Ecology

IPCC. Summary for Policymakers. In (Masson-Delmotte, V., P. Zhai, H.-O. Pörtner, D. Roberts, J. Skea, P.R. Shukla, A. Pirani, W. Moufouma-Okia, C. Péan, R. Pidcock, S. Connors, J.B.R. Matthews, Y. Chen, X. Zhou, M.I. Gomis, E. Lonnoy, T. Maycock, M. Tignor, and T. Waterfield, eds) Global Warming of 1.5°C. An IPCC Special Report on the impacts of global warming of 1.5°C above pre-industrial levels and related global greenhouse gas emission pathways, in the context of strengthening the global response to the threat of climate change, sustainable development, and efforts to eradicate poverty. In Press (2018).Malhi, Y. et al. Climate change and ecosystems: Threats, opportunities and solutions. Philos. Trans. R. Soc. B Biol. Sci. 375(1794), 20190104. https://doi.org/10.1098/rstb.2019.0104 (2020).Article 
CAS 

Google Scholar 
McElwee, P. Climate change and biodiversity loss. Curr. Hist. 120(829), 295–300. https://doi.org/10.1525/curh.2021.120.829.295 (2021).Article 

Google Scholar 
Dickinson, M. G., Orme, C. D. L., Suttle, K. B. & Mace, G. M. Separating sensitivity from exposure in assessing extinction risk from climate change. Sci. Rep. 4(1), 6898. https://doi.org/10.1038/srep06898 (2015).Article 
CAS 

Google Scholar 
UNFCCC (United Nations Framework Convention on Climate Change). Global Warming Potentials http://unfccc.int/ghg_data/items/3825.php (2014).BelhadjSlimen, I., Chniter, M., Najar, T. & Ghram, A. Meta-analysis of some physiologic, metabolic and oxidative responses of sheep exposed to environmental heat stress. Livestock Sci. 229, 179–187. https://doi.org/10.1016/j.livsci.2019.09.026 (2019).Article 

Google Scholar 
Wojtas, K., Cwynar, P. & Kołacz, R. Effect of thermal stress on physiological and blood parameters in merino sheep. Bull. Vet. Inst. Pulawy 58(2), 283–288. https://doi.org/10.2478/bvip-2014-0043 (2014).Article 

Google Scholar 
Gavojdian, D., Cziszter, L. T., Budai, C. & Kusza, S. Effects of behavioral reactivity on production and reproduction traits in Dorper sheep breed. J. Vet. Behav. 10(4), 365–368. https://doi.org/10.1016/j.jveb.2015.03.012 (2015).Article 

Google Scholar 
Mehaba, N., Coloma-Garcia, W., Such, X., Caja, G. & Salama, A. A. K. Heat stress affects some physiological and productive variables and alters metabolism in dairy ewes. J. Dairy Sci. 104(1), 1099–1110. https://doi.org/10.3168/jds.2020-18943 (2021).Article 
CAS 

Google Scholar 
Ramón, M., Díaz, C., Pérez-Guzman, M. D. & Carabaño, M. J. Effect of exposure to adverse climatic conditions on production in Manchega dairy sheep. J. Dairy Sci. 99(7), 5764–6577. https://doi.org/10.3168/jds.2016-10909 (2016).Article 
CAS 

Google Scholar 
Mahjoubi, E. et al. The effect of cyclical and severe heat stress on growth performance and metabolism in Afshari lambs1. J. Anim. Sci. 93(4), 1632–1640. https://doi.org/10.2527/jas.2014-8641 (2015).Article 
CAS 

Google Scholar 
dos Hamilton, T. R. S. et al. Evaluation of lasting effects of heat stress on sperm profile and oxidative status of ram semen and epididymal sperm. Oxid. Med. Cell. Longev. 1–12, 2016. https://doi.org/10.1155/2016/1687657 (2016).Article 
CAS 

Google Scholar 
Romo-Barron, C. B. et al. Impact of heat stress on the reproductive performance and physiology of ewes: A systematic review and meta-analyses. Int. J. Biometeorol. 63(7), 949–962. https://doi.org/10.1007/s00484-019-01707-z (2019).Article 
ADS 

Google Scholar 
Caroprese, M. et al. Glucocorticoid effects on sheep peripheral blood mononuclear cell proliferation and cytokine production under in vitro hyperthermia. J. Dairy Sci. 101(9), 8544–8551. https://doi.org/10.3168/jds.2018-14471 (2018).Article 
CAS 

Google Scholar 
Marcone, G., Kaart, T., Piirsalu, P. & Arney, D. R. Panting scores as a measure of heat stress evaluation in sheep with access and with no access to shade. Appl. Anim. Behav. Sci. 240, 105350. https://doi.org/10.1016/j.applanim.2021.105350 (2021).Article 

Google Scholar 
Van Wettere, W. H. E. J. et al. Review of the impact of heat stress on reproductive performance of sheep. J. Anim. Sci. Biotechnol. 12(1), 26. https://doi.org/10.1186/s40104-020-00537-z (2021).Article 

Google Scholar 
Belhadj Slimen, I., Najar, T., Ghram, A. & Abdrrabba, M. Heat stress effects on livestock: Molecular, cellular and metabolic aspects, a review. J. Anim. Physiol. Anim. Nutr. 100(3), 401–412. https://doi.org/10.1111/jpn.12379 (2016).Article 
CAS 

Google Scholar 
Guo, Z., Gao, S., Ouyang, J., Ma, L. & Bu, D. Impacts of heat stress-induced oxidative stress on the milk protein biosynthesis of dairy cows. Animals 11(3), 726. https://doi.org/10.3390/ani11030726 (2021).Article 

Google Scholar 
Liu, Z. et al. Heat stress in dairy cattle alters lipid composition of milk. Sci. Rep. 7(1), 961. https://doi.org/10.1038/s41598-017-01120-9 (2017).Article 
ADS 
CAS 

Google Scholar 
Krishnan, G. et al. Mitigation of the heat stress impact in Livestock reproduction. In Theriogenology (InTech, 2017).
Google Scholar 
Robertson, S. & Friend, M. Strategies to ameliorate heat stress effects on sheep reproduction. In Climate Change and Livestock Production: Recent Advances and Future Perspectives 175–183 (Springer, 2021). https://doi.org/10.1007/978-981-16-9836-1_15.Chapter 

Google Scholar 
Sawyer, G. & Narayan, E. J. A review on the influence of climate change on sheep reproduction. In Comparative Endocrinology of Animals (Intech Open, 2019). https://doi.org/10.5772/intechopen.86799.Chapter 

Google Scholar 
Maurya, V. P., Sejian, V., Kumar, D. & Naqvi, S. M. K. Biological ability of Malpura rams to counter heat stress challenges and its consequences on production performance in a semi-arid tropical environment. Biol. Rhythm. Res. 49(3), 479–493. https://doi.org/10.1080/09291016.2017.1381451 (2018).Article 

Google Scholar 
Shahat, A. M., Rizzoto, G. & Kastelic, J. P. Amelioration of heat stress-induced damage to testes and sperm quality. Theriogenology 158, 84–96. https://doi.org/10.1016/j.theriogenology.2020.08.034 (2020).Article 
CAS 

Google Scholar 
Singh, K. M. et al. Association of heat stress protein 90 and 70 gene polymorphism with adaptability traits in Indian sheep (Ovis aries). Cell Stress Chaperones 22(5), 675–684. https://doi.org/10.1007/s12192-017-0770-4 (2017).Article 
CAS 

Google Scholar 
Kim, E.-S. et al. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment. Heredity 116(3), 255–264. https://doi.org/10.1038/hdy.2015.94 (2016).Article 
CAS 

Google Scholar 
do Paim, T. P., Alves dos Santos, C., de Faria, D. A., Paiva, S. R. & McManus, C. Genomic selection signatures in Brazilian sheep breeds reared in a tropical environment. Livestock Sci. 258, 104865. https://doi.org/10.1016/j.livsci.2022.104865 (2022).Article 

Google Scholar 
Kusza, S. et al. Kompetitive Allele Specific PCR (KASPTM) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition. PeerJ 6, e4416. https://doi.org/10.7717/peerj.4416 (2018).Article 
CAS 

Google Scholar 
Zhang, Y. et al. Technical note: Development and application of KASP assays for rapid screening of 8 genetic defects in Holstein cattle. J. Dairy Sci. 103(1), 619–624. https://doi.org/10.3168/jds.2019-16345 (2020).Article 
CAS 

Google Scholar 
Chaari, A. Molecular chaperones biochemistry and role in neurodegenerative diseases. Int. J. Biol. Macromol. 131, 396–411. https://doi.org/10.1016/j.ijbiomac.2019.02.148 (2019).Article 
CAS 

Google Scholar 
Tripathy, K., Sodhi, M., Kataria, R. S., Chopra, M. & Mukesh, M. In silico analysis of HSP70 gene family in bovine genome. Biochem. Genet. 59(1), 134–158. https://doi.org/10.1007/s10528-020-09994-7 (2021).Article 
CAS 

Google Scholar 
Rehman, S. et al. Genomic identification, evolution and sequence analysis of the heat-shock protein gene family in buffalo. Genes 11(11), 1388. https://doi.org/10.3390/genes11111388 (2020).Article 
CAS 

Google Scholar 
Huo, C. et al. Chronic heat stress negatively affects the immune functions of both spleens and intestinal mucosal system in pigs through the inhibition of apoptosis. Microbial Pathog. 136, 103672. https://doi.org/10.1016/j.micpath.2019.103672 (2019).Article 
CAS 

Google Scholar 
Morange, M. HSFs in development. In Molecular Chaperones in Health and Disease 153–169 (Springer, 2006). https://doi.org/10.1007/3-540-29717-0_7.Chapter 

Google Scholar 
Hoter, A., El-Sabban, M. & Naim, H. The HSP90 family: Structure, regulation, function, and implications in health and disease. Int. J. Mol. Sci. 19(9), 2560. https://doi.org/10.3390/ijms19092560 (2018).Article 
CAS 

Google Scholar 
Vanselow, J., Vernunft, A., Koczan, D., Spitschak, M. & Kuhla, B. Exposure of lactating dairy cows to acute pre-ovulatory heat stress affects granulosa cell-specific gene expression profiles in dominant follicles. PLoS One 11(8), e0160600. https://doi.org/10.1371/journal.pone.0160600 (2016).Article 
CAS 

Google Scholar 
Joy, A. et al. Resilience of small ruminants to climate change and increased environmental temperature: A review. Animals 10(5), 86. https://doi.org/10.3390/ani10050867 (2020).Article 

Google Scholar 
Saravanan, K. A. et al. Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds. Genomics 113(3), 955–963. https://doi.org/10.1016/j.ygeno.2021.02.009 (2021).Article 
CAS 

Google Scholar 
Singh, A. K., Upadhyay, R. C., Malakar, D., Kumar, S. & Singh, S. V. Effect of thermal stress on HSP70 expression in dermal fibroblast of zebu (Tharparkar) and crossbred (Karan-Fries) cattle. J. Therm. Biol 43, 46–53. https://doi.org/10.1016/j.jtherbio.2014.04.006 (2014).Article 
CAS 

Google Scholar 
Verma, N., Gupta, I. D., Verma, A., Kumar, R. & Das, R. Novel SNPs in HSPB8 gene and their association with heat tolerance traits in Sahiwal indigenous cattle. Trop. Anim. Health Prod. 48(1), 175–180. https://doi.org/10.1007/s11250-015-0938-9 (2016).Article 

Google Scholar 
Al-Thuwaini, T. M., Al-Shuhaib, M. B. S. & Hussein, Z. M. A novel T177P missense variant in the HSPA8 gene associated with the low tolerance of Awassi sheep to heat stress. Trop. Anim. Health Prod. 52(5), 2405–2416. https://doi.org/10.1007/s11250-020-02267-w (2020).Article 

Google Scholar 
Onasanya, G. O. et al. Heterozygous single-nucleotide polymorphism genotypes at heat shock protein 70 gene potentially influence thermo-tolerance among four Zebu breeds of Nigeria. Front. Genet. https://doi.org/10.3389/fgene.2021.642213 (2021).Article 

Google Scholar 
Pascal, C. Researches regarding quality of sheep skins obtained from Karakul from Botosani sheep. Biotechnol. Anim. Husband. 27(3), 1123–1130. https://doi.org/10.2298/BAH1103123P (2011).Article 

Google Scholar 
Kevorkian, S. E. M., Zǎuleţ, M., Manea, M. A., Georgescu, S. E. & Costache, M. Analysis of the ORF region of the prion protein gene in the Botosani Karakul sheep breed from Romania. Turk. J. Vet. Anim. Sci. 35(2), 105–109. https://doi.org/10.3906/vet-0909-124 (2011).Article 
CAS 

Google Scholar 
Kusza, S. et al. Mitochondrial DNA variability in Gyimesi Racka and Turcana sheep breeds. Acta Biochim. Pol. 62(2), 273–280. https://doi.org/10.18388/abp.2015_978 (2015).Article 
CAS 

Google Scholar 
Gavojdian, D. et al. Effects of using indigenous heritage sheep breeds in organic and low-input production systems on production efficiency and animal welfare in Romania. Landbauforschung Volkenrode 66(4), 290–297. https://doi.org/10.3220/LBF1483607712000 (2016).Article 

Google Scholar 
Gavojdian, D. et al. Reproduction efficiency and health traits in Dorper, White Dorper, and Tsigai sheep breeds under temperate European conditions. Asian Australas. J. Anim. Sci. 28(4), 599–603. https://doi.org/10.5713/ajas.14.0659 (2015).Article 
CAS 

Google Scholar 
Kusza, S. et al. The genetic variability of Hungarian Tsigai sheep. Archiv Tierzuch 53(3), 309–317 (2010).
Google Scholar 
Kusza, S. et al. Study of genetic differences among Slovak Tsigai populations using microsatellite markers. Czeh J. Anim. Sci. 54(10), 468–474. https://doi.org/10.17221/1670-CJAS (2009).Article 
CAS 

Google Scholar 
Marcos-Carcavilla, A. et al. Polymorphisms in the HSP90AA1 5′ flanking region are associated with scrapie incubation period in sheep. Cell Stress Chaperones 15(4), 343–349. https://doi.org/10.1007/s12192-009-0149-2 (2010).Article 
CAS 

Google Scholar 
Salces-Ortiz, J. et al. Looking for adaptive footprints in the HSP90AA1 ovine gene. BMC Evol. Biol. 15(1), 7. https://doi.org/10.1186/s12862-015-0280-x (2015).Article 
CAS 

Google Scholar 
Toscano, J. H. B. et al. Innate immune responses associated with resistance against Haemonchus contortus in Morada Nova Sheep. J. Immunol. Res. 2019, 1–10. https://doi.org/10.1155/2019/3562672 (2019).Article 
CAS 

Google Scholar 
Estrada-Reyes, Z. M. et al. Signatures of selection for resistance to Haemonchus contortus in sheep and goats. BMC Genom. 20(1), 735. https://doi.org/10.1186/s12864-019-6150-y (2019).Article 
CAS 

Google Scholar 
Caroprese, M., Bradford, B. J. & Rhoads, R. P. Editorial: Impact of climate change on immune responses in agricultural animals. Front. Vet. Sci. https://doi.org/10.3389/fvets.2021.732203 (2021).Article 

Google Scholar 
FAO/IAEA. Agriculture biotechnology laboratory—handbook of laboratory exercises. Seibersdorf: IAEA Laboratories, 18 (2004).Zsolnai, A. & Orbán, L. Accelerated separation of random complex DNA patterns in gels: Comparing the performance of discontinuous and continuous buffers. Electrophoresis 20(7), 1462–1468. https://doi.org/10.1002/(SICI)1522-2683(19990601)20:7%3c1462::AID-ELPS1462%3e3.0.CO;2-0 (1999).Article 
CAS 

Google Scholar 
Cavalcanti, L. C. G. et al. Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus. Pesq. Agrop. Brasil. 52(8), 615–622. https://doi.org/10.1590/s0100-204×2017000800007 (2017).Article 

Google Scholar 
Li, Y. et al. Heat stress-responsive transcriptome analysis in the liver tissue of Hu sheep. Genes 10(5), 395. https://doi.org/10.3390/genes10050395 (2019).Article 
CAS 

Google Scholar 
Younis, F. Expression pattern of heat shock protein genes in sheep. Mansoura Vet. Med. J. 21(1), 1–5. https://doi.org/10.35943/mvmj.2020.21.001 (2020).Article 

Google Scholar 
Yeh F. C., Boyle R., Yang R. C., Ye Z., Mao J. X. & Yeh D. POPGENE version 1.32. Computer program and documentation distributed by the author. http://www.ualberta.ca/∼fyeh/popgene.html (1999).Lê, S., Josse, J. & Husson, F. FactoMineR: A package for multivariate analysis. J. Stat. Softw. 25(1), 1–18. https://doi.org/10.18637/jss.v025.i01 (2008).Article 

Google Scholar 
Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer. https://ggplot2.tidyverse.org (2016) (ISBN 978-3-319-24277-4).R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ (2020). More

Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010).Article 
CAS 

Google Scholar 
Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737–1742 (2007).Article 
CAS 

Google Scholar 
Brown, B. E. Coral bleaching: causes and consequences. Coral Reefs 16, 129–138 (1997).Article 

Google Scholar 
Hoegh-Guldberg, O. Climate change, coral bleaching and the future of the world’s coral reefs. Mar. Freshw. Res. 50, 839–866 (1999).
Google Scholar 
Scheufen, T., Krämer, W. E., Iglesias-Prieto, R. & Enríquez, S. Seasonal variation modulates coral sensibility to heat-stress and explains annual changes in coral productivity. Sci. Rep. 7, 4937 (2017).Article 

Google Scholar 
Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).Article 
CAS 

Google Scholar 
Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).Article 
CAS 

Google Scholar 
Doney, S. C., Fabry, V. J., Feely, R. A. & Kleypas, J. A. Ocean acidification: the other CO2 problem. Annu. Rev. Mar. Sci. 1, 169–192 (2009).Article 

Google Scholar 
Warner, M. E., Fitt, W. K. & Schmidt, G. W. The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae in hospite from four different species of reef coral: a novel approach. Plant Cell Environ. 19, 291–299 (1996).Article 

Google Scholar 
Iglesias-Prieto, R. Temperature-dependent inactivation of photosystem II in symbiotic dinoflagellates. in Proceedings of the 8th International Coral Reef Symposium (eds. Lessios, H. A. & MacIntyre, I. G.) Vol. 2, 1313–1318 (1997).Takahashi, S., Nakamura, T., Sakamizu, M., van Woesik, R. & Yamasaki, H. Repair machinery of symbiotic photosynthesis as the primary target of heat stress for reef-building corals. Plant Cell Physiol. 45, 251–255 (2004).Article 
CAS 

Google Scholar 
Warner, M. E., Fitt, W. K. & Schmidt, G. W. Damage to photosystem II in symbiotic dinoflagellates: a determinant of coral bleaching. Proc. Natl Acad. Sci. USA 96, 8007–8012 (1999).Article 
CAS 

Google Scholar 
Scheufen, T., Iglesias-Prieto, R. & Enríquez, S. Changes in the number of symbionts and Symbiodinium cell pigmentation modulate differentially coral light absorption and photosynthetic performance. Front. Mar. Sci. 4, 309 (2017).Gómez-Campo, K., Enríquez, S. & Iglesias-Prieto, R. A road map for the development of the bleached coral phenotype. Front. Mar. Sci. 9, 806491 (2022).Dahlhoff, E. A. & Somero, G. N. Effects of temperature on mitochondria from abalone (genus Haliotis): adaptive plasticity and its limits. J. Exp. Biol. 185, 151–168 (1993).Article 

Google Scholar 
Kajiwara, K., Nagai, A. & Ueno, S. Examination of the effect of temperature, light intensity and zooxanthellae concentration on calcification and photosynthesis of scleractinian coral Acropora pulchra. J. Sch. Mar. Sci. Technol. 40, 95–103 (1995).
Google Scholar 
Rodolfo-Metalpa, R., Huot, Y. & Ferrier-Pagès, C. Photosynthetic response of the Mediterranean zooxanthellate coral Cladocora caespitosa to the natural range of light and temperature. J. Exp. Biol. 211, 1579–1586 (2008).Article 
CAS 

Google Scholar 
Marshall, A. T. & Clode, P. Calcification rate and the effect of temperature in a zooxanthellate and an azooxanthellate scleractinian reef coral. Coral Reefs 23, 218–224 (2004).Article 

Google Scholar 
Kleypas, J. A., Buddemeier, R. W. & Gattuso, J.-P. The future of coral reefs in an age of global change. Int. J. Earth Sci. 90, 426–437 (2001).Article 
CAS 

Google Scholar 
Orr, J. C. et al. Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437, 681–686 (2005).Article 
CAS 

Google Scholar 
Ries, J. B., Cohen, A. L. & McCorkle, D. C. Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. Geology 37, 1131–1134 (2009).Article 
CAS 

Google Scholar 
Vasquez-Elizondo, R. M. & Enríquez, S. Coralline algal physiology is more adversely affected by elevated temperature than reduced pH. Sci. Rep. 6, 19030 (2016).Article 
CAS 

Google Scholar 
Anthony, K. R., Kline, D. I., Diaz-Pulido, G., Dove, S. & Hoegh-Guldberg, O. Ocean acidification causes bleaching and productivity loss in coral reef builders. Proc. Natl Acad. Sci. USA 105, 17442–17446 (2008).Article 
CAS 

Google Scholar 
Gattuso, J.-P., Allemand, D. & Frankignoulle, M. Photosynthesis and calcification at cellular, organismal and community levels in coral reefs: A review on interactions and control by carbonate chemistry. Am. Zool. 39, 160–183 (1999).Article 
CAS 

Google Scholar 
Langdon, C. & Aktinson, M. J. Effect of elevated pCO2 on photosynthesis and calcification of corals and interactions with seasonal change in temperature/irradiance and nutrient enrichment. J. Geophys. Res. 110, https://doi.org/10.1029/2004JC002576 (2005).Iglesias-Rodriguez, M. D. et al. Phytoplankton calcification in a high-CO2 world. Science 320, 336–340 (2008).Article 
CAS 

Google Scholar 
Krumhardt, K. M., Lovenduski, N. S., Iglesias-Rodriguez, M. D. & Kleypas, J. A. Coccolithophore growth and calcification in a changing ocean. Prog. Oceanogr. 159, 276–295 (2017).Article 

Google Scholar 
Kleypas, J. A. et al. Impact of Ocean Acidification on Coral Reefs and Other Marine Calcifiers: A Case Guide for Future Research Vol. 88 (2005).Comeau, S., Cornwall, C. E., DeCarlo, T. M., Krieger, E. & McCulloch, M. T. Similar controls on calcification under ocean acidification across unrelated coral reef taxa. Glob. Change Biol. 24, 4857–4868 (2018).Article 

Google Scholar 
Kroeker, K. J. et al. Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming. Glob. Change Biol. 19, 1884–1896 (2013).Article 

Google Scholar 
Hoadley, K. D., Pettay, D. T., Dodge, D. & Warner, M. E. Contrasting physiological plasticity in response to environmental stress within different cnidarians and their respective symbionts. Coral Reefs 35, 529–542 (2016).Article 

Google Scholar 
Langdon, C., Albright, R., Baker, A. & Jones, P. Two threatened Caribbean coral species have contrasting responses to combined temperature and acidification stress. Limnol. Oceanogr. 63, 2450–2464 (2018).Article 
CAS 

Google Scholar 
Agostini, S. et al. The effects of thermal and high-CO2 stresses on the metabolism and surrounding microenvironment of the coral Galaxea fascicularis. C. R. Biol. 336, 384–391 (2013).Article 
CAS 

Google Scholar 
Reynaud, S. et al. Interacting effects of CO2 partial pressure and temperature on photosynthesis and calcification in a scleractinian coral. Glob. Change Biol. 9, 1660–1668 (2003).Article 

Google Scholar 
Klein, S. G. et al. Projecting coral responses to intensifying marine heatwaves under ocean acidification. Glob. Change Biol. 28, 1753–1765 (2022).Article 
CAS 

Google Scholar 
Colombo-Pallotta, M. F., Rodríguez-Román, A. & Iglesias-Prieto, R. Calcification in bleached and unbleached Montastraea faveolata: evaluating the role of oxygen and glycerol. Coral Reefs 29, 899–907 (2010).Article 

Google Scholar 
Holcomb, M., Tambutte, E., Allemand, D. & Tambutte, S. Light enhanced calcification in Stylophora pistillata: effects of glucose, glycerol and oxygen. PeerJ 2, e375 (2014).Article 

Google Scholar 
Herfort, L., Thake, B. & Taubner, I. Bicarbonate stimulation of calcification and photosynthesis in two hermatypic corals. J. Phycol. 44, 91–98 (2008).Article 
CAS 

Google Scholar 
Tremblay, P., Fine, M., Maguer, J. F., Grover, R. & Ferrier-Pagès, C. Photosynthate translocation increases in response to low seawater pH in a coral–dinoflagellate symbiosis. Biogeosciences 10, 3997–4007 (2013).Article 

Google Scholar 
Briggs, A. A. & Carpenter, R. C. Contrasting responses of photosynthesis and photochemical efficiency to ocean acidification under different light environments in a calcifying alga. Sci. Rep. 9, 3986 (2019).Suggett, D. J. et al. Light availability determines susceptibility of reef building corals to ocean acidification. Coral Reefs 32, 327–337 (2013).Article 

Google Scholar 
IPCC. Climate change 2007: The physical science basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change 747–845 (2007).IPCC. Climate change 2021: The physical science basis. Working Group I Contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (2021).Wall, C. B., Fan, T. Y. & Edmunds, P. J. Ocean acidification has no effect on thermal bleaching in the coral Seriatopora caliendrum. Coral Reefs 33, 119–130 (2014).Article 

Google Scholar 
Kuffner, I. B., Andersson, A. J., Jokiel, P. L., Rodgers, K. S. & Mackenzie, F. T. Decreased abundance of crustose coralline algae due to ocean acidification. Nat. Geosci. 1, 114–117 (2008).Article 
CAS 

Google Scholar 
LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580 (2018). e6.Article 
CAS 

Google Scholar 
Kemp, D. W. et al. Spatially distinct and regionally endemic Symbiodinium assemblages in the threatened Caribbean reef-building coral Orbicella faveolata. Coral Reefs 34, 535–547 (2015).Article 

Google Scholar 
Enríquez, S., Méndez, E. R., Hoegh-Guldberg, O. & Iglesias-Prieto, R. Key functional role of the optical properties of coral skeletons in coral ecology and evolution. Proc. Biol. Sci. 284, 20161667 (2017).Enríquez, S., Méndez, E. R. & Iglesias-Prieto, R. Multiple scattering on coral skeletons enhances light absorption by symbiotic algae. Limnol. Oceanogr. 50, 1025–1032 (2005).Article 

Google Scholar 
Skirving, W. et al. Remote sensing of coral bleaching using temperature and light: progress towards an operational algorithm. Remote Sens 10, 18 (2017).Article 

Google Scholar 
Warner, M. E., LaJeunesse, T. C., Robison, J. D. & Thur, R. M. The ecological distribution and comparative photobiology of symbiotic dinoflagellates from reef corals in Belize: Potential implications for coral bleaching. Limnol. Oceanogr. 51, 1887–1897 (2006).Article 

Google Scholar 
Krämer, W., Caamaño-Ricken, I., Richter, C. & Bischof, K. Dynamic regulation of photoprotection determines thermal tolerance of two phylotypes of Symbiodinium clade A at two photon flux densities. Photochem. Photobio. 88, 398–413 (2012).Article 

Google Scholar 
Wall, C. B., Mason, R. A. B., Ellis, W. R., Cunning, R. & Gates, R. D. Elevated pCO2 affects tissue biomass composition, but not calcification, in a reef coral under two light regimes. R. Soc. Open Sci. 4, 170683 (2017).Article 
CAS 

Google Scholar 
Baghdasarian, G. et al. Effects of temperature and pCO2 on population regulation of Symbiodinium spp. in a tropical reef coral. Biol. Bull. 232, 123–139 (2017).Article 

Google Scholar 
Cornwall, C. E. et al. Resistance of corals and coralline algae to ocean acidification: physiological control of calcification under natural pH variability. Proc. R. Soc. B Biol. Sci. 285, 20181168 (2018).Article 

Google Scholar 
DeCarlo, T. M., Comeau, S., Cornwall, C. E. & McCulloch, M. T. Coral resistance to ocean acidification linked to increased calcium at the site of calcification. Proc. R. Soc. B Biol. Sci. 285, 20180564 (2018).Article 

Google Scholar 
Davies, S. W., Marchetti, A., Ries, J. B. & Castillo, K. D. Thermal and pCO2 stress elicit divergent transcriptomic responses in a resilient coral. Front. Mar. Sci. 3, 112 (2016).Article 

Google Scholar 
Hernansanz-Agustín, P. & Enríquez, J. A. Generation of reactive oxygen species by mitochondria. Antioxidants 10, 415 (2021).Article 

Google Scholar 
Acín-Pérez, R. et al. ROS-triggered phosphorylation of complex II by Fgr kinase regulates cellular adaptation to fuel use. Cell Metab. 19, 1020–1033 (2014).Article 

Google Scholar 
Burris, J. E., Porter, J. W. & Laing, W. A. Effects of carbon dioxide concentration on coral photosynthesis. Mar. Biol. 75, 113–116 (1983).Article 
CAS 

Google Scholar 
Muscatine, L., Falkowski, P. G., Dubinsky, Z., Cook, P. A. & McCloskey, L. R. The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral. Proc. R. Soc. Lond. B Biol. Sci. 236, 311–324 (1989).Article 

Google Scholar 
Goiran, C., Al-Moghrabi, S., Allemand, D. & Jaubert, J. Inorganic carbon uptake for photosynthesis by the symbiotic coral/dinoflagellate association I. Photosynthetic performances of symbionts and dependence on sea water bicarbonate. J. Exp. Mar. Biol. Ecol. 199, 207–225 (1996).Article 
CAS 

Google Scholar 
Buxton, L., Badger, M. & Ralph, P. Effects of moderate heat stress and dissolved inorganic carbon concentration on photosynthesis and respiration of Symbiodinium sp. (Dinophyceae) in culture and in symbiosis. J. Phycol. 45, 357–365 (2009).Article 
CAS 

Google Scholar 
Lin, Z., Wang, L., Chen, M. & Chen, J. The acute transcriptomic response of coral-algae interactions to pH fluctuation. Mar. Genomics 42, 32–40 (2018).Article 

Google Scholar 
Ziegler, M. et al. Integrating environmental variability to broaden the research on coral responses to future ocean conditions. Glob. Change Biol. 27, 5532–5546 (2021).Article 
CAS 

Google Scholar 
Cornwall, C. E. et al. Global declines in coral reef calcium carbonate production under ocean acidification and warming. Proc. Natl Acad. Sci. 118, e2015265118 (2021).Article 
CAS 

Google Scholar 
Eyre, B. D. et al. Coral reefs will transition to net dissolving before end of century. Science 359, 908–911 (2018).Article 
CAS 

Google Scholar 
Cyronak, T. & Eyre, B. D. The synergistic effects of ocean acidification and organic metabolism on calcium carbonate (CaCO3) dissolution in coral reef sediments. Mar. Chem. 183, 1–12 (2016).Article 
CAS 

Google Scholar 
Eyre, B. D., Andersson, A. J. & Cyronak, T. Benthic coral reef calcium carbonate dissolution in an acidifying ocean. Nat. Clim. Change 4, 969–976 (2014).Article 
CAS 

Google Scholar 
Bedwell-Ivers, H. E. et al. The role of in hospite zooxanthellae photophysiology and reef chemistry on elevated pCO2 effects in two branching Caribbean corals: Acropora cervicornis and Porites divaricata. ICES J. Mar. Sci. 74, 1103–1112 (2016).Article 

Google Scholar 
Pierrot, D., Lewis, E. & Wallace, D. W. R. MS excel program developed for CO2 system calculations (2006).Cayabyab, N. M. & Enríquez, S. Leaf photoacclimatory responses of the tropical seagrass Thalassia testudinum under mesocosm conditions: a mechanistic scaling-up study. N. Phytol. 176, 108–123 (2007).Article 

Google Scholar 
Smith, S. V. & Kinsey, D. W. In Coral Reefs: Research Methods (eds. Stoddart, D. R. & Johannes, R. E.) 469–484 (UNESCO, 1978).Yao, W. & Byrne, R. H. Simplified seawater alkalinity analysis—application to the potentiometric titration of the total alkalinity and carbonate content in sea water. Deep Sea Res. Part Oceanogr. Res. Pap. 45, 1383–1392 (1998).Article 
CAS 

Google Scholar 
Vasquez-Elizondo, R. M. et al. Absorptance determinations on multicellular tissues. Photosynth. Res. 132, 311–324 (2017).Article 
CAS 

Google Scholar 
Whitaker, J. R. & Granum, P. E. An absolute method for protein determination based on the difference in absorbance at 235 and 280 nm. Anal. Biochem. 109, 156–159 (1980).Article 
CAS 

Google Scholar 
Iglesias-Prieto, R., Matta, J. L., Robins, W. A. & Trench, R. K. Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture. Proc. Natl Acad. Sci. USA 89, 10302–10305 (1992).Article 
CAS 

Google Scholar 
Jeffrey, S. W. & Humphrey, G. F. New spectrophotometric equations for determining chlorophyll a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem. Physiol. Pflanz. 167, 191–194 (1975).Article 
CAS 

Google Scholar  More

Lavelle, P., Blanchart, E., Martin, A., Spain, A. V. & Martin, S. Impact of soil fauna on the properties of soils in the humid tropics. In Myths and Science of Soils of the Tropics (eds Lal, R. & Sanchez, P.) 157–185 (Soil Science Society of America, 1992).
Google Scholar 
Eisenhauer, N. The action of an animal ecosystem engineer: Identification of the main mechanisms of earthworm impacts on soil microarthropods. Pedobiologia 53, 343–352 (2010).Article 

Google Scholar 
Eisenhauer, N. & Eisenhauer, E. The “intestines of the soil”: The taxonomic and functional diversity of earthworms—A review for young ecologists. Preprint at https://doi.org/10.32942/osf.io/tfm5y (2020).Gates, G. E. Burmese earthworms, an introduction to the systematics and biology of megadrile oligochaetes with special reference to South-east Asia. Trans. Amer. Phil. Soc. 62, 1–326. https://doi.org/10.2307/1006214 (1972).Article 

Google Scholar 
Blakemore, R. J. Origin and means of dispersal of cosmopolitan Pontodrilus litoralis (Oligocaheta: Megascolecidae). Eur. J. Soil Biol. 443, S3–S8. https://doi.org/10.1016/j.ejsobi.2007.08.041 (2007).Article 

Google Scholar 
Seesamut, T., Sutcharit, C., Jirapatrasilp, P., Chanabun, R. & Panha, S. Morphological and molecular evidence reveal a new species of the earthworm genus Pontodrilus Perrier, 1874 (Clitellata, Megascolecidae) from Thailand and Peninsular Malaysia. Zootaxa 4496, 218–237. https://doi.org/10.11646/zootaxa.4496.1.18 (2018).Article 

Google Scholar 
Seesamut, T., Jirapatrasilp, P., Chanabun, R., Oba, Y. & Panha, S. Size variation and geographical distribution of the luminous earthworm Pontodrilus litoralis (Grube, 1855) (Clitellata, Megascolecidae) in Southeast Asia and Japan. Zookeys 862, 23–43. https://doi.org/10.3897/zookeys.862.35727 (2019).Article 

Google Scholar 
Seesamut, T., Jirapatrasilp, P., Sutcharit, C., Tongkerd, P. & Panha, S. Mitochondrial genetic population structure and variation of the littoral earthworm Pontodrilus longissimus Seesamut and Panha, 2018 along the coast of Thailand. Eur. J. Soil Biol. 93, 103091. https://doi.org/10.1016/j.ejsobi.2019.103091 (2019).Article 

Google Scholar 
Attrill, M. J. A testable linear model for diversity trends in estuaries. J. Anim. Ecol. 71, 262–269. https://doi.org/10.1046/j.1365-2656.2002.00593.x (2002).Article 

Google Scholar 
McLusky, D. S. & Elliott, M. The Estuarine Ecosystem: Ecology, Threats and Management 3rd edn. (Oxford University Press, 2004).Book 

Google Scholar 
Telesh, I. V. & Khlebovich, V. V. Principal processes within the estuarine salinity gradient: A review. Mar. Pollut. Bull. 61, 149–155. https://doi.org/10.1016/j.marpolbul.2010.02.008 (2010).Article 
CAS 

Google Scholar 
Owojori, O. J. & Reinecke, A. J. Effects of natural (flooding and drought) and anthropogenic (copper and salinity) stressors on the earthworm Aporrectodea caliginosa under field conditions. Appl. Soil Ecol. 44, 156–163. https://doi.org/10.1016/j.apsoil.2009.11.006 (2010).Article 

Google Scholar 
Guzyte, G., Sujetoviene, G. & Zaltauskaite, J. Effects of salinity on earthworm (Eisenia fetida). Environ. Eng. 8, 111 (2011).
Google Scholar 
Ganapati, P. N. & Subba Rao, B. V. S. S. R. Salinity tolerance of a littoral oligochaete, Pontodrilus bermudensis Beddard. Proc. Ind. Nat. Sci. Acad. 38, 350–354 (1972).
Google Scholar 
Subba Rao, B. V. S. S. R. Volume regulation in a euryhaline oligochaete, Pontodrilus bermudensis Beddard. Proc. Indian Acad. Sci. 87, 339–347 (1978).Article 

Google Scholar 
Owojori, O. J., Reinecke, A. J. & Rozanov, A. B. Effects of salinity on partitioning, uptake and toxicity of zinc in the earthworm Eisenia fetida. Soil Biol. Biochem. 40, 2385–2393. https://doi.org/10.1016/j.soilbio.2008.05.019 (2008).Article 
CAS 

Google Scholar 
Seesamut, T. et al. Occurrence of bioluminescent and nonbioluminescent species in the littoral earthworm genus Pontodrilus. Sci. Rep. 11, 8407 (2021).Article 
CAS 

Google Scholar 
Sivinski, J. & Forrest, T. Luminous defense in an earthworm. Fla. Entomol. 66, 517 (1983).Article 

Google Scholar 
Verdes, A. & Gruber, D. F. Glowing worms: Biological, chemical, and functional diversity of bioluminescent annelids. Integr. Comp. Biol. 57, 18–32. https://doi.org/10.1093/icb/icx017 (2017).Article 
CAS 

Google Scholar 
Shimomura, O. & Yampolsky, I. Bioluminescence: Chemical Principles and Methods 3rd edn. (World Scientific, 2019).Book 

Google Scholar 
Easton, E. G. Earthworms (Oligochaeta) from islands of the south-western Pacific, and a note on two species from Papua New Guinea. N. Z. J. Zool. 11, 111–128. https://doi.org/10.1080/03014223.1984.10423750 (1984).Article 

Google Scholar 
Shen, H.-P., Tsai, S.-C. & Tsai, C.-F. Occurrence of the earthworms Pontodrilus litoralis (Grube, 1855), Metaphire houlleti (Perrier, 1872), and Eiseniella tetraedra (Savigny, 1826) from Taiwan. Taiwania 50, 11–21 (2005).
Google Scholar 
Satheeshkumar, P., Khan, A. B. & Senthilkumar, D. Annelida, Oligochaeta, Megascolecidae, Pontodrilus litoralis (Grupe, 1985): First record from Pondicherry mangroves, southeast coast of India. Int. J. Zool. Res. 7, 406–409. https://doi.org/10.3923/ijzr.2011.406.409 (2011).Article 

Google Scholar 
Nguyen, T. T., Nguyen, D. A., Tran, T. T. B. & Blakemore, R. J. A comprehensive checklist of earthworm species and subspecies from Vietnam (Annelida: Clitellata: Oligochaeta: Almidae, Eudrilidae, Glossoscolecidae, Lumbricidae, Megascolecidae, Moniligastridae, Ocnerodrilidae, Octochaetidae). Zootaxa 4140, 1–92. https://doi.org/10.11646/zootaxa.4140.1.1 (2016).Article 

Google Scholar 
Chen, S.-Y., Hsu, C.-H. & Soong, K. How to cross the sea: Testing the dispersal mechanisms of the cosmopolitan earthworm Pontodrilus litoralis. R. Soc. Open Sci. 8, 202297. https://doi.org/10.1098/rsos.202297 (2021).Article 
ADS 

Google Scholar 
Smyth, K. & Elliott, M. Effects of changing salinity on the ecology of the marine environment. In Stressors in the Marine Environment (eds Solan, M. & Whiteley, N. M.) 161–175 (Oxford University Press, 2016).Chapter 

Google Scholar 
Veiga, M. P. T., Gutierre, S. M. M., Castellano, G. C. & Freire, C. A. Tolerance of high and low salinity in the intertidal gastropod Stramonita brasiliensis (Muricidae): Behaviour and maintenance of tissue water content. J. Molluscan Stud. 82, 154–160. https://doi.org/10.1093/mollus/eyv044 (2016).Article 

Google Scholar 
Carley, W. W., Caracciolo, E. A. & Mason, R. T. Cell and coelomic fluid volume regulation in the earthworm Lumbricus terrestris. Comp. Biochem. Physiol. 74, 569–575 (1983).Article 

Google Scholar 
Sharif, F. et al. Salinity tolerance of earthworms and effects of salinity and vermi amendments on growth of Sorghum bicolor. Arch. Agron. Soil Sci. 62, 1169–1181. https://doi.org/10.1080/03650340.2015.1132838 (2016).Article 
CAS 

Google Scholar 
Wu, Z. et al. Effects of salinity on earthworms and the product during vermicomposting of kitchen wastes. Int. J. Environ. Res. Public Health 16, 4737. https://doi.org/10.3390/ijerph16234737 (2019).Article 
CAS 

Google Scholar 
Oglesby, L. C. Volume regulation in aquatic invertebrates. J. Exp. Zool. 215, 289–301 (1981).Article 
CAS 

Google Scholar 
Generlich, O. & Giere, O. Osmoregulation in two aquatic oligochaetes from habitats with different salinity and comparison to other annelids. Hydrobiologia 334, 251–261. https://doi.org/10.1007/BF00017375 (1996).Article 

Google Scholar 
Carregosa, V. et al. Tolerance of Venerupis philippinarum to salinity: Osmotic and metabolic aspects. Comp. Biochem. Physiol. A 171, 36–43. https://doi.org/10.1016/j.cbpa.2014.02.009 (2014).Article 
CAS 

Google Scholar 
Freitas, R. et al. The effects of salinity changes on the polychaete Diopatra neapolitana: Impacts on regenerative capacity and biochemical markers. Aquat. Toxicol. 163, 167–176. https://doi.org/10.1016/j.aquatox.2015.04.006 (2015).Article 
CAS 

Google Scholar 
Rivera-Ingraham, G. A. & Lignot, J. H. Osmoregulation, bioenergetics and oxidative stress in coastal marine invertebrates: Raising the questions for future research. J. Exp. Biol. 220, 1749–1760. https://doi.org/10.1242/jeb.135624 (2017).Article 

Google Scholar 
Munnoli, P. M. & Bhosle, S. Effect of soil cow dung proportion of vermicomposting. J. Sci. Ind. Res. 68, 57–60 (2009).
Google Scholar  More

Takoutsing, B. et al. Assessment of soil health indicators for sustainable production of maize in smallholder farming systems in the highlands of Cameroon. Geoderma 276, 64–73 (2016).Article 
ADS 
CAS 

Google Scholar 
Wenzel, W. W. et al. Soil and land use factors control organic caron status and accumulation in agricultural soils of Lower Austria. Geoderma 409, 115595. https://doi.org/10.1016/j.geoderma.2021.115595 (2022).Article 
ADS 
CAS 

Google Scholar 
Rinot, O., Levy, G. J., Steinberger, Y., Svoray, T. & Eshel, G. Soil health assessment: A critical review of current methodologies and a proposed new approach. Sci. Total. Environ. 648, 1484–1491 (2019).Article 
ADS 
CAS 

Google Scholar 
Veum, K. S., Sudduth, K. A., Kremer, R. J. & Kitchen, R. (2017) Sensor data fusion for soil health assessment. Geoderma 305, 53–61 (2017).Article 
ADS 

Google Scholar 
Nunes, M. R., Van Es, H. M., Schindelbeck, R., Ristow, A. J. & Ryan, M. No-till and cropping system diversification improve soil health and crop yield. Geoderma 328, 30–43 (2018).Article 
ADS 
CAS 

Google Scholar 
Chhipaa, V., Stein, A., Shankar, H., George, K. J. & Alidoost, F. Assessing and transferring soil health information in a hilly terrain. Geoderma 343, 130–138 (2019).Article 
ADS 

Google Scholar 
Oliver, D. P., Bramley, R. G. V., Riches, D., Porter, I. & Edwards, J. A review of soil physical and chemical properties as indicators of soil quality in Australian viticulture. Aust. J. Grape Wine Res. 19, 129–139 (2013).Article 
CAS 

Google Scholar 
Riches, D. et al. Review: soil biological properties as indicators of soil quality in Australian viticulture. Aust. J. Grape Wine Res. 19, 311–323 (2013).CAS 

Google Scholar 
Ritz, K., Black, H. I. J., Campbell, C. D., Harris, J. A. & Wood, C. Selecting biological indicators for monitoring soils: a framework for balancing scientific opinion to assist policy development. Ecol. Ind. 9, 1212–1221 (2009).Article 
CAS 

Google Scholar 
Zhuo, Z., Kirchner, I., Pfahl, S. & Cubasch, U. Climate impact of volcanic eruptions: the sensitivity to eruption season and latitude in MPI-ESM ensemble experiments. Atmos. Chem. Phys. 21, 13425–13442 (2021).Article 
ADS 
CAS 

Google Scholar 
Griffiths, B. S., Bonkowski, M., Roy, J. & Ritz, K. Functional stability, substrate utilisation and biological indicators of soils following environmental impacts. Appl. Soil Ecol. 16(1), 49–61 (2001).Article 

Google Scholar 
Avidano, L., Gamalero, E., Cossa, G. P. & Carraro, E. Characterization of soil health in an Italian polluted site by using microorganisms as bioindicators. Appl. Soil Ecol. 30(1), 21–33 (2005).Article 

Google Scholar 
Pattison, A. B. et al. Development of key soil health indicators for the Australian banana industry. Appl. Soil Ecol. 40(1), 155–164 (2008).Article 

Google Scholar 
Damsma, K. M., Rose, M. T. & Cavagnaro, T. R. Landscape scale survey of indicators of soil health in grazing systems. Soil Res. 53(2), 154–167 (2015).Article 

Google Scholar 
Fine, A. K., van Es, H. M. & Schindelbeck, R. R. Statistics, scoring functions, and regional analysis of a comprehensive soil health database. Soil Sci. Soc. Am. J. 81(3), 589–601 (2016).Article 

Google Scholar 
Roper, W. R., Osmond, D. L., Heitman, J. L., Wagger, M. G. & Reberg-Horton, S. C. Soil Health indicators do not differentiate among agronomic management systems in North Carolina soils. Soil Sci. Soc. Am. J. 81(4), 828–843 (2016).Article 

Google Scholar 
Li, Z. et al. Rapid diagnosis of agricultural soil health: A novel soil health index based on natural soil productivity and human management. J. Environ. Manage. 277, 111402. https://doi.org/10.1016/j.jenvman.2020.111402 (2021).Article 

Google Scholar 
Oren, A. & Steinberger, Y. Catabolic profiles of soil fungal communities along a geographic climatic gradient in Israel. Soil Biol. Biochem. 40, 2578–2587 (2008).Article 
CAS 

Google Scholar 
Yu, J., Glazer, N. & Steinberger, Y. Carbon utilization, microbial biomass, and respiration in biological soil crusts in the Negev Desert. Biol. Fert. Soils 50, 285–293 (2014).Article 
CAS 

Google Scholar 
Van der Putten, W. H. et al. Plant–soil feedbacks: the past, the present and future challenges. J. Ecol. 101, 265–276 (2013).Article 

Google Scholar 
Sherman, C. & Steinberger, Y. Microbial functional diversity associated with plant litter decomposition along a climatic gradient. Microb. Ecol. 64, 399–415 (2012).Article 
CAS 

Google Scholar 
Dwivedi, V. & Soni, P. A review on the role of soil microbial biomass in eco-restoration of degraded ecosystem with special reference to mining areas. J. Appl. Nat. Sci. 3(1), 151–158 (2011).Article 

Google Scholar 
Barreiro, A., Martín, A., Carballas, T. & Díaz-Raviña, M. Long-term response of soil microbial communities to fire and fire-fighting chemicals. Biol. Fertil. Soils 52, 963–975 (2016).Article 
CAS 

Google Scholar 
Soil Science Division Staff. Soil survey manual. In USDA Handbook 18 (ed. Ditzler, C., Scheffe, K. & Monger, H.C.). (Washington, G. P. O., 2017).Campbell, C. D., Chapman, S. J., Cameron, C. M., Davidson, M. S. & Potts, J. M. A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl. Environ. Microbiol. 69, 3593–3599 (2003).Article 
ADS 
CAS 

Google Scholar 
Anderson, J. P. E. & Domsch, K. H. Physiological method for quantitative measurement of microbial biomass in soils. Soil Biol. Biochem. 10, 215–221 (1978).Article 
CAS 

Google Scholar 
Creamer, R. E., Stone, D., Berry, P. & Kuiper, I. Measuring respiration profiles of soil microbial communities across Europe using MicroResp™ method. Appl. Soil Ecol. 97, 36–43 (2016).Article 

Google Scholar 
Oren, A. & Steinberger, Y. Coping with artifacts induced by CaCO3–CO2–H2O equilibria in substrate utilization profiling of calcareous soils. Soil Biol. Biochem. 40, 2569–2577 (2008).Article 
CAS 

Google Scholar 
Zak, J. C., Willig, M. R., Howard, D. L. & Wildman, G. Functional diversity of microbial communities: A quantitative approach. Soil Biol. Biochem. 26(9), 1101–1108 (1994).Article 

Google Scholar 
Hotelling, H. The most predictable criterion. J. Educ. Psychol. 26, 139–142 (1935).Article 

Google Scholar 
Morrison, D. F. Multivariate Statistical Methods 2nd edn. (McGraw-Hill, 1976).MATH 

Google Scholar 
Rencher, A. C. Methods of Multivariate Analysis (Wiley, Uk, 1995).MATH 

Google Scholar 
IBM Corp. Released 2020. IBM SPSS Statistics for Windows, Version 27.0. (Armonk, NY: IBM Corp., 2020)R Core Team. A language and environment for statistical computing (R Foundation for Statistical Computing, 2021).
Google Scholar 
Bartoń K. MuMIn: Multi-Model Inference. R package version 1.46.0, https://CRAN.R-project.org/package=MuMIn, 2022.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).Book 
MATH 

Google Scholar 
Johnson, J. B. & Omland, K. S. Model selection in ecology and evolution. Trends Ecol. Evol. 19, 101–108 (2004).Article 

Google Scholar 
Kiryushin, V. I. The management of soil fertility and productivity of agrocenoses in adaptive-landscape farming systems. Eurasian Soil Sci. 52, 1137–1145 (2019).Article 
ADS 
CAS 

Google Scholar 
Hermans, S. M. et al. Using soil bacterial communities to predict physic-chemical variables and soil quality. Microbiome 8, 79 (2020).Article 
CAS 

Google Scholar 
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U. S. A. 103, 626–631 (2006).Article 
ADS 
CAS 

Google Scholar 
Frey, S. D., Drijber, R., Smith, H. & Melillo, J. M. Microbial biomass, functional capacity, and community structure after 12 years of soil warming. Soil Biol. Biochem. 40, 2904–2907 (2008).Article 
CAS 

Google Scholar 
Powlson, D. S., Brookes, P. C. & Christensen, B. T. Measurement of soil microbial biomass provides an early indication of changes in total soil organic matter due to straw incorporation. Soil Biol. Biochem. 19, 159–164 (1987).Article 
CAS 

Google Scholar 
Brookes, P. C. The use of microbial parameters in monitoring soil pollution by heavy metals. Biol. Fertil. Soils. 19, 269–279 (1995).Article 
CAS 

Google Scholar 
Hermans, S. M. et al. Bacteria as emerging indicators of soil condition. Appl. Environ. Microbiol. 83, e02826-e2916. https://doi.org/10.1128/AEM.02826-16 (2016).Article 

Google Scholar 
Liddicoat, C. et al. Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health?. Environ. Int. 129, 105–117 (2019).Article 

Google Scholar 
Jeanne, T., Parent, S. -É. & Hogue, R. Using a soil bacterial species balance index to estimate potato crop productivity. PLoS ONE 14, e0214089. https://doi.org/10.1371/journal.pone.0214089 (2019).Article 
CAS 

Google Scholar 
Taylor, B. R. & Parkinson, D. Respiration and mass loss rates of aspen and pine leaf litter decomposing in laboratory microcosms. Can. J. Bot. 66, 1948–1959 (1988).Article 

Google Scholar 
Wardle, D. A. & Parkinson, D. Response of the soil microbial biomass to glucose, and selective inhibitors, across a soil moisture gradient. Soil Biol. Biochem. 22, 825–834 (1990).Article 
CAS 

Google Scholar 
Baldrian, P., Merhautová, V., Petránková, M., Cajthaml, T. & Snajdr, J. Distribution of microbial biomass and activity of extracellular enzymes in a hardwood forest soil reflect soil moisture content. Appl. Soil Ecol. 46, 177–182 (2010).Article 

Google Scholar 
Holland, T. C. et al. The response of soil biota to water availability in vineyards. Pedobiol. Int. J. Soil Biol. 56, 9–14 (2013).
Google Scholar 
Yu, J. & Steinberger, Y. Vertical distribution of microbial-community functionality under the canopies of Zygophyllum dumosum and Hammada scoparia in the Negev Desert. Microb. Ecol. 62, 218–227 (2011).Article 

Google Scholar 
Wardle, D. A. & Parkinson, D. Interaction between microclimatic variables and the soil microbial biomass. Biol. Fertil. Soils. 9, 273–280 (1990).Article 

Google Scholar  More

Using a targeted metabolomics approach, we showed that late copepodite stages of the keystone Arctic copepod Calanus glacialis experience important changes in several central energetic pathways following exposure to decreasing pH. These findings shed light on the physiological changes underpinning the effects of OA on fitness related traits such as ingestion rate and metabolic rate previously observed in this species17,18,20.Cellular energy metabolismCellular energy production was altered consistently in both stage CIV and CV, with concentrations of higher energy adenosine phosphates (ATP and ADP) increasing, and concentrations of the lower energy, less-phosphorylated AMP decreasing, with decreasing seawater pH. Moreover, Phospho-L-arginine, which in crustaceans functions as phosphagen in the replenishment of ATP from ADP during transient energy demands32, increased significantly in stage CV. These changes strongly suggest that exposure to low pH affects energy production and expenditure in both developmental stages, although with nuanced differences.NAD+ increased significantly in stage CIV. NAD+ is an essential redox carrier receiving electrons from oxidative processes in the glycolysis, the TCA cycle, and fatty acid oxidation to form NADH. A high NAD+/NADH ratio facilitates higher rates of these reactions and thus potentially higher rates of ATP production (unfortunately, the LC-HRMS could not detect NADH). But most importantly, the produced NADH serves as electron donors to ATP synthesis in the oxidative phosphorylation. For every ATP produced in the oxidative phosphorylation one NADH is oxidised back to NAD+. High rates of ATP production in the oxidative phosphorylation would therefore amass NAD+, as observed in stage CIV. Conversely, ATP production in the glycolysis and TCA cycle consumes NAD+ (9 NAD+ per 4 ATP) and glycolytic ATP production would decrease the NAD+ concentration with decreasing pH.Heterotrophic organisms generally face a trade-off between rate and yield of ATP production. The efficient low rate/high yield production in the TCA cycle/oxidative phosphorylation may prevail under certain circumstances, whereas under other circumstances, the less efficient high rate/low yield production in the glycolysis may predominate33. Because glycolysis and oxidative phosphorylation compete for ADP, the one dominate over the other in terms of rates depending on the substrate being metabolised. In stage CIV copepodites, the TCA cycle pathway was enriched in the MetPA, and metabolites associated with glycolysis and the TCA cycle showed significant changes in their concentrations at decreasing seawater pH. Glucose, the entry point to glycolysis, increased significantly with decreasing pH. High levels of blood glucose (hyperglycemia) have been observed as a general stress response in decapod crustaceans34. Copepods have no circulatory system (although they have a dorsal heart) but might nevertheless react similarly on the cellular level. Along with the significant increase in glucose, lactate decreased significantly with pH in stage CIV. Lactate is an inevitable end product of glycolysis, because lactate dehydrogenase has the highest Vmax of any enzymes in the glycolytic pathway and the Keq for pyruvate to lactate is far in the direction of lactate35. Accordingly, although the glycolysis was not enriched in the MetPA, conceivably because none of its intermediate metabolites were included in the analyses (the protocol did not allow for it), we hypothesise that stage CIV copepodites experience a general down-regulation of glycolysis under decreasing pH. Alternatively, the amassing of glucose and depletion of lactate could also indicate increased gluconeogenesis. Gluconeogenesis occurs during starvation to replenish glycogen stores and ingestion rates did decrease in stage CIV20. But again, we did not target any intermediates in our analyses, and thus cannot firmly conclude on this.Phosphofructokinase-1 is a key regulatory enzyme of glycolysis36. This enzyme is allosterically inhibited by ATP and activated by AMP, and interestingly this regulation is augmented by low pH37,38. Thus, phosphofructokinase-1 could be key to the down-regulation of glycolysis we hypothesise. The fact that we found increasing oxygen consumption with decreasing pH in stage CIV copepodites from the same experiment adds further momentum to this line of thought20. It seems that stage CIV copepodites might experience the so-called Pasteur effect—a decrease in glycolysis at increased levels of oxygen uptake—when exposed to decreasing pH39. Although ATP and AMP were significantly affected also in stage CV, glucose, pyruvate and lactate did not change with decreasing pH, which perhaps indicate absence of the down-regulation of glycolysis we hypothesise for stage CIV. There is, nevertheless, one indication that down-regulation may in fact occur also in this developmental stage. Alpha-glycerophosphate decreased significantly with decreasing pH in stage CV. This molecule is an intermediate in the transfer of electrons from NADH produced by glycolysis in the cytosol to the oxidative phosphorylation in the mitochondria, and decreased concentrations could result from down-regulation of the glycolysis also in stage CV copepodites.The TCA cycle was enriched for stage CIV and most of the measured TCA cycle metabolites (alpha-ketoglutarate, succinate, fumarate, and malate) showed increasing concentrations at decreasing pH. Trigg et al.40 observed a similar increase in concentrations of TCA cycle-related metabolites in the Dungeness crab, Cancer magister (Dana, 1852), at decreased pH and concluded that TCA cycle activity is upregulated under OA. Since NAD+ is the product of the transport of electrons from the TCA cycle to the oxidative phosphorylation in the mitochondria,  the increase in NAD+ concentration we observed in stage CIV could reflect an increase in the flow of electrons from the TCA cycle to the oxidative phosphorylation, and by extension an increase in the energy production by the TCA cycle and the oxidative phosphorylation. There is negative feedback from the TCA cycle to glycolysis through inhibition of phosphofructokinase-1 by citrate, a metabolite of the TCA cycle38. Unfortunately, we did not target citrate in our targeted approach to specifically test this hypothesis, but the amassing of NAD+ do provide additional support to the idea that glycolysis is down-regulated at decreasing pH. Again, there is a less clear picture of how cellular energy metabolism is affected by decreasing pH in stage CV when compared to stage CIV. There was no clear pattern of regulation of TCA metabolites, and the TCA cycle was not enriched in the MetPA. Nevertheless, alpha-ketoglutarate concentrations did increase with decreasing pH in CVs.The glyoxylate/dicarboxylate cycle was also enriched in the pathway analysis, but this is probably also a result of the increases in concentrations of alpha-ketoglutarate, succinate, fumarate, and malate, and we are unable to distinguish it from the TCA cycle based on the set of metabolites analysed.Conclusively, lowered glycolysis due to inhibition of phosphofructokinase-1 and upregulation of the TCA cycle and oxidative phosphorylation at low pH in stage CIV appear plausible causes for the changes in ATP, ADP and AMP concentrations we observed. Alongside these effects, down-regulation of transcription of genes involved in the glycolysis were also present in nauplii of C. glacialis exposed to 35–38 days of low pH conditions16. On the other hand, studies on the acclimatisation and adaptation to OA in another calanoid copepod species, Pseudocalanus acuspes (Giesbrecht, 1881), showed no increase in expression of mitochondrial genes at pHT 7.54, which would have been expected if the TCA cycle or oxidative phosphorylation is upregulated41. Interestingly, De Wit et al.41 also showed natural selection in a large fraction of mitochondrial genes under OA conditions. Even evolutionarily conserved sequences, such as cytochrome oxidase subunit I, were under selection and it was hypothesised that the mitochondrial function of oxidative phosphorylation is a target for natural selection in copepods at low pH41.Besides its role in the transfer of energy from the mitochondria to the cell, ATP is also used to fuel cell homeostasis and active cellular acid–base regulation by activation of ATP-dependent enzymes involved in osmo-ionic- and acid–base regulation. In crustaceans, acid–base status is linked to ion regulation, and is maintained primarily through ion transport mechanisms moving acid and/or base equivalents between the extracellular fluid and the ambient water42. One prominent process in this respect is regulation by Na+/K+-ATPase42,43. While this regulation takes place in the gills of decapod crustaceans43, it is located in the maxillary glands and other specialised organs on the swimming legs of copepods44. Any extensive ATPase mediated pH regulation could have manifested itself by decreasing ATP concentrations, but this is contrary to what we report here. Interestingly, while the pCO2-sensitive isopod Cymodoce truncata (Leach, 1814) is able to maintain its cellular ATP concentration at the expense of the concentration of carbonate anhydrase (an enzyme involved in the cellular transformation of water and CO2 to bicarbonate ions and H+ prior to the ATPase mediated transport of H+ across the cell membrane), the pCO2-tolerant isopod Dynamene bifida (Torelli, 1930) upregulates ATP with no functional compromise to CA concentrations45. Finally, C. glacialis nauplii have shown upregulation of Na+/H+-antiporters independent of ATPase as a response to OA16, which one could hypothesise also may be the case in the copepodites. Arctic populations of the amphipod Gammarus setosus also do not experience increased ATPase activity during OA conditions46. It seems that C. glacialis faces OA without any ATP dependent acid/base regulation activity.Glycolysis is the first step of catabolism of carbohydrates for the production of energy. When down-regulating glycolysis the copepods may be increasingly dedicated to catabolism of amino acids e.g. through oxidative deamination of glutamate and/or catabolism of fatty acids through beta-oxidation to produce the energy they require21. Both lead to the production of molecules entering the TCA cycle and ultimately the oxidative phosphorylation for energy production in the mitochondria.Amino acid metabolismOf the free amino acids which were significantly affected by decreasing pH, the majority decreased in concentration, for both stage CIV and CV copepodites. This could be an indication of changes in protein synthesis at decreasing pH. Supporting this idea, biosynthesis of aminoacyl-tRNA was indicated as significantly enriched in the MetPA in both stage CIV and CV. Aminoacyl-tRNA partakes in the elongation of the protein amino acid chain during protein synthesis and the enrichment was most likely due to the changes in concentration of the many amino acids tested. One probable cause of protein synthesis is the increased demands of enzymes needed to handle stress at low pH, including for example enzymes involved in acid–base- and osmo-regulation or regulation of energy production. Increased protein synthesis caused by OA conditions has been observed in larvae of the purple sea urchin Strongylocentrotus purpuratus (O.F. Müller, 1776), where in vivo rates of protein synthesis and ion transport increased ∼50%47. Costs of protein synthesis are high and have shown to constitute a major part of copepod metabolic demand48 and we did observe significant increases in metabolic rate in copepodite stage CIV from the same experiment20 giving further credit to the idea that protein synthesis was upregulated.An alternate but not mutually exclusive explanation is that the copepods experience increased amino acid catabolism under OA. Glutamate increased in stage CIV accompanied by a significant increase in alpha-ketoglutarate in both stage CIV and CV. Alpha-ketoglutarate is part of the metabolic pathway of glutamine, glutamate and arginine in which glutamate acts as an intermediate in catabolism of these amino acids when it is deaminated to alpha-ketoglutarate to enter the TCA cycle49. Glutamate metabolism (in conjunction with alanine and aspartate metabolism) was significantly enriched in the MetPA in both stage CIV and CV, and these changes could be taken as an indication of a shift towards amino acid catabolism with decreasing pH. The key enzyme catalysing the oxidative deamination of glutamate is glutamate dehydrogenase (GDH), which functions in both directions: deamination of glutamate to form alpha-ketoglutarate or formation of glutamate from alpha-ketoglutarate. Studies on the ribbed mussel, Modiolus dernissus (Dillwyn, 1817), have shown that the balance of this action is strongly pushed towards deamination when pH decreases from 8.0 to 7.550. GDH is activated by ADP, and one could argue that the increase in ADP we observed would work against this shift, but ADP activates GDH mainly in the glutamate forming direction51. The other measured amino acids enter the TCA cycle at different positions we unfortunately could not target in our analyses. Glutamate also partakes in the arginine biosynthesis pathway in which it is transformed to ornithine to enter the urea cycle. Arginine biosynthesis was enriched in the MetPA and it is therefore possible that decreasing pH also changes amino acid catabolism to increase urea excretion. Decreasing pH has a similar depressing effect on amino acid concentration in the gills of the shore crab Carcinus maenas (Linnaeus, 1758) which also has been interpreted as a sign of increased protein catabolism52. Hammer and colleagues52 argued that this increase in catabolism served to buffer H+ by supplying nitrogen to NH4 formation in the cells. All in all, we hypothesise that increased amino acid catabolism, possibly driven by changes in GDH activity, and the down-regulation of glycolysis by inhibition of phosphofructokinase-1 may be major drivers of a shift from carbohydrate metabolism towards catabolism of amino acids.D-glutamine/D-glutamate metabolism was highly enriched in the MetPA in both developmental stages. Several studies show enriched D-glutamine/D-glutamate metabolism in crustaceans [e.g. 53], but they offer no explanation of its function or the reason why it is enriched. While D-glutamate act in neurotransmission, this action is evolutionarily restricted to ctenophores, and biochemical measurements of D-amino acid concentrations have shown absence of D-glutamate in crustaceans54,55.We observed no changes in concentrations of 8-oxy-2-deoxyguanosine, a product of DNA oxidation. Furthermore, regulation of cellular response to oxidative stress is down-regulated in C. glacialis nauplii16, and OA may not induce oxidative stress in C. glacialis.Fatty acid metabolismBesides their importance in energy storage as wax esters, fatty acids are involved in many central processes in cells, most prominently through their function as cell membrane building blocks. Many fatty acids are obtained from the diet but some longer chain fatty acids, such as 20:1n-9 are synthesised de novo in copepods56. Stage CV copepodites experienced increases in most of the targeted free fatty acids (18 of 21) with decreasing pH. Only one of those 18 increased significantly, but since the direction of change were the same in all, we argue that the pattern of change does merit consideration. Conspicuous exceptions were eicosapentaenoic acid (EPA) 20:5n-3 and docosahexaenoic acid (DHA) 22:6n-3, which both decreased significantly. The only other study (to our knowledge) of metabolomic effects of environmental changes in copepods showed the exact same response to starvation in a mix of C. finmarchicus and C. helgolandicus stage CV copepodites, with most fatty acids increasing while EPA and DHA decreased in concentration57. EPA and DHA are key marine polyunsaturated fatty acids (PUFAs) exclusively produced by marine algae. They contribute a major fraction of the fatty acids of cell membrane phospholipids58, and zooplankton reproductive production is highly dependent on especially EPA59. EPA and DHA are key for cell membrane fluidity, which for calanoid copepods is especially important during diapause in the deep during copepodite stage CV60. They have also been linked to diapause buoyancy control, and are selectively metabolized in diapausing copepodites61. The importance of EPA and DHA for cell membrane integrity may be central for the changes we observed. Glycerol-3-phosphate, the precursor for the glycerol backbone of cell membrane phospholipids also decreased significantly and it seems decreasing pH could affect cell membrane turnover.Changing fatty acid concentration could be due to either a change in lipid intake from feeding or increased fatty acid catabolism. While ingestion rates decreased in stage CIV, they were unchanged in stage CV with decreasing pH20. Also, Thalassiosira weissflogii (Grunow) G.Fryxell & Hasle, 1977, the diatom we fed to the copepods, is rich in 16:0, 16:1n-7 and EPA59. The concentrations of 16:0 and 16:1n-7 increased, whereas EPA concentration decreased. If fatty acid concentrations reflected feeding, we would have seen increased concentrations of all three. We therefore believe that the general increases in concentrations of free fatty acids were caused by increasing catabolism of the wax esters stored in stage CV. It may be that due to the metabolic reconfiguration to enter hibernation, stage CV copepodites are already committed to the catabolism of fatty acids through beta-oxidation, and stored wax esters are being hydrolysed to increase the availability of free fatty acids for energy production. Mayor and colleagues57 arrived at the same conclusion. We hypothesise that stress due to low pH increases the organism’s energetic demands, but carbohydrates are not used to accommodate these demands due to the down-regulation of the glycolysis, rather demands are met by hydrolysing and metabolising wax esters in stage CV. The further ramifications of future OA could therefore be a less efficient build-up of wax esters so important for hibernation in this species.Finally, besides their importance for cell membrane fluidity, EPA and DHA are important precursors for eicosanoid endocrine hormones. These hormones are important regulators of, among other processes, ion flux62. As mentioned above, acid base regulation is coupled to osmoregulation in crustaceans42, and the decrease in concentrations of these two specific fatty acids, when all other fatty acid concentrations increased might represent an indication for changing endocrine hormone production to counter adverse whole-organism effects of OA.Changes in metabolite concentrations cannot be directly translated into changes in the rate of the processes they are involved in. However, they do pin-point processes which are affected by the imposed environmental changes. Also, in our analyses we targeted a limited range of molecules. In that respect OA could inflict changes in other important metabolic pathways we did not investigate. The absence of specific biochemical pathways in our analyses and discussion should therefore not be taken as indication that these are not implicated in this species responses to OA.From our previously published study on copepodites from the same incubations, we know that high pCO2/low pH conditions have detrimental effects on the balance between energy input (ingestion) and energy expenditure (metabolism) in stage CIV copepodites but not in stage CV copepodites20. The effects we report here help in this sense to shed light on the metabolic origin of the rather severe effects on energy balance we observed in stage CIV copepodites and the difference in response between stage CIV and CV20. Copepods develop through six nauplii and five copepodite stages before maturation, and while previous studies show negligible effects in stage CV and adults17,18,20, any effects in any developmental stage along the way will affect the fitness of the individual and the recruitment to the population as a whole. In addition, the enhanced fatty acid metabolism observed in stage CV needs further investigation, to determine the magnitude of the fitness implications of the energy diverted away from energy storage for hibernation. More

Azam, F. et al. The ecological role of water-column microbes in the sea. Marine Ecol. Prog. Ser. 10, 257–263 (1983).Fuhrman, J. A. & Caron D. A. in Manual of Environmental Microbiology (eds Yates, M. V. et al.) 4.2.2–4.2.2.-34 (ASM Press, 2016).Gasol, J. M. & Kirchman, D. L. Microbial Ecology of the Oceans (John Wiley & Sons, 2018).Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl Acad. Sci. 105, 7774–7778 (2008).Article 
ADS 
CAS 

Google Scholar 
Gilbert, J. A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132–3139 (2009).Article 
CAS 

Google Scholar 
Gilbert, J. A. et al. Defining seasonal marine microbial community dynamics. ISME J. 6, 298–308 (2012).Article 
CAS 

Google Scholar 
Hatosy, S. M. et al. Beta diversity of marine bacteria depends on temporal scale. Ecology 94, 1898–1904 (2013).Article 

Google Scholar 
Ward, C. S. et al. Annual community patterns are driven by seasonal switching between closely related marine bacteria. ISME J. 11, 1412–1422 (2017).Article 

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

Google Scholar 
Gonzalez, J. M., Sherr, E. B. & Sherr, B. F. Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl. Environ. Microbiol. 56, 583–589 (1990).Article 
ADS 
CAS 

Google Scholar 
Guixa-Boixereu, N., Vaque, D., Gasol, J. M. & Pedros-Alio, C. Distribution of viruses and their potential effect on bacterioplankton in an oligotrophic marine system. Aquat. Microb. Ecol. 19, 205–213 (1999).Article 

Google Scholar 
Šimek, K. et al. Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir. Limnol. Oceanogr. 44, 1634–1644 (1999).Article 
ADS 

Google Scholar 
Hewson, I., Vargo, G. & Fuhrman, J. Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment. Microb. Ecol. 46, 322–336 (2003).Article 
CAS 

Google Scholar 
Schwalbach, M. S., Hewson, I. & Fuhrman, J. A. Viral effects on bacterial community composition in marine plankton microcosms. Aquat. Microb. Ecol. 34, 117–127 (2004).Article 

Google Scholar 
Winter, C., Smit, A., Herndl, G. J. & Weinbauer, M. G. Linking bacterial richness with viral abundance and prokaryotic activity. Limnol. Oceanogr. 50, 968–977 (2005).Article 
ADS 

Google Scholar 
Chow, C.-E. T., Kim, D. Y., Sachdeva, R., Caron, D. A. & Fuhrman, J. A. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME J. 8, 816–829 (2014).Article 
CAS 

Google Scholar 
Suzuki, S. et al. Comparison of community structures between particle-associated and free-living prokaryotes in tropical and subtropical Pacific Ocean surface waters. J. Oceanogr. 73, 383–395 (2017).Article 
CAS 

Google Scholar 
Milici, M. et al. Diversity and community composition of particle‐associated and free‐living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: evidence of dispersal limitation in the Bransfield Strait. Limnol. Oceanogr. 62, 1080–1095 (2017).Article 
ADS 

Google Scholar 
D’ambrosio, L., Ziervogel, K., MacGregor, B., Teske, A. & Arnosti, C. Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison. ISME J. 8, 2167–2179 (2014).Article 

Google Scholar 
Rieck, A., Herlemann, D. P., Jürgens, K. & Grossart, H.-P. Particle-associated differ from free-living bacteria in surface waters of the Baltic Sea. Front. Microbiol. 6, 1297 (2015).Article 

Google Scholar 
Yung, C.-M., Ward, C. S., Davis, K. M., Johnson, Z. I. & Hunt, D. E. Insensitivity of diverse and temporally variable particle-associated microbial communities to bulk seawater environmental parameters. Appl. Environ. Microbiol. 82, 3431–3437 (2016).Article 
ADS 
CAS 

Google Scholar 
Buchan, A., LeCleir, G. R., Gulvik, C. A. & González, J. M. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698 (2014).Article 
CAS 

Google Scholar 
Duret, M. T., Lampitt, R. S. & Lam, P. Prokaryotic niche partitioning between suspended and sinking marine particles. Environ. Microbiol. Rep. 11, 386–400 (2019).Article 
CAS 

Google Scholar 
Crespo, B. G., Pommier, T., Fernández‐Gómez, B. & Pedrós‐Alió, C. Taxonomic composition of the particle‐attached and free‐living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiologyopen 2, 541–552 (2013).Article 
CAS 

Google Scholar 
Mestre, M., Borrull, E., Sala, M. & Gasol, J. M. Patterns of bacterial diversity in the marine planktonic particulate matter continuum. ISME J. 11, 999–1010 (2017).Yeh, Y. C. et al. Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. Environ. Microbiol. 23, 3240–3250 (2021).Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).Article 
CAS 

Google Scholar 
Needham, D. M. et al. Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling. ISME J. 12, 2417 (2018).Article 
CAS 

Google Scholar 
McNichol, J., Berube, P. M., Biller, S. J. & Fuhrman, J. A. Evaluating and improving small subunit rRNA PCR primer coverage for bacteria, archaea, and eukaryotes using metagenomes from global ocean surveys. Msystems 6, e00565–00521 (2021).Article 
CAS 

Google Scholar 
Chow, C. E. T. & Fuhrman, J. A. Seasonality and monthly dynamics of marine myovirus communities. Environ. Microbiol. 14, 2171–2183 (2012).Article 

Google Scholar 
Filée, J., Tétart, F., Suttle, C. A. & Krisch, H. Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc. Natl Acad. Sci. 102, 12471–12476 (2005).Article 
ADS 

Google Scholar 
Pagarete, A. et al. Strong seasonality and interannual recurrence in marine myovirus communities. Appl. Environ. Microbiol. 79, 6253–6259 (2013).Article 
ADS 
CAS 

Google Scholar 
Comeau, A. M. & Krisch, H. M. The capsid of the T4 phage superfamily: the evolution, diversity, and structure of some of the most prevalent proteins in the biosphere. Mol. Biol. Evolution 25, 1321–1332 (2008).Article 
CAS 

Google Scholar 
Needham, D. M. et al. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. ISME J. 7, 1274–1285 (2013).Article 
CAS 

Google Scholar 
Needham, D. M., Sachdeva, R. & Fuhrman, J. A. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME J. 11, 1614–1629 (2017).Article 

Google Scholar 
Ahlgren, N. A., Perelman, J. N., Yeh, Y. C. & Fuhrman, J. A. Multi‐year dynamics of fine‐scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom‐up factors. Environ. Microbiol. 21, 2948–2963 (2019).Article 
CAS 

Google Scholar 
Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A. & Sun, F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 5, 1–20 (2017).Article 

Google Scholar 
Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M. B. VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985 (2015).Article 

Google Scholar 
Ignacio-Espinoza, J. C., Ahlgren, N. A. & Fuhrman, J. A. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nat. Microbiol. 5, 265–271 (2020).Article 
CAS 

Google Scholar 
Brum, J. R. et al. Patterns and ecological drivers of ocean viral communities. Science 348, (2015).Brown, M. V. et al. Global biogeography of SAR11 marine bacteria. Mol. Syst. Biol. 8, 595 (2012).Article 
ADS 

Google Scholar 
Johnson, Z. I. et al. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311, 1737–1740 (2006).Article 
ADS 
CAS 

Google Scholar 
Zwirglmaier, K. et al. Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ. Microbiol. 10, 147–161 (2008).
Google Scholar 
Martiny, A. C., Tai, A. P., Veneziano, D., Primeau, F. & Chisholm, S. W. Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ. Microbiol. 11, 823–832 (2009).Article 

Google Scholar 
Bond, N. A., Cronin, M. F., Freeland, H. & Mantua, N. Causes and impacts of the 2014 warm anomaly in the NE Pacific. Geophys. Res. Lett. 42, 3414–3420 (2015).Article 
ADS 

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

Google Scholar 
Traving, S. J. et al. Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters. Commun. Biol. 4, 1–12 (2021).Article 

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

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

Google Scholar 
Cavole, L. M. et al. Biological impacts of the 2013–2015 warm-water anomaly in the Northeast Pacific: winners, losers, and the future. Oceanography 29, 273–285 (2016).Article 

Google Scholar 
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).Article 
CAS 

Google Scholar 
Needham, D. M. & Fuhrman, J. A. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat. Microbiol. 1, 16005 (2016).Article 
CAS 

Google Scholar 
Grossart, H. P., Levold, F., Allgaier, M., Simon, M. & Brinkhoff, T. Marine diatom species harbour distinct bacterial communities. Environ. Microbiol. 7, 860–873 (2005).Article 
CAS 

Google Scholar 
Teeling, H. et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336, 608–611 (2012).Article 
ADS 
CAS 

Google Scholar 
Chafee, M. et al. Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J. 12, 237–252 (2018).Article 

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

Google Scholar 
Unfried, F. et al. Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms. ISME J. 12, 2894–2906 (2018).Article 
CAS 

Google Scholar 
Francis, T. B. et al. Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom. ISME J. 15, 2336–2350 (2021).Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microb. Ecol. 13, 19–27 (1997).Article 

Google Scholar 
Thingstad, T. F., Våge, S., Storesund, J. E., Sandaa, R.-A. & Giske, J. A theoretical analysis of how strain-specific viruses can control microbial species diversity. Proc. Natl Acad. Sci. 111, 7813–7818 (2014).Article 
ADS 
CAS 

Google Scholar 
Thingstad, T. F., Pree, B., Giske, J. & Våge, S. What difference does it make if viruses are strain-, rather than species-specific? Front. Microbiol. 6, 320 (2015).Article 

Google Scholar 
Prokopowich, C. D., Gregory, T. R. & Crease, T. J. The correlation between rDNA copy number and genome size in eukaryotes. Genome 46, 48–50 (2003).Article 
CAS 

Google Scholar 
Zhu, F., Massana, R., Not, F., Marie, D. & Vaulot, D. Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol. Ecol. 52, 79–92 (2005).Article 
CAS 

Google Scholar 
Sintes, E. & Del Giorgio, P. A. Feedbacks between protistan single-cell activity and bacterial physiological structure reinforce the predator/prey link in microbial foodwebs. Front. Microbiol. 5, 453 (2014).Article 

Google Scholar 
Del Giorgio, P. A. et al. Bacterioplankton community structure: protists control net production and the proportion of active bacteria in a coastal marine community. Limnol. Oceanogr. 41, 1169–1179 (1996).Article 
ADS 

Google Scholar 
Andersson, A., Larsson, U. & Hagström, Å. Size-selective grazing by a microflagellate on pelagic bacteria. Marine Ecol. Prog. Ser. 33, 51–57 (1986).Pernthaler, J. Predation on prokaryotes in the water column and its ecological implications. Nat. Rev. Microbiol. 3, 537–546 (2005).Article 
CAS 

Google Scholar 
Baltar, F. et al. Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions. ISME J. 10, 568–581 (2016).Article 

Google Scholar 
Suzuki, M. T. Effect of protistan bacterivory on coastal bacterioplankton diversity. Aquat. Microb. Ecol. 20, 261–272 (1999).Article 

Google Scholar 
Yokokawa, T. & Nagata, T. Growth and grazing mortality rates of phylogenetic groups of bacterioplankton in coastal marine environments. Appl. Environ. Microbiol. 71, 6799–6807 (2005).Article 
ADS 
CAS 

Google Scholar 
Eren, A. M. et al. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evolution 4, 1111–1119 (2013).Article 

Google Scholar 
Coleman, M. L. & Chisholm, S. W. Code and context: Prochlorococcus as a model for cross-scale biology. Trends Microbiol. 15, 398–407 (2007).Article 
CAS 

Google Scholar 
Scanlan, D. J. et al. Ecological genomics of marine picocyanobacteria. Microbiol. Mol. Biol. Rev. 73, 249–299 (2009).Article 
CAS 

Google Scholar 
Moore, L. R., Rocap, G. & Chisholm, S. W. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393, 464–467 (1998).Article 
ADS 
CAS 

Google Scholar 
Rusch, D. B., Martiny, A. C., Dupont, C. L., Halpern, A. L. & Venter, J. C. Characterization of Prochlorococcus clades from iron-depleted oceanic regions. Proc. Natl Acad. Sci. 107, 16184–16189 (2010).Article 
ADS 
CAS 

Google Scholar 
Larkin, A. A. et al. Persistent El Niño driven shifts in marine cyanobacteria populations. PloS ONE 15, e0238405 (2020).Article 
CAS 

Google Scholar 
Arandia‐Gorostidi, N. et al. Warming the phycosphere: differential effect of temperature on the use of diatom‐derived carbon by two copiotrophic bacterial taxa. Environ. Microbiol. 22, 1381–1396 (2020).Article 

Google Scholar 
Arandia‐Gorostidi, N., Huete‐Stauffer, T. M., Alonso‐Sáez L, G. & Morán, X. A. Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom. Environ. Microbiol. 19, 4493–4505 (2017).Article 

Google Scholar 
Fagan, A. J., Moreno, A. R. & Martiny, A. C. Role of ENSO conditions on particulate organic matter concentrations and elemental ratios in the Southern California Bight. Front. Mar. Sci. 6, 386 (2019).Article 

Google Scholar 
Chang, C. W. et al. Reconstructing large interaction networks from empirical time series data. Ecol. Lett. 24, 2763–2774 (2021).Article 

Google Scholar 
Lie, A. A., Kim, D. Y., Schnetzer, A. & Caron, D. A. Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California. Aquat. Microb. Ecol. 70, 93–110 (2013).Article 

Google Scholar 
Yeh, Y.-C., Needham, D. M., Sieradzki, E. T. & Fuhrman, J. A. Taxon disappearance from microbiome analysis reinforces the value of mock communities as a standard in every sequencing run. MSystems 3, e00023–00018 (2018).Article 

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

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

Google Scholar 
Guillou, L. et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41, D579–D604 (2013).
Google Scholar 
Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. MSystems 2, (2017).Decelle, J. et al. Phyto REF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour. 15, 1435–1445 (2015).Article 
CAS 

Google Scholar 
Amin, S. et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522, 98–101 (2015).Article 
ADS 
CAS 

Google Scholar 
Legendre, P. & Gallagher, E. D. Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271–280 (2001).Article 
ADS 

Google Scholar 
Hill, M. O. & Gauch, H. G. J. Detrended correspondence analysis: an improved ordination technique. Vegetatio 42, 47–58 (1980).Ter Braak, C. J. Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology 67, 1167–1179 (1986).Article 

Google Scholar 
Peres-Neto, P. R., Legendre, P., Dray, S. & Borcard, D. Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87, 2614–2625 (2006).Article 

Google Scholar  More

Sogin, E. M., Leisch, N. & Dubilier, N. Chemosynthetic symbioses. Curr. Biol. 30, R1137–R1142 (2020).Article 
CAS 

Google Scholar 
Dubilier, N., Bergin, C. & Lott, C. Symbiotic diversity in marine animals: The art of harnessing chemosynthesis. Nat. Rev. Microbiol. 6, 725–740 (2008).Article 
CAS 

Google Scholar 
Barry, J. P. et al. Methane-based symbiosis in a mussel, Bathymodiolus platifrons, from cold seeps in Sagami Bay Japan. Invertebr. Biol. 121, 47–54 (2002).Article 

Google Scholar 
Le Pennec, M., Donval, A. & Herry, A. Nutritional strategies of the hydrothermal ecosystem bivalves. Prog. Oceanogr. 24, 71–80 (1990).Article 
ADS 

Google Scholar 
Rau, G. H. & Hedges, J. I. Carbon-13 depletion in a hydrothermal vent mussel: Suggestion of a chemosynthetic food source. Science 203, 648–649 (1979).Article 
ADS 
CAS 

Google Scholar 
Wentrup, C., Wendeberg, A., Schimak, M., Borowski, C. & Dubilier, N. Forever competent: Deep-sea bivalves are colonized by their chemosynthetic symbionts throughout their lifetime. Environ. Microbiol. 16, 3699–3713 (2014).Article 

Google Scholar 
Dattagupta, S., Bergquist, D., Szalai, E., Macko, S. & Fisher, C. Tissue carbon, nitrogen, and sulfur stable isotope turnover in transplanted Bathymodiolus childressi mussels: Relation to growth and physiological condition. Limnol. Oceanogr. 49, 1144–1151 (2004).Article 
ADS 
CAS 

Google Scholar 
Ikuta, T. et al. Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME J. 10, 990–1001 (2016).Article 

Google Scholar 
Takishita, K. et al. Genomic evidence that methanotrophic endosymbionts likely provide deep-sea Bathymodiolus mussels with a sterol intermediate in cholesterol biosynthesis. Genome Biol. Evol. 9, 1148–1160 (2017).Article 

Google Scholar 
Sayavedra, L. et al. Horizontal acquisition followed by expansion and diversification of toxin-related genes in deep-sea bivalve symbionts. BioRxiv 110, 330 (2019).
Google Scholar 
Ponnudurai, R. et al. Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis. ISME J. 11, 463–477 (2017).Article 
CAS 

Google Scholar 
Ponnudurai, R. et al. Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont. Stand Genom. Sci. 12, 1–9 (2017).
Google Scholar 
Kiel, S. The Vent and Seep Biota: Aspects from Microbes to Ecosystems Vol. 33 (Springer Science & Business Media, 2010).
Google Scholar 
Lorion, J. et al. Adaptive radiation of chemosymbiotic deep-sea mussels. Proc. R. Soc. B 280, 20131243 (2013).Article 

Google Scholar 
Nussbaumer, A. D., Fisher, C. R. & Bright, M. Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441, 345–348 (2006).Article 
ADS 
CAS 

Google Scholar 
Gros, O., Liberge, M., Heddi, A., Khatchadourian, C. & Felbeck, H. Detection of the free-living forms of sulfide-oxidizing gill endosymbionts in the lucinid habitat (Thalassia testudinum environment). Appl. Environ. Microbiol. 69, 6264–6267 (2003).Article 
ADS 
CAS 

Google Scholar 
Won, Y.-J. et al. Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus Bathymodiolus. Appl. Environ. Microbiol. 69, 6785–6792 (2003).Article 
ADS 
CAS 

Google Scholar 
Laming, S. R., Gaudron, S. M. & Duperron, S. Lifecycle ecology of deep-sea chemosymbiotic mussels: A review. Front. Mar. Sci. 5, 282 (2018).Article 

Google Scholar 
Laming, S. R., Duperron, S., Cunha, M. R. & Gaudron, S. M. Settled, symbiotic, then sexually mature: Adaptive developmental anatomy in the deep-sea, chemosymbiotic mussel Idas modiolaeformis. Mar. Biol. 161, 1319–1333 (2014).Article 

Google Scholar 
Salerno, J. L. et al. Characterization of symbiont populations in life-history stages of mussels from chemosynthetic environments. Biol. Bull. 208, 145–155 (2005).Article 

Google Scholar 
Wentrup, C., Wendeberg, A., Huang, J. Y., Borowski, C. & Dubilier, N. Shift from widespread symbiont infection of host tissues to specific colonization of gills in juvenile deep-sea mussels. ISME J. 7, 1244–1247 (2013).Article 
CAS 

Google Scholar 
Pennec, M. L. & Beninger, P. G. Ultrastructural characteristics of spermatogenesis in three species of deep-sea hydrothermal vent mytilids. Can. J. Zool. 75, 308–316 (1997).Article 

Google Scholar 
Eckelbarger, K. & Young, C. Ultrastructure of gametogenesis in a chemosynthetic mytilid bivalve (Bathymodiolus childressi) from a bathyal, methane seep environment (northern Gulf of Mexico). Mar. Biol. 135, 635–646 (1999).Article 

Google Scholar 
Ansorge, R. et al. Diversity matters: Deep-sea mussels harbor multiple symbiont strains. bioRxiv 99, 1039 (2019).
Google Scholar 
Petersen, J. M., Wentrup, C., Verna, C., Knittel, K. & Dubilier, N. Origins and evolutionary flexibility of chemosynthetic symbionts from deep-sea animals. Biol. Bull. 223, 123–137 (2012).Article 
CAS 

Google Scholar 
Sayavedra, L. et al. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. Elife 4, e07966 (2015).Article 

Google Scholar 
Ansorge, R. et al. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nat. Microbiol. 4, 2487–2497 (2019).Article 

Google Scholar 
Petersen, J. M. et al. Hydrogen is an energy source for hydrothermal vent symbioses. Nature 476, 176–180 (2011).Article 
ADS 
CAS 

Google Scholar 
Nakamura, K. & Takai, K. Theoretical constraints of physical and chemical properties of hydrothermal fluids on variations in chemolithotrophic microbial communities in seafloor hydrothermal systems. Prog. Earth Planet Sci. 1, 1–24 (2014).Article 
ADS 

Google Scholar 
Perez, M. & Juniper, S. K. Insights into symbiont population structure among three vestimentiferan tubeworm host species at eastern Pacific spreading centers. Appl. Environ. Microbiol. 82, 5197–5205 (2016).Article 
ADS 
CAS 

Google Scholar 
Wilbanks, E. G. et al. Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. ISME J. https://doi.org/10.1038/s41396-022-01242-7 (2022).Article 

Google Scholar 
Rodriguez-Casariego, J. A., Cunning, R., Baker, A. C. & Eirin-Lopez, J. M. Symbiont shuffling induces differential DNA methylation responses to thermal stress in the coral Montastraea cavernosa. Mol. Ecol. 31, 588–602 (2022).Article 
CAS 

Google Scholar 
Triant, D. A. & Whitehead, A. Simultaneous extraction of high-quality RNA and DNA from small tissue samples. J. Hered. 100, 246–250 (2009).Article 
CAS 

Google Scholar 
Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).Article 
CAS 

Google Scholar 
Wick, R. R. et al. Trycycler: Consensus long-read assemblies for bacterial genomes. Genome Biol. 22, 1–17 (2021).Article 

Google Scholar 
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).Article 
CAS 

Google Scholar 
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).Article 
ADS 

Google Scholar 
Krawczyk, P. S., Lipinski, L. & Dziembowski, A. PlasFlow: Predicting plasmid sequences in metagenomic data using genome signatures. Nucleic Acids Res. 46, e35–e35 (2018).Article 

Google Scholar 
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D. & Gurevich, A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34, i142–i150 (2018).Article 
CAS 

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

Google Scholar 
Couvin, D. et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 46, W246–W251 (2018).Article 
CAS 

Google Scholar 
Perez, M., Angers, B., Young, C. R. & Juniper, S. K. Shining light on a deep-sea bacterial symbiont population structure with CRISPR. Microbial. Genom. https://doi.org/10.1099/mgen.0.000625 (2021).Article 

Google Scholar 
Hyatt, D. et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 1–11 (2010).Article 

Google Scholar 
Nielsen, H. Protein Function Prediction 59–73 (Springer, 2017).Book 

Google Scholar 
Krogh, A., Larsson, B., Von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).Article 
CAS 

Google Scholar 
Lagesen, K. et al. RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-31C08 (2007).Article 
ADS 
CAS 

Google Scholar 
Chan, P. P. & Lowe, T. M. Gene Prediction 1–14 (Springer, 2019).
Google Scholar 
Griffiths-Jones, S. et al. Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121–D124 (2005).Article 
CAS 

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 
CAS 

Google Scholar 
Siguier, P., Pérochon, J., Lestrade, L., Mahillon, J. & Chandler, M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34, D32–D36 (2006).Article 
CAS 

Google Scholar 
Bertelli, C. et al. IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 45, W30–W35 (2017).Article 
CAS 

Google Scholar 
Arndt, D. et al. PHASTER: A better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44, W16–W21 (2016).Article 
CAS 

Google Scholar 
Roeselers, G. et al. Complete genome sequence of Candidatus Ruthia magnifica. Stand Genomic Sci. 3, 163–173 (2010).Article 

Google Scholar 
Emms, D. M. & Kelly, S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 1–14 (2019).Article 

Google Scholar 
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).Article 

Google Scholar 
Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).Article 
CAS 

Google Scholar 
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547 (2018).Article 
CAS 

Google Scholar 
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).Article 
CAS 

Google Scholar 
Eren, A. M. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat. Microbiol. 6, 3–6 (2021).Article 
CAS 

Google Scholar 
Darling, A. E., Mau, B. & Perna, N. T. progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147 (2010).Article 
ADS 

Google Scholar 
Tesler, G. GRIMM: Genome rearrangements web server. Bioinformatics 18, 492–493 (2002).Article 
CAS 

Google Scholar 
Cabanettes, F. & Klopp, C. D-GENIES: Dot plot large genomes in an interactive, efficient and simple way. PeerJ 6, e4958 (2018).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 
CAS 

Google Scholar 
Gilchrist, C. L. & Chooi, Y.-H. Clinker & clustermap. js: Automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021).Article 
CAS 

Google Scholar 
Taboada, B., Estrada, K., Ciria, R. & Merino, E. Operon-mapper: A web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics 34, 4118–4120 (2018).Article 
CAS 

Google Scholar 
Søndergaard, D., Pedersen, C. N. & Greening, C. HydDB: A web tool for hydrogenase classification and analysis. Sci. Rep. 6, 1–8 (2016).Article 

Google Scholar 
NCBI Genome Browser. https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/. Accessed 12 March 2022.Mcmullin, E. R., Hourdez, S., Schaeffer, S. W. & Fisher, C. R. Review article phylogeny and biogeography of deep sea vestimentiferan tubeworms and their bacterial symbionts. Symbiosis. 34, 1–41 (2003).
Google Scholar 
Won, Y.-J., Jones, W. J. & Vrijenhoek, R. C. Absence of cospeciation between deep-sea mytilids and their thiotrophic endosymbionts. J. Shellfish Res. 27, 129–138 (2008).Article 

Google Scholar 
Miyazaki, J.-I., Martins, Ld. O., Fujita, Y., Matsumoto, H. & Fujiwara, Y. Evolutionary process of deep-sea Bathymodiolus mussels. PLoS ONE 5, e10363 (2010).Article 
ADS 

Google Scholar 
Bright, M. & Bulgheresi, S. A complex journey: Transmission of microbial symbionts. Nat. Rev. Microbiol. 8, 218–230 (2010).Article 
CAS 

Google Scholar 
Raggi, L., Schubotz, F., Hinrichs, K. U., Dubilier, N. & Petersen, J. M. Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the southern Gulf of Mexico. Environ. Microbiol. 15, 1969–1987 (2013).Article 
CAS 

Google Scholar 
Goris, J. et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91 (2007).Article 
CAS 

Google Scholar 
Meier-Kolthoff, J. P., Auch, A. F., Klenk, H.-P. & Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 14, 1–14 (2013).Article 

Google Scholar 
Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. 102, 2567–2572 (2005).Article 
ADS 
CAS 

Google Scholar 
Ho, P.-T. et al. Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents. BMC Evol. Biol. 17, 1–16 (2017).Article 

Google Scholar 
Romero Picazo, D. et al. Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. ISME J. 13, 2954–2968 (2019).Article 

Google Scholar 
Perez, M. & Juniper, S. K. Is the trophosome of Ridgeia piscesae monoclonal?. Symbiosis 74, 55–65 (2018).Article 
CAS 

Google Scholar 
Polzin, J., Arevalo, P., Nussbaumer, T., Polz, M. F. & Bright, M. Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment. Proc. R. Soc. B 286, 20181281 (2019).Article 
CAS 

Google Scholar 
Russell, S. L. & Cavanaugh, C. M. Intrahost genetic diversity of bacterial symbionts exhibits evidence of mixed infections and recombinant haplotypes. Mol. Biol. Evol. 34, 2747–2761 (2017).Article 
CAS 

Google Scholar 
Breusing, C., Genetti, M., Russell, S. L., Corbett-Detig, R. B. & Beinart, R. A. Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses. Proc. Natl. Acad. Sci. 119, e2115608119 (2022).Article 
CAS 

Google Scholar 
Lan, Y. et al. Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont. ISME J. https://doi.org/10.1038/s41396-022-01261-4 (2022).Article 

Google Scholar 
Anantharaman, K., Breier, J. A., Sheik, C. S. & Dick, G. J. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc. Natl. Acad. Sci. 110, 330–335 (2013).Article 
ADS 
CAS 

Google Scholar 
Fritsch, J. et al. Rubredoxin-related maturation factor guarantees metal cofactor integrity during aerobic biosynthesis of membrane-bound [NiFe] hydrogenase. J. Biol. Chem. 289, 7982–7993 (2014).Article 
CAS 

Google Scholar 
Petersen, J. M. et al. Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation. Nat. Microbiol. 2, 1–11 (2016).Article 

Google Scholar 
Nakagawa, S. et al. Allying with armored snails: The complete genome of gammaproteobacterial endosymbiont. ISME J. 8, 40–51 (2014).Article 
CAS 

Google Scholar 
Vignais, P. M., Billoud, B. & Meyer, J. Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25, 455–501 (2001).Article 
CAS 

Google Scholar 
Perez, M. et al. Divergent paths in the evolutionary history of maternally transmitted clam symbionts. Proc. R. Soc. B 289, 20212137 (2022).Article 
CAS 

Google Scholar 
Li, S. et al. N 4-cytosine DNA methylation is involved in the maintenance of genomic stability in Deinococcus radiodurans. Front. Microbiol. 10, 1905 (2019).Article 

Google Scholar 
Casadesús, J. & Low, D. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70, 830–856 (2006).Article 

Google Scholar 
De Oliveira, A. L., Srivastava, A., Espada-Hinojosa, S. & Bright, M. The complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep-sea hydrothermal vents. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13668 (2022).Article 

Google Scholar 
Ponnudurai, R. et al. Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions. ISME J. 14, 649–656 (2020).Article 
CAS 

Google Scholar 
Yu, N. Y. et al. PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26, 1608–1615 (2010).Article 
CAS 

Google Scholar  More

Odum, E. P. The strategy of ecosystem development. Science 164, 262–270 (1969).Article 
ADS 
CAS 

Google Scholar 
Gorham, E., Vitousek, P. M. & Reiners, W. A. The regulation of element budgets over the course of terrestrial ecosystem succession. Annu. Rev. Ecol. Syst. 10, 53–84 (1979).Article 
CAS 

Google Scholar 
Corman, J. R. et al. Foundations and frontiers of ecosystem science: Legacy of a classic paper (Odum 1969). Ecosystems 22, 1160–1172. https://doi.org/10.1007/s10021-018-0316-3 (2019).Article 

Google Scholar 
Santín, C. et al. Towards a global assessment of pyrogenic carbon from vegetation fires. Glob. Change Biol. 22, 76–91. https://doi.org/10.1111/gcb.12985 (2016).Article 
ADS 

Google Scholar 
Kominoski, J. S., Gaiser, E. E. & Baer, S. G. Advancing theories of ecosystem development through long-term ecological research. Bioscience 68, 554–562. https://doi.org/10.1093/biosci/biy070 (2018).Article 

Google Scholar 
Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gómez-Dans, J. Introduced annual grass increases regional fire activity across the arid western USA (1980–2009). Glob. Change Biol. 19, 173–183. https://doi.org/10.1111/gcb.12046 (2013).Article 
ADS 

Google Scholar 
Abatzoglou, J. T. & Kolden, C. A. Climate change in Western US deserts: Potential for increased wildfire and invasive annual grasses. Rangeland Ecol. Manag. 64(5), 471–478 (2011).Article 

Google Scholar 
Shi, H. et al. Historical cover trends in a sagebrush steppe ecosystem from 1985 to 2013: Links with climate, disturbance, and management. Ecosystems 21, 913–929. https://doi.org/10.1007/s10021-017-0191-3 (2018).Article 

Google Scholar 
Seyfried, M. S. & Wilcox, B. P. Scale and the nature of spatial variability: Field examples having implications for hydrologic modeling. Water Resour. Res. 31, 173–184. https://doi.org/10.1029/94WR02025 (1995).Article 
ADS 

Google Scholar 
Gasch, C. K., Huzurbazar, S. V. & Stahl, P. D. Description of vegetation and soil properties in sagebrush steppe following pipeline burial, reclamation, and recovery time. Geoderma 265, 19–26. https://doi.org/10.1016/j.geoderma.2015.11.013 (2016).Article 
ADS 

Google Scholar 
Huber, D. P. et al. Vegetation and precipitation shifts interact to alter organic and inorganic carbon storage in desert soils. Ecosphere 10, e02655. https://doi.org/10.1002/ecs2.2655 (2019).Article 

Google Scholar 
Knight, D. H., Jones, G. P., Reiners, W. A. & Romme, W. H. Mountains and Plains: The Ecology of Wyoming Landscapes (Yale University Press, 2014).
Google Scholar 
Patton, N. R., Lohse, K. A., Seyfried, M. S., Godsey, S. E. & Parsons, S. Topographic controls on soil organic carbon on soil mantled landscapes. Sci. Rep. 9, 6390. https://doi.org/10.1038/s41598-019-42556-5 (2019).Article 
ADS 
CAS 

Google Scholar 
Schwabedissen, S. G., Lohse, K. A., Reed, S. C., Aho, K. A. & Magnuson, T. S. Nitrogenase activity by biological soil crusts in cold sagebrush steppe ecosystems. Biogeochemistry 134, 57–76. https://doi.org/10.1007/s10533-017-0342-9 (2017).Article 
CAS 

Google Scholar 
You, Y. et al. Biological soil crust bacterial communities vary along climatic and shrub cover gradients within a sagebrush steppe ecosystem. Front. Microbiol. 12, 2365. https://doi.org/10.3389/fmicb.2021.569791 (2021).Article 

Google Scholar 
Burke, I. C., Reiners, W. A. & Olson, R. K. Topographic control of vegetation in a mountain big sagebrush steppe. Vegetation 84, 77–86 (1989).Article 

Google Scholar 
Poulos, M. J., Pierce, J. L., Flores, A. N. & Benner, S. G. Hillslope asymmetry maps reveal widespread, multi-scale organization. Geophys. Res. Lett. 39, 6. https://doi.org/10.1029/2012GL051283 (2012).Article 

Google Scholar 
Smith, T. & Bookhagen, B. Climatic and biotic controls on topographic asymmetry at the global scale. J. Geophys. Res.: Earth Surf. 126, e2020JF005692. https://doi.org/10.1029/2020JF005692Received22 (2021).Article 
ADS 

Google Scholar 
Seyfried, M., Link, T., Marks, D. & Murdock, M. Soil temperature variability in complex terrain measured using fiber-optic distributed temperature sensing. Vadose Zone J. 15, 6. https://doi.org/10.2136/vzj2015.09.0128 (2016).Article 

Google Scholar 
Chambers, J. C. et al. Resilience and resistance of sagebrush ecosystems: Implications for state and transition models and management treatments. Rangel. Ecol. Manage. 67, 440–454. https://doi.org/10.2111/REM-D-13-00074.1 (2014).Article 

Google Scholar 
Chambers, J. C. et al. Operationalizing resilience and resistance concepts to address invasive grass-fire cycles. Front. Ecol. Evol. 7, 2369. https://doi.org/10.3389/fevo.2019.00185 (2019).Article 

Google Scholar 
Boehm, A. R. et al. Slope and aspect effects on seedbed microclimate and germination timing of fall-planted seeds. Rangel. Ecol. Manage. 75, 58–67. https://doi.org/10.1016/j.rama.2020.12.003 (2021).Article 

Google Scholar 
Sankey, J. B., Germino, M. J., Sankey, T. T. & Hoover, A. N. Fire effects on the spatial patterning of soil properties in sagebrush steppe, USA: A meta-analysis. Int. J. Wildl. Fire 21, 545–556. https://doi.org/10.1071/WF11092 (2012).Article 

Google Scholar 
Fellows, A., Flerchinger, G., Seyfried, M. S. & Lohse, K. A. Rapid recovery of mesic mountain big sagebrush gross production and respiration following prescribed fire. Ecosystems 21, 1283–1294. https://doi.org/10.1007/s10021-017-0218-9 (2018).Article 

Google Scholar 
Vega, S. P. et al. Interaction of wind and cold-season hydrologic processes on erosion from complex topography following wildfire in sagebrush steppe. Earth Surf. Process. Landforms https://doi.org/10.1002/esp.4778 (2019).Article 

Google Scholar 
Xie, J., Li, Y., Zhai, C., Li, C. & Lan, Z. CO2 absorption by alkaline soils and its implication to the global carbon cycle. Environ. Geol. 56, 953–961 (2009).Article 
ADS 
CAS 

Google Scholar 
Stanbery, C., Pierce, J. L., Benner, S. G. & Lohse, K. On the rocks: Quantifying storage of inorganic soil carbon on gravels and determining pedon-scale variability. CATENA 157, 436–442. https://doi.org/10.1016/j.catena.2017.06.011 (2017).Article 
CAS 

Google Scholar 
Stanbery, C. et al. Controls on the presence and concentration of soil inorganic carbon in a semi-arid watershed. CATENA https://doi.org/10.2139/ssrn.4267018 (2023).Article 

Google Scholar 
Cerling, T. E. & Quade, J. Stable carbon and oxygen isotopes in soil carbonates. Geophys. Monogr. 78, 217–231 (1993).ADS 

Google Scholar 
Tappa, D. J., Kohn, M. J., McNamara, J. P., Benner, S. G. & Flores, A. N. Isotopic composition of precipitation in a topographically steep, seasonally snow-dominated watershed and implications of variations from the global meteoric water line. Hydrol. Process. 30, 4582–4592. https://doi.org/10.1002/hyp.10940 (2016).Article 
ADS 
CAS 

Google Scholar 
Salomons, W., Goudie, A. & Mook, W. G. Isotopic composition of calcrete deposits from Europe, Africa and India. Earth Surf. Process. 3, 43–57. https://doi.org/10.1002/esp.3290030105 (1978).Article 
CAS 

Google Scholar 
Salomons, W. & Mook, W. G. In Handbook of Environmental Isotope Geochemistry (eds P. Fritz & J. Fontes) Ch. 6, 241–269 (Elsevier, 1986).Bodí, M. B. et al. Wildland fire ash: Production, composition and eco-hydro-geomorphic effects. Earth Sci. Rev. 130, 103–127. https://doi.org/10.1016/j.earscirev.2013.12.007 (2014).Article 
ADS 
CAS 

Google Scholar 
Kéraval, B. et al. Soil carbon dioxide emissions controlled by an extracellular oxidative metabolism identifiable by its isotope signature. Biogeosciences 13, 6353–6362. https://doi.org/10.5194/bg-13-6353-2016 (2016).Article 
ADS 
CAS 

Google Scholar 
Goforth, B. R., Graham, R. C., Hubbert, K. R., Zanner, C. W. & Minnich, R. A. Spatial distribution and properties of ash and thermally altered soils after high-severity forest fire, southern California. Int. J. Wildland Fire 14, 343–354 (2005).Article 

Google Scholar 
Glossner, K. L. et al. Long-term suspended sediment and particulate organic carbon yields from the Reynolds Creek Experimental Watershed and Critical Zone Observatory. Hydrol. Process. 36, e14484. https://doi.org/10.1002/hyp.14484 (2022).Article 
CAS 

Google Scholar 
Seyfried, M. S. et al. Reynolds creek experimental watershed and critical zone observatory. Vadoze Zone J. 17, 180129. https://doi.org/10.2136/vzj2018.07.0129 (2018).Article 
CAS 

Google Scholar 
McIntyre, D. H. Cenozoic geology of the Reynolds Creek Experimental Watershed, Owyhee County, Idaho (Idaho Bureau of Mines and Geology, 1972).Earth Resources Observation and Science (EROS) Center, U. Image of the week: Burned Area Analysis for the Soda Fire, Idaho, https://eros.usgs.gov/media-gallery/image-of-the-week/burned-area-analysis-the-soda-fire-idaho (2015).Jenny, H. Factors of Soil Formation (McGraw-Hill, 1941).Book 

Google Scholar 
Kormos, P. R. et al. 31 years of hourly spatially distributed air temperature, humidity, and precipitation amount and phase from Reynolds Critical Zone Observatory. Earth Syst. Sci. Data 10, 1197–1205. https://doi.org/10.5194/essd-10-1197-2018 (2018).Article 
ADS 

Google Scholar 
Thomas, G. W. In Methods in Soil Analysis. Part 3. Chemical Methods (ed Sparks, D. L. ) (Soil Science Society of America and American Society of Agronomy, 1996).Brodie, C. R. et al. Evidence for bias in C and N concentrations and δ13C composition of terrestrial and aquatic organic materials due to pre-analysis acid preparation methods. Chem. Geol. 282, 67–83. https://doi.org/10.1016/j.chemgeo.2011.01.007 (2011).Article 
ADS 
CAS 

Google Scholar 
Patton, N. P., Lohse, K. A., Seyfried, M. S., Will, R. & Benner, S. G. Lithology and coarse fraction adjusted bulk density estimates for determining total organic carbon stocks in dryland soils. Geoderma 337, 844–852. https://doi.org/10.1016/j.geoderma.2018.10.036 (2019).Article 
ADS 
CAS 

Google Scholar 
McGuire, L. A., Rasmussen, C., Youberg, A. M., Sanderman, J. & Fenerty, B. Controls on the Spatial distribution of near-surface pyrogenic carbon on hillslopes 1 year following wildfire. J. Geophys. Res.: Earth Surf. 126, e2020JF005996. https://doi.org/10.1029/2020JF005996 (2021).Article 
ADS 

Google Scholar 
Jiménez-González, M. A. et al. Spatial distribution of pyrogenic carbon in Iberian topsoils estimated by chemometric analysis of infrared spectra. Sci. Total Env. 790, 148170. https://doi.org/10.1016/j.scitotenv.2021.148170 (2021).Article 
CAS 

Google Scholar 
Baldock, J. A. et al. Quantifying the allocation of soil organic carbon to biologically significant fractions. Soil Res. 51, 561–576. https://doi.org/10.1071/SR12374 (2013).Article 
CAS 

Google Scholar 
Sanderman, J. et al. Soil organic carbon fractions in the Great Plains of the United States: An application of mid-infrared spectroscopy. Biogeochemistry 156, 97–114. https://doi.org/10.1007/s10533-021-00755-1 (2021).Article 
CAS 

Google Scholar 
Sherrod, L. A., Dunn, G., Peterson, G. A. & Kolberg, R. L. Inorganic carbon analysis by modified pressure-calcimeter method. Soil Sci. Soc. Am. J. 66, 299–305 (2002).Article 
ADS 
CAS 

Google Scholar 
Mikutta, R., Kleber, M., Kaiser, K. & Jahn, R. Review. Soil Sci. Soc. Am. J. 69, 120–135. https://doi.org/10.2136/sssaj2005.0120 (2005).Article 
ADS 
CAS 

Google Scholar 
Risk, D., Nickerson, N., Creelman, C., McArthur, G. & Owens, J. Forced Diffusion soil flux: A new technique for continuous monitoring of soil gas efflux. Agric. For. Meteorol. 151, 1622–1631. https://doi.org/10.1016/j.agrformet.2011.06.020 (2011).Article 
ADS 

Google Scholar 
Fierer, N. & Schimel, J. P. Effects of drying–rewetting frequency on soil carbon and nitrogen transformations. Soil Biol. Biochem. 34, 777–787. https://doi.org/10.1016/S0038-0717(02)00007-X (2002).Article 
CAS 

Google Scholar 
Dane, J. H., Topp, G. C. & Campbell, G. S. In Methods of Soil Analysis: Physical Methods. Vol. 4 (ed SSSA) 721–738 (2002). More