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    Functionally distinct T-helper cell phenotypes predict resistance to different types of parasites in a wild mammal

    Abolins, S. et al. The comparative immunology of wild and laboratory mice, Mus musculus domesticus. Nat. Commun. 8, 14811. https://doi.org/10.1038/ncomms14811 (2017).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cox, F. E. G. Concomitant infections, parasites and immune responses. Parasitology 122, S23–S38. https://doi.org/10.1017/S003118200001698X (2001).Article 
    PubMed 

    Google Scholar 
    Seder, R. A., Darrah, P. A. & Roederer, M. T-cell quality in memory and protection: Implications for vaccine design. Nat. Rev. Immunol. 8, 247–258. https://doi.org/10.1038/nri2274 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Demas, G. E., Zysling, D. A., Beechler, B. R., Muehlenbein, M. P. & French, S. S. Beyond phytohaemagglutinin: Assessing vertebrate immune function across ecological contexts. J. Anim. Ecol. 80, 710–730. https://doi.org/10.1111/j.1365-2656.2011.01813.x (2011).Article 
    PubMed 

    Google Scholar 
    Pedersen, A. B. & Babayan, S. A. Wild immunology. Mol. Ecol. 20, 872–880. https://doi.org/10.1111/j.1365-294X.2010.04938.x (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Abolins, S. et al. The ecology of immune state in a wild mammal, Mus musculus domesticus. PLoS Biol. 16, e2003538. https://doi.org/10.1371/journal.pbio.2003538 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ezenwa, V. O. Helminth–microparasite co-infection in wildlife: Lessons from ruminants, rodents and rabbits. Parasite Immunol. 38, 527–534. https://doi.org/10.1111/pim.12348 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Craig, B. H., Tempest, L. J., Pilkington, J. G. & Pemberton, J. M. Metazoan-protozoan parasite co-infections and host body weight in St Kilda Soay sheep. Parasitology 135, 433–441. https://doi.org/10.1017/S0031182008004137 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Graham, A. L. et al. Exposure to viral and bacterial pathogens among Soay sheep (Ovis aries) of the St Kilda archipelago. Epidemiol. Infect. 144, 1879–1888. https://doi.org/10.1017/S0950268816000017 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Murphy, K., Travers, P., Walport, M. & Janeway, C. Janeway’s Immunobiology (Garland Science, 2012).
    Google Scholar 
    Parkin, J. & Cohen, B. An overview of the immune system. Lancet 357, 1777–1789. https://doi.org/10.1016/S0140-6736(00)04904-7 (2001).CAS 
    Article 
    PubMed 

    Google Scholar 
    Mosmann, T. R. & Coffman, R. L. TH1 and TH2 cells: Different patterns of lymphokine secretion lead to different functional properties. Annu. Rev. Immunol. 7, 145–173. https://doi.org/10.1146/annurev.iy.07.040189.001045 (1989).CAS 
    Article 
    PubMed 

    Google Scholar 
    Nakayamada, S., Takahashi, H., Kanno, Y. & O’Shea, J. J. Helper T cell diversity and plasticity. Curr. Opin. Immunol. 24, 297–302. https://doi.org/10.1016/j.coi.2012.01.014 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gerbe, F. et al. Intestinal epithelial tuft cells initiate type 2 mucosal immunity to helminth parasites. Nature 529, 226–230. https://doi.org/10.1038/nature16527 (2016).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Jain, A. & Pasare, C. Innate control of adaptive immunity: Beyond the three-signal paradigm. J. Immunol. (Baltimore, Md.: 1950) 198, 3791–3800. https://doi.org/10.4049/jimmunol.1602000 (2017).CAS 
    Article 

    Google Scholar 
    Schmitt, N. & Ueno, H. Regulation of human helper T cell subset differentiation by cytokines. Curr. Opin. Immunol. 34, 130–136. https://doi.org/10.1016/j.coi.2015.03.007 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Abbas, A. K., Murphy, K. M. & Sher, A. Functional diversity of helper T lymphocytes. Nature 383, 787–793. https://doi.org/10.1038/383787a0 (1996).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Seder, R. A. & Paul, W. E. Acquisition of lymphokine-producing phenotype by CD4+ T cells. Annu. Rev. Immunol. 12, 635–673. https://doi.org/10.1146/annurev.iy.12.040194.003223 (1994).CAS 
    Article 
    PubMed 

    Google Scholar 
    Grencis, R. K. Immunity to helminths: Resistance, regulation, and susceptibility to gastrointestinal nematodes. Annu. Rev. Immunol. 33, 201–225. https://doi.org/10.1146/annurev-immunol-032713-120218 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    O’Garra, A. & Robinson, D. In Advances in Immunology vol. 83 133–162 (Academic Press, 2004).Pereira, L. M. S., Gomes, S. T. M., Ishak, R. & Vallinoto, A. C. R. Regulatory T cell and forkhead box protein 3 as modulators of immune homeostasis. Front. Immunol. https://doi.org/10.3389/fimmu.2017.00605 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Romagnani, S. T-cell subsets (Th1 versus Th2). Ann. Allergy Asthma Immunol. 85, 9–21. https://doi.org/10.1016/S1081-1206(10)62426-X (2000).CAS 
    Article 
    PubMed 

    Google Scholar 
    Sandquist, I. & Kolls, J. Update on regulation and effector functions of Th17 cells. F1000Res 7, 205–205. https://doi.org/10.12688/f1000research.13020.1 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Stockinger, B. & Omenetti, S. The dichotomous nature of T helper 17 cells. Nat. Rev. Immunol. 17, 535–544. https://doi.org/10.1038/nri.2017.50 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Wilson, K., Fenton, A. & Tompkins, D. Wildlife Disease Ecology: Linking Theory to Data and Application (Cambridge University Press, 2019).Book 

    Google Scholar 
    Graham, A. L. Ecological rules governing helminth–microparasite coinfection. PNAS 105, 566–570. https://doi.org/10.1073/pnas.0707221105 (2008).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ezenwa, V. O., Etienne, R. S., Luikart, G., Beja-Pereira, A. & Jolles, A. E. Hidden consequences of living in a wormy world: Nematode-induced immune suppression facilitates tuberculosis invasion in African Buffalo. Am. Nat. 176, 613–624. https://doi.org/10.1086/656496 (2010).Article 
    PubMed 

    Google Scholar 
    Ezenwa, V. O. & Jolles, A. E. Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales. Science 347, 175–177. https://doi.org/10.1126/science.1261714%JScience (2015).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Arriero, E. et al. From the animal house to the field: Are there consistent individual differences in immunological profile in wild populations of field voles (Microtus agrestis)?. PLoS One 12, e0183450. https://doi.org/10.1371/journal.pone.0183450 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jackson, J. A. et al. An immunological marker of tolerance to infection in wild rodents. PLoS Biol. 12, e1001901. https://doi.org/10.1371/journal.pbio.1001901 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Beirne, C., Delahay, R. & Young, A. Sex differences in senescence: The role of intra-sexual competition in early adulthood. Proc. R. Soc. B. 282, 20151086. https://doi.org/10.1098/rspb.2015.1086 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Young, S. et al. Relationships between immune gene expression and circulating cytokine levels in wild house mice. Ecol. Evol. 10, 13860–13871. https://doi.org/10.1002/ece3.6976 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Turner, J. D. et al. Th2 cytokines are associated with reduced worm burdens in a human intestinal helminth infection. J. Infect. Dis. 188, 1768–1775. https://doi.org/10.1086/379370 (2003).CAS 
    Article 
    PubMed 

    Google Scholar 
    Craig, B. H., Pilkington, J. G., Kruuk, L. E. B. & Pemberton, J. M. Epidemiology of parasitic protozoan infections in Soay sheep (Ovis aries L.) on St Kilda. Parasitology 134, 9–21. https://doi.org/10.1017/S0031182006001144 (2006).Article 
    PubMed 

    Google Scholar 
    Maizels, R. M., Hewitson, J. P. & Smith, K. A. Susceptibility and immunity to helminth parasites. Curr. Opin. Immunol. 24, 459–466. https://doi.org/10.1016/j.coi.2012.06.003 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ozmen, O., Adanir, R. & Haligur, M. Immunohistochemical detection of the cytokine and chemokine expression in the gut of lambs and kids with coccidiosis. Small Rumin. Res. 105, 345–350. https://doi.org/10.1016/j.smallrumres.2011.11.010 (2012).Article 

    Google Scholar 
    Woolhouse, M. E. J. Patterns in parasite epidemiology: The peak shift. Parasitol. Today 14, 428–434. https://doi.org/10.1016/S0169-4758(98)01318-0 (1998).CAS 
    Article 
    PubMed 

    Google Scholar 
    Gibson, T. E. & Parfitt, J. W. The effect of age on the development by sheep of resistance to Trichostrongylus colubriformis. Res. Vet. Sci. 13, 529–535 (1972).CAS 
    Article 

    Google Scholar 
    Smith, W. D., Jackson, F., Jackson, E. & Williams, J. Age immunity to Ostertagia circumcincta: Comparison of the local immune responses of 4 1/2- and 10-month-old lambs. J. Comp. Pathol. 95, 235–245. https://doi.org/10.1016/0021-9975(85)90010-6 (1985).CAS 
    Article 
    PubMed 

    Google Scholar 
    Peters, A., Delhey, K., Nakagawa, S., Aulsebrook, A. & Verhulst, S. Immunosenescence in wild animals: Meta-analysis and outlook. Ecol. Lett. 22, 1709–1722. https://doi.org/10.1111/ele.13343 (2019).Article 
    PubMed 

    Google Scholar 
    Sparks, A. M. et al. Natural selection on antihelminth antibodies in a wild mammal population. Am. Nat. 192, 745–760. https://doi.org/10.1086/700115 (2018).Article 
    PubMed 

    Google Scholar 
    Froy, H. et al. Senescence in immunity against helminth parasites predicts adult mortality in a wild mammal. Science 365, 1296–1298. https://doi.org/10.1126/science.aaw5822%JScience (2019).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Nussey, D. H., Watt, K., Pilkington, J. G., Zamoyska, R. & McNeilly, T. N. Age-related variation in immunity in a wild mammal population. Aging Cell 11, 178–180. https://doi.org/10.1111/j.1474-9726.2011.00771.x (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Watson, R. L. et al. Cellular and humoral immunity in a wild mammal: Variation with age & sex and association with overwinter survival. Ecol. Evol. 6, 8695–8705. https://doi.org/10.1002/ece3.2584 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pennock, N. D. et al. T cell responses: Naive to memory and everything in between. Adv. Physiol. Educ. 37, 273–283. https://doi.org/10.1152/advan.00066.2013 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chipeta, J. et al. CD4+and CD8+Cell cytokine profiles in neonates, older children, and adults: Increasing T helper type 1 and T cytotoxic type 1 cell populations with age. Cell. Immunol. 183, 149–156. https://doi.org/10.1006/cimm.1998.1244 (1998).CAS 
    Article 
    PubMed 

    Google Scholar 
    Sakata-Kaneko, S., Wakatsuki, Y., Matsunaga, Y., Usui, T. & Kita, T. Altered Th1/Th2 commitment in human CD4+ T cells with ageing. Clin. Exp. Immunol. 120, 267–273. https://doi.org/10.1046/j.1365-2249.2000.01224.x (2000).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Duddy, M. E., Alter, A. & Bar-Or, A. Distinct profiles of human B cell effector cytokines: A role in immune regulation?. J. Immunol. (Baltimore, Md.: 1950) 172, 3422–3427. https://doi.org/10.4049/jimmunol.172.6.3422 (2004).CAS 
    Article 

    Google Scholar 
    Varma, T. K., Lin, C. Y., Toliver-Kinsky, T. E. & Sherwood, E. R. Endotoxin-induced gamma interferon production: Contributing cell types and key regulatory factors. Clin. Diagn. Lab. Immunol. 9, 530–543. https://doi.org/10.1128/CDLI.9.3.530-543.2002 (2002).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    McNeilly, T. N. et al. Suppression of ovine lymphocyte activation by Teladorsagia circumcincta larval excretory-secretory products. Vet. Res. 44, 70. https://doi.org/10.1186/1297-9716-44-70 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Restif, O. & Amos, W. The evolution of sex-specific immune defences. Proc. R. Soc. B Biol. Sci. 277, 2247–2255. https://doi.org/10.1098/rspb.2010.0188 (2010).Article 

    Google Scholar 
    Hayward, A. D. et al. Heritable, heterogeneous, and costly resistance of sheep against nematodes and potential feedbacks to epidemiological dynamics. Am. Nat. 184, S58–S76. https://doi.org/10.1086/676929 (2014).Article 
    PubMed 

    Google Scholar 
    Sparks, A. M. et al. The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries). PLoS Genet. 15, e1008461. https://doi.org/10.1371/journal.pgen.1008461 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hayward, A. D., Wilson, A. J., Pilkington, J. G., Pemberton, J. M. & Kruuk, L. E. B. Ageing in a variable habitat: Environmental stress affects senescence in parasite resistance in St Kilda Soay sheep. Proc. R. Soc. B. 276, 3477–3485. https://doi.org/10.1098/rspb.2009.0906 (2009).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mosmann, T. R. & Sad, S. The expanding universe of T-cell subsets: Th1, Th2 and more. Immunol. Today 17, 138–146. https://doi.org/10.1016/0167-5699(96)80606-2 (1996).CAS 
    Article 
    PubMed 

    Google Scholar 
    Hassan, M., Hanrahan, J. P., Good, B., Mulcahy, G. & Sweeney, T. A differential interplay between the expression of Th1/Th2/Treg related cytokine genes in Teladorsagia circumcincta infected DRB1*1101 carrier lambs. Vet. Res. 42, 45. https://doi.org/10.1186/1297-9716-42-45 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Noordwijk, A. J. V. & Jong, G. D. Acquisition and allocation of resources: Their influence on variation in life history tactics. Am. Nat. 128, 137–142. https://doi.org/10.1086/284547 (1986).Article 

    Google Scholar 
    Grainger, J. R. et al. Helminth secretions induce de novo T cell Foxp3 expression and regulatory function through the TGF-β pathway. J. Exp. Med. 207, 2331–2341. https://doi.org/10.1084/jem.20101074 (2010).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Smith, K. A. et al. Low-level regulatory T-cell activity is essential for functional type-2 effector immunity to expel gastrointestinal helminths. Mucosal Immunol. 9, 428–443. https://doi.org/10.1038/mi.2015.73 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Beirne, C., Waring, L., McDonald, R. A., Delahay, R. & Young, A. Age-related declines in immune response in a wild mammal are unrelated to immune cell telomere length. Proc. R. Soc. B. 283, 20152949. https://doi.org/10.1098/rspb.2015.2949 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zaros, L. G. et al. Response of resistant and susceptible Brazilian Somalis crossbreed sheep naturally infected by Haemonchus contortus. Parasitol. Res. 113, 1155–1161. https://doi.org/10.1007/s00436-014-3753-8 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Gossner, A., Wilkie, H., Joshi, A. & Hopkins, J. Exploring the abomasal lymph node transcriptome for genes associated with resistance to the sheep nematode Teladorsagia circumcincta. Vet. Res. 44, 68. https://doi.org/10.1186/1297-9716-44-68 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wilkie, H., Gossner, A., Bishop, S. & Hopkins, J. Variations in T cell transcription factor sequence and expression associated with resistance to the sheep nematode Teladorsagia circumcincta. PLoS One 11, e0149644. https://doi.org/10.1371/journal.pone.0149644 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Nussey, D. H., Coulson, T., Festa-Bianchet, M. & Gaillard, J.-M. Measuring senescence in wild animal populations: Towards a longitudinal approach. Funct. Ecol. 22, 393–406. https://doi.org/10.1111/j.1365-2435.2008.01408.x (2008).Article 

    Google Scholar 
    Seguel, M. et al. Immune stability predicts tuberculosis infection risk in a wild mammal. Proc. Biol. Sci. 286, 20191401. https://doi.org/10.1098/rspb.2019.1401 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pemberton, J. M. & Clutton-Brock, T. H. Soay Sheep: Dynamics and Selection in an Island Population (Cambridge University Press, 2004).
    Google Scholar 
    Corripio-Miyar, Y. et al. Phenotypic and functional analysis of monocyte populations in cattle peripheral blood identifies a subset with high endocytic and allogeneic T-cell stimulatory capacity. Vet. Res. 46, 112. https://doi.org/10.1186/s13567-015-0246-4 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kwong, L. S. et al. Development of an ELISA for bovine IL-10. Vet. Immunol. Immunopathol. 85, 213–223. https://doi.org/10.1016/S0165-2427(02)00007-7 (2002).CAS 
    Article 
    PubMed 

    Google Scholar 
    Wattegedera, S. R. et al. Enhancing the toolbox to study IL-17A in cattle and sheep. Vet. Res. 48, 20–20. https://doi.org/10.1186/s13567-017-0426-5 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jackson, F. New technique for obtaining nematode ova from sheep faeces. Lab. Pract. 23, 65–66 (1974).ADS 
    CAS 
    PubMed 

    Google Scholar 
    R Development Core Team. R: A language and environment for statistical computing. Accessed Feb 2020. https://www.R-project.org/ (2019).
    Venables, W. N. & Ripley, B. D. Random and Mixed Effects. In Modern Applied Statistics with S. Statistics and Computing. (2002).Package “corrplot”: visualization of a correlation matrix v. (Version 0.84) (2017).Jari Oksanen, F. et al. vegan: Community Ecology Package. R package version 2.5-6. Accessed Feb 2020. https://CRAN.R-project.org/package=vegan (2019). More

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    Mycorrhizal fungi arbuscular in forage grasses cultivated in Cerrado soil

    Hunke, P., Mueller, E. N., Schröder, B. & Zeilhofer, P. The Brazilian Cerrado: Assessment of water and soil degradation in catchments under intensive agricultural use. Ecohydrology 8, 1154–1180 (2015).Article 

    Google Scholar 
    Klink, C. a. & Machado, R. B. A conservação do Cerrado brasileiro. Megadiversidade 1, 147–155 (2005).Dutra e Silva, S. Challenging the Environmental History of the Cerrado: Science, Biodiversity and Politics on the Brazilian Agricultural Frontier. LAHAC 1, (2020).Nehring, R. Yield of dreams: Marching west and the politics of scientific knowledge in the Brazilian Agricultural Research Corporation (Embrapa). Geoforum 77, 206–217 (2016).Article 

    Google Scholar 
    Taber, A., Navarro, G. & Arribas, M. A. A new park in the Bolivian Gran Chaco—an advance in tropical dry forest conservation and community-based management. Oryx 31, 189 (1997).Article 

    Google Scholar 
    Moura, de, J. B. & Cabral, J. S. R. Mycorrhiza in Central Savannahs: Cerrado and Caatinga. In Mycorrhizal Fungi in South America. vol. 1 (Springer International Publishing, 2019).de Brito Neves, B. B. & Cordani, U. G. Tectonic evolution of South America during the Late Proterozoic. Precambrian Res. 53, 23–40 (1991).ADS 
    Article 

    Google Scholar 
    Laux, J. H., Pimentel, M. M., Dantas, E. L., Armstrong, R. & Junges, S. L. Two neoproterozoic crustal accretion events in the Brasília belt, central Brazil. J. S. Am. Earth Sci. 18, 183–198 (2005).Article 

    Google Scholar 
    Simon, M. F. et al. Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. PNAS 106, 20359–20364 (2009).ADS 
    CAS 
    Article 

    Google Scholar 
    Guimarães Andrade, R. et al. Indicativo de pastagens plantadas em processo de degradação no bioma Cerrado. In XVII Simpósio Brasileiro de Sensoriamento Remot 1585–1592 (INPE, 2015).Arruda, A. B. et al. Resistance of soil to penetration as a parameter indicator of subsolation in crop areas of sugar cane. Sci. Rep. 11, 11780 (2021).ADS 
    CAS 
    Article 

    Google Scholar 
    Bongiorno, G. et al. Sensitivity of labile carbon fractions to tillage and organic matter management and their potential as comprehensive soil quality indicators across pedoclimatic conditions in Europe. Ecol. Ind. 99, 38–50 (2019).CAS 
    Article 

    Google Scholar 
    Dias-Filho, M. B. Desafios da produção animal em pastagens na fronteira agrícola brasileira. Embrapa Amazônia Oriental-Documentos (INFOTECA-E) (2012).Andrade Júnior, J. A. D., Ribeiro De Souza, B., Souza, R. F. & de Moura, J. B. Fixação de carbono em sistemas agroecológicos na região do vale do são patrício, goiás carbon sequestration in agroecological systems in the region of the são patrício valley, goiás. Científic@ Multidiscip. J. ISSN 5, 85–98 (2018).Andrade de Souza Moraes, J. M. et al. Arbuscular mycorrhizal fungi in integrated crop livestock systems with intercropping in the pasture phase in the Cerrado. Rhizosphere 11 (2019).Ofstehage, A. & Nehring, R. No-till agriculture and the deception of sustainability in Brazil. Int. J. Agric. Sustain. 19, 335–348 (2021).Article 

    Google Scholar 
    Thomazini, L. I. Mycorrhiza in plants of the ‘Cerrado’. Plant Soil 41, 707–711 (1974).Article 

    Google Scholar 
    Porcel, R. & Ruiz-Lozano, J. M. Arbuscular mycorrhizal influence on leaf water potential, solute accumulation, and oxidative stress in soybean plants subjected to drought stress. J. Exp. Bot. 55, 1743–1750 (2004).CAS 
    Article 

    Google Scholar 
    Moura, de, J. B., Valentim, N. M., Ventura, M. V. A. & Junior, W. G. V. Taxa de colonização micorrízica sob diferentes sistemas de cultivo no cerrado em cana-de-açúcar. 2, 60–66 (2017).Pirozynski, K. A. Interactions between fungi and plants through the ages. Can. J. Bot. 59, 1824–1827 (1981).Article 

    Google Scholar 
    Muthukumar, T., Udaiyan, K. & Shanmughavel, P. Mycorrhiza in sedges—an overview. Mycorrhiza 14, 65–77 (2004).CAS 
    Article 

    Google Scholar 
    Aliasgharzadeh, N., Rastin, S. N., Towfighi, H. & Alizadeh, A. Occurrence of arbuscular mycorrhizal fungi in saline soils of the Tabriz Plain of Iran in relation to some physical and chemical properties of soil. Mycorrhiza 11, 119–122 (2001).CAS 
    Article 

    Google Scholar 
    Gehring, C. A. & Connell, J. H. Arbuscular mycorrhizal fungi in the tree seedlings of two Australian rain forests: Occurrence, colonization, and relationships with plant performance. Mycorrhiza 16, 89–98 (2006).Article 

    Google Scholar 
    Vestberg, M. Occurrence of some Glomales in Finland. Mycorrhiza 5, 329–336 (1995).Article 

    Google Scholar 
    Khan, A. G. Occurrence and importance of mycorrhizae in aquatic trees of New South Wales, Australia. Mycorrhiza 3, 31–38 (1993).Article 

    Google Scholar 
    Braz, S. P., Urquiaga, S., Alves, B. J. R. & Boddey, R. M. Degradação de Pastagens, Matéria Orgânica do Solo e a Recuperação do Potencial Produtivo em Sistemas de Baixo “Input” Tecnológico na Região dos Cerrados (2004).
    Vieira Jr, W. G. et al. Seasonal variation in mycorrhizal community of different cerrado phytophysiomies. Front. Microbiol. 11 (2020).
    Gerdemann, J. W. & Nicolson, T. H. Spores of mycorrhizal endogone species extracted from soil by wet sieving and decanting. Trans. Br. Mycol. Soc. 46, 235–244 (1963).Article 

    Google Scholar 
    INVAM. International Culture Collection of (Vesicular) Arbuscular Mycorrhizal Fungi | West Virginia University. (2018).SILVA, F. de A. ASSISTAT: Versão 7.7 beta. (DEAG-CTRN-Universidade Federal de Campina Grande, 2008).Hammer, Ø. Past 3.x—the Past of the Future. (Natural History Museum, University of Oslo, 2018).Cavalcanti, A. C. R., Cavallini, M. C. & Lima, N. R. C. de B. Estresse por Déficit Hídrico em Plantas Forrageiras. 50 https://www.infoteca.cnptia.embrapa.br/bitstream/doc/748148/1/doc89.pdf (2009).Alvares, C. A., Stape, J. L., Sentelhas, P. C., De Moraes, J. L. G. & Sparovek, G. Köppen’s climate classification map for Brazil. Metereol Z 22(6), 711–728 (2014).Article 

    Google Scholar 
    Nicolson, T. H. Vesicular-arbuscular mycorrhiza in the Gramineae. Nature 181, 718–719 (1958).ADS 
    Article 

    Google Scholar 
    Soreng, R. J. et al. A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications. J. Syst. Evol. 55, 259–290 (2017).Article 

    Google Scholar 
    Teutscherova, N. et al. Differences in arbuscular mycorrhizal colonization and P acquisition between genotypes of the tropical Brachiaria grasses: Is there a relation with BNI activity?. Biol. Fertil. Soils 55, 325–337 (2019).CAS 
    Article 

    Google Scholar 
    de Miranda, J. C. C. Cerrado: Micorriza Arbuscular, Ocorrência e Manejo. (Embrapa, 2008).Souza, B. R., Moura, J. B., Oliveira, T. C., Ramos, M. L. G. & Lopes Filho, L. C. Arbuscular Mycorrhizal fungi as indicative of soil quality in conservation systems in the region of vale do São Patrício, Goiás. Int. J. Curr. Res. 8, 43307–43311 (2016).
    Google Scholar 
    de Oliveira, T. C. et al. Produtividade da soja em associação ao fungo micorrízico arbuscular Rhizophagus clarus cultivada em condições de campo. Rev. Ciênc. Agrovet. 18, 530–535 (2019).Article 

    Google Scholar 
    Moura, J. B. et al. Arbuscular mycorrhizal fungi associated with bamboo under Cerrado Brazilian vegetation. J. Soil Sci. Plant. Nutr https://doi.org/10.1007/s42729-019-00093-0 (2019).Article 

    Google Scholar 
    Phillips, J. M. & Hayman, D. S. Improved procedures for clearing roots and staining parasitic and vesicular-arbuscular mycorrhizal fungi for rapid assessment of infection. Trans. Br. Mycol. Soc. 55, 158–161 (1970).Article 

    Google Scholar 
    Giovannetti, M. & Mosse, B. An evaluation of techniques for measuring vesicular arbuscular mycorrhizal infection in roots. New Phytol. 84, 489–500 (1980).Article 

    Google Scholar 
    Promita, D. & Mohan, K. Arbuscular mycorrhizal fungal diversity in sugarcane rhizosphere in relation with soil properties. Notulae Scientia Biologicae 4(1), 66–74 (2012).Aquino, S. D. S. et al. Mycorrhizal colonization and diversity and corn genotype yield in soils of the Cerrado region, Brazil. Semin. Cienc. Agrar. 36, 4107–4117 (2015).Article 

    Google Scholar  More

  • in

    Unpacking the complexity of longitudinal movement and recruitment patterns of facultative amphidromous fish

    Beger, M. et al. Conservation planning for connectivity across marine, freshwater, and terrestrial realms. Biol. Cons. 143, 565–575 (2010).Article 

    Google Scholar 
    Roberts, J. H., Angermeier, P. L. & Hallerman, E. M. Distance, dams and drift: What structures populations of an endangered, benthic stream fish?. Freshw. Biol. 58, 2050–2064. https://doi.org/10.1111/fwb.12190 (2013).Article 

    Google Scholar 
    Berejikian, B. A., Campbell, L. A., Moore, M. E. & Grant, J. Large-scale freshwater habitat features influence the degree of anadromy in eight Hood Canal Oncorhynchus mykiss populations. Can. J. Fish. Aquat. Sci. 70, 756–765. https://doi.org/10.1139/cjfas-2012-0491 (2013).Article 

    Google Scholar 
    Falke, J. A. & Fausch, K. D. in American Fisheries Society Symposium. 207–233.Hanski, I. & Simberloff, D. in Metapopulation Biology (eds Ilkka Hanski & Michael E. Gilpin) 5–26 (Academic Press, 1997).Cadrin, S. X., Friedland, K. D. & Waldman, J. R. in Stock Identification Methods (eds Cadrin, S. X., Friedland, K. D. & Waldman, J. R.) 3–6 (Academic Press, 2005).Hughes, J. M., Schmidt, D. J. & Finn, D. S. Genes in streams: Using DNA to understand the movement of freshwater fauna and their riverine habitat. Bioscience 59, 573–583 (2009).Article 

    Google Scholar 
    Gross, M. R., Coleman, R. M. & McDowall, R. M. Aquatic productivity and the evolution of diadromous fish migration. Science 239, 1291–1293 (1988).ADS 
    CAS 
    Article 

    Google Scholar 
    McDowall, R. M. The evolution of diadromy in fishes (revisited) and its place in phylogenetic analysis. Rev. Fish Biol. Fish. 7, 443–462. https://doi.org/10.1023/A:1018404331601 (1997).Article 

    Google Scholar 
    Myers, G. S. Usage of anadromous, catadromous and allied terms for migratory fishes. Copeia 89–97, 1949. https://doi.org/10.2307/1438482 (1949).Article 

    Google Scholar 
    Augspurger, J. M., Warburton, M. & Closs, G. P. Life-history plasticity in amphidromous and catadromous fishes: A continuum of strategies. Rev. Fish Biol. Fish. 27, 177–192. https://doi.org/10.1007/s11160-016-9463-9 (2017).Article 

    Google Scholar 
    McDowall, R. On amphidromy, a distinct form of diadromy in aquatic organisms. Fish Fish. 8, 1–13 (2007).Article 

    Google Scholar 
    David, B. O. et al. To sea or not to sea? Multiple lines of evidence reveal the contribution of non-diadromous recruitment for supporting endemic fish populations within New Zealand’s longest river. Aquat. Conserv. Mar. Freshw. Ecosyst. 29, 1409–1423. https://doi.org/10.1002/aqc.3022 (2019).Article 

    Google Scholar 
    Delgado, L. et al. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol. Ecol. 29, 4857–4870. https://doi.org/10.1111/mec.15686 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Closs, G. P., Hicks, A. S. & Jellyman, P. G. Life histories of closely related amphidromous and non-migratory fish species: A trade-off between egg size and fecundity. Freshw. Biol. 58, 1162–1177. https://doi.org/10.1111/fwb.12116 (2013).Article 

    Google Scholar 
    Górski, K., Habit, E. M., Pingram, M. A. & Manosalva, A. J. Variation of the use of marine resources by Galaxias maculatus in large Chilean rivers. Hydrobiologia 814, 61–73. https://doi.org/10.1007/s10750-015-2542-4 (2018).Article 

    Google Scholar 
    Vega Aguayo, R. et al. Bases biológicas para el cultivo del puye Galaxias maculatus (Jenyns, 1842): Una revisión (2014).Cussac, V. E. et al. New insights into the distribution, physiology and life histories of South American galaxiid fishes, and potential threats to this unique fauna. Diversity https://doi.org/10.3390/d12050178 (2020).Article 

    Google Scholar 
    Hicks, A. S. et al. Lake and species specific patterns of non-diadromous recruitment in amphidromous fish: The importance of local recruitment and habitat requirements. Mar. Freshw. Res. https://doi.org/10.1071/mf16387 (2017).Article 

    Google Scholar 
    Manosalva, A. J. et al. Variation of stomach content and isotopic niche of puye Galaxias maculatus (Jenyns, 1842) in large river systems of southern Chile. Freshw. Biol. 66, 1110–1122. https://doi.org/10.1111/fwb.13703 (2021).CAS 
    Article 

    Google Scholar 
    Milano, D., Aigo, J. C. & Macchi, P. J. Diel patterns in space use, food and metabolic activity of Galaxias maculatus (Pisces: Galaxiidae) in the littoral zone of a shallow Patagonian lake. Aquat. Ecol. 47, 277–290. https://doi.org/10.1007/s10452-013-9443-2 (2013).Article 

    Google Scholar 
    Chapman, A., Morgan, D. L., Beatty, S. J. & Gill, H. S. Variation in life history of land-locked lacustrine and riverine populations of Galaxias maculatus (Jenyns 1842) in Western Australia. Environ. Biol. Fishes 77, 21–37 (2006).Article 

    Google Scholar 
    Barriga, J. P. et al. Intraspecific variation in diet, growth, and morphology of landlocked Galaxias maculatus during its larval period: The role of food availability and predation risk. Hydrobiologia 679, 27–41 (2012).Article 

    Google Scholar 
    Campos, H. Population studies of Galaxias maculatus (Jenyns) (Osteichthys: Galaxiidae) in Chile with reference to the number of vertebrae. Stud. Neotrop. Fauna 9, 55–76. https://doi.org/10.1080/01650527409360470 (1974).Article 

    Google Scholar 
    Rojo, J. H., Fernandez, D. A., Figueroa, D. E. & Boy, C. C. Phenotypic and genetic differentiation between diadromous and landlocked puyen Galaxias maculatus. J. Fish Biol. 96, 956–967. https://doi.org/10.1111/jfb.14285 (2020).Article 
    PubMed 

    Google Scholar 
    Zemlak, T. S., Habit, E. M., Walde, S. J., Carrea, C. & Ruzzante, D. E. Surviving historical Patagonian landscapes and climate: Molecular insights from Galaxias maculatus. BMC Evol. Biol. 10, 1–18 (2010).Article 

    Google Scholar 
    Delgado, M. L., Gorski, K., Habit, E. & Ruzzante, D. E. The effects of diadromy and its loss on genomic divergence: The case of amphidromous Galaxias maculatus populations. Mol. Ecol. 28, 5217–5231. https://doi.org/10.1111/mec.15290 (2019).Article 
    PubMed 

    Google Scholar 
    Delgado, M. L. et al. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol. Ecol. 29, 4857–4870. https://doi.org/10.1111/mec.15686 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Alo, D., Correa, C., Samaniego, H., Krabbenhoft, C. A. & Turner, T. F. Otolith microchemistry and diadromy in Patagonian river fishes. PeerJ 7, e6149. https://doi.org/10.7717/peerj.6149 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Campana, S. E. Chemistry and composition of fish otoliths: Pathways, mechanisms and applications. Mar. Ecol. Prog. Ser. 188, 263–297 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    Schulz-Mirbach, T., Ladich, F., Plath, M. & Heß, M. Enigmatic ear stones: What we know about the functional role and evolution of fish otoliths. Biol. Rev. 94, 457–482 (2019).Article 

    Google Scholar 
    Campana, S. E. Otolith science entering the 21st century. Mar. Freshw. Res. 56, 485–495 (2005).Article 

    Google Scholar 
    Ahn, H. et al. Effect of water temperature on embryonic development and hatching time of the Japanese eel Anguilla japonica. Aquaculture 330, 100–105 (2012).Article 

    Google Scholar 
    Avigliano, E., Velasco, G. & Volpedo, A. V. Use of lapillus otolith microchemistry as an indicator of the habitat of Genidens barbus from different estuarine environments in the southwestern Atlantic Ocean. Environ. Biol. Fishes 98, 1623–1632. https://doi.org/10.1007/s10641-015-0387-3 (2015).Article 

    Google Scholar 
    Whitledge, G. W. Otolith microchemistry and isotopic composition as potential indicators of fish movement between the Illinois River drainage and Lake Michigan. J. Great Lakes Res. 35, 101–106. https://doi.org/10.1016/j.jglr.2008.10.003 (2009).CAS 
    Article 

    Google Scholar 
    Kraus, R. T. & Secor, D. H. Incorporation of strontium into otoliths of an estuarine fish. J. Exp. Mar. Biol. Ecol. 302, 85–106. https://doi.org/10.1016/j.jembe.2003.10.004 (2004).CAS 
    Article 

    Google Scholar 
    Volk, E. C., Blakley, A., Schroder, S. L. & Kuehner, S. M. Otolith chemistry reflects migratory characteristics of Pacific salmonids: Using otolith core chemistry to distinguish maternal associations with sea and freshwaters. Fish. Res. 46, 251–266 (2000).Article 

    Google Scholar 
    Vignon, M. Extracting environmental histories from sclerochronological structures—Recursive partitioning as a mean to explore multi-elemental composition of fish otolith. Ecol. Inform. 30, 159–169. https://doi.org/10.1016/j.ecoinf.2015.10.002 (2015).Article 

    Google Scholar 
    Teichert, N. et al. Site fidelity and movements of an amphidromous goby revealed by otolith multi-elemental signatures along a tropical watershed. Ecol. Freshw. Fish 27, 834–846. https://doi.org/10.1111/eff.12396 (2018).Article 

    Google Scholar 
    Elsdon, T. S. & Gillanders, B. M. Fish otolith chemistry influenced by exposure to multiple environmental variables. J. Exp. Mar. Biol. Ecol. 313, 269–284. https://doi.org/10.1016/j.jembe.2004.08.010 (2004).CAS 
    Article 

    Google Scholar 
    Vivancos, A. et al. Hydrological connectivity drives longitudinal movement of endangered endemic Chilean darter Percilia irwini (Eigenmann, 1927). J Fish Biol 98, 33–43. https://doi.org/10.1111/jfb.14554 (2021).Article 
    PubMed 

    Google Scholar 
    Percie du Sert, N. et al. Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0. PLOS Biology 18, e3000411. https://doi.org/10.1371/journal.pbio.3000411 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Warburton, M. L., Reid, M. R., Stirling, C. H. & Closs, G. Validation of depth-profiling LA-ICP-MS in otolith applications. Can. J. Fish. Aquat. Sci. 74, 572–581 (2017).CAS 
    Article 

    Google Scholar 
    Paton, C., Hellstrom, J., Paul, B., Woodhead, J. & Hergt, J. Iolite: Freeware for the visualisation and processing of mass spectrometric data. J. Anal. At. Spectrom. 26, 2508–2518. https://doi.org/10.1039/C1JA10172B (2011).CAS 
    Article 

    Google Scholar 
    Woodhead, J. et al. A guide to depth profiling and imaging applications of LA-ICP-MS. Laser Ablation ICP-MS Earth Sci. Curr. Pract. Outst. Issues 40, 135–145 (2008).CAS 

    Google Scholar 
    Veinott, G., Westley, P. A. H., Purchase, C. F., Warner, L. & Gillanders, B. Experimental evidence simultaneously confirms and contests assumptions implicit to otolith microchemistry research. Can. J. Fish. Aquat. Sci. 71, 356–365. https://doi.org/10.1139/cjfas-2013-0224 (2014).Article 

    Google Scholar 
    Brophy, D., Jeffries, T. E. & Danilowicz, B. S. Elevated manganese concentrations at the cores of clupeid otoliths: Possible environmental, physiological, or structural origins. Mar. Biol. 144, 779–786. https://doi.org/10.1007/s00227-003-1240-3 (2004).CAS 
    Article 

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

    Google Scholar 
    Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46. https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x (2001).Article 

    Google Scholar 
    McArdle, B. H. & Anderson, M. J. Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology 82, 290–297. https://doi.org/10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2 (2001).Article 

    Google Scholar 
    Brown, R. J., Campana, S. & Severin, K. P. Otolith chemistry analyses indicate that water Sr: Ca is the primary factor influencing otolith Sr: Ca for freshwater and diadromous fish but not for marine fish. Can. J. Fish. Aquat. Sci. 66, 1790–1808. https://doi.org/10.1139/f09-112 (2009).CAS 
    Article 

    Google Scholar 
    Humston, R. et al. Isotope geochemistry reveals ontogeny of dispersal and exchange between main-river and tributary habitats in smallmouth bass Micropterus dolomieu. J. Fish Biol. 90, 528–548. https://doi.org/10.1111/jfb.13073 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Dingle, H. & Drake, V. A. What is migration?. Bioscience 57, 113–121 (2007).Article 

    Google Scholar 
    Hogan, J. D., Blum, M. J., Gilliam, J. F., Bickford, N. & McIntyre, P. B. Consequences of alternative dispersal strategies in a putatively amphidromous fish. Ecology 95, 2397–2408 (2014).Article 

    Google Scholar 
    Kelley, J. L., Grierson, P. F., Collin, S. P. & Davies, P. M. Habitat disruption and the identification and management of functional trait changes. Fish Fish. 19, 716–728. https://doi.org/10.1111/faf.12284 (2018).Article 

    Google Scholar 
    Vivancos, A. et al. Hydrological connectivity drives longitudinal movement of endangered endemic Chilean darter Percilia irwini (Eigenmann, 1927). J. Fish Biol. 98, 33–43 (2020).Article 

    Google Scholar 
    Hicks, A. S., Closs, G. P. & Swearer, S. E. Otolith microchemistry of two amphidromous galaxiids across an experimental salinity gradient: A multi-element approach for tracking diadromous migrations. J. Exp. Mar. Biol. Ecol. 394, 86–97 (2010).Article 

    Google Scholar 
    Miller, J. A. Effects of water temperature and barium concentration on otolith composition along a salinity gradient: Implications for migratory reconstructions. J. Exp. Mar. Biol. Ecol. 405, 42–52. https://doi.org/10.1016/j.jembe.2011.05.017 (2011).CAS 
    Article 

    Google Scholar 
    Walsh, C. T. & Gillanders, B. M. Extrinsic factors affecting otolith chemistry—Implications for interpreting migration patterns in a diadromous fish. Environ. Biol. Fishes 101, 905–916. https://doi.org/10.1007/s10641-018-0746-y (2018).Article 

    Google Scholar 
    Walther, B. D. & Limburg, K. E. The use of otolith chemistry to characterize diadromous migrations. J. Fish Biol. 81, 796–825. https://doi.org/10.1111/j.1095-8649.2012.03371.x (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Hicks, A. S. et al. Lake and species specific patterns of non-diadromous recruitment in amphidromous fish: The importance of local recruitment and habitat requirements. Mar. Freshw. Res. 68, 2315–2323 (2017).Article 

    Google Scholar 
    Hickford, M. J. & Schiel, D. R. Population sinks resulting from degraded habitats of an obligate life-history pathway. Oecologia 166, 131–140 (2011).ADS 
    Article 

    Google Scholar 
    Barriga, J., Battini, M. & Cussac, V. Annual dynamics variation of a landlocked Galaxias maculatus (Jenyns 1842) population in a Northern Patagonian river: Occurrence of juvenile upstream migration. J. Appl. Ichthyol. 23, 128–135 (2007).Article 

    Google Scholar 
    Huey, J. A. et al. Is variable connectivity among populations of a continental gobiid fish driven by local adaptation or passive dispersal?. Freshw. Biol. 59, 1672–1686 (2014).CAS 
    Article 

    Google Scholar 
    Catlin, A. K., Collier, K. J. & Duggan, I. C. Zooplankton generation following inundation of floodplain soils: Effects of vegetation type and riverine connectivity. Mar. Freshw. Res. https://doi.org/10.1071/mf15273 (2017).Article 

    Google Scholar 
    Górski, K., Collier, K. J., Duggan, I. C., Taylor, C. M. & Hamilton, D. P. Connectivity and complexity of floodplain habitats govern zooplankton dynamics in a large temperate river system. Freshw. Biol. 58, 1458–1470. https://doi.org/10.1111/fwb.12144 (2013).Article 

    Google Scholar 
    Sturrock, A. M. et al. Quantifying physiological influences on otolith microchemistry. Methods Ecol. Evol. 6, 806–816. https://doi.org/10.1111/2041-210x.12381 (2015).Article 

    Google Scholar 
    Doubleday, Z. A., Izzo, C., Woodcock, S. H. & Gillanders, B. M. Relative contribution of water and diet to otolith chemistry in freshwater fish. Aquat. Biol. 18, 271–280. https://doi.org/10.3354/ab00511 (2013).Article 

    Google Scholar 
    Elsdon, T. S. et al. Oceanography and Marine Biology 303–336 (CRC Press, 2008).
    Google Scholar 
    Izzo, C., Doubleday, Z. A., Schultz, A. G., Woodcock, S. H. & Gillanders, B. M. Contribution of water chemistry and fish condition to otolith chemistry: Comparisons across salinity environments. J Fish Biol 86, 1680–1698. https://doi.org/10.1111/jfb.12672 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Walther, B. D. The art of otolith chemistry: interpreting patterns by integrating perspectives. Mar. Freshw. Res. 70, 1643–1658 (2019).CAS 
    Article 

    Google Scholar 
    Hüssy, K. et al. Trace element patterns in otoliths: The role of biomineralization. Rev. Fish. Sci. Aquacult. 29, 1–33 (2020).
    Google Scholar 
    Nazir, A. & Khan, M. A. Spatial and temporal variation in otolith chemistry and its relationship with water chemistry: Stock discrimination of Sperata aor. Ecol. Freshw. Fish 28, 499–511. https://doi.org/10.1111/eff.12471 (2019).Article 

    Google Scholar 
    Vera-Escalona, I., Habit, E. & Ruzzante, D. E. Invasive species and postglacial colonization: Their effects on the genetic diversity of a Patagonian fish. Proc. Biol. Sci. 286, 20182567. https://doi.org/10.1098/rspb.2018.2567 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar  More

  • in

    Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes

    Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ, Ring D, et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol. 2016;2:16215.CAS 
    PubMed 

    Google Scholar 
    Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 2015;517:205–8.CAS 
    PubMed 

    Google Scholar 
    He M, Shi B. Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics. Cell Biosci. 2017;7:54.PubMed 
    PubMed Central 

    Google Scholar 
    Ma W, Mao Q, Xia W, Dong G, Yu C, Jiang F. Gut microbiota shapes the efficiency of cancer therapy. Front Microbiol. 2019;10:1050.PubMed 
    PubMed Central 

    Google Scholar 
    Rodriguez J, Hiel S, Neyrinck AM, Le Roy T, Potgens SA, Leyrolle Q, et al. Discovery of the gut microbial signature driving the efficacy of prebiotic intervention in obese patients. Gut 2020;69:1975–87.CAS 
    PubMed 

    Google Scholar 
    Schubert AM, Sinani H, Schloss PD. Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. mBio 2015;6:e00974.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vivarelli S, Salemi R, Candido S, Falzone L, Santagati M, Stefani S, et al. Gut microbiota and cancer: From pathogenesis to therapy. Cancers (Basel). 2019;11:38.Pasolli E, Truong DT, Malik F, Waldron L, Segata N. Machine learning meta-analysis of large metagenomic datasets: Tools and biological insights. PLoS Comput Biol. 2016;12:e1004977.PubMed 
    PubMed Central 

    Google Scholar 
    Walters WA, Xu Z, Knight R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 2014;588:4223–33.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rastelli M, Knauf C, Cani PD. Gut microbes and health: A focus on the mechanisms linking microbes, obesity, and related disorders. Obes (Silver Spring) 2018;26:792–800.
    Google Scholar 
    Sonnenburg JL, Backhed F. Diet-microbiota interactions as moderators of human metabolism. Nature 2016;535:56–64.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science 2012;336:1255–62.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Koskella B, Hall LJ, Metcalf CJE. The microbiome beyond the horizon of ecological and evolutionary theory. Nat Ecol Evol. 2017;1:1606–15.PubMed 

    Google Scholar 
    Walter J, Ley R. The human gut microbiome: Ecology and recent evolutionary changes. Annu Rev Microbiol. 2011;65:411–29.CAS 
    PubMed 

    Google Scholar 
    Walter J, Maldonado-Gomez MX, Martinez I. To engraft or not to engraft: An ecological framework for gut microbiome modulation with live microbes. Curr Opin Biotechnol. 2018;49:129–39.CAS 
    PubMed 

    Google Scholar 
    Le Roy T, Debedat J, Marquet F, Da-Cunha C, Ichou F, Guerre-Millo M, et al. Comparative evaluation of microbiota engraftment following fecal microbiota transfer in mice models: Age, kinetic and microbial status matter. Front Microbiol. 2018;9:3289.PubMed 

    Google Scholar 
    Maldonado-Gomez MX, Martinez I, Bottacini F, O’Callaghan A, Ventura M, van Sinderen D, et al. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe. 2016;20:515–26.CAS 
    PubMed 

    Google Scholar 
    Martinez I, Maldonado-Gomez MX, Gomes-Neto JC, Kittana H, Ding H, Schmaltz R, et al. Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly. Elife. 2018;7:e36521.Podlesny D, Durdevic M, Paramsothy S, Kaakoush NO, Högenauer C, Gorkiewicz G, et al. Intraspecies strain exclusion, antibiotic pretreatment, and donor selection control microbiota engraftment after fecal transplantation. medRxiv. 2021;08.18.21262200.Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, et al. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 2016;352:586–89.CAS 
    PubMed 

    Google Scholar 
    Seekatz AM, Aas J, Gessert CE, Rubin TA, Saman DM, Bakken JS, et al. Recovery of the gut microbiome following fecal microbiota transplantation. mBio 2014;5:e00893–00814.PubMed 
    PubMed Central 

    Google Scholar 
    Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, et al. Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing. mBio. 2012;3:e00338–12.Hardin G. The competitive exclusion principle. Science 1960;131:1292–7.CAS 
    PubMed 

    Google Scholar 
    Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S, Weber TC, et al. Like will to like: Abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010;6:e1000711.PubMed 
    PubMed Central 

    Google Scholar 
    Chesson P. Mechanisms of maintenance of species diversity. Annu Rev Ecol Syst. 2000;31:343–66.
    Google Scholar 
    Grainger TN, Letten AD, Gilbert B, Fukami T. Applying modern coexistence theory to priority effects. Proc Natl Acad Sci USA. 2019;116:6205–10.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lee SM, Donaldson GP, Mikulski Z, Boyajian S, Ley K, Mazmanian SK. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 2013;501:426–9.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Onderdonk A, Marshall B, Cisneros R, Levy SB. Competition between congenic Escherichia coli K-12 strains in vivo. Infect Immun. 1981;32:74–9.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci USA. 2013;110:9066–71.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shin NR, Lee JC, Lee HY, Kim MS, Whon TW, Lee MS, et al. An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut 2014;63:727–35.CAS 

    Google Scholar 
    Dingemanse C, Belzer C, van Hijum SA, Gunthel M, Salvatori D, den Dunnen JT, et al. Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice. Carcinogenesis 2015;36:1388–96.CAS 
    PubMed 

    Google Scholar 
    Png CW, Linden SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol. 2010;105:2420–8.CAS 
    PubMed 

    Google Scholar 
    Zhai R, Xue X, Zhang L, Yang X, Zhao L, Zhang C. Strain-specific anti-inflammatory properties of two Akkermansia muciniphila strains on chronic colitis in mice. Front Cell Infect Microbiol. 2019;9:239.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 2011;9:e1001221.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pudlo NA, Urs K, Crawford R, Pirani A, Atherly T, Jimenez R, et al. Phenotypic and genomic diversification in complex carbohydrate-degrading human gut bacteria. mSystems. 2022;7:e0094721.Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, et al. The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol. 2016;1:16131.CAS 
    PubMed 

    Google Scholar 
    Weldon L, Abolins S, Lenzi L, Bourne C, Riley EM, Viney M. The gut microbiota of wild mice. PLoS One. 2015;10:e0134643.PubMed 
    PubMed Central 

    Google Scholar 
    Segura Munoz RR, Quach T, Gomes-Neto JC, Xian Y, Pena PA, Weier S, et al. Stearidonic-enriched soybean oil modulates obesity, glucose metabolism, and fatty acid profiles independently of Akkermansia muciniphila. Mol Nutr Food Res. 2020;64:e2000162.PubMed 
    PubMed Central 

    Google Scholar 
    Bindels LB, Segura Munoz RR, Gomes-Neto JC, Mutemberezi V, Martinez I, Salazar N, et al. Resistant starch can improve insulin sensitivity independently of the gut microbiota. Microbiome 2017;5:12.PubMed 
    PubMed Central 

    Google Scholar 
    Chen IA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 2019;47:D666–D677.CAS 
    PubMed 

    Google Scholar 
    Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000;132:365–86.CAS 
    PubMed 

    Google Scholar 
    Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, et al. Genomes OnLine database (GOLD) v.7: Updates and new features. Nucleic Acids Res.2019;47:D649–D659.CAS 
    PubMed 

    Google Scholar 
    Schneeberger M, Everard A, Gomez-Valades AG, Matamoros S, Ramirez S, Delzenne NM, et al. Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice. Sci Rep. 2015;5:16643.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gomes-Neto JC, Mantz S, Held K, Sinha R, Segura Munoz RR, Schmaltz R, et al. A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice. J Microbiol Methods. 2017;135:52–62.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gomes-Neto JC, Kittana H, Mantz S, Segura Munoz RR, Schmaltz RJ, Bindels LB, et al. A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself. Sci Rep. 2017;7:17707.PubMed 
    PubMed Central 

    Google Scholar 
    Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018;7:1338.PubMed 
    PubMed Central 

    Google Scholar 
    Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754–60.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Garcia-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Gotz S, Tarazona S, et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 2012;28:2678–79.CAS 
    PubMed 

    Google Scholar 
    Thomsen MCF, Hasman H, Westh H, Kaya H, Lund O. RUCS: rapid identification of PCR primers for unique core sequences. Bioinformatics 2017;33:3917–21.PubMed 
    PubMed Central 

    Google Scholar 
    Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394–1403.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.PubMed 
    PubMed Central 

    Google Scholar 
    Genome [Internet] (2004). National Library of Medicine (US), National Center for Biotechnology Information: Bethesda (MD). https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/1218/Genome [Internet] (2004). National Library of Medicine (US), National Center for Biotechnology Information: Bethesda (MD). https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/1598/Beghini F, McIver LJ, Blanco-Miguez A, Dubois L, Asnicar F, Maharjan S, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021;10:e65088.Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 2015;3:e1029.PubMed 
    PubMed Central 

    Google Scholar 
    Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43:6761–71.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC. Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PLoS One 2009;4:e7979.PubMed 
    PubMed Central 

    Google Scholar 
    El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res 2019;47:D427–D432.CAS 
    PubMed 

    Google Scholar 
    The UniProt Consortium. The universal protein resource (UniProt). Nucleic Acids Res 2008;36:D190–195.
    Google Scholar 
    Obadia B, Guvener ZT, Zhang V, Ceja-Navarro JA, Brodie EL, Ja WW, et al. Probabilistic invasion underlies natural gut microbiome stability. Curr Biol 2017;27:1999–2006 e1998.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Meszena G, Gyllenberg M, Pasztor L, Metz JA. Competitive exclusion and limiting similarity: A unified theory. Theor Popul Biol. 2006;69:68–87.PubMed 

    Google Scholar 
    Cavender-Bares J, Kozak KH, Fine PV, Kembel SW. The merging of community ecology and phylogenetic biology. Ecol Lett. 2009;12:693–715.PubMed 

    Google Scholar 
    Tramontano M, Andrejev S, Pruteanu M, Klunemann M, Kuhn M, Galardini M, et al. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nat Microbiol 2018;3:514–22.CAS 
    PubMed 

    Google Scholar 
    Derrien M, Vaughan EE, Plugge CM, de Vos WM. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 2004;54:1469–1476.CAS 
    PubMed 

    Google Scholar 
    Walker AW, Lawley TD. Therapeutic modulation of intestinal dysbiosis. Pharm Res 2013;69:75–86.CAS 

    Google Scholar 
    Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol 2016;1:16140.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Perez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, et al. Gut microbiota disturbance during antibiotic therapy: A multi-omic approach. Gut 2013;62:1591–1601.CAS 
    PubMed 

    Google Scholar 
    Adler PB, Hillerislambers J, Levine JM. A niche for neutrality. Ecol Lett. 2007;10:95–104.PubMed 

    Google Scholar 
    Levine JM, HilleRisLambers J. The importance of niches for the maintenance of species diversity. Nature 2009;461:254–57.CAS 
    PubMed 

    Google Scholar 
    Forstner G. Signal transduction, packaging and secretion of mucins. Annu Rev Physiol. 1995;57:585–605.CAS 
    PubMed 

    Google Scholar 
    Ottman N, Davids M, Suarez-Diez M, Boeren S, Schaap PJ, Martins Dos Santos VAP, et al. Genome-scale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle. Appl Environ Microbiol. 2017;83:e01014-17.Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE, Tasseva G et al. Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Appl Environ Microbiol. 2017;83:e00132–17.Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, et al. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet. 2011;7:e1001314.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, et al. Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell 2017;171:1015–1028 e1013.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Karcher N, Nigro E, Puncochar M, Blanco-Miguez A, Ciciani M, Manghi P, et al. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biol. 2021;22:209.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365.Mark Welch JL, Hasegawa Y, McNulty NP, Gordon JI, Borisy GG. Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice. Proc Natl Acad Sci USA. 2017;114:E9105–E9114.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Whitaker WR, Shepherd ES, Sonnenburg JL. Tunable expression tools enable single-cell strain distinction in the gut microbiome. Cell 2017;169:538–546. e512.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Becken B, Davey L, Middleton DR, Mueller KD, Sharma A, Holmes ZC, et al. Genotypic and phenotypic diversity among human isolates of Akkermansia muciniphila. mBio. 2021;12:e00478–21.Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 2017;27:626–38.
    Google Scholar 
    Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science 2013;341:1237439.PubMed 
    PubMed Central 

    Google Scholar 
    Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, et al. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol. 2018;3:347–355.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24:133–45 e135.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Korpela K, Costea P, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, et al. Selective maternal seeding and environment shape the human gut microbiome. Genome Res. 2018;28:561–8.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Freitag TL, Hartikainen A, Jouhten H, Sahl C, Meri S, Anttila VJ, et al. Minor effect of antibiotic pre-treatment on the engraftment of donor microbiota in fecal transplantation in mice. Front Microbiol. 2019;10:2685.PubMed 
    PubMed Central 

    Google Scholar 
    Ji SK, Yan H, Jiang T, Guo CY, Liu JJ, Dong SZ, et al. Preparing the gut with antibiotics enhances gut microbiota reprogramming efficiency by promoting xenomicrobiota colonization. Front Microbiol. 2017;8:1208.PubMed 
    PubMed Central 

    Google Scholar 
    Divya Ganeshan S, Hosseinidoust Z. Phage therapy with a focus on the human microbiota. Antibiotics (Basel). 2019;8:131.Ramachandran G, Bikard D. Editing the microbiome the CRISPR way. Philos Trans R Soc Lond B Biol Sci. 2019;374:20180103.CAS 
    PubMed 
    PubMed Central 

    Google Scholar  More

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    How colonialism fed the flames of Australia’s catastrophic wildfires

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    The unprecedented fires that devastated parts of Australia in 2020 can be attributed in part to colonialism1.

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    ReferencesMariani, M. et al. Front. Ecol. Environ. https://doi.org/10.1002/fee.2395 (2022).Article 

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    Alternative stable states of the forest mycobiome are maintained through positive feedbacks

    van der Heijden, M. G. A., Martin, F. M., Selosse, M.-A. & Sanders, I. R. Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytol. 205, 1406–1423 (2015).Article 

    Google Scholar 
    McGuire, K. L. Common ectomycorrhizal networks may maintain monodominance in a tropical rain forest. Ecology 88, 567–574 (2007).Article 

    Google Scholar 
    Selosse, M.-A., Richard, F., He, X. & Simard, S. W. Mycorrhizal networks: des liaisons dangereuses? Trends Ecol. Evol. 21, 621–628 (2006).Article 

    Google Scholar 
    Simard, S. W. et al. Net transfer of carbon between ectomycorrhizal tree species in the field. Nature 388, 579–582 (1997).CAS 
    Article 

    Google Scholar 
    Klein, T., Siegwolf, R. T. W. & Korner, C. Belowground carbon trade among tall trees in a temperate forest. Science 352, 342–344 (2016).CAS 
    Article 

    Google Scholar 
    Franklin, O., Näsholm, T., Högberg, P. & Högberg, M. N. Forests trapped in nitrogen limitation—an ecological market perspective on ectomycorrhizal symbiosis. New Phytol. 203, 657–666 (2014).CAS 
    Article 

    Google Scholar 
    Phillips, R. P., Brzostek, E. & Midgley, M. G. The mycorrhizal-associated nutrient economy: a new framework for predicting carbon–nutrient couplings in temperate forests. New Phytol. 199, 41–51 (2013).CAS 
    Article 

    Google Scholar 
    Cheng, L. et al. Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2. Science 337, 1084–1087 (2012).CAS 
    Article 

    Google Scholar 
    Averill, C. & Hawkes, C. V. Ectomycorrhizal fungi slow soil carbon cycling. Ecol. Lett. 19, 937–947 (2016).Article 

    Google Scholar 
    Fukami, T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).Article 

    Google Scholar 
    Steidinger, B. S. et al. Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature 569, 404–408 (2019).CAS 
    Article 

    Google Scholar 
    Averill, C., Turner, B. L. & Finzi, A. C. Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505, 543–545 (2014).CAS 
    Article 

    Google Scholar 
    Terrer, C., Vicca, S., Hungate, B. A., Phillips, R. P. & Prentice, I. C. Mycorrhizal association as a primary control of the CO2 fertilization effect. Science 353, 72–74 (2016).CAS 
    Article 

    Google Scholar 
    Read, D. J. Mycorrhizas in ecosystems. Experientia 47, 376–391 (1991).Article 

    Google Scholar 
    Lu, M. & Hedin, L. O. Global plant–symbiont organization and emergence of biogeochemical cycles resolved by evolution-based trait modelling. Nat. Ecol. Evol. 3, 239–250 (2019).Blanchet, F. G., Cazelles, K. & Gravel, D. Co‐occurrence is not evidence of ecological interactions. Ecol. Lett. 23, 1050–1063 (2020).Article 

    Google Scholar 
    Connor, E. F. & Simberloff, D. The assembly of species communities: chance or competition? Ecology 60, 1132 (1979).Article 

    Google Scholar 
    Molofsky, J. & Bever, J. D. A novel theory to explain species diversity in landscapes: positive frequency dependence and habitat suitability. Proc. R. Soc. Lond. B 269, 2389–2393 (2002).Article 

    Google Scholar 
    Mayfield, M. M. & Levine, J. M. Opposing effects of competitive exclusion on the phylogenetic structure of communities: phylogeny and coexistence. Ecol. Lett. 13, 1085–1093 (2010).Article 

    Google Scholar 
    Beisner, B., Haydon, D. & Cuddington, K. Alternative stable states in ecology. Front. Ecol. Environ. 1, 376–382 (2003).Article 

    Google Scholar 
    Averill, C., Dietze, M. C. & Bhatnagar, J. M. Continental-scale nitrogen pollution is shifting forest mycorrhizal associations and soil carbon stocks. Glob. Change Biol. 24, 4544–4553 (2018).Article 

    Google Scholar 
    Frelich, L. E., Calcote, R. R., Davis, M. B. & Pastor, J. Patch formation and maintenance in an old-growth hemlock-hardwood forest. Ecology 74, 513–527 (1993).Article 

    Google Scholar 
    Davis, M. B., Calcote, R. R., Sugita, S. & Takahara, H. Patchy invasion and the origin of a hemlock-hardwood forest mosaic. Ecology 79, 2641–2659 (1998).
    Google Scholar 
    Jo, I., Fei, S., Oswalt, C. M., Domke, G. M. & Phillips, R. P. Shifts in dominant tree mycorrhizal associations in response to anthropogenic impacts. Sci. Adv. 5, eaav6358 (2019).CAS 
    Article 

    Google Scholar 
    Staver, A. C., Archibald, S. & Levin, S. A. The global extent and determinants of savanna and forest as alternative biome states. Science 334, 230–232 (2011).CAS 
    Article 

    Google Scholar 
    Chen, L. et al. Differential soil fungus accumulation and density dependence of trees in a subtropical forest. Science 366, 124–128 (2019).CAS 
    Article 

    Google Scholar 
    Averill, C., Bhatnagar, J. M., Dietze, M. C., Pearse, W. D. & Kivlin, S. N. Global imprint of mycorrhizal fungi on whole-plant nutrient economics. Proc. Natl Acad. Sci. USA 16, 23163–23168 (2019). https://doi.org/10.1073/pnas.1906655116Hodge, A. & Fitter, A. H. Substantial nitrogen acquisition by arbuscular mycorrhizal fungi from organic material has implications for N cycling. Proc. Natl Acad. Sci. USA 107, 13754–13759 (2010).CAS 
    Article 

    Google Scholar 
    Fernandez, C. W. & Kennedy, P. G. Revisiting the ‘Gadgil effect’: do interguild fungal interactions control carbon cycling in forest soils? New Phytol. 209, 1382–1394 (2016).CAS 
    Article 

    Google Scholar 
    The Forest Inventory and Analysis Database: Database Description and User Guide Version 7.0 for Phase 2 (USDA Forest Service, 2018).Johnson, D. J., Beaulieu, W. T., Bever, J. D. & Clay, K. Conspecific negative density dependence and forest diversity. Science 336, 904–907 (2012).CAS 
    Article 

    Google Scholar 
    van den Hoogen, J. et al. Soil nematode abundance and functional group composition at a global scale. Nature 572, 194–198 (2019).Article 

    Google Scholar 
    NRSP-3 (National Atmospheric Deposition Program, 2015).Wood, S. N. Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models: estimation of semiparametric generalized linear models. J. R. Stat. Soc. B 73, 3–36 (2011).Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).Hartigan, J. & Hartigan, P. The dip test of unimodality. Ann. Stat. 13, 70–84 (1985).Article 

    Google Scholar 
    Dickie, I. A., Hurst, J. M. & Bellingham, P. J. Comment on ‘conspecific negative density dependence and forest diversity’. Science 338, 469–469 (2012).CAS 
    Article 

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

    Google Scholar 
    Omernik, J. M. & Griffith, G. E. Ecoregions of the conterminous United States: evolution of a hierarchical spatial framework. Environ. Manag. 54, 1249–1266 (2014).Article 

    Google Scholar 
    Masek, J. G. et al. North American forest disturbance mapped from a decadal Landsat record. Remote Sens. Environ. 112, 2914–2926 (2008).Article 

    Google Scholar 
    Averill, C. colinaverill/altSS_forest_mycorrhizas: First release to establish Zenodo DOI for Nature Ecology & Evolution. Zenodo https://zenodo.org/record/5744063 (2021). More

  • in

    Mycorrhizal dominance reduces local tree species diversity across US forests

    Smith, S. E. & Read, D. J. Mycorrhizal Symbiosis (Academic Press, 2008).Tedersoo, L., Bahram, M. & Zobel, M. How mycorrhizal associations drive plant population and community biology. Science 367, eaba1223 (2020).CAS 
    Article 

    Google Scholar 
    Connell, J. H. & Lowman, M. D. Low-diversity tropical rain forests: some possible mechanisms for their existence. Am. Nat. 134, 88–119 (1989).Article 

    Google Scholar 
    Brundrett, M. in Advances in Ecological Research, Vol. 21 (eds Begon M. et al.) 171–313 (Academic Press, 1991).Allen, E. B. et al. Patterns and regulation of mycorrhizal plant and fungal diversity. Plant Soil 170, 47–62 (1995).CAS 
    Article 

    Google Scholar 
    Laliberté, E., Lambers, H., Burgess, T. I. & Wright, S. J. Phosphorus limitation, soil-borne pathogens and the coexistence of plant species in hyperdiverse forests and shrublands. New Phytol. 206, 507–521 (2015).Article 

    Google Scholar 
    Bennett, J. A. et al. Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics. Science 355, 181–184 (2017).CAS 
    Article 

    Google Scholar 
    Teste, F. P. et al. Plant-soil feedback and the maintenance of diversity in Mediterranean-climate shrublands. Science 355, 173–176 (2017).CAS 
    Article 

    Google Scholar 
    van der Heijden, M. G. A., Martin, F. M., Selosse, M.-A. & Sanders, I. R. Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytol. 205, 1406–1423 (2015).CAS 
    Article 

    Google Scholar 
    Burrill, E. A. et al. The Forest Inventory and Analysis Database: Database Description and User Guide Version 8.0 for Phase 2 (U.S. Department of Agriculture, Forest Service, 2018).Jo, I., Fei, S., Oswalt, C. M., Domke, G. M. & Phillips, R. P. Shifts in dominant tree mycorrhizal associations in response to anthropogenic impacts. Sci. Adv. 5, eaav6358 (2019).CAS 
    Article 

    Google Scholar 
    Jo, I. & Fei, S. Responses of Dominant Tree-Mycorrhizal Associations to Anthropogenic Impacts in the USA (Purdue Univ. Research Repository, 2019).Read, D. J. Mycorrhizas in ecosystems. Experientia 47, 376–391 (1991).Article 

    Google Scholar 
    Laliberté, E., Zemunik, G. & Turner, B. L. Environmental filtering explains variation in plant diversity along resource gradients. Science 345, 1602–1605 (2014).Article 

    Google Scholar 
    Ricklefs, R. E. Community diversity: relative roles of local and regional processes. Science 235, 167–171 (1987).CAS 
    Article 

    Google Scholar 
    Cleland, D. T. et al. Ecological Subregions: Sections and Subsections for the Conterminous United States. General Technical Report WO-76D (U.S. Department of Agriculture, 2007).Tedersoo, L. & Bahram, M. Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes. Biol. Rev. Camb. Philos. Soc. 94, 1857–1880 (2019).Article 

    Google Scholar 
    Taylor, D. L. et al. A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecol. Monogr. 84, 3–20 (2014).Article 

    Google Scholar 
    Mariotte, P. et al. Plant–soil feedback: bridging natural and agricultural sciences. Trends Ecol. Evol. 33, 129–142 (2018).Article 

    Google Scholar 
    Zemunik, G., Turner, B. L., Lambers, H. & Laliberté, E. Diversity of plant nutrient-acquisition strategies increases during long-term ecosystem development. Nat. Plants 1, 15050 (2015).CAS 
    Article 

    Google Scholar 
    van der Heijden, M. G. A. et al. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396, 69–72 (1998).CAS 
    Article 

    Google Scholar 
    Maherali, H. & Klironomos, J. N. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316, 1746–1748 (2007).CAS 
    Article 

    Google Scholar 
    Lin, G., McCormack, M. L. & Guo, D. Arbuscular mycorrhizal fungal effects on plant competition and community structure. J. Ecol. 103, 1224–1232 (2015).CAS 
    Article 

    Google Scholar 
    Hartnett, D. C. & Wilson, G. W. T. The role of mycorrhizas in plant community structure and dynamics: lessons from grasslands. Plant Soil 244, 319–331 (2002).CAS 
    Article 

    Google Scholar 
    Mangan, S. A. et al. Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466, 752–755 (2010).CAS 
    Article 

    Google Scholar 
    Peh, K. S.-H., Lewis, S. L. & Lloyd, J. Mechanisms of monodominance in diverse tropical tree-dominated systems. J. Ecol. 99, 891–898 (2011).Article 

    Google Scholar 
    ter Steege, H. et al. Hyperdominance in the Amazonian tree flora. Science 342, 1243092 (2013).Article 

    Google Scholar 
    Newman, E. I. & Reddell, P. Relationship between mycorrhizal infection and diversity in vegetation: evidence from the Great Smoky Mountains. Funct. Ecol. 2, 259–262 (1988).Article 

    Google Scholar 
    Bahram, M. et al. Plant nutrient-acquisition strategies drive topsoil microbiome structure and function. New Phytol. 227, 1189–1199 (2020).CAS 
    Article 

    Google Scholar 
    Beisner, B. E., Haydon, D. T. & Cuddington, K. Alternative stable states in ecology. Front. Ecol. Environ. 1, 376–382 (2003).Article 

    Google Scholar 
    Zhu, K., Woodall, C. W. & Clark, J. S. Failure to migrate: lack of tree range expansion in response to climate change. Glob. Change Biol. 18, 1042–1052 (2012).Article 

    Google Scholar 
    Phillips, R. P., Brzostek, E. & Midgley, M. G. The mycorrhizal-associated nutrient economy: a new framework for predicting carbon–nutrient couplings in temperate forests. New Phytol. 199, 41–51 (2013).CAS 
    Article 

    Google Scholar 
    Jenkins, C. N., Van Houtan, K. S., Pimm, S. L. & Sexton, J. O. US protected lands mismatch biodiversity priorities. Proc. Natl Acad. Sci. USA 112, 5081–5086 (2015).CAS 
    Article 

    Google Scholar 
    Chao, A., Chiu, C.-H. & Jost, L. Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. Annu. Rev. Ecol. Evol. Syst. 45, 297–324 (2014).Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2018).Bürkner, P.-C. brms: an R package for Bayesian multilevel models using Stan. J. Stat. Softw. 80, 1–28 (2017).Article 

    Google Scholar 
    Dowle, M. & Srinivasan, A. data.table: Extension of ‘data.frame’ R package version 1.14.0 https://CRAN.R-project.org/package=data.table (2017).Wickham, H., Francois, R., Henry, L. & Müller, K. dplyr: A grammar of data manipulation. R package version 1.0.2 https://CRAN.R-project.org/package=dplyr (2017).Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).Book 

    Google Scholar 
    Kassambara, A. ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 3.3.3 https://CRAN.R-project.org/package=ggpubr (2018).Dunnington, D. ggspatial: Spatial Data Framework for ggplot2. R package version 1.1.1 https://CRAN.R-project.org/package=ggspatial (2018).Hijmans, R. J. raster: Geographic Data Analysis and Modeling. R package version 3.4-5 https://CRAN.R-project.org/package=raster (2019).Wickham, H. Reshaping data with the reshape Package. J. Stat. Softw. 21, 1–20 (2007).Article 

    Google Scholar 
    Pebesma, E. Simple features for R: standardized support for spatial vector data. R. J. 10, 439–446 (2018).Article 

    Google Scholar 
    Wickham, H. & Henry, L. tidyr: Tidy messy data. R package version 1.1.0 https://CRAN.R-project.org/package=tidyr (2019).Oksanen, J. et al. vegan: Community ecology package. R package version 2.5-6 https://cran.r-project.org/web/packages/vegan/index.html (2017).Forest Inventory and Analysis; https://apps.fs.usda.gov/fia/datamart/CSV/ENTIRE.zipCarteron, A. alexiscarter/mycorrhiza_tree_diversity: custom code https://doi.org/10.5281/ZENODO.5713273 (2021). More

  • in

    Carbon parks could secure essential ecosystems for climate stabilization

    Anderegg, W. R. L. AGU Advances 2, e2021AV000490 (2021).Article 

    Google Scholar 
    Goldstein, A. et al. Nat. Clim. Chang. 10, 287–295 (2020).CAS 
    Article 

    Google Scholar 
    Tanneberger, F. et al. Adv. Sustain. Syst. 5, 2000146 (2021).CAS 
    Article 

    Google Scholar 
    Paustian, K. et al. Nature 532, 49–57 (2016).CAS 
    Article 

    Google Scholar 
    Magill, B. Biden climate plan to save forests pivots on swamps, wetland (1). Bloomberg Law, https://go.nature.com/3gzaYKM (2 November 2021).Meier, J. Designating Dark Sky Areas: Actors and Interests (Routledge, 2014).Climate Action Reserve. Key Accounting Principles for Improved Forest Management Projects within the Forest Protocol (Climate Action Reserve, 2019).Verified Carbon Standard. VM0007 REDD+ Methodology Framework (REDD+ MF), v1.6. verra.org, https://go.nature.com/3GCEKbZ (8 September 2020).PCAF. The Global GHG Accounting and Reporting Standard for the Financial Industry (Partnership for Carbon Accounting Financials, 2021).Xu, J., Morris, P. J., Liu, J. & Holden, J. Catena 160, 134–140 (2018).Article 

    Google Scholar 
    Yu, Z., Loisel, J., Brosseau, D. P., Beilman, D. W. & Hunt, S. J. Geophys. Res. Lett. 37, L13402 (2010).
    Google Scholar 
    Loisel, J. et al. Nat. Clim. Chang. 11, 70–77 (2021).Article 

    Google Scholar 
    Leifeld, J., Wüst-Galley, C. & Page, S. Nat. Clim. Chang. 9, 945–947 (2019).CAS 
    Article 

    Google Scholar 
    Leifeld, J. & Menichetti, L. Nat. Commun. 9, 1071 (2018).CAS 
    Article 

    Google Scholar 
    Juffe-Bignoli, D. et al. Protected Planet Report 2014 (UNEP-WCMC: 2014).Hoyos-Santillan, J., Miranda, A., Lara, A., Rojas, M. & Sepulveda-Jauregui, A. Science 366, 1207–1208 (2019).Article 

    Google Scholar 
    von Unger, M. & Emmer, I. Carbon Market Incentives to Conserve, Restore and Enhance Soil Carbon. (The Nature Conservancy, 2018).Bonn, A. et al. (eds). Peatland Restoration and Ecosystem Services: Science, Policy and Practice (Cambridge Univ. Press, 2016).Buotte, P. C., Law, B. E., Ripple, W. J. & Berner, L. T. Ecol. Appl. 30, e02039 (2020).Article 

    Google Scholar 
    Soto-Navarro, C. et al. Phil. Trans. R. Soc. Lond. B 375, 20190128 (2020).CAS 
    Article 

    Google Scholar  More