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    Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

    1.
    Ceballos, G. & Ehrlich, P. R. Mammal population losses and the extinction crisis. Science 296, 904–907 (2002).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 
    2.
    Cardinale, B. J. et al. Biodiversity loss and its impact on humanity. Nature 486, 59–67 (2012).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    3.
    Gámez-Virués, S. et al. Landscape simplification filters species traits and drives biotic homogenization. Nat. Commun. 6, 8568 (2015).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    4.
    Haddad, N. M. et al. Habitat fragmentation and its lasting impact on Earth’s ecosystems. Sci. Adv. 1, e1500052 (2015).
    ADS  PubMed  PubMed Central  Article  Google Scholar 

    5.
    Tilman, D. et al. Future threats to biodiversity and pathways to their prevention. Nature 546, 73–81 (2017).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    6.
    Mittell, E. A., Nakagawa, S. & Hadfield, J. D. Are molecular markers useful predictors of adaptive potential? Ecol. Lett. 18, 772–778 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    7.
    Vilas, A., Pérez-Figueroa, A., Quesada, H. & Caballero, A. Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity. Mol. Ecol. 24, 4419–4432 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    8.
    Crandall, K. A., Bininda-Emonds, O. R. P., Mace, G. M. & Wayne, R. K. Considering evolutionary processes in conservation biology. Trends Ecol. Evol. 15, 290–295 (2000).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    9.
    Paz-Vinas, I. et al. Systematic conservation planning for intraspecific genetic diversity. Proc. R. Soc. B Biol. Sci. 285, 20172746 (2018).
    Article  Google Scholar 

    10.
    Eckert, C. G., Samis, K. E. & Lougheed, S. C. Genetic variation across species’ geographical ranges: the central-marginal hypothesis and beyond. Mol. Ecol. 17, 1170–1188 (2008).
    CAS  PubMed  Article  Google Scholar 

    11.
    Attard, C. R. M. et al. Low genetic diversity in pygmy blue whales is due to climate-induced diversification rather than anthropogenic impacts. Biol. Lett. 11, 20141037 (2015).
    PubMed  PubMed Central  Article  Google Scholar 

    12.
    Ma, G., Rudolf, V. H. W. & Ma, C. Extreme temperature events alter demographic rates, relative fitness, and community structure. Glob. Chang. Biol. 21, 1794–1808 (2015).
    ADS  PubMed  Article  Google Scholar 

    13.
    Johnson, D. W., Freiwald, J. & Bernardi, G. Genetic diversity affects the strength of population regulation in a marine fish. Ecology 97, 627–639 (2016).
    CAS  PubMed  Google Scholar 

    14.
    Coates, D. J., Byrne, M. & Moritz, C. Genetic diversity and conservation units: dealing with the species-population continuum in the age of genomics. Front. Ecol. Evol. 6, 165 (2018).
    Article  Google Scholar 

    15.
    Willoughby, J. R. et al. The reduction of genetic diversity in threatened vertebrates and new recommendations regarding IUCN conservation rankings. Biol. Conserv. 191, 495–503 (2015).
    Article  Google Scholar 

    16.
    Blanchet, S., Prunier, J. G. & De Kort, H. Time to go bigger: emerging patterns in macrogenetics. Trends Genet. 33, 579–580 (2017).
    CAS  PubMed  Article  Google Scholar 

    17.
    Bruford, M. W., Davies, N., Dulloo, M. E., Faith, D. P. & Walters, M. In The GEO Handbook on Biodiversity Observation Networks 107–128 (Springer International Publishing, 2017).

    18.
    Hamrick, J. L. & Godt, M. J. W. Effects of life history traits on genetic diversity in plant species. Philos. Trans. R. Soc. B Biol. Sci. 351, 1291–1298 (1996).
    ADS  Article  Google Scholar 

    19.
    Cahill, A. E. & Levinton, J. S. Genetic differentiation and reduced genetic diversity at the northern range edge of two species with different dispersal modes. Mol. Ecol. 25, 515–526 (2016).
    PubMed  Article  Google Scholar 

    20.
    Gelmi-Candusso, T. A., Heymann, E. W. & Heer, K. Effects of zoochory on the spatial genetic structure of plant populations. Mol. Ecol. 26, 5896–5910 (2017).
    PubMed  Article  Google Scholar 

    21.
    Vranckx, G., Jacquemyn, H., Muys, B. & Honnay, O. Meta-analysis of susceptibility of woody plants to loss of genetic diversity through habitat fragmentation. Conserv. Biol. 26, 228–237 (2012).
    PubMed  Article  PubMed Central  Google Scholar 

    22.
    Eo, S. H., Doyle, J. M. & DeWoody, J. A. Genetic diversity in birds is associated with body mass and habitat type. J. Zool. 283, 220–226 (2011).
    Article  Google Scholar 

    23.
    Davey, C. M., Chamberlain, D. E., Newson, S. E., Noble, D. G. & Johnston, A. Rise of the generalists: evidence for climate driven homogenization in avian communities. Glob. Ecol. Biogeogr. 21, 568–578 (2012).
    Article  Google Scholar 

    24.
    Romiguier, J. et al. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515, 261–263 (2014).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    25.
    Doyle, J. M., Hacking, C. C., Willoughby, J. R., Sundaram, M. & DeWoody, J. A. Mammalian genetic diversity as a function of habitat, body size, trophic class, and conservation status. J. Mammal. 96, 564–572 (2015).
    Article  Google Scholar 

    26.
    Miller, J. E. D., Damschen, E. I., Harrison, S. P. & Grace, J. B. Landscape structure affects specialists but not generalists in naturally fragmented grasslands. Ecology 96, 3323–3331 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    27.
    Dalongeville, A., Andrello, M., Mouillot, D., Albouy, C. & Manel, S. Ecological traits shape genetic diversity patterns across the Mediterranean Sea: a quantitative review on fishes. J. Biogeogr. 43, 845–857 (2016).
    Article  Google Scholar 

    28.
    Mitton, J. B. & Lewis, W. M. Relationships between genetic variability and life history features of bony fishes. Evolution 43, 1712–1723 (1989).
    PubMed  Article  PubMed Central  Google Scholar 

    29.
    Vachon, F., Whitehead, H. & Frasier, T. R. What factors shape genetic diversity in cetaceans? Ecol. Evol. 8, 1554–1572 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    30.
    Jackson, J. M. et al. Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude. Mol. Ecol. 27, 2926–2942 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    31.
    Yannic, G. et al. Genetic diversity in caribou linked to past and future climate change. Nat. Clim. Chang. 4, 132–137 (2014).
    ADS  Article  Google Scholar 

    32.
    Lira-Noriega, A. & Manthey, J. D. Relationship of genetic diversity and niche centrality: a survey and analysis. Evolution 68, 1082–1093 (2014).
    PubMed  Article  PubMed Central  Google Scholar 

    33.
    Duncan, S. I., Crespi, E. J., Mattheus, N. M. & Rissler, L. J. History matters more when explaining genetic diversity within the context of the core-periphery hypothesis. Mol. Ecol. 24, 4323–4336 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    34.
    Garner, T. W. J., Pearman, P. B. & Angelone, S. Genetic diversity across a vertebrate species’ range: a test of the central-peripheral hypothesis. Mol. Ecol. 13, 1047–1053 (2004).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    35.
    Munwez, I. et al. The change in genetic diversity down the core-edge gradient in the eastern spadefoot toad (Pelobates syriacus). Mol. Ecol. 19, 2675–2689 (2010).
    Article  CAS  Google Scholar 

    36.
    Jones, M. E., Paetkau, D., Geffen, E. & Moritz, C. Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore. Mol. Ecol. 13, 2197–2209 (2004).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    37.
    White, T. A. & Searle, J. B. Genetic diversity and population size: island populations of the common shrew, Sorex araneus. Mol. Ecol. 16, 2005–2016 (2007).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    38.
    Conord, C., Gurevitch, J. & Fady, B. Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basin. Ecol. Evol. 2, 2600–2614 (2012).
    PubMed  PubMed Central  Article  Google Scholar 

    39.
    Whitlock, R. Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis. J. Ecol. 102, 857–872 (2014).
    PubMed  PubMed Central  Article  Google Scholar 

    40.
    García-Verdugo, C. et al. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates. Mol. Ecol. 24, 726–741 (2015).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    41.
    Patiño, J. et al. A roadmap for island biology: 50 fundamental questions after 50 years of The Theory of Island Biogeography. J. Biogeogr. 44, 963–983 (2017).
    Article  Google Scholar 

    42.
    Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature 405, 907–913 (2000).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    43.
    Schluter, D. & Pennell, M. W. Speciation gradients and the distribution of biodiversity. Nature 546, 48–55 (2017).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    44.
    Miraldo, A. et al. An Anthropocene map of genetic diversity. Sci 353, 1532–1535 (2016).
    ADS  CAS  Article  Google Scholar 

    45.
    Hirao, A. S. et al. Genetic diversity within populations of an arctic-alpine species declines with decreasing latitude across the Northern Hemisphere. J. Biogeogr. 44, 2740–2751 (2017).
    Article  Google Scholar 

    46.
    Kim, M.-S., Richardson, B. A., McDonald, G. I. & Klopfenstein, N. B. Genetic diversity and structure of western white pine (Pinus monticola) in North America: a baseline study for conservation, restoration, and addressing impacts of climate change. Tree Genetics & Genomes, 7. PLoS Genet. 1, 11–21 (2011).
    Google Scholar 

    47.
    Adams, R. I. & Hadly, E. A. Genetic diversity within vertebrate species is greater at lower latitudes. Evol. Ecol. 27, 133–143 (2013).
    Article  Google Scholar 

    48.
    Gratton, P. et al. Which latitudinal gradients for genetic diversity? Trends Ecol. Evol. 32, 724–726 (2017).
    PubMed  Article  PubMed Central  Google Scholar 

    49.
    Lumibao, C. Y., Hoban, S. M. & McLachlan, J. Ice ages leave genetic diversity ‘hotspots’ in Europe but not in Eastern North America. Ecol. Lett. 20, 1459–1468 (2017).
    PubMed  Article  PubMed Central  Google Scholar 

    50.
    Schoville, S. D. et al. Adaptive genetic variation on the landscape: methods and cases. Annu. Rev. Ecol. Evol. Syst. 43, 23–43 (2012).
    Article  Google Scholar 

    51.
    Manel, S. et al. Global determinants of freshwater and marine fish genetic diversity. Nat. Commun. 11, 1–9 (2020).
    ADS  Article  CAS  Google Scholar 

    52.
    Socolar, J. B., Gilroy, J. J., Kunin, W. E. & Edwards, D. P. How should beta-diversity inform biodiversity conservation? Trends Ecol. Evol. 31, 67–80 (2016).
    PubMed  Article  PubMed Central  Google Scholar 

    53.
    Browne, L., Ottewell, K., Sork, V. L. & Karubian, J. The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm. Mol. Ecol. 27, 3159–3173 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    54.
    Laughlin, D. C. & Messier, J. Fitness of multidimensional phenotypes in dynamic adaptive landscapes. Trends Ecol. Evol. 30, 487–496 (2015).
    PubMed  Article  PubMed Central  Google Scholar 

    55.
    Raffard, A., Santoul, F., Cucherousset, J. & Blanchet, S. The community and ecosystem consequences of intraspecific diversity: a meta-analysis. Biol. Rev. 94, 648–661 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    56.
    Nybom, H. & Bartish, I. V. Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspect. Plant Ecol. Evol. Syst. 3, 93–114 (2000).
    Article  Google Scholar 

    57.
    Honnay, O. & Jacquemyn, H. Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation. Conserv. Biol. 21, 823–831 (2007).
    PubMed  Article  PubMed Central  Google Scholar 

    58.
    Jarne, P. & Auld, J. R. Animals mix it up too: the distribution of self-fertilization among hermaphroditic animals. Evolution 60, 1816–1824 (2006).
    PubMed  Article  PubMed Central  Google Scholar 

    59.
    Suggitt, A. J. et al. Extinction risk from climate change is reduced by microclimatic buffering. Nat. Clim. Chang. 8, 713–717 (2018).
    ADS  Article  Google Scholar 

    60.
    Lawrence, E. R. & Fraser, D. J. Latitudinal biodiversity gradients at three levels: linking species richness, population richness and genetic diversity. Glob. Ecol. Biogeogr. 29, 770–788 (2020).
    Article  Google Scholar 

    61.
    Mariette, S., Le Corre, V., Austerlitz, F. & Kremer, A. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Mol. Ecol. 11, 1145–1156 (2002).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    62.
    Chapman, J. R., Nakagawa, S., Coltman, D. W., Slate, J. & Sheldon, B. C. A quantitative review of heterozygosity-fitness correlations in animal populations. Mol. Ecol. 18, 2746–2765 (2009).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    63.
    Brown, S. C., Wigley, T. M. L., Otto-Bliesner, B. L., Rahbek, C. & Fordham, D. A. Persistent Quaternary climate refugia are hospices for biodiversity in the Anthropocene. Nat. Clim. Chang. 10, 244–248 (2020).
    ADS  Article  Google Scholar 

    64.
    Storey, J., Bass, A., Dabney, A. & Robinson, D. qvalue: Q-value estimation for false discovery rate control. R package version 2.14.1. https://doi.org/10.1111/ele.12303 (2019).

    65.
    Nowakowski, A. J. et al. Thermal biology mediates responses of amphibians and reptiles to habitat modification. Ecol. Lett. 21, 345–355 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    66.
    Stevens, V. M. et al. A comparative analysis of dispersal syndromes in terrestrial and semi-terrestrial animals. Ecol. Lett. 17, 1039–1052 (2014).
    PubMed  Article  PubMed Central  Google Scholar 

    67.
    Bilton, D. T., Freeland, J. R. & Okamura, B. Dispersal in freshwater invertebrates. Annu. Rev. Ecol. Syst. 32, 159–181 (2001).
    Article  Google Scholar 

    68.
    Kappes, H. & Haase, P. Slow, But Steady: Dispersal of Freshwater Molluscs (Springer, 2012).

    69.
    Grace, J. B. et al. Integrative modelling reveals mechanisms linking productivity and plant species richness. Nature 529, 390–393 (2016).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    70.
    Brun, P. et al. The productivity-biodiversity relationship varies across diversity dimensions. Nat. Commun. 10, 5691 (2019).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    71.
    McGlynn, T. P., Weiser, M. D. & Dunn, R. R. More individuals but fewer species: testing the ‘more individuals hypothesis’ in a diverse tropical fauna. Biol. Lett. 6, 490–493 (2010).
    PubMed  PubMed Central  Article  Google Scholar 

    72.
    Binks, R. M., Millar, M. A. & Byrne, M. Not all rare species are the same: contrasting patterns of genetic diversity and population structure in two narrow-range endemic sedges. Biol. J. Linn. Soc. 114, 873–886 (2015).
    Article  Google Scholar 

    73.
    Aguilar, R., Quesada, M., Ashworth, L., Herrerias-Diego, Y. & Lobo, J. Genetic consequences of habitat fragmentation in plant populations: Susceptible signals in plant traits and methodological approaches. Mol. Ecol. 17, 5177–5188 (2008).
    PubMed  Article  PubMed Central  Google Scholar 

    74.
    Cardillo, M. et al. Evolution: multiple causes of high extinction risk in large mammal species. Science 309, 1239–1241 (2005).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    75.
    LaManna, J. A. et al. Plant diversity increases with the strength of negative density dependence at the global scale. Science 356, 1389–1392 (2017).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    76.
    Mittelbach, G. G. A matter of time for tropical diversity. Nature 550, 51–52 (2017).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    77.
    Usinowicz, J. et al. Temporal coexistence mechanisms contribute to the latitudinal gradient in forest diversity. Nature 550, 105–108 (2017).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    78.
    Eziz, A. et al. Drought effect on plant biomass allocation: a meta-analysis. Ecol. Evol. 7, 11002–11010 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    79.
    Siepielski, A. M. et al. Precipitation drives global variation in natural selection. Science 355, 959–962 (2017).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    80.
    Martin, T. E. Age-related mortality explains life history strategies of tropical and temperate songbirds. Science 349, 966–970 (2015).
    ADS  CAS  PubMed  Article  Google Scholar 

    81.
    Winemiller, K. O., Fitzgerald, D. B., Bower, L. M. & Pianka, E. R. Functional traits, convergent evolution, and periodic tables of niches. Ecol. Lett. 18, 737–751 (2015).
    PubMed  PubMed Central  Article  Google Scholar 

    82.
    Kuussaari, M. et al. Extinction debt: a challenge for biodiversity conservation. Trends Ecol. Evol. 24, 564–571 (2009).
    PubMed  Article  Google Scholar 

    83.
    Talluto, M. V., Boulangeat, I., Vissault, S., Thuiller, W. & Gravel, D. Extinction debt and colonization credit delay range shifts of eastern North American trees. Nat. Ecol. Evol. 1, 1–6 (2017).
    Article  Google Scholar 

    84.
    Cronk, Q. Plant extinctions take time: many plant species may already be functionally extinct. Science 353, 446–447 (2016).
    ADS  CAS  PubMed  Article  Google Scholar 

    85.
    Aguilar, R. et al. Habitat fragmentation reduces plant progeny quality: a global synthesis. Ecol. Lett. 22, 1163–1173 (2019).
    PubMed  Article  Google Scholar 

    86.
    González, A. V., Gómez‐Silva, V., Ramírez, M. J. & Fontúrbel, F. E. Meta‐analysis of the differential effects of habitat fragmentation and degradation on plant genetic diversity. Conserv. Biol. 34, 711–720 (2019).
    PubMed  Article  Google Scholar 

    87.
    Wood, J. L. A., Yates, M. C. & Fraser, D. J. Are heritability and selection related to population size in nature? Meta-analysis and conservation implications. Evol. Appl. 9, 640–657 (2016).
    PubMed  PubMed Central  Article  Google Scholar 

    88.
    Yates, M. C., Bowles, E. & Fraser, D. J. Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish. Proc. R. Soc. B Biol. Sci. 286, 20191989 (2019).
    CAS  Article  Google Scholar 

    89.
    De Kort, H., Mergeay, J., Jacquemyn, H. & Honnay, O. Transatlantic invasion routes and adaptive potential in North American populations of the invasive glossy buckthorn, Frangula alnus. Ann. Bot. 118, 1089–1099 (2016).
    PubMed  PubMed Central  Article  Google Scholar 

    90.
    Jordan, R., Hoffmann, A. A., Dillon, S. K. & Prober, S. M. Evidence of genomic adaptation to climate in Eucalyptus microcarpa: Implications for adaptive potential to projected climate change. Mol. Ecol. 26, 6002–6020 (2017).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    91.
    Wogan, G. O. U., Yuan, M. L., Mahler, D. L. & Wang, I. J. Genome-wide epigenetic isolation by environment in a widespread Anolis lizard. Mol. Ecol. 29, 40–55 (2020).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    92.
    Schmid, M. W. et al. Contribution of epigenetic variation to adaptation in Arabidopsis. Nat. Commun. 9, 4446 (2018).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    93.
    Rey, O. et al. Linking epigenetics and biological conservation: towards a conservation epigenetics perspective. Funct. Ecol. 34, 414–427 (2020).
    Article  Google Scholar 

    94.
    Mace, G. M. et al. Aiming higher to bend the curve of biodiversity loss. Nat. Sustain. 1, 448–451 (2018).
    Article  Google Scholar 

    95.
    Jetz, W. et al. Essential biodiversity variables for mapping and monitoring species populations. Nat. Ecol. Evolution 3, 539–551 (2019).
    Article  Google Scholar 

    96.
    Crandall, E. D., Taffel, J. R. & Barber, P. H. High gene flow due to pelagic larval dispersal among South Pacific archipelagos in two amphidromous gastropods (Neritomorpha: Neritidae). Heredity 104, 563–572 (2010).
    CAS  PubMed  Article  Google Scholar 

    97.
    Faurby, S. & Barber, P. H. Theoretical limits to the correlation between pelagic larval duration and population genetic structure. Mol. Ecol. 21, 3419–3432 (2012).
    PubMed  Article  Google Scholar 

    98.
    Álvarez-Noriega, M. et al. Global biogeography of marine dispersal potential. Nat. Ecol. Evol. 4, 1196–1203, https://doi.org/10.1038/s41559-020-1238-y (2020).
    Article  PubMed  Google Scholar 

    99.
    Mueller, T. & Fagan, W. F. Search and navigation in dynamic environments—from individual behaviors to population distributions. Oikos 117, 654–664 (2008).
    Article  Google Scholar 

    100.
    Willoughby, J. R. et al. Biome and migratory behaviour significantly influence vertebrate genetic diversity. Biol. J. Linn. Soc. 121, 446–457 (2017).
    Article  Google Scholar 

    101.
    Martin, A. E. & Fahrig, L. Habitat specialist birds disperse farther and are more migratory than habitat generalist birds. Ecology 99, 2058–2066 (2018).
    PubMed  Article  Google Scholar 

    102.
    Tellier, A. Persistent seed banking as eco‐evolutionary determinant of plant nucleotide diversity: novel population genetics insights. N. Phytol. 221, 725–730 (2019).
    CAS  Article  Google Scholar 

    103.
    Ayre, D., O’Brien, E., Ottewell, K. & Whelan, R. The accumulation of genetic diversity within a canopy-stored seed bank. Mol. Ecol. 19, 2640–2650 (2010).
    PubMed  Article  Google Scholar 

    104.
    Campbell, D. R., Brody, A. K., Price, M. V., Waser, N. M. & Aldridge, G. Is plant fitness proportional to seed set? An experiment and a spatial model. Am. Nat. 190, 818–827 (2017).
    PubMed  Article  PubMed Central  Google Scholar 

    105.
    Angeloni, F., Ouborg, N. J. & Leimu, R. Meta-analysis on the association of population size and life history with inbreeding depression in plants. Biol. Conserv. 144, 35–43 (2011).
    Article  Google Scholar 

    106.
    Nei, M., Maruyama, T. & Chakraborty, R. The Bottleneck effect and genetic variability in populations. Evolution 29, 1–10 (1975).
    PubMed  Article  Google Scholar 

    107.
    Kimura, M. The neutral theory of molecular evolution (Cambridge University Press: Cambridge [Cambridgeshire], 1983).

    108.
    Nagylaki, T. The effective size of a subdivided population. Genetics 149, 1599–1604 (1997).
    Google Scholar 

    109.
    Poirier, M.-A., Coltman, D. W., Pelletier, F., Jorgenson, J. & Festa-Bianchet, M. Genetic decline, restoration and rescue of an isolated ungulate population. Evol. Appl. 12, 1318–1328 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    110.
    Dures, S. G. et al. A century of decline: loss of genetic diversity in a southern African lion-conservation stronghold. Divers. Distrib. 25, 870–879 (2019).
    Article  Google Scholar 

    111.
    Nakagawa, S. & Cuthill, I. C. Effect size, confidence interval and statistical significance: a practical guide for biologists. Biol. Rev. 82, 591–605 (2007).
    PubMed  Article  PubMed Central  Google Scholar 

    112.
    Burnham, K. P. & Anderson, D. R. In Sociological Methods & Research 33, (Sage PublicationsSage CA, Thousand Oaks, 2002). More

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    Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia

    Ice environment
    Physicochemical analyses of individual ice blocks were conducted to observe eventual differences that could be attributed to spatially related gradual freezing–melting and fresh ice deposition, and to characterize the habitat that enables long-term survival of ice microbiota. All ice samples contained low concentrations of salts, indicating that they originated from recent clean snow. Concentrations of anions in the upper layers, Ice-1 and Ice-2, were similar. However, the bottom layer Ice-3 had distinctly higher electrical conductivity (EC), hardness and alkalinity, less nitrate, and more sulphate. This could indicate that this ice stratum includes a higher proportion of percolation water, which contains more ions than rain and snow as shown by the differences between the percolation water from the cave Planinska jama (that was used for preparing growth media) and the ice, as shown in Table 1. Total organic carbon (TOC) concentrations in the ice were in a range typical of karst streams22, and above the minimum values reported for surface streams, i.e. 0.1–36.6 mg/l23, indicating a significant input of organic matter for the underground ecosystem. TOC indicates an available in situ source of carbon for the ice microbiome. Nitrogen expressed as nitrate did not exhibit high values in ice samples (Table 1). In this respect, a parallel can be drawn with karst sediments, where microbes are commonly limited more by carbon and phosphorus than by nitrogen24.
    Table 1 Characteristics of ice samples from Paradana.
    Full size table

    Besides EC and temperature, pH and dissolved oxygen are additionaly two influential parametres that can affect the abundance and taxonomic structure of microbial communities. pH was found to drive the shift in the community structure not only in habitats such as freshwater, marine sediments or soils but also in cold habitats as Antarctic soils25. In the current samples, the pH effect on the microbial community structure is less evident because all the values are rather similar (Table 1). Cave ice habitats with incoming waterflow are probably not oxygen depleted; on the contrary, for example in Antarctic lakes, glacial meltwater inflow is responsible for oxygen supersaturation26.
    Isotopically, the Ice-3 stratum was significantly lighter than the stratum represented by Ice-1 and Ice-2 (Table 1). Correlation of δ2H and deuterium excess did not indicate any effect of kinetic fractionation during water freezing. Thus, intersection of the freezing-line determined by stable isotopes in samples Ice-1 to Ice-3 (δ2H = 6.48δ18O + 2.88) with the local meteoric-water line (LMWL) constructed for the precipitation station at Postojna (Supplementary Fig. S1) (δ2H = 7.95 δ18O + 12.13), provided the δ18O value − 6.3‰ for the original water before freezing. It represents relatively enriched water, but such a value is not uncommon in daily precipitation in Slovenia27. The ice lake in Paradana is presumably formed by the refreezing of water from melting snow accumulated during the winter months20, with some contribution of water dripping from the cave ceiling. November and December 2015 had only a few days with precipitation in Postojna (5 and 4, respectively). However, January and February 2016 had 12 and 20 days with precipitation and monthly totals were high, 152 mm and 312 mm, respectively. The air temperature data adjusted for the elevation difference between Postojna and the Trnovski gozd karst plateau (about 600 m) indicate that about one third of the precipitation in January and one half in February probably fell as snow. The rest was probably a mixture of solid and liquid precipitation, but heavy rains could have occurred as well (e.g. about 55.5 mm of precipitation was measured in Postojna on February 8–9, with mean daily air temperatures between 8 °C and 9 °C). Isotopic composition of precipitation varied significantly between and also during individual events. It is known that snow cover can preserve the isotopic composition of the original snowfalls for long periods28. However, individual snowfalls can mix at the entrance of the cave and the isotopic composition of snow accumulated in the cave can also be influenced by thaws caused by temporary increases of air temperature or rainfall. The isotopic composition of snowmelt water that eventually refreezes in the cave is therefore the result of many processes. Further research with better temporal and spatial resolution of samples and sampling of snowmelt water would be needed to improve knowledge on the dynamics and sources of ice formation. LMWLs known from the literature for other precipitation stations in Slovenia, i.e. Kozina, Portorož and Ljubljana that are given in Supplementary Fig. S1 provided δ18O values for the original water, which we consider too high (− 3.0‰ for LMWL from Portorož, − 3.8‰ for LMWL from Ljubljana and − 5,1‰ for LMWL from Kozina). Postojna is the closest precipitation station to the Paradana and the data on isotopic composition of precipitation cover the period of ice sampling (Supplementary Fig. S2). Therefore, the LMWL at Postojna could be the best representation of the isotopic composition of precipitation supplying water to the Paradana Ice Cave (after considering the elevation difference between the two sites, which is about 600 m).
    When analysed in more detail, results obtained using the approach described above (to calculate the isotopic composition of the water that formed the sampled ice) also revealed the sensitivity of the constructed LMWL, the length of data series and extreme values. This is illustrated by records of isotopically very light precipitation in November and December 2015 (δ18O − 17.6‰ and − 14.2 δ18O, respectively). Although such isotopically light precipitation occurred in just two of the 27 months of the observation period, the two values changed the LMWL intercept significantly. However, because they did occur, they cannot be disregarded in the LMWL construction. Daily precipitation data indicate that in both cases monthly values were influenced dominantly by precipitation that fell during just one day (precipitation on those days represented almost the entire monthly precipitation). The LMWL intercept at Postojna without those two months would be 8.3, i.e. closely similar to values in Ljubljana and Kozina. Long-term data from Ljubljana show that the δ18O value of monthly precipitation was lower than − 16.0‰ (values around − 14.0‰ were quite abundant until 1986 and after 2004) in only 5 months in the years 1981–2010. Thus, precipitation with notable isotopically light values, as observed in Postojna between 21 and 23 November 2015 (92% of the precipitation fell on 22 November) appears to be rare in the study area. Nevertheless, it was observed, and it influenced the intercept of LMWL significantly.
    It is worth noting that the δ18O values of Ice-1 and Ice-2 are higher than those reported for the Paradana Ice Cave by Carey et al.20. Deuterium excess is also significantly higher than the mean value reported for samples from different depths of ice by Carey et al.20. The difference in δ18O values could be related to different sampling sites. Carey et al.20 sampled the wall ice, whereas the samples collected during this study represent the frozen lake. Investigation of the difference in deuterium levels would be especially interesting. It could point at the input (either by overland flow from the cave entrance or by percolation from the vadose zone) of water from the autumn/winter months, with precipitation from the Eastern Mediterranean air masses having particularly high d-excess (up to 22‰). The Western Mediterranean air masses have d-excess of about 14‰, whereas air masses from the Atlantic have values of only about 10‰29. Late autumn to early winter precipitation in Slovenia (October to December) regularly exhibits high d-excess27. Unfortunately, the available data are insufficient to support analysis of the reason for high deuterium excess of the ice in detail. Study samples also display far lower concentrations of chloride, sulphate and nitrate than samples collected by Carey et al.20.
    Concentration of microbes in cave ice
    The upper ice stratum represented by Ice-1 and Ice-2 had comparable microbial load expressed in total ATP concentration and total cell counts, whereas the Ice-3 block exhibited significantly higher values (Table 1). Interestingly, the total cell counts of microorganisms in the ice samples was similar (4.67 × 104–15.15 × 104) to that recorded in the Pivka River (SW Slovenia) at the ponor connecting to the karst underground, i.e. 4.29 × 104–12.38 × 104, 30. A large proportion (51.0–85.4%) of entrapped microbes in the ice were viable, showing that they were able to survive ice formation and melting, or even several freezing–melting cycles. A relatively high cell viability can be linked to the availability of compatible solutes, indicated by correspondingly high TOC (Table 1). Not only do sugars and polyols increase microbial resistance to freezing, they can also be used inside the cell as carbon and nitrogen sources31. Higher concentration of salts in Ice-3 block was accompanied by the highest total cell counts and percentage of viable cells (Table 1). In ice from Scărişoara Cave total cell counts varied from 0.84 × 103 to 3.14 × 104 cells/ml with corresponding viability from 28.2 to 84.9%, but no correlation was observed between the ice age (0–13,000 years BP) or depth (0–25 m) and the total number of cells or viability14.
    The media types used in this study differed in their ability to stimulate the growth of colonies. In general, nutrient-poor media and low temperatures resulted in higher colony counts in all samples. This phenomenon has been reported previously in cave microbiology, but was not correlated with phylogenetic diversity of microbes obtained on the growth media32. After 28 days of incubation, samples grown on the oligotrophic medium with percolation water (PWA) and cultivated at 10 °C produced the highest colony counts (Table 2). In context this indicates that cave percolation water contains soluble compounds that are not present in tap water and which support the growth of cave-ice microorganisms. With respect to individual samples, the highest colony counts were found in the Ice-3 sample, i.e., 167.37‰ of all cell biomass, determined by flow cytometry (Table 2), and this sample also contained the highest concentration of nutrients (Table 1). Cultivable anaerobic bacteria and fungi were detected in all the ice samples (Table 2).
    Table 2 Colony counts (colony-forming units—CFU/ml) and their proportion to total cell counts determined by flow cytometry (‰) at different cultivation conditions and media.
    Full size table

    Communities in the ice blocks differed in the representation of r-strategists, with their predominance in the Ice-1, and a big difference between Ice-1 and Ice-2, the two ice samples from the same stratum. Interestingly, a more-uniform community structure in terms of r-strategists was displayed in ice block Ice-2–Ice-3 (Table 1). R-strategists commonly dominate in uncrowded and unstable habitats where resources are temporarily abundant and available; with development of a community, r-strategists are gradually replaced by the slow-growing equilibrium K-strategists33.
    Cultivation on different media showed that the ice contained metabolically diverse microorganisms, aerobic and anaerobic bacteria and fungi. Two species of yellow-green algae were also recovered in cultures from samples Ice-2 and Ice-3. The two cultivated species, Chloridella glacialis and Ellipsoidion perminimum (for identification see Supplementary Fig. S3), were also found in green ice from Antarctica34. It is known from results of previous studies that algae in ice can survive and even grow under such adverse conditions34,35,36. They can also be well adapted to low light and low water temperature; for example they can thrive under ice- and snow-cover where the available photosynthetic photon flux density is only around the photosynthetic compensation point37. In these terms, and particularly in ice caves with available light, algae and cyanobacteria should not be overlooked as an important part of the ice microbial community. Interestingly, in Himalayan-type glaciers, the algae-rich layers in ice cores were suggested as providing accurate boundary markers of annual layers38. It remains unclear whether algae can be applied similarly as boundary markers in cave ice. Their existence is already known from some caves, for example in Hungary in a small ice cave colonizing surfaces of the ice39, Romania in Scarişoara Ice Cave at the ice/water interface40 and in New Mexico, USA, in Zuni Ice Cave giving the distinctive greenish patina of the layered ice35.
    Bacterial community structure
    Previous study of ice from the Paradana Ice Cave showed that it probably originates from local rainfall that reaches the cave as drip water after dissolving bedrock while percolating from the surface, and from snow that includes dust particles20. Thus, the largely impacted cave ice in Paradana has different sources, each bringing along a diverse and adaptable microbiota. 16S metagenomic analysis was conducted to describe the taxonomic composition of bacteria found in different ice blocks. Quality filtration of sequence readings gave a total number of 120,381 sequences in the three studied samples (Table 3). The number of operational taxonomic units (OTUs) varied from 185 in Ice-2 to 304 in Ice-1. This pattern was in alignment with values of alpha diversity parameters: extrapolated richness (Chao1), abundance-based coverage estimator (ACE) and Shannon index (Table 3). The rarefaction curves indicated that the diversity had been sampled sufficiently (Supplementary Fig. S4).
    Table 3 Number of reads, OTUs, taxon richness and diversity indexes for cave ice samples.
    Full size table

    A Venn diagram of the distribution of 441 distinct OTUs found in the three studied samples is presented in Fig. 1. Observations showed that 119 OTUs (28.3%) occurred in all three samples and can be interpreted as “a core microbiome”. Three of these OTUs dominated microbial communities in individual samples (relative abundance range 14.5–56.5%) and corresponded to the members of the genera Pseudomonas, Lysobacter, and Sphingomonas, as discussed below. These were followed in abundance by Polaromonas, Flavobacterium, Rhodoferax, Nocardioides, and Pseudonocardia (relative abundance range 3.3–6.9%). Another 35 OTUs had relative abundance above 0.5% and the remaining 76 OTUs had relative abundance below 0.5%. The unique OTUs probably contribute to the variability due to internal variations within the ice block caused by incoming snow or the freezing of percolation water. For example, samples Ice-2 and Ice-3 were cut from the same ice block in a vertical ice profile, but differed in their content of dark, particulate, organic inclusions.
    Figure 1

    Prokaryotic OTU distribution in cave ice. The Venn diagram indicates the number of distinct and shared OTUs in ice samples Ice-1, Ice-2 and Ice-3.

    Full size image

    Members of 29 bacterial phyla were detected in the cave ice microbiome (Fig. 2, Supplementary Fig. S5). All samples were dominated by Proteobacteria, with relative abundances of 79.1% in Ice-2, 65.5% in Ice-3 and 55.9% in Ice-1.
    Figure 2

    Relative abundance of phyla in the cave-ice samples. Phyla with relative abundance  1% of phylotypes in at least one sample and corresponded to Firmicutes, Cyanobacteria and Gemmatimonadetes. Phototrophic bacterial phylotypes belonging to Cyanobacteria were recovered from all three samples. They represented 1.3% of phylotypes in sample Ice-1, but only 0.6% and 0.3% in samples Ice-2 and Ice-3 respectively, from where algae, C. glacialis and E. perminimum, were obtained via cultivation.
    Phyla whose relative abundance was less than 1% were grouped together and classified as “Rare phyla”. These phyla comprised 2.2%, 1.5% and 1.2% of Ice-1, Ice-2, and Ice-3, respectively. Their relative abundance is presented in Supplementary Fig. S5.
    Among the 31 classes detected in this study, members of Gammaproteobacteria were most abundant and represented 20.1% (Ice-1), 45.3% (Ice-2) and 42.5% (Ice-3) of total detected phylotypes (Fig. 3A). This proteobacterial group was also most abundant in the ice from Scărişoara Cave14. Actinobacteria represented the second most abundant group of phylotypes, with its relative abundances declining from 30.8% in Ice-1 to 26.2% in Ice-3 and 11.7% in Ice-2. Other notably abundant classes were Alpha- and Betaproteobacteria, whose abundances ranged from 9.6 to 26.3% and from 6.9 to 12.3%, respectively.
    Figure 3

    Heat-map analysis of the relative abundance of members of cave-ice prokaryotic communities at class (A) and genus (B) levels in Ice-1, Ice-2 and Ice-3. Phylotypes whose relative abundances at class level were  More

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    Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

    Construction of RUGs from rumen sequencing data
    We produced 979G of Illumina sequencing data from 4 cows, 2 sheep, 4 red deer and 2 reindeer samples, then performed a metagenomic assembly of single samples and a co-assembly of all samples. This created a set of 391 dereplicated genomes (99% ANI (average nucleotide identity)) with estimated completeness ≥ 80% and estimated contamination ≤ 10% (Fig. 1). 284 of these genomes were produced from the single-sample assemblies and 107 were produced from the co-assemblies. 172 genomes were > 90% complete with contamination  90% complete with More

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    Heat dissipation in subterranean rodents: the role of body region and social organisation

    Tested animals
    Altogether 73 individuals from seven species of subterranean rodents differing in body mass, phylogenetic relatedness, and sociality were studied (Table 1). All animals were adult non-breeders, or their breeding history was unknown in solitary species, but none of them showed signs of recent breeding, which may theoretically influence measured parameters. For the purpose of this study, we used the following taxa. African mole-rats (Bathyergidae): the social Ansell’s mole-rat Fukomys anselli (Burda, Zima, Scharff, Macholán & Kawalika 1999) occupies the miombo in a small area near Zambia’s capital Lusaka; another social species of the genus Fukomys is named here as Fukomys “Nsanje” because founders of the breeding colony were captured near town Nsanje in south Malawi. Although we used name Fukomys darlingi (Thomas 1895) for mole-rats from this population in previous studies (e.g.38,49), its taxonomic status is still not resolved; the social common mole-rat Cryptomys hottentotus hottentotus (Lesson, 1826) occurs in mesic and semi-arid regions of southern Africa; the solitary Cape dune mole-rat Bathyergus suillus (Schreber, 1782) inhabits sandy soils along the south-western coast of South Africa; and the solitary Cape mole-rat Georychus capensis (Pallas, 1778) occupies mesic areas of the South Africa50. In addition, we studied the social coruro Spalacopus cyanus (Molina, 1782) (Octodontidae) occupying various habitats in Chile51; and the solitary Upper Galilee Mountains blind mole rat Nannospalax galili (Nevo, Ivanitskaya & Beiles 2001) (Spalacidae) from Israel52. Further information about the species including number of individuals used in the study, their physiology and ecology is shown in Table 1.
    All experiments were done on captive animals. Georychus capensis, C. hottentotus, and B. suillus, were captured about four months before the experiment, and kept in the animal facility at the University of Pretoria, South Africa (temperature: 23 °C; humidity: 40–60%, photoperiod: 12L:12D). The animals were housed in plastic boxes with wood shavings used as a bedding. Cryptomys hottentotus and G. capensis were fed with sweet potatoes; B. suillus with sweet potatoes, carrots, and fresh grass. Fukomys anselli, F. “Nsanje”, N. galili, and S. cyanus were kept for at least three years in captivity (or born in captivity) before the experiment in the animal facility at the University of South Bohemia in České Budějovice, Czech Republic (temperature: African mole-rats 25 °C, N. galili and S. cyanus 23 °C; humidity: 40–50%, photoperiod: 12L:12D). The animals were kept in terraria with peat as a substrate and fed with carrots, potatoes, sweet potatoes, beetroot, apple, and rodent dry food mix ad libitum.
    Experimental design
    We measured Tb and Ts in all species at six Tas (10, 15, 20, 25, 30 and 35 °C). Each individual of all species was measured only once in each Ta. Measurements were conducted in temperature controlled experimental rooms in České Budějovice and Pretoria. Each animal was tested on two experimental days.
    The animals were placed in the experimental room individually in plastic buckets with wood shavings as bedding. On the first day, the experimental procedure started at Ta 25 °C. They spent 60 min of initial habituation in the first Ta after which Tb and Ts were measured as described in the following paragraphs. The Ta was then increased to 30 °C and 35 °C, respectively. After the experimental room reached the focal Ta, the animals were left minimally 30 min in each Ta to acclimate, and the measurements were repeated. Considering their relatively small body size, tested animals were very likely in thermal equilibrium after this period because mammals of a comparable body mass are thermally equilibrated after similar period of acclimation53,54,55,56. On the second day, the procedure was repeated with the initial Ta 20 °C and decreasing to 15 °C and 10 °C, respectively. The time span between the measurements of the same individual in different Ta was at least 150 min. Between experimental days, the animals were kept at 25 °C in the experimental room (individuals of social species were housed together with their family members).
    Body temperature measurements
    We used two sets of equipment to measure animal Tb and Ts. In B. suillus, G. capensis, and C. hottentotus, Tb was measured by intraperitoneally injected PIT tags ( More

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    Global maps of twenty-first century forest carbon fluxes

    1.
    IPCC Climate Change 2014: Synthesis Report (eds Core Writing Team, Pachauri, R. K. & Meyer L. A.) (IPCC, 2014).
    2.
    IPCC Special Report on Climate Change, Desertification, Land Degradation, Sustainable Land Management, Food Security, and Greenhouse Gas Fluxes in Terrestrial Ecosystems (IPCC, 2019).

    3.
    Adoption of the Paris Agreement FCCC/CP/2015/10/Add.1 (UNFCCC, 2015).

    4.
    Klein Goldewijk, K., Beusen, A., Doelman, J. & Stehfest, E. New anthropogenic land use estimates for the Holocene: HYDE 3.2. Earth Syst. Sci. Data 9, 927–953 (2017).
    Article  Google Scholar 

    5.
    Griscom, B. W. et al. National mitigation potential from natural climate solutions in the tropics. Philos. Trans. R. Soc. B 375, 20190126 (2020).
    CAS  Article  Google Scholar 

    6.
    Friedlingstein, P. et al. Global carbon budget 2019. Earth Syst. Sci. Data 11, 1783–1838 (2019).
    Article  Google Scholar 

    7.
    Houghton, R. A. & Nassikas, A. A. Global and regional fluxes of carbon from land use and land cover change 1850–2015. Glob. Biogeochem. Cycles 31, 456–472 (2017).
    CAS  Article  Google Scholar 

    8.
    Hansis, E., Davis, S. J. & Pongratz, J. Relevance of methodological choices for accounting of land use change carbon fluxes. Glob. Biogeochem. Cycles 29, 1230–1246 (2015).
    CAS  Article  Google Scholar 

    9.
    Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).
    CAS  Article  Google Scholar 

    10.
    IPCC. 2006 IPCC Guidelines for National Greenhouse Gas Inventories Vol. 4 (eds Eggleston, S. et al.) (IGES, 2006).

    11.
    IPCC. 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories Vol. 4 (eds Buendia, E. C. et al.) (IPCC, 2019).

    12.
    Grassi, G. et al. Reconciling global-model estimates and country reporting of anthropogenic forest CO2 sinks. Nat. Clim. Change 8, 914–920 (2018).
    CAS  Article  Google Scholar 

    13.
    Lee, D., Llopis, P., Waterworth, R., Roberts, G. & Pearson, T. Approaches to REDD+ Nesting: Lessons Learned from Country Experiences (World Bank, 2018).

    14.
    Streck, C. et al. Options for Enhancing REDD+ Collaboration in the Context of Article 6 of the Paris Agreement (Meridian Institute, 2017).

    15.
    Hansen, M. C. et al. High-resolution global maps of 21st-century forest cover change. Science 342, 850–853 (2013).
    CAS  Article  Google Scholar 

    16.
    World Database on Protected Areas User Manual (UNEP, 2016); https://www.protectedplanet.net/en/resources/wdpa-manual

    17.
    Curtis, P. G., Slay, C. M., Harris, N. L., Tyukavina, A. & Hansen, M. C. Classifying drivers of global forest loss. Science 361, 1108–1111 (2018).
    CAS  Article  Google Scholar 

    18.
    Saatchi, S. S. et al. Benchmark map of forest carbon stocks in tropical regions across three continents. Proc. Natl Acad. Sci. USA 108, 9899–9904 (2011).
    CAS  Article  Google Scholar 

    19.
    PRODES Deforestation (INPE, 2019); http://www.obt.inpe.br/OBT/assuntos/programas/amazonia/prodes

    20.
    Ogle, S. M.et al. Delineating managed land for reporting national greenhouse gas emissions and removals to the United Nations framework convention on climate change. Carbon Balance Manag. 13, 9 (2018).

    21.
    Pearson, T. R., Brown, S., Murray, L. & Sidman, G. Greenhouse gas emissions from tropical forest degradation: an underestimated source. Carbon Balance Manag. 12, 3 (2017).
    Article  Google Scholar 

    22.
    Ahlström, A. et al. The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink. Science 348, 895–899 (2015).
    Article  Google Scholar 

    23.
    Van Der Werf, G. R. et al. Global fire emissions estimates during 1997–2016. Earth Syst. Sci. Data 9, 697–720 (2017).
    Article  Google Scholar 

    24.
    Kirschbaum, M. U., Zeng, G., Ximenes, F., Giltrap, D. L. & Zeldis, J. R. Towards a more complete quantification of the global carbon cycle. Biogeosciences 16, 831–846 (2019).

    25.
    Global Forest Observations Initiative. Integration of Remote-sensing and Ground-based Observations for Estimation of Emissions and Removals of Greenhouse Gases in Forests 2nd edn (FAO, 2016).

    26.
    Potapov, P. et al. Annual continuous fields of woody vegetation structure in the Lower Mekong region from 2000–2017 Landsat time-series. Remote Sens. Environ. 232, 111278 (2019).
    Article  Google Scholar 

    27.
    Federici, S., Lee, D. & Herold, M. Forest Mitigation: A Permanent Contribution to the Paris Agreement? (Climate and Land Use Alliance, 2017).

    28.
    Romijn, E. et al. Assessing change in national forest monitoring capacities of 99 tropical countries. Ecol. Manag. 352, 109–123 (2015).
    Article  Google Scholar 

    29.
    Cook-Patton, S. Mapping potential carbon capture from global natural forest regrowth. Nature 585, 545–550 (2020).
    CAS  Article  Google Scholar 

    30.
    The Global Stocktake (UNFCCC, 2015); https://unfccc.int/topics/science/workstreams/global-stocktake-referred-to-in-article-14-of-the-paris-agreement

    31.
    Austin, K. et al. Shifting patterns of oil palm driven deforestation in Indonesia and implications for zero-deforestation commitments. Land Use Policy 69, 41–48 (2017).
    Article  Google Scholar 

    32.
    Gaveau, D. L. et al. Four decades of forest persistence, clearance and logging on Borneo. PLoS ONE 9, e101654 (2014).
    Article  Google Scholar 

    33.
    Miettinen, J., Shi, C. & Liew, S. C. Land cover distribution in the peatlands of Peninsular Malaysia, Sumatra and Borneo in 2015 with changes since 1990. Glob. Ecol. Conserv. 6, 67–78 (2016).
    Article  Google Scholar 

    34.
    Gunarso, P., Hartoyo, M., Agus, F. & Killeen, T. in Reports from the Technical Panels of the 2nd Greenhouse Gas Working Group of the Roundtable on Sustainable Palm Oil (eds Killeen, T. J. & Goon, J.) 29–64 (RSPO, 2013).

    35.
    Giri, C. et al. Status and distribution of mangrove forests of the world using earth observation satellite data. Glob. Ecol. Biogeogr. 20, 154–159 (2011).
    Article  Google Scholar 

    36.
    Simard, M. et al. Mangrove canopy height globally related to precipitation, temperature and cyclone frequency. Nat. Geosci. 12, 40–45 (2019).
    CAS  Article  Google Scholar 

    37.
    Baccini, A. et al. Estimated carbon dioxide emissions from tropical deforestation improved by carbon-density maps. Nat. Clim. Change 2, 182–185 (2012).
    CAS  Article  Google Scholar 

    38.
    Zarin, D. J. et al. Can carbon emissions from tropical deforestation drop by 50% in 5 years? Glob. Change Biol. 22, 1336–1347 (2016).
    Article  Google Scholar 

    39.
    Mokany, K., Raison, R. J. & Prokushkin, A. S. Critical analysis of root: shoot ratios in terrestrial biomes. Glob. Change Biol. 12, 84–96 (2006).
    Article  Google Scholar 

    40.
    IPCC Supplement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories: Wetlands (eds Hiraishi, T. et al.) (IPCC, 2014).

    41.
    Methodological Tool: Estimation of Carbon Stocks and Change in Carbon Stocks in Dead Wood and Litter in A/R CDM Project Activities (UNFCCC, 2013); https://cdm.unfccc.int/methodologies/ARmethodologies/tools/ar-am-tool-12-v3.0.pdf

    42.
    Hengl, T. et al. SoilGrids250m: global gridded soil information based on machine learning. PLoS ONE 12, e0169748 (2017).
    Article  Google Scholar 

    43.
    Sanderman, J. et al. A global map of mangrove forest soil carbon at 30 m spatial resolution. Environ. Res. Lett. 13, 055002 (2018).
    Article  Google Scholar 

    44.
    Giglio, L., Boschetti, L., Roy, D. P., Humber, M. L. & Justice, C. O. The Collection 6 MODIS burned area mapping algorithm and product. Remote Sens. Environ. 217, 72–85 (2018).
    Article  Google Scholar 

    45.
    Global Ecological Zones for FAO Forest Reporting: 2010 Update (FAO, 2012).

    46.
    Brus, D. et al. Statistical mapping of tree species over Europe. Eur. J. Res. 131, 145–157 (2012).
    Article  Google Scholar 

    47.
    Del Lungo, A., Ball, J. & Carle, J. Global Planted Forests Thematic Study: Results and Analysis (FAO, 2006); http://www.fao.org/forestry/12139-03441d093f070ea7d7c4e3ec3f306507.pdf

    48.
    Portugal National Greenhouse Gas Inventory submitted to the UNFCCC, 1990–2018 (UNFCCC, 2020).

    49.
    Harris, N. L., Goldman, E. D. & Gibbes, S. Spatial Database on Planted Trees Version 1.0 https://www.wri.org/publication/spatialdatabase-planted-trees (WRI, 2019).

    50.
    Smith, J. E., Heath, L. S., Skog, K. E. & Birdsey, R. A. Methods for Calculating Forest Ecosystem and Harvested Carbon with Standard Estimates for Forest Types of the United States General Technical Report (USDA, Forest Service, 2006); https://doi.org/10.2737/NE-GTR-343

    51.
    Ruefenacht, B. et al. Conterminous US and Alaska forest type mapping using forest inventory and analysis data. Photogramm. Eng. Remote Sensing 74, 1379–1388 (2008).
    Article  Google Scholar 

    52.
    Pan, Y. et al. Age structure and disturbance legacy of North American forests. Biogeosciences 8, 715–732 (2011) .
    Article  Google Scholar 

    53.
    Turubanova, S., Potapov, P. V., Tyukavina, A. & Hansen, M. C. Ongoing primary forest loss in Brazil, Democratic Republic of the Congo, and Indonesia. Environ. Res. Lett. 13, 074028 (2018).
    Article  Google Scholar 

    54.
    Potapov, P. et al. The last frontiers of wilderness: tracking loss of intact forest landscapes from 2000 to 2013. Sci. Adv. 3, e1600821 (2017).
    Article  Google Scholar 

    55.
    Roman-Cuesta, R. M. et al. Hotspots of gross emissions from the land use sector: patterns, uncertainties, and leading emission sources for the period 2000–2005 in the tropics. Biogeosciences 13, 4253–4269 (2016).
    CAS  Article  Google Scholar 

    56.
    Carter, S. et al. Agriculture-driven deforestation in the tropics from 1990–2015: emissions, trends and uncertainties. Environ. Res. Lett. 13, 014002 (2017).
    Article  Google Scholar  More

  • in

    Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments

    1.
    Zoumis T, Schmidt A, Grigorova L, Calmano W. Contaminants in sediments: remobilisation and demobilisation. Sci Total Environ. 2001;266:195–202.
    CAS  PubMed  Article  Google Scholar 
    2.
    SØNdergaard M, Jeppesen E, Lauridsen TL, Skov C, Van Nes EH, Roijackers R, et al. Lake restoration: successes, failures and long-term effects. J Appl Ecol. 2007;44:1095–105.
    Article  CAS  Google Scholar 

    3.
    Zhao CS, Yang Y, Yang ST, Xiang H, Wang F, Chen X, et al. Impact of spatial variations in water quality and hydrological factors on the food-web structure in urban aquatic environments. Water Res. 2019;153:121–33.
    CAS  PubMed  Article  Google Scholar 

    4.
    Wang C, Zhai W, Shan B. Oxygen microprofile in the prepared sediments and its implication for the sediment oxygen consuming process in a heavily polluted river of China. Environ Sci Pollut Res Int. 2016;23:8634–43.
    CAS  PubMed  Article  Google Scholar 

    5.
    Liu B, Han RM, Wang WL, Yao H, Zhou F. Oxygen microprofiles within the sediment-water interface studied by optode and its implication for aeration of polluted urban rivers. Environ Sci Pollut Res Int. 2017;24:9481–94.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    6.
    Rysgaard S, Risgaard-Petersen N, Sloth NP, Jensen K, Nielsen LP. Oxygen regulation of nitrification and denitrification in sediments. Limnol Oceanogr. 2003;39:1643–52.
    Article  Google Scholar 

    7.
    Broman E, Sachpazidou V, Pinhassi J, Dopson M. Oxygenation of hypoxic coastal Baltic Sea sediments impacts on chemistry, microbial community composition, and metabolism. Front Microbiol. 2017;8:2453–2453.
    PubMed  PubMed Central  Article  Google Scholar 

    8.
    Zheng B, Wang L, Liu L. Bacterial community structure and its regulating factors in the intertidal sediment along the Liaodong Bay of Bohai Sea, China. Microbiol Res. 2014;169:585–92.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    9.
    Yu P, Wang J, Chen J, Guo J, Yang H, Chen Q. Successful control of phosphorus release from sediments using oxygen nano-bubble-modified minerals. Sci Total Environ. 2019;663:654–61.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    10.
    Papageorgiou N, Kalantzi I, Karakassis I. Effects of fish farming on the biological and geochemical properties of muddy and sandy sediments in the Mediterranean Sea. Mar Environ Res. 2010;69:326–36.
    CAS  PubMed  Article  Google Scholar 

    11.
    Pfeffer C, Larsen S, Song J, Dong MD, Besenbacher F, Meyer RL, et al. Filamentous bacteria transport electrons over centimetre distances. Nature. 2012;491:218–21.
    CAS  PubMed  Article  Google Scholar 

    12.
    Nielsen LP, Risgaard-Petersen N. Rethinking sediment biogeochemistry after the discovery of electric currents. Annu Rev Mar Sci. 2015;7:425–42.
    Article  Google Scholar 

    13.
    Burdorf LDW, Tramper A, Seitaj D, Meire L, Hidalgo-Martinez S, Zetsche E-M, et al. Long-distance electron transport occurs globally in marine sediments. Biogeosciences. 2017;14:683–701.
    CAS  Article  Google Scholar 

    14.
    Sandfeld T, Marzocchi U, Petro C, Schramm A, Risgaard-Petersen N. Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments. ISME J. 2020;14:1233–46.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    15.
    Muller H, Bosch J, Griebler C, Damgaard LR, Nielsen LP, Lueders T, et al. Long-distance electron transfer by cable bacteria in aquifer sediments. ISME J. 2016;10:2010–9.
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    16.
    Malkin SY, Rao AM, Seitaj D, Vasquez-Cardenas D, Zetsche EM, Hidalgo-Martinez S, et al. Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor. ISME J. 2014;8:1843–54.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    17.
    Rao AMF, Malkin SY, Hidalgo-Martinez S, Meysman FJR. The impact of electrogenic sulfide oxidation on elemental cycling and solute fluxes in coastal sediment. Geochim et Cosmochim Acta. 2016;172:265–86.
    CAS  Article  Google Scholar 

    18.
    Marzocchi U, Palma E, Rossetti S, Aulenta F, Scoma A. Parallel artificial and biological electric circuits power petroleum decontamination: the case of snorkel and cable bacteria. Water Res. 2020;173:115520.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    19.
    Kjeldsen KU, Schreiber L, Thorup CA, Boesen T, Bjerg JT, Yang T, et al. On the evolution and physiology of cable bacteria. Proc Natl Acad Sci USA. 2019;116:19116–25.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    20.
    Schauer R, Risgaard-Petersen N, Kjeldsen KU, Bjerg JJT, Jorgensen BB, Schramm A, et al. Succession of cable bacteria and electric currents in marine sediment. ISME J. 2014;8:1314–22.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    21.
    Burdorf LDW, Malkin SY, Bjerg JT, van Rijswijk P, Criens F, Tramper A, et al. The effect of oxygen availability on long-distance electron transport in marine sediments. Limnol Oceanogr. 2018;63:1799–816.
    CAS  Article  Google Scholar 

    22.
    Zhou J, Deng Y, Luo F, He Z, Yang Y. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. mBio. 2011;2:e00122-11.
    Article  Google Scholar 

    23.
    Faust K, Raes J. Microbial interactions: from networks to model. Nat Rev Microbiol. 2012;10:538–50.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    24.
    Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X. Functional molecular ecological networks. mBio. 2010;1:e00169–110.
    PubMed  PubMed Central  Google Scholar 

    25.
    Barberán A, Bates ST, Casamayor EO, Fierer N. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 2012;6:343–51.
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    26.
    Tu Q, Yan Q, Deng Y, Michaletz ST, Buzzard V, Weiser MD, et al. Biogeographic patterns of microbial co-occurrence ecological networks in six American forests. Soil Biol Biochem. 2020;148:107897.
    CAS  Article  Google Scholar 

    27.
    Hu A, Ju F, Hou L, Li J, Yang X, Wang H, et al. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ Microbiol. 2017;19:4993–5009.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    28.
    Deng Y, Jiang YH, Yang Y, He Z, Luo F, Zhou J. Molecular ecological network analyses. BMC Bioinform. 2012;13:113.
    Article  Google Scholar 

    29.
    Kruskal JB. Nonmetric multidimensional scaling: a numerical method. Psychometrika. 1964;29:115–29.
    Article  Google Scholar 

    30.
    Guo X, Feng J, Shi Z, Zhou X, Yuan M, Tao X, et al. Climate warming leads to divergent succession of grassland microbial communities. Nat Clim Change. 2018;8:813–8.
    Article  Google Scholar 

    31.
    Legendre P, Legendre LF. Numerical ecology. 3rd ed. Oxford, UK: Elsevier; 2012.

    32.
    van den Wollenberg AL. Redundancy analysis an alternative for canonical correlation analysis. Psychometrika. 1977;42:207–19.
    Article  Google Scholar 

    33.
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2018. https://www.R-project.org/.

    34.
    Goslee SC, Urban DL. The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw. 2007;22:1–19.
    Article  Google Scholar 

    35.
    Luo Y, Hui D, Zhang D. Elevated CO2 stimulates net accumulations of carbon and nitrogen in land ecosystems: a meta-analysis. Ecology. 2006;87:53–63.
    PubMed  Article  Google Scholar 

    36.
    Scholz VV, Meckenstock RU, Nielsen LP, Risgaard-Petersen N. Cable bacteria reduce methane emissions from rice-vegetated soils. Nat Commun. 2020;11:1878.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    37.
    Risgaard-Petersen N, Kristiansen M, Frederiksen RB, Dittmer AL, Bjerg JT, Trojan D, et al. Cable bacteria in freshwater sediments. Appl Environ Microbiol. 2015;81:6003–11.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    38.
    Coates JD, Anderson RT, Lovley DR. Oxidation of polycyclic aromatic hydrocarbons under sulfate-reducing conditions. Appl Environ Microbiol. 1996;62:1099–101.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    39.
    Coates JD, Chakraborty R, McInerney MJ. Anaerobic benzene biodegradation—a new era. Res Microbiol. 2002;153:621–8.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    40.
    Matturro B, Cruz Viggi C, Aulenta F, Rossetti S. Cable bacteria and the bioelectrochemical snorkel: the natural and engineered facets playing a role in hydrocarbons degradation in marine sediments. Front Microbiol. 2017;8:952.
    PubMed  PubMed Central  Article  Google Scholar 

    41.
    Huisingh J, McNeill JJ, Matrone G. Sulfate reduction by a Desulfovibrio species isolated from sheep rumen. Appl Microbiol. 1974;28:489–97.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    42.
    Gupta A, Dutta A, Sarkar J, Panigrahi MK, Sar P. Low-abundance members of the Firmicutes facilitate bioremediation of soil impacted by highly acidic mine drainage from the Malanjkhand Copper Project, India. Front Microbiol. 2018;9:2882–2882.
    PubMed  PubMed Central  Article  Google Scholar 

    43.
    Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, et al. Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol. 2017;8:682–682.
    PubMed  PubMed Central  Article  Google Scholar 

    44.
    Coates JD, Councell T, Ellis DJ, Lovley DR. Carbohydrate oxidation coupled to Fe(III) reduction, a novel form of anaerobic metabolism. Anaerobe. 1998;4:277–82.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    45.
    Caccavo F Jr., Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol. 1994;60:3752–9.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    46.
    Loesche WJ. Oxygen sensitivity of various anaerobic bacteria. Appl Microbiol. 1969;18:723–7.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    47.
    Duncan SH, Louis P, Thomson JM, Flint HJ. The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol. 2009;11:2112–22.
    PubMed  Article  PubMed Central  Google Scholar 

    48.
    Borin S, Brusetti L, Mapelli F, D’Auria G, Brusa T, Marzorati M, et al. Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin. Proc Natl Acad Sci USA. 2009;106:9151–6.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    49.
    Yun Y, Wang H, Man B, Xiang X, Zhou J, Qiu X, et al. The relationship between pH and bacterial communities in a single karst ecosystem and its implication for soil acidification. Front Microbiol. 2016;7:1955–1955.
    PubMed  PubMed Central  Article  Google Scholar 

    50.
    Sohn JH, Kwon KK, Kang JH, Jung HB, Kim SJ. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol. 2004;54:1483–7.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    51.
    Rodriguez-Conde S, Molina L, González P, García-Puente A, Segura A. Degradation of phenanthrene by Novosphingobium sp. HS2a improved plant growth in PAHs-contaminated environments. Appl Microbiol Biotechnol. 2016;100:10627–36.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    52.
    Sha S, Zhong J, Chen B, Lin L, Luan T. Novosphingobium guangzhouense sp. nov., with the ability to degrade 1-methylphenanthrene. Int J Syst Evolut Microbiol. 2017;67:489–97.
    CAS  Article  Google Scholar 

    53.
    Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): a review. Front Microbiol. 2016;7:1369.
    PubMed  PubMed Central  Google Scholar 

    54.
    Yan Z, Zhang Y, Wu H, Yang M, Zhang H, Hao Z, et al. Isolation and characterization of a bacterial strain Hydrogenophaga sp. PYR1 for anaerobic pyrene and benzo[a]pyrene biodegradation. RSC Adv. 2017;7:46690–8.
    CAS  Article  Google Scholar 

    55.
    Weiss JV, Rentz JA, Plaia T, Neubauer SC, Merrill-Floyd M, Lilburn T, et al. Characterization of neutrophilic Fe(II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov. Geomicrobiol J. 2007;24:559–70.
    CAS  Article  Google Scholar 

    56.
    Lenchi N, Inceoğlu O, Kebbouche-Gana S, Gana ML, Llirós M, Servais P, et al. Diversity of microbial communities in production and injection waters of Algerian oilfields revealed by 16S rRNA gene Amplicon 454 pyrosequencing. PLoS ONE. 2013;8:e66588.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    57.
    Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R, Timmis KN. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol. 2001;67:1874–84.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    58.
    Xu P, Xiao E, Zeng L, He F, Wu Z. Enhanced degradation of pyrene and phenanthrene in sediments through synergistic interactions between microbial fuel cells and submerged macrophyte Vallisneria spiralis. J Soils Sediment. 2019;19:2634–49.
    CAS  Article  Google Scholar 

    59.
    Singleton DR, Jones MD, Richardson SD, Aitken MD. Pyrosequence analyses of bacterial communities during simulated in situ bioremediation of polycyclic aromatic hydrocarbon-contaminated soil. Appl Microbiol Biotechnol. 2013;97:8381–91.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    60.
    Lu XY, Zhang T, Fang HH. Bacteria-mediated PAH degradation in soil and sediment. Appl Microbiol Biotechnol. 2011;89:1357–71.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    61.
    Wang C, Huang Y, Zhang Z, Wang H. Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium. AMB Express. 2018;8:67.
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    62.
    Dastgheib SM, Amoozegar MA, Khajeh K, Shavandi M, Ventosa A. Biodegradation of polycyclic aromatic hydrocarbons by a halophilic microbial consortium. Appl Microbiol Biotechnol. 2012;95:789–98.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    63.
    Vasquez-Cardenas D, van de Vossenberg J, Polerecky L, Malkin SY, Schauer R, Hidalgo-Martinez S, et al. Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments. ISME J. 2015;9:1966–78.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    64.
    Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, et al. Single-cell genome and group-specific dsrAB sequencing implicate marine members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling. mBio. 2016;7:e00266-16.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    65.
    Liang B, Wang L-Y, Mbadinga SM, Liu J-F, Yang S-Z, Gu J-D, et al. Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation. AMB Express. 2015;5:117–117.
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    66.
    Logan BE, Rossi R, Ragab AA, Saikaly PE. Electroactive microorganisms in bioelectrochemical systems. Nat Rev Microbiol. 2019;17:307–19.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    67.
    Pisciotta JM, Zaybak Z, Call DF, Nam J-Y, Logan BE. Enrichment of microbial electrolysis cell biocathodes from sediment microbial fuel cell bioanodes. Appl Environ Microbiol. 2012;78:5212–9.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    68.
    Wang B, Zhang H, Yang Y, Xu M. Diffusion and filamentous bacteria jointly govern the spatiotemporal process of sulfide removal in sediment microbial fuel cells. Chem Eng J. 2021;405:126680.
    CAS  Article  Google Scholar 

    69.
    Li X, Li Y, Zhang X, Zhao X, Sun Y, Weng L, et al. Long-term effect of biochar amendment on the biodegradation of petroleum hydrocarbons in soil microbial fuel cells. Sci Total Environ. 2019;651:796–806.
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    70.
    Malvankar NS, King GM, Lovley DR. Centimeter-long electron transport in marine sediments via conductive minerals. ISME J. 2015;9:527–31.
    CAS  PubMed  Article  Google Scholar 

    71.
    Bjerg JT, Boschker HTS, Larsen S, Berry D, Schmid M, Millo D, et al. Long-distance electron transport in individual, living cable bacteria. Proc Natl Acad Sci USA. 2018;115:5786–91.
    CAS  PubMed  Article  Google Scholar 

    72.
    Meysman FJR, Cornelissen R, Trashin S, Bonné R, Martinez SH, van der Veen J, et al. A highly conductive fibre network enables centimetre-scale electron transport in multicellular cable bacteria. Nat Commun. 2019;10:4120.
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    73.
    Teske A. Cable bacteria, living electrical conduits in the microbial world. Proc Natl Acad Sci USA. 2019;116:18759.
    CAS  PubMed  Article  Google Scholar 

    74.
    Risgaard-Petersen N, Revil A, Meister P, Nielsen LP. Sulfur, iron-, and calcium cycling associated with natural electric currents running through marine sediment. Geochim et Cosmochim Acta. 2012;92:1–13.
    CAS  Article  Google Scholar 

    75.
    Risgaard-Petersen N, Damgaard LR, Revil A, Nielsen LP. Mapping electron sources and sinks in a marine biogeobattery. J Geophys Res Biogeosci. 2014;119:1475–86.
    CAS  Article  Google Scholar  More

  • in

    The role of host promiscuity in the invasion process of a seaweed holobiont

    Sample collection
    Algae were sampled from August 27th to September 21st (2017) from seven populations also collected for Bonthond et al. [28], including three native populations; Akkeshi (Japan), Soukanzan (Japan), Rongcheng (China); and four non-native populations; Pleudihen-sur-Rance (France), Nordstrand (Germany), Cape Charles Beach (Viriginia) and Tomales Bay (California, Fig. 1, Table S1). Individuals fixed to hard substratum (see [30]) were sampled at least a meter apart from one another and stored in separate plastic bags. As A. vermiculophyllum has a complex, haplodiplontic life-cycle only diploids were included in the experiment. Life-cycle stages were identified in the field with a dissecting microscope or post-hoc by microsatellite genotyping [31]. After transport in coolers and storage at 4 °C in the lab, bags with algae were shipped to Germany, arriving within 4–6 days after collection. In the climate room (15 °C), individuals were transferred to separate transparent aquaria with transparent lids, containing 1.75 L artificial seawater (ASW) prepared from tap water and 24 gL−1 artificial sea salt without CaCO3 (high CaCO3 concentrations increase disease risk, Weinberger data unpublished) and exposed to 12 h of light per day (86.0 µmol m−2s−1 at the water surface). Aquaria were moderately aerated with aeration stones. Per population, four diploid individuals were acclimated over 31–32 days to climate room conditions prior to starting the experiment. Water was exchanged weekly with new ASW enriched with 2 mL Provasoli-Enrichment Solution (PES; [32]). At the start of the experiment, wet weight was recorded and individuals were divided into two parts of ~10 g each and placed into two plastic tanks with 1.75 L water and 2 mL PES (Fig. 1).
    Fig. 1: Schematic overview of the sampling design and experimental process.

    Algae were collected from native populations Rongcheng (ron), Soukanzan (sou) and Akkeshi (akk) and non-native populations Tomales Bay (tmb), Cape Charles Beach (ccb), Pleudihen-sur-Rance (fdm) and Nordstrand (nor). In the climate room algae were acclimated for 5 weeks and divided into two thalli. One of the thalli was treated for three days with an antibiotic mixture after which both groups were monitored for six weeks, during which the treated algae received inoculum with each water change. Microbiota samples were taken in the field (tfield), directly after disturbance (t0) and after 1, 2, 4 and 6 weeks (t1, t2, t4 and t6).

    Full size image

    Experimental setup
    To rigorously disturb the microbial community, one of each of the pairs of aquaria containing the same algal individual was treated with a combination of antibiotics, aiming to increase the effectivity (10 mgL−1 ampicillin, 10 mgL−1 streptomycin, 10 mgL−1 chloramphenicol) and the other (control) remained untreated. All experimental work was conducted with disposable gloves and sterilized equipment, to minimize contamination. After three days, the water was removed from all tanks (treated and control) and the wet weight was recorded for all algae. All individuals were rinsed with one 1.75 L volume ASW and re-incubated in 1.75 L ASW. Subsequently, both groups received new ASW with 2 mL PES weekly and individuals treated with antibiotics received also 2 mL inoculum. The inoculum was prepared from individuals of all 7 populations, following the procedure to remove epibiota as described in Bonthond et al. [28]. Briefly, apical fragments of 1 g were separated from the thallus and transferred to 50 mL tubes containing 15 ± 1 glass beads (3 mm) and 15 mL ASW and vortexed for 6 min to separate epibiota from the algal tissue. In total, 8 samples were prepared from one individual per population. The resulting suspensions were pooled and mixed with glycerol (20% final glycerol concentration), aliquoted in 50 mL tubes and stored at −20 °C. For each water exchange, a new aliquot was defrosted at room temperature and added to the water of treated algae. Wet weight was recorded weekly with water exchanges. Before weighing the individual on aluminum foil, it was dipped twice on a separate aluminum foil sheet, to reduce attached water in a systematic way. Endo- and epiphytic microbiota were sampled in the field (tfield, [28]), at the start of the experiment (t0), after one week (t1), two weeks (t2), four weeks (t4) and six weeks (t6, Fig. 1). To equalize acclimation times across populations the experiment was stacked into five groups (Table S2). At each sampling moment, 0.5 or 1 g of tissue was separated from all individuals with sterilized forceps and epibiota were extracted similarly to the preparation of the inoculum. The resulting suspension was filtered through 0.2 µm pore size PCTA filters. Both the filters and the remaining tissue were preserved at −20 °C.
    DNA extraction and amplicon sequencing
    Tissue samples were defrosted, rinsed with absolute ethanol and DNA free water to remove hydro- and moderately lipophilic cells and molecules from the surface and cut to fragments with sterilized scissors. DNA was then extracted from these fragments (endobiota) and from preserved filters (epibiota) using the ZYMO Fecal/soil microbe kit (D6102; ZYMO-Research, Irvine, CA, USA), following the manufacturer’s protocol. Although this method to separate endo- and epibiota was shown to resolve distinct communities [28], tightly attached epiphytic cells may not be completely removed from the surface and detectable in endophytic samples as well. Two 16S-V4 amplicon libraries, over which the samples were divided in a balanced manner, were prepared as in Bonthond et al. [28], following the two-step PCR strategy from Gohl et al. [33], using the same set of 16S-V4 target primers and indexing primers. The libraries were sequenced on the Illumina MiSeq platform (2×300 PE) at the Max-Planck-Institute for Evolutionary Biology (Plön, Germany), including four negative DNA extraction controls and four negative and positive PCR controls (mock communities; ZYMO-D6311). The fastq files were de-multiplexed (0 mismatches). Relevant field samples from Bonthond et al. [28] were combined with the new dataset and assembled, quality filtered and classified altogether with Mothur v1.43.0 [34] using the SILVA-alignment release 132 [35]. Sequences were clustered within 3% dissimilarity into OTUs using the opticlust algorithm. Mitochondrial, chloroplast, eukaryotic and unclassified sequences were removed. To prepare the community matrix we discarded singleton OTUs (in the full dataset), samples with More

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    Author Correction: Expert assessment of future vulnerability of the global peatland carbon sink

    Department of Geography, Texas A&M University, College Station, TX, USA
    J. Loisel

    Department of Geography, University of Exeter, Exeter, UK
    A. V. Gallego-Sala, M. J. Amesbury, D. J. Charman & T. P. Roland

    Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
    M. J. Amesbury, A. Korhola, M. Väliranta, S. Juutinen, K. Minkkinen & S. Piilo

    Department of Geography and Geotop Research Center, University of Quebec at Montreal, Montreal, Quebec, Canada
    G. Magnan & M. Garneau

    Magister of Environment and Soil Science Department, Tanjungpura University, Pontianak, Indonesia
    G. Anshari

    Department of Geography and Environment, University of Hawaii at Manoa, Honolulu, HI, USA
    D. W. Beilman

    Department of Ecology and Territory, Pontificial Xavierian University, Bogota, Colombia
    J. C. Benavides

    Organic Geochemistry Unit, School of Chemistry, and School of Earth Sciences, University of Bristol, Bristol, UK
    J. Blewett & B. D. A. Naafs

    Environmental Studies Program and Earth and Oceanographic Science Department, Bowdoin College, Brunswick, ME, USA
    P. Camill

    Department of Geology, Chulalongkorn University, Bangkok, Thailand
    S. Chawchai

    Department of Geography, University of California, Los Angeles, Los Angeles, CA, USA
    A. Hedgpeth

    Max Planck Institute for Meteorology, Hamburg, Germany
    T. Kleinen & V. Brovkin

    Faculty of Engineering, Chemical and Environmental Engineering, University of Nottingham, Nottingham, UK
    D. Large

    Centro de Investigación GAIA Antártica, University of Magallanes, Punta Arenas, Chile
    C. A. Mansilla

    Climate and Environmental Physics, Physics Institute and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
    J. Müller & F. Joos

    Consortium Érudit, Université de Montréal, Montreal, Quebec, Canada
    S. van Bellen

    Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
    J. B. West

    Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA, USA
    Z. Yu

    Institute for Peat and Mire Research, School of Geographical Sciences, Northeast Normal University, Changchun, China
    Z. Yu

    Department of Environmental Studies, Mount Holyoke College, South Hadley, MA, USA
    J. L. Bubier

    Department of Geography, McGill University, Montreal, Quebec, Canada
    T. Moore

    Department of Physical Geography, Stockholm University, Stockholm, Sweden
    A. B. K. Sannel

    School of Geography, Geology and the Environment, University of Leicester, Leicester, UK
    S. Page

    Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
    M. Bechtold & W. Swinnen

    School of Geography & Sustainable Development, University of St Andrews, St Andrews, UK
    L. E. S. Cole

    Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, USA
    J. P. Chanton

    Department of Bioscience, Aarhus University, Roskilde, Denmark
    T. R. Christensen

    Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
    M. A. Davies & S. A. Finkelstein

    Instituto Franco-Argentino para el Estudio del Clima y sus Impactos, Buenos Aires, Argentina
    F. De Vleeschouwer

    Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH, USA
    S. Frolking & C. Treat

    Department of Geobotany and Plant Ecology, University of Lodz, Lodz, Poland
    M. Gałka

    Laboratoire d’Ecologie Fonctionnelle et Environnement, UMR 5245, CNRS-UPS-INPT, Toulouse, France
    L. Gandois

    Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
    N. Girkin

    Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
    L. I. Harris

    Stockholm Environment Institute, University of York, York, UK
    A. Heinemeyer

    Max Planck Institute for Biogeochemistry, Jena, Germany
    A. M. Hoyt

    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    A. M. Hoyt

    Florence Bascom Geoscience Center, United States Geological Survey, Reston, VA, USA
    M. C. Jones

    Department of Marine and Coastal Environmental Science, Texas A&M University at Galveston, Galveston, TX, USA
    K. Kaiser

    Department of Biology, University of Victoria, Victoria, British Columbia, Canada
    T. Lacourse

    Faculty of Geographical and Geological Sciences, Climate Change Ecology Research Unit, Adam Mickiewicz University, Poznań, Poland
    M. Lamentowicz

    Natural Resources Institute Finland (Luke), Helsinki, Finland
    T. Larmola

    Agroscope, Zurich, Switzerland
    J. Leifeld

    Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki, Finland
    A. Lohila

    Finnish Meteorological Institute, Climate System Research, Helsinki, Finland
    A. Lohila

    Department of Geography, Royal Holloway, University of London, Egham, UK
    A. M. Milner

    Department of Forest Sciences, University of Helsinki, Helsinki, Finland
    K. Minkkinen

    School of Earth and Environmental Sciences, University of Queensland, Brisbane, Queensland, Australia
    P. Moss

    Lamont-Doherty Earth Observatory, Palisades, NY, USA
    J. Nichols

    National Park Service, Washington DC, WA, USA
    J. O’Donnell

    Department of Environment & Geography, University of York, York, UK
    R. Payne

    Department of Chemistry, and Department of Geological and Environmental Science, Hope College, Holland, MI, USA
    M. Philben

    Department of Geography and Environmental Science, University of Reading, Reading, UK
    A. Quillet

    Department of Applied Earth Sciences, Uva Wellassa University, Badulla, Sri Lanka
    A. S. Ratnayake

    School of Biosciences, University of Nottingham, Nottingham, UK
    S. Sjögersten

    Département de Géographie, Université de Montréal, Montréal, Québec, Canada
    O. Sonnentag & J. Talbot

    Geography, School of Natural and Built Environment, Queen’s University Belfast, Belfast, UK
    G. T. Swindles

    Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
    A. C. Valach

    Department of Environment and Sustainability, Grenfell Campus, Memorial University, Corner Brook, Newfoundland, Canada
    J. Wu More