Aran, A., L. Lin, L. A. Finn, K. Weiner, P. Peppard, T. Young, and E. Mignot. 2011. Post-streptococcal antibodies are associated with metabolic syndrome in a population-based cohort. PloS one 6:e25017.
Binks, P. R., C. E. French, S. Nicklin, and N. C. Bruce. 1996. Degradation of pentaerythritol tetranitrate by Enterobacter cloacae PB2. Appl. Environ. Microbiol. 62:1214-1219.
Boersma, M. 2000. The nutritional quality of P‐limited algae for Daphnia. Limnology and Oceanography 45:1157-1161.
Boersma, M., N. Aberle, F. M. Hantzsche, K. L. Schoo, K. H. Wiltshire, and A. M. Malzahn. 2008. Nutritional limitation travels up the food chain. International Review of Hydrobiology 93:479-488.
Bolyen, E., J. R. Rideout, M. R. Dillon, N. A. Bokulich, C. C. Abnet, G. A. Al-Ghalith, H. Alexander, E. J. Alm, M. Arumugam, and F. Asnicar. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37:852-857.
Brett, M. T., D. C. Müller‐Navarra, and P. Sang‐Kyu. 2000. Empirical analysis of the effect of phosphorus limitation on algal food quality for freshwater zooplankton. Limnology and Oceanography 45:1564-1575.
Buchfink, B., C. Xie, and D. H. Huson. 2015. Fast and sensitive protein alignment using DIAMOND. Nature methods 12:59-60.
Burns, A. R., W. Z. Stephens, K. Stagaman, S. Wong, J. F. Rawls, K. Guillemin, and B. J. Bohannan. 2016. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. The ISME journal 10:655-664.
Callens, M., E. Macke, K. Muylaert, P. Bossier, B. Lievens, M. Waud, and E. Decaestecker. 2016. Food availability affects the strength of mutualistic host–microbiota interactions in Daphnia magna. The ISME journal 10:911-920.
Callens, M., H. Watanabe, Y. Kato, J. Miura, and E. Decaestecker. 2018a. Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia. Microbiome 6:56.
Callens, M., H. Watanabe, Y. Kato, J. Miura, and E. Decaestecker. 2018b. Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia. Microbiome 6:1-12.
Camacho, C., G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer, and T. L. Madden. 2009. BLAST+: architecture and applications. BMC bioinformatics 10:421.
Chave, J. 2004. Neutral theory and community ecology. Ecology letters 7:241-253.
Chen, W., Y. Pan, L. Yu, J. Yang, and W. Zhang. 2017. Patterns and processes in marine microeukaryotic community biogeography from Xiamen coastal waters and intertidal sediments, southeast China. Frontiers in microbiology 8:1912.
Cho, M.-J., Y.-H. Kim, K. Shin, Y.-K. Kim, Y.-S. Kim, and T.-J. Kim. 2010. Symbiotic adaptation of bacteria in the gut of Reticulitermes speratus: Low endo-β-1, 4-glucanase activity. Biochemical and biophysical research communications 395:432-435.
Conroy, J. D., W. J. Edwards, R. A. Pontius, D. D. Kane, H. Zhang, J. F. Shea, J. N. Richey, and D. A. Culver. 2005. Soluble nitrogen and phosphorus excretion of exotic freshwater mussels (Dreissena spp.): potential impacts for nutrient remineralisation in western Lake Erie. Freshwater Biology 50:1146-1162.
Cruden, D. L., and A. Markovetz. 1984. Microbial aspects of the cockroach hindgut. Archives of microbiology 138:131-139.
Donaldson, G. P., S. M. Lee, and S. K. Mazmanian. 2016. Gut biogeography of the bacterial microbiota. Nature Reviews Microbiology 14:20-32.
Edgar, R. C., B. J. Haas, J. C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200.
Elser, J. J., K. Hayakawa, and J. Urabe. 2001. Nutrient limitation reduces food quality for zooplankton: Daphnia response to seston phosphorus enrichment. Ecology 82:898-903.
Elser, J. J., and J. Urabe. 1999. The stoichiometry of consumer‐driven nutrient recycling: theory, observations, and consequences. Ecology 80:735-751.
Glibert, P. M., D. Fullerton, J. M. Burkholder, J. C. Cornwell, and T. M. Kana. 2011. Ecological stoichiometry, biogeochemical cycling, invasive species, and aquatic food webs: San Francisco Estuary and comparative systems. Reviews in Fisheries Science 19:358-417.
Golz, A.-L., A. Burian, and M. Winder. 2015. Stoichiometric regulation in micro-and mesozooplankton. Journal of Plankton Research 37:293-305.
Gong, W., H. Paerl, and A. Marchetti. 2018. Eukaryotic phytoplankton community spatiotemporal dynamics as identified through gene expression within a eutrophic estuary. Environmental microbiology 20:1095-1111.
Grasshoff, K., K. Kremling, and M. Ehrhardt. 2009. Methods of seawater analysis. John Wiley & Sons.
Haas, B. J., A. Papanicolaou, M. Yassour, M. Grabherr, P. D. Blood, J. Bowden, M. B. Couger, D. Eccles, B. Li, and M. Lieber. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature protocols 8:1494-1512.
Hambright, K., N. Hairston, W. Schaffner, and R. Howarth. 2007. Grazer control of nitrogen fixation: synergisms in the feeding ecology of two freshwater crustaceans. Fundamental and Applied Limnology/Archiv für Hydrobiologie 170:89-101.
Hansen, K. D., S. E. Brenner, and S. Dudoit. 2010. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic acids research 38:e131-e131.
Harold, F. M. 1966. Inorganic polyphosphates in biology: structure, metabolism, and function. Bacteriological Reviews 30:772.
Harris, K. D., N. J. Bartlett, and V. K. Lloyd. 2012. Daphnia as an emerging epigenetic model organism. Genetics research international 2012.
Hessen, D. O., G. I. Ågren, T. R. Anderson, J. J. Elser, and P. C. De Ruiter. 2004. Carbon sequestration in ecosystems: the role of stoichiometry. Ecology 85:1179-1192.
Hirota, R., A. Kuroda, J. Kato, and H. Ohtake. 2010. Bacterial phosphate metabolism and its application to phosphorus recovery and industrial bioprocesses. Journal of bioscience and bioengineering 109:423-432.
Hooda, S., B. M. V. Boler, M. C. R. Serao, J. M. Brulc, M. A. Staeger, T. W. Boileau, S. E. Dowd, G. C. Fahey Jr, and K. S. Swanson. 2012. 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber. The Journal of nutrition 142:1259-1265.
Kan, Y., and J. Pan. 2010. A ONE‐SHOT SOLUTION TO BACTERIAL AND FUNGAL CONTAMINATION IN THE GREEN ALGA CHLAMYDOMONAS REINHARDTII CULTURE BY USING AN ANTIBIOTIC COCKTAIL 1. Journal of Phycology 46:1356-1358.
Kasubuchi, M., S. Hasegawa, T. Hiramatsu, A. Ichimura, and I. Kimura. 2015. Dietary gut microbial metabolites, short-chain fatty acids, and host metabolic regulation. Nutrients 7:2839-2849.
Klüttgen, B., U. Dülmer, M. Engels, and H. Ratte. 1994. ADaM, an artificial freshwater for the culture of zooplankton. Water research 28:743-746.
Kortstee, G. J., K. J. Appeldoorn, C. F. Bonting, E. W. van Niel, and H. W. van Veen. 1994. Biology of polyphosphate-accumulating bacteria involved in enhanced biological phosphorus removal. FEMS microbiology reviews 15:137-153.
Kulakova, A. N., D. Hobbs, M. Smithen, E. Pavlov, J. A. Gilbert, J. P. Quinn, and J. W. McGrath. 2011. Direct quantification of inorganic polyphosphate in microbial cells using 4′-6-diamidino-2-phenylindole (DAPI). Environmental science & technology 45:7799-7803.
Langmead, B., and S. L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nature methods 9:357.
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079.
Li, J., and M. Dittrich. 2019. Dynamic polyphosphate metabolism in cyanobacteria responding to phosphorus availability. Environmental microbiology 21:572-583.
Li, Y., Y. Neng, T. Y. Wong, W.-X. Wang, and H. Liu. 2019a. Interaction of antibacterial silver nanoparticles and microbiota-dependent holobiont revealed by metatranscriptomic analysis. Environmental Science: Nano.
Li, Y., N. Yan, T. Y. Wong, W.-X. Wang, and H. Liu. 2019b. Interaction of antibacterial silver nanoparticles and microbiota-dependent holobionts revealed by metatranscriptomic analysis. Environmental Science: Nano 6:3242-3255.
Liu, H., S. Tan, J. Xu, W. Guo, X. Xia, and S. Yan Cheung. 2017. Interactive regulations by viruses and dissolved organic matter on the bacterial community. Limnology and Oceanography 62:S364-S380.
Macke, E., M. Callens, L. De Meester, and E. Decaestecker. 2017a. Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria. Nature communications 8:1608.
Macke, E., M. Callens, L. Meester, and E. Decaestecker. 2017b. Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria. Nature communications 8:1608.
Mandal, S., R. Abbott Wilkins, and J. B. Shurin. 2018. Compensatory grazing by Daphnia generates a trade‐off between top‐down and bottom‐up effects across phytoplankton taxa. Ecosphere 9:e02537.
Marchet, C., L. Lecompte, A. Limasset, L. Bittner, and P. Peterlongo. 2020. A resource-frugal probabilistic dictionary and applications in bioinformatics. Discrete Applied Mathematics 274:92-102.
Marie, D., F. Partensky, S. Jacquet, and D. Vaulot. 1997. Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I. Appl. Environ. Microbiol. 63:186-193.
Meng, A., C. Marchet, E. Corre, P. Peterlongo, A. Alberti, C. Da Silva, P. Wincker, E. Pelletier, I. Probert, and J. Decelle. 2018. A de novo approach to disentangle partner identity and function in holobiont systems. Microbiome 6:105.
Mullan, A., J. Quinn, and J. McGrath. 2002. Enhanced phosphate uptake and polyphosphate accumulation in Burkholderia cepacia grown under low-pH conditions. Microbial ecology 44:69-77.
Orsini, L., D. Gilbert, R. Podicheti, M. Jansen, J. B. Brown, O. S. Solari, K. I. Spanier, J. K. Colbourne, D. B. Rusch, and E. Decaestecker. 2016. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific data 3:160030.
Pan, Y., J. Yang, G. B. McManus, S. Lin, and W. Zhang. 2019. Insights into protist diversity and biogeography in intertidal sediments sampled across a range of spatial scales. Limnology and Oceanography.
Panáček, A., L. Kvítek, M. Smékalová, R. Večeřová, M. Kolář, M. Röderová, F. Dyčka, M. Šebela, R. Prucek, and O. Tomanec. 2018. Bacterial resistance to silver nanoparticles and how to overcome it. Nature Nanotechnology 13:65-71.
Pearson, W. R., T. Wood, Z. Zhang, and W. Miller. 1997. Comparison of DNA sequences with protein sequences. Genomics 46:24-36.
Ploug, H., M. H. Iversen, and G. Fischer. 2008. Ballast, sinking velocity, and apparent diffusivity within marine snow and zooplankton fecal pellets: Implications for substrate turnover by attached bacteria. Limnology and Oceanography 53:1878-1886.
Power, M., K. Guiguer, and D. Barton. 2003. Effects of temperature on isotopic enrichment in Daphnia magna: implications for aquatic food‐web studies. Rapid Communications in Mass Spectrometry 17:1619-1625.
Prahl, F. G., and R. Carpenter. 1979. The role of zooplankton fecal pellets in the sedimentation of polycyclic aromatic hydrocarbons in Dabob Bay, Washington. Geochimica et Cosmochimica Acta 43:1959-1972.
Qiao, Y., J. Sun, Z. Xie, Y. Shi, and G. Le. 2014. Propensity to high-fat diet-induced obesity in mice is associated with the indigenous opportunistic bacteria on the interior of Peyer’s patches. Journal of clinical biochemistry and nutrition 55:120-128.
Reid, N. M., S. L. Addison, L. J. Macdonald, and G. Lloyd-Jones. 2011. Biodiversity of active and inactive bacteria in the gut flora of wood-feeding huhu beetle larvae (Prionoplus reticularis). Appl. Environ. Microbiol. 77:7000-7006.
Ríos-Covián, D., P. Ruas-Madiedo, A. Margolles, M. Gueimonde, C. G. de los Reyes-Gavilán, and N. Salazar. 2016. Intestinal short chain fatty acids and their link with diet and human health. Frontiers in microbiology 7:185.
Rippka, R., J. Deruelles, J. B. Waterbury, M. Herdman, and R. Y. Stanier. 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology 111:1-61.
Robertson, G., J. Schein, R. Chiu, R. Corbett, M. Field, S. D. Jackman, K. Mungall, S. Lee, H. M. Okada, and J. Q. Qian. 2010. De novo assembly and analysis of RNA-seq data. Nature methods 7:909-912.
Robinson, M. D., D. J. McCarthy, and G. K. Smyth. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
Shoemaker, K. M., S. Duhamel, and P. H. Moisander. 2019. Copepods promote bacterial community changes in surrounding seawater through farming and nutrient enrichment. Environmental microbiology 21:3737-3750.
Sloan, W. T., M. Lunn, S. Woodcock, I. M. Head, S. Nee, and T. P. Curtis. 2006. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environmental microbiology 8:732-740.
Sommer, U. 2002. Competition and coexistence in plankton communities. Pages 79-108 Competition and coexistence. Springer.
Steinberg, D. K., and M. R. Landry. 2017. Zooplankton and the ocean carbon cycle. Annual Review of Marine Science 9:413-444.
Sterner, R. W., J. Clasen, W. Lampert, and T. Weisse. 1998. Carbon: phosphorus stoichiometry and food chain production. Ecology Letters 1:146-150.
Sterner, R. W., and J. J. Elser. 2002. Ecological stoichiometry: the biology of elements from molecules to the biosphere. Princeton university press.
Suzuki‐Ohno, Y., M. Kawata, and J. Urabe. 2012. Optimal feeding under stoichiometric constraints: a model of compensatory feeding with functional response. Oikos 121:569-578.
Tang, K. W. 2005. Copepods as microbial hotspots in the ocean: effects of host feeding activities on attached bacteria. Aquatic Microbial Ecology 38:31-40.
Tang, K. W., R. N. Glud, A. Glud, S. Rysgaard, and T. G. Nielsen. 2011. Copepod guts as biogeochemical hotspots in the sea: evidence from microelectrode profiling of Calanus spp. Limnology and Oceanography 56:666-672.
Tang, K. W., V. Turk, and H.-P. Grossart. 2010. Linkage between crustacean zooplankton and aquatic bacteria. Aquatic Microbial Ecology 61:261-277.
Vital, M., A. C. Howe, and J. M. Tiedje. 2014. Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data. MBio 5:e00889-00814.
Vrede, T., T. Andersen, and D. O. Hessen. 1999. Phosphorus distribution in three crustacean zooplankton species. Limnology and Oceanography 44:225-229.
Xu, J., H. Jing, L. Kong, M. Sun, P. J. Harrison, and H. Liu. 2013. Effect of seawater–sewage cross-transplants on bacterial metabolism and diversity. Microbial ecology 66:60-72.
Zhai, S., S. Qin, L. Li, L. Zhu, Z. Zou, and L. Wang. 2019. Dietary butyrate suppresses inflammation through modulating gut microbiota in high-fat diet-fed mice. FEMS microbiology letters 366:fnz153.
Zhang, S., H. Liu, B. Chen, and C.-J. Wu. 2015. Effects of diet nutritional quality on the growth and grazing of Noctiluca scintillans. Marine Ecology Progress Series 527:73-85.
Zhang, S., H. Liu, P. M. Glibert, C. Guo, and Y. Ke. 2017. Effects of prey of different nutrient quality on elemental nutrient budgets in Noctiluca scintillans. Scientific reports 7:7622.