. J. Seasonal and spatial patterns of heterotrophic bacterial production, respiration, and biomass in the subarctic NE Pacific. Deep Sea Res. Part II Top. Stud. Oceanogr. 46, 2557–2578 (1999).25.Harrison, P. J. Station Papa Time Series: insights into ecosystem dynamics. J. Oceanogr. 58, 259–264 (2002).CAS 
    Article 

    Google Scholar 
    26.Mende, D. R. et al. Environmental drivers of a microbial genomic transition zone in the ocean’s interior. Nat. Microbiol. 2, 1367–1373 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    27.Pommier, T. et al. Global patterns of diversity and community structure in marine bacterioplankton. Mol. Ecol. 16, 867–880 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    28.Cram, J. A. et al. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J. 9, 563–580 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    29.Freeland, H. J. Evidence of change in the winter mixed layer in the Northeast Pacific Ocean: a problem revisited. Atmos. Ocean 51, 126–133 (2013).CAS 
    Article 

    Google Scholar 
    30.Stevens, H. & Ulloa, O. Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific. Environ. Microbiol. 10, 1244–1259 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    31.Bryant, J. A., Stewart, F. J., Eppley, J. M. & DeLong, E. F. Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology 93, 1659–1673 (2012).PubMed 
    Article 

    Google Scholar 
    32.Muck, S. et al. Niche differentiation of aerobic and anaerobic ammonia oxidizers in a high latitude deep oxygen minimum zone. Front. Microbiol. 10, 2141 (2019).33.Medina Faull, L., Mara, P., Taylor, G. T. & Edgcomb, V. P. Imprint of trace dissolved oxygen on prokaryoplankton community structure in an oxygen minimum zone. Front. Mar. Sci. 7, 360 (2020).34.Reji, L., Tolar, B. B., Chavez, F. P. & Francis, C. A. Depth-differentiation and seasonality of planktonic microbial assemblages in the monterey bay upwelling system. Front. Microbiol. 11, 1075 (2020).35.Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nat. Rev. Microbiol. 10, 381–394 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    36.Tsementzi, D. et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536, 179–183 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    37.Choi, D. H., Karen, Selph & Noh, J. H. Niche partitioning of picocyanobacterial lineages in the oligotrophic northwestern Pacific Ocean. ALGAE 30, 223–232 (2015).38.Johnson, Z. I. et al. Niche partitioning among prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311, 1737–1740 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    39.Sohm, J. A. et al. Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron. ISME J. 10, 333–345 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    40.Not, F. et al. in Advances in Botanical Research (ed. Piganeau, G.) vol. 64, 1–53 (Academic Press, 2012).41.Lutz, M., Dunbar, R. & Caldeira, K. Regional variability in the vertical flux of particulate organic carbon in the ocean interior. Glob. Biogeochemical Cycles 16, 11-1–11–18 (2002).
    Google Scholar 
    42.Richardson, T. L., Jackson, G. A., Ducklow, H. W. & Roman, M. R. Carbon fluxes through food webs of the eastern equatorial Pacific: an inverse approach. Deep Sea Res. Part I: Oceanographic Res. Pap. 51, 1245–1274 (2004).CAS 
    Article 

    Google Scholar 
    43.Michaels, A. F. & Silver, M. W. Primary production, sinking fluxes and the microbial food web. Deep Sea Res. Part A. Oceanographic Res. Pap. 35, 473–490 (1988).Article 

    Google Scholar 
    44.Dufrêne, M. & Legendre, P. Species assemblages and indicator species:the need for a flexible asymmetrical approach. Ecol. Monogr. 67, 345–366 (1997).
    Google Scholar 
    45.Cáceres, M. D., Legendre, P. & Moretti, M. Improving indicator species analysis by combining groups of sites. Oikos 119, 1674–1684 (2010).Article 

    Google Scholar 
    46.Shade, A. et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 5, e01371-14 (2014).47.Thrash, J. C. et al. Metabolic Roles of Uncultivated Bacterioplankton lineages in the Northern Gulf of Mexico “Dead Zone”. mBio 8, e01017-17 (2017).48.Kirchman, D. L. The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiol Ecol. 39, 91–100 (2002).CAS 
    PubMed 

    Google Scholar 
    49.Alonso, C., Warnecke, F., Amann, R. & Pernthaler, J. High local and global diversity of Flavobacteria in marine plankton. Environ. Microbiol. 9, 1253–1266 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    50.Teeling, H. et al. Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. eLife 5, e11888 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    51.Selje, N., Simon, M. & Brinkhoff, T. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427, 445 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    52.Buchan, A., González, J. M. & Moran, M. A. Overview of the marine Roseobacter lineage. Appl. Environ. Microbiol. 71, 5665–5677 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    53.Luo, H. & Moran, M. A. Evolutionary ecology of the marine roseobacter clade. Microbiol. Mol. Biol. Rev. 78, 573–587 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    54.Simon, M. et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J. 11, 1483–1499 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    55.Sato, S. et al. Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal. Sci. Rep. 10, 9449 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Sañudo-Wilhelmy, S. A., Gómez-Consarnau, L., Suffridge, C. & Webb, E. A. The role of B vitamins in marine biogeochemistry. Annu. Rev. Mar. Sci. 6, 339–367 (2014).Article 

    Google Scholar 
    57.Landa, M. et al. Sulfur metabolites that facilitate oceanic phytoplankton–bacteria carbon flux. ISME J. 13, 2536–2550 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    58.Georges, A. A., El-Swais, H., Craig, S. E., Li, W. K. & Walsh, D. A. Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton. ISME J. 8, 1301–1313 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    59.Baker, B. J., Lazar, C. S., Teske, A. P. & Dick, G. J. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome 3, 14 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Andrei, A.-Ş. et al. Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. ISME J 13, 1056–1071 (2019).61.Fukunaga, Y. et al. Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes. J. Gen. Appl. Microbiol. 55, 267–275 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    62.Gade, D., Stührmann, T., Reinhardt, R. & Rabus, R. Growth phase dependent regulation of protein composition in Rhodopirellula baltica. Environ. Microbiol. 7, 1074–1084 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    63.Luecker, S., Nowka, B., Rattei, T., Spieck, E. & Daims, H. The genome of nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front. Microbiol. 4, 27 (2013).64.Winder, M. & Schindler, D. E. Climate change uncouples trophic interactions in an aquatic ecosystem. Ecology 85, 2100–2106 (2004).Article 

    Google Scholar 
    65.Brown, M. V. et al. Global biogeography of SAR11 marine bacteria. Mol. Syst. Biol. 8, 595 (2012).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    66.Haro‐Moreno, J. M. et al. Ecogenomics of the SAR11 clade. Environ. Microbiol 22, 1748–1763 (2020).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    67.Grote, J. et al. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3, e00252–12 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    68.Giovannoni, S. J. SAR11 Bacteria: The Most Abundant Plankton in the Oceans. Annu. Rev. Mar. Sci. 9, 231–255 (2017).Article 

    Google Scholar 
    69.Getz, E. W., Tithi, S. S., Zhang, L. & Aylward, F. O. Parallel evolution of genome streamlining and cellular bioenergetics across the marine radiation of a bacterial phylum. mBio. 9, e01089-18 (2018).70.Aylward, F. O. & Santoro, A. E. Heterotrophic thaumarchaea with small genomes are widespread in the dark ocean. mSystems 5, e00415-20 (2020).71.Prosser, J. I. & Nicol, G. W. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ. Microbiol. 10, 2931–2941 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    72.Santoro, A. E., Casciotti, K. L. & Francis, C. A. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environ. Microbiol. 12, 1989–2006 (2010).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    73.Horak, R. E. A. et al. Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea. ISME J. 7, 2023–2033 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    74.Qin, W. et al. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. PNAS 111, 12504–12509 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    75.Rinke, C. et al. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J. 13, 663 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    76.Haro-Moreno, J. M., Rodriguez-Valera, F., López-García, P., Moreira, D. & Martin-Cuadrado, A.-B. New insights into marine group III Euryarchaeota, from dark to light. ISME J. 11, 1102–1117 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    77.Orsi, W. D. et al. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. ISME J. 10, 2158–2173 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Orsi, W. D. et al. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME J. 9, 1747–1763 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    79.Hugoni, M. et al. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc. Natl Acad. Sci. USA 110, 6004–6009 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    80.Matheus Carnevali, P. B. et al. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat. Commun. 10, 463 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    81.Saw, J. H. W. et al. Pangenomics analysis reveals diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria. mBio 11, e02975-19 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    82.Alonso‐Sáez, L., Díaz‐Pérez, L. & Morán, X. A. G. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton. Environ. Microbiol. 17, 3766–3780 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    83.Lambert, S. et al. Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations. ISME J. 13, 388–401 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    84.Mehrshad, M., Rodriguez-Valera, F., Amoozegar, M. A., López-García, P. & Ghai, R. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME J. 12, 655–668 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    85.Mullins, T. D., Britschgi, T. B., Krest, R. L. & Giovannoni, S. J. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40, 148–158 (1995).CAS 
    Article 

    Google Scholar 
    86.Acinas, S. G., Antón, J. & Rodríguez-Valera, F. Diversity of free-living and attached bacteria in offshore western mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microbiol. 65, 514–522 (1999).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    87.Hoarfrost, A. et al. Global ecotypes in the ubiquitous marine clade SAR86. ISME J. 14, 178–188 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    88.Alonso-Sáez, L., Galand, P. E., Casamayor, E. O., Pedrós-Alió, C. & Bertilsson, S. High bicarbonate assimilation in the dark by Arctic bacteria. ISME J. 4, 1581–1590 (2010).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    89.Swan, B. K. et al. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296–1300 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    90.Maldonado, M. T., Boyd, P. W., Harrison, P. J. & Price, N. M. Co-limitation of phytoplankton growth by light and Fe during winter in the NE subarctic Pacific Ocean. Deep Sea Res. Part II: Topical Stud. Oceanogr. 46, 2475–2485 (1999).CAS 
    Article 

    Google Scholar 
    91.Peña, M. A. & Varela, D. E. Seasonal and interannual variability in phytoplankton and nutrient dynamics along Line P in the NE subarctic Pacific. Prog. Oceanogr. 75, 200–222 (2007).Article 

    Google Scholar 
    92.Whitney, F. A., Wong, C. S. & Boyd, P. W. Interannual variability in nitrate supply to surface waters of the Northeast Pacific Ocean. Mar. Ecol. Prog. Ser. 170, 15–23 (1998).CAS 
    Article 

    Google Scholar 
    93.Crawford, W., Galbraith, J. & Bolingbroke, N. Line P ocean temperature and salinity, 1956–2005. Prog. Oceanogr. 75, 161–178 (2007).Article 

    Google Scholar 
    94.Whitney, F. A. & Freeland, H. J. Variability in upper-ocean water properties in the NE Pacific Ocean. Deep Sea Res. Part II: Topical Stud. Oceanogr. 46, 2351–2370 (1999).CAS 
    Article 

    Google Scholar 
    95.Whitney, F. A., Freeland, H. J. & Robert, M. Persistently declining oxygen levels in the interior waters of the eastern subarctic Pacific. Prog. Oceanogr. 75, 179–199 (2007).Article 

    Google Scholar 
    96.Siegel, D. A. et al. Prediction of the Export and Fate of Global Ocean Net Primary Production: The EXPORTS Science Plan. Front. Mar. Sci. 3, 030 (2016).97.Buesseler, K. O. et al. High-resolution spatial and temporal measurements of particulate organic carbon flux using thorium-234 in the northeast Pacific Ocean during the EXport Processes in the Ocean from RemoTe Sensing field campaign. Elementa: Sci. Anthrop. 8, (2020).98.Stephens, B. M. et al. Organic matter composition at ocean station papa affects its bioavailability, bacterioplankton growth efficiency and the responding taxa. Front. Mar. Sci. 7, 590273 (2020).99.Mackinson, B. L., Moran, S. B., Lomas, M. W., Stewart, G. M. & Kelly, R. P. Estimates of micro-, nano-, and picoplankton contributions to particle export in the northeast Pacific. Biogeosciences 12, 3429–3446 (2015).Article 

    Google Scholar 
    100.Fisher, J. et al. Copepod responses to, and recovery from, the recent marine heatwave in the Northeast Pacific. PICES Sci. 2019: Notes Sci. Board Chair 28, 65 (2020).
    Google Scholar 
    101.Batten, S. D. et al. Interannual variability in lower trophic levels on the Alaskan Shelf. Deep Sea Res. Part II: Topical Stud. Oceanogr. 147, 58–68 (2018).Article 

    Google Scholar 
    102.Geider, R. & Roche, J. L. Redfield revisited: variability of C:N:P in marine microalgae and its biochemical basis. Eur. J. Phycol. 37, 1–17 (2002).Article 

    Google Scholar 
    103.Wohlers, J. et al. Changes in biogenic carbon flow in response to sea surface warming. Proc.Natl. Acad. Sci. USA 106, 7067–7072 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    104.Bif, M. B. & Hansell, D. A. Seasonality of dissolved organic carbon in the upper Northeast Pacific Ocean. Glob. Biogeochem. Cycles 33, 526–539 (2019).CAS 
    Article 

    Google Scholar 
    105.Ferrer-González, F. X. et al. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME J. https://doi.org/10.1038/s41396-020-00811-y. (2020).106.Gies, E. A., Konwar, K. M., Beatty, J. T. & Hallam, S. J. Illuminating microbial dark matter in meromictic Sakinaw Lake. Appl. Environ. Microbiol. 80, 6807–6818 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    107.Pachiadaki, M. G. et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179, 1623–1635.e11 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    108.Fuhrman, J. A. et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl Acad. Sci. USA 103, 13104–13109 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    109.Ono, T., Shiomoto, A. & Saino, T. Recent decrease of summer nutrients concentrations and future possible shrinkage of the subarctic North Pacific high-nutrient low-chlorophyll region. Global Biogeochemical Cycles 22, GB3027 (2008).110.Walsh, D. A., Zaikova, E. & Hallam, S. J. Small Volume (1-3L) Filtration of Coastal Seawater Samples. JoVE https://doi.org/10.3791/1163 (2009).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    111.Barwell-Clarke, J. & Whitney, F. Institute of Ocean Sciences nutrient Methods and Analysis. (1996).112.Zapata, M., Rodríguez, F. & Garrido, J. L. Separation of chlorophylls and carotenoids from marine phytoplankton: a new HPLC method using a reversed phase C8 column and pyridine-containing mobile phases. Mar. Ecol. Prog. Ser. 195, 29–45 (2000).CAS 
    Article 

    Google Scholar 
    113.Nemcek, N. & Peña, M. A. Institute of Ocean Sciences Protocols for Phytoplankton Pigment Analysis by HPLC. (2014).114.Wright, J. J., Lee, S., Zaikova, E., Walsh, D. A. & Hallam, S. J. DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation. J. Vis. Exp. e1352, https://doi.org/10.3791/1352 (2009).115.Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    116.Rivers, A. R. iTag amplicon sequencing for taxonomix identification at JGI. http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2013/05/iTagger-methods-1.pdf (2016).117.Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    118.Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    119.Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    120.Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    121.Yilmaz, P. et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 42, D643–D648 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    122.Bolyen, E. et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Nat. Biotechnol. 37, 852–857 (2019).123.R Core Team. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, 2018).124.Rstudio Team. Rstudio: Integrated Development Environment for R (Rstudio Inc, 2016).125.Faust, K. & Raes, J. CoNet app: inference of biological association networks using Cytoscape. F1000Res 5, 1519 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    126.Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498–2504 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Identification of ecological networks and nodes in Fujian province based on green and blue corridors

    1.Garcia-Garcia, M. J., Christien, L., García-Escalona, E. & González-García, C. Sensitivity of green spaces to the process of urban planning: Three case studies of Madrid (Spain). Cities 100, 102655. https://doi.org/10.1016/j.cities.2020.102655 (2020).Article 

    Google Scholar 
    2.Kondo, M. C., Fluehr, J. M., McKeon, T. & Branas, C. C. Urban green space and its impact on human health. Environ. Res. Public Health 15(3), 445. https://doi.org/10.3390/ijerph15030445 (2018).Article 

    Google Scholar 
    3.Nesbitt, L. et al. The social and economic value of cultural ecosystem services provided by urban forests in North America: A review and suggestions for future research. Urban For. Urban Green. 25, 103–111. https://doi.org/10.1016/j.ufug.2017.05.005 (2017).Article 

    Google Scholar 
    4.Hasan, S. S., Zhen, L., Miah, G., Ahamed, T. & Samie, A. Impact of land use change on ecosystem services: A review. Environ. Dev. 34, 100527. https://doi.org/10.1016/j.envdev.2020.100527 (2020).Article 

    Google Scholar 
    5.Kolodziejczyk, B. et al. Frontiers 2018/19: Emerging issues of environmental concern. United Nations Environment Programme, Nairobi, 24–37 (2019).6.Steffen, W., Crutzen, P. J. & McNeill, J. R. The anthropocene: Are humans now overwhelming the great forces of nature. Hum. Environ. 36(8), 614–621. https://doi.org/10.1579/0044-7447(2007)36[614:TAAHNO]2.0.CO;2 (2007).CAS 
    Article 

    Google Scholar 
    7.CC & SC. Views on Accelerating the Ecological Civilization Construction (2015).8.Ministry of Housing and Urban-Rural Development (MHURD). City Green Space Planning Standards, GB/T51346-2019 (2019).9.Raei, E. et al. Multi-objective decision-making for green infrastructure planning (LID-BMPs) in urban storm water management under uncertainty. J. Hydrol. 579, 124091. https://doi.org/10.1016/j.jhydrol.2019.124091 (2019).CAS 
    Article 

    Google Scholar 
    10.Tzoulas, K. et al. Promoting ecosystem and human health in urban areas using Green Infrastructure: A literature review. Landsc. Urban Plan. 81(3), 167–178. https://doi.org/10.1016/j.landurbplan.2007.02.001 (2007).Article 

    Google Scholar 
    11.Xiao, F., Shu, J. & Zhang, L. Research on applying minimal cumulative resistance model in urban land ecological suitability assessment: As an example of Xiamen City. Acta Ecol. Sin. 30(2), 421–428 (2010).
    Google Scholar 
    12.Zhao, S., Ma, Y., Wang, J. & You, X. Landscape pattern analysis and ecological network planning of Tianjin City. Urban For. Urban Green. 46, 126479. https://doi.org/10.1016/j.ufug.2019.126479 (2019).Article 

    Google Scholar 
    13.Davies, C. & Lafortezza, R. Urban green infrastructure in Europe: Is greenspace planning and policy compliant? Land Use Policy 69, 93–101. https://doi.org/10.1016/j.landusepol.2017.08.018 (2017).Article 

    Google Scholar 
    14.Central Committee & State Council (CC & SC). Views on establishment and monitoring of Territorial Space Planning system (2019).15.Zhou, Q. et al. China’s Green space system planning: Development, experiences, and characteristics. Urban For. Urban Green. 60, 127017. https://doi.org/10.1016/j.ufug.2021.127017 (2021).Article 

    Google Scholar 
    16.Zhou, X., Zhang, S. & Zhu, D. Impact of urban water networks on microclimate and PM25 distribution in downtown areas: A case study of wuhan. Build. Environ. 203, 108073. https://doi.org/10.1016/j.buildenv.2021.108073 (2021).Article 

    Google Scholar 
    17.Ministry of Natural Resources (MNR). Guidelines for Formulation of Provincial Territorial Space Planning (Trial) (2020).18.Rushdi, A. M. A. & Hassan, A. K. Reliability of migration between habitat patches with heterogeneous ecological corridors. Ecol. Model. 304, 1–10. https://doi.org/10.1016/j.ecolmodel.2015.02.014 (2015).Article 

    Google Scholar 
    19.Wang, T., Li, H. & Huang, Y. The complex ecological network’s resilience of the Wuhan metropolitan area. Ecol. Ind. 130, 108101. https://doi.org/10.1016/j.ecolind.2021.108101 (2021).Article 

    Google Scholar 
    20.Wu, H. et al. A novel remote sensing ecological vulnerability index on large scale: A case study of the China-Pakistan Economic Corridor region. Ecol. Ind. 129, 107955. https://doi.org/10.1016/j.ecolind.2021.107955 (2021).Article 

    Google Scholar 
    21.Janauer, G. A. Ecohydrology: Fusing concepts and scales. Ecol. Eng. 16(1), 9–16. https://doi.org/10.1016/S0925-8574(00)00072-0 (2000).Article 

    Google Scholar 
    22.Rinaldo, A., Gatto, M. & Rodriguez-Iturbe, I. River networks as ecological corridors: A coherent ecohydrological perspective. Adv. Water Resour. 112, 27–58. https://doi.org/10.1016/j.advwatres.2017.10.005 (2018).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Fletcher, T. D. et al. SUDS, LID, BMPs, WSUD and more: The evolution and application of terminology surrounding urban drainage. Urban Water J. 12(7), 525–542. https://doi.org/10.1080/1573062X.2014.916314 (2015).Article 

    Google Scholar 
    24.Nieuwenhuis, E., Cuppen, E., Langeveld, J. & Bruijn, H. Towards the integrated management of urban water systems: Conceptualizing integration and its uncertainties. J. Clean. Prod. 280(2), 124977. https://doi.org/10.1016/j.jclepro.2020.124977 (2021).Article 

    Google Scholar 
    25.Knaapen, J. P., Scheffer, M. & Harms, B. Estimating habitat isolation in landscape planning. Landscape Urban Plann. 23(1), 1–16. https://doi.org/10.1016/0169-2046(92)90060-D (1992).Article 

    Google Scholar 
    26.Yu, K. Security patterns and surface model in landscape ecological planning. Landscape Urban Plann. 36(1), 1–17. https://doi.org/10.1016/S0169-2046(96)00331-3 (1996).Article 

    Google Scholar 
    27.Yu, K. Landscape ecological security pattern of biological protection. Acta Ecologica Sinica 1, 3–5 (1999).
    Google Scholar 
    28.Zhang, Z., Meerow, S., Newell, J. P. & Lindquist, M. Enhancing landscape connectivity through multifunctional green infrastructure corridor modeling and design. Urban For. Urban Green. 38, 305–317. https://doi.org/10.1016/j.ufug.2018.10.014 (2019).Article 

    Google Scholar 
    29.Fu, Y., Shi, X., He, J., Yuan, Y. & Qu, L. Identification and optimization strategy of county ecological security pattern: A case study in the Loess Plateau, China. Ecol. Ind. 112, 106030. https://doi.org/10.1016/j.ecolind.2019.106030 (2020).Article 

    Google Scholar 
    30.Kong, F., Yin, H., Nakagoshi, N. & Zong, Y. Urban green space network development for biodiversity conservation: Identification based on graph theory and gravity modeling. Landsc. Urban Plan. 95, 16–27. https://doi.org/10.1016/j.landurbplan.2009.11.001 (2010).Article 

    Google Scholar 
    31.Kong, F. & Yin, H. Construction of Jinan urban green space ecological network. Acta Ecol. Sin. 4, 1711–1719 (2008).
    Google Scholar 
    32.Linehan, J., Gross, M. & Finn, J. Greenway planning: Developing a landscape ecological network approach. Landsc. Urban Plan. 33(1–3), 179–193. https://doi.org/10.1016/0169-2046(94)02017-A (1995).Article 

    Google Scholar 
    33.Yang, H., Chen, W. & Chen, X. Regional ecological network planning for biodiversity conservation: A case study of China’s Poyang lake eco-economic region. Pol. J. Environ. Stud. 26(4), 1825–1833. https://doi.org/10.15244/pjoes/68877 (2017).Article 

    Google Scholar 
    34.Fahrig, L. Rethinking patch size and isolation effects: The habitat amount hypothesis. J. Biogeogr. 40(9), 1649–1663. https://doi.org/10.1111/jbi.12130 (2013).Article 

    Google Scholar 
    35.Gilbert-Norton, L., Wilson, R., Stevens, J. R. & Beard, K. H. A meta-analytic review of corridor effectiveness. Conserv. Biol. 24(3), 660–668. https://doi.org/10.1111/j.1523-1739.2010.01450.x (2010).Article 
    PubMed 

    Google Scholar 
    36.Saura, S. & Torné, J. Conefor Sensinode 2.2: A software package for quantifying the importance of habitat patches for landscape connectivity. Environ. Model. Softw. 24(1), 135–139. https://doi.org/10.1016/j.envsoft.2008.05.005 (2009).Article 

    Google Scholar 
    37.Saura, S., Vogt, P., Velázquez, J., Hernando, A. & Tejera, R. Key structural forest connectors can be identified by combining landscape spatial pattern and network analyses. For. Ecol. Manag. 262(2), 150–160. https://doi.org/10.1016/j.foreco.2011.03.017 (2011).Article 

    Google Scholar 
    38.Bueno, J. A., Tsihrintzis, V. A. & Alvarez, L. South Florida greenways: a conceptual framework for the ecological reconnectivity of the region. Landsc. Urban Plan. 33(1–3), 247–266. https://doi.org/10.1016/0169-2046(94)02021-7 (1995).Article 

    Google Scholar 
    39.Cook, E. A. Landscape structure indices for assessing urban ecological networks. Landsc. Urban Plan. 58(2–4), 269–280. https://doi.org/10.1016/S0169-2046(01)00226-2 (2002).Article 

    Google Scholar 
    40.Dalton, R., Garlick, J., Minshull, R. & Robinson, A. Networks in Geography (Phillip, 1973).
    Google Scholar 
    41.Forman, R. T. T. & Godron, M. Landscape Ecology (Wiley, 1986).
    Google Scholar 
    42.Haggett, P. & Chorley, R. J. Network Analysis in Geography (Edward Arnold, 1972).
    Google Scholar 
    43.Yu, K. The identification method of landscape ecological strategic points and the surface model of theoretical geography. J. Geog. Sci. S1, 3–5 (1998).
    Google Scholar 
    44.Yu, Q. et al. Optimization of ecological node layout and stability analysis of ecological network in desert oasis: A typical case study of ecological fragile zone located at Deng Kou County (Inner Mongolia). Ecol. Indic. 84, 304–318. https://doi.org/10.1016/j.ecolind.2017.09.002 (2018).Article 

    Google Scholar 
    45.Zhang, Y. & Yu, B. Evaluation of urban ecological network space and its structure optimization. Acta Ecol. Sin. 36(21), 6969–6984 (2016).
    Google Scholar 
    46.Hong, W. et al. Sensitivity evaluation and land-use control of urban ecological corridors: A case study of Shenzhen, China. Land Use Policy 62, 316–325. https://doi.org/10.1016/j.landusepol.2017.01.010 (2017).Article 

    Google Scholar 
    47.Monaco, R., Negrini, G., Salizzoni, E., Soares, A. J. & Voghera, A. Inside-outside park planning: A mathematical approach to assess and support the design of ecological connectivity between Protected Areas and the surrounding landscape. Ecol. Eng. 149, 105748. https://doi.org/10.1016/j.ecoleng.2020.105748 (2020).Article 

    Google Scholar 
    48.Morandi, D. T. et al. Delimitation of ecological corridors between conservation units in the Brazilian Cerrado using a GIS and AHP approach. Ecol. Ind. 115, 106440. https://doi.org/10.1016/j.ecolind.2020.106440 (2020).Article 

    Google Scholar 
    49.Santos, J. S. et al. Delimitation of ecological corridors in the Brazilian Atlantic Forest. Ecol. Ind. 88, 414–424. https://doi.org/10.1016/j.ecolind.2018.01.011 (2018).Article 

    Google Scholar 
    50.Dai, L., Liu, Y., Luo, X. I. & the MCR and, ,. DOI models to construct an ecological security network for the urban agglomeration around Poyang Lake, China. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2020.141868 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    51.Ferreira, C. S. S. et al. Spatiotemporal variability of hydrologic soil properties and the implications for overland flow and land management in a peri-urban Mediterranean catchment. J. Hydrol. 525, 249–263. https://doi.org/10.1016/j.jhydrol.2015.03.039 (2015).ADS 
    Article 

    Google Scholar 
    52.Kalantari, Z. et al. Assessing flood probability for transportation infrastructure based on catchment characteristics, sediment connectivity and remotely sensed soil moisture. Sci. Total Environ. 661, 393–406. https://doi.org/10.1016/j.scitotenv.2019.01.009 (2019).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    53.Kalantari, Z., Ferreira, C. S. S., Walsh, R. P. D., Ferreira, A. J. D. & Destouni, G. Urbanization development under climate change: Hydrological responses in a peri-urban Mediterranean catchment. Land Degrad. Dev. 28, 2207–2221. https://doi.org/10.1002/ldr.2747 (2017).Article 

    Google Scholar 
    54.Grillakis, M. G. et al. Initial soil moisture effects on flash flood generation: A comparison between basins of contrasting hydro-climatic conditions. J. Hydrol. 541(A), 206–217. https://doi.org/10.1016/j.jhydrol.2016.03.007 (2016).ADS 
    Article 

    Google Scholar 
    55.Zhang, K., Fong, T. & Chui, M. A comprehensive review of spatial allocation of LID-BMP-GI practices: Strategies and optimization tools. Sci. Total Environ. 621, 915–929. https://doi.org/10.1016/j.scitotenv.2017.11.281 (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    56.Liu, Z., Lin, Y., De Meulder, B. & Wang, S. Heterogeneous landscapes of urban greenways in Shenzhen: Traffic impact, corridor width and land use. Urban For. Urban Green. 126, 785. https://doi.org/10.1016/j.ufug.2020.126785 (2020).Article 

    Google Scholar 
    57.Wakefield, S. Great expectations: Waterfront redevelopment and the Hamilton Harbour Waterfront Trail. Cities 24(4), 298–310. https://doi.org/10.1016/j.cities.2006.11.001 (2007).Article 

    Google Scholar 
    58.Rimaze, D., Machumu, A., Mremi, R. & Eustace, A. Diversity and abundance of wild mammals between different accommodation facilities in the Kwakuchinja Wildlife Corridor, Tanzania. Sci. Afr. 9, e00480. https://doi.org/10.1016/j.sciaf.2020.e00480 (2020).Article 

    Google Scholar 
    59.Franco, D., Mannino, I. & Zanetto, G. The impact of agroforestry networks on scenic beauty estimation: The role of a landscape ecological network on a socio-cultural process. Landsc. Urban Plan. 62(3), 119–138. https://doi.org/10.1016/S0169-2046(02)00127-5 (2003).Article 

    Google Scholar 
    60.Wu, X. et al. Increasing green infrastructure-based ecological resilience in urban systems: A perspective from locating ecological and disturbance sources in a resource-based city. Sustain. Cities Soc. 61, 102354. https://doi.org/10.1016/j.scs.2020.102354 (2020).Article 

    Google Scholar 
    61.Yang, C., Zeng, W. & Yang, X. Coupling coordination evaluation and sustainable development pattern of geo-ecological environment and urbanization in Chongqing municipality, China. Sustain. Cities Soc. 61, 102271. https://doi.org/10.1016/j.scs.2020.102271 (2020).Article 

    Google Scholar 
    62.Yang, J., Zeng, C. & Cheng, Y. Spatial influence of ecological networks on land use intensity. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2020.137151 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    63.Théau, J., Bernier, A. & Fournier, R. A. An evaluation framework based on sustainability-related indicators for the comparison of conceptual approaches for ecological networks. Ecol. Indic. 52, 444–457. https://doi.org/10.1016/j.ecolind.2014.12.029 (2015).Article 

    Google Scholar 
    64.Neri, M., Jameli, D., Bernard, E. & Melo, F. P. L. Green versus green? Adverting potential conflicts between wind power generation and biodiversity conservation in Brazil. Perspect. Ecol. Conserv. 17(3), 131–135. https://doi.org/10.1016/j.pecon.2019.08.004 (2019).Article 

    Google Scholar 
    65.Zeng, Y. & Zhong, L. Identifying conflicts tendency between nature-based tourism development and ecological protection in China. Ecol. Indic. 109, 105791. https://doi.org/10.1016/j.ecolind.2019.105791 (2020).Article 

    Google Scholar 
    66.Cunha, N. S. & Magalhães, M. R. Methodology for mapping the national ecological network to mainland Portugal: A planning tool towards a green infrastructure. Ecol. Ind. 104, 802–818. https://doi.org/10.1016/j.ecolind.2019.04.050 (2019).Article 

    Google Scholar 
    67.Dong, J., Peng, J., Liu, Y., Qiu, S. & Han, Y. Integrating spatial continuous wavelet transform and kernel density estimation to identify ecological corridors in megacities. Landsc. Urban Plan. 199, 103815. https://doi.org/10.1016/j.landurbplan.2020.103815 (2020).Article 

    Google Scholar 
    68.Gasanov, G. et al. Data on the productivity of plant cover of the main types of soils of the North-Western precaspian in connection with the dynamics of ecological factors. Data Brief 24, 103713. https://doi.org/10.1016/j.dib.2019.103713 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    69.Montis, A. D. et al. Resilient ecological networks: A comparative approach. Land Use Policy 89, 104207. https://doi.org/10.1016/j.landusepol.2019.104207 (2019).Article 

    Google Scholar 
    70.Du, H. et al. Urban blue-green space planning based on thermal environment simulation: A case study of Shanghai, China. Ecol. Indic. 106, 105501. https://doi.org/10.1016/j.ecolind.2019.105501 (2020).Article 

    Google Scholar 
    71.Guo, X. et al. The impact of onshore wind power projects on ecological corridors and landscape connectivity in Shanxi, China. J. Clean. Prod. 254, 120075. https://doi.org/10.1016/j.jclepro.2020.120075 (2020).Article 

    Google Scholar 
    72.Li, J., Wang, Y., Ni, Z., Chen, S. & Xia, B. An integrated strategy to improve the microclimate regulation of green-blue-grey infrastructures in specific urban forms. J. Clean. Prod. 271, 122555. https://doi.org/10.1016/j.jclepro.2020.122555 (2020).Article 

    Google Scholar 
    73.Afriyanie, D. et al. Re-framing urban green spaces planning for flood protection through socio-ecological resilience in Bandung City, Indonesia. Cities 101, 102710. https://doi.org/10.1016/j.cities.2020.102710 (2020).Article 

    Google Scholar 
    74.Ioan-Cristian, I. et al. Integrating urban blue and green areas based on historical evidence. Urban For. Urban Green. 34, 217–225. https://doi.org/10.1016/j.ufug.2018.07.001 (2019).Article 

    Google Scholar 
    75.Jaung, W. L., Carrasco, R., Ahmad, S., Tan, P. Y. & Richards, D. R. Temperature and air pollution reductions by urban green spaces are highly valued in a tropical city-state. Urban For. Urban Green. https://doi.org/10.1016/j.ufug.2020.126827 (2020).Article 

    Google Scholar 
    76.La Sorte, F. A., Aronson, M. F. J., Lepczyk, C. A. & Horton, K. G. Area is the primary correlate of annual and seasonal patterns of avian species richness in urban green spaces. Landsc. Urban Plan. 203, 103892. https://doi.org/10.1016/j.landurbplan.2020.103892 (2020).Article 

    Google Scholar 
    77.Moradpour, M. & Hosseini, V. An investigation into the effects of green space on air quality of an urban area using CFD modeling. Urban Clim. 34, 100686. https://doi.org/10.1016/j.uclim.2020.100686 (2020).Article 

    Google Scholar 
    78.Nouri, H., Borujeni, S. C. & Hoekstra, A. Y. The blue water footprint of urban green spaces: An example for Adelaide, Australia. Landsc. Urban Plan. 190, 103613. https://doi.org/10.1016/j.landurbplan.2019.103613 (2019).Article 

    Google Scholar 
    79.Sikuzani, Y. U. et al. Tree diversity and structure on green space of urban and peri-urban zones: The case of Lubumbashi City in the Democratic Republic of Congo. Urban For. Urban Green. 41, 67–74. https://doi.org/10.1016/j.ufug.2019.03.008 (2019).Article 

    Google Scholar  More

  • in

    Enhancement of extreme events through the Allee effect and its mitigation through noise in a three species system

    One of the most interesting observations from the time series presented in the section above is the following: when the magnitude of the Allee parameter (theta) is low, vegetation and prey densities are confined to low values. However, the predator densities deviate very significantly away from their mean. Now for very small (theta) the system is attracted to a periodic orbit, and so the large deviations are completely correlated with time and occur periodically. So they cannot be considered to be extreme events, as they are neither aperiodic, nor rare. But for larger (theta), both predator and prey densities can sometime shoot up over 7 standard deviations away from the mean value. This is evident clearly in Fig. 2c,e where one can see that both predator and prey populations exceed the (7sigma) threshold from time to time. The instants at which prey and predator populations exceed the (7sigma) threshold are now completely uncorrelated with time. This is consistent with the underlying chaotic dynamics that emerges under increasing Allee parameter (theta).In order to illustrate this, we mark the time instances at which a population exceeds the (7sigma) threshold, for different values of Allee parameter (theta). Figure 4 shows this for the vegetation, prey and predator populations. The density of points signifying the occurrence of extreme events is clearly the highest for the predator population. This indicates that the predator population has the greatest propensity for large deviations. It is also clear that vegetation has the least number of extreme events in the same time window. The uncorrelated nature of the extreme events is also evident in the scatter of these points, except in the small periodic windows that occur for certain special ranges of (theta). The increasing density of these points also illustrate the increasing probability of extreme events in the populations with increasing Allee parameter (theta).Figure 4Figure marking the time instances at which a population exceeds the (7sigma) threshold, for different values of Allee parameter (theta), for the case of (top to bottom) vegetation, prey and predator populations.Full size imageIn order to understand the phenomena quantitatively, we first estimate the maximum densities of vegetation, prey and predator populations (denoted by (u_{max}), (v_{max}) and (w_{max}) respectively) for varying the Allee parameter (theta). To estimate this, we find the global maximum of the populations sampled over a time interval (T=1000), averaged over a large set of random initial conditions.Figure 5 shows (u_{max}), (v_{max}) and (w_{max}), for Allee parameter (theta in [0,theta _{c})), scaled by their values at (theta = 0). These scaled maxima help us gauge the relative change in the maximum population densities arising due to the Allee effect. It is evident from our simulation results that the magnitude of the global maximum of vegetation does not change very significantly for increasing Allee parameter (theta), with its magnitude around (theta _c) being approximately 4 fold the value at (theta =0). However, the magnitude of maximum prey and predator populations change very significantly with respect to Allee parameter (theta) and exceeds over 10 fold the value obtained for (theta =0).Figure 5Global maximum of vegetation (u_{max}) (blue), prey (v_{max}) (red) and predator (black) populations, with respect to the Allee parameter (theta), scaled by their values obtained for (theta =0). Clearly, when Allee parameter (theta) is sufficiently large, the maximum prey and predator populations are an order of magnitude larger than that obtained in systems with no Allee effect.Full size imageWe then go on to numerically calculate the probability density of the vegetation, prey, and predator population densities, for increasing Allee effect parameter (theta). The tail of this probability density function reflects the influence of the Allee effect on the probability of obtaining extreme events. To illustrate this, we show the probability density function for the prey population in Fig. 6, for three different values of (theta). Extreme events are confined to the tail of the distribution that lie beyond the vertical red line, marking the (mu + 7 sigma) value in the figure. So it is clear from these probability distributions that the Allee effect in prey population promotes the occurrence of extreme events as the tail of the distribution is flatter and extends further with increasing Allee parameter (theta).Figure 6Probability Density Function (PDF) of the prey population v, for the system given by Eq. (1), with increasing magnitude of (theta) with (a) (theta =0), (b) (theta =0.015) and (c) (theta =0.02). The threshold for extreme event (mu + 7sigma) is denoted by vertical red dashed line.Full size imageIn order to ascertain that the extreme values are uncorrelated and aperiodic we examine the time intervals between successive extreme events in the population. Figure 7 (left panel) shows representative results for the return map of the intervals between extreme events in the prey population and it is clearly shows no regularity. The probability distribution of the intervals is also Poisson distributed and so the extreme population buildups are uncorrelated aperiodic events, as clearly evident from the right panel of the figure.Figure 7(Left) Return Map of (Delta t_{i+1}) versus (Delta t_i), and (right) Probability distribution of (Delta t_i) fitted with exponentially decaying function, where (Delta t_i) is the ith interval between successive extreme events, where an extreme event is defined at the instant when the prey population crosses the (mu +7sigma) line (cf. Fig. 2). Here (theta =0.024).Full size imageIn order to further quantify how Allee effect influences extreme events, we estimate the probability of obtaining large deviations, in a large sample of initial states tracked over a long period of time. We denote this probability by (P_{ext}), and we calculate it by following a large set of random initial conditions and recording the number of occurrences of the population crossing the threshold value in a prescribed period of time, with this time window being several orders of magnitude larger than the mean oscillation period. This time-averaged and ensemble-averaged quantity yields a good estimate of (P_{ext}). With no loss of generality, we choose the threshold for determining extreme events to be (mu + 7 sigma), i.e. when the variable crosses the (7 sigma) level, it is labelled as extreme.This probability, estimated for all three populations is shown in Fig. 8. First, it is clear from Fig. 8, that the probability of the occurrence of extreme events is the lowest for vegetation, and the highest for predator populations, for any value of the Allee parameter (theta in [0,theta _{c})). We also observe that, for values of the Allee parameter (theta) lower than a critical value denoted by (theta ^{u}_{c}) the probability of obtaining extreme events in the vegetation population tends to zero. Beyond the critical value (theta ^u_c), the vegetation population starts to exhibit extreme events. A similar trend emerges for the prey population. However, the critical value of the Allee parameter (theta) necessary for the emergence of a finite probability of extreme events, denoted by (theta ^{v}_{c}), is much smaller than (theta ^u_c). So for the prey population, a weaker Allee effect can induce extreme events.Figure 8Probability of obtaining extreme event in unit time ((P_{ext})), with respect to Allee parameter (theta), estimated by sampling a time series of length (T=5000), and averaging over 500 random initial states. Here we consider that an extreme event occurs when a population level crosses the threshold (mu + 7sigma). (P_{ext}) for vegetation, prey and predator are displayed in blue, red and black colors respectively. Note that there exists a narrow periodic window around (theta sim 0.02) (cf. Fig. 9), and so the large deviations in this window of Allee parameter are not associated with true extreme events, as they occur periodically.Full size imageNote that some mechanisms have been proposed for the generation of extreme events in deterministic dynamical systems, which typically have been excitable systems. These include interior crisis, Pomeau-Manneville intermittency, and the breakdown of quasiperiodic motion. However the extreme events generated by these mechanisms occur typically at very specific critical points in parameter space, or narrow windows around it. The first important difference in our system here is that the extreme events do not emerge only at some special values alone. Rather, there is a broad range in Allee parameter space where extreme events have a very significant presence. This makes our extreme event phenomenon more robust, and thus increases its potential observability. This also rules out the intermittency-induced mechanisms that have been proposed, as is evident through the lack of sudden expansion in attractor size in our bifurcation diagram (Fig. 3) in general.However, interestingly, the system does have one parameter window where there is attractor widening and this gives rise to a markedly enhanced extreme event count. The peak observed in Fig. 8 can be directly correlated with a sudden attractor widening leading to a marked increase of extreme event in a narrow window of parameter space located near the crisis (see Fig. 9). Additionally, for a narrow window around (theta sim 0.02), the emergent dynamics is periodic. So the large deviations are no longer uncorrelated, and so they are not extreme events in the true sense.Figure 9Bifurcation diagram of prey populations with respect to Allee parameter, in the range (theta in [0.0189 : 0.0191]). Here we display the local maxima of the prey population. The parameter values in Eq. (1) are as mentioned in the text.Full size imageLastly we notice that the predator population shows extreme events for all values of (theta in [0,theta _{c})). So the predator population is most prone to experiencing unusually large deviations from the mean. We also observe that the probability of occurrence of extreme events in the predator population is not affected significantly by the Allee effect. This is in marked contrast to the case of vegetation and prey, where the Allee effect crucially influences the advent of extreme events. Also, for the predator population there is no marked transition from zero to finite (P_{ext}) under increasing Allee parameter (theta), as evident for vegetation and prey populations. More

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    Field evidence for microplastic interactions in marine benthic invertebrates

    1.Geyer, R., Jambeck, J. R. & Law, K. L. Production, use and fate of all plastics ever made. Sci. Adv. 3, e1700782 (2017).2.Napper, I. E. & Thompson, R. C. Marine plastic pollution: other than microplastic in Waste: A Handbook for Management, Second Edition (ed. Letcher, T. & Vallero, D.) chapter 22, 425–442 (Academic Press, 2019).3.Eriksen, M. et al. Plastic pollution in the world’s oceans: more than 5 trillion plastic pieces weighing over 250,000 tons afloat at sea. PLoS ONE 9, e111913 (2014).4.Sharma, S. & Chatterjee, S. Microplastic pollution, a threat to marine ecosystem and human health: a short review. Environ. Sci. Pollut. Res. 24, 21530–21547 (2017).Article 

    Google Scholar 
    5.Rocha-Santos, T. & Duarte, A. C. A critical overview of the analytical approaches to the occurrence, the fate and the behavior or microplastics in the environment. TrAC Trends Anal. Chem. 65, 47–53 (2015).CAS 
    Article 

    Google Scholar 
    6.Cózar, A. et al. Plastic accumulation in the mediterranean sea. PLoS ONE 10, e0121762 (2015).7.Suaria, G. & Aliani, S. Floating debris in the Mediterranean Sea. Mar. Pollut. Bull. 86, 494–504 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Auta, H. S., Emenike, C. U. & Fauziah, S. H. Distribution and importance of microplastics in the marine environment: A review of the sources, fate, effects, and potential solutions. Environ. Int. 102, 165–176 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    9.Woodall, L. C. et al. The deep sea is a major sink for microplastic debris. R. Soc. Open Sci. 1, 140317 (2014).10.Kershaw, P., Turra, A. & Galgani, F. Guidelines for the monitoring and assessment of plastic litter in the ocean. GESAMP Reports and Studies No. 99 (2019).11.Desforges, J. P. W., Galbraith, M. & Ross, P. S. Ingestion of microplastics by zooplankton in the Northeast Pacific Ocean. Arch. Environ. Contam. Toxicol. 69, 320–330 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Van Cauwenberghe, L., Claessens, M., Vandegehuchte, M. B. & Janssen, C. R. Microplastics are taken up by mussels (Mytilus edulis) and lugworms (Arenicola marina) living in natural habitats. Environ. Pollut. 199, 10–17 (2015).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    13.Setälä, O., Norkko, J. & Lehtiniemi, M. Feeding type affects microplastic ingestion in a coastal invertebrate community. Mar. Pollut. Bull. 102, 95–101 (2016).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    14.Amelineau, F. et al. Microplastic pollution in the Greenland Sea: Background levels and selective contamination of planktivorous diving seabirds. Environ. Pollut. 219, 1131–1139 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Zhu, J. et al. Cetaceans and microplastics: First report of microplastic ingestion by a coastal delphinid Sousa chinensis. Sci. Total Environ. 659, 649–654 (2019).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    16.Sbrana, A. et al. Spatial variability and influence of biological parameters on microplastic ingestion by Boops boops (L.) along the Italian coasts (Western Mediterranean Sea). Environ. Pollut. 263, 114429 (2020).17.De Sa, L. C., Luís, L. G. & Guilhermino, L. Effects of microplastics on juveniles of the common goby (Pomatoschistus microps): confusion with prey, reduction of the predatory performance and efficiency, and possible influence of developmental conditions. Environ. Pollut. 196, 359–362 (2015).Article 
    CAS 

    Google Scholar 
    18.Gallitelli, L., Cera, A., Cesarini, G., Pietrelli, L. & Scalici, M. Preliminary indoor evidences of microplastic effects on freshwater benthic macroinvertebrates. Sci. Rep. 11, 720 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Karlsson, T. M. et al. Screening for microplastics in sediment, water, marine invertebrates and fish: Method development and microplastic accumulation. Mar. Pollut. Bull. 122, 403–408 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    20.Bour, A., Avio, C. G., Gorbi, S., Regoli, F. & Hylland, K. Presence of microplastics in benthic and epibenthic organisms: Influence of habitat, feeding mode and trophic level. Environ. Pollut. 243, 1217–1225 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Díaz-Castañeda, V., & Reish, D. Polychaetes in environmental studies in Annelids as Model Systems in the Biological Sciences (ed. Shain, D. H.) chapter 11, 205–227 (Wiley, 2009).22.Gusmão, F. et al. In situ ingestion of microfibres by meiofauna from sandy beaches. Environ. Pollut. 216, 584–590 (2016).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    23.Missawi, O. et al. Abundance and distribution of small microplastics (≤ 3 μm) in sediments and seaworms from the Southern Mediterranean coasts and characterisation of their potential harmful effects. Environ. Pollut. 263, 114634 (2020).24.Piarulli, S. et al. Do different habits affect microplastics contents in organisms? A trait-based analysis on salt marsh species. Mar. Pollut. Bull. 153, 110983 (2020).25.Knutsen, et al. Microplastic accumulation by tube-dwelling, suspension feeding polychaetes from the sediment surface: A case study from the Norwegian Continental Shelf. Mar. Environ. Res. 161, 105073 (2020).26.Lusher, A. L., Welden, N. A., Sobral, P. & Cole, M. Sampling, isolating and identifying microplastics ingested by fish and invertebrates. Anal. Methods 9, 1346–1360 (2017).Article 

    Google Scholar 
    27.Foekema, E. M. et al. Plastics in North Sea fish. Environ. Sci. Technol. 47, 8818–8824 (2013).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    28.Rochman, C. M. et al. Anthropogenic debris in seafood: Plastic debris and fibers from textiles in fish and bivalves sold for human consumption. Sci. Rep. 5, 1–10 (2015).Article 
    CAS 

    Google Scholar 
    29.Avio, C. G., Gorbi, S. & Regoli, F. Experimental development of a new protocol for extraction and characterization of microplastics in fish tissues: First observations in commercial species from Adriatic Sea. Mar. Environ. Res. 111, 18–26 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Li, J., Yang, D., Li, L., Jabeen, K. & Shi, H. Microplastics in commercial bivalves from China. Environ. Pollut. 207, 190–195 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Claessens, M., Van Cauwenberghe, L., Vandegehuchte, M. B. & Janssen, C. R. New techniques for the detection of microplastics in sediments and field collected organisms. Mar. Pollut. Bull. 70, 227–233 (2013).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    32.Bianchi, J. et al. Food preference determines the best suitable digestion protocol for analysing microplastic ingestion by fish. Mar. Pollut. Bull. 154, 1–9 (2020).Article 
    CAS 

    Google Scholar 
    33.Cole, M. et al. Isolation of microplastics in biota-rich seawater samples and marine organisms. Sci. Rep. 4, 4528 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    34.Dehaut, A. et al. Microplastics in seafood: Benchmark protocol for their extraction and characterization. Environ. Pollut. 215, 223–233 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    35.Phuong, N. N., Poirier, L., Pham, Q. T., Lagarde, F. & Zalouk-Vergnoux, A. Factors influencing the microplastic contamination of bivalves from the French Atlantic coast: Location, season and/or mode of life?. Mar. Pollut. Bull. 129, 664–674 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    36.Valente, T. et al. Exploring microplastic ingestion by three deepwater elasmobranch species: a case study from the Tyrrhenian Sea. Environ. Pollut. 253, 342–350 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    37.Thompson, R. C. et al. Lost at sea: Where is all the plastic?. Science 304, 838 (2004).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    38.Mathalon, A. & Hill, P. Microplastic fibers in the intertidal ecosystem surrounding Halifax Harbor Nova Scotia. Mar. Pollut. Bull. 81, 69–79 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.Setälä, O., Fleming-Lehtinen, V. & Lehtiniemi, M. Ingestion and transfer of microplastics in the planktonic food web. Environ. Pollut. 185, 77–83 (2014).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    40.Jang, M., Shim, W. J., Han, G. M., Song, Y. K. & Hong, S. H. Formation of microplastics by polychaetes (Marphysa sanguinea) inhabiting expanded polystyrene marine debris. Mar. Pollut. Bull. 131, 365–369 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    41.Naidu, S. A., Rao, V. R. & Ramu, K. Microplastics in the benthic invertebrates from the coastal waters of Kochi Southeastern Arabian Sea. Environ. Geochem. Health 40, 1377–1383 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    42.Revel, M. et al. (2018). Accumulation and immunotoxicity of microplastics in the estuarine worm Hediste diversicolor in environmentally relevant conditions of exposure. Environ. Sci. Pollut. Res. 27, 3574–3583 (2018).43.Näkki, P., Setälä, O. & Lehtiniemi, M. Seafloor sediments as microplastic sinks in the northern Baltic Sea-Negligible upward transport of buried microplastics by bioturbation. Environ. Pollut. 249, 74–81 (2019).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    44.Amin, R. M., Sohaimi, E. S., Anuar, S. T. & Bachok, Z. Microplastic ingestion by zooplankton in Terengganu coastal waters, southern South China Sea. Mar. Pollut. Bull. 150, 110616 (2020).45.Jang, M. et al. A close relationship between microplastic contamination and coastal area use pattern. Water Res. 171, 115400 (2020).46.Torre, M., Digka, N., Anastasopoulou, A., Tsangaris, C. & Mytilineou, C. Anthropogenic microfibres pollution in marine biota. A new and simple methodology to minimize airborne contamination. Mar. Pollut. Bull. 113, 55–61 (2016).47.Courtene-Jones, W., Quinn, B., Murphy, F., Gary, S. F. & Narayanaswamy, B. E. Optimisation of enzymatic digestion and validation of specimen preservation methods for the analysis of ingested microplastics. Anal. Methods 9, 1437–1445 (2017).CAS 
    Article 

    Google Scholar 
    48.Digka, N., Tsangaris, C., Torre, M., Anastasopoulou, A. & Zeri, C. Microplastics in mussels and fish from the Northern Ionian Sea. Mar. Pollut. Bull. 135, 30–40 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    49.Ding, J. et al. Detection of microplastics in local marine organisms using a multi-technology system. Anal. Methods 11, 78–87 (2019).CAS 
    Article 

    Google Scholar 
    50.Botterell, Z. L. et al. Bioavailability and effects of microplastics on marine zooplankton: A review. Environ. Pollut. 245, 98–110 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    51.Huerta Lwanga, E. et al. Microplastics in the Terrestrial Ecosystem: Implications for Lumbricus terrestris (Oligochaeta, Lumbricidae). Environ. Sci. Technol. 50, 2685–2691 (2016).52.Hurley, R. R., Woodward, J. C. & Rothwell, J. J. Ingestion of microplastics by freshwater Tubifex worms. Environ. Sci. Technol. 51, 12844–12851 (2017).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.Kowalski, N., Reichardt, A. M. & Waniek, J. J. Sinking rates of microplastics and potential implications of their alteration by physical, biological, and chemical factors. Mar. Pollut. Bull. 109, 310–319 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    54.PlasticsEurope. Plastics – the Facts 2019. An analysis of European plastics production, demand and waste data, p. 42 (2019). FINAL web version Plastics the facts2019 14102019.pdf.55.Horton, T. et al. World Register of Marine Species (2021). https://doi.org/10.14284/170.56.Currie, D. R., McArthur, M. A. & Cohen, B. F. Reproduction and distribution of the invasive European fanworm Sabella spallanzanii (Polychaeta: Sabellidae) in Port Phillip Bay, Victoria Australia. Mar. Biol. 136, 645–656 (2000).Article 

    Google Scholar 
    57.Giangrande, A. et al. Utilization of the filter feeder polychaete Sabella. Aquac. Int. 13, 129–136 (2005).Article 

    Google Scholar 
    58.Stabili, L., Licciano, M., Giangrande, A., Fanelli, G. & Cavallo, R. A. Sabella spallanzanii filter-feeding on bacterial community: ecological implications and applications. Mar. Environ. Res. 61, 74–92 (2006).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    59.Schulze, A., Grimes, C. J. & Rudek, T. E. Tough, armed and omnivorous: Hermodice carunculata (Annelida: Amphinomidae) is prepared for ecological challenges. J. Mar. Biolog. Assoc. U. K. 97, 1075–1080 (2017).CAS 
    Article 

    Google Scholar 
    60.Jumars, P. A., Dorgan, K. M. & Lindsay, S. M. Diet of worms emended: an update of polychaete feeding guilds. Annu. Rev. Mar. Sci. 7, 497–520 (2015).ADS 
    Article 

    Google Scholar 
    61.Nel, H. A., Hean, J. W., Noundou, X. S. & Froneman, P. W. Do microplastic loads reflect the population demographics along the southern African coastline?. Mar. Pollut. Bull. 115, 115–119 (2016).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    62.Stolte, A., Forster, S., Gerdts, G. & Schubert, H. Microplastic concentrations in beach sediments along the German Baltic coast. Mar. Pollut. Bull. 99, 216–229 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    63.Karami, A. et al. A high-performance protocol for extraction of microplastics in fish. Sci. Total Environ. 578, 485–494 (2017).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    64.Hermsen, E., Mintenig, S. M., Besseling, E. & Koelmans, A. A. Quality criteria for the analysis of microplastic in biota samples: A critical review. Environ. Sci. Technol. 52, 10230–10240 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    65.Developer Core Team, R. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing (2019).66.Hui, W., Gel, Y. R. & Gastwirth, J. L. Lawstat: An R package for law, public policy and biostatistics. J. Stat. Softw. 28, 1–26 (2008).Article 

    Google Scholar 
    67.Ripley, B. et al. Support Functions and Datasets for Venables and Ripley’s MASS (4th edition) (Springer, 2002).68.Breheny, P. & Burchett, W. Visualization of regression models using visreg. R. J. 9, 56–71 (2017).Article 

    Google Scholar  More

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    Exploring the potential effect of COVID-19 on an endangered great ape

    Study site and demographic dataThe study was carried out in Volcanoes National Park, the Rwandan part of the Virunga massif, which is further shared with Uganda and the Democratic Republic of the Congo. We focused on habituated mountain gorilla groups monitored by the Dian Fossey Gorilla Fund’s Karisoke Research Center, often referred to as the Karisoke subpopulation. Since 1967, groups in this subpopulation have been followed on a near daily basis. Through the mid-2000s, the Karisoke groups generally numbered three but over the last decade, group fission events and new group formations resulted in an average of ten groups in the region (see42,43). During daily observations, detailed demographic data are recorded, such as group composition, birthdate and death date, group transfers (for further details see Strier et al.50). The data used for this study covers demographic data from 1967 to 2018 and includes 396 recognized individuals.Epidemiological dataWe obtained published data on four variables that control the disease dynamics of COVID-19 in humans, namely (a) the basic reproductive number (R0)34,35, (b) the infection fatality rate (IFR) based on estimates from China and Italy24,25,36,37, (c) the probability of developing immunity and (d) the duration of immunity37,38,39,41.Stochastic projection modelWe used the stochastic projection model proposed by Colchero et al.51, that models population dynamics for both sexes on fully age-dependent demographic rates. The model incorporates the yearly variance–covariance between demographic rates, while it accounts for infanticide as a function of the number of silverbacks (mature males > 12 years old) in the population51. Because of this relationship between infanticide and number of silverbacks, this source of mortality changes in time and cannot be assumed to be part of the infant mortality rate. To explore the extinction probability for the Karisoke subpopulation as a function of different diseases, we gathered information from the model on the proportion of individuals that died for each disease and the frequency of outbreaks (i.e., how often outbreaks occurred).Demographic-epidemiological projection model for COVID-19We constructed a predictive population model that combines the species’ baseline demographic rates with a model based on the susceptible-infected-recovered-susceptible (SIRS) framework. As the baseline demographic rates, we used the age-specific mortality and fecundity estimated by Colchero et al.51 for mountain gorillas (Karisoke subpopulation). We defined four epidemiological stages, namely (a) susceptible, (b) infected, (c) immune and (d) dead, each of which we further divided into a fully age-specific structure (Fig. 1). Based on recent research on COVID-19 on humans, we assumed that the dynamics of the model allowed for the recovered individuals to be divided into either susceptible or immune37,38,39,41. Furthermore, we incorporated the potential age-specific infection fatality rate (IFR) based on current estimates from medical and epidemiological research24,25,36,37, adjusted to the lifespan of the gorillas by means of the logistic function$$qleft(xright)=frac{{q}_{M}}{1+{text{exp}}left[-0.2left(x-25right)right]},$$
    (1)
    where qM is the maximum infected mortality probability. Similarly, we modeled the probability of developing immunity as a function of the strength of the disease, which, based on recent research, we measured as mirroring Eq. (1) as$$mleft(xright)=frac{{M}_{I}}{1+{text{exp}}left[-0.2left(x-25right)right]},$$
    (2)
    where MI is the maximum immunity probability (Fig. 2B).To explore the potential impact of COVID-19 on the growth rate of the Karisoke mountain gorilla subpopulation, we varied four of the critical epidemiological variables, namely (a) the basic reproductive number, R0, from 0.5 to 6 (which helps to simulate factors such as increased group density, which may increase the likelihood of transmission), (b) the maximum infected mortality probability, qM = (0.3, 0.6) (Fig. 2A), (c) the immunity duration, TI to 1, 3, 6, and 12 months, and (d) the maximum immunity probability, MI, from 0.2 to 0.8 (Fig. 2B). As time units we used year fractions in half months (i.e., t1 − t0 = 0.5/12), which allowed us to simplify the model, based on current information on the average time of serial interval and incubation period in humans21. This implementation assumes that susceptible individuals could become infected at the beginning of the time interval, while infected individuals in time interval t would either recover (immune or susceptible) or die in t + 1.The deterministic structure of the model implies that the number of individuals in each sex, age and epidemiological stage was given by the possible contribution from the other stages 1/2 month before. This is, the number of susceptible individuals of age x at time t is given by the difference equation$$begin{aligned} n_{s,x,t} & = p_{x – 1} left{ {n_{s,x – 1,t – 1} + n_{i,x – 1,t – 1} left[ {1 – qleft( {x – 1} right)} right]left[ {1 – mleft( {x – 1} right)} right]} right} \ & quad + n_{{m,x – T_{i} ,t – T_{i} }} prodlimits_{{j = x – T_{i} :j > 0}}^{x – 1} {p_{j} – n_{i,x,t} } , \ end{aligned}$$where the ns,x,t is the number of susceptible individuals of age x at time t, and subscripts i and m refer to infected and immune individuals, respectively. For simplicity of notation, we do not include a subscript for sex, although the model does distinguish between sexes. The probability px is the age-specific survival probability. Functions q(x) and m(x) are as in Eqs. (1) and (2). Similarly, the number of immune individuals at time t and age x are$${n}_{m,x,t}={n}_{i,x-1,t-1}left[1-qleft(x-1right)right]mleft(xright)+sum_{{j:0le jle {T}_{i}wedge x-j >0}}{p}_{x-j}{n}_{i,x-j,t-j}.$$We incorporated this mechanistic structure into a stochastic model, where all contributions from time t to t + 1 were drawn from binomial or Poisson distributions. For instance, the total new number of infected individuals, Ni,t, was obtained as a random draw from a Poisson distribution with expected value$$Eleft[{N}_{i,t}right]={text{min}}left[{{R}_{0}N}_{i,t-1},{N}_{t}right],$$where Nt is the total number of individuals in the study subpopulation. We then distributed randomly these individuals into different available ages and sex corresponding to the term ni,x,t, in the susceptible equation above. The number of newborns, Bx,t, at each age for which there were available females at time t was drawn from a binomial distribution with expected value$$Eleft[{B}_{x,t}right]=left({n}_{s,x,t}+{n}_{m,x,t}right){f}_{x}$$where fx is the age-specific average female fecundity rate and ns,x,t and nm,x,t refers to the number of susceptible and immune females, respectively, of age x at time t. The sex of each newborn was then determined by means of a Bernoulli draw with probability given by the proportion of males in the population. Thus, if the draw produced 1 for that individual, it became a male, and if 0 a female.For each scenario, we ran stochastic simulations for 2000 iterations for 10 years and recorded the average number of individuals at each age–sex and epidemiological state at every month. We then ran long-term stochastic simulations for four scenarios with R0 = 3 and maximum immunity probability MI = 0.2. For these, we recorded also the number of subpopulations that went extinct at each month. More

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    A global model to forecast coastal hardening and mitigate associated socioecological risks

    1.Dugan, J., Airoldi, L., Chapman, G. & Walker, S. in Treatise on Estuarine and Coastal Science Vol. 8 (eds Wolanski, E. & McLusky, D.) 17–41 (2011).2.Bugnot, A. B. et al. Current and projected global extent of marine built structures. Nat. Sustain. 4, 33–41 (2020).Article 

    Google Scholar 
    3.Connell, S. D. Floating pontoons create novel habitats for subtidal epibiota. J. Exp. Mar. Biol. Ecol. 247, 183–194 (2000).CAS 
    Article 

    Google Scholar 
    4.Glasby, T., Connell, S., Holloway, M. & Hewitt, C. Nonindigenous biota on artificial structures: could habitat creation facilitate biological invasions? Mar. Biol. 151, 887–895 (2007).Article 

    Google Scholar 
    5.Heery, E. C. et al. Identifying the consequences of ocean sprawl for sedimentary habitats. J. Exp. Mar. Biol. Ecol. 492, 31–48 (2017).Article 

    Google Scholar 
    6.Scherner, F. et al. Coastal urbanization leads to remarkable seaweed species loss and community shifts along the SW Atlantic. Mar. Pollut. Bull. 76, 106–115 (2013).CAS 
    Article 

    Google Scholar 
    7.Malerba, M. E., White, C. R. & Marshall, D. J. The outsized trophic footprint of marine urbanization. Front. Ecol. Environ. 17, 400–406 (2019).Article 

    Google Scholar 
    8.Dafforn, K. A., Glasby, T. M. & Johnston, E. L. Comparing the invasibility of experimental “reefs” with field observations of natural reefs and artificial structures. PLoS ONE 7, e38124 (2012).CAS 
    Article 

    Google Scholar 
    9.Airoldi, L., Turon, X., Perkol-Finkel, S. & Rius, M. Corridors for aliens but not for natives: effects of marine urban sprawl at a regional scale. Divers. Distrib. 21, 755–768 (2015).Article 

    Google Scholar 
    10.Hayes, K. R., Inglis, G. J. & Barry, S. C. The assessment and management of marine pest risks posed by shipping: the Australian and New Zealand experience. Front. Mar. Sci. https://doi.org/10.3389/fmars.2019.00489 (2019).11.Floerl, O., Inglis, G., Dey, K. L. & Smith, A. The importance of transport hubs in stepping-stone invasions. J. Appl. Ecol. 46, 37–45 (2009).Article 

    Google Scholar 
    12.Kaluza, P., Kolzsch, A., Gastner, M. T. & Blasius, B. The complex network of global cargo ship movements. J. R. Soc. Interface 7, 1093–1103 (2010).Article 

    Google Scholar 
    13.Aguirre, D. et al. Loved to pieces: toward the sustainable management of the Waitematā Harbour and Hauraki Gulf. Reg. Stud. Mar. Sci. 8, 220–233 (2016).Article 

    Google Scholar 
    14.Molnar, J. L., Gamboa, R. L., Revenga, C. & Spalding, M. D. Assessing the global threat of invasive species to marine biodiversity. Front. Ecol. Environ. 6, 485–492 (2008).Article 

    Google Scholar 
    15.Seto, K. C., Güneralp, B. & Hutyra, L. R. Global forecasts of urban expansion to 2030 and direct impacts on biodiversity and carbon pools. Proc. Natl Acad. Sci. USA 109, 16083–16088 (2012).CAS 
    Article 

    Google Scholar 
    16.Neumann, B., Vafeidis, A. T., Zimmermann, J. & Nicholls, R. J. Future coastal population growth and exposure to sea-level rise and coastal flooding—a global assessment. PLoS ONE 10, e0118571 (2015).Article 
    CAS 

    Google Scholar 
    17.Kulp, S. A. & Strauss, B. H. New elevation data triple estimates of global vulnerability to sea-level rise and coastal flooding. Nat. Commun. 10, 4844 (2019).CAS 
    Article 

    Google Scholar 
    18.Lombard, A. T. et al. Practical approaches and advances in spatial tools to achieve multi-objective marine spatial planning. Front. Mar. Sci. https://doi.org/10.3389/fmars.2019.00166 (2019).19.Pelling, M. & Blackburn, S. Megacities and the Coast: Risk, Resilience and Transformation (Routledge, 2013).20.Sutton-Grier, A. E., Wowk, K. & Bamford, H. Future of our coasts: the potential for natural and hybrid infrastructure to enhance the resilience of our coastal communities, economies and ecosystems. Environ. Sci. Policy 51, 137–148 (2015).Article 

    Google Scholar 
    21.Keller, R., Drake, J., Drew, M. & Lodge, D. Linking environmental conditions and ship movements to estimate invasive species transport across the global shipping network. Divers. Distrib. 17, 93–102 (2011).Article 

    Google Scholar 
    22.How Can We Meet Increasing Demand for Ports in the Upper North Island? A Report for the Upper North Island Strategic Alliance (PricewaterhouseCoopers, 2012).23.Ernst & Young Port Future Study. A Report Prepared for Auckland Council (Auckland Council, 2016).24.NZIER Bigger Ships—Past, Present and Future Implications for New Zealand Supply Chains (New Zealand Economic Research Institute, 2017).25.Hino, M., Belanger, S. T., Field, C. B., Davies, A. R. & Mach, K. J. High-tide flooding disrupts local economic activity. Sci. Adv. 5, eaau2736 (2019).Article 

    Google Scholar 
    26.United Nations Review of Maritime Transport 109 (United Nations Conference on Trade and Development, 2019).27.Ferrario, F., Iveša, L., Jaklin, A., Perkol-Finkel, S. & Airoldi, L. The overlooked role of biotic factors in controlling the ecological performance of artificial marine habitats. J. Appl. Ecol. 53, 16–24 (2016).Article 

    Google Scholar 
    28.Firth, L. et al. Ocean sprawl: challenges and opportunities for biodiversity management in a changing world. Oceanogr. Mar. Biol. 54, 189–262 (2016).
    Google Scholar 
    29.Mayer-Pinto, M. et al. Functional and structural responses to marine urbanisation. Environ. Res. Lett. 13, 014009 (2018).Article 

    Google Scholar 
    30.Bannister, J., Sievers, M., Bush, F. & Bloecher, N. Biofouling in marine aquaculture: a review of recent research and developments. Biofouling 35, 631–648 (2019).CAS 
    Article 

    Google Scholar 
    31.Colautti, R. I., Bailey, S. A., van Overdijk, C. D. A., Amundsen, K. & MacIsaac, H. J. Characterised and projected costs of nonindigenous species in Canada. Biol. Invasions 8, 45–59 (2006).Article 

    Google Scholar 
    32.Mazur, K., Bath, A., Curtotti, R. & Summerson, R. An Assessment of the Non-market Value of Reducing the Risk of Marine Pest Incursions in Australia’s Waters (Australian Bureau of Agricultural and Resource Economics and Sciences, 2018).33.Hatami, R. et al. Improving New Zealand’s Marine Biosecurity Surveillance Programme Biosecurity New Zealand Technical Paper No. 2021/01 (Ministry for Primary Industries, 2021).34.Sardain, A., Sardain, E. & Leung, B. Global forecasts of shipping traffic and biological invasions to 2050. Nat. Sustain. 2, 274–282 (2019).Article 

    Google Scholar 
    35.Monios, J., Bergqvist, R. & Woxenius, J. Port-centric cities: the role of freight distribution in defining the port-city relationship. J. Transp. Geogr. 66, 53–64 (2018).Article 

    Google Scholar 
    36.The Ocean Economy in 2030 (Organisation for Economic Co-operation and Development, 2016).37.Halpern, B. S. et al. Recent pace of change in human impact on the world’s ocean. Sci. Rep. 9, 11609 (2019).Article 
    CAS 

    Google Scholar 
    38.Dafforn, K. A. et al. Marine urbanization: an ecological framework for designing multifunctional artificial structures. Front. Ecol. Environ. 13, 82–90 (2015).Article 

    Google Scholar 
    39.Diggon, S. et al. The marine plan partnership: Indigenous community-based marine spatial planning. Mar. Policy https://doi.org/10.1016/j.marpol.2019.04.014 (2019).40.Noble, M. M., Harasti, D., Pittock, J. & Doran, B. Understanding the spatial diversity of social uses, dynamics, and conflicts in marine spatial planning. J. Environ. Manag. 246, 929–940 (2019).Article 

    Google Scholar 
    41.Abhinav, K. A. et al. Offshore multi-purpose platforms for a blue growth: a technological, environmental and socio-economic review. Sci. Total Environ. 734, 138256 (2020).CAS 
    Article 

    Google Scholar 
    42.Jacob, C., Buffard, A., Pioch, S. & Thorin, S. Marine ecosystem restoration and biodiversity offset. Ecol. Eng. 120, 585–594 (2018).Article 

    Google Scholar 
    43.Hopkins, G. A. et al. Continuous bubble streams for controlling marine biofouling on static artificial structures. PeerJ 9, e11323 (2021).Article 

    Google Scholar 
    44.Vucko, M. J. et al. Cold spray metal embedment: an innovative antifouling technology. Biofouling 28, 239–248 (2012).CAS 
    Article 

    Google Scholar 
    45.Atalah, J., Newcombe, E. M., Hopkins, G. A. & Forrest, B. M. Potential biocontrol agents for biofouling on artificial structures. Biofouling 30, 999–1010 (2014).CAS 
    Article 

    Google Scholar 
    46.Airoldi, L. et al. Emerging solutions to return nature to the urban ocean. Ann. Rev. Mar. Sci. 13, 445–477 (2021).Article 

    Google Scholar 
    47.Keeley, N., Wood, S. A. & Pochon, X. Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment. Ecol. Indic. 85, 1044–1057 (2018).CAS 
    Article 

    Google Scholar 
    48.Zaiko, A., Pochon, X., Garcia-Vazquez, E., Olenin, S. & Wood, S. A. Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: management and surveillance of non-indigenous species. Front. Mar. Sci. https://doi.org/10.3389/fmars.2018.00322 (2018).49.Cristescu, M. E. Can environmental RNA revolutionize biodiversity science? Trends Ecol. Evol. 34, 694–697 (2019).Article 

    Google Scholar 
    50.Chakravarthy, K., Charters, F. & Cochrane, T. The impact of urbanisation on New Zealand freshwater quality. Policy Q. 15, 17–21 (2019).Article 

    Google Scholar 
    51.Gittman, R. K. et al. Engineering away our natural defenses: an analysis of shoreline hardening in the US. Front. Ecol. Environ. 13, 301–307 (2015).Article 

    Google Scholar 
    52.Hume, T. M., Snelder, T., Weatherhead, M. & Liefting, R. A controlling factor approach to estuary classification. Ocean Coast. Manag. 50, 905–929 (2007).Article 

    Google Scholar 
    53.Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).Article 

    Google Scholar 
    54.Prasad, A. M., Iverson, L. R. & Liaw, A. Newer classification and regression tree techniques: bagging and random forests for ecological prediction. Ecosystems 9, 181–199 (2006).Article 

    Google Scholar 
    55.Olden, J. D., Lawler, J. J. & Poff, N. L. Machine learning methods without tears: a primer for ecologists. Q. Rev. Biol. 83, 171–193 (2008).Article 

    Google Scholar 
    56.Kursa, M. B. & Rudnicki, W. R. Feature selection with the boruta package. J. Stat. Softw. 36, 1–13 (2010).Article 

    Google Scholar 
    57.Zuur, A. F., Leno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. 1, 3–14 (2010).Article 

    Google Scholar 
    58.Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002).
    Google Scholar 
    59.Kuhn, M. et al. caret: Classification and Regression Training (CRAN, 2019); https://CRAN.R-project.org/package=caret60.Ministry for the Environment & Stats NZ. New Zealand’s Environmental Reporting Series: Environment Aotearoa 2019 (Ministry for the Environment, 2019). More