Ecology

Reich, P. B. et al. The evolution of plant functional variation: traits, spectra, and strategies. Int. J. Plant Sci. 164, S143–S164 (2003).
Google Scholar 
Cornelissen, J. H. C. et al. A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Aust. J. Bot. 51, 335–380 (2003).
Google Scholar 
Liu, X. J. & Ma, K. P. Plant functional traits concepts, applications and future directions. Sci. Sin. Vitae 45, 325–339 (2015).
Google Scholar 
Diaz, S., Cabido, M. & Casanoves, F. Plant functional traits and environmental filters at a regional scale. J. Veg. Sci. 9, 113–122 (1998).
Google Scholar 
Kraft, N. J. B., Godoy, O. & Levine, J. M. Plant functional traits and the multidimensional nature of species coexistence. Proc. Natl Acad. Sci. USA 112, 797–802 (2015).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Barton, K. E. Tougher and thornier: general patterns in the induction of physical defence traits. Func. Ecol. 30, 181–187 (2016).
Google Scholar 
Adler, P. B., Fajardo, A., Kleinhesselink, A. R. & Kraft, N. J. B. Trait-based tests of coexistence mechanisms. Ecol. Lett. 16, 1294–1306 (2013).PubMed 

Google Scholar 
Wright, S. J. et al. Functional traits and the growth–mortality trade-off in tropical trees. Ecology 91, 3664–3674 (2010).PubMed 

Google Scholar 
Wright, I. J. et al. The worldwide leaf economics spectrum. Nature 428, 821–827 (2004).ADS 
CAS 
PubMed 

Google Scholar 
Ruiz-Jaen, M. C. & Potvin, C. Can we predict carbon stocks in tropical ecosystems from tree diversity? Comparing species and functional diversity in a plantation and a natural forest. New Phytol. 189, 978–987 (2011).PubMed 

Google Scholar 
Grubb, P. J. A positive distrust in simplicity-lessons from plant defences and from competition among plants and among animals. J. Ecol. 80, 585–610 (1992).
Google Scholar 
Hanley, M. E., Lamont, B. B., Fairbanks, M. M. & Rafferty, C. M. Plant structural traits and their role in anti-herbivore defence. Perspect. Plant Ecol. 8, 157–178 (2007).
Google Scholar 
Burns, K. C. Spinescence in the New Zealand flora: parallels with Australia. N. Z. J. Bot. 54, 273–289 (2016).
Google Scholar 
Goheen, J. R., Young, T. P., Keesing, F. & Palmer, T. M. Consequences of herbivory by native ungulates for the reproduction of a savanna tree. J. Ecol. 95, 129–138 (2007).
Google Scholar 
Goldel, B., Kissling, W. D. & Svenning, J.-C. Geographical variation and environmental correlates of functional trait distributions in palms (Arecaceae) across the New World. Bot. J. Linn. Soc. 179, 602–617 (2015).
Google Scholar 
Alves-Silva, E. & Del-Claro, K. Herbivory causes increases in leaf spinescence and fluctuating asymmetry as a mechanism of delayed induced resistance in a tropical savanna tree. Plant Ecol. Evol. 149, 73–80 (2016).
Google Scholar 
Cooper, S. M. & Ginnett, T. F. Spines protect plants against browsing by small climbing mammals. Oecologia 113, 219–221 (1998).ADS 
PubMed 

Google Scholar 
Charles-Dominique, T. et al. Spiny plants, mammal browsers, and the origin of African savannas. Proc. Natl Acad. Sci. USA 113, E5572–E5579 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ratnam, J., Tomlinson, K. W., Rasquinha, D. N. & Sankaran, M. Savannahs of Asia: antiquity, biogeography, and an uncertain future. Philos. Trans. R. Soc. B. 371, 20150305 (2016).
Google Scholar 
Scholes, R. & Archer, S. Tree-grass interactions in savannas. Annu. Rev. Ecol. Syst. 28, 517–544 (1997).
Google Scholar 
Cerling, T. E. Development of grasslands and savannas in East Africa during the Neogene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 97, 241–247 (1992).
Google Scholar 
Brown, R. W. Additions to the flora of the Green River formation. U. S. Geol. Surv. Prof. Paper, U. S. Gov. Print. Off. 154-J, 279–292 (1929).Manchester, S. Oligocene fossil plants of the John Day Formation, Oregon. Or. Geol. 49, 115d–127d (1987).
Google Scholar 
Meyer, H. W. & Manchester, S. R. Oligocene Bridge Creek flora of the John Day Formation, Oregon (Univ. California Press, 1997).Lancucka-Srodoniowa, M. Tortonian flora from the “Gdow Bay” in the south of Poland. Acta Palaeobot. 7, 1–134 (1966).
Google Scholar 
Yuan, J. et al. Rapid drift of the Tethyan Himalaya terrane before two-stage India-Asia collision. Natl Sci. Rev. 8, nwaa173 (2021).PubMed 

Google Scholar 
Spicer, R. A. et al. Why the ‘Uplift of the Tibetan Plateau’is a myth. Natl Sci. Rev. 8, nwaa091 (2021).PubMed 

Google Scholar 
Spicer, R. A. Tibet, the Himalaya, Asian monsoons and biodiversity–In what ways are they related? Plant Divers. 39, 233–244 (2017).PubMed 
PubMed Central 

Google Scholar 
DeCelles, P. G., Kapp, P., Gehrels, G. E. & Ding, L. Paleocene-Eocene foreland basin evolution in the Himalaya of southern Tibet and Nepal: implications for the age of initial India-Asia collision. Tectonics 33, 824–849 (2014).ADS 

Google Scholar 
Royden, L. H., Burchfiel, B. C. & van der Hilst, R. D. The geological evolution of the Tibetan Plateau. Science 321, 1054–1058 (2008).ADS 
CAS 
PubMed 

Google Scholar 
Deng, T., Wu, F. X., Zhou, Z. K. & Su, T. Tibetan Plateau: an evolutionary junction for the history of modern biodiversity. Sci. China Earth Sci. 63, 172–187 (2020).ADS 

Google Scholar 
Favre, A. et al. The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas. Biol. Rev. 90, 236–253 (2015).PubMed 

Google Scholar 
Su, T. et al. A Middle Eocene lowland humid subtropical “Shangri-La” ecosystem in central Tibet. Proc. Natl Acad. Sci. USA 117, 32989–32995 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Scientific Expedition Team to the Qinghai-Xizang Plateau. Vegetation of Xizang (Tibet) (Sci. Press, 1988).Liu. X. H. Paleoelevation History and Evolution of the Cenozoic Lunpola basin, Central Tibet. Doctoral thesis (Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 2018).Xiong, Z. Y. et al. The rise and demise of the Paleogene Central Tibetan Valley. Sci. Adv. 8, eabj0944 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Reichgelt, T., West, C. K. & Greenwood, D. R. The relation between global palm distribution and climate. Sci. Rep. 8, 4721 (2018).ADS 
PubMed 
PubMed Central 

Google Scholar 
Farnsworth, A. et al. Paleoclimate model-derived thermal lapse rates: towards increasing precision in paleoaltimetry studies. Earth Planet. Sci. Lett. 564, 116903 (2021).CAS 

Google Scholar 
Spicer, R. A. et al. Why do foliar physiognomic climate estimates sometimes differ from those observed? Insights from taphonomic information loss and a CLAMP case study from the Ganges Delta. Palaeogeogr. Palaeoclimatol. Palaeoecol. 302, 381–395 (2011).
Google Scholar 
Walter, H. Vegetation of the Earth and Ecological Systems of the Geo-biosphere (Springer Berlin Heidelb., 1973).Burley, J. Encyclopedia of Forest Sciences (Acad. Press, 2004).Deng, T. et al. A mammalian fossil from the Dingqing Formation in the Lunpola Basin, northern Tibet, and its relevance to age and paleo-altimetry. Sci. Bull. 57, 261–269 (2012).CAS 

Google Scholar 
Ma, P. F. et al. Late Oligocene-early Miocene evolution of the Lunpola Basin, central Tibetan Plateau, evidences from successive lacustrine records. Gondwana Res. 48, 224–236 (2017).ADS 

Google Scholar 
Hempson, G. P., Archibald, S. & Bond, W. J. A continent-wide assessment of the form and intensity of large mammal herbivory in Africa. Science 350, 1056–1061 (2015).ADS 
CAS 
PubMed 

Google Scholar 
Spicer, R. A. The formation and interpretation of plant fossil assemblages. Adv. Bot. Res. 16, 95–191 (1989).
Google Scholar 
Gibson, D. J. Grasses and Grassland Ecology (Oxford Univ. Press, 2009).Eltringham, S. K. The Hippos: Natural History and Conservation (Princeton Univ. Press, 1999).Jiang, H. et al. Oligocene Koelreuteria (Sapindaceae) from the Lunpola Basin in central Tibet and its implication for early diversification of the genus. J. Asian Earth Sci. 175, 99–108 (2019).ADS 

Google Scholar 
Liu, J. et al. Biotic interchange through lowlands of Tibetan Plateau suture zones during Paleogene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 524, 33–40 (2019).
Google Scholar 
Jia, L. B. et al. First fossil record of Cedrelospermum (Ulmaceae) from the Qinghai-Tibetan Plateau: implications for morphological evolution and biogeography. J. Syst. Evol. 57, 94–104 (2019).
Google Scholar 
Su, T. et al. No high Tibetan Plateau until the Neogene. Sci. Adv. 5, eaav2189 (2019).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, Y. L., Li, B. Y. & Zheng, D. A discussion on the boundary and area of the Tibetan Plateau in China. Geol. Res. 21, 1–8 (2002).
Google Scholar 
Yao, T. D. et al. From Tibetan Plateau to Third Pole and Pan-Third Pole. Bull. Chin. Acad. Sci. 32, 924–931 (2017).
Google Scholar 
Spicer, R. A., Farnsworth, A. & Su, T. Cenozoic topography, monsoons and biodiversity conservation within the Tibetan Region: an evolving story. Plant Divers. 42, 229–254 (2020).PubMed 
PubMed Central 

Google Scholar 
Liu, X. H., Xu, Q. & Ding, L. Differential surface uplift: Cenozoic paleoelevation history of the Tibetan Plateau. Sci. China Earth Sci. 59, 2105–2120 (2016).ADS 
CAS 

Google Scholar 
Ding, L., Li, Z. Y. & Song, P. P. Core fragments of Tibetan Plateau from Gondwanaland united in Northern Hemisphere. Bull. Chin. Acad. Sci. 32, 945–950 (2017).
Google Scholar 
Deng, T. & Ding, L. Paleoaltimetry reconstructions of the Tibetan Plateau: progress and contradictions. Natl Sci. Rev. 2, 417–437 (2015).CAS 

Google Scholar 
Li, S. F. et al. Orographic evolution of northern Tibet shaped vegetation and plant diversity in eastern Asia. Sci. Adv. 7, eabc7741 (2021).ADS 
PubMed 
PubMed Central 

Google Scholar 
Ding, L. et al. The Andean-type Gangdese Mountains: Paleoelevation record from the Paleocene–Eocene Linzhou Basin. Earth Planet. Sci. Lett. 392, 250–264 (2014).ADS 
CAS 

Google Scholar 
Deng, T. et al. Review: implications of vertebrate fossils for paleo-elevations of the Tibetan Plateau. Glob. Planet. Change 174, 58–69 (2019).ADS 

Google Scholar 
Westerhold, T. et al. An astronomically dated record of Earth’s climate and its predictability over the last 66 million years. Science 369, 1383–1387 (2020).ADS 
CAS 
PubMed 

Google Scholar 
Nemani, R. R. et al. Climate-driven increases in global terrestrial net primary production from 1982 to 1999. Science 300, 1560–1563 (2003).ADS 
CAS 
PubMed 

Google Scholar 
Hopkins, W. G. Introduction to Plant Physiology (John Wiley & Sons, 1999).Sun, J. M., Liu, W. G., Liu, Z. H. & Fu, B. H. Effects of the uplift of the Tibetan Plateau and retreat of Neotethys ocean on the stepwise aridification of mid-latitude Asian interior. Bull. Chin. Acad. Sci. 32, 951–958 (2017).
Google Scholar 
Zong, G. F. Cenezoic Mammals and Environment of Hengduan Mountains Region (China Ocean Press, 1996).Deng, T. et al. An Oligocene giant rhino provides insights into Paraceratherium evolution. Commun. Biol. 4, 639 (2021).PubMed 
PubMed Central 

Google Scholar 
Young, T. P., Stanton, M. L. & Christian, C. E. Effects of natural and simulated herbivory on spine lengths of Acacia drepanolobium in Kenya. Oikos 101, 171–179 (2003).
Google Scholar 
Karban, R. & Myers, J. H. Induced plant responses to herbivory. Annu. Rev. Ecol. Syst. 20, 331–348 (1989).
Google Scholar 
Huntly, N. Herbivores and the dynamics of communities and ecosystems. Annu. Rev. Ecol. Syst. 22, 477–503 (1991).
Google Scholar 
Asner, G. P. et al. Large-scale impacts of herbivores on the structural diversity of African savannas. Proc. Natl Acad. Sci. USA 106, 4947–4952 (2009).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sankaran, M., Augustine, D. J. & Ratnam, J. Native ungulates of diverse body sizes collectively regulate long‐term woody plant demography and structure of a semi‐arid savanna. J. Ecol. 101, 1389–1399 (2013).
Google Scholar 
Staver, A. C. & Bond, W. J. Is there a ‘browse trap’? Dynamics of herbivore impacts on trees and grasses in an African savanna. J. Ecol. 102, 595–602 (2014).
Google Scholar 
Bakker, E. S. et al. Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation. Proc. Natl Acad. Sci. USA 113, 847–855 (2016).ADS 
CAS 
PubMed 

Google Scholar 
Spicer, R. A. et al. The topographic evolution of the Tibetan Region as revealed by palaeontology. Palaeobio. Palaeoenv. 101, 213–243 (2021).
Google Scholar 
Rowley, D. B. & Currie, B. S. Palaeo-altimetry of the late Eocene to Miocene Lunpola basin, central Tibet. Nature 439, 677–681 (2006).ADS 
CAS 
PubMed 

Google Scholar 
Sun, J. M. et al. Palynological evidence for the latest Oligocene-early Miocene paleoelevation estimate in the Lunpola Basin, central Tibet. Palaeogeogr. Palaeoclimatol. Palaeoecol. 399, 21–30 (2014).
Google Scholar 
DeCelles, P. G., Kapp, P., Ding, L. & Gehrels, G. E. Late Cretaceous to middle Tertiary basin evolution in the central Tibetan Plateau: Changing environments in response to tectonic partitioning, aridification, and regional elevation gain. Geol. Soc. Am. Bull. 119, 654–680 (2007).ADS 

Google Scholar 
Tang, H. et al. Extinct genus Lagokarpos reveals a biogeographic connection between Tibet and other regions in the Northern Hemisphere during the Paleogene. J. Syst. Evol. 57, 670–677 (2019).
Google Scholar 
Wang, T. X. et al. Fossil fruits of Illigera (Hernandiaceae) from the Eocene of central Tibetan Plateau. J. Syst. Evol. 59, 1276–1286 (2021).
Google Scholar 
Del Rio, C. et al. Asclepiadospermum gen. nov., the earliest fossil record of Asclepiadoideae (Apocynaceae) from the early Eocene of central Qinghai-Tibetan Plateau, and its biogeographic implications. Am. J. Bot. 107, 126–138 (2020).PubMed 

Google Scholar 
Xu, Z. Y. The Tertiary and its petroleum potential in the Lunpola Basin, Tibet. Oil Gas. Geol. 1, 153–158 (1980).
Google Scholar 
Zhang, K. X. et al. Paleogene-Neogene stratigraphic realm and sedimentary sequence of the Qinghai-Tibet Plateau and their response to uplift of the plateau. Sci. China Earth Sci. 53, 1271–1294 (2010).ADS 

Google Scholar 
Wu, Y. F. & Chen, Y. Y. Fossil cyprinid fishes from the late Tertiary of north Xizang, China. Vertebrata Palasiat. 18, 15–20 (1980).
Google Scholar 
Wu, F. X., Miao, D. S., Chang, M. M., Shi, G. L. & Wang, N. Fossil climbing perch and associated plant megafossils indicate a warm and wet central Tibet during the late Oligocene. Sci. Rep. 7, 878 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Cai, C. Y., Huang, D. Y., Wu, F. X., Zhao, M. & Wang, N. Tertiary water striders (Hemiptera, Gerromorpha, Gerridae) from the central Tibetan Plateau and their palaeobiogeographic implications. J. Asian Earth Sci. 175, 121–127 (2017).ADS 

Google Scholar 
Low, S. L. et al. Oligocene Limnobiophyllum (Araceae) from the central Tibetan Plateau and its evolutionary and palaeoenvironmental implications. J. Syst. Palaeontol. 18, 415–431 (2020).
Google Scholar 
Bell, A. D. & Bryan, A. Plant Form: An Illustrated Guide to Flowering Plant Morphology (Timber Press, 2008).Zanne, A. E. et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).ADS 
CAS 
PubMed 

Google Scholar 
Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
Google Scholar 
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 35, 526–528 (2019).CAS 
PubMed 

Google Scholar 
Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E. & Challenger, W. GEIGER: investigating evolutionary radiations. Bioinformatics. 24, 129–131 (2008).CAS 
PubMed 

Google Scholar 
Maddison, W. P. Confounding asymmetries in evolutionary diversification and character change. Evolution 60, 1743–1746 (2006).PubMed 

Google Scholar 
Forest, C. E., Molnar, P. & Emanuel, K. A. Palaeoaltimetry from energy conservation principles. Nature 374, 347–350 (1995).ADS 
CAS 

Google Scholar 
Valdes, P. J. et al. The BRIDGE HadCM3 family of climate models: HadCM3@ Bristol v1.0. Geosci. Model Dev. 10, 3715–3743 (2017).ADS 
CAS 

Google Scholar 
Gough, D. O. Solar interior structure and luminosity variations. Sol. Phys. 74, 21–34 (1981).ADS 
CAS 

Google Scholar 
Foster, G. L., Royer, D. L. & Lunt, D. J. Future climate forcing potentially without precedent in the last 420 million years. Nat. Commun. 8, 14845 (2017).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cox, P. M. Description of the “TRIFFID” Dynamic Global Vegetation Model. 1–16 (Met Office Hadley Centre, 2001).Cox, P., Huntingford, C. & Harding, R. A canopy conductance and photosynthesis model for use in a GCM land surface scheme. J. Hydrol. 212, 79–94 (1998).ADS 

Google Scholar 
McInerney, F. A., Strömberg, C. A. E. & White, J. W. C. The Neogene transition from C3 to C4 grasslands in North America stable carbon isotope ratios of fossil phytoliths. Paleobiology 37, 23–49 (2011).
Google Scholar 
Lu, H. Y. et al. Phytoliths as quantitative indicators for the reconstruction of past environmental conditions in China II: palaeoenvironmental reconstruction in the Loess Plateau. Quat. Sci. Rev. 25, 945–959 (2006).ADS 

Google Scholar  More

The copy numbers for 16S and ITS1 rRNA, and the sequencing depth for all samples are presented in Supplementary File 3 (qPCR data, Sequencing Rarefaction Curves). An average of 14,265.25 reads per housefly sample for the V4 16SrRNA and 16,149.4 reads per housefly sample for the ITS1 were retained after quality filtering. After quality filtering of the egg-laying substrate samples, an average of 10,371.75 reads were retained per sample for the V4 16SrRNA, and an average of 25,479.75 reads were retained per sample for the ITS1 region. The extracted DNA from newly emerged adult houseflies of the Spanish laboratory strain (12 samples in total, newly emerged adults, three replicates from four generations, strain SP100) returned a low copy number for the fungal ITS1 (qPCR data, Supplementary File 3) and a low number of acquired sequencing reads; they were therefore omitted from any further analysis of the fungal microbiota. In addition, the mitochondrial COI phylogeny showed that the Dutch wild-caught strain and the Dutch laboratory strain, which were sampled from the same locality at different times, are in close proximity and form a separate clade from the Spanish lab strain phylotypes (Supplementary File 2).The housefly microbiota alpha-diversity is determined by sampling environmentAbsolute richness (number of ASVs), Shannon index, and Phylogenetic diversity for all housefly strains and developmental stages are shown in Fig. 1. The highest bacterial alpha diversity was observed for the wild-caught housefly population GK0. Strain was an important factor for separating Shannon biodiversity levels both for newly emerged (F = 4.37, P  More

Huxley, J. Evolution. The Modern Synthesis (Allen & Unwin, 1942).Bay, R. A. & Palumbi, S. R. Rapid acclimation ability mediated by transcriptome changes in reef-building corals. Genome Biol. Evol. 7, 1602–1612 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Palumbi, S. R., Barshis, D. J., Traylor-Knowles, N. & Bay, R. A. Mechanisms of reef coral resistance to future climate change. Science 344, 895–898 (2014).CAS 
PubMed 

Google Scholar 
Bang, C. et al. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? Zoology 127, 1–19 (2018).PubMed 

Google Scholar 
Fraune, S., Forêt, S. & Reitzel, A. M. Using Nematostella vectensis to study the interactions between genome, epigenome, and bacteria in a changing environment. Front. Mar. Sci. 3, 1–8 (2016).
Google Scholar 
Kolodny, O. & Schulenburg, H. Opinion piece Microbiome-mediated plasticity directs host evolution along several distinct time scales. Phil. Trans. R. Soc. B 375, 20190589 (2020).Reshef, L., Koren, O., Loya, Y., Zilber-Rosenberg, I. & Rosenberg, E. The coral probiotic hypothesis. Environ. Microbiol. 8, 2068–2073 (2006).CAS 
PubMed 

Google Scholar 
Webster, N. S. & Reusch, T. B. H. Microbial contributions to the persistence of coral reefs. ISME J. 11, 2167–2174 (2017).PubMed 
PubMed Central 

Google Scholar 
Totton, A. K. The British sea anemones. Nature 135, 977–978 (1935).
Google Scholar 
Hand, C. & Uhlinger, K. R. The unique, widely distributed, estuarine sea anemone, Nematostella vectensis Stephenson: a review, new facts, and questions. Estuaries 17, 501–501 (1994).
Google Scholar 
Darling, J. A., Reitzel, A. M. & Finnerty, J. R. Regional population structure of a widely introduced estuarine invertebrate: Nematostella vectensis Stephenson in New England. Mol. Ecol. 13, 2969–2981 (2004).CAS 
PubMed 

Google Scholar 
Darling, J. A. et al. Rising starlet: the starlet sea anemone, Nematostella vectensis. BioEssays 27, 211–221 (2005).CAS 
PubMed 

Google Scholar 
Hand, C. & Uhlinger, K. R. The culture, sexual and asexual reproduction, and growth of the sea anemone Nematostella vectensis. Biol. Bull. 182, 169–176 (1992).CAS 
PubMed 

Google Scholar 
Pearson, C. V. M., Rogers, A. D. & Sheader, M. The genetic structure of the rare lagoonal sea anemone, Nematostella vectensis Stephenson (Cnidaria; Anthozoa) in the United Kingdom based on RAPD analysis. Mol. Ecol. 11, 2285–2293 (2002).CAS 
PubMed 

Google Scholar 
Reitzel, A. M., Darling, J. A., Sullivan, J. C. & Finnerty, J. R. Global population genetic structure of the starlet anemone Nematostella vectensis: multiple introductions and implications for conservation policy. Biol. Invasions 10, 1197–1213 (2008).
Google Scholar 
Stefanik, D. J., Friedman, L. E. & Finnerty, J. R. Collecting, rearing, spawning and inducing regeneration of the starlet sea anemone, Nematostella vectensis. Nat. Protoc. 8, 916–923 (2013).PubMed 

Google Scholar 
Fritzenwanker, J. H. & Technau, U. Induction of gametogenesis in the basal cnidarian Nematostella vectensis (Anthozoa). Dev. Genes Evol. 212, 99–103 (2002).PubMed 

Google Scholar 
Mortzfeld, B. M. et al. Response of bacterial colonization in Nematostella vectensis to development, environment, and biogeography. Environ. Microbiol. 18, 1764–1781 (2016).PubMed 

Google Scholar 
Baldassarre, L. et al. Contribution of maternal and paternal transmission to bacterial colonization in Nematostella vectensis. Front. Microbiol. 12, 2892 (2021).
Google Scholar 
Domin, H. et al. Predicted bacterial interactions affect in vivo microbial colonization dynamics in Nematostella. Front. Microbiol. 9, 728 (2018).Guest, J. J. R. et al. Contrasting patterns of coral bleaching susceptibility in 2010 suggest an adaptive response to thermal stress. PLoS ONE 7, e33353–e33353 (2012).CAS 
PubMed 
PubMed Central 

Google Scholar 
Puisay, A., Pilon, R., Goiran, C. & Hédouin, L. Thermal resistances and acclimation potential during coral larval ontogeny in Acropora pulchra. Mar. Environ. Res. 135, 1–10 (2018).CAS 
PubMed 

Google Scholar 
Van Oppen, M. J. H., Oliver, J. K., Putnam, H. M. & Gates, R. D. Building coral reef resilience through assisted evolution. Proc. Natl Acad. Sci. USA 112, 2313 (2015).
Google Scholar 
Torda, G. et al. Rapid adaptive responses to climate change in corals. Nat. Clim. Change 7, 627–636 (2017).
Google Scholar 
Yu, Xiaopeng et al. Thermal acclimation increases heat tolerance of the scleractinian coral Acropora pruinosa,. Sci. Total Environ. 733, 139319–139319 (2020).CAS 
PubMed 

Google Scholar 
Jury, C. P. & Toonen, R. J. Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans. Proc. R. Soc. B Biol. Sci. 286, 20190614–20190614 (2019).
Google Scholar 
Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G. & van Woesik, R. A global analysis of coral bleaching over the past two decades. Nat. Commun. 10, 5 (2019).
Google Scholar 
Thomas, L. et al. Mechanisms of thermal tolerance in reef-building corals across a fine-grained environmental mosaic: lessons from Ofu,. Am. Samoa. Front. Mar. Sci. 4, 434 (2018).
Google Scholar 
Oliver, T. A. & Palumbi, S. R. Many corals host thermally resistant symbionts in high-temperature habitat. Coral Reefs 30, 241–250 (2011).
Google Scholar 
Kenkel, C. D. & Matz, M. V. Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nat. Ecol. Evol. 1, 14 (2017).Barker, V. Exceptional thermal tolerance of coral reefs in American Samoa a review. Curr. Clim. Change Rep. 4, 427 (2018).
Google Scholar 
Bourne, D., Iida, Y., Uthicke, S. & Smith-Keune, C. Changes in coral-associated microbial communities during a bleaching event. ISME J. 2, 350–63 (2008).CAS 
PubMed 

Google Scholar 
Carrier, T. J. & Reitzel, A. M. The hologenome across environments and the implications of a host-associated microbial repertoire. Front. Microbiol. 8, 802 (2017).Koren, O. & Rosenberg, E. Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl. Environ. Microbiol. 72, 5254–5259 (2006).CAS 
PubMed 
PubMed Central 

Google Scholar 
Littman, R., Willis, B. L. & Bourne, D. G. Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef. Environ. Microbiol. Rep. 3, 651–60 (2011).CAS 
PubMed 

Google Scholar 
Ziegler, M., Seneca, F. O., Yum, L. K., Palumbi, S. R. & Voolstra, C. R. Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat. Commun. 8, 14213–14213 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Thurber, R. V. et al. Metagenomic analysis of stressed coral holobionts. Environ. Microbiol. 11, 2148–2163 (2009).CAS 

Google Scholar 
van Oppen, M. J. H. & Blackall, L. L. Coral microbiome dynamics, functions and design in a changing world. Nat. Rev. Microbiol. 17, 557–567 (2019).PubMed 

Google Scholar 
Moran, N. A. & Yun, Y. Experimental replacement of an obligate insect symbiont. Proc. Natl Acad. Sci. USA 112, 2093–2096 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ainsworth, T. D. T. et al. The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME J. 9, 2261–2274 (2015).CAS 

Google Scholar 
Hester, E. R., Barott, K. L., Nulton, J., Vermeij, M. J. A. & Rohwer, F. L. Stable and sporadic symbiotic communities of coral and algal holobionts. ISME J. 10, 1157–1169 (2016).CAS 
PubMed 

Google Scholar 
Bourne, D. G., Morrow, K. M. & Webster, N. S. Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Annu. Rev. Microbiol. 70, 340 (2016).
Google Scholar 
Pollock, F. J. et al. Reduced diversity and stability of coral-associated bacterial communities and suppressed immune function precedes disease onset in corals. R. Soc. Open Sci. 6, 31312497 (2019).Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723–735 (2008).CAS 
PubMed 

Google Scholar 
Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4, 457–469 (2003).CAS 
PubMed 

Google Scholar 
Hehemann, J. H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912 (2010).CAS 
PubMed 

Google Scholar 
Bourne, D. G. Microbiological assessment of a disease outbreak on corals from Magnetic Island (Great Barrier Reef, Australia). Coral Reefs 24, 304–312 (2005).
Google Scholar 
Leach, W. B., Carrier, T. J. & Reitzel, A. M. Diel patterning in the bacterial community associated with the sea anemone Nematostella vectensis. Ecol. Evol. 9, 9935–9947 (2019).PubMed 
PubMed Central 

Google Scholar 
Pootakham, W. et al. Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea. MicrobiologyOpen 8, e935 (2019).Webster, N. Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification. Sci. Rep. 6, 19324 (2016).Van, K. L., Ae, A., Schupp, P. & Slattery, M. The distribution of dimethylsulfoniopropionate in tropical Pacific coral reef invertebrates. Coral Reefs 25, 321–327 (2006).
Google Scholar 
Rypien, K. L., Ward, J. R. & Azam, F. Antagonistic interactions among coral-associated bacteria. Environ. Microbiol. 12, 28–39 (2010).CAS 
PubMed 

Google Scholar 
Blazejak, A., Erséus, C., Amann, R. & Dubilier, N. Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (oligochaeta) from the Peru margin. Appl. Environ. Microbiol. 71, 1553–1561 (2005).CAS 
PubMed 
PubMed Central 

Google Scholar 
Dubilier, N. et al. Phylogenetic diversity of bacterial endosymbionts in the gutless marine oligochete Olavius loisae (Annelida). Mar. Ecol. Prog. Ser. 178, 271–280 (1999).
Google Scholar 
Rincón-Rosales, R., Lloret, L., Ponce, E. & Martínez-Romero, E. Erratum: Rhizobia with different symbiotic efficiencies nodulate Acaciella angustissima in Mexico, including Sinorhizobium chiapanecum sp. nov. which has common symbiotic genes with Sinorhizobium mexicanum (FEMS Microbiology Ecology (2009) 67 (103-117)). FEMS Microbiol. Ecol. 68, 255–255 (2009).
Google Scholar 
Rosenberg, E. & DeLong, E. F., Stackebrandt, E., Lory, S., Thompson, F. The Prokaryotes—Prokaryotic Biology and Symbiotic Associations. (Springer, 2013).Kimura, H., Higashide, Y. & Naganuma, T. Endosymbiotic microflora of the Vestimentiferan Tubeworm (Lamellibrachia sp.) from a Bathyal Cold Seep. Mar. Biotechnol. 5, 593–603 (2003).CAS 

Google Scholar 
Melillo, A. A., Bakshi, C. S. & Melendez, J. A. Francisella tularensis antioxidants harness reactive oxygen species to restrict macrophage signaling and cytokine production. J. Biol. Chem. 285, 27553–27560 (2010).CAS 
PubMed 
PubMed Central 

Google Scholar 
Rabadi, S. M. et al. Antioxidant defenses of Francisella tularensis modulate macrophage function and production of proinflammatory cytokines. J. Biol. Chem. 291, 5009–5021 (2016).CAS 
PubMed 

Google Scholar 
McBride, M. J. in The Prokaryotes: Other Major Lineages of Bacteria and The Archaea. Vol. 9783642389542, 643–676 (Springer-Verlag Berlin Heidelberg, 2014).Augustin, R., Fraune, S. & Bosch, T. C. G. How Hydra senses and destroys microbes. Semin. Immunol. 22, 54–58 (2010).CAS 
PubMed 

Google Scholar 
Augustin, R. et al. A secreted antibacterial neuropeptide shapes the microbiome of Hydra. Nat. Commun. 8, 698 (2017).Franzenburg, S. et al. Distinct antimicrobial peptide expression determines host species-specific bacterial associations. Proc. Natl Acad. Sci. USA 110, E3730–E3738 (2013).CAS 
PubMed 
PubMed Central 

Google Scholar 
Fraune, S., Abe, Y. & Bosch, T. C. G. G. Disturbing epithelial homeostasis in the metazoan Hydra leads to drastic changes in associated microbiota. Environ. Microbiol. 11, 2361–9 (2009).CAS 
PubMed 

Google Scholar 
Brennan, J. J. et al. Sea anemone model has a single Toll-like receptor that can function in pathogen detection, NF-κB signal transduction, and development. Proc. Natl Acad. Sci. USA 114, E10122–E10131 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Sullivan, J. C. et al. Two alleles of NF-κB in the sea anemone Nematostella vectensis are widely dispersed in nature and encode proteins with distinct activities. PLoS ONE 4, e7311 (2009).Wolenski, F. S. et al. Characterization of the core elements of the NF-B signaling pathway of the sea anemone Nematostella vectensis. Mol. Cell. Biol. 31, 1076–1087 (2011).CAS 
PubMed 

Google Scholar 
Gáliková, M., Klepsatel, P., Senti, G. & Flatt, T. Steroid hormone regulation of C. elegans and Drosophila aging and life history. Exp. Gerontol. 46, 141–147 (2011).PubMed 

Google Scholar 
Taubenheim, J., Kortmann, C. & Fraune, S. Function and evolution of nuclear receptors in environmental-dependent postembryonic development. Front. Cell Dev. Biol. 9, 653792 (2021).PubMed 
PubMed Central 

Google Scholar 
Becker, P. B. & Workman, J. L. Nucleosome remodeling and epigenetics. Cold Spring Harb. Perspect. Biol. 5, a017905–a017905 (2013).PubMed 
PubMed Central 

Google Scholar 
Barno, A. R., Villela, H. D. M., Aranda, M., Thomas, T. & Peixoto, R. S. Host under epigenetic control: a novel perspective on the interaction between microorganisms and corals. BioEssays 43, 2100068.Reitzel, A. M. et al. Physiological and developmental responses to temperature by the sea anemone Nematostella vectensis. Mar. Ecol. Prog. Ser. 484, 115–130 (2013).
Google Scholar 
Chua, C. M., Leggat, W., Moya, A. & Baird, A. H. Temperature affects the early life history stages of corals more than near future ocean acidification. Mar. Ecol. Prog. Ser. 475, 85–92 (2013).
Google Scholar 
Ericson, J. A. et al. Combined effects of two ocean change stressors, warming and acidification, on fertilization and early development of the Antarctic echinoid Sterechinus neumayeri. Polar Biol. 35, 1027–1034 (2012).
Google Scholar 
Sheppard Brennand, H., Soars, N., Dworjanyn, S. A., Davis, A. R. & Byrne, M. Impact of ocean warming and ocean acidification on larval development and calcification in the sea urchin Tripneustes gratilla. PLoS ONE 5, e11372 (2010).Bernal, M. A. et al. Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish. Mol. Ecol. 27, 4516–4528 (2018).CAS 
PubMed 

Google Scholar 
Clark, M. S. et al. Molecular mechanisms underpinning transgenerational plasticity in the green sea urchin Psammechinus miliaris. Sci. Rep. 9, 1–12 (2019).
Google Scholar 
Donelson, J. et al. Rapid transgenerational acclimation of a tropical reef fish to climate change. Nat. Clim. Change 2, 30–32 (2012).
Google Scholar 
Miller, G. M., Watson, S. A., Donelson, J. M., McCormick, M. I. & Munday, P. L. Parental environment mediates impacts of increased carbon dioxide on a coral reef fish. Nat. Clim. Change 2, 858–861 (2012).CAS 

Google Scholar 
Munday, P. L. Transgenerational acclimation of fishes to climate change and ocean acidification. F1000Prime Rep. 6, 99–99 (2014).PubMed 
PubMed Central 

Google Scholar 
Ryu, T. et al. An epigenetic signature for within-generational plasticity of a reef fish to ocean warming. Front. Mar. Sci. 7, 284 (2020).Veilleux, H. et al. Molecular processes of transgenerational acclimation to a warming ocean. Nat. Clim. Change 5, 1074–1078 (2015).CAS 

Google Scholar 
Zhao, C. et al. Transgenerational effects of ocean warming on the sea urchin Strongylocentrotus intermedius. Ecotoxicol. Environ. Saf. 151, 212–219 (2018).CAS 
PubMed 

Google Scholar 
Eirin-Lopez, J. M. & Putnam, H. M. Marine Environmental Epigenetics. Annu. Rev. Mar. Sci. 11, 335–368 (2019).
Google Scholar 
Fallet, M., Luquet, E., David, P. & Cosseau, C. Epigenetic inheritance and intergenerational effects in mollusks. Gene 729, 144166–144166 (2020).CAS 
PubMed 

Google Scholar 
Putnam, H. M. & Gates, R. D. Preconditioning in the reef-building coral Pocillopora damicornis and the potential for trans-generational acclimatization in coral larvae under future climate change conditions. J. Exp. Biol. 218, 2365–2372 (2015).PubMed 

Google Scholar 
Daxinger, L. & Whitelaw, E. Transgenerational epigenetic inheritance: more questions than answers. Genome Res. 20, 1623–1628 (2010).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ptashne, M. Epigenetics: core misconcept. Proc. Natl Acad. Sci. USA 110, 7101–7103 (2013).CAS 
PubMed 
PubMed Central 

Google Scholar 
Rivera, H. E., Chen, C.-Y., Gibson, M. C. & Tarrant, A. M. Plasticity in parental effects confers rapid larval thermal tolerance in the estuarine anemone Nematostella vectensis. J. Exp. Biol. 224, jeb236745 (2021).Hirose, E. & Fukuda, T. Vertical transmission of photosymbionts in the colonial ascidian Didemnum molle: The larval tunic prevents symbionts from attaching to the anterior part of larvae. Zool. Sci. 23, 669–674 (2006).
Google Scholar 
Padilla-Gamiño, J. L., Pochon, X., Bird, C., Concepcion, G. T. & Gates, R. D. From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata. PLoS ONE 7, e38440–e38440 (2012).PubMed 
PubMed Central 

Google Scholar 
Sharp, K. H., Eam, B., John Faulkner, D. & Haygood, M. G. Vertical transmission of diverse microbes in the tropical sponge Corticium sp. Appl. Environ. Microbiol. 73, 622–629 (2007).CAS 
PubMed 

Google Scholar 
Sipkema, D. et al. Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission. Environ. Microbiol. 17, 3807–3821 (2015).CAS 
PubMed 

Google Scholar 
Apprill, A., Marlow, H. Q., Martindale, M. Q. & Rappé, M. S. The onset of microbial associations in the coral Pocillopora meandrina. ISME J. 3, 685–699 (2009).PubMed 

Google Scholar 
Sharp, K. H., Distel, D. & Paul, V. J. Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides. ISME J. 6, 790–801 (2012).CAS 
PubMed 

Google Scholar 
Lesser, M. P., Stat, M. & Gates, R. D. The endosymbiotic dinoflagellates (Symbiodinium sp.) of corals are parasites and mutualists. Coral Reefs 32, 603–611 (2013).
Google Scholar 
Ceh, J., Raina, J. B., Soo, R. M., van Keulen, M. & Bourne, D. G. Coral-bacterial communities before and after a coral mass spawning event on Ningaloo Reef. PLoS ONE 7, e36920 (2012).Ricardo, G. F., Jones, R. J., Negri, A. P. & Stocker, R. That sinking feeling: suspended sediments can prevent the ascent of coral egg bundles. Sci. Rep. 6, 21567 (2016).Leite, D. C. A. D. et al. Broadcast spawning coral Mussismilia Hispida can vertically transfer its associated bacterial core. Front. Microbiol. 8, 176–176 (2017).PubMed 
PubMed Central 

Google Scholar 
Epstein, H. E. et al. Microbiome engineering: enhancing climate resilience in corals. Front. Ecol. Environ. 17, 108 (2019).
Google Scholar 
Peixoto, R. S. et al. Beneficial microorganisms for corals (BMC) Proposed mechanisms for coral health and resilience. Front. Microbiol. 8, 341 (2017).PubMed 
PubMed Central 

Google Scholar 
Chakravarti, L. J., Beltran, V. H. & van Oppen, M. J. H. Rapid thermal adaptation in photosymbionts of reef-building corals. Glob. Change Biol. 23, 4675–4688 (2017).
Google Scholar 
Damjanovic, K., Blackall, L. L., Webster, N. S. & van Oppen, M. J. H. H. The contribution of microbial biotechnology to mitigating coral reef degradation. Microb. Biotechnol. 10, 1236–1243 (2017).PubMed 
PubMed Central 

Google Scholar 
Damjanovic, K., Van Oppen, M. J. H., Menéndez, P. & Blackall, L. L. Experimental inoculation of coral recruits with marine bacteria indicates scope for microbiome manipulation in Acropora tenuis and Platygyra daedalea. Front. Microbiol. 10, 1702 (2019).Rosado, P. M. et al. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 13, 921–936 (2019).CAS 
PubMed 

Google Scholar 
Fraune, S. et al. Bacteria-bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance. ISME J. 9, 1543–1556 (2015).CAS 
PubMed 

Google Scholar 
Fadrosh, D. W. et al. An improved dual-indexing approach for multiplexed 16 S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2, 6 (2014).PubMed 
PubMed Central 

Google Scholar 
Rausch, P. et al. Analysis of factors contributing to variation in the C57BL/6 J fecal microbiota across German animal facilities. Int. J. Med. Microbiol. 306, 343–355 (2016).PubMed 

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

Google Scholar 
Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439–1237439 (2013).PubMed 
PubMed Central 

Google Scholar 
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60–R60 (2011).PubMed 
PubMed Central 

Google Scholar 
Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Shao, M. & Kingsford, C. accurate assembly of transcripts through phase-preserving graph decomposition. Nat. Biotechnol. 35, 1167–1169 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Niknafs, Y. S., Pandian, B., Iyer, H. K., Chinnaiyan, A. M. & Iyer, M. K. TACO produces robust multisample transcriptome assemblies from RNA-seq. Nat. Methods 14, 68–70 (2016).PubMed 
PubMed Central 

Google Scholar 
Pertea, M. & Pertea, G. GFF Utilities: GffRead and GffCompare. F1000Research 9, 304–304 (2020).
Google Scholar 
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).PubMed 
PubMed Central 

Google Scholar 
Liao, Y., Smyth, G. K. & Shi, W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).CAS 
PubMed 

Google Scholar 
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550–550 (2014).PubMed 
PubMed Central 

Google Scholar 
Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29–R29 (2014).PubMed 
PubMed Central 

Google Scholar  More

Understanding the source and fate of microplastics (plastic debris  More

Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbial community function at the single-cell level. Nat Rev Microbiol. 2020;18:241–56.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, et al. The 2018 correlative microscopy techniques roadmap. J Phys D: Appl Phys. 2018;51:443001.Article 
CAS 

Google Scholar 
Endesfelder U. Advances in correlative single-molecule localization microscopy and electron microscopy. NanoBioImaging. 2015;1:29–37.Article 

Google Scholar 
Osborn M, Webster RE, Weber K. Individual microtubules viewed by immunofluorescence and electron microscopy in the same PtK2 cell. J Cell Biol. 1978;77:27–38.Article 

Google Scholar 
Webster RE, Osborn M, Weber K. Visualization of the same PtK2 cytoskeletons by both immunofluorescence and low power electron microscopy. Exp Cell Res. 1978;117:47–61.CAS 
PubMed 
Article 

Google Scholar 
Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, et al. Correlative Light- and Electron Microscopy with chemical tags. J Struct Biol. 2014;186:205–13.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lange F, Agui-Gonzalez P, Riedel D, Phan NTN, Jakobs S, Rizzoli SO. Correlative fluorescence microscopy, transmission electron microscopy and secondary ion mass spectrometry (CLEM-SIMS) for cellular imaging. Plos One. 2021;16:e0240768.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pirozzi NM, Hoogenboom JP, Giepmans BNG. ColorEM: analytical electron microscopy for element-guided identification and imaging of the building blocks of life. Histochem Cell Biol. 2018;150:509–20.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Loussert-Fonta C, Toullec G, Paraecattil AA, Jeangros Q, Krueger T, Escrig S, et al. Correlation of fluorescence microscopy, electron microscopy, and NanoSIMS stable isotope imaging on a single tissue section. Commun Biol. 2020;3:362.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Joosten B, Willemse M, Fransen J, Cambi A, van den Dries K. Super-resolution correlative light and electron microscopy (SR-CLEM) reveals novel ultrastructural insights into dendritic cell podosomes. Front Immunol. 2018;9:1–14.Article 
CAS 

Google Scholar 
Woehl TJ, Kashyap S, Firlar E, Perez-Gonzalez T, Faivre D, Trubitsyn D, et al. Correlative electron and fluorescence microscopy of magnetotactic bacteria in liquid: toward in vivo imaging. Sci Rep. 2014;4:6854.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li J, Zhang H, Menguy N, Benzerara K, Wang F, Lin X, et al. Single-cell resolution of uncultured magnetotactic bacteria via fluorescence-coupled electron microscopy. Appl Environ Microbiol. 2017;83:e00409–17.PubMed 
PubMed Central 

Google Scholar 
Qian XX, Santini CL, Kosta A, Menguy N, Le Guenno H, Zhang W, et al. Juxtaposed membranes underpin cellular adhesion and display unilateral cell division of multicellular magnetotactic prokaryotes. Environ Microbiol. 2020;22:1481–94.CAS 
PubMed 
Article 

Google Scholar 
McGlynn SE, Chadwick GL, O’Neill A, Mackey M, Thor A, Deerinck TJ, et al. Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy. Appl Environ Microbiol. 2018;84:e00399–18.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY, Aslan H, et al. Novel prosthecate bacteria from the candidate phylum Acetothermia. ISME J. 2018;126:2225–37.Article 
CAS 

Google Scholar 
Hapca S, Baveye PC, Wilson C, Lark RM, Otten W. Three-dimensional mapping of soil chemical characteristics at micrometric scale by combining 2D SEM-EDX data and 3D X-Ray CT images. PLoS One. 2015;10:e0137205.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Schluter S, Eickhorst T, Mueller CW. Correlative imaging reveals holistic view of soil microenvironments. Environ Sci Technol. 2019;53:829–37.PubMed 
Article 
CAS 

Google Scholar 
Marlow J, Spietz R, Kim KY, Ellisman M, Girguis P, Hatzenpichler R. Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment. Environ Microbiol. 2021;23:4756–77.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Musat N, Musat F, Weber PK, Pett-Ridge J. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol. 2016;41:114–21.CAS 
PubMed 
Article 

Google Scholar 
Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, et al. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci USA. 2015;112:E194–203.CAS 
PubMed 

Google Scholar 
Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, et al. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol. 2007;9:1878–89.CAS 
PubMed 
Article 

Google Scholar 
Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol. 2020;70:5972–6016.CAS 
PubMed 
Article 

Google Scholar 
Keim CN, Martins JL, de Barros HL, Lins U, MF Structure, behavior, ecology and diversity of multicellular magnetotactic prokaryotes. Magnetoreception and magnetosomes in bacteria. (Springer, Berlin, Heidelberg, 2006):103–32.Abreu F, Silva KT, Martins JL, Lins U. Cell viability in magnetotactic multicellular prokaryotes. Int Microbiol. 2006;9:267–72.CAS 
PubMed 

Google Scholar 
Abreu F, Martins JL, Silveira TS, Keim CN, de Barros HG, Filho FJ, et al. ‘Candidatus Magnetoglobus multicellularis’, a multicellular, magnetotactic prokaryote from a hypersaline environment. Int J Syst Evol Microbiol. 2007;57:1318–22.CAS 
PubMed 
Article 

Google Scholar 
Abreu F, Silva KT, Leao P, Guedes IA, Keim CN, Farina M, et al. Cell adhesion, multicellular morphology, and magnetosome distribution in the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis. Microsc Microanal. 2013;19:535–43.CAS 
PubMed 
Article 

Google Scholar 
Faivre D, Schuler D. Magnetotactic bacteria and magnetosomes. Chem Rev. 2008;108:4875–98.CAS 
PubMed 
Article 

Google Scholar 
Greening C, Lithgow T. Formation and function of bacterial organelles. Nat Rev Microbiol. 2020;18:677–89.CAS 
PubMed 
Article 

Google Scholar 
Uebe R, Schuler D. Magnetosome biogenesis in magnetotactic bacteria. Nat Rev Microbiol. 2016;14:621–37.CAS 
PubMed 
Article 

Google Scholar 
Shapiro OH, Hatzenpichler R, Buckley DH, Zinder SH, Orphan VJ. Multicellular photo-magnetotactic bacteria. Env Microbiol Rep. 2011;3:233–8.Article 

Google Scholar 
Simmons SL, Edwards KJ. Unexpected diversity in populations of the many-celled magnetotactic prokaryote. Environ Microbiol. 2007;9:206–15.CAS 
PubMed 
Article 

Google Scholar 
Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, et al. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environ Microbiol. 2014;16:3398–415.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen JA, Buckley DH, et al. The Green Berry Consortia of the Sippewissett Salt Marsh: millimeter-sized aggregates of diazotrophic unicellular cyanobacteria. Front Microbiol. 2017;8:1–12.Article 

Google Scholar 
Larsen S, Nielsen LP, Schramm A. Cable bacteria associated with long-distance electron transport in New England salt marsh sediment. Env Microbiol Rep. 2015;7:175–9.CAS 
Article 

Google Scholar 
Salman V, Yang TT, Berben T, Klein F, Angert E, Teske A. Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh. ISME J. 2015;9:2503–14.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Mackey KRM, Hunter-Cevera K, Britten GL, Murphy LG, Sogin ML, Huber JA. Seasonal succession and spatial patterns of synechococcus microdiversity in a salt marsh estuary revealed through 16S rRNA gene oligotyping. Front Microbiol. 2017;8.Bowen JL, Morrison HG, Hobbie JE, Sogin ML. Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. ISME J. 2012;6:2014–23.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lewis AT, Gaifulina R, Isabelle M, Dorney J, Woods ML, Lloyd GR, et al. Mirrored stainless steel substrate provides improved signal for Raman spectroscopy of tissue and cells. J Raman Spectrosc. 2017;48:119–25.CAS 
PubMed 
Article 

Google Scholar 
Eder SH, Gigler AM, Hanzlik M, Winklhofer M. Sub-micrometer-scale mapping of magnetite crystals and sulfur globules in magnetotactic bacteria using confocal Raman micro-spectrometry. PLoS One. 2014;9:e107356.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Stoecker K, Dorninger C, Daims H, Wagner M. Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl Environ Microbiol. 2010;76:922–6.CAS 
PubMed 
Article 

Google Scholar 
Daims H, Stoecker K, Wagner M. Fluorescence in situ hybridization for the detection of prokaryotes. Taylor & Francis, 2004; Mol Microbial Ecol:208–28.Daims H, Brühl A, Amann R, Schleifer K-H, Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol. 1999;22:434–44.CAS 
PubMed 
Article 

Google Scholar 
Stahl DA, Amann RI. Development and application of nucleic acid probes. Stackebrandt E and Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. John Wiley & Sons; 1991. p. 205–48.Behrens S, Ruhland C, Inacio J, Huber H, Fonseca A, Spencer-Martins I, et al. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol. 2003;69:1748–58.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wallner G, Amann R, Beisker W. Optimizing fluorescent insitu hybridization with ribosomal-Rna-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry. 1993;14:136–43.CAS 
PubMed 
Article 

Google Scholar 
Zimmermann M, Escrig S, Hubschmann T, Kirf MK, Brand A, Inglis RF, et al. Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS. Front Microbiol. 2015;6:243.PubMed 
PubMed Central 
Article 

Google Scholar 
Grieb A, Bowers RM, Oggerin M, Goudeau D, Lee J, Malmstrom RR, et al. A pipeline for targeted metagenomics of environmental bacteria. Microbiome. 2020;8:21.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Meyer NR, Fortney JL, Dekas AE. NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity. Environ Microbiol. 2021;23:81–98.CAS 
PubMed 
Article 

Google Scholar 
Musat N, Stryhanyuk H, Bombach P, Adrian L, Audinot JN, Richnow HH. The effect of FISH and CARD-FISH on the isotopic composition of (13)C- and (15)N-labeled Pseudomonas putida cells measured by nanoSIMS. Syst Appl Microbiol. 2014;37:267–76.CAS 
PubMed 
Article 

Google Scholar 
Amann R, Fuchs BM. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol. 2008;6:339–48.CAS 
PubMed 
Article 

Google Scholar 
Lee KS, Landry Z, Pereira FC, Wagner M, Berry D, Huang WE, et al. Raman microspectroscopy for microbiology. Nat Rev Methods Primers. 2021;1:1–25.Article 
CAS 

Google Scholar 
Wang Y, Huang WE, Cui L, Wagner M. Single-cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol. 2016;41:34–42.CAS 
PubMed 
Article 

Google Scholar 
Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol. 2015;91:1–16.Article 
CAS 

Google Scholar 
Li J, Liu P, Tamaxia A, Zhang H, Liu Y, Wang J, et al. Diverse intracellular inclusion types within magnetotactic bacteria: implications for biogeochemical cycling in aquatic environments. J Geophys Res Biogeosci. 2021;126:e2021JG006310.CAS 

Google Scholar 
Matanfack GA, Taubert M, Guo S, Houhou R, Bocklitz T, Kusel K, et al. Influence of carbon sources on quantification of deuterium incorporation in heterotrophic bacteria: a Raman-stable isotope labeling approach. Anal Chem. 2020;92:11429–37.CAS 
PubMed 
Article 

Google Scholar 
Amor M, Tharaud M, Gelabert A, Komeili A. Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle. Environ Microbiol. 2020;22:823–31.CAS 
PubMed 
Article 

Google Scholar 
Farina M, Esquivel DMS, Debarros HGPL. Magnetic iron-sulfur crystals from a magnetotactic microorganism. Nature. 1990;343:256–8.CAS 
Article 

Google Scholar 
Wenter R, Wanner G, Schuler D, Overmann J. Ultrastructure, tactic behaviour and potential for sulfate reduction of a novel multicellular magnetotactic prokaryote from North Sea sediments. Environ Microbiol. 2009;11:1493–505.PubMed 
Article 

Google Scholar 
Zhang R, Chen YR, Du HJ, Zhang WY, Pan HM, Xiao T, et al. Characterization and phylogenetic identification of a species of spherical multicellular magnetotactic prokaryotes that produces both magnetite and greigite crystals. Res Microbiol. 2014;165:481–9.CAS 
PubMed 
Article 

Google Scholar 
Teng Z, Zhang Y, Zhang W, Pan H, Xu J, Huang H, et al. Diversity and characterization of multicellular magnetotactic prokaryotes from coral reef habitats of the Paracel Islands, South China Sea. Front Microbiol. 2018;9:2135.PubMed 
PubMed Central 
Article 

Google Scholar 
Bourdoiseau J-A, Jeannin M, Rémazeilles C, Sabot R, Refait P. The transformation of mackinawite into greigite studied by Raman spectroscopy. J Raman Spectrosc. 2011;42:496–504.CAS 
Article 

Google Scholar 
Mann S, Sparks NH, Board RG. Magnetotactic bacteria: microbiology, biomineralization, palaeomagnetism and biotechnology. Adv Microb Physiol. 1990;31:125–81.CAS 
PubMed 
Article 

Google Scholar 
Posfai M, Buseck PR, Bazylinski DA, Frankel RB. Iron sulfides from magnetotactic bacteria: structure, composition, and phase transitions. Am Mineral. 1998;83:1469–81.CAS 
Article 

Google Scholar 
Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science. 2006;313:1642–5.CAS 
PubMed 
Article 

Google Scholar 
Rust MJ, Bates M, Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods. 2006;3:793–5.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol. 2014;16:2568–90.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Smriga S, Samo TJ, Malfatti F, Villareal J, Azam F. Individual cell DNA synthesis within natural marine bacterial assemblages as detected by ‘click’ chemistry. Aquat Microb Ecol. 2014;72:269–80.Article 

Google Scholar 
Siegrist MS, Whiteside S, Jewett JC, Aditham A, Cava F, Bertozzi CR. (D)-Amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem Biol. 2013;8:500–5.CAS 
PubMed 
Article 

Google Scholar 
Keim CN, Abreu F, Lins U, Lins de Barros H, Farina M. Cell organization and ultrastructure of a magnetotactic multicellular organism. J Struct Biol. 2004;145:254–62.PubMed 
Article 

Google Scholar  More

Falkowski, P. et al. The global carbon cycle: a test of our knowledge of Earth as a system. Science 290, 291–296 (2000).Article 

Google Scholar 
McMahon, S. & Parnell, J. Weighing the deep continental biosphere. FEMS Microbiol. Ecol. 87, 113–120 (2014).Article 

Google Scholar 
Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).Article 

Google Scholar 
Gleeson, T., Befus, K. M., Jasechko, S., Luijendijk, E. & Cardenas, M. B. The global volume and distribution of modern groundwater. Nat. Geosci. 9, 161–167 (2016).Article 

Google Scholar 
Stevanović, Z. Karst waters in potable water supply: a global scale overview. Environ. Earth Sci. 78, 662 (2019).Article 

Google Scholar 
Poulson, T. L. & White, W. B. The cave environment. Science 165, 971–981 (1969).Article 

Google Scholar 
Rusterholtz, K. J. & Mallory, L. M. Density, activity, and diversity of bacteria indigenous to a karstic aquifer. Microb. Ecol. 28, 79–99 (1994).Article 

Google Scholar 
Smith, H. J. et al. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol. Ecol. 94, fiy191 (2018).
Google Scholar 
Alexander, M. Introduction to Soil Microbiology (Wiley, 1977).Griebler, C. & Lueders, T. Microbial biodiversity in groundwater ecosystems. Freshw. Biol. 54, 649–677 (2009).Article 

Google Scholar 
Krumholz, L. R., McKinley, J. P., Ulrich, G. A. & Suflita, J. M. Confined subsurface microbial communities in Cretaceous rock. Nature 386, 64–66 (1997).Article 

Google Scholar 
Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3, 328–336 (2018).Article 

Google Scholar 
Magnabosco, C. et al. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust. ISME J. 10, 730–741 (2016).Article 

Google Scholar 
Stevens, T. O. & McKinley, J. P. Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270, 450–455 (1995).Article 

Google Scholar 
Tiago, I. & Veríssimo, A. Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization. Environ. Microbiol. 15, 1687–1706 (2013).Article 

Google Scholar 
Mccollom, T. M. & Amend, J. P. A thermodynamic assessment of energy requirements for biomass synthesis by chemolithoautotrophic micro-organisms in oxic and anoxic environments. Geobiology 3, 135–144 (2005).Article 

Google Scholar 
Momper, L., Jungbluth, S. P., Lee, M. D. & Amend, J. P. Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J. 11, 2319–2333 (2017).Article 

Google Scholar 
Jewell, T. N. M., Karaoz, U., Brodie, E. L., Williams, K. H. & Beller, H. R. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. ISME J. 10, 2106–2117 (2016).Article 

Google Scholar 
Herrmann, M., Rusznyák, A. & Akob, D. M. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl. Environ. Microbiol. 81, 2384–2394 (2015).Peterson, B. J. Aquatic primary productivity and the 14C–CO2 method: a history of the productivity problem. Annu. Rev. Ecol. Syst. 11, 359–385 (1980).Article 

Google Scholar 
Viviani, D. A., Karl, D. M. & Church, M. J. Variability in photosynthetic production of dissolved and particulate organic carbon in the North Pacific Subtropical Gyre. Front. Mar. Sci. 2, 73 (2015).Article 

Google Scholar 
Kohlhepp, B. et al. Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate–siliciclastic alternations of the Hainich CZE, central Germany. Hydrol. Earth Syst. Sci. 21, 6091–6116 (2017).Article 

Google Scholar 
Pedersen, K. & Ekendahl, S. Assimilation of CO2 and introduced organic compounds by bacterial communities in groundwater from southeastern Sweden deep crystalline bedrock. Microb. Ecol. 23, 1–14 (1992).Article 

Google Scholar 
Partensky, F. & Garczarek, L. Prochlorococcus: advantages and limits of minimalism. Ann. Rev. Mar. Sci. 2, 305–331 (2010).Article 

Google Scholar 
Karl, D. M., Hebel, D. V., Björkman, K. & Letelier, R. M. The role of dissolved organic matter release in the productivity of the oligotrophic North Pacific Ocean. Limnol. Oceanogr. 43, 1270–1286 (1998).Article 

Google Scholar 
Liang, Y. et al. Estimating primary production of picophytoplankton using the carbon-based ocean productivity model: a preliminary study. Front. Microbiol. 8, 1926 (2017).Article 

Google Scholar 
Steinberg, D. K. et al. Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biogeochemistry. Deep Sea Res. 2 48, 1405–1447 (2001).Article 

Google Scholar 
Gundersen, K., Orcutt, K. M., Purdie, D. A., Michaels, A. F. & Knap, A. H. Particulate organic carbon mass distribution at the Bermuda Atlantic Time-series Study (BATS) site. Deep Sea Res. 2 48, 1697–1718 (2001).Article 

Google Scholar 
Karl, D. M. & Lukas, R. The Hawaii Ocean Time-series (HOT) program: background, rationale and field implementation. Deep Sea Res. 2 43, 129–156 (1996).Article 

Google Scholar 
Martiny, A. C., Vrugt, J. A. & Lomas, M. W. Concentrations and ratios of particulate organic carbon, nitrogen, and phosphorus in the global ocean. Sci. Data 1, 140048 (2014).Article 

Google Scholar 
Martiny, A. C., Vrugt, J. A. & Lomas, M. W. Data from: Concentrations and ratios of particulate organic carbon, nitrogen, and phosphorus in the global ocean. Dryad https://doi.org/10.5061/dryad.d702p (2015).Schwab, V. F. et al. 14C-free carbon Is a major contributor to cellular biomass in geochemically distinct groundwater of shallow sedimentary bedrock aquifers. Water Resour. Res. 55, 2104–2121 (2019).Article 

Google Scholar 
Taubert, M. et al. Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater. ISME J 16, 1153–1162 (2022).Article 

Google Scholar 
Rimstidt, J. D. & Vaughan, D. J. Pyrite oxidation: a state-of-the-art assessment of the reaction mechanism. Geochim. Cosmochim. Acta 67, 873–880 (2003).Article 

Google Scholar 
Lin, W. et al. Genomic insights into the uncultured genus “Candidatus Magnetobacterium” in the phylum Nitrospirae. ISME J. 8, 2463–2477 (2014).Article 

Google Scholar 
Kato, S. et al. Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits. Environ. Microbiol. 20, 862–877 (2018).Article 

Google Scholar 
Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).Article 

Google Scholar 
Kojima, H., Watanabe, T. & Fukui, M. Sulfuricaulis limicola gen. nov., sp. nov., a sulfur oxidizer isolated from a lake. Int. J. Syst. Evol. Microbiol. 66, 266–270 (2016).Article 

Google Scholar 
Strous, M., Van Gerven, E., Kuenen, J. G. & Jetten, M. Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing (anammox) sludge. Appl. Environ. Microbiol. 63, 2446–2448 (1997).Article 

Google Scholar 
Ji, X., Wu, Z., Sung, S. & Lee, P.-H. Metagenomics and metatranscriptomics analyses reveal oxygen detoxification and mixotrophic potentials of an enriched anammox culture in a continuous stirred-tank reactor. Water Res. 166, 115039 (2019).Article 

Google Scholar 
Dalsgaard, T. et al. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression in anammox and denitrification in the oxygen minimum zone off northern Chile. mBio 5, e01966 (2014).Article 

Google Scholar 
Smith, R. L., Böhlke, J. K., Song, B. & Tobias, C. R. Role of anaerobic ammonium oxidation (anammox) in nitrogen removal from a freshwater aquifer. Environ. Sci. Technol. 49, 12169–12177 (2015).Article 

Google Scholar 
Strous, M., Heijnen, J. J., Kuenen, J. G. & Jetten, M. S. M. The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms. Appl. Microbiol. Biotechnol. 50, 589–596 (1998).Article 

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

Google Scholar 
Rittmann, B. E. & McCarty, P. L. Environmental Biotechnology: Principles and Applications (McGraw-Hill Education, 2001).Zhang, Y. et al. Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. Proc. Natl. Acad. Sci. USA 117, 4823–4830 (2020).Article 

Google Scholar 
Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).Article 

Google Scholar 
Lehmann, R. & Totsche, K. U. Multi-directional flow dynamics shape groundwater quality in sloping bedrock strata. J. Hydrol. 580, 124291 (2020).Article 

Google Scholar 
Küsel, K. et al. How deep can surface signals be traced in the Critical Zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape. Front. Earth Sci. 4, 32 (2016).Article 

Google Scholar 
Yan, L. et al. Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Res. 170, 115341 (2019).Article 

Google Scholar 
Pack, M. A. et al. A method for measuring methane oxidation rates using low levels of 14C-labeled methane and accelerator mass spectrometry: methane oxidation rates by AMS. Limnol. Oceanogr. Methods 9, 245–260 (2011).Article 

Google Scholar 
Nielsen, E. S. The use of radio-active carbon (C14) for measuring organic production in the sea. ICES J. Mar. Sci. 18, 117–140 (1952).Article 

Google Scholar 
Xu, X. et al. Modifying a sealed tube zinc reduction method for preparation of AMS graphite targets: reducing background and attaining high precision. Nucl. Instrum. Methods Phys. Res. B 259, 320–329 (2007).Article 

Google Scholar 
Merser, S. Acetabulum online interactive statistical calculators. Accessed Feb, 2021. https://acetabulum.dk/anova.htmlBermuda Oceanographic Timeseries, accessed 21 Oct 2020, http://batsftp.bios.edu/BATS/production/bats_primary_production.txtHawaiian Oceanographic Timeseries, accessed 21 Oct 2020, ftp://ftp.soest.hawaii.edu/hot/primary_productionHawaiian Oceanographic Timeseries, accessed 21 Oct 2020, https://hahana.soest.hawaii.edu/FTP/hot/microscopy/EPIslides.txtKumar, S. et al. Nitrogen loss from pristine carbonate-rock aquifers of the Hainich Critical Zone Exploratory (Germany) is primarily driven by chemolithoautotrophic anammox processes. Front. Microbiol. 8, 1951 (2017).Article 

Google Scholar 
Füssel, J. et al. Nitrite oxidation in the Namibian oxygen minimum zone. ISME J. 6, 1200–1209 (2012).Article 

Google Scholar 
McIlvin, M. R. & Altabet, M. A. Chemical conversion of nitrate and nitrite to nitrous oxide for nitrogen and oxygen isotopic analysis in freshwater and seawater. Anal. Chem. 77, 5589–5595 (2005).Article 

Google Scholar 
Dalsgaard, T., Thamdrup, B., Farías, L. & Revsbech, N. P. Anammox and denitrification in the oxygen minimum zone of the eastern South Pacific. Limnol. Oceanogr. 57, 1331–1346 (2012).Article 

Google Scholar 
Thamdrup, B. et al. Anaerobic ammonium oxidation in the oxygen-deficient waters off northern Chile. Limnol. Oceanogr. 51, 2145–2156 (2006).Article 

Google Scholar 
Taubert, M. et al. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environ. Microbiol. 20, 369–384 (2018).Article 

Google Scholar 
Bushnell, B. BBMap (SourceForge, 2014); http://sourceforge.net/projects/bbmapBornemann, T. L. V. et al. Geological degassing enhances microbial metabolism in the continental subsurface. Preprint at bioRxiv https://doi.org/10.1101/2020.03.07.980714 (2020).Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).Article 

Google Scholar 
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).Article 

Google Scholar 
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).Article 

Google Scholar 
Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016).Article 

Google Scholar 
Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain bacteria. Nature 523, 208–211 (2015).Article 

Google Scholar 
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).Article 

Google Scholar 
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).Article 

Google Scholar 
Murat Eren, A. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).Article 

Google Scholar 
Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).Article 

Google Scholar 
Graham, E. D., Heidelberg, J. F. & Tully, B. J. Potential for primary productivity in a globally-distributed bacterial phototroph. ISME J. 12, 1861–1866 (2018).Article 

Google Scholar 
Kanehisa, M., Sato, Y. & Morishima, K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726–731 (2016).Article 

Google Scholar 
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).Article 

Google Scholar 
Pelikan, C. et al. Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics. Environ. Microbiol. 18, 2994–3009 (2016).Article 

Google Scholar 
Lücker, S., Nowka, B., Rattei, T., Spieck, E. & Daims, H. The genome of Nitrospina gracilis Illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front. Microbiol. 4, 27 (2013).Article 

Google Scholar 
Orellana, L. H., Rodriguez-R, L. M. & Konstantinidis, K. T. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Res. 45, e14 (2017).
Google Scholar 
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2020).
Google Scholar 
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).Article 

Google Scholar 
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-0501-8 (2020).Matsen, F. A., Kodner, R. B. & Armbrust, E. V. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11, 538 (2010).Article 

Google Scholar 
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90 K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).Article 

Google Scholar 
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).Article 

Google Scholar 
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).Article 

Google Scholar 
Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).Article 

Google Scholar 
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).Article 

Google Scholar 
Emiola, A. & Oh, J. High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage. Nat. Commun. 9, 4956 (2018).Article 

Google Scholar 
Wegner, C.-E. et al. Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of the elements nitrogen, sulfur, and carbon. Appl. Environ. Microbiol. 85, e02346-18 (2019).Article 

Google Scholar 
R: A Language and Environment for Statistical Computing (R Core Team, 2018).RStudio: Integrated Development Environment for R (RStudio Team, 2016).Wickham, H. et al. Welcome to the tidyverse. J. Open Source Softw. 4, 1686 (2019).Article 

Google Scholar 
Neuwirth, E. RColorBrewer: ColorBrewer Palettes. R package version 1.1-2. https://CRAN.R-project.org/package=RColorBrewer (2014). More

Weiss, S. et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 10, 1669–1681 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Djokic, T., Kranendonk, M. J. V., Campbell, K. A., Walter, M. R. & Ward, C. R. Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits. Nat. Commun. 8, 1–9 (2017).
Google Scholar 
Damer, B. & Deamer, D. The Hot Spring Hypothesis for an origin of life. Astrobiology 20, 429–452 (2020).ADS 
PubMed 
PubMed Central 

Google Scholar 
Van Kranendonk, M. J. et al. Elements for the origin of life on land: a deep-time perspective from the Pilbara Craton of Western Australia. Astrobiology 21, 39–59 (2021).ADS 
PubMed 

Google Scholar 
Colman, D. R. et al. Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. ISME J. 14, 1316–1331 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Anbar, A. D. & Knoll, A. H. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297, 1137–1142 (2002).ADS 
CAS 
PubMed 

Google Scholar 
Lloyd, K. G. et al. Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. mSystems 3, 431 (2018).
Google Scholar 
Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015).CAS 
PubMed 

Google Scholar 
Nunoura, T. et al. Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ. Microbiol. 7, 1967–1984 (2005).CAS 
PubMed 

Google Scholar 
Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2010).PubMed 
PubMed Central 

Google Scholar 
Rinke, C. et al. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat. Microbiol. 6, 946–959 (2021).CAS 
PubMed 

Google Scholar 
Hua, Z.-S. et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat. Commun. 9, 1–11 (2018).ADS 

Google Scholar 
Takami, H., Arai, W., Takemoto, K., Uchiyama, I. & Taniguchi, T. Functional classification of uncultured ‘Candidatus Caldiarchaeum subterraneum’ using the Maple system. PLoS ONE 10, e0132994 (2015).PubMed 
PubMed Central 

Google Scholar 
Beam, J. P. et al. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community. ISME J. 10, 210–224 (2016).CAS 
PubMed 

Google Scholar 
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).ADS 
CAS 
PubMed 

Google Scholar 
Cole, J. K. et al. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME J. 7, 718–729 (2013).CAS 
PubMed 

Google Scholar 
Peacock, J. P. et al. Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS ONE 8, e59927 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kletzin, A. & Adams, M. W. W. Tungsten in biological systems. FEMS Microbiol. Rev. 18, 5–63 (1996).CAS 
PubMed 

Google Scholar 
Hagedoorn, P. L. et al. Purification and characterization of the tungsten enzyme aldehyde:ferredoxin oxidoreductase from the hyperthermophilic denitrifier Pyrobaculum aerophilum. J. Biol. Inorg. Chem. 10, 259–269 (2005).CAS 
PubMed 

Google Scholar 
de Vries, S. et al. Adaptation to a high-tungsten environment: Pyrobaculum aerophilum contains an active tungsten nitrate reductase. Biochemistry 49, 9911–9921 (2010).PubMed 

Google Scholar 
Bräsen, C., Esser, D., Rauch, B. & Siebers, B. Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol. Mol. Biol. Rev. 78, 89–175 (2014).Kato, S. et al. Long-term cultivation and metagenomics reveal ecophysiology of previously uncultivated thermophiles involved in biogeochemical nitrogen cycle. Microbes Environ. 33, 107–110 (2018).PubMed 
PubMed Central 

Google Scholar 
Costa, K. C. et al. Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles 13, 447–459 (2009).CAS 
PubMed 

Google Scholar 
Mukund, S. & Adams, M. W. The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase. Evidence for its participation in a unique glycolytic pathway. J. Biol. Chem. 266, 14208–14216 (1991).CAS 
PubMed 

Google Scholar 
Mukund, S. & Adams, M. W. W. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase, a novel tungsten-containing enzyme with a potential glycolytic role in the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 270, 8389–8392 (1995).CAS 
PubMed 

Google Scholar 
Roy, R. et al. Purification and molecular characterization of the tungsten-containing formaldehyde ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus: the third of a putative five-member tungstoenzyme family. J. Bacteriol. 181, 1171–1180 (1999).CAS 
PubMed 
PubMed Central 

Google Scholar 
Roy, R. & Adams, M. W. W. Characterization of a fourth tungsten-containing enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 184, 6952–6956 (2002).CAS 
PubMed 
PubMed Central 

Google Scholar 
Bevers, L. E., Bol, E., Hagedoorn, P.-L. & Hagen, W. R. WOR5, a novel tungsten-containing aldehyde oxidoreductase from Pyrococcus furiosus with a broad substrate specificity. J. Bacteriol. 187, 7056–7061 (2005).CAS 
PubMed 
PubMed Central 

Google Scholar 
Habib, U. & Hoffman, M. Effect of molybdenum and tungsten on the reduction of nitrate in nitrate reductase, a DFT study. Chem. Cent. J. 11, 1–12 (2017).
Google Scholar 
Liao, R.-Z. Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J. Biol. Inorg. Chem. 18, 175–181 (2013).CAS 
PubMed 

Google Scholar 
Qian, H.-X. & Liao, R.-Z. QM/MM study of tungsten-dependent benzoyl-coenzyme A reductase: rationalization of regioselectivity and predication of W vs Mo selectivity. Inorg. Chem. 57, 10667–10678 (2018).CAS 
PubMed 

Google Scholar 
Liu, Y.-F., Liao, R.-Z., Ding, W.-J., Yu, J.-G. & Liu, R.-Z. Theoretical investigation of the first-shell mechanism of acetylene hydration catalyzed by a biomimetic tungsten complex. JBIC 16, 745–752 (2011).CAS 
PubMed 

Google Scholar 
Kerr, P. F. Tungsten-bearing manganese deposit at Golconda, Nevada. Geol. Soc. Am. Bull. 51, 1359–1390 (1940).ADS 
CAS 

Google Scholar 
Mukund, S. & Adams, M. W. W. Molybdenum and vanadium do not replace tungsten in the catalytically active forms of the three tungstoenzymes in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 178, 163–167 (1996).CAS 
PubMed 
PubMed Central 

Google Scholar 
Debnar-Daumler, C., Seubert, A., Schmitt, G. & Heider, J. Simultaneous involvement of a tungsten-containing aldehyde:ferredoxin oxidoreductase and a phenylacetaldehyde dehydrogenase in anaerobic phenylalanine metabolism. J. Bacteriol. 196, 483–492 (2014).PubMed 
PubMed Central 

Google Scholar 
Scott, I. M. et al. A new class of tungsten-containing oxidoreductase in Caldicellulosiruptor, a genus of plant biomass-degrading thermophilic bacteria. Appl. Environ. Microbiol. 81, 7339–7347 (2015).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Scott, I. M. et al. The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis. J. Biol. Chem. 294, 9995–10005 (2019).CAS 
PubMed 
PubMed Central 

Google Scholar 
Johnson, J. L., Rajagopalan, K. V., Mukund, S. & Adams, M. W. Identification of molybdopterin as the organic component of the tungsten cofactor in four enzymes from hyperthermophilic Archaea. J. Biol. Chem. 268, 4848–4852 (1993).CAS 
PubMed 

Google Scholar 
Chan, M. K., Mukund, S., Kletzin, A., Adams, M. W. & Rees, D. C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science 267, 1463–1469 (1995).ADS 
CAS 
PubMed 

Google Scholar 
Glass, J. B. et al. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane‐oxidizing microbial consortia in sulphidic marine sediments. Environ. Microbiol. 16, 1592–1611 (2014).CAS 
PubMed 

Google Scholar 
Li, G.-W., Burkhardt, D., Gross, C. & Weissman, J. S. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157, 624–635 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Behrens, S. et al. Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl. Environ. Microbiol. 74, 3143–3150. https://doi.org/10.1128/AEM.00191-08 (2008).Knapik, K., Becerra, M. & González-Siso, M.-I. Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain. Sci. Rep. 9, 11195 (2019).ADS 
PubMed 
PubMed Central 

Google Scholar 
Roy, R., Dhawan, I. K., Johnson, M. K., Rees, D. C. & Adams, M. W. Aldehyde Ferredoxin Oxidoreductase. 266 (American Cancer Society, 2011).Sevcenco, A.-M. et al. The tungsten metallome of Pyrococcus furiosus. Metallomics 1, 395–402 (2009).CAS 
PubMed 

Google Scholar 
Sakuraba, H. & Ohshima, T. Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway. J. Biosci. Bioeng. 93, 441–448 (2002).CAS 
PubMed 

Google Scholar 
Ma, K., Hutchins, A., Sung, S.-J. S. & Adams, M. W. W. Pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon, Pyrococcus furiosus, functions as a CoA-dependent pyruvate decarboxylase. Proc. Natl Acad. Sci. USA 94, 9608–9613 (1997).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mai, X. & Adams, M. W. Characterization of a fourth type of 2-keto acid-oxidizing enzyme from a hyperthermophilic archaeon: 2-ketoglutarate ferredoxin oxidoreductase from Thermococcus litoralis. J. Bacteriol. 178, 5890–5896 (1996).CAS 
PubMed 
PubMed Central 

Google Scholar 
Adams, M. W. W. & Kletzin, A. Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic archaea. Adv. Prot. Chem. 48, 101–180 (1996).CAS 

Google Scholar 
Mulkidjanian, A. Y., Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Evolutionary primacy of sodium bioenergetics. Biol. Direct 3, 1–19 (2008).
Google Scholar 
Heider, J., Ma, K. & Adams, M. W. W. Purification, characterization, and metabolic function of tungsten-containing aldehyde ferredoxin oxidoreductase from the hyperthermophilic and proteolytic archaeon Thermococcus strain ES-1. J. Bacteriol. 177, 4757–4764 (1995).CAS 
PubMed 
PubMed Central 

Google Scholar 
Schut, G. J. et al. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol. Rev. 37, 182–203 (2013).CAS 
PubMed 

Google Scholar 
Kuhns, M., Trifunović, D., Huber, H. & Müller, V. The Rnf complex is a Na+ coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima. Commun. Biol. 3, 1–10 (2020).
Google Scholar 
Sapra, R., Verhagen, M. F. J. M. & Adams, M. W. W. Purification and characterization of a membrane-bound hydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 182, 3423–3428 (2000).CAS 
PubMed 
PubMed Central 

Google Scholar 
Sapra, R., Bagramyan, K. & Adams, M. W. W. A simple energy-conserving system: Proton reduction coupled to proton translocation. Proc. Natl Acad. Sci. USA 100, 7545–7550 (2003).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Schut, G. J. et al. The role of geochemistry and energetics in the evolution of modern respiratory complexes from a proton-reducing ancestor. Biochim. Biophys. Acta Bioenerg. 1857, 958–970 (2016).CAS 

Google Scholar 
Juszczak, A., Aono, S. & Adams, M. W. The extremely thermophilic eubacterium, Thermotoga maritima, contains a novel iron-hydrogenase whose cellular activity is dependent upon tungsten. J. Biol. Chem. 266, 13834–13841 (1991).CAS 
PubMed 

Google Scholar 
Selig, M., Xavier, K. B., Santos, H. & Schönheit, P. Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga. Arch. Microbiol. 167, 217–232 (1997).CAS 
PubMed 

Google Scholar 
Zhang, Y. & Gladyshev, V. N. Molybdoproteomes and evolution of molybdenum utilization. J. Mol. Biol. 379, 881–899 (2008).CAS 
PubMed 
PubMed Central 

Google Scholar 
Anbar, A. D. et al. A whiff of oxygen before the Great Oxidation Event? Science 317, 1903–1906 (2007).Neubert, N., Nägler, T. F. & Böttcher, M. E. Sulfidity controls molybdenum isotope fractionation into euxinic sediments: evidence from the modern Black Sea. Geology 36, 775–778 (2008).ADS 
CAS 

Google Scholar 
Helz, G. R. et al. Mechanism of molybdenum removal from the sea and its concentration in black shales: EXAFS evidence. Geochim. Cosmochim. Acta 60, 3631–3642 (1996).ADS 
CAS 

Google Scholar 
Shen, Y., Buick, R. & Canfield, D. E. Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410, 77–81 (2001).ADS 
CAS 
PubMed 

Google Scholar 
Dodsworth, J. A. et al. Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov. Int. J. Sys. Evol. Microbiol. 64, 2119–2127 (2014).CAS 

Google Scholar 
Hanada, S., Hiraishi, A., Shimada, K. & Matsuura, K. Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. Int. J. Sys. Evol. Microbiol. 45, 676–681 (1995).CAS 

Google Scholar 
Murugapiran, S. K. et al. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Stand. Genom. Sci. 7, 449–468 (2013).CAS 

Google Scholar 
Kozich, J. J., Westcott, S. L., Baker, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina Sequencing Platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).Friel, A. D. et al. Microbiome shifts associated with the introduction of wild atlantic horseshoe crabs (Limulus polyphemus) into a touch-tank exhibit. Front. Microbiol. 11, 1398 (2020).Hamilton, T. L., Peters, J. W., Skidmore, M. L. & Boyd, E. S. Molecular evidence for an active endogenous microbiome beneath glacial ice. ISME J. 7, 1402–1412 (2013).CAS 
PubMed 
PubMed Central 

Google Scholar 
Courtois, S. et al. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3, 431–439 (2001).CAS 
PubMed 

Google Scholar 
Pernthaler, A. & Pernthaler, J. In Protocols for Nucleic Acid Analysis by Nonradioactive Probes 353, 153–164 (Humana Press, 2007).Pett-Ridge, J. & Weber, P. K. In Microbial Systems Biology 91–136 (Humana, New York, NY, 2022). https://doi.org/10.1007/978-1-0716-1585-0_6Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2020).CAS 

Google Scholar 
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 1–11 (2010).
Google Scholar 
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).Aziz, R. K. et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9, 1–15 (2008).
Google Scholar 
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164–1165 (2011).CAS 
PubMed 

Google Scholar 
Kück, P. & Longo, G. C. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front. Zool. 11, 1–8 (2014).
Google Scholar 
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Jacox, E., Chauve, C., Szöllősi, G. J., Ponty, Y. & Scornavacca, C. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32, 2056–2058 (2016).CAS 
PubMed 

Google Scholar 
Chevenet, F. et al. SylvX: a viewer for phylogenetic tree reconciliations. Bioinformatics 32, 608–610 (2016).CAS 
PubMed 

Google Scholar 
Csűös, M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26, 1910–1912 (2010).
Google Scholar 
Yang, J. et al. The I-TASSER Suite: protein structure and function prediction. Nat. Methods 12, 7–8 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Wu, S., Skolnick, J. & Zhang, Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 5, 17 (2007).PubMed 
PubMed Central 

Google Scholar 
Holm, L. & Rosenstrïm, P. I. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545–W549 (2010).CAS 
PubMed 
PubMed Central 

Google Scholar 
Holm, L. Benchmarking fold detection by DaliLite v.5. Bioinformatics 35, 5326–5327 (2019).CAS 
PubMed 

Google Scholar 
MacQueen, J. In Some Methods for Classification and Analysis of Multivariate Observations 1, 281–297 (1967).Ma, K. & Adams, M. W. W. Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur. J. Bacteriol. 176, 6509–6517 (1994).CAS 
PubMed 
PubMed Central 

Google Scholar  More

Fink, D. et al. Crowdsourcing meets ecology: he misphere wide spatiotemporal species distribution models. AI Mag. 35, 19–30. https://doi.org/10.1609/aimag.v35i2.2533 (2014).Article 

Google Scholar 
Chandler, M. et al. Contribution of citizen science towards international biodiversity monitoring. Biol. Cons. 213, 280–294. https://doi.org/10.1016/j.biocon.2016.09.004 (2017).Article 

Google Scholar 
Schmeller, D. S. et al. Advantages of volunteer-based biodiversity monitoring in Europe. Conserv. Biol. 23, 307–316. https://doi.org/10.1111/j.1523-1739.2008.01125.x (2009).Article 
PubMed 

Google Scholar 
Boakes, E. H. et al. Distorted views of biodiversity: Spatial and temporal bias in species occurrence data. PLoS Biol. https://doi.org/10.1371/journal.pbio.1000385 (2010).Article 
PubMed 
PubMed Central 

Google Scholar 
Follett, R. & Strezov, V. An analysis of citizen science based research: Usage and publication patterns. PLoS ONE https://doi.org/10.1371/journal.pone.0143687 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Zattara, E. E. & Aizen, M. A. Worldwide occurrence records suggest a global decline in bee species richness. One Earth 4, 114–123. https://doi.org/10.1016/j.oneear.2020.12.005 (2021).ADS 
Article 

Google Scholar 
Dickinson, J. L. et al. The current state of citizen science as a tool for ecological research and public engagement. Front. Ecol. Environ. 10, 291–297. https://doi.org/10.1890/110236 (2012).Article 

Google Scholar 
Kosmala, M., Wiggins, A., Swanson, A. & Simmons, B. Assessing data quality in citizen science. Front. Ecol. Environ. 14, 551–560. https://doi.org/10.1002/fee.1436 (2016).Article 

Google Scholar 
Bayraktarov, E. et al. Do big unstructured biodiversity data mean more knowledge?. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2018.00239 (2019).Article 

Google Scholar 
Burgess, H. K. et al. The science of citizen science: Exploring barriers to use as a primary research tool. Biol. Cons. 208, 113–120. https://doi.org/10.1016/j.biocon.2016.05.014 (2017).Article 

Google Scholar 
Isaac, N. J. B. & Pocock, M. J. O. Bias and information in biological records. Biol. J. Lin. Soc. 115, 522–531. https://doi.org/10.1111/bij.12532 (2015).Article 

Google Scholar 
August, T., Fox, R., Roy, D. B. & Pocock, M. J. O. Data-derived metrics describing the behaviour of field-based citizen scientists provide insights for project design and modelling bias. Sci. Rep. https://doi.org/10.1038/s41598-020-67658-3 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Boakes, E. H. et al. Patterns of contribution to citizen science biodiversity projects increase understanding of volunteers’ recording behaviour. Sci. Rep. https://doi.org/10.1038/srep33051 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Di Cecco, G. J. et al. Observing the observers: How participants contribute data to iNaturalist and implications for biodiversity science. Bioscience 71, 1179–1188. https://doi.org/10.1093/biosci/biab093 (2021).Article 

Google Scholar 
Kamp, J., Oppel, S., Heldbjerg, H., Nyegaard, T. & Donald, P. F. Unstructured citizen science data fail to detect long-term population declines of common birds in Denmark. Divers. Distrib. 22, 1024–1035. https://doi.org/10.1111/ddi.12463 (2016).Article 

Google Scholar 
Altwegg, R. & Nichols, J. D. Occupancy models for citizen-science data. Methods Ecol. Evol. 10, 8–21. https://doi.org/10.1111/2041-210x.13090 (2019).Article 

Google Scholar 
Courter, J. R., Johnson, R. J., Stuyck, C. M., Lang, B. A. & Kaiser, E. W. Weekend bias in citizen science data reporting: Implications for phenology studies. Int. J. Biometeorol. 57, 715–720. https://doi.org/10.1007/s00484-012-0598-7 (2013).ADS 
Article 
PubMed 

Google Scholar 
Amano, T., Lamming, J. D. L. & Sutherland, W. J. Spatial gaps in global biodiversity information and the role of citizen science. Bioscience 66, 393–400. https://doi.org/10.1093/biosci/biw022 (2016).Article 

Google Scholar 
Geldmann, J. et al. What determines spatial bias in citizen science? Exploring four recording schemes with different proficiency requirements. Divers. Distrib. 22, 1139–1149. https://doi.org/10.1111/ddi.12477 (2016).Article 

Google Scholar 
Girardello, M. et al. Gaps in butterfly inventory data: A global analysis. Biol. Cons. 236, 289–295. https://doi.org/10.1016/j.biocon.2019.05.053 (2019).Article 

Google Scholar 
Husby, M., Hoset, K. S. & Butler, S. Non-random sampling along rural-urban gradients may reduce reliability of multi-species farmland bird indicators and their trends. Ibis https://doi.org/10.1111/ibi.12896 (2021).Article 

Google Scholar 
Petersen, T. K., Speed, J. D. M., Grøtan, V. & Austrheim, G. Species data for understanding biodiversity dynamics: The what, where and when of species occurrence data collection. Ecol. Solut. Evid. https://doi.org/10.1002/2688-8319.12048 (2021).Article 

Google Scholar 
Egerer, M., Lin, B. B. & Kendal, D. Towards better species identification processes between scientists and community participants. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2019.133738 (2019).Article 
PubMed 

Google Scholar 
Jimenez, M. F., Pejchar, L. & Reed, S. E. Tradeoffs of using place-based community science for urban biodiversity monitoring. Conserv. Sci. Pract. https://doi.org/10.1111/csp2.338 (2021).Article 

Google Scholar 
Branchini, S. et al. Using a citizen science program to monitor coral reef biodiversity through space and time. Biodivers. Conserv. 24, 319–336. https://doi.org/10.1007/s10531-014-0810-7 (2015).Article 

Google Scholar 
Snall, T., Kindvall, O., Nilsson, J. & Part, T. Evaluating citizen-based presence data for bird monitoring. Biol. Cons. 144, 804–810. https://doi.org/10.1016/j.biocon.2010.11.010 (2011).Article 

Google Scholar 
Gardiner, M. M. et al. Lessons from lady beetles: Accuracy of monitoring data from US and UK citizen-science programs. Front. Ecol. Environ. 10, 471–476. https://doi.org/10.1890/110185 (2012).Article 

Google Scholar 
Troudet, J., Grandcolas, P., Blin, A., Vignes-Lebbe, R. & Legendre, F. Taxonomic bias in biodiversity data and societal preferences. Sci. Rep. https://doi.org/10.1038/s41598-017-09084-6 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Johansson, F. et al. Can information from citizen science data be used to predict biodiversity in stormwater ponds?. Sci. Rep. https://doi.org/10.1038/s41598-020-66306-0 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Everett, G. & Geoghegan, H. Initiating and continuing participation in citizen science for natural history. BMC Ecol. https://doi.org/10.1186/s12898-016-0062-3 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Richter, A. et al. The social fabric of citizen science drivers for long-term engagement in the German butterfly monitoring scheme. J. Insect Conserv. 22, 731–743. https://doi.org/10.1007/s10841-018-0097-1 (2018).Article 

Google Scholar 
MacPhail, V. J., Gibson, S. D. & Colla, S. R. Community science participants gain environmental awareness and contribute high quality data but improvements are needed: Insights from Bumble Bee Watch. PeerJ https://doi.org/10.7717/peerj.9141 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Maund, P. R. et al. What motivates the masses: Understanding why people contribute to conservation citizen science projects. Biol. Conserv. https://doi.org/10.1016/j.biocon.2020.108587 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Moczek, N., Nuss, M. & Kohler, J. K. Volunteering in the citizen science project “Insects of Saxony”—The larger the island of knowledge, the longer the bank of questions. Insects https://doi.org/10.3390/insects12030262 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Branchini, S. et al. Participating in a citizen science monitoring program: Implications for environmental education. PLoS ONE https://doi.org/10.1371/journal.pone.0131812 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Kelemen-Finan, J., Scheuch, M. & Winter, S. Contributions from citizen science to science education: An examination of a biodiversity citizen science project with schools in Central Europe. Int. J. Sci. Educ. 40, 2078–2098. https://doi.org/10.1080/09500693.2018.1520405 (2018).Article 

Google Scholar 
Deguines, N., Prince, K., Prevot, A. C. & Fontaine, B. Assessing the emergence of pro-biodiversity practices in citizen scientists of a backyard butterfly survey. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2020.136842 (2020).Article 
PubMed 

Google Scholar 
Peter, M., Diekötter, T., Höffler, T. & Kremer, K. Biodiversity citizen science: Outcomes for the participating citizens. People Nat. 3, 294–311. https://doi.org/10.1002/pan3.10193 (2021).Article 

Google Scholar 
Phillips, T. B., Bailey, R. L., Martin, V., Faulkner-Grant, H. & Bonter, D. N. The role of citizen science in management of invasive avian species: What people think, know, and do. J. Environ. Manage. https://doi.org/10.1016/j.jenvman.2020.111709 (2021).Article 
PubMed 

Google Scholar 
Parrish, J. K. et al. Hoping for optimality or designing for inclusion: Persistence, learning, and the social network of citizen science. Proc. Natl. Acad. Sci. U.S.A. 116, 1894–1901. https://doi.org/10.1073/pnas.1807186115 (2019).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Mac Domhnaill, C., Lyons, S. & Nolan, A. The citizens in citizen science: Demographic, socioeconomic, and health characteristics of biodiversity recorders in Ireland. Citiz. Sci.: Theory Pract. 5, 16. https://doi.org/10.5334/cstp.283 (2020).Article 

Google Scholar 
van der Wal, R., Sharma, N., Mellish, C., Robinson, A. & Siddharthan, A. The role of automated feedback in training and retaining biological recorders for citizen science. Conserv. Biol. 30, 550–561. https://doi.org/10.1111/cobi.12705 (2016).Article 
PubMed 

Google Scholar 
Bloom, E. H. & Crowder, D. W. Promoting data collection in pollinator citizen science projects. Citiz. Sci.: Theory Pract. 5, 3. https://doi.org/10.5334/cstp.217 (2020).Article 

Google Scholar 
Johnston, A., Fink, D., Hochachka, W. M. & Kelling, S. Estimates of observer expertise improve species distributions from citizen science data. Methods Ecol. Evol. 9, 88–97. https://doi.org/10.1111/2041-210x.12838 (2018).Article 

Google Scholar 
Kelling, S. et al. Using semistructured surveys to improve citizen science data for monitoring biodiversity. Bioscience 69, 170–179. https://doi.org/10.1093/biosci/biz010 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Koen, B., Loosveldt, G., Vandenplas, C. & Stoop, I. Response rates in the european social survey: Increasing, decreasing, or a matter of fieldwork efforts?. Surv. Methods: Insights Field https://doi.org/10.13094/SMIF-2018-00003 (2018).Article 

Google Scholar 
Gideon, L. Handbook of Survey Methodology for the Social Sciences (Springer, 2012).Book 

Google Scholar 
Wolf, C., Joye, D., Smith, T. W. & Fu, Y. C. The SAGE Handbook of Survey Methodology (SAGE Publications Ltd, 2016).Book 

Google Scholar 
Richter, A. et al. Motivation and support services in citizen science insect monitoring: A cross-country study. Biol. Conserv. 263, 109325. https://doi.org/10.1016/j.biocon.2021.109325 (2021).Article 

Google Scholar 
Johnston, A., Moran, N., Musgrove, A., Fink, D. & Baillie, S. R. Estimating species distributions from spatially biased citizen science data. Ecol. Model. https://doi.org/10.1016/j.ecolmodel.2019.108927 (2020).Article 

Google Scholar 
Isaac, N. J. B., van Strien, A. J., August, T. A., de Zeeuw, M. P. & Roy, D. B. Statistics for citizen science: Extracting signals of change from noisy ecological data. Methods Ecol. Evol. 5, 1052–1060. https://doi.org/10.1111/2041-210x.12254 (2014).Article 

Google Scholar 
Liao, H.-I., Yeh, S.-L. & Shimojo, S. Novelty vs. familiarity principles in preference decisions: Task context of past experience matters. Front. Psychol. https://doi.org/10.3389/fpsyg.2011.00043 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Park, J., Shimojo, E. & Shimojo, S. Roles of familiarity and novelty in visual preference judgments are segregated across object categories. Proc. Natl. Acad. Sci. U.S.A. 107, 14552–14555. https://doi.org/10.1073/pnas.1004374107 (2010).ADS 
Article 
PubMed 

Google Scholar 
Tiago, P., Gouveia, M. J., Capinha, C., Santos-Reis, M. & Pereira, H. M. The influence of motivational factors on the frequency of participation in citizen science activities. Nat. Conserv.-Bulg. https://doi.org/10.3897/natureconservation.18.13429 (2017).Article 

Google Scholar 
Davis, A., Taylor, C. E. & Martin, J. M. Are pro-ecological values enough? Determining the drivers and extent of participation in citizen science programs. Hum. Dimens. Wildl. 24, 501–514. https://doi.org/10.1080/10871209.2019.1641857 (2019).Article 

Google Scholar 
Bell, S. et al. What counts? Volunteers and their organisations in the recording and monitoring of biodiversity. Biodivers. Conserv. 17, 3443–3454. https://doi.org/10.1007/s10531-008-9357-9 (2008).Article 

Google Scholar 
Toomey, A. H. & Domroese, M. C. Can citizen science lead to positive conservation attitudes and behaviors?. Hum. Ecol. Rev. 20, 50–62 (2013).Article 

Google Scholar 
Dennis, E. B., Morgan, B. J. T., Brereton, T. M., Roy, D. B. & Fox, R. Using citizen science butterfly counts to predict species population trends. Conserv. Biol. 31, 1350–1361. https://doi.org/10.1111/cobi.12956 (2017).Article 
PubMed 

Google Scholar 
Callaghan, C. T., Poore, A. G. B., Major, R. E., Rowley, J. J. L. & Cornwell, W. K. Optimizing future biodiversity sampling by citizen scientists. Proc. R. Soc. B-Biol. Sci. https://doi.org/10.1098/rspb.2019.1487 (2019).Article 

Google Scholar 
Outhwaite, C. L., Gregory, R. D., Chandler, R. E., Collen, B. & Isaac, N. J. B. Complex long-term biodiversity change among invertebrates, bryophytes and lichens. Nat. Ecol. Evol. 4, 384. https://doi.org/10.1038/s41559-020-1111-z (2020).Article 
PubMed 

Google Scholar 
Bowler, D. E. et al. Winners and losers over 35 years of dragonfly and damselfly distributional change in Germany. Divers. Distrib. https://doi.org/10.1111/ddi.13274 (2021).Article 

Google Scholar  More