Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter
1.
Chen M, Zeng G, Zhang J, Xu P, Chen A, Lu L. Global landscape of total organic carbon, nitrogen and phosphorus in lake water. Sci Rep. 2015;5:15043.
CAS PubMed PubMed Central Article Google Scholar
2.
Toming K, Kotta J, Uuemaa E, Sobek S, Kutser T, Tranvik LJ. Predicting lake dissolved organic carbon at a global scale. Sci Rep. 2020;10:8471.
CAS PubMed PubMed Central Article Google Scholar
3.
Tranvik LJ, Downing JA, Cotner JB, Loiselle SA, Striegl RG, Ballatore TJ, et al. Lakes and reservoirs as regulators of carbon cycling and climate. Limnol Oceanogr. 2009;54:2298–314.
CAS Article Google Scholar
4.
Tranvik LJ, Cole JJ, Prairie YT. The study of carbon in inland waters-from isolated ecosystems to players in the global carbon cycle. Limnol Oceanogr Lett. 2018;3:41–48.
Article Google Scholar
5.
Jaffé R, McKnight D, Maie N, Cory R, McDowell WH, Campbell JL. Spatial and temporal variations in DOM composition in ecosystems: the importance of long-term monitoring of optical properties. J Geophys Res Biogeosci. 2008;113:G04032.
Article CAS Google Scholar
6.
Crump BC, Kling GW, Bahr M, Hobbie JE. Bacterioplankton community shifts in an Arctic Lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol. 2003;69:2253–68.
PubMed PubMed Central Article Google Scholar
7.
Fasching C, Behounek B, Singer GA, Battin TJ. Microbial degradation of terrigenous dissolved organic matter and potential consequences for carbon cycling in brown-water streams. Sci Rep. 2014;4:4981.
CAS PubMed PubMed Central Article Google Scholar
8.
Yakimovich KM, Emilson EJS, Carson MA, Tanentzap AJ, Basiliko N, Mykytczuk NCS. Plant litter type dictates microbial communities responsible for greenhouse gas production in amended lake sediments. Front Microbiol. 2018;9:2662.
PubMed PubMed Central Article Google Scholar
9.
Attermeyer K, Hornick T, Kayler ZE, Bahr A, Zwirnmann E, Grossart HP, et al. Enhanced bacterial decomposition with increasing addition of autochthonous to allochthonous carbon without any effect on bacterial community composition. Biogeosciences. 2014;11:1479–89.
Article Google Scholar
10.
Fabian J, Zlatanovic S, Mutz M, Premke K. Fungal-bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality. ISME J. 2017;11:415–25.
CAS PubMed Article PubMed Central Google Scholar
11.
Quigley LNM, Edwards A, Steen AD, Buchan A. Characterization of the interactive effects of labile and recalcitrant organic matter on microbial growth and metabolism. Front Microbiol. 2019;10:493.
PubMed PubMed Central Article Google Scholar
12.
Tranvik LJ. Degradation of dissolved organic matter in humic waters by bacteria. In: Hessen DOTLJ, editor. Aquatic Humic Substances. Berlin, Heidelberg: Springer; 1998.
13.
Søndergaard M, Borch NH, Riemann B. Dynamics of biodegradable DOC produced by freshwater plankton communities. Aquat Micro Ecol. 2000;23:73–83.
Article Google Scholar
14.
Berg B, McClaugherty C. Initial litter chemical composition. Plant Litter. 2014;3:53–83.
Article Google Scholar
15.
Bugg TD, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep. 2011;28:1883–96.
CAS PubMed Article PubMed Central Google Scholar
16.
Klotzbücher T, Kaiser K, Guggenberger G, Gatzek C, Kalbitz K. A new conceptual model for the fate of lignin in decomposing plant litter. Ecology. 2011;92:1052–62.
PubMed Article PubMed Central Google Scholar
17.
Grey J, Jones RI, Sleep D. Seasonal changes in the importance of the source of organic matter to the diet of zooplankton in Loch Ness, as indicated by stable isotope analysis. Limnol Oceanogr. 2001;46:505–13.
Article Google Scholar
18.
Cole JJ, Carpenter SR, Kitchell JF, Pace ML. Pathways of organic carbon utilization in small lakes: results from a whole-lake 13C addition and coupled model. Limnol Oceanogr. 2002;47:1664–75.
CAS Article Google Scholar
19.
Guenet B, Danger M, Abbadie L, Lacroix G. Priming effect: bridging the gap between terrestrial and aquatic ecology. Ecology. 2010;91:2850–61.
PubMed Article PubMed Central Google Scholar
20.
Bianchi TS. The role of terrestrially derived organic carbon in the coastal ocean: a changing paradigm and the priming effect. Proc Natl Acad Sci USA. 2011;108:19473–81.
CAS PubMed Article PubMed Central Google Scholar
21.
Bengtsson MM, Attermeyer K, Catalán N. Interactive effects on organic matter processing from soils to the ocean: are priming effects relevant in aquatic ecosystems? Hydrobiologia. 2018;822:1–17.
CAS Article Google Scholar
22.
Kuzyakov Y, Friedel JK, Stahr K. Review of mechanisms and quantification of priming effects. Soil Biol Biochem. 2000;32:1485–98.
CAS Article Google Scholar
23.
Bianchi TS, Ward ND. Editorial: the role of priming in terrestrial and aquatic ecosystems. Front Earth Sci. 2019;7:321.
Article Google Scholar
24.
Halvorson HM, Francoeur SN, Findlay RH, Kuehn KA. Algal-mediated priming effects on the ecological stoichiometry of leaf litter decomposition: a meta-analysis. Front Earth Sci. 2019;7:76.
Article Google Scholar
25.
Kayler ZE, Premke K, Gessler A, Gessner MO, Griebler C, Hilt S, et al. Integrating aquatic and terrestrial perspectives to improve insights into organic matter cycling at the landscape scale. Front Earth Sci. 2019;7:127.
Article Google Scholar
26.
Danger M, Cornut J, Chauvet E, Chavez P, Elger A, Lecerf A. Benthic algae stimulate leaf litter decomposition in detritus-based headwater streams: a case of aquatic priming effect? Ecology. 2013;94:1604–13.
PubMed Article PubMed Central Google Scholar
27.
Guenet B, Danger M, Harrault L, Allard B, Jauset-Alcala M, Bardoux G, et al. Fast mineralization of land-born C in inland waters: first experimental evidences of aquatic priming effect. Hydrobiologia. 2013;721:35–44.
Article CAS Google Scholar
28.
Ward ND, Sawakuchi HO, Richey JE, Keil RG, Bianchi TS. Enhanced aquatic respiration associated with mixing of clearwater tributary and turbid Amazon river waters. Front Earth Sci. 2019;7:101.
Article Google Scholar
29.
Bianchi TS, Thornton DCO, Yvon-Lewis SA, King GM, Eglinton TI, Shields MR, et al. Positive priming of terrestrially derived dissolved organic matter in a freshwater microcosm system. Geophys Res Lett. 2015;42:5460–67.
CAS Article Google Scholar
30.
Tang KW, Gladyshev MI, Dubovskaya OP, Kirillin G, Grossart H-P. Zooplankton carcasses and non-predatory mortality in freshwater and inland sea environments. J Plankton Res. 2014;36:597–612.
CAS Article Google Scholar
31.
Cauchie HM, Jaspar-Versali MF, Hoffmann L, Thomé JP. Analysis of the seasonal variation in biochemical composition of Daphnia magna Straus (Crustacea: Branchiopoda: Anomopoda) from an aerated wastewater stabilisation pond. Ann Limnol. 1999;35:223–31.
Article Google Scholar
32.
Smirnov NN. Physiology of the Cladocera, 2nd ed., London, Academic Press: Elsevier; 2017.
33.
Dubovskaya OP, Tang KW, Gladyshev MI, Kirillin G, Buseva Z, Kasprzak P, et al. Estimating in situ zooplankton non-predation mortality in an oligo-mesotrophic lake from sediment trap data: caveats and reality check. PLoS ONE. 2015;10:e0131431.
PubMed PubMed Central Article CAS Google Scholar
34.
Kirillin G, Grossart H-P, Tang KW. Modeling sinking rate of zooplankton carcasses: effects of stratification and mixing. Limnol Oceanogr. 2012;57:881–94.
Article Google Scholar
35.
Tang KW, Hutalle KML, Grossart HP. Microbial abundance, composition and enzymatic activity during decomposition of copepod carcasses. Aquat Micro Ecol. 2006;45:219–27.
Article Google Scholar
36.
Tang KW, Bickel SL, Dziallas C, Grossart HP. Microbial activities accompanying decomposition of cladoceran and copepod carcasses under different environmental conditions. Aquat Micro Ecol. 2009;57:89–100.
Article Google Scholar
37.
Kolmakova OV, Gladyshev MI, Fonvielle JA, Ganzert L, Hornick T, Grossart HP. Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling. Environ Microbiol. 2019;21:34–49.
CAS PubMed Article PubMed Central Google Scholar
38.
Corno G, Salka I, Pohlmann K, Hall AR, Grossart HP. Interspecific interactions drive chitin and cellulose degradation by aquatic microorganisms. Aquat Micro Ecol. 2015;76:27–37.
Article Google Scholar
39.
Masigol H, Khodaparast SA, Woodhouse JN, Rojas‐Jimenez K, Fonvielle J, Rezakhani F, et al. The contrasting roles of aquatic fungi and oomycetes in the degradation and transformation of polymeric organic matter. Limnol Oceanogr. 2019;64:2662–78.
CAS Article Google Scholar
40.
Gessner MO, Chauvet E. Importance of stream microfungi in controlling breakdown rates of leaf litter. Ecology. 1994;75:1807–17.
Article Google Scholar
41.
Grossart HP, Van den Wyngaert S, Kagami M, Wurzbacher C, Cunliffe M, Rojas-Jimenez K. Fungi in aquatic ecosystems. Nat Rev Microbiol. 2019;17:339–54.
CAS PubMed Article PubMed Central Google Scholar
42.
Osono T. Functional diversity of ligninolytic fungi associated with leaf litter decomposition. Ecol Res. 2019;35:30–43.
Article CAS Google Scholar
43.
Taube R, Ganzert L, Grossart HP, Gleixner G, Premke K. Organic matter quality structures benthic fatty acid patterns and the abundance of fungi and bacteria in temperate lakes. Sci Total Environ. 2018;610-611:469–81.
CAS PubMed Article PubMed Central Google Scholar
44.
Cragg SM, Beckham GT, Bruce NC, Bugg TD, Distel DL, Dupree P, et al. Lignocellulose degradation mechanisms across the Tree of Life. Curr Opin Chem Biol. 2015;29:108–19.
CAS PubMed PubMed Central Article Google Scholar
45.
Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J. 2019;13:413–29.
CAS PubMed Article PubMed Central Google Scholar
46.
Kuikman PJ, Jansen AG, van Veen JA, Zehnder AJB. Protozoan predation and the turnover of soil organic carbon and nitrogen in the presence of plants. Biol Fertil Soils. 1990;10:22–28.
CAS Article Google Scholar
47.
White DC, Davis WM, Nickels JS, King JD, Bobbie RJ. Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia. 1979;40:51–62.
CAS PubMed Article PubMed Central Google Scholar
48.
Romaní AM, Fischer H, Mille-Lindblom C, Tranvik LJ. Interactions of bacteria and fungi on decomposing litter: differential extracellular enzyme activities. Ecology. 2006;87:2559–69.
PubMed Article PubMed Central Google Scholar
49.
Hutalle-Schmelzer KM, Zwirnmann E, Kruger A, Grossart HP. Changes in pelagic bacteria communities due to leaf litter addition. Micro Ecol. 2010;60:462–75.
Article Google Scholar
50.
Smith EJ, Davison W, Hamilton-Taylor J. Methods for preparing synthetic freshwaters. Water Res. 2002;36:1286–96.
CAS PubMed Article PubMed Central Google Scholar
51.
Attermeyer K, Premke K, Hornick T, Hilt S, Grossart HP. Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats. Ecology. 2013;94:2754–66.
PubMed Article PubMed Central Google Scholar
52.
Halbedel S (2015) Protocol for CO2 sampling in waters by the use of the headspaceequilibration technique, based on the simple gas equation; second update. Protoc Exch. https://assets.researchsquare.com/files/nprot-4275/v1/manuscript.pdf
53.
Cheng W. Measurement of rhizosphere respiration and organic matter decomposition using natural 13C. Plant Soil. 1996;183:263–68.
CAS Article Google Scholar
54.
Taube R, Fabian J, Van den Wyngaert S, Agha R, Baschien C, Gerphagnon M, et al. Potentials and limitations of quantification of fungi in freshwater environments based on PLFA profiles. Fungal Ecol. 2019;41:256–68.
Article Google Scholar
55.
Zhang Z, Qu Y, Li S, Feng K, Wang S, Cai W, et al. Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa. Sci Rep. 2017;7:4837.
PubMed PubMed Central Article CAS Google Scholar
56.
Mangelsdorf K, Karger C, Zink K-G. Phospholipids as life markers in geological habitats. Hydrocarbons, oils and lipids: diversity, origin, chemistry and fate. 2019. pp. 1–29.
57.
Frostegård Å, Tunlid A, Bååth E. Microbial biomass measured as total lipid phosphate in soils of different organic content. J Microbiol Methods. 1991;14:151–63.
Article Google Scholar
58.
Nercessian O, Noyes E, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. Appl Environ Microbiol. 2005;71:6885–99.
CAS PubMed PubMed Central Article Google Scholar
59.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
CAS PubMed Article PubMed Central Google Scholar
60.
Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, et al. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys. 2015;10:1–43.
Article Google Scholar
61.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
CAS PubMed PubMed Central Article Google Scholar
62.
Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018;6:140.
PubMed PubMed Central Article Google Scholar
63.
De Caceres M, Legendre P. Associations between species and groups of sites: indices and statistical inference. Ecology. 2009;90:3566–74.
PubMed Article PubMed Central Google Scholar
64.
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinforma. 2008;9:559.
Article CAS Google Scholar
65.
Taipale SJ, Kainz MJ, Brett MT. Diet-switching experiments show rapid accumulation and preferential retention of highly unsaturated fatty acids in Daphnia. Oikos. 2011;120:1674–82.
Article Google Scholar
66.
Corno G, Jurgens K. Structural and functional patterns of bacterial communities in response to protist predation along an experimental productivity gradient. Environ Microbiol. 2008;10:2857–71.
PubMed Article PubMed Central Google Scholar
67.
Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012;6:1007–17.
CAS PubMed Article PubMed Central Google Scholar
68.
Song HK, Song W, Kim M, Tripathi BM, Kim H, Jablonski P, et al. Bacterial strategies along nutrient and time gradients, revealed by metagenomic analysis of laboratory microcosms. FEMS Microbiol Ecol. 2017;93:fix114.
Article CAS Google Scholar
69.
Bardgett RD, Kandeler E, Tscherko D, Hobbs PJ, Bezemer TM, Jones TH, et al. Below-ground microbial community development in a high temperature world. Oikos. 1999;85:193–203.
Article Google Scholar
70.
Hammel KE, Kapich AN, Jensen KA, Ryan ZC. Reactive oxygen species as agents of wood decay by fungi. Enzym Micro Technol. 2002;30:445–53.
CAS Article Google Scholar
71.
Rojas-Jimenez K, Fonvielle JA, Ma H, Grossart H-P. Transformation of humic substances by the freshwater Ascomycete Cladosporium sp. Limnol Oceanogr. 2017;62:1955–62.
CAS Article Google Scholar
72.
Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, et al. Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci USA. 2001;98:4136–41.
CAS PubMed Article PubMed Central Google Scholar
73.
Zheng W, Lehmann A, Ryo M, Valyi KK, Rillig MC. Growth rate trades off with enzymatic investment in soil filamentous fungi. Sci Rep. 2020;10:11013.
CAS PubMed PubMed Central Article Google Scholar
74.
Bärlocher F, Boddy L. Aquatic fungal ecology—How does it differ from terrestrial? Fungal Ecol. 2016;19:5–13.
Article Google Scholar
75.
Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A. Enzymes of early-diverging, zoosporic fungi. Appl Microbiol Biotechnol. 2019;103:6885–902.
CAS PubMed PubMed Central Article Google Scholar
76.
Janusz G, Pawlik A, Swiderska-Burek U, Polak J, Sulej J, Jarosz-Wilkolazka A, et al. Laccase properties, physiological functions, and evolution. Int J Mol Sci. 2020;21:966.
CAS PubMed Central Article Google Scholar
77.
Catalán N, Kellerman AM, Peter H, Carmona F, Tranvik LJ. Absence of a priming effect on dissolved organic carbon degradation in lake water. Limnol Oceanogr. 2015;60:159–68.
Article Google Scholar
78.
Bengtsson MM, Wagner K, Burns NR, Herberg ER, Wanek W, Kaplan LA, et al. No evidence of aquatic priming effects in hyporheic zone microcosms. Sci Rep. 2014;4:5187.
CAS PubMed PubMed Central Article Google Scholar
79.
Tanentzap AJ, Fitch A, Orland C, Emilson EJS, Yakimovich KM, Osterholz H, et al. Chemical and microbial diversity covary in fresh water to influence ecosystem functioning. Proc Natl Acad Sci USA. 2019;116:24689–95.
CAS PubMed Article PubMed Central Google Scholar
80.
Orland C, Emilson EJS, Basiliko N, Mykytczuk NCS, Gunn JM, Tanentzap AJ. Microbiome functioning depends on individual and interactive effects of the environment and community structure. ISME J. 2019;13:1–11.
CAS PubMed Article PubMed Central Google Scholar
81.
Winder M, Sommer U. Phytoplankton response to a changing climate. Hydrobiologia. 2012;698:5–16.
Article Google Scholar
82.
Pothoven SA, Fahnenstiel GL. Spatial and temporal trends in zooplankton assemblages along a nearshore to offshore transect in southeastern Lake Michigan from 2007 to 2012. J Gt Lakes Res. 2015;41:95–103.
Article Google Scholar
83.
Selmeczy GB, Abonyi A, Krienitz L, Kasprzak P, Casper P, Telcs A, et al. Old sins have long shadows: climate change weakens efficiency of trophic coupling of phyto- and zooplankton in a deep oligo-mesotrophic lowland lake (Stechlin, Germany)—a causality analysis. Hydrobiologia. 2018;831:101–17.
Article CAS Google Scholar More