Philippa Kaur

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.This is a summary of: Sauterey, B. et al. Early Mars habitability and global cooling by H2-based methanogens. Nat. Astron. https://doi.org/10.1038/s41550-022-01786-w (2022). More

Howe, B. M. et al. Observing the oceans acoustically. Front. Mar. Sci. 6, 426. https://doi.org/10.3389/fmars.2019.00426 (2019).Article 

Google Scholar 
Molenaar, M. M., Hill, D., Webster, P., Fidan, E. & Birch, B. First downhole application of distributed acoustic sensing for hydraulic-fracturing monitoring and diagnostics. SPE Drill. Complet. 27, 32–38. https://doi.org/10.2118/140561-PA (2012).Article 

Google Scholar 
Lindsey, N. J. et al. Fiber-optic network observations of earthquake wavefields. Geophys. Res. Lett. 44, 11792–11799. https://doi.org/10.1002/2017GLO75722 (2017).Article 
ADS 

Google Scholar 
Jousset, P. et al. Dynamic strain determination using fibre-optic cables allows imaging of seismological and structural features. Nat. Commun. 9, 1–11. https://doi.org/10.1038/s41467-018-04860-y (2018).Article 
CAS 

Google Scholar 
Ajo-Franklin, J. B. et al. Distributed acoustic sensing using dark fiber for near-surface characterization and broadband seismic event detection. Sci. Rep. 9, 1–14. https://doi.org/10.1038/s41598-018-36675-8 (2019).Article 
CAS 

Google Scholar 
Williams, E. F. et al. Distributed sensing of microseisms and teleseisms with submarine dark fibers. Nat. Commun. 10, 1–11. https://doi.org/10.1038/s41467-019-13262-7 (2019).Article 
CAS 

Google Scholar 
Lindsey, N. J., Dawe, T. C. & Ajo-Franklin, J. B. Illuminating seafloor faults and ocean dynamics with dark fiber distributed acoustic sensing. Science 366, 1103–1107. https://doi.org/10.1126/science.aay5881 (2019).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Sladen, A. et al. Distributed sensing of earthquakes and ocean-solid Earth interactions on seafloor telecom cables. Nat. Commun. 10, 5777. https://doi.org/10.1038/s41467-019-13793-z (2019).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Williams, E. F. et al. Surface gravity wave interferometry and ocean current monitoring with ocean-bottom DAS. J. Geophys. Res. Oceans 127, e2021JC018375. https://doi.org/10.1029/2021JC018375 (2022).Article 
ADS 

Google Scholar 
Zhan, Z. et al. Optical polarization-based seismic and water wave sensing on transoceanic cables. Science 371, 931–936. https://doi.org/10.1126/science.abe6648 (2021).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Waagaard, O. H. et al. Real-time low noise distributed acoustic sensing in 171 km low loss fiber. OSA Contin. 4, 688–701. https://doi.org/10.1364/OSAC.408761 (2021).Article 
CAS 

Google Scholar 
Rivet, D., de Cacqueray, B., Sladen, A., Roques, A. & Calbris, G. Preliminary assessment of ship detection and trajectory evaluation using distributed acoustic sensing on an optical fiber telecom cable. J. Acoust. Soc. Am. 149, 2615–2627. https://doi.org/10.1121/10.0004129 (2021).Article 
ADS 
PubMed 

Google Scholar 
Taweesintananon, K., Landrø, M., Brenne, J. K. & Haukanes, A. Distributed acoustic sensing for near-surface imaging using submarine telecommunication cable: a case study in the Trondheimsfjord, Norway. Geophysics 86, B303–B320. https://doi.org/10.1190/geo2020-0834.1 (2021).Article 

Google Scholar 
Matsumoto, H. et al. Detection of hydroacoustic signals on a fiber-optic submarine cable. Sci. Rep. 11, 2797. https://doi.org/10.1038/s41598-021-82093-8 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bouffaut, L. et al. Eavesdropping at the speed of light: Distributed acoustic sensing of baleen whales in the Arctic. Front. Mar. Sci. 9, 901348. https://doi.org/10.3389/fmars.2022.901348 (2022).Article 

Google Scholar 
Jones, N. The quest for quieter seas. Nature 568, 158–161. https://doi.org/10.1038/d41586-019-01098-6 (2019).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Williams, R. et al. Chronic ocean noise and cetacean population models. J. Cetacean Res. Manag. 21, 85–94. https://doi.org/10.47536/jcrm.v21i1.202 (2020).Article 

Google Scholar 
Roman, J. et al. Whales as marine ecosystem engineers. Front. Ecol. Environ. 12, 377–385. https://doi.org/10.1890/130220 (2014).Article 

Google Scholar 
Pershing, A. J., Christensen, L. B., Record, N. R., Sherwood, G. D. & Stetson, P. B. The impact of whaling on the ocean carbon cycle: Why bigger was better. PLoS ONE 5, 1–9. https://doi.org/10.1371/journal.pone.0012444 (2010).Article 
CAS 

Google Scholar 
IUCN – SSC Cetacean Specialist Group. Status of the World’s cetaceans (2021). https://iucn-csg.org/status-of-the-worlds-cetaceans/.Bailey, H. et al. Behavioural estimation of blue whale movements in the Northeast Pacific from state-space model analysis of satellite tracks. Endanger. Species Res. 10, 93–106. https://doi.org/10.3354/esr00239 (2010).Article 

Google Scholar 
Thomas, P. O., Reeves, R. R. & Brownell, R. L. Jr. Status of the world’s baleen whales. Mar. Mamm. Sci. 32, 682–734. https://doi.org/10.1111/mms.12281 (2016).Article 

Google Scholar 
Grigoli, F. et al. Current challenges in monitoring, discrimination, and management of induced seismicity related to underground industrial activities: A European perspective. Rev. Geophys. 55, 310–340. https://doi.org/10.1002/2016RG000542 (2017).Article 
ADS 

Google Scholar 
Bigg, G. R. & Hanna, E. Impacts and effects of ocean warming on the weather. In: Laffoley, D. & Baxter, J. M. (eds.) Explaining ocean warming: Causes, scale, effects and consequences, 359–372, https://doi.org/10.2305/IUCN.CH.2016.08.en (International Union for Conservation of Nature and Natural Resources (IUCN), Gland, Switzerland, 2016).Hartog, A. H. An Introduction to Distributed Optical Fibre Sensors 1st edn. (CRC Press, 2017). https://doi.org/10.1201/9781315119014.Book 

Google Scholar 
Lin, J., Fang, S., Li, X., Wu, R. & Zheng, H. Seismological observations of ocean swells induced by Typhoon Megi using dispersive microseisms recorded in coastal areas. Remote Sens.https://doi.org/10.3390/rs10091437 (2018).Article 

Google Scholar 
Munk, W. H., Miller, G. R., Snodgrass, F. E., Barber, N. F. & Deacon, G. E. R. Directional recording of swell from distant storms. Philos. Trans. R. Soc. Lond. Ser. A Math. Phys. Sci. 255, 505–584. https://doi.org/10.1098/rsta.1963.0011 (1963).Article 
ADS 

Google Scholar 
Mellinger, D. K. & Clark, C. W. Blue whale (balaenoptera musculus) sounds from the North Atlantic. J. Acoust. Soc. Am. 114, 1108–1119. https://doi.org/10.1121/1.1593066 (2003).Article 
ADS 
PubMed 

Google Scholar 
Ou, H., Au, W. W., Van Parijs, S., Oleson, E. M. & Rankin, S. Discrimination of frequency-modulated baleen whale downsweep calls with overlapping frequencies. J. Acoust. Soc. Am. 137, 3024–3032. https://doi.org/10.1121/1.4919304 (2015).Article 
ADS 
PubMed 

Google Scholar 
Saito, T. & Tsushima, H. Synthesizing ocean bottom pressure records including seismic wave and tsunami contributions: Toward realistic tests of monitoring systems. J. Geophys. Res. Solid Earth 121, 8175–8195. https://doi.org/10.1002/2016JB013195 (2016).Article 
ADS 

Google Scholar 
Rørstadbotnen, R. A. et al. Analysis of a local earthquake in the Arctic using a 120 km long fibre-optic cable. In 83rd EAGE Annual Conference & Exhibition, vol. 2022 of Conference Proceedings, 1–5, https://doi.org/10.3997/2214-4609.202210404 (European Association of Geoscientists & Engineers, 2022).Bromirski, P. D. & Duennebier, F. K. The near-coastal microseism spectrum: Spatial and temporal wave climate relationships. J. Geophys. Res. Solid Earth 107, ESE 5-1-20. https://doi.org/10.1029/2001JB000265 (2002).Article 

Google Scholar 
Pasch, R. J. National hurricane center tropical cyclone report: Tropical storm Edouard (AL052020). Technical report, National Oceanic and Atmospheric Administration (2021). https://www.nhc.noaa.gov/data/tcr/AL052020_Edouard.pdf.Gobato, R. & Heidari, A. Cyclone Bomb hits Southern Brazil in 2020. J. Atmos. Sci. Res. 3, 8–12. https://doi.org/10.30564/jasr.v3i3.2163 (2020).Article 

Google Scholar 
Khalid, A., de Lima, Ad. S., Cassalho, F., Miesse, T. & Ferreira, C. Hydrodynamic and wave responses during storm surges on the Southern Brazilian Coast: A real-time forecast system. Water 12, 3397. https://doi.org/10.3390/w12123397 (2020).Article 

Google Scholar 
Ćirić, J. Weather warning for Central Highland, Northwest Iceland (2020). https://www.icelandreview.com/travel/weather-warning-for-central-highland-northwest-iceland/.Schoeman, R. P., Patterson-Abrolat, C. & Plön, S. A global review of vessel collisions with marine animals. Front. Mar. Sci. 7, 292. https://doi.org/10.3389/fmars.2020.00292 (2020).Article 

Google Scholar 
Ringrose, P. S. et al. Storage of carbon dioxide in saline aquifers: Physicochemical processes, key constraints, and scale-up potential. Annu. Rev. Chem. Biomol. Eng. 12, 471–494. https://doi.org/10.1146/annurev-chembioeng-093020-091447 (2021).Article 
CAS 
PubMed 

Google Scholar 
Nishimura, T. et al. Source location of volcanic earthquakes and subsurface characterization using fiber-optic cable and distributed acoustic sensing system. Sci. Rep. 11, 6319. https://doi.org/10.1038/s41598-021-85621-8 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ardhuin, F. & Herbers, T. H. C. Noise generation in the solid Earth, oceans and atmosphere, from nonlinear interacting surface gravity waves in finite depth. J. Fluid Mech. 716, 316–348. https://doi.org/10.1017/jfm.2012.548 (2013).Article 
ADS 
MATH 

Google Scholar 
Airy, G. B. Encyclopaedia Metropolitana (1817–1845), vol. 3 of Mixed Sciences, chap. Tides and waves (London, 1841).Craik, A. D. The origins of water wave theory. Annu. Rev. Fluid Mech. 36, 1–28. https://doi.org/10.1146/annurev.fluid.36.050802.122118 (2004).Article 
ADS 
MathSciNet 
MATH 

Google Scholar 
Matsumoto, H., Inoue, S. & Ohmachi, T. Dynamic response of bottom water pressure due to the 2011 Tohoku earthquake. J. Disaster Res. 7, 468–475. https://doi.org/10.20965/jdr.2012.p0468 (2012).Article 

Google Scholar 
Landrø, M. & Hatchell, P. Normal modes in seismic data: Revisited. Geophysics 77, W27–W40. https://doi.org/10.1190/geo2011-0094.1 (2012).Article 
ADS 

Google Scholar  More

Theurillat, J.-P. & Guisan, A. Potential impact of climate change on vegetation in the European Alps: A review. Clim. Change 50, 77–109 (2001).CAS 

Google Scholar 
Diaz, H. F. & Eischeid, J. K. Disappearing “alpine tundra” Köppen climatic type in the western United States. Geophys. Res. Lett. 34, L18707 (2007).ADS 

Google Scholar 
Dirnböck, T., Essl, F. & Rabitsch, W. Disproportional risk for habitat loss of high-altitude endemic species under climate change. Glob. Change Biol. 17, 990–996 (2011).ADS 

Google Scholar 
Myers, N., Mittermeier, R. A., Mittermeier, C. G., Da Fonseca, G. A. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403, 853–858 (2000).ADS 
CAS 
PubMed 

Google Scholar 
Pauli, H., Gottfried, M., Dirnböck, T., Dullinger, S. & Grabherr, G. Assessing the long-term dynamics of endemic plants at summit habitats. In Alpine Biodiversity in Europe (eds. Nagy, L., Grabherr, G., Körner, C., & Thompson, D. B.) 195–207 (Springer, 2003).Cogoni, D., Sulis, E., Bacchetta, G. & Fenu, G. The unpredictable fate of the single population of a threatened narrow endemic Mediterranean plant. Biodivers. Conserv. 28, 1799–1813 (2019).
Google Scholar 
Cursach, J., Besnard, A., Rita, J. & Fréville, H. Demographic variation and conservation of the narrow endemic plant Ranunculus weyleri. Acta Oecol. 53, 102–109 (2013).ADS 

Google Scholar 
Dibner, R. R., DeMarche, M. L., Louthan, A. M. & Doak, D. F. Multiple mechanisms confer stability to isolated populations of a rare endemic plant. Ecol. Monogr. 89, e01360 (2019).
Google Scholar 
Boyce, M. S., Haridas, C. V., Lee, C. T., NCEAS Stochastic Demography Working Group. Demography in an increasingly variable world. Trends Ecol. Evol. 21, 141–148 (2006).PubMed 

Google Scholar 
Buckley, Y. M. et al. Causes and consequences of variation in plant population growth rate: A synthesis of matrix population models in a phylogenetic context. Ecol. Lett. 13, 1182–1197 (2010).PubMed 

Google Scholar 
Abbott, R. E., Doak, D. F. & DeMarche, M. L. Portfolio effects, climate change, and the persistence of small populations: Analyses on the rare plant Saussurea weberi. Ecology 98, 1071–1081 (2017).PubMed 

Google Scholar 
Villellas, J., Doak, D. F., García, M. B. & Morris, W. F. Demographic compensation among populations: What is it, how does it arise and what are its implications?. Ecol. Lett. 18, 1139–1152 (2015).PubMed 

Google Scholar 
Doak, D. F. & Morris, W. F. Demographic compensation and tipping points in climate-induced range shifts. Nature 467, 959–962 (2010).ADS 
CAS 
PubMed 

Google Scholar 
García-Camacho, R., Albert, M. J. & Escudero, A. Small-scale demographic compensation in a high-mountain endemic: The low edge stands still. Plant Ecol. Divers. 5, 37–44 (2012).
Google Scholar 
Andrello, M. et al. Accounting for stochasticity in demographic compensation along the elevational range of an alpine plant. Ecol. Lett. 23, 870–880 (2020).PubMed 

Google Scholar 
Valladares, F. et al. The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change. Ecol. Lett. 17, 1351–1364 (2014).PubMed 

Google Scholar 
Ægisdóttir, H. H., Kuss, P. & Stöcklin, J. Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation. Ann. Bot. 104, 1313–1322 (2009).PubMed 
PubMed Central 

Google Scholar 
Morente-López, J. et al. Geography and environment shape landscape genetics of Mediterranean alpine species Silene ciliata Poiret. (Caryophyllaceae). Front. Plant Sci. 9, 1698 (2018).PubMed 
PubMed Central 

Google Scholar 
Franks, S. J., Weber, J. J. & Aitken, S. N. Evolutionary and plastic responses to climate change in terrestrial plant populations. Evol. Appl. 7, 123–139 (2014).PubMed 

Google Scholar 
Jeong, H., Cho, Y.-C. & Kim, E. Differential plastic responses to temperature and nitrogen deposition in the subalpine plant species, Primula farinosa subsp. modesta. AoB Plants 13, plab061 (2021).ADS 
PubMed 
PubMed Central 

Google Scholar 
Sulis, E., Bacchetta, G., Cogoni, D. & Fenu, G. From global to local scale: Where is the best for conservation purpose?. Biodivers. Conserv. 30, 183–200 (2021).
Google Scholar 
Hambler, D. & Dixon, J. Primula farinosa L. J. Ecol. 91, 694–705 (2003).
Google Scholar 
Arnold, E. & Richards, A. On the occurrence of unilateral incompatibility in Primula section Aleuritia Duby and the origin of Primula scotica Hook. Bot. J. Linn. Soc. 128, 359–368 (1998).
Google Scholar 
Tribsch, A. Areas of endemism of vascular plants in the eastern Alps in relation to Pleistocene glaciation. J. Biogeogr. 31, 747–760 (2004).
Google Scholar 
Chung, J.-M., Son, S.-W., Kim, S.-Y., Park, G.-W. & Kim, S.-S. Genetic diversity and geographic differentiation in the endangered Primula farinosa subsp. modesta, a subalpine endemic to Korea. Korean J. Plant. Taxon. 43, 236–243 (2013).
Google Scholar 
Lindborg, R. & Ehrlén, J. Evaluating the extinction risk of a perennial herb: Demographic data versus historical records. Conserv. Biol. 16, 683–690 (2002).
Google Scholar 
Caswell, H. Matrix Population Models, 2nd ed (Sinauer Associates Inc, 2000).Salguero-Gómez, R. & De Kroon, H. Matrix projection models meet variation in the real world. J. Ecol. 98, 250–254 (2010).
Google Scholar 
Jongejans, E. et al. Region versus site variation in the population dynamics of three short-lived perennials. J. Ecol. 98, 279–289 (2010).
Google Scholar 
Jongejans, E. & De Kroon, H. Space versus time variation in the population dynamics of three co-occurring perennial herbs. J. Ecol. 93, 681–692 (2005).
Google Scholar 
Suggitt, A. J. et al. Habitat microclimates drive fine-scale variation in extreme temperatures. Oikos 120, 1–8 (2011).
Google Scholar 
Tomimatsu, H. & Ohara, M. Demographic response of plant populations to habitat fragmentation and temporal environmental variability. Oecologia 162, 903–911 (2010).ADS 
PubMed 

Google Scholar 
Kudernatsch, T., Fischer, A., Bernhardt-Römermann, M. & Abs, C. Short-term effects of temperature enhancement on growth and reproduction of alpine grassland species. Basic Appl. Ecol. 9, 263–274 (2008).
Google Scholar 
Kim, E. & Donohue, K. Local adaptation and plasticity of Erysimum capitatum to altitude: Its implications for responses to climate change. J. Ecol. 101, 796–805 (2013).
Google Scholar 
Forbis, T. A. Seedling demography in an alpine ecosystem. Am. J. Bot. 90, 1197–1206 (2003).PubMed 

Google Scholar 
Yenni, G., Adler, P. B. & Ernest, S. M. Strong self-limitation promotes the persistence of rare species. Ecology 93, 456–461 (2012).PubMed 

Google Scholar 
Doak, D. F. Source-sink models and the problem of habitat degradation: General models and applications to the Yellowstone grizzly. Conserv. Biol. 9, 1370–1379 (1995).
Google Scholar 
Lesica, P. & Crone, E. E. Arctic and boreal plant species decline at their southern range limits in the Rocky Mountains. Ecol. Lett. 20, 166–174 (2017).PubMed 

Google Scholar 
Oldfather, M. F. & Ackerly, D. D. Microclimate and demography interact to shape stable population dynamics across the range of an alpine plant. New Phytol. 222, 193–205 (2019).PubMed 

Google Scholar 
Ågren, J., Fortunel, C. & Ehrlén, J. Selection on floral display in insect-pollinated Primula farinosa: Effects of vegetation height and litter accumulation. Oecologia 150, 225–232 (2006).ADS 
PubMed 

Google Scholar 
Ehrlén, J., Syrjänen, K., Leimu, R., Begona Garcia, M. & Lehtilä, K. Land use and population growth of Primula veris: An experimental demographic approach. J. Appl. Ecol. 42, 317–326 (2005).
Google Scholar 
Ehrlén, J. & Morris, W. F. Predicting changes in the distribution and abundance of species under environmental change. Ecol. Lett. 18, 303–314 (2015).PubMed 
PubMed Central 

Google Scholar 
Stubben, C. & Milligan, B. Estimating and analyzing demographic models using the popbio package in R. J. Stat. Softw. 22, 1–23 (2007).
Google Scholar 
Weiss, N. Package ‘wPerm’. https://cran.r-project.org/web/packages/wPerm/wPerm.pdf. (2015).Frossard, J. & Renaud, O. Permutation tests for regression, ANOVA, and comparison of signals: The permuco package. J. Stat. Softw. 99, 1–32 (2021).
Google Scholar  More

Meghana, M. & Shastri, Y. Sustainable valorization of sugar industry waste: Status, opportunities, and challenges. Biores. Technol. 303, 122929 (2020).CAS 

Google Scholar 
Petrescu, D. C., Vermeir, I. & Petrescu-Mag, R. M. Consumer understanding of food quality, healthiness, and environmental impact: a cross-national perspective. IJERPH 17, 169 (2019).PubMed Central 

Google Scholar 
Kassam, A., Friedrich, T., Shaxson, F. & Pretty, J. The spread of conservation agriculture: justification, sustainability and uptake. Int. J. Agric. Sustain. 7, 292–320 (2009).
Google Scholar 
Malviya, M. K. et al. Sugarcane microbiome: role in sustainable production. In Microbiomes and Plant Health 225–242 (Elsevier, 2021). https://doi.org/10.1016/B978-0-12-819715-8.00007-0.Chapter 

Google Scholar 
Sandhu, H. S., Wratten, S. D. & Cullen, R. Organic agriculture and ecosystem services. Environ. Sci. Policy 13, 1–7 (2010).CAS 

Google Scholar 
Schipanski, M. E. et al. Balancing multiple objectives in organic feed and forage cropping systems. Agr. Ecosyst. Environ. 239, 219–227 (2017).
Google Scholar 
Knapp, S. & van der Heijden, M. G. A. A global meta-analysis of yield stability in organic and conservation agriculture. Nat. Commun. 9, 3632 (2018).ADS 
PubMed 
PubMed Central 

Google Scholar 
Bender, S. F., Wagg, C. & van der Heijden, M. G. A. An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends Ecol. Evol. 31, 440–452 (2016).PubMed 

Google Scholar 
Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).CAS 
PubMed 

Google Scholar 
Chialva, M., Lanfranco, L. & Bonfante, P. The plant microbiota: composition, functions, and engineering. Curr. Opin. Biotechnol. 73, 135–142 (2022).CAS 
PubMed 

Google Scholar 
Dastogeer, K. M. G., Tumpa, F. H., Sultana, A., Akter, M. A. & Chakraborty, A. Plant microbiome–an account of the factors that shape community composition and diversity. Curr. Plant Biol. 23, 100161 (2020).
Google Scholar 
Yang, B., Wang, Y. & Qian, P.-Y. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC Bioinformat. 17, 135 (2016).
Google Scholar 
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).CAS 
PubMed 

Google Scholar 
Wright, R. J., Gibson, M. I. & Christie-Oleza, J. A. Understanding microbial community dynamics to improve optimal microbiome selection. Microbiome 7, 85 (2019).PubMed 
PubMed Central 

Google Scholar 
Praeg, N. & Illmer, P. Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms. Sci. Rep. 10, 22324 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
de Souza, R. S. C. et al. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci. Rep. 6, 28774 (2016).ADS 
PubMed 
PubMed Central 

Google Scholar 
Tayyab, M. et al. Sugarcane cultivars manipulate rhizosphere bacterial communities’ structure and composition of agriculturally important keystone taxa. 3 Biotech. 12, 32 (2022).PubMed 

Google Scholar 
Tayyab, M. et al. Sugarcane cultivar-dependent changes in assemblage of soil rhizosphere fungal communities in subtropical ecosystem. Environ. Sci. Pollut. Res. 29, 20795–20807 (2022).
Google Scholar 
Dakora, F. D., Matiru, V. N. & Kanu, A. S. Rhizosphere ecology of lumichrome and riboflavin, two bacterial signal molecules eliciting developmental changes in plants. Front. Plant Sci. 6, 700 (2015).PubMed 
PubMed Central 

Google Scholar 
Chapelle, E., Mendes, R., Bakker, P. A. H. & Raaijmakers, J. M. Fungal invasion of the rhizosphere microbiome. ISME J. 10, 265–268 (2016).CAS 
PubMed 

Google Scholar 
Teheran-Sierra, L. G. et al. Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect. Microbiol. Res. 247, 126729 (2021).CAS 
PubMed 

Google Scholar 
de Carvalho, L. A. L. et al. Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome. Microbiol. Res. 252, 126866 (2021).PubMed 

Google Scholar 
Henneron, L. et al. Fourteen years of evidence for positive effects of conservation agriculture and organic farming on soil life. Agron. Sustain. Dev. 35, 169–181 (2015).
Google Scholar 
Hartmann, M., Frey, B., Mayer, J., Mäder, P. & Widmer, F. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 9, 1177–1194 (2015).PubMed 

Google Scholar 
Tayyab, M. et al. Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms. Environ. Sci. Pollut. Res. 28, 48080–48096 (2021).CAS 

Google Scholar 
Pang, Z. et al. Soil Metagenomics reveals effects of continuous sugarcane cropping on the structure and functional pathway of rhizospheric microbial community. Front. Microbiol. 12, 627569 (2021).PubMed 
PubMed Central 

Google Scholar 
Orr, C. H., Stewart, C. J., Leifert, C., Cooper, J. M. & Cummings, S. P. Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems. J. Appl. Microbiol. 119, 208–214 (2015).CAS 
PubMed 

Google Scholar 
Brasil. Lei no 10.831, de 23 de dezembro de 2003. Dispõe sobre a agricultura orgânica e dá outras providências. In Publicado no Diário Oficial da União de 24/12/2003 (2003).Europea, C. Reglamento (CE) no 834/2007 del Consejo, de 28 de junio de 2007, sobre producción y etiquetado de los productos ecológicos y por el que se deroga el Reglamento (CEE) no 2092/91. D. Of. Unión Eur. 20, 1–23 (2007).
Google Scholar 
Council of the European Union. 889/2008, “Commission Regulation 889/2008/EC of 5 September 2008 laying down detailed rules for the implementation of Council Regulation (EC) No 834/2007 on organic production and labelling of organic products with regard to organic production, labelling and control”. Off. J. Eur. Union (L) 250, 18–19 (2007).
Google Scholar 
de Andrade, J. C., Cantarella, H. & Quaggio, J. A. Análise química para avaliação da fertilidade de solos tropicais. (2001).Donagema, G. K., de Campos, D. B., Calderano, S. B., Teixeira, W. G. & Viana, J. M. Manual de métodos de análise de solo. In Embrapa Solos-Documentos (INFOTECA-E) (2011).Kassambara, A. ggpubr: ‘ggplot2’ Based Publication Ready Plots. (2020). at R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2020). At Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D. & Dangl, J. L. Practical innovations for high-throughput amplicon sequencing. Nat. Methods 10, 999–1002 (2013).CAS 
PubMed 

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

Google Scholar 
Renaud, G., Stenzel, U., Maricic, T., Wiebe, V. & Kelso, J. deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics 31, 770–772 (2015).CAS 
PubMed 

Google Scholar 
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014).CAS 
PubMed 

Google Scholar 
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).CAS 
PubMed 

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

Google Scholar 
Cole, J. R. et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642 (2014).CAS 
PubMed 

Google Scholar 
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lahti, L. & Shetty, S. Microbiome R package. (2012).Oksanen, J. et al. vegan: Community Ecology Package. (2019). At Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).PubMed 
PubMed Central 

Google Scholar 
Dhariwal, A. et al. MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 45, W180–W188 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Douglas, G. M. et al. PICRUSt2: an improved and extensible approach for metagenome inference. Bioinformatics https://doi.org/10.1101/672295 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Parks, D. H., Tyson, G. W., Hugenholtz, P. & Beiko, R. G. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30, 3123–3124 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Kohl, M., Wiese, S. & Warscheid, B. Cytoscape: software for visualization and analysis of biological networks. In Data Mining in Proteomics (eds Hamacher, M. et al.) 291–303 (Humana Press, Totowa, NJ, 2011). https://doi.org/10.1007/978-1-60761-987-1_18.Chapter 

Google Scholar 
Assenov, Y., Ramírez, F., Schelhorn, S.-E., Lengauer, T. & Albrecht, M. Computing topological parameters of biological networks. Bioinformatics 24, 282–284 (2008).CAS 
PubMed 

Google Scholar 
Shen, Z. et al. Deep 16S rRNA pyrosequencing reveals a bacterial community associated with banana fusarium wilt disease suppression induced by bio-organic fertilizer application. PLoS One 9, e98420 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
Yun, Y. et al. The relationship between pH and bacterial communities in a single karst ecosystem and its implication for soil acidification. Front. Microbiol. 7, 1955 (2016).PubMed 
PubMed Central 

Google Scholar 
Wu, Y., Zeng, J., Zhu, Q., Zhang, Z. & Lin, X. pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution. Sci. Rep. 7, 40093 (2017).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, R. et al. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities. PLoS One 7, e51897 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bill, M., Chidamba, L., Gokul, J. K., Labuschagne, N. & Korsten, L. Bacterial community dynamics and functional profiling of soils from conventional and organic cropping systems. Appl. Soil. Ecol. 157, 103734 (2021).
Google Scholar 
Xun, W., Shao, J., Shen, Q. & Zhang, R. Rhizosphere microbiome: Functional compensatory assembly for plant fitness. Comput. Struct. Biotechnol. J. 19, 5487–5493 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Semenov, M. V., Krasnov, G. S., Semenov, V. M. & van Bruggen, A. Mineral and organic fertilizers distinctly affect fungal communities in the crop rhizosphere. JoF 8, 251 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Wang, Z., Li, Y., Li, T., Zhao, D. & Liao, Y. Tillage practices with different soil disturbance shape the rhizosphere bacterial community throughout crop growth. Soil Tillage Res. 197, 104501 (2020).
Google Scholar 
Gdanetz, K. & Trail, F. The wheat microbiome under four management strategies, and potential for endophytes in disease protection. Phytobiom. J. 1, 158–168 (2017).
Google Scholar 
Lazcano, C. et al. The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions. Sci. Rep. 11, 3188 (2021).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Leys, N. M. E. J. et al. Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 70, 1944–1955 (2004).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yin, C. et al. Role of bacterial communities in the natural suppression of rhizoctonia solani bare patch disease of wheat (Triticum aestivum L.). Appl. Environ. Microbiol. 79, 7428–7438 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Stewart, A. & Hill, R. Applications of trichoderma in plant growth promotion. In Biotechnology and Biology of Trichoderma 415–428 (Elsevier, 2014). https://doi.org/10.1016/B978-0-444-59576-8.00031-X.Chapter 

Google Scholar 
Banerjee, S. et al. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol. Biochem. 97, 188–198 (2016).CAS 

Google Scholar 
Andargie, M., Congyi, Z., Yun, Y. & Li, J. Identification and evaluation of potential bio-control fungal endophytes against Ustilagonoidea virens on rice plants. World J. Microbiol. Biotechnol. 33, 120 (2017).PubMed 

Google Scholar 
Orrù, L. et al. How tillage and crop rotation change the distribution pattern of fungi. Front. Microbiol. 12, 634325 (2021).PubMed 
PubMed Central 

Google Scholar 
van der Heijden, M. G. A. & Hartmann, M. Networking in the plant microbiome. PLoS Biol. 14, e1002378 (2016).PubMed 
PubMed Central 

Google Scholar 
Wang, W. et al. Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River. Sci. Rep. 6, 35046 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Silva, T. M. et al. Degradation of 2,4-D herbicide by microorganisms isolated from Brazilian contaminated soil. Braz. J. Microbiol. 38, 522–525 (2007).
Google Scholar 
Laura, M., Snchez-Salinas, E., Gonzlez, E. D. & Luisa, M. Pesticide biodegradation: mechanisms, genetics and strategies to enhance the process. In Biodegradation – Life of Science (ed. Chamy, R.) (InTech, 2013). https://doi.org/10.5772/56098.Chapter 

Google Scholar 
Upadhyay, L. S. B. & Dutt, A. Microbial detoxification of residual organophosphate pesticides in agricultural practices. In Microbial Biotechnology (eds Patra, J. K. et al.) 225–242 (Springer Singapore, Singapore, 2017). https://doi.org/10.1007/978-981-10-6847-8_10.Chapter 

Google Scholar 
Hassan, Y. I., Lepp, D., He, J. & Zhou, T. Draft genome sequences of Devosia sp. strain 17-2-E-8 and Devosia riboflavina strain IFO13584. Genome Announ. https://doi.org/10.1128/genomeA.00994-14 (2014).Article 

Google Scholar 
Talwar, C. et al. Defining the environmental adaptations of genus Devosia: insights into its expansive short peptide transport system and positively selected genes. Sci. Rep. 10, 1151 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, F., Chen, L., Zhang, J., Yin, J. & Huang, S. Bacterial community structure after long-term organic and inorganic fertilization reveals important associations between soil nutrients and specific taxa involved in nutrient transformations. Front. Microbiol. 8, 187 (2017).PubMed 
PubMed Central 

Google Scholar 
Ho, A., Lonardo, D. P. D. & Bodelier, P. L. E. Revisiting life strategy concepts in environmental microbial ecology. Microbiol. Ecol. https://doi.org/10.1093/femsec/fix006 (2017).Article 

Google Scholar 
Lupatini, M., Korthals, G. W., de Hollander, M., Janssens, T. K. S. & Kuramae, E. E. Soil microbiome is more heterogeneous in organic than in conventional farming system. Front. Microbiol. 7, 2064 (2017).PubMed 
PubMed Central 

Google Scholar 
Wang, H. et al. Eight years of manure fertilization favor copiotrophic traits in paddy soil microbiomes. Eur. J. Soil Biol. 106, 103352 (2021).CAS 

Google Scholar 
Fließbach, A., Oberholzer, H.-R., Gunst, L. & Mäder, P. Soil organic matter and biological soil quality indicators after 21 years of organic and conventional farming. Agric. Ecosyst. Environ. 118, 273–284 (2007).
Google Scholar 
Lewin, G. R. et al. Evolution and ecology of Actinobacteria and their bioenergy applications. Annu. Rev. Microbiol. 70, 235–254 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Karanja, E. N. et al. Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya. PLoS One 15, e0236574 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Francioli, D. et al. Mineral versus organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front. Microbiol. 7, 1446 (2016).PubMed 
PubMed Central 

Google Scholar 
Paungfoo-Lonhienne, C. et al. Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Sci. Rep. 5, 8678 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Pang, Z. et al. Liming positively modulates microbial community composition and function of sugarcane fields. Agronomy 9, 808 (2019).CAS 

Google Scholar 
Aira, M., Gómez-Brandón, M., Lazcano, C., Bååth, E. & Domínguez, J. Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities. Soil Biol. Biochem. 42, 2276–2281 (2010).CAS 

Google Scholar 
Ma, M. et al. Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols. MicrobiologyOpen 7, e00597 (2018).PubMed 
PubMed Central 

Google Scholar 
Bellenger, J. P., Darnajoux, R., Zhang, X. & Kraepiel, A. M. L. Biological nitrogen fixation by alternative nitrogenases in terrestrial ecosystems: a review. Biogeochemistry 149, 53–73 (2020).
Google Scholar 
Schmidt, J. E. et al. Effects of agricultural management on rhizosphere microbial structure and function in processing tomato plants. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.01064-19 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Agler, M. T. et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, e1002352 (2016).PubMed 
PubMed Central 

Google Scholar 
Lin, Y. et al. Nitrosospira cluster 8a plays a predominant role in the nitrification process of a subtropical Ultisol under long-term inorganic and organic fertilization. Appl. Environ. Microbiol. 84, e01031-e1118 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Chu, H. et al. Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil. Appl. Environ. Microbiol. 73, 485–491 (2007).ADS 
CAS 
PubMed 

Google Scholar 
Xun, W. et al. Specialized metabolic functions of keystone taxa sustain soil microbiome stability. Microbiome 9, 35 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar  More

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol. 2021;39:499–509.CAS 
PubMed 

Google Scholar 
Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15:579–90.CAS 
PubMed 

Google Scholar 
Cordovez V, Dini-Andreote F, Carrión VJ, Raaijmakers JM. Ecology and evolution of plant microbiomes. Annu Rev Microbiol. 2019;73:69–88.CAS 
PubMed 

Google Scholar 
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607–21.CAS 
PubMed 

Google Scholar 
Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, et al. The plant microbiome: From ecology to reductionism and beyond. Annu Rev Microbiol. 2020;74:81–100.CAS 
PubMed 

Google Scholar 
Schmidt R, Ulanova D, Wick LY, Bode HB, Garbeva P. Microbe-driven chemical ecology: past, present and future. ISME J. 2019;13:2656–63.PubMed 
PubMed Central 

Google Scholar 
Tyc O, Song C, Dickschat JS, Vos M, Garbeva P. The ecological role of volatile and soluble secondary metabolites produced by soil bacteria. Trends Microbiol. 2017;25:280–92.CAS 
PubMed 

Google Scholar 
Romero D, Traxler MF, López D, Kolter R. Antibiotics as signal molecules. Chem Rev. 2011;111:5492–505.CAS 
PubMed 
PubMed Central 

Google Scholar 
Traxler MF, Seyedsayamdost MR, Clardy J, Kolter R. Interspecies modulation of bacterial development through iron competition and siderophore piracy. Mol Microbiol. 2012;86:628–44.CAS 
PubMed 
PubMed Central 

Google Scholar 
Bernal P, Llamas MA, Filloux A. Type VI secretion systems in plant-associated bacteria. Environ Microbiol. 2018;20:1–15.PubMed 

Google Scholar 
Okada BK, Seyedsayamdost MR. Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiol Rev. 2017;41:19–33.CAS 
PubMed 

Google Scholar 
Zhang C, Straight PD. Antibiotic discovery through microbial interactions. Curr Opin Microbiol. 2019;51:64–71.CAS 
PubMed 

Google Scholar 
Traxler MF, Kolter R. Natural products in soil microbe interactions and evolution. Nat Prod Rep. 2015;32:956–70.CAS 
PubMed 

Google Scholar 
Müller DB, Vogel C, Bai Y, Vorholt JA. The plant microbiota: systems-level insights and perspectives. Annu Rev Genet. 2016;50:211–34.PubMed 

Google Scholar 
Anckaert A, Arias AA, Hoff G, Calonne-Salmon M, Declerck S, Ongena M. The use of Bacillus spp. as bacterial biocontrol agents to control plant diseases. In: Köhl J, Ravensberg W, editors. Microbial bioprotectants for plant disease management. Cambridge, UK: Burleigh Dodds Science Publishing; 2022. p. 1–54.Dunlap CA. Taxonomy of registered Bacillus spp. strains used as plant pathogen antagonists. Biol Control. 2019;134:82–86.
Google Scholar 
Ye M, Tang X, Yang R, Zhang H, Li F, Tao F, et al. Characteristics and application of a novel species of Bacillus: Bacillus velezensis. ACS Chem Biol. 2018;13:500–5.CAS 
PubMed 

Google Scholar 
Grubbs KJ, Bleich RM, Santa Maria KC, Allen SE, Farag S, Shank EA, et al. Large-scale bioinformatics analysis of Bacillus genomes uncovers conserved roles of natural products in bacterial physiology. mSystems 2017;2:e00040–17.CAS 
PubMed 
PubMed Central 

Google Scholar 
Harwood CR, Mouillon J-MM, Pohl S, Arnau J. Secondary metabolite production and the safety of industrially important members of the Bacillus subtilis group. FEMS Microbiol Rev. 2018;42:721–38.CAS 
PubMed 
PubMed Central 

Google Scholar 
Köhl J, Kolnaar R, Ravensberg WJ. Mode of action of microbial biological control agents against plant diseases: Relevance beyond efficacy. Front Plant Sci. 2019;10:1–19.
Google Scholar 
Li Y, Rebuffat S. The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology. J Biol Chem. 2020;295:34–54.Andrić S, Meyer T, Ongena M. Bacillus responses to plant-associated fungal and bacterial communities. Front Microbiol. 2020;11:1350.PubMed 
PubMed Central 

Google Scholar 
Zhang L, Sun C. Fengycins, cyclic lipopeptides from marine Bacillus subtilis strains, kill the plant-pathogenic fungus Magnaporthe grisea by inducing reactive oxygen species production and chromatin condensation. Appl Environ Microbiol. 2018;84:e00445–18.CAS 
PubMed 
PubMed Central 

Google Scholar 
Molina-Santiago C, Vela-Corcía D, Petras D, Díaz-Martínez L, Pérez-Lorente AI, Sopeña-Torres S, et al. Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence. Cell Rep. 2021;36:109449.CAS 
PubMed 
PubMed Central 

Google Scholar 
Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, et al. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nat Commun. 2019;10:1919.PubMed 
PubMed Central 

Google Scholar 
Almoneafy AA, Kakar KU, Nawaz Z, Li B, Saand MA, Chun-lan Y, et al. Tomato plant growth promotion and antibacterial related-mechanisms of four rhizobacterial Bacillus strains against Ralstonia solanacearum. Symbiosis 2014;63:59–70.CAS 

Google Scholar 
Kakar KU, Duan Y-P, Nawaz Z, Sun G, Almoneafy AA, Hassan MA, et al. A novel rhizobacterium Bk7 for biological control of brown sheath rot of rice caused by Pseudomonas fuscovaginae and its mode of action. Eur J Plant Pathol. 2014;138:819–34.
Google Scholar 
Raynaud X, Nunan N. Spatial ecology of bacteria at the microscale in soil. PLoS ONE. 2014;9:e87217.PubMed 
PubMed Central 

Google Scholar 
Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H, van Noort V, et al. The ever-expanding Pseudomonas genus: description of 43 new species and partition of the Pseudomonas putida group. Microorganisms. 2021;9:1–24.
Google Scholar 
Hua GKH, Höfte M. The involvement of phenazines and cyclic lipopeptide sessilin in biocontrol of Rhizoctonia root rot on bean (Phaseolus vulgaris) by Pseudomonas sp. CMR12a is influenced by substrate composition. Plant Soil. 2015;388:243–53.CAS 

Google Scholar 
Ma Z, Hoang Hua GKH, Ongena M, Höfte M. Role of phenazines and cyclic lipopeptides produced by Pseudomonas sp. CMR12a in induced systemic resistance on rice and bean. Environ Microbiol Rep. 2016;8:896–904.PubMed 

Google Scholar 
Olorunleke FE, Hua GKH, Kieu NP, Ma Z, Höfte M. Interplay between orfamides, sessilins and phenazines in the control of Rhizoctonia diseases by Pseudomonas sp. CMR12a. Environ Microbiol Rep. 2015;7:774–81.CAS 
PubMed 

Google Scholar 
van Gestel J, Vlamakis H, Kolter R. From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate. PLoS Biol. 2015;13:1–29.
Google Scholar 
Nihorimbere V, Cawoy H, Seyer A, Brunelle A, Thonart P, Ongena M. Impact of rhizosphere factors on cyclic lipopeptide signature from the plant beneficial strain Bacillus amyloliquefaciens S499. FEMS Microbiol Ecol. 2012;79:176–91.CAS 
PubMed 

Google Scholar 
Hoff G, Arias AA, Boubsi F, Pršić J, Meyer T, Ibrahim HMM, et al. Surfactin stimulated by pectin molecular patterns and root exudates acts as a key driver of the Bacillus-plant mutualistic interaction. MBio 2021;12:e01774–21.CAS 
PubMed Central 

Google Scholar 
Andrić S, Meyer T, Rigolet A, Prigent-Combaret C, Höfte M, Balleux G, et al. Lipopeptide interplay mediates molecular interactions between soil bacilli and pseudomonads. Microbiol Spectr. 2021;9:e0203821.PubMed 

Google Scholar 
Pluskal T, Castillo S, Villar-Briones A, Orešič M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinform. 2010;11:395.
Google Scholar 
Li W, Godzik A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.CAS 
PubMed 

Google Scholar 
Bodenhofer U, Bonatesta E, Horejš-Kainrath C, Hochreiter S. msa: an R package for multiple sequence alignment. Bioinformatics. 2015;31:3997–9.CAS 
PubMed 

Google Scholar 
Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004;20:289–90.CAS 
PubMed 

Google Scholar 
Ivica Letunic PB. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–W296.PubMed 
PubMed Central 

Google Scholar 
R Core Team (2020). R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020.Steinke K, Mohite OS, Weber T, Kovács ÁT. Phylogenetic distribution of secondary metabolites in the Bacillus subtilis species complex. mSystems. 2021;6:2–10.
Google Scholar 
Molinatto G, Puopolo G, Sonego P, Moretto M, Engelen K, Viti C, et al. Complete genome sequence of Bacillus amyloliquefaciens subsp. plantarum S499, a rhizobacterium that triggers plant defences and inhibits fungal phytopathogens. J Biotechnol. 2016;238:56–59.CAS 
PubMed 

Google Scholar 
Fan B, Wang C, Song X, Ding X, Wu L, Wu H, et al. Bacillus velezensis FZB42 in 2018: The gram-positive model strain for plant growth promotion and biocontrol. Front Microbiol. 2018;9:3389.
Google Scholar 
Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol. 2012;13:614–29.PubMed 
PubMed Central 

Google Scholar 
Scholz R, Vater J, Budiharjo A, Wang Z, He Y, Dietel K, et al. Amylocyclicin, a novel circular bacteriocin produced by Bacillus amyloliquefaciens FZB42. J Bacteriol. 2014;196:1842–52.PubMed 
PubMed Central 

Google Scholar 
Lembrechts JJ, van den Hoogen J, Aalto J, Ashcroft MB, De Frenne P, Kemppinen J, et al. Global maps of soil temperature. Glob Chang Biol. 2022;28:3110–44.CAS 
PubMed 
PubMed Central 

Google Scholar 
Blake C, Christensen MN, Kovacs AT. Molecular aspects of plant growth promotion and protection by Bacillus subtilis. Mol Plant-Microbe Interact. 2021;34:15–25.CAS 
PubMed 

Google Scholar 
Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol. 2021;19:600–14.CAS 
PubMed 

Google Scholar 
D’aes J, Hua GKH, De Maeyer K, Pannecoucque J, Forrez I, Ongena M, et al. Biological control of Rhizoctonia root rot on bean by phenazine- and cyclic lipopeptide-producing Pseudomonas CMR12a. Phytopathology. 2011;101:996–1004.PubMed 

Google Scholar 
Grandchamp GM, Caro L, Shank EA. Pirated siderophores promote sporulation in Bacillus subtilis. Appl Environ Microbiol. 2017;83:e03293–16.CAS 
PubMed 
PubMed Central 

Google Scholar 
Miethke M, Klotz O, Linne U, May JJ, Beckering CL, Marahiel MA. Ferri-bacillibactin uptake and hydrolysis in Bacillus subtilis. Mol Microbiol. 2006;61:1413–27.CAS 
PubMed 

Google Scholar 
Pi H, Helmann JD. Genome-wide characterization of the fur regulatory network reveals a link between catechol degradation and bacillibactin metabolism in Bacillus subtilis. MBio. 2018;9:1–15.
Google Scholar 
Adler C, Corbalán NS, Seyedsayamdost MR, Pomares MF, de Cristóbal RE, Clardy J, et al. Catecholate siderophores protect bacteria from pyochelin toxicity. PLoS ONE. 2012;7:e46754.CAS 
PubMed 
PubMed Central 

Google Scholar 
Trottmann F, Franke J, Ishida K, García-Altares M, Hertweck C. A pair of bacterial siderophores releases and traps an intercellular signal molecule: an unusual case of natural nitrone bioconjugation. Angew Chem. 2019;58:200–4.CAS 

Google Scholar 
Mongkolsuk S, Helmann JD. Regulation of inducible peroxide stress responses. Mol Microbiol. 2002;45:9–15.CAS 
PubMed 

Google Scholar 
Cox CD, Rinehart KL, Moore ML, Cook JC. Pyochelin: novel structure of an iron-chelating growth promoter for Pseudomonas aeruginosa. Proc Natl Acad Sci USA. 1981;78:4256–60.CAS 
PubMed 
PubMed Central 

Google Scholar 
Youard ZA, Mislin GLA, Majcherczyk PA, Schalk IJ, Reimmann C. Pseudomonas fluorescens CHA0 produces enantio-pyochelin, the optical antipode of the Pseudomonas aeruginosa siderophore pyochelin. J Biol Chem. 2007;282:35546–53.CAS 
PubMed 

Google Scholar 
Ronnebaum TA, Lamb AL. Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study. Curr Opini Struct Biol. 2018;53:1–11.CAS 

Google Scholar 
Seipke RF, Song L, Bicz J, Laskaris P, Yaxley AM, Challis GL, et al. The plant pathogen Streptomyces scabies 87-22 has a functional pyochelin biosynthetic pathway that is regulated by TetR- and AfsR-family proteins. Microbiology. 2011;157:2681–93.CAS 
PubMed 

Google Scholar 
Gu S, Wei Z, Shao Z, Friman VP, Cao K, Yang T, et al. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nat Microbiol. 2020;5:1002–10.CAS 
PubMed 
PubMed Central 

Google Scholar 
Komaki H, Ichikawa N, Hosoyama A, Hamada M, Igarashi Y. In silico analysis of PKS and NRPS gene clusters in arisostatin-and kosinostatin-producers and description of Micromonospora okii sp. nov. Antibiotics. 2021;10:1447.CAS 
PubMed 
PubMed Central 

Google Scholar 
Engelbrecht A, Saad H, Gross H, Kaysser L. Natural products from Nocardia and their role in pathogenicity. Micro Physiol. 2021;31:217–32.
Google Scholar 
Inahashi Y, Zhou S, Bibb MJ, Song L, Al-Bassam MM, Bibb MJ, et al. Watasemycin biosynthesis in Streptomyces venezuelae: thiazoline C-methylation by a type B radical-SAM methylase homologue. Chem Sci. 2017;8:2823–31.CAS 
PubMed 
PubMed Central 

Google Scholar 
Song J, Qiu S, Zhao J, Han C, Wang Y, Sun X, et al. Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Nat Microbiol. 2019;12:470–80.
Google Scholar 
Sayed AM, Abdel-Wahab NM, Hassan HM, Abdelmohsen UR. Saccharopolyspora: an underexplored source for bioactive natural products. J Appl Microbiol. 2020;128:314–29.CAS 
PubMed 

Google Scholar 
Nordstedt NP, Jones ML. Genomic analysis of Serratia plymuthica MBSA-MJ1: A plant growth promoting rhizobacteria that improves water stress tolerance in greenhouse ornamentals. Front Microbiol. 2021;12:653556.PubMed 
PubMed Central 

Google Scholar 
Zhalnina K, Louie KB, Hao Z, Mansoori N, Da Rocha UN, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470–80.CAS 
PubMed 

Google Scholar 
Takahashi Y, Malisorn K, Kanchanasin P, Phongsopitanun W, Tanasupawat S, Spain AM, et al. Actinomadura rhizosphaerae sp. nov., isolated from rhizosphere soil of the plant Azadirachta indica. ISME J 2018;68:3012–6.
Google Scholar 
Takahashi Y. Genus Kitasatospora, taxonomic features and diversity of secondary metabolites. J Antibiot. 2017;70:506–13.CAS 

Google Scholar 
Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species: Incidence, ecological roles and adaptations. Microbiol Res. 2015;174:33–47.PubMed 

Google Scholar 
Walterson AM, Stavrinides J. Pantoea: Insights into a highly versatile and diverse genus within the Enterobacteriaceae. J Basic Microbiol. 2015;39:33–47.
Google Scholar 
Sungthong R, Nakaew N. The genus Nonomuraea: a review of a rare actinomycete taxon for novel metabolites. J Basic Microbiol. 2015;55:554–65.PubMed 

Google Scholar 
Müller S, Strack SN, Ryan SE, Kearns DB, Kirby JR. Predation by Myxococcus xanthus induces Bacillus subtilis to form spore-filled megastructures. Appl Environ Microbiol. 2015;81:203–10.PubMed 

Google Scholar 
Straight PD, Fischbach MA, Walsh CT, Rudner DZ, Kolter R. A singular enzymatic megacomplex from Bacillus subtilis. Proc Natl Acad Sci USA. 2007;104:305–10.CAS 
PubMed 

Google Scholar 
Barger SR, Hoefler BC, Cubillos-Ruiz A, Russell WK, Russell DH, Straight PD. Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis. Antonie van Leeuwenhoek. 2012;102:435–45.CAS 
PubMed 

Google Scholar 
Ogran A, Yardeni EH, Keren-Paz A, Bucher T, Jain R, Gilhar O, et al. The plant host induces antibiotic production to select the most-beneficial colonizers. Appl Environ Microbiol. 2019;85:1–15.
Google Scholar 
Rosenberg G, Steinberg N, Oppenheimer-Shaanan Y, Olender T, Doron S, Ben-Ari J, et al. Not so simple, not so subtle: The interspecies competition between Bacillus simplex and Bacillus subtilis and its impact on the evolution of biofilms. npj Biofilms Microbiomes. 2016;2:15027.PubMed 
PubMed Central 

Google Scholar 
Straight PD, Willey JM, Kolter R. Interactions between Streptomyces coelicolor and Bacillus subtilis: Role of surfactants in raising aerial structures. J Bacteriol. 2006;188:4918–25.CAS 
PubMed 
PubMed Central 

Google Scholar 
Hoefler BC, Gorzelnik KV, Yang JY, Hendricks N, Dorrestein PC, Straight PD. Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition. Proc Natl Acad Sci USA. 2012;109:13082–7.CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu Y, Kyle S, Straight PD. Antibiotic stimulation of a Bacillus subtilis migratory response. mSphere 2018;3:e00586–17.CAS 
PubMed 
PubMed Central 

Google Scholar 
Qi G, Zhu F, Du P, Yang X, Qiu D, Yu Z, et al. Lipopeptide induces apoptosis in fungal cells by a mitochondria-dependent pathway. Peptides. 2010;31:1978–86.CAS 
PubMed 

Google Scholar 
McCully LM, Bitzer AS, Seaton SC, Smith LM, Silby MW. Interspecies social spreading: interaction between two sessile soil bacteria leads to emergence of surface motility. mSphere. 2019;4:e00696–18.CAS 
PubMed 
PubMed Central 

Google Scholar 
Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016;14:563–75.CAS 
PubMed 

Google Scholar 
Townsley L, Shank EA. Natural-product antibiotics: cues for modulating bacterial biofilm formation. Trends Microbiol. 2017;25:1016–26.CAS 
PubMed 
PubMed Central 

Google Scholar 
Sun X, Xu Z, Xie J, Hesselberg-Thomsen V, Tan T, Zheng D, et al. Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. ISME J. 2022;16:774–87.CAS 
PubMed 

Google Scholar 
Dumas Z, Ross-Gillespie A, Kümmerli R. Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments. Proc R Soc B Biol Sci. 2013;280:20131055.
Google Scholar 
Lee N, Kim W, Chung J, Lee Y, Cho S, Jang KS, et al. Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus. ISME J. 2020;14:1111–24.CAS 
PubMed 
PubMed Central 

Google Scholar 
Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol. 2020;18:152–63.CAS 
PubMed 

Google Scholar 
Niehus R, Picot A, Oliveira NM, Mitri S, Foster KR. The evolution of siderophore production as a competitive trait. Evolution. 2017;71:1443–55.CAS 
PubMed 

Google Scholar 
Ho YN, Lee HJ, Hsieh CT, Peng CC, Yang YL. Chemistry and biology of salicyl-capped siderophores. Stud Nat Prod Chem. 2018;59:431–90.Schalk IJ, Rigouin C, Godet J. An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization. Environ Microbiol. 2020;22:1447–66.PubMed 

Google Scholar 
Deveau A, Gross H, Palin B, Mehnaz S, Schnepf M, Leblond P, et al. Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions. FEMS Microbiol Ecol. 2016;92:1–11.
Google Scholar 
Jenul C, Keim K, Jens J, Zeiler MJ, Schilcher K, Schurr M, et al. Pyochelin biotransformation shapes bacterial competition. bioRxiv. 2022. https://doi.org/10.1101/2022.04.18.486787.Ho YN, Hoo SY, Wang BW, Hsieh CT, Lin CC, Sun CH, et al. Specific inactivation of an antifungal bacterial siderophore by a fungal plant pathogen. ISME J. 2021;15:1858–61.CAS 
PubMed 
PubMed Central 

Google Scholar 
Lopez-Medina E, Fan D, Coughlin LA, Ho EX, Lamont IL, Reimmann C, et al. Candida albicans inhibits Pseudomonas aeruginosa virulence through suppression of pyochelin and pyoverdine biosynthesis. PLoS Pathog. 2015;11:1–34.
Google Scholar 
Meisel JD, Panda O, Mahanti P, Schroeder FC, Kim DH. Chemosensation of bacterial secondary metabolites modulates neuroendocrine signaling and behavior of C. elegans. Cell. 2014;159:267–80.CAS 
PubMed 
PubMed Central 

Google Scholar 
Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol. 2017;38:155–63.PubMed 
PubMed Central 

Google Scholar 
Saad MM, Eida AA, Hirt H, Doerner P. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. J Exp Bot. 2020;71:3878–901.CAS 
PubMed 
PubMed Central 

Google Scholar 
Ansari FA, Ahmad I. Fluorescent Pseudomonas -FAP2 and Bacillus licheniformis interact positively in biofilm mode enhancing plant growth and photosynthetic attributes. Sci Rep. 2019;9:4547.PubMed 
PubMed Central 

Google Scholar 
Domenech J, Reddy MS, Kloepper JW, Ramos B, Gutierrez-Mañero J. Combined application of the biological product LS213 with Bacillus, Pseudomonas or Chryseobacterium for growth promotion and biological control of soil-borne diseases in pepper and tomato. BioControl. 2006;51:245–58.CAS 

Google Scholar 
Powers MJ, Sanabria-Valentín E, Bowers AA, Shank EA. Inhibition of cell differentiation in Bacillus subtilis by Pseudomonas protegens. J Bacteriol. 2015;197:2129–38.CAS 
PubMed 
PubMed Central 

Google Scholar  More

Precht, W. F., Gintert, B. E., Robbart, M. L., Fura, R. & van Woesik, R. Unprecedented disease-related coral mortality in Southeastern Florida. Sci. Rep. 6, 31374 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
NOAA. Stony Coral Tissue Loss Disease Case Definition. NOAA, Silver Spring, MD 10 (2018).Aeby, G. S. et al. Pathogenesis of a tissue loss disease affecting multiple species of corals along the Florida Reef Tract. Front Mar. Sci. 6, 00678 (2019).
Google Scholar 
Landsberg, J. H. et al. Stony coral tissue loss disease in Florida is associated with disruption of host–zooxanthellae physiology. Front Mar. Sci. 7, 576013 (2020).
Google Scholar 
Neely, K. L., Macaulay, K. A., Hower, E. K. & Dobler, M. A. Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease. PeerJ 8, 9289 (2020).
Google Scholar 
Shilling, E. N., Combs, I. R. & Voss, J. D. Assessing the effectiveness of two intervention methods for stony coral tissue loss disease on Montastraea cavernosa. Sci. Rep. 11, 8566 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Walker, B. K., Turner, N. R., Noren, H. K. G., Buckley, S. F. & Pitts, K. A. Optimizing stony coral tissue loss disease (SCTLD) intervention treatments on Montastraea cavernosa in an endemic zone. Front Mar. Sci. 8, 666224 (2021).
Google Scholar 
Work, T. M. et al. Viral-like particles are associated with endosymbiont pathology in Florida corals affected by stony coral tissue loss disease. Front Mar. Sci. 8, 750658 (2021).
Google Scholar 
Veglia, A. J. et al. Alphaflexivirus genomes in stony coral tissue loss disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands. Microbiol. Resource Announc. 11, e01199-e1221 (2022).CAS 

Google Scholar 
Rosales, S. M. et al. Bacterial metabolic potential and micro-eukaryotes enriched in stony coral tissue loss disease lesions. Front Mar. Sci. 8, 776859 (2022).
Google Scholar 
Rosales, S. M., Clark, A. S., Huebner, L. K., Ruzicka, R. R. & Muller, E. M. Rhodobacterales and Rhizobiales are associated with stony coral tissue loss disease and its suspected sources of transmission. Front. Microbiol. 11, 681 (2020).PubMed 
PubMed Central 

Google Scholar 
Studivan, M. S. et al. Reef sediments can act as a stony coral tissue loss disease vector. Front Mar. Sci. 8, 815698 (2022).
Google Scholar 
Meyer, J. L. et al. Microbial community shifts associated with the ongoing stony coral tissue loss disease outbreak on the Florida Reef Tract. Front. Microbiol. 10, 2244 (2019).PubMed 
PubMed Central 

Google Scholar 
Ushijima, B. et al. Disease diagnostics and potential coinfections by Vibrio coralliilyticus during an ongoing coral disease outbreak in Florida. Front. Microbiol. 11, 2682 (2020).
Google Scholar 
Meiling, S. S. et al. Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure. Front Mar. Sci. 8, 670829 (2021).
Google Scholar 
Becker, C. C., Brandt, M., Miller, C. A. & Apprill, A. Microbial bioindicators of stony coral tissue loss disease identified in corals and overlying waters using a rapid field-based sequencing approach. Environ. Microbiol. 24, 1166–1182 (2021).PubMed 

Google Scholar 
Dobbelaere, T., Muller, E. M., Gramer, L. J., Holstein, D. M. & Hanert, E. Coupled epidemio-hydrodynamic modeling to understand the spread of a deadly coral disease in Florida. Front Mar. Sci. 7, 591881 (2020).
Google Scholar 
Dobbelaere, T. et al. Connecting the dots: Transmission of stony coral tissue loss disease from the Marquesas to the Dry Tortugas. Front Mar. Sci. 9, 778938 (2022).
Google Scholar 
Muller, E. M., Sartor, C., Alcaraz, N. I. & van Woesik, R. Spatial epidemiology of the stony-coral-tissue-loss disease in Florida. Front Mar. Sci. 7, 00163 (2020).
Google Scholar 
Sharp, W. C., Shea, C. P., Maxwell, K. E., Muller, E. M. & Hunt, J. H. Evaluating the small-scale epidemiology of the stony-coral-tissue-loss-disease in the middle Florida Keys. PLoS ONE 15, e0241871 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Williamson, O. M., Dennison, C. E., O’Neil, K. L. & Baker, A. C. Susceptibility of Caribbean brain coral recruits to stony coral tissue loss disease (SCTLD). Front Mar. Sci. 9, 821165 (2022).
Google Scholar 
Noonan, K. R. & Childress, M. J. Association of butterflyfishes and stony coral tissue loss disease in the Florida Keys. Coral Reefs 39, 1581–1590 (2020).
Google Scholar 
Dahlgren, C., Pizarro, V., Sherman, K., Greene, W. & Oliver, J. Spatial and temporal patterns of stony coral tissue loss disease outbreaks in the Bahamas. Front Mar. Sci. 8, 682114 (2021).
Google Scholar 
Rosenau, N. A. et al. Considering commercial vessels as potential vectors of stony coral tissue loss disease. Front Mar. Sci. 8, 709764 (2021).
Google Scholar 
Roth, L., Kramer, P., Doyle, E. & O’Sullivan, C. Caribbean SCTLD Dashboard. Available www.agrra.org. Accessed 06 Mar 2021. (2020).Brandt, M. E. et al. The emergence and initial impact of stony coral tissue loss disease (SCTLD) in the United States Virgin Islands. Front Mar. Sci. 8, 715329 (2021).
Google Scholar 
Bailey, S. A. et al. Trends in the detection of aquatic non-indigenous species across global marine, estuarine and freshwater ecosystems: A 50-year perspective. Divers. Distrib. 26, 1780–1797 (2020).MathSciNet 

Google Scholar 
Hewitt, C. L., Gollasch, S. & Minchin, D. The vessel as a vector: Biofouling, ballast water and sediments. In Biological Invasions in Marine Ecosystems Vol. 204 (eds Rilov, G. & Crooks, J. A.) 117–131 (Springer, 2009).
Google Scholar 
Zabin, C. J. et al. Small boats provide connectivity for nonindigenous marine species between a highly invaded international port and nearby coastal harbors. Manag. Biol. Invas. 5, 97–112 (2014).
Google Scholar 
Ashton, G. V., Zabin, C. J., Davidson, I. C. & Ruiz, G. M. Recreational boats routinely transfer organisms and promote marine bioinvasions. Biol. Invas. 24, 1083–1096 (2022).
Google Scholar 
Drake, L. A., Doblin, M. A. & Dobbs, F. C. Potential microbial bioinvasions via ships’ ballast water, sediment, and biofilm. Mar. Pollut. Bull. 55, 333–341 (2007).CAS 
PubMed 

Google Scholar 
Pagenkopp Lohan, K. M., Fleischer, R. C., Carney, K. J., Holzer, K. K. & Ruiz, G. M. Amplicon-based pyrosequencing reveals high diversity of protistan parasites in ships’ ballast water: Implications for biogeography and infectious diseases. Microb. Ecol. 71, 530–542 (2015).PubMed 

Google Scholar 
Ruiz, G. M. et al. Global spread of microorganisms by ships. Nature 408, 49–50 (2000).ADS 
CAS 
PubMed 

Google Scholar 
Hwang, J., Park, S. Y., Lee, S. & Lee, T. K. High diversity and potential translocation of DNA viruses in ballast water. Mar. Pollut. Bull. 137, 449–455 (2018).CAS 
PubMed 

Google Scholar 
Shikuma, N. J. & Hadfield, M. G. Marine biofilms on submerged surfaces are a reservoir for Escherichia coli and Vibrio cholerae. Biofouling 26, 39–46 (2009).
Google Scholar 
Aguirre-Macedo, M. L. et al. Ballast water as a vector of coral pathogens in the Gulf of Mexico: The case of the Cayo Arcas coral reef. Mar. Pollut. Bull. 56, 1570–1577 (2008).CAS 
PubMed 

Google Scholar 
Bruno, J. F. The coral disease triangle. Nat. Clim. Chang. 5, 302–303 (2015).ADS 

Google Scholar 
Lakshmi, E., Priya, M. & Achari, V. S. An overview on the treatment of ballast water in ships. Ocean Coast. Manag. 199, 105296 (2021).
Google Scholar 
Petersen, N. B., Madsen, T., Glaring, M. A., Dobbs, F. C. & Jørgensen, N. O. G. Ballast water treatment and bacteria: Analysis of bacterial activity and diversity after treatment of simulated ballast water by electrochlorination and UV exposure. Sci. Total Environ. 648, 408–421 (2019).ADS 
CAS 
PubMed 

Google Scholar 
Romero-Martínez, L., Moreno-Andrés, J., Acevedo-Merino, A. & Nebot, E. Evaluation of ultraviolet disinfection of microalgae by growth modeling: Application to ballast water treatment. J. Appl. Phycol. 28, 2831–2842 (2016).
Google Scholar 
First, M. R. et al. Stratification of living organisms in ballast tanks: How do organism concentrations vary as ballast water is discharged?. Environ. Sci. Technol. 47, 4442–4448 (2013).ADS 
CAS 
PubMed 

Google Scholar 
Drake, L. A. et al. Microbial ecology of ballast water during a transoceanic voyage and the effects of open-ocean exchange. Mar. Ecol. Prog. Ser. 233, 13–20 (2002).ADS 

Google Scholar 
Khandeparker, L., Kuchi, N., Desai, D. V. & Anil, A. C. Changes in the ballast water tank bacterial community during a trans-sea voyage: Elucidation through next generation DNA sequencing. J. Environ. Manag. 273, 111018 (2020).
Google Scholar 
Ruiz, G. M., Lorda, J., Arnwine, A. & Lion, K. Shipping patterns associated with the Panama Canal: Effects on biotic exchange? In Bridging Divides Vol. 83 (eds Gollasch, S. et al.) 113–126 (Springer, 2006).
Google Scholar 
Pagano, A., Wang, G., Sánchez, O., Ungo, R. & Tapiero, E. The impact of the Panama Canal expansion on Panama’s maritime cluster. Marit. Policy Manag. 43, 164–178 (2016).
Google Scholar 
Muirhead, J. R., Minton, M. S., Miller, W. A. & Ruiz, G. M. Projected effects of the Panama Canal expansion on shipping traffic and biological invasions. Divers. Distrib. 21, 75–87 (2015).
Google Scholar 
Ros, M. et al. The Panama Canal and the transoceanic dispersal of marine invertebrates: Evaluation of the introduced amphipod Paracaprella pusilla Mayer, 1890 in the Pacific Ocean. Mar. Environ. Res. 99, 204–211 (2014).ADS 
CAS 
PubMed 

Google Scholar 
Stehouwer, P. P., Buma, A. & Peperzak, L. A comparison of six different ballast water treatment systems based on UV radiation, electrochlorination and chlorine dioxide. Environ. Technol. 36, 2094–2104 (2015).CAS 
PubMed 

Google Scholar 
Wu, Y., Li, Z., Du, W. & Gao, K. Physiological response of marine centric diatoms to ultraviolet radiation, with special reference to cell size. J. Photochem. Photobiol., B 153, 1–6 (2015).CAS 

Google Scholar 
Aguirre, L. E. et al. Diatom frustules protect DNA from ultraviolet light. Sci. Rep. 8, 5138 (2018).ADS 
PubMed 
PubMed Central 

Google Scholar 
First, M. R. & Drake, L. A. Life after treatment: Detecting living microorganisms following exposure to UV light and chlorine dioxide. J. Appl. Phycol. 26, 227–235 (2014).CAS 

Google Scholar 
Liebich, V., Stehouwer, P. P. & Veldhuis, M. Re-growth of potential invasive phytoplankton following UV-based ballast water treatment. Aquat. Invas. 7, 29–36 (2012).
Google Scholar 
Hess-Erga, O. K., Moreno-Andrés, J., Enger, Ø. & Vadstein, O. Microorganisms in ballast water: Disinfection, community dynamics, and implications for management. Sci. Total Environ. 657, 704–716 (2019).ADS 
CAS 
PubMed 

Google Scholar 
Endresen, Ø., Lee Behrens, H., Brynestad, S., Bjørn Andersen, A. & Skjong, R. Challenges in global ballast water management. Mar. Pollut. Bull. 48, 615–623 (2004).CAS 
PubMed 

Google Scholar 
Vorkapić, A., Radonja, R. & Zec, D. Cost efficiency of ballast water treatment systems based on ultraviolet irradiation and electrochlorination. Promet Traffic Transp. 30, 343–348 (2018).
Google Scholar 
King, D., Hagan, P., Riggio, M. & Wright, D. Preview of global ballast water treatment markets. J. Mar. Eng. Technol. 11, 3–15 (2012).
Google Scholar 
Wang, Z., Saebi, M., Corbett, J. J., Grey, E. K. & Curasi, S. R. Integrated biological risk and cost model analysis supports a geopolitical shift in ballast water management. Environ. Sci. Technol. 55, 12791–12800 (2021).CAS 
PubMed 

Google Scholar 
Moreno-Andrés, J. & Peperzak, L. Operational and environmental factors affecting disinfection byproducts formation in ballast water treatment systems. Chemosphere 232, 496–505 (2019).ADS 
PubMed 

Google Scholar 
David, M., Linders, J., Gollasch, S. & David, J. Is the aquatic environment sufficiently protected from chemicals discharged with treated ballast water from vessels worldwide? A decadal environmental perspective and risk assessment. Chemosphere 207, 590–600 (2018).ADS 
CAS 
PubMed 

Google Scholar 
U.S. Environmental Protection Agency. Generic protocol for the verification of ballast water treatment technology, version 5.1. Report number EPA/600/R-10/146. Washington, D.C. 157 (2010).Evans, J. S., Paul, V. J., Ushijima, B. & Kellogg, C. A. Combining tangential flow filtration and size fractionation of mesocosm water as a method for the investigation of waterborne coral diseases. Biol. Methods Protocols 7, bpac007 (2022).
Google Scholar 
Fujimoto, M. et al. Application of Ion Torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity. PLoS ONE 9, e107534 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
United States Coast Guard. Ballast Water Best Management Practices to Reduce the Likelihood of Transporting Pathogens That May Spread Stony Coral Tissue Loss Disease. Marine Safety Information Bulletin 07–19. Washington, D.C. 2 (2019).Bolton, J. R. & Linden, K. G. Standardization of methods for fluence (UV dose) determination in bench-scale UV experiments. J. Environ. Eng. 129, 209–215 (2003).CAS 

Google Scholar 
Enochs, I. C. et al. The influence of diel carbonate chemistry fluctuations on the calcification rate of Acropora cervicornis under present day and future acidification conditions. J. Exp. Mar. Biol. Ecol. 506, 135–143 (2018).CAS 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Preprint at https://www.r-project.org/ (2019).Therneau, T. M. survival: A package for survival analysis in R. R package version 3.2–13. (2021).Kassambara, A., Kosinski, M. & Biecek, P. survminer: Drawing survival curves using “ggplot2”. R package version 0.4.9. (2021).Bakalar, G. Review of interdisciplinary devices for detecting the quality of ship ballast water. Springerplus 3, 468 (2014).PubMed 
PubMed Central 

Google Scholar 
Water Environmental Federation & American Public Health Association. Standard methods for the examination of water and wastewater. Washington, D.C. 21 (2005).Steinberg, M. K., Lemieux, E. J. & Drake, L. A. Determining the viability of marine protists using a combination of vital, fluorescent stains. Mar. Biol. 158, 1431–1437 (2011).
Google Scholar 
Oksanen, J. et al. vegan: Community ecology package. R package version 2.0–10. (2015).Martinez Arbizu, P. pairwiseAdonis: Pairwise multilevel comparison using adonis. R package version 0.4. (2020).Studivan, MS. Mstudiva/SCTLD-ballast-transmission: Stony coral tissue loss disease ballast transmission and treatment (Version 1.0), Zenodo, https://doi.org/10.5281/zenodo.6561517 (2022). More

Urbanization is fast progressing in the Global South, requiring new solutions for infrastructure, services, industrial development and land and energy use for these regions. In this context, fast-growing cities in Africa can take on a leadership role in driving climate change mitigation and adaptation, disaster risk reduction and sustainable development.
Credit: Stefan Rotter / Alamy Stock PhotoCities in Africa and elsewhere in the Global South continue to grapple with the challenge of delivering equitable services, infrastructure, housing and action to respond to climate change extremes and disasters. One well-known problem is a mismatch between the pace of urban growth and the slower development of basic services and critical infrastructure. This results in, for example, deficient sanitation, water supply systems and localized waste management for large parts of the population, which in turn contribute substantially to heightened poverty and inequality. For inclusive, equitable, prosperous and climate-resilient cities, urban management needs to integrate low-income communities into the urban economy by ensuring access to water, sanitation, energy transition, waste management, poverty reduction and by improving resilience through innovative solutions.
Credit: Patrick J. Endres/Corbis Documentary/GettySuch an equitable urban transition requires changes in the urban infrastructure, and land and energy use, as well as water and ecosystem management. The key research question in this field is to find ways to ensure city-wide access to infrastructure and services, while minimizing emissions and resource use, and building resilience to climate change impacts. In this regard, cities in the Global South and Africa in particular can serve as examples for other parts of the world as they have the potential to adopt disruptive, innovative yet practical solutions to low emissions, resource minimization and resilience building.
Credit: Nature Picture Library / Alamy Stock PhotoFor example, rapid urbanization creates the opportunity to develop economic structures in African cities that strongly integrate waste by promoting recovery, recycling, re-use and repair for lengthening lifecycles. Such a circular economy can create business opportunities, while also reducing resource use, thus creating a pathway for sustainable development. Another potential solution is hybrid systems for urban water management that are off-grid and utilize multiple water sources and treatment but that can also connect to centralized water systems. Business models for micro-to-medium enterprises have the potential to integrate some of the low-income groups through these kinds of technology and building social resilience.
Credit: Images of Africa Photobank / Alamy Stock PhotoThese examples are part of a broader assessment of urban infrastructure innovations, their disruption of centralized systems and rethinking of urban form for more compact, walkable, co-located land use for low carbon intensity towards net-zero cities. However, to translate research on these new solutions into action, a shift is necessary in the planning, governing and managing of cities so as to allow for opportunities for leapfrogging to emerge and expand the possibilities of urban development for inclusive and resilient African cities. More

Suttle CA. Marine viruses-major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12.CAS 
PubMed 

Google Scholar 
Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature 1999;399:541–8.CAS 
PubMed 

Google Scholar 
Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature 2009;459:207–12.CAS 
PubMed 

Google Scholar 
Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66.CAS 
PubMed 

Google Scholar 
Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, et al. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol. 2020;18:21–34.CAS 
PubMed 

Google Scholar 
Rosenwasser S, Ziv C, Creveld SGV, Vardi A. Virocell metabolism: metabolic innovations during host-virus interactions in the ocean. Trends Microbiol. 2016;24:821–32.CAS 
PubMed 

Google Scholar 
Fuchsman CA, Carlson MCG, Garcia Prieto D, Hays MD, Rocap G. Cyanophage host-derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific. Environ Microbiol. 2021;23:2782–2800.CAS 
PubMed 

Google Scholar 
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 2016;537:689–93.CAS 
PubMed 

Google Scholar 
Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 2019;177:1109–23.CAS 
PubMed 
PubMed Central 

Google Scholar 
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, et al. Patterns and ecological drivers of ocean viral communities. Science 2015;348:1261498.PubMed 

Google Scholar 
Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol. 2020;18:125–38.CAS 
PubMed 

Google Scholar 
Sullivan MB, Waterbury JB, Chisholm SW. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 2003;424:1047–51.CAS 
PubMed 

Google Scholar 
Mann NH. Phages of the marine cyanobacterial picophytoplankton. FEMS Microbiol Rev. 2003;27:17–34.CAS 
PubMed 

Google Scholar 
Ni T, Zeng Q. Diel infection of cyanobacteria by cyanophages. Front Mar Sci. 2016;2:123.
Google Scholar 
Flombaum P, Gallegos JL, Gordillo RA, Rincon J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA 2013;110:9824–9.CAS 
PubMed 
PubMed Central 

Google Scholar 
Biller SJ, Berube PM, Lindell D, Chisholm SW. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol 2015;13:13–27.CAS 
PubMed 

Google Scholar 
Proctor LM, Fuhrman JA. Viral mortality of marine-bacteria and cyanobacteria. Nature 1990;343:60–62.
Google Scholar 
Carlson MCG, Ribalet F, Maidanik I, Durham BP, Hulata Y, Ferron S, et al. Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean. Nat Microbiol 2022;7:570–80.CAS 
PubMed 
PubMed Central 

Google Scholar 
Matteson AR, Loar SN, Pickmere S, DeBruyn JM, Ellwood MJ, Boyd PW, et al. Production of viruses during a spring phytoplankton bloom in the South Pacific Ocean near of New Zealand. FEMS Microbiol Ecol 2012;79:709–19.CAS 
PubMed 

Google Scholar 
Ribalet F, Swalwell J, Clayton S, Jimenez V, Sudek S, Lin Y, et al. Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre. Proc Natl Acad Sci USA. 2015;112:8008–12.CAS 
PubMed 
PubMed Central 

Google Scholar 
Demory D, Liu R, Chen Y, Zhao F, Coenen AR, Zeng Q, et al. Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage. mSystems 2020;5:e00586–19.CAS 
PubMed 
PubMed Central 

Google Scholar 
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D. Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 2011;474:604–8.CAS 
PubMed 

Google Scholar 
Marston MF, Pierciey FJ Jr, Shepard A, Gearin G, Qi J, Yandava C, et al. Rapid diversification of coevolving marine Synechococcus and a virus. Proc Natl Acad Sci USA 2012;109:4544–9.CAS 
PubMed 
PubMed Central 

Google Scholar 
Xiao X, Guo W, Li X, Wang C, Chen X, Lin X, et al. Viral lysis alters the optical properties and biological availability of dissolved organic matter derived from Prochlorococcus picocyanobacteria. Appl Environ Microbiol. 2021;87:e02271–20.CAS 
PubMed 
PubMed Central 

Google Scholar 
Xiao X, Zeng Q, Zhang R, Jiao N. Prochlorococcus viruses—From biodiversity to biogeochemical cycles. Sci China Earth Sci. 2018;61:1728–36.
Google Scholar 
Jover LF, Effler TC, Buchan A, Wilhelm SW, Weitz JS. The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat Rev Microbiol. 2014;12:519–28.CAS 
PubMed 

Google Scholar 
Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Viruses inhibit CO2 fixation in the most abundant phototrophs on earth. Curr Biol 2016;26:1585–9.CAS 
PubMed 

Google Scholar 
Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, et al. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J. 2015;9:1352–64.PubMed 
PubMed Central 

Google Scholar 
Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 2005;3:e144.PubMed 
PubMed Central 

Google Scholar 
Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, Sarracino D, et al. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’. Environ Microbiol. 2009;11:2935–51.CAS 
PubMed 
PubMed Central 

Google Scholar 
Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, et al. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol. 2010;12:3035–56.CAS 
PubMed 
PubMed Central 

Google Scholar 
Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, Lindell D. A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proc Natl Acad Sci USA 2012;109:2037–42.CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang S, Wang K, Jiao N, Chen F. Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environ Microbiol. 2012;14:540–58.CAS 
PubMed 

Google Scholar 
Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, et al. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environ Microbiol. 2013;15:1356–76.CAS 
PubMed 

Google Scholar 
Dekel-Bird NP, Avrani S, Sabehi G, Pekarsky I, Marston MF, Kirzner S, et al. Diversity and evolutionary relationships of T7-like podoviruses infecting marine cyanobacteria. Environ Microbiol. 2013;15:1476–91.CAS 
PubMed 

Google Scholar 
Huang S, Wilhelm SW, Jiao N, Chen F. Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences. ISME J. 2010;4:1243–51.PubMed 

Google Scholar 
Baran N, Goldin S, Maidanik I, Lindell D. Quantification of diverse virus populations in the environment using the polony method. Nat Microbiol. 2018;3:62–72.CAS 
PubMed 

Google Scholar 
Chow C-ET, Suttle CA. Biogeography of viruses in the sea. Annu Rev Virol. 2015;2:41–66.CAS 
PubMed 

Google Scholar 
Chen F, Lu JR. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl Environ Microbiol. 2002;68:2589–94.CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang S, Zhang S, Jiao N, Chen F. Comparative genomic and phylogenomic analyses reveal a conserved core genome shared by estuarine and oceanic cyanopodoviruses. PLoS One. 2015;10:e0142962.PubMed 
PubMed Central 

Google Scholar 
Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, et al. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: A “horned’ bacteriophage of marine Synechococcus. J Mol Biol. 2007;368:966–81.CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang S, Sun Y, Zhang S, Long L. Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection. Microbiologyopen 2021;10:e1150.CAS 
PubMed 

Google Scholar 
Wang K, Chen F. Prevalence of highly host-specific cyanophages in the estuarine environment. Environ Microbiol. 2008;10:300–12.CAS 
PubMed 

Google Scholar 
Chen F, Wang K, Huang S, Cai H, Zhao M, Jiao N, et al. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. Environ Microbiol. 2009;11:2884–92.PubMed 

Google Scholar 
Goldin S, Hulata Y, Baran N, Lindell D. Quantification of T4-like and T7-like cyanophages using the polony method show they are significant members of the virioplankton in the North Pacific Subtropical Gyre. Front Microbiol. 2020;11:1210.PubMed 
PubMed Central 

Google Scholar 
Nasko DJ, Chopyk J, Sakowski EG, Ferrell BD, Polson SW, Wommack KE. Family A DNA polymerase phylogeny uncovers diversity and replication gene organization in the virioplankton. Front Microbiol. 2018;9:3053.PubMed 
PubMed Central 

Google Scholar 
Dekel-Bird NP, Sabehi G, Mosevitzky B, Lindell D. Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea. Environ Microbiol. 2015;17:1286–99.CAS 
PubMed 

Google Scholar 
Hanson CA, Marston MF, Martiny JBH. Biogeographic variation in host range phenotypes and taxonomic composition of marine cyanophage isolates. Front Microbiol. 2016;7:983.PubMed 
PubMed Central 

Google Scholar 
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 2003;424:1042–7.CAS 
PubMed 

Google Scholar 
Chen B, Wang L, Song S, Huang B, Sun J, Liu H. Comparisons of picophytoplankton abundance, size, and fluorescence between summer and winter in northern South China Sea. Cont Shelf Res. 2011;31:1527–40.
Google Scholar 
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, et al. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 2007;449:83–86.CAS 
PubMed 

Google Scholar 
Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, et al. Pelagiphages in the Podoviridae family integrate into host genomes. Environ Microbiol. 2019;21:1989–2001.CAS 
PubMed 

Google Scholar 
Leptihn S, Gottschalk J, Kuhn A. T7 ejectosome assembly: A story unfolds. Bacteriophage 2016;6:e1128513.CAS 
PubMed 
PubMed Central 

Google Scholar 
Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc Natl Acad Sci USA 2011;108:E757–64.CAS 
PubMed 
PubMed Central 

Google Scholar 
Zeng Q, Chisholm SW. Marine viruses exploit their host’s two-component regulatory system in response to resource limitation. Curr Biol 2012;22:124–8.CAS 
PubMed 

Google Scholar 
Zeng Q, Bonocora RP, Shub DA. A free-standing homing endonuclease targets an intron insertion site in the psbA gene of cyanophages. Curr Biol. 2009;19:218–22.CAS 
PubMed 

Google Scholar 
Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 2005;438:86–89.CAS 
PubMed 

Google Scholar 
Breitbart M, Thompson LR, Suttle CA, Sullivan MB. Exploring the vast diversity of marine viruses. Oceanography. 2007;20:135–9.
Google Scholar 
Kazlauskas D, Venclovas C. Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size. Nucleic Acids Res. 2011;39:8291–305.CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, et al. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol. 2010;17:830–6.CAS 
PubMed 
PubMed Central 

Google Scholar 
Dai W, Fu C, Raytcheva D, Flanagan J, Khant HA, Liu XG, et al. Visualizing virus assembly intermediates inside marine cyanobacteria. Nature 2013;502:707–10.CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu R, Liu Y, Chen Y, Zhan Y, Zeng Q. Cyanobacterial viruses exhibit diurnal rhythms during infection. Proc Natl Acad Sci USA 2019;116:14077–82.CAS 
PubMed 
PubMed Central 

Google Scholar 
Maidanik I, Kirzner S, Pekarski I, Arsenieff L, Tahan R, Carlson MCG, et al. Cyanophages from a less virulent clade dominate over their sister clade in global oceans. ISME J. 2022;16:2169–80.CAS 
PubMed 
PubMed Central 

Google Scholar 
Shitrit D, Hackl T, Laurenceau R, Raho N, Carlson MCG, Sabehi G, et al. Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages. ISME J. 2022;16:488–99.CAS 
PubMed 

Google Scholar 
Liang Y, Wang L, Wang Z, Zhao J, Yang Q, Wang M, et al. Metagenomic analysis of the diversity of DNA viruses in the surface and deep sea of the South China Sea. Front Microbiol. 2019;10:1951.PubMed 
PubMed Central 

Google Scholar 
Pedrós-Alió C, Potvin M, Lovejoy C. Diversity of planktonic microorganisms in the Arctic Ocean. Prog Oceanogr. 2015;139:233–43.
Google Scholar 
Luo E, Eppley JM, Romano AE, Mende DR, DeLong EF. Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. ISME J. 2020;14:1304–15.CAS 
PubMed 
PubMed Central 

Google Scholar 
Steidinger BS, Crowther TW, Liang J, Van Nuland ME, Werner GDA, Reich PB, et al. Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature 2019;569:404–8.CAS 
PubMed 

Google Scholar 
Xie X, Wu T, Zhu M, Jiang G, Xu Y, Wang X, et al. Comparison of random forest and multiple linear regression models for estimation of soil extracellular enzyme activities in agricultural reclaimed coastal saline land. Ecol Indic. 2021;120:106925.CAS 

Google Scholar 
Lee SJ, Richardson CC. Choreography of bacteriophage T7 DNA replication. Curr Opin Chem Biol. 2011;15:580–6.CAS 
PubMed 
PubMed Central 

Google Scholar 
Kulczyk AW, Richardson CC. The replication system of bacteriophage T7. Enzymes. 2016;39:89–136.CAS 
PubMed 

Google Scholar 
Benkovic SJ, Valentine AM, Salinas F. Replisome-mediated DNA replication. Annu Rev Biochem. 2001;70:181–208.CAS 
PubMed 

Google Scholar 
Johnson A, O’Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu Rev Biochem. 2005;74:283–315.CAS 
PubMed 

Google Scholar 
Seco EM, Zinder JC, Manhart CM, Lo Piano A, McHenry CS, Ayora S. Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro. Nucleic Acids Res. 2013;41:1711–21.CAS 
PubMed 

Google Scholar 
Mruwat N, Carlson MCG, Goldin S, Ribalet F, Kirzner S, Hulata Y, et al. A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances. ISME J. 2021;15:41–54.CAS 
PubMed 

Google Scholar 
Moore LR, Rocap G, Chisholm SW. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 1998;393:464–7.CAS 
PubMed 

Google Scholar 
Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. Photosynth Res. 2015;126:71–97.CAS 
PubMed 

Google Scholar 
Edwards KF, Steward GF, Schvarcz CR. Making sense of virus size and the tradeoffs shaping viral fitness. Ecol Lett. 2021;24:363–73.PubMed 

Google Scholar 
Moore LR, Coe A, Zinser ER, Saito MA, Sullivan MB, Lindell D, et al. Culturing the marine cyanobacterium Prochlorococcus. Limnol Oceanogr Methods. 2007;5:353–62.CAS 

Google Scholar 
Hyman P, Abedon ST. Bacteriophage host range and bacterial resistance. Adv Appl Microbiol. 2010;70:217–48.CAS 
PubMed 

Google Scholar 
Fridman S, Flores-Uribe J, Larom S, Alalouf O, Liran O, Yacoby I, et al. A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nat Microbiol. 2017;2:1350–7.CAS 
PubMed 

Google Scholar 
Fang X, Liu Y, Zhao Y, Chen Y, Liu R, Qin QL, et al. Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products. Environ Microbiol. 2019;21:2015–28.CAS 
PubMed 

Google Scholar 
John SG, Mendez CB, Deng L, Poulos B, Kauffman AK, Kern S, et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ Microbiol Rep. 2011;3:195–202.CAS 
PubMed 
PubMed Central 

Google Scholar 
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.CAS 
PubMed 
PubMed Central 

Google Scholar 
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27:863–4.CAS 
PubMed 
PubMed Central 

Google Scholar 
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:1–10.
Google Scholar 
Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012;28:1420–8.CAS 
PubMed 

Google Scholar 
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–9.CAS 
PubMed 

Google Scholar 
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.CAS 
PubMed 
PubMed Central 

Google Scholar 
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic Inference in the genomic era. Mol Biol Evol. 2020;37:2461–2461.PubMed 
PubMed Central 

Google Scholar 
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–22.CAS 
PubMed 

Google Scholar 
Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Pena MJ, Martinez JM, et al. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun. 2017;8:15892.CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang Z, Qin F, Chen F, Chu X, Luo H, Zhang R, et al. Culturing novel and abundant pelagiphages in the ocean. Environ Microbiol 2021;23:1145–61.CAS 
PubMed 

Google Scholar 
Buchholz HH, Michelsen ML, Bolanos LM, Browne E, Allen MJ, Temperton B. Efficient dilution-to-extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. ISME J. 2021;15:1585–98.CAS 
PubMed 
PubMed Central 

Google Scholar 
Qin F, Du S, Zhang Z, Ying H, Wu Y, Zhao G, et al. Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group. ISME J. 2022;16:1363–75.CAS 
PubMed 
PubMed Central 

Google Scholar  More