Seviour RJ, Kragelund C, Kong Y, Eales K, Nielsen JL, Nielsen PH. Ecophysiology of the Actinobacteria in activated sludge systems. Antonie Van Leeuw J Microb. 2008;94:21–33.
Jiang X-T, Ye L, Ju F, Wang Y-L, Zhang T. Toward an intensive longitudinal understanding of activated sludge bacterial assembly and dynamics. Environ Sci Technol. 2018;52:8224–32.
Google Scholar
Fiałkowska E, Pajdak-Stós A. The role of Lecane rotifers in activated sludge bulking control. Water Res. 2008;42:2483–90.
Google Scholar
Madoni P. Protozoa in wastewater treatment processes: a minireview. Ital J Zool. 2011;78:3–11.
Ye L, Mei R, Liu W-T, Ren H, Zhang X-X. Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes. Microbiome. 2020;8:16.
Google Scholar
Peces M, Astals S, Jensen P, Clarke W. Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community. Water Res. 2018;141:366–76.
Google Scholar
Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, et al. Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nat Microbiol. 2019;4:1183–95.
Google Scholar
Cox HH, Deshusses MA. Biomass control in waste air biotrickling filters by protozoan predation. Biotechnol Bioeng. 1999;62:216–24.
Google Scholar
Madoni P. A sludge biotic index (SBI) for the evaluation of the biological performance of activated sludge plants based on the microfauna analysis. Water Res. 1994;28:67–75.
Google Scholar
Ratsak C, Maarsen K, Kooijman S. Effects of protozoa on carbon mineralization in activated sludge. Water Res. 1996;30:1–12.
Google Scholar
Pogue AJ, Gilbride KA. Impact of protozoan grazing on nitrification and the ammonia- and nitrite-oxidizing bacterial communities in activated sludge. Can J Microbiol. 2007;53:559–71.
Google Scholar
Esteban G, Tellez C, Bautista LM. Dynamics of ciliated protozoa communities in activated-sludge process. Water Res. 1991;25:967–72.
Madoni P, Davoli D, Chierici E. Comparative analysis of the activated sludge microfauna in several sewage treatment works. Water Res. 1993;27:1485–91.
Google Scholar
Otto S, Harms H, Wick LY. Effects of predation and dispersal on bacterial abundance and contaminant biodegradation. FEMS Microbiol Ecol. 2017;93:fiw241.
Google Scholar
Peralta-Maraver I, Reiss J, Robertson AL. Interplay of hydrology, community ecology and pollutant attenuation in the hyporheic zone. Sci Total Environ. 2018;610:267–75.
Google Scholar
Yang JW, Wu W, Chung C-C, Chiang K-P, Gong G-C, Hsieh C-H. Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning—interplay between nanoflagellates and bacterioplankton. ISME J. 2018;12:1532–42.
Google Scholar
Seiler C, van Velzen E, Neu TR, Gaedke U, Berendonk TU, Weitere M. Grazing resistance of bacterial biofilms: a matter of predators’ feeding trait. FEMS Microbiol Ecol. 2017;93:fix112.
Burian A, Nielsen JM, Winder M. Food quantity-quality interactions and their impact on consumer behavior and trophic transfer. Ecol Monogr. 2020;90:e01395.
Schmitz OJ. Effects of predator functional diversity on grassland ecosystem function. Ecology. 2009;90:2339–45.
Google Scholar
Estes JA, Terborgh J, Brashares JS, Power ME, Berger J, Bond WJ, et al. Trophic downgrading of planet Earth. Science. 2011;333:301–6.
Google Scholar
Cardinale BJ, Duffy JE, Gonzalez A, Hooper DU, Perrings C, Venail P, et al. Biodiversity loss and its impact on humanity. Nature. 2012;486:59–67.
Google Scholar
Isbell F, Calcagno V, Hector A, Connolly J, Harpole WS, Reich PB, et al. High plant diversity is needed to maintain ecosystem services. Nature. 2011;477:199–202.
Google Scholar
Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun. 2016;7:10541.
Google Scholar
McCann KS. The diversity–stability debate. Nature. 2000;405:228.
Google Scholar
Pennekamp F, Pontarp M, Tabi A, Altermatt F, Alther R, Choffat Y, et al. Biodiversity increases and decreases ecosystem stability. Nature. 2018;563:109–12.
Google Scholar
Saikaly PE, Oerther DB. Diversity of dominant bacterial taxa in activated sludge promotes functional resistance following toxic shock loading. Microb Ecol. 2011;61:557–67.
Google Scholar
Worm B, Lotze HK, Hillebrand H, Sommer U. Consumer versus resource control of species diversity and ecosystem functioning. Nature. 2002;417:848–51.
Google Scholar
Gauzens B, Legendre S, Lazzaro X, Lacroix G. Intermediate predation pressure leads to maximal complexity in food webs. Oikos. 2016;125:595–603.
Chase JM, Biro EG, Ryberg WA, Smith KG. Predators temper the relative importance of stochastic processes in the assembly of prey metacommunities. Ecol Lett. 2009;12:1210–8.
Google Scholar
Paine RT. Food web complexity and species diversity. Am Nat. 1966;100:65–75.
Gliwicz ZM, Wursbaugh WA, Szymanska E. Absence of predation eliminates coexistence: experience from the fish–zooplankton interface. Fifty years after the “Homage to Santa Rosalia”: old and new paradigms on biodiversity in aquatic ecosystems. Springer; 2010. p. 103–17.
Terborgh JW. Toward a trophic theory of species diversity. Proc Natl Acad Sci USA. 2015;112:11415–22.
Google Scholar
Kondoh M. Unifying the relationships of species richness to productivity and disturbance. Proc R Soc B-Biol Sci. 2001;268:269–71.
Google Scholar
Hutchinson GE. The paradox of the plankton. Am Nat. 1961;95:137–45.
Al-Shahwani S, Horan N. The use of protozoa to indicate changes in the performance of activated sludge plants. Water Res. 1991;25:633–8.
Google Scholar
Torsvik V, Øvreås L, Thingstad TF. Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science. 2002;296:1064–6.
Google Scholar
Papadimitriou C, Papatheodoulou A, Takavakoglou V, Zdragas A, Samaras P, Sakellaropoulos G, et al. Investigation of protozoa as indicators of wastewater treatment efficiency in constructed wetlands. Desalination. 2010;250:378–82.
Google Scholar
Rossberg AG. Food webs and biodiversity: foundations, models, data. John Wiley & Sons; 2013.
Vage S, Bratbak G, Egge J, Heldal M, Larsen A, Norland S, et al. Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs. Ecol Lett. 2018;21:1440–52.
Google Scholar
Landry M, Hassett R. Estimating the grazing impact of marine micro-zooplankton. Mar Biol. 1982;67:283–8.
Dolan J, Gallegos C, Moigis A. Dilution effects on microzooplankton in dilution grazing experiments. Mar Ecol Prog Ser. 2000;200:127–39.
Google Scholar
Dottorini G, Michaelsen TY, Kucheryavskiy S, Andersen KS, Kristensen JM, Peces M, et al. Mass-immigration determines the assembly of activated sludge microbial communities. Proc Natl Acad Sci USA; 2021;118:e2021589118.
Google Scholar
Stevens-Garmon J, Drewes JE, Khan SJ, McDonald JA, Dickenson ERV. Sorption of emerging trace organic compounds onto wastewater sludge solids. Water Res. 2011;45:3417–26.
Google Scholar
Gasol JM, Morán XAG. Flow cytometric determination of microbial abundances and its use to obtain indices of community structure and relative activity. Hydrocarbon and lipid microbiology protocols. Springer; 2015. p. 159–87.
Ram AP, Chaibi-Slouma S, Keshri J, Colombet J, Sime-Ngando T. Functional responses of bacterioplankton diversity and metabolism to experimental bottom-up and top-down forcings. Microb Ecol. 2016;72:347–58.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.
Google Scholar
Hugerth LW, Muller EE, Hu YO, Lebrun LA, Roume H, Lundin D, et al. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. Plos One. 2014;9:e95567.
Google Scholar
D’Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, et al. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genom. 2016;17:55.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–D596.
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. Plos One. 2010;5:10.
Faith DP. Conservation evaluation and phylogenetic diversity. Biol Conserv. 1992;61:1–10.
Tsirogiannis C, Sandel B. PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments. Ecography. 2016;39:709–14.
Wobbrock JO, Findlater L, Gergle D, Higgins JJ, Acm. The aligned rank transform for nonparametric factorial analyses using only ANOVA procedures. Association Computing Machinery: New York; 2011.
Burnham KP, Anderson DR. Model selection and multimodel interference: a practical information—theoretic approach. Springer: New York, USA; 2002.
Arndt D, Xia J, Liu Y, Zhou Y, Guo AC, Cruz JA, et al. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 2012;40:W88–W95.
Google Scholar
R Development Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria; 2015. ISBN 3-900051-07-0, http://wwwR-projectorg.
Calbet A, Landry MR. Phytoplankton growth, microzooplankton grazing, and carbon cycling in marine systems. Limnol Oceanogr. 2004;49:51–57.
Google Scholar
Kiorboe T. How zooplankton feed: mechanisms, traits and trade-offs. Biol Rev. 2011;86:311–39.
Google Scholar
Juergens K, Matz C. Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Antonie Van Leeuw J Microb. 2002;81:413–34.
Hammill E, Kratina P, Beckerman A, Anholt BR. Precise time interactions between behavioural and morphological defences. Oikos. 2010;119:494–9.
Pernthaler J. Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol. 2005;3:537–46.
Google Scholar
Visser MD, Muller‐Landau HC, Wright SJ, Rutten G, Jansen PA. Tri‐trophic interactions affect density dependence of seed fate in a tropical forest palm. Ecol Lett. 2011;14:1093–1100.
Google Scholar
Bagchi R, Gallery RE, Gripenberg S, Gurr SJ, Narayan L, Addis CE, et al. Pathogens and insect herbivores drive rainforest plant diversity and composition. Nature. 2014;506:85–88.
Google Scholar
Kratina P, Vos M, Anholt BR. Species diversity modulates predation. Ecology. 2007;88:1917–23.
Google Scholar
Jaworski CC, Bompard A, Genies L, Amiens-Desneux E, Desneux N. Preference and prey switching in a generalist predator attacking local and invasive alien pests. Plos One. 2013;8:e82231.
Google Scholar
Coblentz KE, DeLong JP. Predator‐dependent functional responses alter the coexistence and indirect effects among prey that share a predator. Oikos. 2020;129:1404–14.
Madoni P. Estimates of ciliated protozoa biomass in activated sludge and biofilm. Bioresour Technol. 1994;48:245–9.
Google Scholar
Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E. The influence of functional diversity and composition on ecosystem processes. Science. 1997;277:1300–2.
Google Scholar
Sato Y, Hori T, Navarro RR, Habe H, Ogata A. Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor. Appl Microbiol Biot. 2016;100:6447–56.
Google Scholar
Cardinale BJ, Wright JP, Cadotte MW, Carroll IT, Hector A, Srivastava DS, et al. Impacts of plant diversity on biomass production increase through time because of species complementarity. Proc Natl Acad Sci USA. 2007;104:18123–8.
Google Scholar
Srivastava DS, Cadotte MW, MacDonald AAM, Marushia RG, Mirotchnick N. Phylogenetic diversity and the functioning of ecosystems. Ecol Lett. 2012;15:637–48.
Google Scholar
Yachi S, Loreau M. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci USA. 1999;96:1463–8.
Google Scholar
Mori AS, Isbell F, Seidl R. β-diversity, community assembly, and ecosystem functioning. Trends Ecol Evol. 2018;33:549–64.
Google Scholar
Hammill E, Hawkins CP, Greig HS, Kratina P, Shurin JB, Atwood TB. Landscape heterogeneity strengthens the relationship between β‐diversity and ecosystem function. Ecology. 2018;99:2467–75.
Google Scholar
Ellingsen KE, Yoccoz NG, Tveraa T, Frank KT, Johannesen E, Anderson MJ, et al. The rise of a marine generalist predator and the fall of beta diversity. Glob Change Biol. 2020;26:2897–907.
Weisse T. The significance of inter-and intraspecific variation in bacterivorous and herbivorous protists. Antonie Van Leeuw J Microb. 2002;81:327–41.
Nierychlo M, Andersen KS, Xu Y, Green N, Jiang C, Albertsen M, et al. MiDAS 3: an ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge. Water Res. 2020;182:115955.
Google Scholar
Source: Ecology - nature.com
