More stories

  • in

    Are endemic species necessarily ecological specialists? Functional variability and niche differentiation of two threatened Dianthus species in the montane steppes of northeastern Iran

    Plant functional variability
    In total, 78 species occurred (cover ≥ 5%) at the different sites, creating the set of species over which CSR strategies were assessed (Fig. 2; Table S2). A clear dominance of relatively stress-tolerant strategies was evident across the sites; indeed, most species showed a proportion of S exceeding 50% (Fig. 2, Supplementary Figs. S1, S2).
    Figure 2

    CSR classification of four sites related to Dianthus pseudocrinitus (a–d) showing the relative importance of the C, S and R axes for sympatric (non-Dianthus) species within the plant community (left side) and the individuals of D. pseudocrinitus (right side) in each site (a Rein; b Misino; c Biu Pass; d Rakhtian). The species are represented in gray scale according to their mean cover (%). The numbering indicated in the circles corresponds to Table S2. The small triangles show the community weighted mean (CWM) strategies at each site for the sympatric species and the individuals of D. pseudocrinitus.

    Full size image

    Dianthus pseudocrinitus was the only Dianthus species that exhibited general functional divergence, ranging from strong ruderalism at the Rein site (R; C:S:R = 12.0:7.2:80.8%), an intermediate strategy at Rakhtian and Misino (S/SR; C:S:R = 2.8:75.9:21.3%; and C:S:R = 7.4:70.5:22.1%, respectively), to strong stress-tolerance at the Biu Pass site (S; C:S:R = 6.8:82.3:10.9%) (Fig. 2). Differences among D. pseudocrinitus populations at different sites were apparent for S-selection (ANOVA on arcsine transformed data, predictor variables were sites and response variables were the percentage CSR-scores; f = 34.386, dfnumerator = 3, dfdenominator = 37, p = 0.000) and R-selection (f = 43.707, dfnumerator = 3, dfdenominator = 37, p = 0.000) but not for C-selection (f = 2.801, dfnumerator = 3, dfdenominator = 37, p = 0.054), with a Tukey’s post-hoc multiple comparison on data for R-selection (i.e. the highest f-value), suggesting that populations at all sites differed from one another, except for those at Misino and Rakhtian.
    In terms of interspecific differences, analysis of variance (ANOVA) showed that D. pseudocrinitus differed significantly from the community mean at the Rein site in terms of R-selection (f = 46.982, dfnumerator = 16, dfdenominator = 146, p = 0.000) and S-selection (f = 44.601, dfnumerator = 16, dfdenominator = 146, p = 0.000; arcsine transformed data, with species (i.e. taxa present in the plant community) as the predictor variables and percentage CSR-scores as the response variables). Crucially, that D. pseudocrinitus exhibited extensive intraspecific variability was evident as extreme values of strategy variance (s2) compared to the intraspecific variability of sympatric species at the Rakhtian and Rein sites (Table 1). Note that the CSR strategy variability evident for sympatric species is presented in greater detail in Fig. S3.
    Table 1 Variance (s2) in C-, S-, and R-selection values (%) for D. pseudocrinitus and other species at the (a) Rein and (b) Rakhrian sites, with species ordered according to decreasing variance in R-selection (n = 10).
    Full size table

    Dianthus polylepis subsp. polylepis exhibited an extreme stress-tolerant strategy (C:S:R = 0.1:99.1:0.8%) across all sites (Fig. S1). Most sympatric species at sites of D. polylepis subsp. polylepis represented a broadly stress-tolerant strategy (Fig. S1), but interspecific functional variability was evident, including subordinate species (mean cover percentage 5.5–9.0%) with relatively generalist, intermediate strategies (Fig. S1). Intraspecific differences in Dianthus polylepis subsp. polylepis between sites were apparent for C-selection (ANOVA on arcsine transformed data, predictor variables were sites and response variables the percentage CSR-scores; f = 7.599, dfnumerator = 5, dfdenominator = 48, p = 0.000) and S-selection (f = 6.686, dfnumerator = 5, dfdenominator = 48, p = 0.000) and R-selection (f = 8.099, dfnumerator = 5, dfdenominator = 48, p = 0.000), with a Tukey’s post-hoc multiple comparison on data for R-selection (i.e. the highest f-value) suggesting that the population at Bezd was distinct from other sites.
    Dianthus polylepis subsp. binaludensis exhibited an extremely stress-tolerant strategy (C:S:R = 0.5:99.5:0.0%) at all sites except Zoshk, where it exhibited an intermediate S/SR strategy (Fig. S2). Intraspecific differences in D. polylepis subsp. binaludensis between sites were apparent for C-selection (ANOVA on arcsine transformed data, predictor variables were sites and response variables the percentage CSR-scores; f = 2.801, dfnumerator = 4, dfdenominator = 46, p = 0.054), S-selection (f = 25.796, dfnumerator = 4, dfdenominator = 46, p = 0.000) and R-selection (f = 18.476, dfnumerator = 4, dfdenominator = 46, p = 0.000), with a Tukey’s post-hoc multiple comparison on data for S-selection (i.e. the highest f-value) suggesting that the population at Zoshk was distinct from other sites. At Zoshk, Dahane Jaji and Dizbad, D. polylepis subsp. binaludensis exhibited significantly lower C-selection (p ≤ 0.05) with respect to the community mean (t tests within site on arcsine-transformed data).
    Site and environmental variables
    The canonical correspondence analysis (CCA) (Fig. 3) was constrained by a matrix of soil and topographic data and bioclimatic variables. Seven soil variables (clay, silt, sand, EC, P, CEC and organic carbon) and 15 bioclimatic variables were eliminated from the environmental data set owing to high collinearity (VIF  > 10). Soil organic matter, pH, N, K, lime, elevation, and aspect were the edaphic/topographic variables exhibiting the highest levels of significance (p  More

  • in

    Nitrogen challenges in global livestock systems

    1.
    Sutton, M. A. et al. Our Nutrient World: The Challenge to Produce More Food and Energy with Less Pollution. Global Overview of Nutrient Management (Centre for Ecology and Hydrology, Edinburgh on behalf of the Global Partnership on Nutrient Management and the International Nitrogen Initiative, 2013).
    2.
    Uwizeye, A. et al. Nat. Food https://doi.org/10.1038/s43016-020-0113-y (2020).
    Article  Google Scholar 

    3.
    Clark, M. & Tilman, D. Environ. Res. Lett. 12, 064016 (2017).
    ADS  Article  Google Scholar 

    4.
    Lassaletta, L. et al. Sci. Total Environ. 665, 739–751 (2019).
    ADS  CAS  Article  Google Scholar 

    5.
    Chadwick, D. R. et al. Front. Agr. Sci. Eng. 7, 45–55 (2020).
    ADS  Article  Google Scholar 

    6.
    Zhang, C. et al. Resour. Conserv. Recycl. 144, 65–73 (2019).
    Article  Google Scholar 

    7.
    Spiegal, S. et al. Agric. Syst. 182, 102813 (2020).
    Article  Google Scholar 

    8.
    Mueller, N. D. et al. Global Biogeochem. Cycles 31, 245–257 (2017).
    ADS  CAS  Google Scholar 

    9.
    van Grinsven, H. J. M. et al. Reg. Environ. Change 18, 2403–2415 (2018).
    Article  Google Scholar 

    10.
    Bai, Z. et al. Nat. Sustain. 2, 888 (2019).
    Article  Google Scholar  More

  • in

    Spatial data of Ixodes ricinus instar abundance and nymph pathogen prevalence, Scandinavia, 2016–2017

    1.
    Estrada-Peña, A., De, J. & de la Fuente, J. The ecology of ticks and epidemiology of tick-borne viral diseases. Antiviral Res.108, 104–128 (2014).
    Article  Google Scholar 
    2.
    Vu Hai, V. et al. Monitoring human tick-borne disease risk and tick bite exposure in Europe: Available tools and promising future methods. Ticks Tick. Borne. Dis.5, 607–619 (2014).
    Article  Google Scholar 

    3.
    Jaenson, T. G. T., Jaenson, D. G. E., Eisen, L., Petersson, E. & Lindgren, E. Changes in the geographical distribution and abundance of the tick Ixodes ricinus during the past 30 years in Sweden. Parasit. Vectors5, 8 (2012).
    Article  Google Scholar 

    4.
    Skarphédinsson, S., Jensen, P. M. & Kristiansen, K. Survey of tickborne infections in Denmark. Emerg. Infect. Dis.11, 1055–1061 (2005).
    Article  Google Scholar 

    5.
    Michelet, L. et al. High-throughput screening of tick-borne pathogens in Europe. Front. Cell. Infect. Microbiol.4, 103 (2014).
    Article  Google Scholar 

    6.
    Heyman, P. et al. A clear and present danger: tick-borne diseases in Europe. Expert Rev. Anti. Infect. Ther.8, 33–50 (2010).
    Article  Google Scholar 

    7.
    Medlock, J. M. et al. Driving forces for changes in geographical distribution of Ixodes ricinus ticks in Europe. Parasit. Vectors6, 1–11 (2013).
    Article  Google Scholar 

    8.
    Jore, S. et al. Multi-source analysis reveals latitudinal and altitudinal shifts in range of Ixodes ricinus at its northern distribution limit. Parasit. Vectors4, 1–11 (2011).
    Article  Google Scholar 

    9.
    Kjelland, V. et al. Tick-borne encephalitis virus, Borrelia burgdorferi sensu lato, Borrelia miyamotoi, Anaplasma phagocytophilum and Candidatus Neoehrlichia mikurensis in Ixodes ricinus ticks collected from recreational islands in southern Norway. Ticks Tick. Borne. Dis.9, 1098–1102 (2018).
    Article  Google Scholar 

    10.
    Rizzoli, A. et al. Ixodes ricinus and Its Transmitted Pathogens in Urban and Peri-Urban Areas in Europe: New Hazards and Relevance for Public Health. Front. Public Heal.2, 251 (2014).
    Google Scholar 

    11.
    Klitgaard, K., Kjær, L. J., Isbrand, A., Hansen, M. F. & Bødker, R. Multiple infections in questing nymphs and adult female Ixodes ricinus ticks collected in a recreational forest in Denmark. Ticks Tick. Borne. Dis.10, 1060–1065 (2019).
    Article  Google Scholar 

    12.
    Pedersen, B. N. et al. Distribution of Neoehrlichia mikurensis in Ixodes ricinus ticks along the coast of Norway: The western seaboard is a low‐prevalence region. Zoonoses Public Health zph. 12662, https://doi.org/10.1111/zph.12662 (2019).

    13.
    Jenkins, A. et al. Detection of Candidatus Neoehrlichia mikurensis in Norway up to the northern limit of Ixodes ricinus distribution using a novel real time PCR test targeting the groEL gene. BMC Microbiol.19, 199 (2019).
    Article  Google Scholar 

    14.
    Lindgren, E. & Gustafson, R. Tick-borne encephalitis in Sweden and climate change. Lancet (London, England)358, 16–18 (2001).
    CAS  Article  Google Scholar 

    15.
    Del Fabbro, S., Gollino, S., Zuliani, M. & Nazzi, F. Investigating the relationship between environmental factors and tick abundance in a small, highly heterogeneous region. J. Vector Ecol.40, 107–116 (2015).
    Article  Google Scholar 

    16.
    Nazzi, F. et al. Ticks and Lyme borreliosis in an alpine area in northeast Italy. Med. Vet. Entomol.24, 220–6 (2010).
    CAS  PubMed  Google Scholar 

    17.
    Jaenson, T. G. T. et al. Risk indicators for the tick Ixodes ricinus and Borrelia burgdorferi sensu lato in Sweden. Med. Vet. Entomol.23, 226–237 (2009).
    CAS  Article  Google Scholar 

    18.
    Hudson, P. J. et al. Tick-borne encephalitis virus in northern Italy: molecular analysis, relationships with density and seasonal dynamics of Ixodes ricinus. Med. Vet. Entomol.15, 304–313 (2001).
    MathSciNet  CAS  Article  Google Scholar 

    19.
    Hubalek, Z., Halouzka, J. & Juricova, Z. Longitudinal surveillance of the tick Ixodes ricinusfor borreliae. Med. Vet. Entomol.17, 46–51 (2003).
    CAS  Article  Google Scholar 

    20.
    Mysterud, A. et al. Tick abundance, pathogen prevalence, and disease incidence in two contrasting regions at the northern distribution range of Europe. Parasit. Vectors11, 309 (2018).
    Article  Google Scholar 

    21.
    Jensen, P. M. & Hansen, H. Spatial Risk Assessment for Lyme Borreliosis in Denmark. Scand. J. Infect. Dis.32, 545–550 (2000).
    CAS  Article  Google Scholar 

    22.
    Moutailler, S. et al. Co-infection of Ticks: The Rule Rather Than the Exception. PLoS Negl. Trop. Dis.10, e0004539 (2016).
    Article  Google Scholar 

    23.
    Reye, A. L. et al. Prevalence of Tick-Borne Pathogens in Ixodes ricinus and Dermacentor reticulatus Ticks from Different Geographical Locations in Belarus. PLoS One8, e54476 (2013).
    ADS  CAS  Article  Google Scholar 

    24.
    Estrada-Peña, A. Distribution, Abundance, and Habitat Preferences of Ixodes ricinus (Acari: Ixodidae) in Northern Spain. J. Med. Entomol.38, 361–370 (2001).
    Article  Google Scholar 

    25.
    Estrada-Pena, A. & De La Fuente, J. Species interactions in occurrence data for a community of tick-transmitted pathogens. Sci. Data3, 2–4 (2016).
    Article  Google Scholar 

    26.
    Estrada-Peña, A. et al. An updated meta-analysis of the distribution and prevalence of Borrelia burgdorferi s.l. in ticks in Europe. Int. J. Health Geogr.17, 41 (2018).
    Article  Google Scholar 

    27.
    Soleng, A. & Kjelland, V. Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum in Ixodes ricinus ticks in Brønnøysund in northern Norway. Ticks Tick. Borne. Dis.4, 218–221 (2013).
    Article  Google Scholar 

    28.
    Øines, Ø., Radzijevskaja, J., Paulauskas, A. & Rosef, O. Prevalence and diversity of Babesia spp. in questing Ixodes ricinus ticks from Norway. Parasit. Vectors5, 156 (2012).
    Article  Google Scholar 

    29.
    Strnad, M., Hönig, V., Růžek, D., Grubhoffer, L. & Rego, R. O. M. Europe-Wide Meta-Analysis of Borrelia burgdorferi Sensu Lato Prevalence in Questing Ixodes ricinus Ticks. Appl. Environ. Microbiol. 83 (2017).

    30.
    Hornok, S. et al. Occurrence of ticks and prevalence of Anaplasma phagocytophilum and Borrelia burgdorferi s.l. in three types of urban biotopes: Forests, parks and cemeteries. Ticks Tick. Borne. Dis.5, 785–789 (2014).
    Article  Google Scholar 

    31.
    Moutailler, S. et al. Co-infection of Ticks: The Rule Rather Than the Exception. PLoS Negl Trop Dis.10(3), e0004539 (2016).
    Article  Google Scholar 

    32.
    Reye, A. L. et al. Pathogen prevalence in questing and feeding ticks. figshare https://plos.figshare.com/articles/_Pathogen_prevalence_in_questing_and_feeding_ticks_/174458 (2013).

    33.
    Estrada-Peña, A. & De La Fuente, J. Data from: Species interactions in occurrence data for a community of tick-transmitted pathogens. Dryad https://doi.org/10.5061/dryad.2h3f2 (2016).

    34.
    Estrada-Peña, A. et al. Correlation of Borrelia burgdorferi sensu lato prevalence in questing Ixodes ricinus ticks with specific abiotic traits in the western palearctic. Appl. Environ. Microbiol.77, 3838–45 (2011).
    Article  Google Scholar 

    35.
    Estrada-Peña, A. Data from: The dataset of ticks in South America. Dryad https://doi.org/10.5061/dryad.860473k (2019).

    36.
    Kjær, L. J. et al. Predicting and mapping human risk of exposure to Ixodes ricinus nymphs using climatic and environmental data, Denmark, Norway and Sweden, 2016. Eurosurveillance24, 1800101 (2019).
    Article  Google Scholar 

    37.
    Kjær, L. J. et al. Predicting the spatial abundance of Ixodes ricinus ticks in southern Scandinavia using environmental and climatic data. Sci. Rep.9, 18144 (2019).
    ADS  Article  Google Scholar 

    38.
    Corine Land Cover 2006 raster data. European Environment Agency, https://www.eea.europa.eu/data-and-maps/data/clc-2006-raster (2010).

    39.
    Scharlemann, J. P. W. et al. Global Data for Ecology and Epidemiology: A Novel Algorithm for Temporal Fourier Processing MODIS Data. PLoS One3, e1408 (2008).
    ADS  Article  Google Scholar 

    40.
    R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, http://www.r-project.org (2018).

    41.
    Hijmans, R. J. raster: Geographic Data Analysis and Modeling. R package version2, 6–7 (2017).
    Google Scholar 

    42.
    Gray, J. S. & Lohan, G. The development of a sampling method for the tick Ixodes ricinus and its use in a redwater fever area. Ann. Appl. Biol.101, 421–427 (1982).
    Article  Google Scholar 

    43.
    Klitgaard, K., Chriél, M., Isbrand, A., Jensen, T. K. & Bødker, R. Identification of Dermacentor reticulatus Ticks Carrying Rickettsia raoultii on Migrating Jackal, Denmark. Emerg. Infect. Dis.23, 2072–2074 (2017).
    Article  Google Scholar 

    44.
    Jaenson, T. G. T. et al. First evidence of established populations of the taiga tick Ixodes persulcatus (Acari: Ixodidae) in Sweden. Parasit. Vectors9, 377 (2016).
    Article  Google Scholar 

    45.
    Klitgaard, K. et al. Screening for multiple tick-borne pathogens in Ixodes ricinus ticks from birds in Denmark during spring and autumn migration seasons. Ticks Tick. Borne. Dis.10, 546–552 (2019).
    Article  Google Scholar 

    46.
    Cowling, D. W., Gardner, I. A. & Johnson, W. O. Comparison of methods for estimation of individual-level prevalence based on pooled samples. Prev. Vet. Med.39, 211–25 (1999).
    CAS  Article  Google Scholar 

    47.
    Kjær, L. J. et al. A large-scale screening for the taiga tick, Ixodes persulcatus, and the meadow tick, Dermacentor reticulatus, in southern Scandinavia, 2016. Parasit. Vectors12, 338 (2019).
    Article  Google Scholar 

    48.
    Kjær, L. J. et al. Spatial data of Ixodes ricinus instar abundance and nymph pathogen prevalence, Scandinavia, 2016–2017. figshare https://doi.org/10.6084/m9.figshare.c.4938270 (2020). More

  • in

    Seasonal and environmental variation in volatile emissions of the New Zealand native plant Leptospermum scoparium in weed-invaded and non-invaded sites

    1.
    Li, S., Wang, P., Yuan, W., Su, Z. & Bullard, S. H. Endocidal regulation of secondary metabolites in the producing organisms. Sci. Rep. 6, 29315. https://doi.org/10.1038/srep29315 (2016).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 
    2.
    Dudareva, N., Negre, F., Nagegowda, D. A. & Orlova, I. Plant volatiles: recent advances and future perspectives. Crit. Rev. Plant Sci. 25, 417–440. https://doi.org/10.1080/07352680600899973 (2006).
    CAS  Article  Google Scholar 

    3.
    Holopainen, J. K. Multiple functions of inducible plant volatiles. Trends Plant Sci. 9, 529–533. https://doi.org/10.1016/j.tplants.2004.09.006 (2004).
    CAS  Article  PubMed  Google Scholar 

    4.
    Dudareva, N., Klempien, A., Muhlemann, J. K. & Kaplan, I. Biosynthesis, function and metabolic engineering of plant volatile organic compounds. New Phytol. 198, 16–32. https://doi.org/10.1111/nph.12145 (2013).
    CAS  Article  PubMed  Google Scholar 

    5.
    Effah, E., Holopainen, J. K. & Clavijo McCormick, A. Potential roles of volatile organic compounds in plant competition. Perspect. Plant Ecol. Evol. Syst. 38, 58–63. https://doi.org/10.1016/j.ppees.2019.04.003 (2019).
    Article  Google Scholar 

    6.
    Flamini, G., Tebano, M. & Cioni, P. L. Volatiles emission patterns of different plant organs and pollen of Citrus limon. Anal. Chim. Acta 589, 120–124 (2007).
    CAS  Article  Google Scholar 

    7.
    Holopainen, J. K. & Gershenzon, J. Multiple stress factors and the emission of plant VOCs. Trends Plant Sci. 15, 176–184. https://doi.org/10.1016/j.tplants.2010.01.006 (2010).
    CAS  Article  PubMed  Google Scholar 

    8.
    Bracho-Nunez, A., Welter, S., Staudt, M. & Kesselmeier, J. Plant-specific volatile organic compound emission rates from young and mature leaves of Mediterranean vegetation. J. Geophys. Res. Atmos. https://doi.org/10.1029/2010jd015521 (2011).
    Article  Google Scholar 

    9.
    Vivaldo, G., Masi, E., Taiti, C., Caldarelli, G. & Mancuso, S. The network of plants volatile organic compounds. Sci. Rep. 7, 1–18 (2017).
    CAS  Article  Google Scholar 

    10.
    Himanen, S. J. et al. Birch (Betula spp.) leaves adsorb and re-release volatiles specific to neighbouring plants—a mechanism for associational herbivore resistance? New Phytol. 186, 722–732. https://doi.org/10.1111/j.1469-8137.2010.03220.x (2010).
    CAS  Article  PubMed  Google Scholar 

    11.
    Camacho-Coronel, X., Molina-Torres, J. & Heil, M. Sequestration of exogenous volatiles by plant cuticular waxes as a mechanism of passive associational resistance: a proof of concept. Front. Plant Sci. https://doi.org/10.3389/fpls.2020.00121 (2020).
    Article  PubMed  PubMed Central  Google Scholar 

    12.
    Clavijo McCormick, A. Can plant–natural enemy communication withstand disruption by biotic and abiotic factors?. Ecol. Evol. 6, 8569–8582. https://doi.org/10.1002/ece3.2567 (2016).
    Article  PubMed  PubMed Central  Google Scholar 

    13.
    Shiojiri, K. et al. Functions of plant infochemicals in tritrophic interactions between plants, herbivores and carnivorous natural enemies. Jpn. J. Appl. Entomol. Zool. 46, 117–133 (2002).
    CAS  Article  Google Scholar 

    14.
    Pichersky, E. & Gershenzon, J. The formation and function of plant volatiles: perfumes for pollinator attraction and defense. Curr. Opin. Plant Biol. 5, 237–243 (2002).
    CAS  Article  Google Scholar 

    15.
    Kigathi, R. N., Weisser, W. W., Reichelt, M., Gershenzon, J. & Unsicker, S. B. Plant volatile emission depends on the species composition of the neighboring plant community. BMC Plant Biol. 19, 58. https://doi.org/10.1186/s12870-018-1541-9 (2019).
    Article  PubMed  PubMed Central  Google Scholar 

    16.
    Effah, E. et al. Natural variation in volatile emissions of the invasive weed Calluna vulgaris in New Zealand. Plants 9, 283 (2020).
    Article  Google Scholar 

    17.
    Inderjit, S. et al. Volatile chemicals from leaf litter are associated with invasiveness of a Neotropical weed in Asia. Ecology 92, 316–324. https://doi.org/10.1890/10-0400.1 (2011).
    CAS  Article  PubMed  Google Scholar 

    18.
    Broz, A. K. et al. Plant neighbor identity influences plant biochemistry and physiology related to defense. BMC Plant Biol. 10, 115. https://doi.org/10.1186/1471-2229-10-115 (2010).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    19.
    Corbin, J. D. & D’Antonio, C. M. Competition between native perennial and exotic annual grasses: implications for an historical invasion. Ecology 85, 1273–1283. https://doi.org/10.1890/02-0744 (2004).
    Article  Google Scholar 

    20.
    Leger, E. A. & Espeland, E. K. Perspective: coevolution between native and invasive plant competitors: implications for invasive species management. Evol. Appl. 3, 169–178. https://doi.org/10.1111/j.1752-4571.2009.00105.x (2010).
    Article  PubMed  PubMed Central  Google Scholar 

    21.
    Alvarez-Suarez, J. M., Gasparrini, M., Forbes-Hernández, T. Y., Mazzoni, L. & Giampieri, F. The composition and biological activity of honey: a focus on Manuka honey. Foods 3, 420–432 (2014).
    Article  Google Scholar 

    22.
    Almasaudi, S. B. et al. Antioxidant, anti-inflammatory, and antiulcer potential of manuka honey against gastric ulcer in rats. Oxid. Med. Cell. Longev. 2016, 3643824 (2016).
    Article  Google Scholar 

    23.
    Ronghua, Y., Mark, A. F. & Wilson, J. B. Aspects of the ecology of the indigenous shrub Leptospermum scoparium (Myrtaceae) in New Zealand. N. Z. J. Bot. 22, 483–507. https://doi.org/10.1080/0028825X.1984.10425282 (1984).
    Article  Google Scholar 

    24.
    Stephens, J. M. C., Molan, P. C. & Clarkson, B. D. A review of Leptospermum scoparium (Myrtaceae) in New Zealand. N. Z. J. Bot. 43, 431–449. https://doi.org/10.1080/0028825X.2005.9512966 (2005).
    Article  Google Scholar 

    25.
    Smale, M. C. Ecology of Dracophyllum subulatum-dominant heathland on frost flats at Rangitaiki and north Pureora, central North Island New Zealand. N. Z. J. Bot. 28, 225–248. https://doi.org/10.1080/0028825X.1990.10412311 (1990).
    Article  Google Scholar 

    26.
    Rogers, G. M. North Island seral tussock grasslands 1. Origins and land-use history. N. Z. J. Bot. 32, 271–286. https://doi.org/10.1080/0028825X.1994.10410471 (1994).
    Article  Google Scholar 

    27.
    Bagnall, A. Heather at Tongariro. A study of a weed introduction. Tussock Grassl. Mountainlands Inst. Rev. 41, 17–21 (1982).
    Google Scholar 

    28.
    Buddenhagen, C. E. Broom Control Monitoring at Tongariro National Park. (Department of Conservation, 2000).

    29.
    Perry, N. B. et al. Essential oils from New Zealand manuka and kanuka: chemotaxonomy of Leptospermum. Phytochemistry 44, 1485–1494. https://doi.org/10.1016/S0031-9422(96)00743-1 (1997).
    CAS  Article  Google Scholar 

    30.
    Douglas, M. H. et al. Essential oils from New Zealand manuka: triketone and other chemotypes of Leptospermum scoparium. Phytochemistry 65, 1255–1264. https://doi.org/10.1016/j.phytochem.2004.03.019 (2004).
    CAS  Article  PubMed  Google Scholar 

    31.
    Guenther, A. B., Zimmerman, P. R., Harley, P. C., Monson, R. K. & Fall, R. Isoprene and monoterpene emission rate variability: model evaluations and sensitivity analyses. J. Geophys. Res. Atmos. 98, 12609–12617. https://doi.org/10.1029/93jd00527 (1993).
    ADS  Article  Google Scholar 

    32.
    Pratt, J. D., Keefover-Ring, K., Liu, L. Y. & Mooney, K. A. Genetically based latitudinal variation in Artemisia californica secondary chemistry. Oikos 123, 953–963. https://doi.org/10.1111/oik.01156 (2014).
    Article  Google Scholar 

    33.
    Soler, C. C. L., Proffit, M., Bessière, J.-M., Hossaert-McKey, M. & Schatz, B. Evidence for intersexual chemical mimicry in a dioecious plant. Ecol. Lett. 15, 978–985. https://doi.org/10.1111/j.1461-0248.2012.01818.x (2012).
    Article  PubMed  Google Scholar 

    34.
    Anderson, M. J. Permutational multivariate analysis of variance. Department of Statistics, University of Auckland, Auckland 26, 32–46 (2005).

    35.
    Anderson, M. J. Permutational multivariate analysis of variance (PERMANOVA). Wiley statsref: statistics reference online, 1–15 (2014).

    36.
    Copolovici, L. & Niinemets, Ü. In Deciphering Chemical Language of Plant Communication 35–59 (Springer, 2016).

    37.
    Valolahti, H., Kivimäenpää, M., Faubert, P., Michelsen, A. & Rinnan, R. Climate change-induced vegetation change as a driver of increased subarctic biogenic volatile organic compound emissions. Glob. Change Biol. 21, 3478–3488. https://doi.org/10.1111/gcb.12953 (2015).
    ADS  Article  Google Scholar 

    38.
    Laothawornkitkul, J., Taylor, J. E., Paul, N. D. & Hewitt, C. N. Biogenic volatile organic compounds in the Earth system. New Phytol. 183, 27–51. https://doi.org/10.1111/j.1469-8137.2009.02859.x (2009).
    CAS  Article  PubMed  Google Scholar 

    39.
    Loreto, F. & Schnitzler, J.-P. Abiotic stresses and induced BVOCs. Trends Plant Sci. 15, 154–166. https://doi.org/10.1016/j.tplants.2009.12.006 (2010).
    CAS  Article  PubMed  Google Scholar 

    40.
    Possell, M. & Loreto, F. In Biology, Controls and Models of Tree Volatile Organic Compound Emissions 209–235 (Springer, Berlin, 2013).

    41.
    Peñuelas, J. & Staudt, M. BVOCs and global change. Trends Plant Sci. 15, 133–144. https://doi.org/10.1016/j.tplants.2009.12.005 (2010).
    CAS  Article  PubMed  Google Scholar 

    42.
    Pare, P. W. & De Tumlinson, J. H. De novo biosynthesis of volatiles induced by insect herbivory in cotton plants. Plant Physiol. 114, 1161. https://doi.org/10.1104/pp.114.4.1161 (1997).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    43.
    Holopainen, J. & Blande, J. Where do herbivore-induced plant volatiles go?. Front. Plant Sci. https://doi.org/10.3389/fpls.2013.00185 (2013).
    Article  PubMed  PubMed Central  Google Scholar 

    44.
    Niinemets, Ü, Kännaste, A. & Copolovici, L. Quantitative patterns between plant volatile emissions induced by biotic stresses and the degree of damage. Front. Plant Sci. https://doi.org/10.3389/fpls.2013.00262 (2013).
    Article  PubMed  PubMed Central  Google Scholar 

    45.
    Litt, A. R., Cord, E. E., Fulbright, T. E. & Schuster, G. L. Effects of invasive plants on arthropods. Conserv. Biol. 28, 1532–1549. https://doi.org/10.1111/cobi.12350 (2014).
    Article  PubMed  Google Scholar 

    46.
    Dicke, M. & Baldwin, I. T. The evolutionary context for herbivore-induced plant volatiles: beyond the ‘cry for help’. Trends Plant Sci. 15, 167–175. https://doi.org/10.1016/j.tplants.2009.12.002 (2010).
    CAS  Article  PubMed  Google Scholar 

    47.
    Clavijo McCormick, A., Unsicker, S. B. & Gershenzon, J. The specificity of herbivore-induced plant volatiles in attracting herbivore enemies. Trends Plant Sci. 17, 303–310. https://doi.org/10.1016/j.tplants.2012.03.012 (2012).
    CAS  Article  PubMed  Google Scholar 

    48.
    Turlings, T. C. J. & Erb, M. Tritrophic interactions mediated by herbivore-induced plant volatiles: mechanisms, ecological relevance, and application potential. Annu. Rev. Entomol. 63, 433–452. https://doi.org/10.1146/annurev-ento-020117-043507 (2018).
    CAS  Article  PubMed  Google Scholar 

    49.
    Bernasconi, M. L., Turlings, T. C. J., Ambrosetti, L., Bassetti, P. & Dorn, S. Herbivore-induced emissions of maise volatiles repel the corn leaf aphid, Rhopalosiphum maidis. Entomol. Exp. Appl. 87, 133–142. https://doi.org/10.1046/j.1570-7458.1998.00315.x (1998).
    CAS  Article  Google Scholar 

    50.
    De Moraes, C. M., Mescher, M. C. & Tumlinson, J. H. Caterpillar-induced nocturnal plant volatiles repel conspecific females. Nature 410, 577–580. https://doi.org/10.1038/35069058 (2001).
    ADS  CAS  Article  PubMed  Google Scholar 

    51.
    Clavijo McCormick, A. et al. Herbivore-induced volatile emission in black poplar: regulation and role in attracting herbivore enemies. Plant Cell Environ. 37, 1909–1923. https://doi.org/10.1111/pce.12287 (2014).
    Article  PubMed  Google Scholar 

    52.
    Irmisch, S. et al. Herbivore-induced poplar cytochrome P450 enzymes of the CYP71 family convert aldoximes to nitriles which repel a generalist caterpillar. Plant J. 80, 1095–1107. https://doi.org/10.1111/tpj.12711 (2014).
    CAS  Article  PubMed  Google Scholar 

    53.
    Ehrenfeld, J. G. Effects of exotic plant invasions on soil Nutrient cycling processes. Ecosystems 6, 503–523. https://doi.org/10.1007/s10021-002-0151-3 (2003).
    CAS  Article  Google Scholar 

    54.
    Vallés, S. M., Fernández, J. B. G., Dellafiore, C. & Cambrollé, J. Effects on soil, microclimate and vegetation of the native-invasive Retama monosperma (L.) in coastal dunes. Plant Ecol. 212, 169–179. https://doi.org/10.1007/s11258-010-9812-z (2011).
    Article  Google Scholar 

    55.
    Rogers, G. M. Demography, and post-control response of heather in the central north island. Sci. Conserv. 9, 20 (1995).
    Google Scholar 

    56.
    Fogarty, G. & Facelli, J. M. Growth and competition of Cytisus scoparius, an invasive shrub, and Australian native shrubs. Plant Ecol. 144, 27–35. https://doi.org/10.1023/A:1009808116068 (1999).
    Article  Google Scholar 

    57.
    Haubensak, K. A. & Parker, I. M. Soil changes accompanying invasion of the exotic shrub Cytisus scoparius in glacial outwash prairies of western Washington [USA]. Plant Ecol. 175, 71–79. https://doi.org/10.1023/B:VEGE.0000048088.32708.58 (2004).
    Article  Google Scholar 

    58.
    Caldwell, B. A. Effects of invasive scotch broom on soil properties in a Pacific coastal prairie soil. Appl. Soil. Ecol. 32, 149–152. https://doi.org/10.1016/j.apsoil.2004.11.008 (2006).
    Article  Google Scholar 

    59.
    Chen, Y., Schmelz, E. A., Wäckers, F. & Ruberson, J. R. Cotton plant, Gossypium hirsutum L., defense in response to nitrogen fertilization. J. Chem. Ecol. 34, 1553–1564. https://doi.org/10.1007/s10886-008-9560-x (2008).
    CAS  Article  PubMed  Google Scholar 

    60.
    Peñuelas, J. & Llusià, J. Influence of intra- and inter-specific Interference on terpene emission by Pinus Halepensis and Quercus Ilex seedlings. Biol. Plant. 41, 139–143. https://doi.org/10.1023/A:1001789222741 (1998).
    Article  Google Scholar 

    61.
    Ormeño, E., Fernandez, C. & Mévy, J. P. Plant coexistence alters terpene emission and content of Mediterranean species. Phytochemistry 68, 840–852. https://doi.org/10.1016/j.phytochem.2006.11.033 (2007).
    CAS  Article  PubMed  Google Scholar 

    62.
    Kigathi, R. N., Weisser, W. W., Veit, D., Gershenzon, J. & Unsicker, S. B. Plants suppress their emission of volatiles when growing with conspecifics. J. Chem. Ecol. 39, 537–545. https://doi.org/10.1007/s10886-013-0275-2 (2013).
    CAS  Article  PubMed  Google Scholar 

    63.
    Ishizaki, S., Shiojiri, K., Karban, R. & Ohara, M. Effect of genetic relatedness on volatile communication of sagebrush (Artemisia tridentata). J. Plant Interact. 6, 193–193 (2011).
    CAS  Article  Google Scholar 

    64.
    Wason, E. L. & Hunter, M. D. Genetic variation in plant volatile emission does not result in differential attraction of natural enemies in the field. Oecologia 174, 479–491 (2014).
    ADS  Article  Google Scholar 

    65.
    Karban, R. & Shiojiri, K. Self-recognition affects plant communication and defense. Ecol. Lett. 12, 502–506 (2009).
    Article  Google Scholar  More

  • in

    Minimal fatal shocks in multistable complex networks

    Minimal fatal shock
    The first step in identifying the MiFaS for a given system is to define a desired state (mathbf {X_0}). We then assume that, prior to perturbations, the system resides on (mathbf {X_0}) and that a shock—applied at (t=0)—kicks the system’s state instantaneously to (mathbf {X}(0)). A shock—now defined as (mathbf {x}(0) = mathbf {X}(0)-mathbf {X_0})—is said to be fatal if (mathbf {X}(0)) is located outside the basin of (mathbf {X_0}) and non-fatal if (mathbf {X}(0)) is located within the basin of (mathbf {X_0}). Accordingly, the MiFaS is a vector which displays the shortest distance between the desired state and its basin boundary and the corresponding direction in state space (Fig. 1a).
    Figure 1

    Representation of the Minimal Fatal Shock and the related search algorithm. (a) The MiFaS (red arrow) is the smallest perturbation to the desired state (mathbf {X_0}) which puts the system outside the basin of (mathbf {X_0}) and into the basin of an alternative attractor (mathbf {X_a}). (b) The search algorithm starts with a relatively large perturbation magnitude. The related subspace of allowed initial conditions is given by the largest circle and the direction of maximum amplification is displayed by the green arrow. As the magnitude of allowed perturbations is reduced, the direction of maximum amplification converges towards the MiFaS. Color coding marks the objective function (distance to the desired state after a short integration time) with dark colors displaying large values and bright colors small values. This figure was generated using MATLAB version R2020a (https://www.mathworks.com/).

    Full size image

    The second essential step, is defining a norm for the perturbation size. It is important to note that the use of a certain norm is not only a technical but also an interpretative decision. Throughout this work, we use the Euclidean distance to the desired state (mathbf {X_0}) to quantify the magnitude d of a perturbation

    $$begin{aligned} d ; = , ||mathbf {x}(0) || , = , ||mathbf {X}(0) – mathbf {X_0}||. end{aligned}$$
    (1)

    To determine the MiFaS, we develop a search algorithm which is based on the minimal seed approach41 and which can be divided into two stages, the global random initialization (stage I) and the local non-random optimization (stage II).
    In stage I, we randomly draw initial conditions from a shrinking subspace in state space to find a fatal shock with a preferably small magnitude d (see “Methods” and Supplementary Fig. S1). Stage II starts with the smallest fatal shock received from stage I (Supplementary Fig. S1). From this point on, we take two seemingly opposing steps. First, we adapt the direction of (mathbf {x}(0)) in order to move (mathbf {X}(0)) away from the basin of (mathbf {X_0}) while keeping d fixed. Second, we move (mathbf {X}(0)) towards the basin by reducing d by a step size (Delta d). By repeating these two steps iteratively, we attain smaller and smaller fatal shocks which finally converge towards a local MiFaS (see Fig. 1b and Supplementary Fig. S1). It is important to note that the outcome of the search—and thus the achieved local MiFaS—is dependent on the initialization in stage I. Accordingly, to attain the global MiFaS, we need to run the search algorithm multiple times and select the minimum of the local MiFaS as the global one.
    Figure 2

    Minimal Fatal Shock for an exemplary plant–pollinator network. (a) Direction of the MiFaS. The perturbation vector is scaled to a length of 1. The relative contribution of each element of the vector (node in the network) to the overall perturbation is represented by the area and the color saturation of the respective squares and circles. A pink coloring denotes a loss and a green coloring a gain in species abundance at the respective node. Squares portray pollinators and circles plants. Species being lost after the perturbation are marked by the yellow shaded region. Placement of the vertices is based on the Kamada–Kawai algorithm66 obtained from python-igraph version 0.7.1 (https://igraph.org/). (b) Transient behavior following the MiFaS. Dark gray area shows the situation before the perturbation (desired state). Lighter gray area shows how the state variables are altered due to the perturbation. Light gray area depicts the transient behavior after the system has been perturbed. (c) Evolution over a longer time span. Vertical line displays the time interval shown in (b). The figure was generated using MATLAB version R2020a (https://www.mathworks.com/).

    Full size image

    The centerpiece of the outlined algorithm is the adaptation of the direction of (mathbf {x}(0)) during stage II, which aims at maximizing the distance between (mathbf {X}(0)) and the basin boundary of (mathbf {X_0}). However, since this distance is not easily accessible, it is approximated by an objective function which can be maximized within a constraint optimization. For the two applications we present here, the objective function can be thought of as the amplification of the shock over a preselected time T (see “Methods” for specific definition). The mechanism behind this is that trajectories close to the basin boundary stay close to it for long times as they move along the stable manifold of a saddle-type state while trajectories far off the boundary approach an alternative attractor faster and thus lead to earlier and stronger amplifications.
    In summary, as a result of the optimization procedure we obtain the magnitude of the smallest distance to the basin boundary which can be utilized as a quantitative measure of global stability and the direction of the perturbation in the high-dimensional phase space.
    Plant–pollinator networks
    In our first example, we consider a simple model of mutualism which captures the crucial aspects of a system of plants and their corresponding pollinators43,45. The mutualistic system is described as a bipartite network, with one set of nodes representing a number of (N_P) plant species and one set representing a number of (N_A) animal species whose dynamics are given by

    $$begin{aligned} frac{mathrm {d} P_i}{mathrm {d} t} ,&= , alpha P_i , – , sum _{k=1}^{N_P} beta _{ik} P_i P_k , + , frac{sum _{j=1}^{N_A} gamma _{ij} A_j P_i}{1 + h sum _{j=1}^{N_A} gamma _{ij} A_j},nonumber \ frac{mathrm {d} A_j}{mathrm {d} t} ,&= , alpha A_j , – , sum _{l=1}^{N_A} {tilde{beta }}_{jl} A_j A_l , + , frac{sum _{i=1}^{N_P} {tilde{gamma }}_{ji} P_i A_j}{1 + h sum _{i=1}^{N_P} {tilde{gamma }}_{ji} P_i}, end{aligned}$$
    (2)

    where (P_i) denotes the abundance of plant species i ((i=1, ldots , N_P)) and (A_j) the abundance of animal species j ((j=1, ldots , N_A)). In Eq. (2), the parameter (alpha) gives the intrinsic growth rate, (beta _{ik}) (({tilde{beta }}_{jl})) the competitive pressure of plant (animal) species k (l) on plant (animal) species i (j), (gamma _{ij}) (({tilde{gamma }}_{ji})) the benefit plant (animal) species i (j) obtains from animal (plant) species j (i) and h the handling time for pollination. As a general principle, we assume the benefit a species gains from pollination to be obligatory for its own growth, an assumption which is necessary to obtain multistability in this model57. Therefore, we choose the net growth rate (alpha le 0).
    In order to keep the parametrization as simple as possible, we set (alpha), (beta _{ii}) (({tilde{beta }}_{jj})) and h to be equal for all species. To reduce the complexity of the overall interaction pattern, we assume all-to-all coupling for the interspecific competition between species within one set, whereby (beta _{ik}=beta _0/(N_{P}-1)) for (i ne k) (({tilde{beta }}_{jl}=beta _0/(N_{A}-1)) for (j ne l)). By contrast, a mutualistic interaction between an animal and a plant species can either be absent, in which case (gamma _{ij}=0) (({tilde{gamma }}_{ji}=0)), or present, in which case (gamma _{ij}=gamma _0/kappa _i) (({tilde{gamma }}_{ji}=gamma _0/{tilde{kappa }}_j)), where (kappa _i) (({tilde{kappa }}_j)) denotes the degree or the number of mutualistic partners of plant (animal) species i (j). This formulation corresponds to a full trade-off between the benefit a species attains from one partner and the number of partners this species has45. An important aspect of the chosen parametrization is that species solely differ on account of their position in the mutualistic network. In the following, we determine the MiFaS for realistic plant–pollinator networks from the Web of Life Database58 representing networks from different geographic locations across various climate zones (see Supplementary Fig. S5 and Supplementary Table S2). With (alpha = -0.3), (beta _{ii}=1.0), (beta _0 = 1.0), (gamma _0 = 4.5) and (h=0.1), we choose the model parameters in a way that ensures that each of the studied systems possesses a state in which all species coexist. This ’desired’ state (mathbf {X_0}) is opposed to multiple ’undesired’ states in which one or more species are gone extinct (the MiFaS is actually fatal).
    To interpret the results, it is useful to state some general considerations first. Due to the mutualism, the growth of a species depends on the abundance of its mutualistic partners. As the growth of these partners can also depend on further other partners, these further partners indirectly support the growth of the first species. We could continue building this chain of dependencies but essential is that species being close to each other within the network and especially those sharing partners benefit from each other. On the other hand, due to competition high abundances of one species directly impede the growth of all species within the same group (animals or plants). Hence, the net effect which an increase or decrease of a species’ abundance has on another species depends on the interplay between the two processes. The indirect benefits can either balance or enhance the negative effects due to competition depending on whether species are close (balance) or far apart (enhance).
    At first, we compute the minimal fatal shock (MiFaS) for an exemplary network from Morant Point in Jamaica (Fig. 2a). The topology of this system is characterized by an asymmetric division into a small tree-like part and a large core, i.e. a large mostly well connected component. This topological division is mirrored in the direction of the MiFaS which is visualized by the color-coding. A small negatively perturbed part consisting of the tree-like periphery (nodes within the yellow shaded region in Fig. 2a) plus its single non-peripheral neighbor is opposed to the rest of the network which is positively perturbed. This division exemplifies how the mutualistic and competitive interactions between species shape the system’s response to perturbations. In the tree-shaped part of the network, all species are close to each other but far away from most other species. Furthermore, due to the sole connection between the two characteristic structural parts of the network, the share of partners between the two is minimal. As a result, the interdependency of species within the tree-shaped part is extremely high. Accordingly, the loss of abundance of any species in the tree-like structure—as it is the case in the MiFaS (Fig. 2)—significantly affects all other species in this tree-like periphery. On the contrary, the competitive stress due to species within the large component is high as it is not balanced by the indirect benefits. It is actually even enhanced as the increase of abundance of one species boosts the growth of its partners which again enhances the competive stress on the peripheral tree-like structure.
    Figure 3

    Magnitudes of 59 and direction of six MiFaS in plant–pollinator networks. The 59 networks are ordered, from low to high, and labeled according to their respective magnitude of the MiFaS. In addition, the direction of the MiFaS is shown for six exemplary networks. Perturbation vectors are scaled to a length of 1. The relative contribution of each element of the vector (node in the network) to the overall perturbation is represented by the area and the color saturation of the respective squares and circles. A pink coloring denotes a loss and a green coloring a gain in species abundance at the respective node. Squares portray pollinators and circles plants. Species being lost after the perturbation are marked by the yellow shaded region. Placement of the vertices is based on the Kamada–Kawai algorithm66 obtained from python-igraph version 0.7.1 (https://igraph.org/). The figure was generated using MATLAB version R2020a (https://www.mathworks.com/).

    Full size image

    After the system has been hit by the MiFaS, all ten species within the tree-like periphery are lost in the long run (Fig. 2c and yellow shaded region in Fig. 2a). The remaining species—except for the single neighbor of the periphery—tend to higher abundances as the competitive pressure on them is relaxed. Accordingly, the new asymptotic state (Fig. 2c) again shows that the net impact of the peripheral species on most other species has been negative. Apart from the new asymptotic state, the transient leading there (Fig. 2b,c) is of interest as well. In fact, the transient behavior is typical for an initial state close to the basin boundary which is made up by the stable manifold of a saddle point. The transient at first moves towards the saddle fast (Fig. 2b), stays in its vicinity for some time as the repulsion is weak and finally settles on an attractor which, in this case, is the undesired state of partial extinction (Fig. 2c).
    Figure 4

    Minimal Fatal Shock in the Great Britain power grid. (a) Direction of the MiFaS. The perturbation vector is scaled to a length of 1. The relative contribution of each element of the vector (node in the network) to the overall perturbation is represented by the area and the color saturation of the respective squares and circles. A blue coloring denotes a deceleration and a pink coloring an acceleration at the respective node. Squares portray consumers and circles generators. Width of transmission line scales with respective initial transmission load. (b) Blow-up of tree-like structure in (a). (c, d) Transient behavior following the MiFaS. (c) Time series of the loads on the transmission lines included in (b). Colors of highlighted loads correspond to colors of transmission lines in (b), remaining loads are depicted in white. (d) Time series of the frequency deviations of all oscillators, color coding corresponds to perturbation magnitude and direction at each node. The figure was generated using MATLAB version R2020a (https://www.mathworks.com/).

    Full size image

    Overall, we examine the MiFaS for a total of 59 plant–pollinator systems, each being based on one of the real-world network topologies. For comparison, we order the networks from sensitive to robust according to the magnitude of their respective MiFaS and depict the direction of the MiFaS for five further exemplary systems (Fig. 3).
    Figure 5

    Local Minimal Fatal Shocks in the Great Britain power grid. Direction of the local MiFaS. The perturbation vectors are scaled to a length of 1. The relative contribution of each element of the vector (node in the network) to the overall perturbation is represented by the area and the color saturation of the respective squares and circles. A blue coloring denotes a deceleration and a pink coloring an acceleration at the respective node. Squares portray consumers and circles generators. (a–d) Blow-ups of the significantly perturbed area of four local MiFaS which correspond to different outcomes of the optimization process. Highlighted edges represent the trigger transmission line of the particular perturbation. The figure was generated using MATLAB version R2020a (https://www.mathworks.com/).

    Full size image

    Some characteristics found for the MiFaS of the exemplary network (Fig. 2) prove to be generally valid. For each system, the division of the MiFaS into a small negatively perturbed part and a larger but weaker positively perturbed part displays how mutualistic interdependency and competition shape the system’s response to perturbations. In this context, the negatively perturbed part marks the weakest point of the network at whose outer edge the extinction occurs. Speaking in ecological terms, we find these weak points always being associated with specialization and the distribution of negative perturbations depends on the nature of the caused interdependency: in the exemplary system (network 1 in Fig. 3), where the specialization among all species within the tree-like structure is rather mutual, all involved species are significantly perturbed (the same for network 13 and partly for network 4, Fig. 3). However, the more asymmetric the specialization gets—meaning that many specialists are connected to a single generalist—the stronger the negative perturbation focuses on this generalist (networks 4 (rightarrow) 26 (rightarrow) 27 (rightarrow) 49, Fig. 3). This perturbation structure proofs to be efficient as the dependency of the generalist on each single specialist is low but its cumulated dependency on all specialized partners is high. A perturbation at the generalist therefore induces a negative feedback whose strength also depends on the number of connections the generalist has to other-non-specialized species. Accordingly, network 49 is much more robust than network 26 as the decisive generalist is highly connected to the core.
    The positive contribution to the overall MiFaS marks the impact of competitive forces which depends on the global interdependency among species. In the case of a single well-connected core and a periphery which only consists of specialists being directly connected to this core, indirect positive effects between species balance competive effects as all species are close and well connected. Accordingly, we do not find any significant contribution of positive perturbations to the overall MiFaS (networks 37, 49, Fig. 3). The contrary is the case if the core is not well build, meaning that only a few connections between important hub nodes exist (networks 4, 26) or if—due to strong reciprocal specialization—a larger peripheral structure exists (networks 1, 13). In such cases, positive perturbations at rather central core-species contribute significantly to the overall MiFaS and thus to the extinction of peripheral species. In summary, a strong global interdependency among all species favors a system’s robustness whereas a strong local interdependency paired with a weak global interdependency depicts the worst case scenario.
    Great Britain power grid
    As a second example we consider a coarse-grained model of a power grid which exhibits synchronization dynamics. In this framework, a power grid is described as a network of Kuramoto-like13 second order phase oscillators whose dynamics are given by

    $$begin{aligned} frac{mathrm {d} phi _i}{mathrm {d} t}&= omega _i nonumber \ frac{mathrm {d} omega _i}{mathrm {d} t}&= P_i – alpha omega _i + sum ^N_{j=1} K_{ji} , sin (phi _j-phi _i), end{aligned}$$
    (3)

    where (phi _i) and (omega _i) denote the phase and frequency deviation of oscillator i from a grid’s rated frequency (which will hereinafter be referred to as phase and frequency). The parameters (alpha) and (P_i) are the grid’s damping constant and the net power input/output of oscillator i, respectively. The capacities of the transmission lines and therefore also the topology of the grid are contained in the matrix K, with (K_{ji}=K_{ij} >0) if oscillators i and j are connected and (K_{ij}=0) otherwise.
    As an example, we consider the Great Britain power grid which consists of 120 nodes and 165 transmission lines59. For reasons of simplification, we assume one half of the oscillators to be generators ((P_i=+P_0)) and one half to be consumers ((P_i=-P_0)) whose distribution within the grid we draw randomly (see Fig. 5). Furthermore, we choose the same maximum capacity for all transmission lines, either (K_{ij}=K_0) or (K_{ij}=0). In a realistic parameter setting of this model, one ’desired’ synchronized state ((phi _i=const) and (omega _i=0) for all i) representing stable operation competes with several ’undesired’ non-synchronized states. With (alpha =0.1), (P_0=1.0) and (K_0=5.0), we choose the model parameters accordingly. In this setting, the MiFaS represents the smallest perturbation to the synchronous state which induces a shift to one of the non-synchronous states interpreted as a power outage.
    The combination of frequencies and phases is actually problematic when determining the MiFaS since they differ in units. We therefore only take into account perturbations in the frequencies (omega). In this context, choosing the frequencies (omega) instead of the phases (phi) seems reasonable as disturbances usually occur due to fluctuations in the power generation or consumption60. Such parametric disturbances would first affect the frequencies via (mathrm {d}omega /mathrm {d}t) (Eq. 3). Furthermore, considering only frequencies allows a clearer depiction of the MiFaS, since the corresponding vector contains exactly one entry per node of the power grid.
    Examining one random realization of the power grid (Fig. 4a), we find that, like in the exemplary plant–pollinator network, the MiFaS is associated with a tree-like structure including the most peripheral nodes of the network (according to the resistance centrality proposed by61, see Supplementary Fig. S7). In fact, the same structure is highlighted by some of the eigenmodes of the graph Laplacian (see Supplementary Fig. S8). However, apart from the observation that the MiFaS is orthogonal to a neutral perturbation affecting all oscillators in the same way which is equivalent to its first eigenmode, we find no simple connection to the graph Laplacian (see Supplementary Information).
    In order to understand the effectiveness of the MiFaS, it is instructive to have a closer look at how the desynchronization occurs after the system has been hit by the MiFaS (Fig. 4c,d). The desynchronization is triggered by an overload on the transmission line which connects the seven northermost oscillators to the rest of the grid (Fig. 4b). Due to the accumulation of consumers within this tree-like structure (5 consumers towards 2 generators), already in the unperturbed state, the load—(K sin (phi _j – phi _i)) for the line connecting nodes j and i—on the ’trigger transmission line’ is comparatively close to its maximum capacity K (see Fig. 4c). Intuitively, a strong deceleration of oscillators inside plus an acceleration of oscillators outside the tree-like structure seems to be an efficient way to induce an overload. Indeed, we find the strongest negative perturbations at the seven oscillators within (Fig. 4b) as well as positive perturbations at several oscillators outside the tree-like structure. However, in the northern part of the grid, the overall MiFaS roughly follows a broad gradient distribution with negative perturbations on both sides of the trigger transmission line and the strongest positive perturbations at rather distant nodes in the northwest of Great Britain. This distribution is efficient as the perturbations in frequencies first have to be transferred into phase deviations to induce an overload. A relatively smooth gradient ensures that the arising phase deviations are balanced slowly and thus a large transmission load can build up.
    This transfer can be observed in the first stage of the transient following the MiFaS (Fig. 4c,d). In this stage, the system evolves rather smoothly towards a point where the frequency deviations of all oscillators are close to zero but where, at the same time, the transmission load on the trigger line (red line in Fig. 4) has passed its maximum capacity. The system subsequently enters a stage in which both transmission loads as well as frequencies oscillate erratically until the oscillations suddenly collapse and the system settles on an undesired attractor. It is remarkable that the final overload (green line in Fig. 4) is not located on the line which triggered the desynchronization but on a line deeper in the tree-like structure (Fig. 4c). The final overload is similar to a cutoff of two consumers from the rest of the grid, as the frequencies in the two departed components evolve more or less independently. It is however important to note that this particular undesired state represents only one of several possible outcomes. Indeed, already the slightest variation (smaller than the finite precision of the search algorithm) of the initial perturbation can lead to a different non-synchronous asymptotic state, although the trigger transmission line is always the same. Such high sensitivity is often an indicator for complexly intervowen basins of attraction, characteristic to many highly multistable systems62.
    In order to gain more insights into how certain topological features harm a power grid’s stability against shocks, we examine some of the local MiFaS inducing power outages (Fig. 5). These local minima correspond to different outcomes of the applied optimization scheme for the same network topology and parametrization and thus represent further close but less crucial distances between the desired state and its basin boundary. As we are interested in distinct topological weak points of the grid, we take into account only those local minima which differ in the involved trigger transmission line (highlighted edges in Fig. 5).
    The local MiFaS, and in particular the examination of the associated trigger transmission lines, reveal two mutually reinforcing sources for the emergence of weak points. Firstly, desynchronization events are triggered on transmission bottlenecks which result from the loose connection between a peripheral subgraph and the rest of the grid. Four out of five of the shown local MiFaS (Fig. 4 and Fig. 5a–c) are actually related to the most pronounced case of such a bottleneck which is a bridge, i.e. a single edge connecting two subnetworks. Secondly, the accumulation of oscillators of the same type within a subgraph induces a local mismatch between power generation and consumption (Fig. 4 and Fig. 5a–d). We find each of the shown local MiFaS to be related to such a local mismatch. Already in the unperturbed state, this mismatch has to be balanced by a high initial load on the connecting transmission line(s) which in turn results in a low threshold for an overload (Fig. 5d). This overload is then triggered by the MiFaS by reinforcing the generation/consumption imbalance between the two subgraphs. Accordingly, all fatal shocks involve strong frequency perturbations with a sign according to the already established power mismatch in the peripheral subgraph and frequency perturbations in the opposite direction in adjacent areas of the grid. However, as in the global MiFaS, the boundary between positive and negative perturbations is not sharp but more (Fig. 5a,c,d) or less (Fig. 5b) follows a kind of gradient.
    Of particular interest is the local MiFaS shown in Fig. 5c as its underlying topological motif is quite common in the network: a node with degree 1, also termed ’dead end’32. Apart from the two dead ends within trees (Fig. 5a,b), the portrayed dead end is the one being most sensitive to perturbations despite or seemingly because it is connected to a rather central node of degree 6 (see also Supplementary Fig. S7). For none of the surroundings of the other dead ends, which are all adjacent to lower degree nodes, we find a local MiFaS of similar low magnitude. Accordingly, we conclude that a rather central position of the node from which the peripheral subgraph branches off might actually harm its robustness against particular perturbations. More

  • in

    Geobiochemistry characteristics of rare earth elements in soil and ground water: a case study in Baotou, China

    Distribution characteristics of REEs in ground water
    In this study, ground water samples were collected from 18 ground water monitoring wells around tailings ponds and their chemical characteristics were also having been determined, as showed in Figure S1. Fe, Mn2+, Cl−, SO42−, ammonia nitrogen and total hardness showed the same trend and decreased with distance. The ground water environmental quality standard (III Grade, National Standard Bureau of PR China, GB3838-2002, the water quality above III Grade can be used for living and drinking after treatment, but the water quality below III Grade was bad and cannot be used as drinking water source) was used as the evaluation standard. The ratio of the number of wells with Fe, Mn2+, Cl−, SO42−, ammonia nitrogen and total hardness exceeding the standard in the total number of wells was 33.33%, 61.11%, 66.67%, 77.78%, 100% and 81.25%, respectively.
    In order to study the accumulation of REEs in ground water, the concentration of REEs in 18 ground water samples around the tailings pond were measured. The total REEs concentrations in ground water ranged from 0.0820 to 12.3 μg/L, and rare earth in the ground water accumulated in the southeast of the tailings pond (Fig. 2). In addition, the concentrations of REEs in ground water around the tailings pond decreased in the order of Ce  > La  > Nd  > Pr  > Gd  > Sm  > Dy  > Er  > Eu  > Yb  > Tb  > Ho  > Tm  > Lu. Chondrite-normalized REEs patterns for ground waters around the tailings were shown in Fig. 4b and Table 1. The well points have the same normalization pattern with a predominance of LREEs over HREEs.
    Figure 2

    Distribution of rare earth elements in the ground water surrounding the rare earth tailings pond (μg/L).

    Full size image

    Table 1 Distribution characteristics of REEs in ground water surrounding tailings pond.
    Full size table

    The distribution patterns of REEs in ground water were characterized by obvious fractionation of LREEs and HREEs with the LREEs/HREEs ratios of 2.77 ~ 25.9, and (La/Yb)N of 1.445 ~ 50.67. The degree of LREEs fractionation with (La/Sm)N of 0.5806 ~ 5.216. Most sampling points presented the positive anomaly of Ce and Eu, however, GW1, GW5, GW6, GW9, GW10, GW13 and GW6 were negative anomalies of Ce, while GW1, GW5, GW7 and GW8 were negative anomalies of Eu. Individual anomalies showed differentiation between selected elements (Ce and Eu) and the other REEs (Table 1).
    Baotou environmental monitoring station, Inner Mongolia, China detected ground water leakage around the pond, and various degrees of ground water pollution were found with relatively lower metals concentration and higher anionic concentration21,22,23. Therefore, in addition to REEs, for our ground water correlation analysis we chose to also look at Fe, Mn2+, Cl−, SO42−, ammonia nitrogen and some other ions (HCO3−, total hardness). Correlation analysis showed that total hardness (r = 0.541, p  More

  • in

    Differential impact of thermal and physical permafrost disturbances on High Arctic dissolved and particulate fluvial fluxes

    1.
    Woo, M. K. Permafrost Hydrology (Springer, New York, 2012).
    Google Scholar 
    2.
    Braun, C., Hardy, D. R., Bradley, R. S. & Retelle, M. J. Streamflow and suspended sediment transfer to Lake Sophia, Cornwallis Island, Nunavut, Canada. Arct. Antarct. Alp. Res. 32(4), 456–465. https://doi.org/10.1080/15230430.2000.12003390 (2000).
    Article  Google Scholar 

    3.
    Woo, M. K. & McCann, B. S. Climatic variability, climatic change, runoff, and suspended sediment regimes in northern Canada. Phys. Geogr. 15(3), 201–226. https://doi.org/10.1080/02723646.1994.10642513 (1994).
    Article  Google Scholar 

    4.
    Frey, K. E. & McClelland, J. W. Impacts of permafrost degradation on arctic river biogeochemistry. Hydrol. Process. 23, 169–182. https://doi.org/10.1002/hyp.7196 (2009).
    ADS  CAS  Article  Google Scholar 

    5.
    Lafrenière, M. J. et al. Chapter 6: Drivers, trends and uncertainties of changing freshwater systems. In From Science to Policy in the Eastern Canadian Arctic: An Integrated Regional Impact Study (IRIS) of Climate Change and Modernization (eds Bell, T. & Brown, T. M.) (ArcticNet, Halifax, 2018).
    Google Scholar 

    6.
    Post, E. et al. The polar regions in a 2°C warmer world. Sci. Adv. 5(12), eaaw9883. https://doi.org/10.1126/sciadv.aaq9883 (2019).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    7.
    Kokelj, S. V., Lantz, T. C., Tunnicliffe, J., Segal, R. & Lacelle, D. Climate-drive thaw of permafrost preserved glacial landscapes, northwestern Canada. Geology 45(4), 371–374. https://doi.org/10.1130/G38626.1 (2017).
    ADS  Article  Google Scholar 

    8.
    Kokelj, S. V. et al. Thawing of massive ground ice in mega slumps drives increases in stream sediment and solute flux across a range of watershed scales. J. Geophys. Res. Earth Surf. 118, 681–692. https://doi.org/10.1002/jgrf.20063 (2013).
    ADS  Article  Google Scholar 

    9.
    Rudy, A. C. A., Lamoureux, S. F., Kokelj, S. V., Smith, I. R. & England, J. H. Accelerating thermokarst transforms ice-cored terrain triggering a downstream cascade to the ocean. Geophys. Res. Lett. 44(21), 11080–11087. https://doi.org/10.1002/2017GL074912 (2017).
    ADS  Article  Google Scholar 

    10.
    Malone, L., Lacelle, D., Kokelj, S. & Clark, I. D. Impacts of hillslope thaw slumps on the geochemistry of permafrost catchments (Stony Creek watershed, NWT, Canada). Chem. Geol. 356, 38–49. https://doi.org/10.1016/j.chemgeo.2013.07.010 (2013).
    ADS  CAS  Article  Google Scholar 

    11.
    Kokelj, S. V. & Jorgenson, M. T. Advances in thermokarst research. Permafr. Periglac. Process. 24, 108–119. https://doi.org/10.1002/ppp.1779 (2013).
    Article  Google Scholar 

    12.
    Lantz, T. C. & Kokelj, S. V. Increasing rates of retrogressive thaw slump activity in the Mackenzie Delta region, N.W.T., Canada. Geophys. Res. Lett. 35, L06502. https://doi.org/10.1029/2007/GL032433 (2008).
    ADS  Article  Google Scholar 

    13.
    Lewkowicz, A. G. & Way, R. G. Extremes of summer climate trigger thousands of thermokarst landslides in a High Arctic environment. Nat. Commun. 10, 1329. https://doi.org/10.1038/s41467-019-09314-7(2019) (2019).
    ADS  Article  PubMed  PubMed Central  Google Scholar 

    14.
    Bowden, W. B. et al. Sediment and nutrient delivery from thermokarst features in the foothills of the North Slope, Alaska: potential impacts on headwater stream ecosystems. J. Geophys. Res. 113, G02026. https://doi.org/10.1029/2007JG000470 (2008).
    ADS  CAS  Article  Google Scholar 

    15.
    Lafrenière, M. J. & Lamoureux, S. F. Effects of changing permafrost conditions on hydrological processes and fluvial fluxes. Earth Sci. Rev. 191, 212–223. https://doi.org/10.1016/j.earscirev.2019.02.018 (2019).
    ADS  CAS  Article  Google Scholar 

    16.
    Kokelj, S. V. & Burn, C. R. Geochemistry of the active layer and near-surface permafrost, Mackenzie Delta region, Northwest Territories, Canada. Can. J. Earth Sci. 42(1), 37–48. https://doi.org/10.1139/E04-089 (2005).
    ADS  CAS  Article  Google Scholar 

    17.
    Keller, K., Blum, J. D. & Kling, G. W. Stream geochemistry as an indicator of increasing permafrost thaw depth in an arctic watershed. Chem. Geol. 273, 76–81. https://doi.org/10.1016/j.chemgeo.2010.02.013 (2010).
    ADS  CAS  Article  Google Scholar 

    18.
    Vonk, J. E. et al. A centennial record of fluvial organic matter input from the discontinuous permafrost catchment of Lake Torneträsk. J. Geophys. Res. 117, G03018. https://doi.org/10.1029/2011JG001887 (2012).
    Article  Google Scholar 

    19.
    Tank, S. E., Fellman, J. B., Hood, E. & Kritzberg, E. S. Beyond respiration: controls on lateral carbon fluxes across the terrestrial-aquatic interface. Limnol. Oceanogr. Lett. 3, 76–88. https://doi.org/10.1002/lol2.10065 (2018).
    Article  Google Scholar 

    20.
    Abbott, B. W., Jones, J. B., Godsey, S. E., Larouche, J. R. & Bowden, W. B. Patterns and persistence of hydrologic carbon and nutrient export from collapsing upland permafrost. Biogeosciences 12, 3725–3740. https://doi.org/10.5194/bg-12-3725-2015 (2015).
    ADS  CAS  Article  Google Scholar 

    21.
    Tarnocai, C. et al. Soil organic carbon pools in the northern circumpolar permafrost region. Glob. Biogeochem. Cycles 23, GB2023. https://doi.org/10.1029/2008GB003327 (2009).
    ADS  CAS  Article  Google Scholar 

    22.
    Hugelius, G. et al. Estimated stocks of circumpolar permafrost carbon with quantified uncertainty ranges and identified data gaps. Biogeosciences 11, 6573–6593. https://doi.org/10.5194/bg-11-6573-2014 (2014).
    ADS  Article  Google Scholar 

    23.
    Schuur, E. A. G. et al. Climate change and the permafrost carbon feedback. Nature 520, 171–179. https://doi.org/10.1038/nature14338 (2015).
    ADS  CAS  Article  PubMed  Google Scholar 

    24.
    Semiletov, I. P. et al. Carbon transport by the Lena River from its headwaters to the Arctic Ocean, with emphasis on fluvial input of terrestrial organic carbon vs. carbon transport by coastal erosion. Biogeosciences 8, 2407–2426. https://doi.org/10.5194/bg-8-2407-2011 (2011).
    ADS  CAS  Article  Google Scholar 

    25.
    Schädel, C. et al. Divergent patterns of experimental and model-derived permafrost ecosystem carbon dynamics in response to Arctic warming. Environ. Res. Lett. 13, 105002. https://doi.org/10.1088/1748-9326/aae0ff (2018).
    ADS  CAS  Article  Google Scholar 

    26.
    Dean, J. F. et al. East Siberian Arctic inland waters emit mostly contemporary carbon. Nat. Commun. 11, 1627. https://doi.org/10.1038/s41467-020-15511-6 (2020).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    27.
    O’Donnell, J. A. et al. DOM composition and transformation in boreal forest soils: The effects of temperature and organic-horizon decomposition state. J. Geophys. Res. 121(10), 2727–2744. https://doi.org/10.1002/2016JG003431 (2016).
    CAS  Article  Google Scholar 

    28.
    Tank, S. E. et al. Landscape-level controls on dissolved carbon flux from diverse catchments of the circumboreal. Glob. Biogeochem. Cycles 26, GB0E02. https://doi.org/10.1029/2012GB004299 (2012).
    CAS  Article  Google Scholar 

    29.
    Thienpont, J. R. et al. Biological responses to permafrost thaw slumping in Canadian Arctic lakes. Freshw. Biol. 58, 337–353. https://doi.org/10.1111/fwb.12061 (2012).
    Article  Google Scholar 

    30.
    Vonk, J. et al. High biolability of ancient permafrost carbon upon thaw. Geophys. Res. Lett. 40(11), 2689–2693. https://doi.org/10.1002/grl.50348 (2013).
    ADS  CAS  Article  Google Scholar 

    31.
    Littlefair, C. A., Tank, S. E. & Kokelj, S. V. Retrogressive thaw slumps temper dissolved organic carbon delivery to streams of the Peel Plateau, NWT, Canada. Biogeosciences 14, 5487–5505. https://doi.org/10.5194/bg-14-5487-2017 (2017).
    ADS  CAS  Article  Google Scholar 

    32.
    Fouché, J., Lafrenière, M. J., Rutherford, K. & Lamoureux, S. F. Seasonal hydrology and permafrost disturbance impacts on dissolved organic matter composition in High Arctic headwater catchments. Arct. Sci. 3, 378–405. https://doi.org/10.1139/as-2016-0031 (2017).
    Article  Google Scholar 

    33.
    Lamoureux, S. F. & Lafrenière, M. J. Seasonal fluxes and age of particulate organic carbon exported from Arctic catchments impacted by localized permafrost slope disturbances. Environ. Res. Lett. 9, 045002. https://doi.org/10.1088/1748-9326/9/4/045002 (2014).
    ADS  CAS  Article  Google Scholar 

    34.
    Guo, L., Ping, C.-L. & Macdonald, R. W. Mobilization pathways of organic carbon from permafrost to arctic rivers in a changing climate. Geophys. Res. Lett. 34, L13603. https://doi.org/10.1029/2007GL030689 (2007).
    ADS  CAS  Article  Google Scholar 

    35.
    Schreiner, K. M., Bianchi, T. S. & Rosenheim, B. E. Evidence for permafrost thaw and transport from an Alaskan North Slope watershed. Geophys. Res. Lett. 41, 3117–3126. https://doi.org/10.1002/2014GL059514 (2014).
    ADS  Article  Google Scholar 

    36.
    Wang, J.-J. et al. Differences in riverine and pond water dissolved organic matter composition and sources in Canadian High Arctic watersheds affected by active layer detachments. Environ. Sci. Technol. 52, 1062–1071. https://doi.org/10.1021/acs.est.7b05506 (2018).
    ADS  CAS  Article  PubMed  Google Scholar 

    37.
    Guo, L. & Macdonald, R. W. Source and transport of terrigenous organic matter in the upper Yukon River: evidence from isotope (δ13C, Δ14C, and δ15N) composition of dissolved, colloidal, and particulate phases. Glob. Biogeochem. Cycles 20, GB2011. https://doi.org/10.1029/2005GB002593 (2006).
    ADS  CAS  Article  Google Scholar 

    38.
    Bintanja, R. & Andry, O. Towards a rain-dominated Arctic. Nat. Clim. Change 7, 263–267. https://doi.org/10.1038/nclimate3240 (2017).
    ADS  Article  Google Scholar 

    39.
    Bintanja, A. The impact of Arctic warming on increased rainfall. Sci. Rep. 8, 16001. https://doi.org/10.1038/s41598-018-34450-3 (2018).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    40.
    Lewis, T., Lafrenière, M. J. & Lamoureux, S. F. Hydrochemical and sedimentary responses of paired High Arctic watersheds to unusual climate and permafrost change, Cape Bounty, Melville Island, Canada. Hydrol. Process. 26, 2003–2018. https://doi.org/10.1002/hyp.8335 (2012).
    ADS  Article  Google Scholar 

    41.
    Beel, C. R., Lamoureux, S. F. & Orwin, J. F. Fluvial response to a period of hydrometeorological change and landscape disturbance in the Canadian High Arctic. Geophys. Res. Lett. 45(19), 10446–10455. https://doi.org/10.1029/2018GL079660 (2018).
    ADS  Article  Google Scholar 

    42.
    Roberts, K. E. et al. Climate and permafrost effects on the chemistry and ecosystems of High Arctic lakes. Sci. Rep. 7, 13292. https://doi.org/10.1038/s41598-017-13658-9 (2017).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    43.
    Lamoureux, S. F., Lafrenière, M. J. & Favaro, E. A. Erosion dynamics following localized permafrost slope disturbances. Geophys. Res. Lett. 41(15), 5499–5505. https://doi.org/10.1002/2014GL060677 (2014).
    ADS  Article  Google Scholar 

    44.
    Lamhonwah, D., Lafrenière, M. J., Lamoureux, S. F. & Wolfe, B. B. Multi-year impacts of permafrost disturbance and thermal perturbation on High Arctic stream chemistry. Arct. Sci. 3, 254–276. https://doi.org/10.1139/as-2016-0024 (2017).
    Article  Google Scholar 

    45.
    Lamoureux, S. F. & Lafrenière, M. J. More than just snowmelt: integrated watershed science for changing climate and permafrost at the Cape Bounty Arctic Watershed Observatory. WIREs Water 5(1), e1255. https://doi.org/10.1002/wat2.1255 (2017).
    Article  Google Scholar 

    46.
    Hodgson, D. A., Vincent, J.-S. & Fyles, J. G. Quaternary Geology of Central Melville Island, Northwest Territories. Geological Survey of Canada, Paper 83-16. https://doi.org/10.4095/119784 (1984).

    47.
    Soil Classification Working Group. The Canadian System of Soil Classification 3rd edn, Vol. 1646 (Agriculture and Agri-Food Canada Publication, Revised, 1998). https://sis.agr.gc.ca/cansis/publications/manuals/1998-cssc-ed3/index.html

    48.
    Grewer, D. M., Lafrenière, M. J., Lamoureux, S. F. & Simpson, M. J. Redistribution of soil organic matter by permafrost disturbance in the Canadian High Arctic. Biogeochemistry 128(3), 397–415. https://doi.org/10.1007/s10533-016-0215-7 (2016).
    CAS  Article  Google Scholar 

    49.
    Walker, D. A. et al. The Circumpolar Arctic vegetation map. J. Veg. Sci. 16, 267–282. https://doi.org/10.1111/j.1654-1103.2005.tb02365.x (2005).
    Article  Google Scholar 

    50.
    Favaro, E. A. & Lamoureux, S. F. Antecedent controls on rainfall runoff response and sediment transport in a High Arctic catchment. Geogr. Ann. Phys. Geogr. 96(4), 433–446. https://doi.org/10.1111/geoa.12063 (2014).
    Article  Google Scholar 

    51.
    Taylor, J. R. An Introduction to Error Analysis: The Study of Uncertainties in Physical Measurements (University Science Books, Mill Valley, 1982).
    Google Scholar 

    52.
    Watt, W. E., Lathem, K. W., Neill, C. R., Richards, T. L. & Rousselle, J. Hydrology of Floods in Canada: A Guide to Planning and Design (National Research Council of Canada, Ottawa, 1989).
    Google Scholar 

    53.
    Government of Canada – Environment and Natural Resources. Historical Climate Data. www.climat.meteo.gc.ca (2017).

    54.
    Singh, V. Elementary Hydrology (Prentice Hall, Upper Saddle River, 1992).
    Google Scholar 

    55.
    Emmerton, C. A., Lesack, L. F. W. & Vincent, W. F. Mackenzie River nutrient delivery to the Arctic Ocean and effects of the Mackenzie Delta during open water conditions. Glob. Biogeochem. Cycles 22, GB1024. https://doi.org/10.1029/2006GB002856 (2008).
    ADS  CAS  Article  Google Scholar 

    56.
    Gareis, J. A. L. & Lesack, L. F. W. Fluxes of particulates and nutrients during hydrologically defined seasonal periods in an ice-affect great Arctic river, the Mackenzie. Water Resour. Res. 53, 6109–6132. https://doi.org/10.1002/2017WR020623 (2017).
    ADS  CAS  Article  Google Scholar 

    57.
    Kennedy, P., Kennedy, H. & Papadimitriou, S. The effect of acidification on the determination of organic carbon, total nitrogen and their stable isotopic composition in algae and marine sediment. Rapid Commun. Mass Spectrom. 19, 1063–1068. https://doi.org/10.1002/rcm.1889 (2005).
    ADS  CAS  Article  PubMed  Google Scholar 

    58.
    Komada, T., Anderson, M. R. & Dorfmeier, C. L. Carbonate removal from coastal sediments for the determination of organic carbon and its isotopic signatures, δ13C and Δ14C: comparison of fumigation and direct acidification by hydrochloric acid. Limnol. Oceanogr. Methods 6, 254–262. https://doi.org/10.4319/lom.2008.6.254 (2008).
    CAS  Article  Google Scholar 

    59.
    Searcy, J. K. & Hardison, C. H. Double-mass curves. In Manual of Hydrology: Part 1. General Surface-Water Techniques. Water-Supply Paper 1541-B (US Geological Survey, 1960).

    60.
    Spencer, R. G. M. et al. Detecting the signature of permafrost thaw in Arctic rivers. Geophys. Res. Lett. 42, 2830–2835. https://doi.org/10.1002/2015GL063498 (2015).
    ADS  Article  Google Scholar 

    61.
    Benner, R., Benitez-Nelson, B., Kaiser, K. & Amon, R. M. W. Export of young terrigenous dissolved organic carbon from rivers to the Arctic Ocean. Geophys. Res. Lett. 31, L05305. https://doi.org/10.1029/2003GL019251 (2004).
    ADS  CAS  Article  Google Scholar 

    62.
    Raymond, P. et al. Flux and age of dissolved organic carbon exported to the Arctic Ocean: a carbon isotopic study of the five largest Arctic rivers. Glob. Biogeochem. Cycles 21, GB4011. https://doi.org/10.1029/2007GB002934 (2007).
    ADS  CAS  Article  Google Scholar 

    63.
    Striegl, R. G., Dornblaser, M. M., Aiken, G. R., Wickland, K. P. & Raymond, P. A. Carbon export and cycling by the Yukon, Tanana, and Porcupine rivers, Alaska 2001–2005. Water Resour. Res. 43, W02411. https://doi.org/10.1029/2006WR005201 (2007).
    ADS  CAS  Article  Google Scholar 

    64.
    Drake, T. W. et al. The ephemeral signature of permafrost carbon in an Arctic fluvial network. JGR Biogeosci. 123(5), 1475–1485. https://doi.org/10.1029/2017JG004311 (2018).
    CAS  Article  Google Scholar 

    65.
    Pautler, B. G., Simpson, A. J., McNally, D. J., Lamoureux, S. F. & Simpson, M. J. Arctic permafrost active layer detachments stimulate microbial activity and degradation of soil organic matter. Environ. Sci. Technol. 44, 4076–4082. https://doi.org/10.1021/es903685j (2010).
    ADS  CAS  Article  PubMed  Google Scholar 

    66.
    Grewer, D. M., Lafrenière, M. J., Lamoureux, S. F. & Simspon, M. J. Potential shifts in Canadian High Arctic sedimentary organic matter composition with permafrost active layer detachments. Org. Geochem. 79, 1–13. https://doi.org/10.1016/j.orggeochem.2014.11.007 (2015).
    CAS  Article  Google Scholar 

    67.
    Kalbitz, K., Schwesig, D., Rethemeyer, J. & Matzner, E. Stabilization of dissolved organic matter by sorption to the mineral soil. Soil Biol. Biochem. 37(7), 1319–1331. https://doi.org/10.1016/j.soilbio.2004.11.028 (2005).
    CAS  Article  Google Scholar 

    68.
    Owens, P. N., Petticrew, E. L. & van der Perk, M. Sediment response to catchment disturbances. J. Soils Sediments 10, 591–596. https://doi.org/10.1007/s11368-010-0235-1 (2010).
    Article  Google Scholar 

    69.
    Grosse, G. et al. Vulnerability of high-latitude soil organic carbon in North America to disturbance. J. Geophys. Res. 116, G00K06. https://doi.org/10.1029/2010JG001507 (2011).
    CAS  Article  Google Scholar 

    70.
    Vonk, J. E. et al. Reviews and syntheses: effects of permafrost thaw on Arctic aquatic ecosystems. Biogeosciences 12, 7129–7167. https://doi.org/10.5194/bg-12-7129-2015 (2015).
    ADS  CAS  Article  Google Scholar 

    71.
    Schuur, E. A. G. et al. Expert assessment of vulnerability of permafrost carbon to climate change. Clim. Change 119, 359–374. https://doi.org/10.1007/s10584-013-0730-7 (2013).
    ADS  CAS  Article  Google Scholar 

    72.
    Vonk, J. E., van Dongen, B. E. & Gustafsson, Ö. Selective preservation of old organic carbon fluvially released from sub-Arctic soils. Geophys. Res. Lett. 37, L11605. https://doi.org/10.1029/2010GL042909 (2010).
    ADS  CAS  Article  Google Scholar 

    73.
    Gordeev, V. V. & Kravchishina, M. D. River flux of dissolved organic carbon (DOC) and particulate organic carbon (POC) to the Arctic Ocean: what are the consequences of the global changes. In Influence of Climate Change on the Changing Arctic and sub-Arctic Conditions (eds Nihoul, J. C. J. & Kostianoy, A. G.) 145–161 (Springer, Berlin, 2009).
    Google Scholar 

    74.
    Rudy, A. C. A., Lamoureux, S. F., Treitz, P. & Collingwood, A. Identifying permafrost slope disturbance using multi-temporal optical satellite images and change detection techniques. Cold Reg. Sci. Technol. 88, 37–49. https://doi.org/10.1016/j.coldregions.2012.12.008 (2013).
    Article  Google Scholar  More

  • in

    Bacterial chemolithoautotrophy via manganese oxidation

    1.
    Beijerinck, M. Oxydation des mangancarbonates durch Bakterien und Schimmelpilze. Folia Microbiol. (Delft) 2, 123–134 (1913).
    Google Scholar 
    2.
    Nealson, K. H., Tebo, B. M. & Rosson, R. A. Occurrence and mechanisms of microbial oxidation of manganese. Adv. Appl. Microbiol. 33, 279–318 (1988).
    CAS  Google Scholar 

    3.
    Tebo, B. M., Johnson, H. A., McCarthy, J. K. & Templeton, A. S. Geomicrobiology of manganese(II) oxidation. Trends Microbiol. 13, 421–428 (2005).
    CAS  Google Scholar 

    4.
    Hansel, C. & Learman, D. R. in Ehrlich’s Geomicrobiology (eds Ehrlich, H. L. et al.) 401–452 (CRC, 2015).

    5.
    Myers, C. R. & Nealson, K. H. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 1319–1321 (1988).
    ADS  CAS  Google Scholar 

    6.
    Lovley, D. R. & Phillips, E. J. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl. Environ. Microbiol. 54, 1472–1480 (1988).
    CAS  PubMed  PubMed Central  Google Scholar 

    7.
    Winogradsky, S. Über schwefelbakterien. Bot. Ztg 45, 489ff (1887).
    Google Scholar 

    8.
    Kelly, D. P. & Wood, A. P. in The Prokaryotes: Prokaryotic Communities and Ecophysiology (eds Rosenberg, E. et al.) 275–287 (Springer, 2013).

    9.
    Daims, H. et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504–509 (2015).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    10.
    Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005).
    ADS  Google Scholar 

    11.
    Strous, M. et al. Missing lithotroph identified as new planctomycete. Nature 400, 446–449 (1999).
    ADS  CAS  Google Scholar 

    12.
    van Kessel, M. A. H. J. et al. Complete nitrification by a single microorganism. Nature 528, 555–559 (2015).
    ADS  PubMed  PubMed Central  Google Scholar 

    13.
    Watson, S. W. & Waterbury, J. B. Characteristics of two marine nitrite oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus mobilis nov. gen. nov. sp. Arch. Mikrobiol. 77, 203–230 (1971).
    Google Scholar 

    14.
    Lovley, D. R., Holmes, D. E. & Nevin, K. P. in Advances in Microbial Physiology (ed Poole, R. K.) 219–286 (Elsevier, 2004).

    15.
    Henkel, J. V. et al. A bacterial isolate from the Black Sea oxidizes sulfide with manganese(IV) oxide. Proc. Natl Acad. Sci. USA 116, 12153–12155 (2019).
    CAS  Google Scholar 

    16.
    Ghiorse, W. C. & Ehrlich, H. L. Microbial biomineralization of iron and manganese. Catena Suppl. 21, 75–99 (1992).
    Google Scholar 

    17.
    Ehrlich, H. L. & Salerno, J. C. Energy coupling in Mn2+ oxidation by a marine bacterium. Arch. Microbiol. 154, 12–17 (1990).
    CAS  Google Scholar 

    18.
    Ehrlich, H. L. Manganese as an energy source for bacteria. Environ. Biogeochem. 2, 633–644 (1976).
    CAS  Google Scholar 

    19.
    Dick, G. J. et al. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl. Environ. Microbiol. 74, 2646–2658 (2008).
    CAS  PubMed  PubMed Central  Google Scholar 

    20.
    Nealson, K. H. in The Prokaryotes (eds Dworkin, M. et al.) 222–231 (Springer, 2006).

    21.
    van Veen, W. L. Biological oxidation of manganese in soils. Antonie van Leeuwenhoek 39, 657–662 (1973).
    Google Scholar 

    22.
    Morgan, J. J. Kinetics of reaction between O2 and Mn(II) species in aqueous solutions. Geochim. Cosmochim. Acta 69, 35–48 (2005).
    ADS  CAS  Google Scholar 

    23.
    Kits, K. D. et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549, 269–272 (2017).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    24.
    Flagan, S. F. & Leadbetter, J. R. Utilization of capsaicin and vanillylamine as growth substrates by Capsicum (hot pepper)-associated bacteria. Environ. Microbiol. 8, 560–565 (2006).
    CAS  PubMed  PubMed Central  Google Scholar 

    25.
    Kanzler, B. E. M., Pfannes, K. R., Vogl, K. & Overmann, J. Molecular characterization of the nonphotosynthetic partner bacterium in the consortium “Chlorochromatium aggregatum”. Appl. Environ. Microbiol. 71, 7434–7441 (2005).
    CAS  PubMed  PubMed Central  Google Scholar 

    26.
    Emerson, D. & Moyer, C. Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63, 4784–4792 (1997).
    CAS  PubMed  PubMed Central  Google Scholar 

    27.
    Neidhardt, F. C. Escherichia coli and Salmonella: Cellular and Molecular Biology, vol. 1 (ASM, 1996).

    28.
    Kostanjšek, R., Pašić, L., Daims, H. & Sket, B. Structure and community composition of sprout-like bacterial aggregates in a dinaric karst subterranean stream. Microb. Ecol. 66, 5–18 (2013).
    Google Scholar 

    29.
    Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012).
    ADS  CAS  Google Scholar 

    30.
    Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).
    CAS  Google Scholar 

    31.
    Castelle, C. et al. A new iron-oxidizing/O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans. J. Biol. Chem. 283, 25803–25811 (2008).
    CAS  PubMed  PubMed Central  Google Scholar 

    32.
    Jeans, C. et al. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2, 542–550 (2008).
    CAS  Google Scholar 

    33.
    Croal, L. R., Jiao, Y. & Newman, D. K. The fox operon from Rhodobacter strain SW2 promotes phototrophic Fe(II) oxidation in Rhodobacter capsulatus SB1003. J. Bacteriol. 189, 1774–1782 (2007).
    CAS  Google Scholar 

    34.
    Jiao, Y. & Newman, D. K. The pio operon is essential for phototrophic Fe(II) oxidation in Rhodopseudomonas palustris TIE-1. J. Bacteriol. 189, 1765–1773 (2007).
    CAS  Google Scholar 

    35.
    He, S., Barco, R. A., Emerson, D. & Roden, E. E. Comparative genomic analysis of neutrophilic iron(II) oxidizer genomes for candidate genes in extracellular electron transfer. Front. Microbiol. 8, 1584 (2017).
    PubMed  PubMed Central  Google Scholar 

    36.
    Richardson, D. J. et al. The ‘porin-cytochrome’ model for microbe-to-mineral electron transfer. Mol. Microbiol. 85, 201–212 (2012).
    CAS  Google Scholar 

    37.
    Luther, G. W., III. Manganese(II) oxidation and Mn(IV) reduction in the environment—two one-electron transfer steps versus a single two-electron Step. Geomicrobiol. J. 22, 195–203 (2005).
    CAS  Google Scholar 

    38.
    Lücker, S. et al. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl Acad. Sci. USA 107, 13479–13484 (2010).
    ADS  Google Scholar 

    39.
    Mundinger, A. B., Lawson, C. E., Jetten, M. S. M., Koch, H. & Lücker, S. Cultivation and transcriptional analysis of a canonical Nitrospira under stable growth conditions. Front. Microbiol. 10, 1325 (2019).
    PubMed  PubMed Central  Google Scholar 

    40.
    Koch, H. et al. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science 345, 1052–1054 (2014).
    ADS  CAS  Google Scholar 

    41.
    Levicán, G., Ugalde, J. A., Ehrenfeld, N., Maass, A. & Parada, P. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9, 581 (2008).
    PubMed  PubMed Central  Google Scholar 

    42.
    Berg, I. A. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl. Environ. Microbiol. 77, 1925–1936 (2011).
    CAS  PubMed  PubMed Central  Google Scholar 

    43.
    Thauer, R. K., Jungermann, K. & Decker, K. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 41, 100–180 (1977).
    CAS  PubMed  PubMed Central  Google Scholar 

    44.
    Baradaran, R., Berrisford, J. M., Minhas, G. S. & Sazanov, L. A. Crystal structure of the entire respiratory complex I. Nature 494, 443–448 (2013).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    45.
    Chadwick, G. L., Hemp, J., Fischer, W. W. & Orphan, V. J. Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications. ISME J. 12, 2668–2680 (2018).
    CAS  PubMed  PubMed Central  Google Scholar 

    46.
    Lücker, 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).
    PubMed  PubMed Central  Google Scholar 

    47.
    Watson, S. W., Bock, E., Valois, F. W., Waterbury, J. B. & Schlosser, U. Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium. Arch. Microbiol. 144, 1–7 (1986).
    Google Scholar 

    48.
    Hippe, H. Leptospirillum gen. nov. (ex Markosyan 1972), nom. rev., including Leptospirillum ferrooxidans sp. nov. (ex Markosyan 1972), nom. rev. and Leptospirillum thermoferrooxidans sp. nov. (Golovacheva et al. 1992). Int. J. Syst. Evol. Microbiol. 50, 501–503 (2000).
    Google Scholar 

    49.
    Henry, E. A. et al. Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch. Microbiol. 161, 62–69 (1994).
    CAS  Google Scholar 

    50.
    Lin, X., Kennedy, D., Fredrickson, J., Bjornstad, B. & Konopka, A. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford site. Environ. Microbiol. 14, 414–425 (2012).
    CAS  Google Scholar 

    51.
    Flagan, S., Ching, W.-K. & Leadbetter, J. R. Arthrobacter strain VAI-A utilizes acyl-homoserine lactone inactivation products and stimulates quorum signal biodegradation by Variovorax paradoxus. Appl. Environ. Microbiol. 69, 909–916 (2003).
    CAS  PubMed  PubMed Central  Google Scholar 

    52.
    Leadbetter, J. R. & Greenberg, E. P. Metabolism of acyl-homoserine lactone quorum-sensing signals by Variovorax paradoxus. J. Bacteriol. 182, 6921–6926 (2000).
    CAS  PubMed  PubMed Central  Google Scholar 

    53.
    Krumbein, W. E. & Altmann, H. J. A new method for the detection and enumeration of manganese oxidizing and reducing microorganisms. Helgol. Wiss. Meeresunters. 25, 347–356 (1973).
    CAS  Google Scholar 

    54.
    Emerson, D. & Revsbech, N. P. Investigation of an iron-oxidizing microbial mat community located near Aarhus, Denmark: laboratory studies. Appl. Environ. Microbiol. 60, 4032–4038 (1994).
    CAS  PubMed  PubMed Central  Google Scholar 

    55.
    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  Google Scholar 

    56.
    Illumina. 16S Metagenomic sequencing library preparation, https://support.illumina.com/downloads/16s_metagenomic_sequencing_library_preparation.html (2013).

    57.
    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
    CAS  PubMed  PubMed Central  Google Scholar 

    58.
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
    CAS  Google Scholar 

    59.
    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
    CAS  Google Scholar 

    60.
    Lane, D. J. in Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt, E. & Goodfellow, M.) 115–175 (John Wiley & Sons, 1991).

    61.
    Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).
    CAS  PubMed  PubMed Central  Google Scholar 

    62.
    Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
    CAS  Google Scholar 

    63.
    Schönmann, S. et al. 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environ. Microbiol. 11, 779–800 (2009).
    Google Scholar 

    64.
    Greuter, D., Loy, A., Horn, M. & Rattei, T. probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016. Nucleic Acids Res. 44, D586–D589 (2016).
    CAS  Google Scholar 

    65.
    Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919–1925 (1990).
    CAS  PubMed  PubMed Central  Google Scholar 

    66.
    Stoecker, K., Dorninger, C., Daims, H. & Wagner, M. Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl. Environ. Microbiol. 76, 922–926 (2010).
    CAS  PubMed  PubMed Central  Google Scholar 

    67.
    Schramm, A., Fuchs, B. M., Nielsen, J. L., Tonolla, M. & Stahl, D. A. Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environ. Microbiol. 4, 713–720 (2002).
    CAS  PubMed  PubMed Central  Google Scholar 

    68.
    Daims, H., Stoecker, K. & Wagner, M. in Molecular Microbial Ecology (eds Osborn, M. A. and Smith, C. J.) 208–228 (Taylor & Francis, 2004).

    69.
    Daims, H., Lücker, S. & Wagner, M. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8, 200–213 (2006).
    CAS  Google Scholar 

    70.
    Taylor, G. J. & Crowder, A. A. Use of the DCB technique for extraction of hydrous iron oxides from roots of wetland plants. Am. J. Bot. 70, 1254 (1983).
    CAS  Google Scholar 

    71.
    Polerecky, L. et al. Look@NanoSIMS—a tool for the analysis of nanoSIMS data in environmental microbiology. Environ. Microbiol. 14, 1009–1023 (2012).
    CAS  Google Scholar 

    72.
    Brewer, P. G. & Spencer, D. W. Colorimetric determination of manganse in anoxic waters. Limnol. Oceanogr. 16, 107–110 (1971).
    ADS  CAS  Google Scholar 

    73.
    Oldham, V. E., Miller, M. T., Jensen, L. T. & Luther, G. W. Revisiting Mn and Fe removal in humic rich estuaries. Geochim. Cosmochim. Acta 209, 267–283 (2017).
    ADS  CAS  Google Scholar 

    74.
    Suzuki, M. T., Taylor, L. T. & DeLong, E. F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl. Environ. Microbiol. 66, 4605–4614 (2000).
    CAS  PubMed  PubMed Central  Google Scholar 

    75.
    William, S., Feil, H. & Copeland, A. Bacterial genomic DNA isolation using CTAB, Department of Energy Joint Genome Institute, https://jgi.doe.gov/user-programs/pmo-overview/protocols-sample-preparation-information/ (2012).

    76.
    Arkin, A. P. et al. KBase: the United States Department of Energy systems biology knowledgebase. Nat. Biotechnol. 36, 566–569 (2018).
    CAS  PubMed  PubMed Central  Google Scholar 

    77.
    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
    CAS  PubMed  PubMed Central  Google Scholar 

    78.
    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
    MathSciNet  CAS  PubMed  PubMed Central  Google Scholar 

    79.
    Karst, S. M., Kirkegaard, R. H. & Albertsen, M. mmgenome: a toolbox for reproducible genome extraction from metagenomes. Preprint at https://www.biorxiv.org/content/ 10.1101/059121v1.full (2016).

    80.
    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
    CAS  PubMed  PubMed Central  Google Scholar 

    81.
    Chen, I. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).
    CAS  Google Scholar 

    82.
    NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 46, D8–D13 (2018).
    Google Scholar 

    83.
    Bagos, P. G., Liakopoulos, T. D., Spyropoulos, I. C. & Hamodrakas, S. J. PRED-TMBB: a web server for predicting the topology of β-barrel outer membrane proteins. Nucleic Acids Res. 32, W400–W404 (2004).
    CAS  PubMed  PubMed Central  Google Scholar 

    84.
    Federhen, S. The NCBI taxonomy database. Nucleic Acids Res. 40, D136–D143 (2012).
    CAS  Google Scholar 

    85.
    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
    CAS  PubMed  PubMed Central  Google Scholar 

    86.
    Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).
    CAS  PubMed  PubMed Central  Google Scholar 

    87.
    Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
    PubMed  PubMed Central  Google Scholar 

    88.
    Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).
    CAS  PubMed  PubMed Central  Google Scholar 

    89.
    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
    CAS  PubMed  PubMed Central  Google Scholar 

    90.
    Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
    PubMed  PubMed Central  Google Scholar 

    91.
    Lever, M. A. et al. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types. Front. Microbiol. 6, 476 (2015).
    PubMed  PubMed Central  Google Scholar 

    92.
    Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
    CAS  Google Scholar 

    93.
    Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).
    CAS  PubMed  Google Scholar 

    94.
    Pimentel, H., Bray, N. L., Puente, S., Melsted, P. & Pachter, L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat. Methods 14, 687–690 (2017).
    CAS  Google Scholar 

    95.
    van Waasbergen, L. G., Hildebrand, M. & Tebo, B. M. Identification and characterization of a gene cluster involved in manganese oxidation by spores of the marine Bacillus sp. strain SG-1. J. Bacteriol. 178, 3517–3530 (1996).
    PubMed  PubMed Central  Google Scholar 

    96.
    Jung, W. K. & Schweisfurth, R. Manganese oxidation by an intracellular protein of a Pseudomonas species. Z. Allg. Mikrobiol. 19, 107–115 (1979).
    CAS  Google Scholar 

    97.
    Esteve-Núñez, A., Rothermich, M., Sharma, M. & Lovley, D. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7, 641–648 (2005).
    Google Scholar 

    98.
    Neubauer, S. C., Emerson, D. & Megonigal, J. P. Life at the energetic edge: kinetics of circumneutral iron oxidation by lithotrophic iron-oxidizing bacteria isolated from the wetland-plant rhizosphere. Appl. Environ. Microbiol. 68, 3988–3995 (2002).
    CAS  PubMed  PubMed Central  Google Scholar 

    99.
    Nowka, B., Daims, H. & Spieck, E. Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Appl. Environ. Microbiol. 81, 745–753 (2015).
    PubMed  PubMed Central  Google Scholar 

    100.
    Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W. & Bock, E. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164, 16–23 (1995).
    CAS  Google Scholar 

    101.
    Kim, S. & Lee, S. B. Catalytic promiscuity in dihydroxy-acid dehydratase from the thermoacidophilic archaeon Sulfolobus solfataricus. J. Biochem. 139, 591–596 (2006).
    CAS  Google Scholar 

    102.
    Safarian, S. et al. Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Science 352, 583–586 (2016).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    103.
    Lovley, D. R. & Phillips, E. J. P. Manganese inhibition of microbial iron reduction in anaerobic sediments. Geomicrobiol. J. 6, 145–155 (1988).
    CAS  Google Scholar 

    104.
    Perez-Benito, J. F., Arias, C. & Amat, E. A kinetic study of the reduction of colloidal manganese dioxide by oxalic acid. J. Colloid Interface Sci. 177, 288–297 (1996).
    ADS  CAS  Google Scholar  More