Ecology

Gao, Y., Schofield, O. M. & Leustek, T. Characterization of sulfate assimilation in marine algae focusing on the enzyme 5′-adenylylsulfate reductase. Plant Physiol. 123, 1087–1096 (2000).CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang, C.-W., Walker, M. E., Fedrizzi, B., Gardner, R. C. & Jiranek, V. Hydrogen sulfide and its roles in Saccharomyces cerevisiae in a winemaking context. FEMS Yeast Res. 17, 058 (2017).
Google Scholar 
Kopriva, S., Calderwood, A., Weckopp, S. C. & Koprivova, A. Plant sulfur and big data. Plant Sci. 241, 1–10 (2015).CAS 
PubMed 

Google Scholar 
Shibagaki, N. & Grossman, A. The state of sulfur metabolism in algae: From ecology to genomics. In Sulfur Metabolism in Phototrophic Organisms (eds Hell, C. D. R. et al.) 231–267 (Springer, 2008).
Google Scholar 
Fakhraee, M. & Katsev, S. Organic sulfur was integral to the Archean sulfur cycle. Nat. Commun. 10, 1–8 (2019).CAS 

Google Scholar 
Ho, T. Y. et al. The elemental composition of some marine phytoplankton 1. J. Phycol. 39, 1145–1159 (2003).CAS 

Google Scholar 
Jørgensen, B. B. Unravelling the sulphur cycle of marine sediments. Environ. Microbiol. 21, 3533–3538 (2019).PubMed 

Google Scholar 
El Mahrad, B. et al. Social-environmental analysis for the management of coastal lagoons in North Africa. Front. Environ. Sci. 8, 37 (2020).
Google Scholar 
Srarfi, F. Etude géochimique et état de pollution de la lagune de Bizerte. These de doctorat, Univ. Tunis el Manar 122 (2007).FAO. La Situation Mondiale Des Pêches et de L’aquaculture 2020 (Food & Agriculture Organisation, 2020).
Google Scholar 
Soto, D. & Wurmann, C. The Future of Ocean Governance and Capacity Development 379–384 (Brill Nijhoff, 2019).
Google Scholar 
Ran, W. et al. Storage of starch and lipids in microalgae: Biosynthesis and manipulation by nutrients. Bioresour. Technol. 291, 121894 (2019).CAS 
PubMed 

Google Scholar 
Aikawa, S. et al. Improving polyglucan production in cyanobacteria and microalgae via cultivation design and metabolic engineering. Biotechnol. J. 10, 886–898 (2015).CAS 
PubMed 

Google Scholar 
Klok, A., Lamers, P., Martens, D., Draaisma, R. & Wijffels, R. Edible oils from microalgae: Insights in TAG accumulation. Trends Biotechnol. 32, 521–528 (2014).CAS 
PubMed 

Google Scholar 
Yuan, Y. et al. Enhancing carbohydrate productivity of Chlorella sp. AE10 in semi-continuous cultivation and unraveling the mechanism by flow cytometry. Appl. Biochem. 185, 419–433 (2018).CAS 

Google Scholar 
Rodríguez, M. C., Matulewicz, M. C., Noseda, M., Ducatti, D. & Leonardi, P. I. Agar from Gracilaria gracilis (Gracilariales, Rhodophyta) of the Patagonic coast of Argentina-Content, structure and physical properties. Biores. Technol. 100, 1435–1441 (2009).
Google Scholar 
Lee, W.-K. et al. Factors affecting yield and gelling properties of agar. J. Appl. Phycol. 29, 1527–1540 (2017).
Google Scholar 
Fethi, M. & Ghedifa, A. B. Optimum ranges of combined abiotic factor for Gracilaria gracilis aquaculture. J. Appl. Phycol. 31, 3025–3040 (2019).
Google Scholar 
Friedlander, M. Inorganic nutrition in pond cultivated Gracilaria conferta (Rhodophyta): Nitrogen, phosphate and sulfate. J. Appl. Phycol. 13, 279–286 (2001).CAS 

Google Scholar 
Lee, W.-K., Namasivayam, P. & Ho, C.-L. Effects of sulfate starvation on agar polysaccharides of Gracilaria species (Gracilariaceae, Rhodophyta) from Morib, Malaysia. J. Appl. Phycol. 26, 1791–1799 (2014).CAS 

Google Scholar 
Carfagna, S. et al. Impact of sulfur starvation in autotrophic and heterotrophic cultures of the extremophilic microalga Galdieria phlegrea (Cyanidiophyceae). Plant Cell Physiol. 57, 1890–1898 (2016).CAS 
PubMed 

Google Scholar 
Collén, P. N., Camitz, A., Hancock, R. D., Viola, R. & Pedersén, M. Effect of nutrient deprivation and resupply on metabolites and enzymes related to carbon allocation in gracilaria tenuistipitata (rhodophyta) 1. J. Phycol. 40, 305–314 (2004).
Google Scholar 
Collier, J. L. & Grossman, A. A small polypeptide triggers complete degradation of light-harvesting phycobiliproteins in nutrient-deprived cyanobacteria. EMBO J. 13, 1039–1047 (1994).CAS 
PubMed 
PubMed Central 

Google Scholar 
Richaud, C., Zabulon, G., Joder, A. & Thomas, J.-C. Nitrogen or sulfur starvation differentially affects phycobilisome degradation and expression of the nblA gene in Synechocystis strain PCC 6803. J. Bacteriol. 183, 2989–2994 (2001).CAS 
PubMed 
PubMed Central 

Google Scholar 
Lloyd, A. G., Dodgson, K. S. & Rose, F. A. Infrared studies on sulphate esters I. Polysaccharide sulphates. Biochim. Biophys. Acta 46, 108–115 (1961).CAS 
PubMed 

Google Scholar 
Kawachi, M. & Noël, M.-H. Sterilization and sterile technique. In Algal Culturing Techniques (ed. Anderson, R. A.) 65–81 (Academic Press, 2005).
Google Scholar 
Harrison, P. J. & Berges, J. A. Marine culture media. In Algal Culturing Techniques (ed. Anderson, R. A.) 21–34 (Academic Press, 2005).
Google Scholar 
Guiry, M. & Cunningham, E. Photoperiodic and temperature responses in the reproduction of north-eastern Atlantic Gigartina acicularis (Rhodophyta: Gigartinales). Phycologia 23, 357–367 (1984).
Google Scholar 
Kolmert, Å., Wikström, P. & Hallberg, K. B. A fast and simple turbidimetric method for the determination of sulfate in sulfate-reducing bacterial cultures. J. Microbiol. Methods 41, 179–184 (2000).CAS 
PubMed 

Google Scholar 
Destombe, C., Godin, J., Nocher, M., Richerd, S. & Valero, M. In Fourteenth International Seaweed Symposium (eds Brown, M. T. & Lahaye, M.) 131–137 (Springer, 1993).
Google Scholar 
Rueness, J. & Tananger, T. In Eleventh International Seaweed Symposium (eds Bird, C. J. & Ragan, M. A.) 303–307 (Springer, 1984).
Google Scholar 
Shea, R. & Chopin, T. Effects of germanium dioxide, an inhibitor of diatom growth, on the microscopic laboratory cultivation stage of the kelp, Laminaria saccharina. J. Appl. Phycol. 19, 27–32 (2007).CAS 

Google Scholar 
Dawes, C., Orduna-Rojas, J. & Robledo, D. Response of the tropical red seaweed Gracilaria cornea to temperature, salinity and irradiance. J. Appl. Phycol. 10, 419–425 (1998).
Google Scholar 
Yaphe, W. & Arsenault, G. Improved resorcinol reagent for the determination of fructose, and of 3, 6-anhydrogalactose in polysaccharides. Anal. Biochem. 13, 143–148 (1965).CAS 

Google Scholar 
Mensi, F., Ksouri, J., Seale, E., Romdhane, M. S. & Fleurence, J. A statistical approach for optimization of R-phycoerythrin extraction from the red algae Gracilaria verrucosa by enzymatic hydrolysis using central composite design and desirability function. J. Appl. Phycol. 24, 915–926 (2012).CAS 

Google Scholar 
Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. T. & Smith, F. Colorimetric method for determination of sugars and related substances. Anal. Chem. 28, 350–356 (1956).CAS 

Google Scholar 
Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254 (1976).CAS 
PubMed 

Google Scholar 
Sörbo, B. Sulfate: Turbidimetric and nephelometric methods. Methods Enzymol. 143, 3–6 (1987).PubMed 

Google Scholar 
Redmond, S., Green, L., Yarish, C., Kim, J. & Neefus, C. New England Seaweed Culture Handbook (University of Connecticut Sea Garent, 2014).
Google Scholar 
Kakita, H. & Kamishima, H. Effects of environmental factors and metal ions on growth of the red alga Gracilaria chorda Holmes (Gracilariales, Rhodophyta). J. Appl. Phycol. 18, 469–474 (2006).CAS 

Google Scholar 
Berges, J. A., Franklin, D. J. & Harrison, P. J. Evolution of an artificial seawater medium: Improvements in enriched seawater, artificial water over the last two decades. J. Phycol. 37, 1138–1145 (2001).
Google Scholar 
Shpigun, L. K., Kolotyrkina, I. Y. & Zolotov, Y. A. Experience with flow-injection analysis in marine chemical research. Anal. Chim. Acta 261, 307–314 (1992).CAS 

Google Scholar 
Cosano, J., de Castro, M. & Valcarcel, M. Flow injection analysis of water. Part 1: Automatic preconcentration determination of sulphate, ammonia and iron (II)/iron (III). J. Autom. Chem. 15, 141–146 (1993).CAS 

Google Scholar 
Van Staden, J. & Taljaard, R. Determination of sulphate in natural waters and industrial effluents by sequential injection analysis. Anal. Chim. Acta 331, 271–280 (1996).
Google Scholar 
Petersen, S. P. & Ahring, B. K. Analysis of sulfate in sewage sludge using ion chromatographic techniques. J. Microbiol. Methods 12, 225–230 (1990).CAS 

Google Scholar 
Rand, M., Greenberg, A., Taras, K. & Franson, M. Standard Methods for the Examination of Water and Waste Water (American Public Health Association, 1975).
Google Scholar 
Wanner, G., Henkelmann, G., Schmidt, A. & Köst, H.-P. Nitrogen and sulfur starvation of the cyanobacterium Synechococcus 6301 an ultrastructural, morphometrical, and biochemical comparison. Zeitschrift Naturforschung C 41, 741–750 (1986).CAS 

Google Scholar 
Molloy, F. & Bolton, J. The effect of season and depth on the growth of Gracilaria gracilis at Lüderitz, Namibia. Bot. Mar. 39, 407–414 (1996).
Google Scholar 
Mensi, F., Nasraoui, S., Bouguerra, S., Ben Ghedifa, A. & Chalghaf, M. Effect of lagoon and sea water depth on Gracilaria gracilis growth and biochemical composition in the northeast of Tunisia. Sci. Rep. 10, 1–12 (2020).
Google Scholar 
Mensi, F., Ksouri, J., Hammami, W. & Romdhane, M. État des connaissances et perspectives de recherches sur la culture de Gracilariales (Gracilaria et Gracilariopsis): Application a la lagune de Bizerte. Bull. Inst. Natn. Scien. Tech. Mer Salammbô 41, 101–119 (2014).
Google Scholar 
Sugimoto, K., Sato, N. & Tsuzuki, M. Utilization of a chloroplast membrane sulfolipid as a major internal sulfur source for protein synthesis in the early phase of sulfur starvation in Chlamydomonas reinhardtii. FEBS Lett. 581, 4519–4522 (2007).CAS 
PubMed 

Google Scholar 
Cakmak, T. et al. Nitrogen and sulfur deprivation differentiate lipid accumulation targets of Chlamydomonas reinhardtii. Bioengineered 3, 343–346 (2012).PubMed 
PubMed Central 

Google Scholar 
Ostaszewska-Bugajska, M., Rychter, A. M. & Juszczuk, I. M. Antioxidative and proteolytic systems protect mitochondria from oxidative damage in S-deficient Arabidopsis thaliana. J. Plant Physiol. 186, 25–38 (2015).PubMed 

Google Scholar 
Zhang, L. et al. Sulfur deficiency-induced glucosinolate catabolism attributed to two β-glucosidases, BGLU28 and BGLU30, is required for plant growth maintenance under sulfur deficiency. Plant Cell Physiol. 61, 803–813 (2020).CAS 
PubMed 

Google Scholar 
Takahashi, H., Kopriva, S., Giordano, M., Saito, K. & Hell, R. Sulfur assimilation in photosynthetic organisms: Molecular functions and regulations of transporters and assimilatory enzymes. Annu. Rev. Plant biol. 62, 157–184 (2011).CAS 
PubMed 

Google Scholar 
Butterfield, N. J. Bangiomorpha pubescens n. gen., n. sp.: Implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386–404 (2000).
Google Scholar 
Collier, J. L. & Grossman, A. R. Chlorosis induced by nutrient deprivation in Synechococcus sp. strain PCC 7942: Not all bleaching is the same. J. Bacteriol. 174, 4718–4726. https://doi.org/10.1128/jb.174.14.4718-4726.1992 (1992).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Kaur, H. et al. Cys-Gly specific dipeptidase Dug1p from S. cerevisiae binds promiscuously to di-, tri-, and tetra-peptides: Peptide-protein interaction, homology modeling, and activity studies reveal a latent promiscuity in substrate recognition. Biochimie 93, 175–186. https://doi.org/10.1016/j.biochi.2010.09.008 (2011).CAS 
Article 
PubMed 

Google Scholar 
Said, R. B. et al. Effects of depth and initial fragment weights of Gracilaria gracilis on the growth, agar yield, quality, and biochemical composition. J. Appl. Phycol. 30, 2499–2512 (2018).
Google Scholar 
Bird, K. T. Agar production and quality from Gracilaria sp. strain G—16: Effects of environmental factors. Bot. Mar. 31, 33–38 (1988).
Google Scholar 
Cote, G. & Hanisak, M. Production and properties of native agars from Gracilaria tikvahiae and other red algae. Bot. Mar. 29, 359–366 (1986).CAS 

Google Scholar 
Lahaye, M. & Yaphe, W. Effects of seasons on the chemical structure and gel strength of Gracilaria pseudoverrucosa agar (Gracilariaceae, Rhodophyta). Carbohydr. Polym. 8, 285–301 (1988).CAS 

Google Scholar 
Yaphe, W. Eleventh International Seaweed Symposium 171–174 (Springer, 1984).
Google Scholar 
Duckworth, M., Hong, K. & Yaphe, W. The agar polysaccharides of Gracilaria species. Carbohydr. Res. 18, 1–9 (1971).CAS 

Google Scholar 
Rotem, A., Roth-Bejerano, N. & Arad, S. Effect of controlled environmental conditions on starch and agar contents of Gracilaria sp. (Rhodophyceae) 1. J. Phycol. 22, 117–121 (1986).CAS 

Google Scholar 
Arad, S. M., Lerental, Y. B. & Dubinsky, O. Effect of nitrate and sulfate starvation on polysaccharide formation in Rhodella reticulata. Bioresour. Technol. 42, 141–148 (1992).CAS 

Google Scholar  More

Carpenter, K. E. et al. One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321, 560–563 (2008).CAS 
PubMed 
Article 

Google Scholar 
Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. 9, 4921–4932 (2018).PubMed 
PubMed Central 
Article 
CAS 

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

Google Scholar 
Rosenberg, E. & Zilber-Rosenberg, I. Microbes drive evolution of animals and plants: the hologenome concept. mBio 7, e01395 (2016).CAS 
PubMed 
PubMed Central 
Article 

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

Google Scholar 
Reshef, L., Koren, O., Loya, Y., Zilber-Rosenberg, I. & Rosenberg, E. The coral probiotic hypothesis. Environ. Microbiol. 8, 2068–2073 (2006).CAS 
PubMed 
Article 

Google Scholar 
Ainsworth, T. D., Thurber, R. V. & Gates, R. D. The future of coral reefs: a microbial perspective. Trends Ecol. Evol. 25, 233–240 (2010).PubMed 
Article 

Google Scholar 
Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426–429 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Freter, R. The fatal enteric cholera infection in the guinea pig, achieved by inhibition of normal enteric flora. J. Infect. Dis. 97, 57–65 (1955).CAS 
PubMed 
Article 

Google Scholar 
Corr, S. C. et al. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc. Natl. Acad. Sci. USA 104, 7617–7621 (2007).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kamada, N. et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336, 1325–1329 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Khosravi, A. et al. Gut microbiota promote hematopoiesis to control bacterial infection. Cell Host Microbe 15, 374–381 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li, J., Kuang, W. Q., Long, L. J. & Zhang, S. Production of quorum-sensing signals by bacteria in the coral mucus layer. Coral Reefs 36, 1235–1241 (2017).Article 

Google Scholar 
Alagely, A., Krediet, C. J., Ritchie, K. B. & Teplitski, M. Signaling-mediated cross-talk modulates swarming and biofilm formation in a coral pathogen Serratia marcescens. ISME J. 5, 1609–1620 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Krediet, C. J., Ritchie, K. B., Alagely, A. & Teplitski, M. Members of native coral microbiota inhibit glycosidases and thwart colonization of coral mucus by an opportunistic pathogen. ISME J. 7, 980–990 (2013).CAS 
PubMed 
Article 

Google Scholar 
Thompson, F. L., Hoste, B., Thompson, C. C., Huys, G. & Swings, G. The coral bleaching Vibrio shiloi Kushmaro et al. 2001 is a later synonym of Vibrio mediterranei Pujalte and Garay 1986. Syst. Appl. Microbiol. 24, 516–519 (2001).CAS 
PubMed 
Article 

Google Scholar 
Santoro, E. P. et al. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci. Adv. 7, eabg3088 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tang, K. H. et al. Antagonism between coral pathogen Vibrio coralliilyticus and other bacteria in the gastric cavity of scleractinian coral Galaxea fascicularis. Sci. China-Earth Sci. 63, 157–166 (2020).CAS 
Article 

Google Scholar 
Zhou, Y. Q. et al. Identification of bacteria-derived urease in the coral gastric cavity. Sci. China-Earth Sci. 63, 1553–1563 (2020).CAS 
Article 

Google Scholar 
Chen, B. et al. Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea. Sci. Total Environ. 765, 142690 (2021).CAS 
PubMed 
Article 

Google Scholar 
Tout, J. et al. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis. Front. Microbiol. 6, 432 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Savary, R. et al. Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea. Proc. Natl. Acad. Sci. USA 118, e2023298118 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Vezzulli, L. et al. Vibrio infections triggering mass mortality events in a warming Mediterranean Sea. Environ. Microbiol. 12, 2007–2019 (2010).CAS 
PubMed 
Article 

Google Scholar 
Rosenberg, E. & Falkovitz, L. The Vibrio shiloi/Oculina patagonica model system of coral bleaching. Annu. Rev. Microbiol. 58, 143–159 (2004).CAS 
PubMed 
Article 

Google Scholar 
Gibbin, E. et al. Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral. ISME J. 13, 989–1003 (2019).CAS 
PubMed 
Article 

Google Scholar 
Kimes, N. E. et al. Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J. 6, 835–846 (2012).CAS 
PubMed 
Article 

Google Scholar 
Banin, E., Vassilakos, D., Orr, E., Martinez, R. J. & Rosenberg, E. Superoxide dismutase is a virulence factor produced by the coral bleaching pathogen Vibrio shiloi. Curr. Microbiol. 46, 418–422 (2003).CAS 
PubMed 
Article 

Google Scholar 
Meron, D. et al. Role of flagella in virulence of the coral pathogen Vibrio coralliilyticus. Appl. Environ. Microbiol. 75, 5704–5707 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rubio-Portillo, E. et al. Virulence as a side effect of interspecies interaction in Vibrio coral pathogens. mBio 11, e00201-20 (2020).Rubio-Portillo, E., Yarza, P., Penalver, C., Ramos-Espla, A. A. & Anton, J. New insights into Oculina patagonica coral diseases and their associated Vibrio spp. communities. ISME J. 8, 1794–1807 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Bourne, D. G. et al. Microbial disease and the coral holobiont. Trends Microbiol. 17, 554–562 (2009).CAS 
PubMed 
Article 

Google Scholar 
Ben-Haim, Y., Zicherman-Keren, M. & Rosenberg, E. Temperature-regulated bleaching and lysis of the coral Pocillopora damicornis by the novel pathogen Vibrio coralliilyticus. Appl. Environ. Microbiol. 69, 4236–4242 (2003).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gavish, A. R., Shapiro, O. H., Kramarsky-Winter, E. & Vardi, A. Microscale tracking of coral–vibrio interactions. ISME Commun. 1, 18 (2021).Shapiro, O. H. et al. Vortical ciliary flows actively enhance mass transport in reef corals. Proc. Natl. Acad. Sci. USA 111, 13391–13396 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Shapiro, O. H., Kramarsky-Winter, E., Gavish, A. R., Stocker, R. & Vardi, A. A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals. Nat. Commun. 7, 10860 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chen, D. D. et al. Identification and characterization of microsatellite markers for scleractinian coral Galaxea fascicularis and its symbiotic zooxanthellae. Conservation. Genet. Resour. 5, 741–743 (2013).Article 

Google Scholar 
Parks, D. H. et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat. Biotechnol. 38, 1079–1086 (2020).CAS 
PubMed 
Article 

Google Scholar 
Liu, X. et al. Symbiosis of a P2-family phage and deep-sea Shewanella putrefaciens. Environ. Microbiol. 21, 4212–4232 (2019).CAS 
PubMed 
Article 

Google Scholar 
Wang, P. et al. Eliminating mcr-1-harbouring plasmids in clinical isolates using the CRISPR/Cas9 system. J. Antimicrob. Chemother. 74, 2559–2565 (2019).CAS 
PubMed 
Article 

Google Scholar 
Zeng, Z. et al. Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis. ISME J. 10, 2787–2800 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Wang, X. et al. Cryptic prophages help bacteria cope with adverse environments. Nat. Commun. 1, 147 (2010).Bardwell, J. C., McGovern, K. & Beckwith, J. Identification of a protein required for disulfide bond formation in vivo. Cell 67, 581–589 (1991).CAS 
PubMed 
Article 

Google Scholar 
Wang, X., Kim, Y. & Wood, T. K. Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms. ISME J. 3, 1164–1179 (2009).CAS 
PubMed 
Article 

Google Scholar 
Wood, T. K., Gonzalez Barrios, A. F., Herzberg, M. & Lee, J. Motility influences biofilm architecture in Escherichia coli. Appl. Microbiol. Biotechnol. 72, 361–367 (2006).CAS 
PubMed 
Article 

Google Scholar 
Song, S., Guo, Y., Kim, J. S., Wang, X. & Wood, T. K. Phages mediate bacterial self-recognition. Cell Rep. 27, 737–749 (2019).CAS 
PubMed 
Article 

Google Scholar 
Krediet, C. J., Carpinone, E. M., Ritchie, K. B. & Teplitski, M. Characterization of the gacA-dependent surface and coral mucus colonization by an opportunistic coral pathogen Serratia marcescens PDL100. FEMS Microbiol. Ecol. 84, 290–301 (2013).CAS 
PubMed 
Article 

Google Scholar 
Guo, Y., Lin, J. & Wang, X. Rapid detection of temperate bacteriophage using a simple motility assay. Environ. Microbiol. Rep. 13, 728–734 (2021).CAS 
PubMed 
Article 

Google Scholar 
Tang, K. et al. Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment. Nucleic Acids Res. 49, e128 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ding, J. Y., Shiu, J. H., Chen, W. M., Chiang, Y. R. & Tang, S. L. Genomic insight into the host–endosymbiont relationship of Endozoicomonas montiporae CL-33(T) with its coral host. Front. Microbiol. 7, 251 (2016).PubMed 
PubMed Central 

Google Scholar 
Yang, C. S. et al. Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata. Int. J. Syst. Evol. Microbiol. 60, 1158–1162 (2010).CAS 
PubMed 
Article 

Google Scholar 
Schreiber, L., Kjeldsen, K. U., Obst, M., Funch, P. & Schramm, A. Description of Endozoicomonas ascidiicola sp nov., isolated from Scandinavian ascidians. Syst. Appl. Microbiol. 39, 313–318 (2016).CAS 
PubMed 
Article 

Google Scholar 
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lu, S. N. et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 48, D265–D268 (2020).CAS 
PubMed 
Article 

Google Scholar 
Mai-Prochnow, A. et al. Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several Gram-negative bacteria. J. Bacteriol. 190, 5493–5501 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Campillo-Brocal, J. C., Lucas-Elio, P. & Sanchez-Amat, A. Identification in Marinomonas mediterranea of a novel quinoprotein with glycine oxidase activity. MicrobiologyOpen 2, 684–694 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chacon-Verdu, M. D., Gomez, D., Solano, F., Lucas-Elio, P. & Sanchez-Amat, A. LodB is required for the recombinant synthesis of the quinoprotein l-lysine-epsilon-oxidase from Marinomonas mediterranea. Appl. Microbiol. Biotechnol. 98, 2981–2989 (2014).CAS 
PubMed 
Article 

Google Scholar 
Gomez, D., Lucas-Elio, P., Solano, F. & Sanchez-Amat, A. Both genes in the Marinomonas mediterranea lodAB operon are required for the expression of the antimicrobial protein lysine oxidase. Mol. Microbiol. 75, 462–473 (2010).CAS 
PubMed 
Article 

Google Scholar 
Piewngam, P. et al. Pathogen elimination by probiotic Bacillus via signalling interference. Nature 562, 532–537 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zipperer, A. et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature 535, 511–516 (2016).CAS 
PubMed 
Article 

Google Scholar 
Selva, L. et al. Killing niche competitors by remote-control bacteriophage induction. Proc. Natl. Acad. Sci. USA 106, 1234–1238 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Regev-Yochay, G., Trzcinski, K., Thompson, C. M., Malley, R. & Lipsitch, M. Interference between Streptococcus pneumoniae and Staphylococcus aureus: in vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae. J. Bacteriol. 188, 4996–5001 (2006).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Paul, J. H. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2, 579–589 (2008).CAS 
PubMed 
Article 

Google Scholar 
Frazao, N., Sousa, A., Lassig, M. & Gordo, I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc. Natl. Acad. Sci. USA 116, 17906–17915 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yu, M. et al. Purification and characterization of antibacterial compounds of Pseudoalteromonas flavipulchra JG1. Microbiology-SGM 158, 835–842 (2012).CAS 
Article 

Google Scholar 
James, S. G., Holmstrom, C. & Kjelleberg, S. Purification and characterization of a novel antibacterial protein from the marine bacterium D2. Appl. Environ. Microbiol. 62, 2783–2788 (1996).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lucas-Elio, P., Gomez, D., Solano, F. & Sanchez-Amat, A. The antimicrobial activity of marinocine, synthesized by Marinomonas mediterranea, is due to hydrogen peroxide generated by its lysine oxidase activity. J. Bacteriol. 188, 2493–2501 (2006).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Imlay, J. A. & Linn, S. Mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide. J. Bacteriol. 169, 2967–2976 (1987).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Los, J. M., Los, M., Wegrzyn, G. & Wegrzyn, A. Differential efficiency of induction of various lambdoid prophages responsible for production of Shiga toxins in response to different induction agents. Microb. Pathog. 47, 289–298 (2009).CAS 
PubMed 
Article 

Google Scholar 
Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466–470 (2016).CAS 
PubMed 
Article 

Google Scholar 
Howard-Varona, C., Hargreaves, K. R., Abedon, S. T. & Sullivan, M. B. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 11, 1511–1520 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Arkin, A. P. et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat. Biotechnol. 36, 566–569 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Luo, P., He, X. Y., Liu, Q. T. & Hu, C. Q. Developing universal genetic tools for rapid and efficient deletion mutation in Vibrio species based on suicide T-vectors carrying a novel counterselectable marker, vmi480. PLoS ONE 10, e0144465 (2015).Wang, P. et al. Development of an efficient conjugation-based genetic manipulation system for Pseudoalteromonas. Microb. Cell Fact. 14, 11 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Bertani, L. E. & Bertani, G. Preparation and characterization of temperate, non-inducible bacteriophage P2 (host: Escherichia coli). J. Gen. Virol. 6, 201–212 (1970).CAS 
PubMed 
Article 

Google Scholar 
Garneau, J. R., Depardieu, F., Fortier, L. C., Bikard, D. & Monot, M. PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep. 7, 8292 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Pratt, L. A. & Kolter, R. Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol. Microbiol. 30, 285–293 (1998).CAS 
PubMed 
Article 

Google Scholar 
Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Brynildsrud, O., Bohlin, J., Scheffer, L. & Eldholm, V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 17, 238 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).CAS 
PubMed 
PubMed Central 
Article 

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

Google Scholar 
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yilmaz, P. et al. The SILVA and ‘All-species Living Tree Project (LTP)’ taxonomic frameworks. Nucleic Acids Res. 42, D643–D648 (2014).CAS 
PubMed 
Article 

Google Scholar 
Chong, J., Liu, P., Zhou, G. & Xia, J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat. Protoc. 15, 799–821 (2020).CAS 
PubMed 
Article 

Google Scholar 
Nagpal, S., Singh, R., Yadav, D. & Mande, S. S. MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks. Nucleic Acids Res. 48, W572–W579 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar  More

Study siteThe study was conducted at the Center for Applied Research on the Environment and Sustainability (CARES) at The American University in Cairo, New Cairo, Egypt (30°01′11.7″N 31°29′59.8″E) from 12/Nov/2019 until 31st/March/2020. The experiment was carried out in a greenhouse-controlled environment with temperatures ranging from 18 to 23 °C and relative humidity between 60 and 70% during the growing period.Experimental designThe proposed design starts by treating brackish water using RO membrane separation technology, powered by an on-grid 10 kW photovoltaic solar panel as shown in Fig. 1. The permeate (freshwater) from the RO facility is directed to the aquaculture units of capacity of 1 m3, where the fish effluents are used as irrigation water and as the sole source of fertilizers for the crops.Figure 1Schematic Integrated model design. T1 Deep water culture system without sand, T2 Sandponics system with sand from October, T3 Sandponics system with sand from Beni suef, T4 Sandponics system with sand from Fayoum.Full size imageThe study followed a completely randomized design with four variants, i.e., an aquaponic deep-water culture system (T1) and three sandponics systems (T2–T4). The three sandponics systems were established with different sand collected from different sand locations in Egypt during the period between September and October 2019.Initially, an exploratory field trip was set to six different locations in Egypt to collect sand samples for lab analysis aimed at sourcing the most suitable sand for the system under study with regards to both the physical and chemical parameters. These areas include Ismailia Governorate; 30°34′55.2″N 31°50′08.1″E, 6th October governorate; 29°54′49.8″N 31°05′51.5″E, Benu Suef governorate; 28°53′18.4″N 30°45′12.9″E, Al-Minya governorate; 28.725799, 30.630305, and two sites from Fayoum governorate; 29°05′07.4″N 30°49′39.9″E.From the six locations in Egypt, preliminary sand analysis was carried out, and sand samples were also collected for both physical and chemical lab analysis at the Soil and Water Lab at the Agricultural Research Center in Dokki, Egypt. Following a thorough technical, field, mechanical, and lab chemical evaluation of the six sand samples from six locations, three sand locations/types were selected for experimentation that seemed fit and suitable for the current study. The criteria parameters for the shortlisting of sand included water retention potential of the sand by the percolation process, testing the carbonates level in the soil, the turbidity of the sand, porosity percentage and drainage potential of the sand. The three locations included 6th October (T2), Benu Suef (T3), and Fayoum site 2 (T4). In the second week of November 2019, ten cubic meter tracks of sand from the three above locations were set to collect sand from these areas to the research facility at CARES where the experiment was carried out.The study was carried out with two systems/setups, i.e., an aquaponic Deep Water Culture (DWC) and SP systems. The DWC model comprises a 1 m3 fish tank, a settlement tank, a mechanical filter, a biological filter, three grow beds, and a drainage tank. This system being the most practiced aquaponics technique was considered as the control. Fish effluent water flowed from the fish tank to the settlement tank to filter big solid wastes through the mechanical filter to remove the smaller solid wastes and the biological filter for the nitrification process. Then filtered water continues to the grow beds, where overflow drains into the drainage tank and back to the fish tank in a closed system.On the other hand, the variable in the three IAVS systems is the sand source. This system comprises three independent set-ups: a 1 m3 fish tank, three grow beds, and a drainage tank. Fish effluents flowed from the fish tank directly to the sand grow beds where water was supplied through irrigation drip lines using diaghram emitters connected with valves to ensure uniformity of water application to each grow bed.All the fish tanks were installed with the same fish stock size of 30 Nile tilapia (Oreochromis niloticus) from an existing fish stock at the research center with an average initial weight of 244 g and the same amount of water, initially 850L per tank. The fish was sourced from an already existing aquaponics system at the research center to avoid any transportation stress effects and related shocks on the small fish, leading to a lot of mortality cases. The fish were fed 3–4 times daily with commercial pellets containing 30% proteins, 5% crude lipid, 6% crude fiber, 13% Ash, and 9% moisture content supplied by Skretting Egypt. The feeding pattern and frequency were according to the fish body biomass percentage of 2–3% depending on the growth stage and upon reaching satiation.DesalinationThe experiment was entirely run with desalinated water produced from a desalination facility at the center. The desalination technology used was Reverse Osmosis (RO); in batch mode; using a Sea Water Pump with Energy Recovery Unit (model Danfoss-APP1.0/APM1.2). The RO membrane used is Hydraunatic SWC5-4040, from Lenntech company with an average salt rejection of 99.7%. Three modules were connected in a series arrangement (3 Pressure Vessels each equipped with a single module). Synthesized brackish water was prepared by dissolving industrial grade sodium chloride (sea salt) from El-Arish Governorate, Egypt. The salt chemical properties are presented in Table 1. Feedwater salinity was 10 mg/L, with an equivalent osmotic pressure equal to 8.61 bars. The osmotic pressure was calculated using Van’t Hoff relation. Permeate Total Dissolved Solids (TDS) was 192 mg/L, and brine TDS was 13.1 g/L as shown in Table 2.Table 1 Chemical properties of the used salt.Full size tableTable 2 Chemical properties of water samples used.Full size tableThe average pure water flux is 9.5 LMH and was calculated by dividing the permeate volume by the product of membrane surface area and time. Each batch run produced around 4 m3 of permeate, which was enough to irrigate the designated plant beds. The estimated average permeate recovery for the RO process is 22% and salt rejection exceeded 98.7%. The differential pressure between membrane inlet and outlet was equal to 1 bar, where membrane inlet pressure was 16 bars, and the outlet was 15 bars. The RO process operated at an average transmembrane pressure equal to 16 bars and an average permeate and brine flow rates equivalent to 3.49 and 12.41 Lpm, respectively. All experiment runs were performed at 25 °C.Plant materials and cultivation practiceSwiss chard bright lights (Beta vulgaris subsp. cicia) seeds were imported from Seed kingdom seed company in the USA. Seeds were sown in ¼ inch holes in a seed starting mix containing perlite and vermiculite and irrigated with a hand mist sprayer daily to keep the growing media always moist. Sowing was done on the 12th of November 2019, and seedlings were transplanted when they were 40 days old. Seedlings were transplanted into raised grow beds made of fiberglass material measuring 1.8 × 1.2 × 0.6 m for each of the four systems. The beds were raised off the ground by 0.5 m to allow drainage water from the bed to be collected and circulated back to the fish tank. Each bed was constructed with a drainage pipe at the bottom covered with a mesh net to prevent water blockage by the sand. Also, a 5 cm layer of small gravel was uniformly laid at the bottom of the beds to facilitate drainage, followed by sand with a height of 50 cm.In the IAVS systems, plants were irrigated using manually punched diaphragm emitters, and the irrigation flow rate was controlled using small plastic valves at the start of every irrigation tube. Emitters were installed in drip tubing at a 30 cm distance as well the tubing lines were also placed 30 cm between each other. Seedlings were transplanted 5 cm away from the emitters at 30 cm between rows and 30 cm within the row. Since the water was pumped with submersible pumps to the grow beds, regulatory pressure valves were installed in between the pump and the main irrigation line, and then water flows through the emitters into the row furrows. Water would then saturate in the sand and eventually drain at the bottom into drainage tanks and pumped back to the fish tanks.To maintain the water quality, two full cycles of water recirculation were run every day. Every irrigation cycle recirculated 25% of the fish tank, and complete drainage was allowed for a maximum of two hours. Plants were harvested upon reaching maturity for three cuts, except with the T1, which could not grow back after the second cut. Plants took 52 days from transplanting to reach the first cut, 20 days from cut 1 to cut 2, and as well 23 days from cut 2 to reach cut 3. Measurable crop parameters included plant height at harvesting/cutting, leaf area, number of leaves per plant, chlorophyll content, fresh weight per plant, and nutrient composition. Since the focus of SP is on the crops, fish were only measured to monitor their relative growth in terms of weight gained at harvesting/cutting time.Measurement of crop parametersPlants were cut 5 cm above the soil surface, and agronomical trait measurements from a representative sample of 12 plants per replicate were taken as follows.Plant heights were taken using a foot ruler and averages determined. Leaf number was obtained as the number of leaves counted per plant and averages determined. Leaf area was calculated according to the equation reported by Yeshitila and Taye16.$${text{Leaf}} , {text{ Area }}left( {{text{cm}}^{{2}} } right) = , – {422}.{973} + { 22}.{752}0{text{L }}left( {{text{cm}}} right) , + { 8}.{text{31W }}left( {{text{cm}}} right)$$where L and W represent the leaf length and Leaf width respectively, − 422.973 is a constant relating to the shape of the leaf of Swiss chard developed by the author under citation.Chlorophyll content was measured using MC-100 chlorophyll meter from Apogee Instruments, Inc, and data was expressed as SPAD averages. Fresh weight was measured using a digital weighing balance and data expressed as g/plant.Sand testSand samples were obtained and sent for analysis at the Soils, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt. The Electrical conductivity (EC) values were measured from the sand paste extract; pH values were taken from sand suspensions at ratio of 1:2.5 as described by Estefan17. The available nitrogen in the sand sample was extracted using potassium chloride (KCl) as an extractable solution with the ratio of (5gm sand to 50 ml KCl) and determined using the micro- kjeldahl method. Available potassium was determined using a flame photometer, and the other elements in the sand sample were determined by using inductively coupled plasma (ICP) Spectrometry (model Ultima 2 JY Plasma)18,19. The physical and chemical characteristics of the used sand are presented in Table 3.Table 3 (a): Chemical analysis of field sand samples, (b): Available macro, micronutrients, and heavy metals content of the sand samples.Full size tableWater analysisEvery 15 days, a measured amount of desalinated water was added to a standard mark of 850L in the fish tanks to compensate for the consumed amount of water in the system. Fish water quality parameters such as water temperature, pH, and dissolved oxygen (DO) was closely monitored using automated digital Nilebot technologies by Conative labs to fit the ideal required levels as reported by Somerville et al.20. In contrast, ammonia, nitrite, and nitrate were adjusted using an API test kit every week. These parameters’ recorded values were as follows: water temperature ranged between 25 and 28 °C, DO range between 6–7 mg/L, and pH between 6.5 and 7.0. Ammonia levels were kept below 1 mg/L. Elements in water samples were determined according to EPA methods18 using inductively coupled plasma (ICP) Spectrometry (model Ultima 2 JY Plasma) as presented in Table 4.Table 4 Water sample analysis for the different systems’ fish tanks and sump tanks.Full size tableNutritive composition analysisAccording to Official methods of analysis from the association of official analytical chemists (A.O.A.C) (1990), moisture content and Vitamin C were determined. Vitamin A was determined according to the procedures described by Aremu and Nweze21. Briefly, 100 g of the sample were homogenized, from which 1 g was obtained and soaked in 5 mL methanol for two hours at room temperature in the dark for complete extraction of a pro-vitamin A carotenoid, β-carotene. Separation of the β-carotene layer was achieved through the addition of hexane to the sample, and moisture was removed using sodium sulphonate. The absorbance of the layer was measured at 436 nm using hexane as a blank. β-carotene was calculated using the formula:$$beta {text{-carotene }}left( {{mu g}/{1}00{text{ g}}} right) , = {text{ Absorbance }}left( {text{436 nm}} right) , times {text{ V }} times {text{ D }} times { 1}00 , times { 1}00/{text{W }} times {text{ Y}}$$where: V = total volume of the extract; D = Dilution factor; W = Sample weight; Y = Percentage dry matter content of the sample.Vitamin A was then determined according to the concept of Retinol Equivalent (RE) of the β-carotene content of the vegetables using the standard conversion formula. Total hydrolyzable carbohydrates were determined as glucose using phenol–sulfuric acid reagent as described by Michel22.Vitamin C content was determined using dichlorophenol indophenol reagent. As such, 10 g of fresh leaf tissues, were crushed using a motor and pestle in the presence of 10 ml metaphosphoric acid 6% (Merck). This was followed by centrifugation at 4000×g for 5 min at 4 °C. Five mL of the supernatant were transferred into an Erlenmeyer flask, and 20 mL of 3% metaphosphoric acid were added. The extract was titrated by dichlorophenol indophenol (Sigma-Aldrich) until a rose color was observed. Vitamin C (mg/100 g FW) was then calculated and based on the standard curve of l-Ascorbic acid (Merck) concentrations.For the determination of protein and mineral content, 0.5 g of dried samples were digested using sulfuric acid (H2SO4) and hydrogen peroxide (H2O2) as described by Cottenie23. From the extracted sample, the following minerals were determined:Nitrogen was determined according to the procedures described by Plummer24. Briefly, 5 mL of the digestive solution was distilled with 10 mL of sodium hydroxide (NaOH) for 10 min to obtain ammonia. Back titration was then used to determine the amount of nitrogen present in ammonia. Protein content was calculated by multiplying total nitrogen by 6.25 according to methods of AOAC25.Phosphorus content was determined calorimetrically (660 nm) according to the procedures described by Jackson26. Potassium, Calcium, and Sodium were determined against a standard using a flame-photometer (JEN way flame photometer) as described by Piper27. Magnesium (Mg), Copper (Cu), Manganese (Mn), Zinc (Zn), and Iron (Fe) content were determined using Atomic Absorption Spectrophotometer, Pyeunican SP1900, according to methods described by Liu28.The moisture percentage of leaf samples was determined by weighing the fresh weight for each sample (Fw), then dried for 72 h at 80 °C. The dry matter weight was record as Dw. The leaf water content was then calculated as the following:$${text{Moisture}};{text{ content }}left( % right) , = , left( {{text{Fw}} – {text{Dw}}} right) , /{text{ Fw}} * {1}00$$Statistical analysisStatistical comparisons among means of more than two groups were performed with analysis of variance (ANOVA) using SPSS V22, and the difference in means was analyzed by Tukey’s test at α = 0.05. Statistical differences were considered significant at P ≤ 0.05 in triplicates and data expressed as mean ± S.D.Plant materialAll plant materials and related procedures in this study were done in accordance with the guidelines of the Institutional Review Board of the American University in Cairo and the Ministry of Agriculture and Land Reclamation in Egypt.Ethics approvalThis study followed the guidelines and approval of Committee of Animal Welfare and Research Ethics, Faculty of Agriculture, Kafrelsheikh University, Egypt. More

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.This is a summary of: Quinton, J. N. et al. Tillage exacerbates the vulnerability of cereal crops to drought. Nat. Food https://doi.org/10.1038/s43016-022-00533-8 (2022). More

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Google Scholar  More

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Google Scholar  More