Abstract
The cyanobacterium Microcystis aeruginosa is a globally distributed bloom-forming organism that degrades freshwater systems around the world. Factors that drive its dispersion, diversification and success remain, however, poorly understood. To develop insight into cellular-level responses to nutrient drivers of eutrophication, RNA sequencing was coupled to a comprehensive metabolomics survey of M. aeruginosa sp. NIES 843 grown in various nutrient-reduced conditions. Transcriptomes were generated for cultures grown in nutrient-replete (with nitrate as the nitrogen (N) source), nitrogen-reduced (with nitrate, urea or ammonium acting as the N sources) and phosphate-reduced conditions. Extensive expression differences (up to 696 genes for urea-grown cells) relative to the control treatment were observed, demonstrating that the chemical variant of nitrogen available to cells affected transcriptional activity. Of particular note, a high number of transposase genes (up to 81) were significantly and reproducibly up-regulated relative to the control when grown on urea. Conversely, phosphorus (P) reduction resulted in a significant cessation in transcription of transposase genes, indicating that variation in nutrient chemistry may influence transcription of transposases and may impact the highly mosaic genomic architecture of M. aeruginosa. Corresponding metabolomes showed comparably few differences between treatments, suggesting broad changes to gene transcription are required to maintain metabolic homeostasis under nutrient reduction. The combined observations provide novel and extensive insight into the complex cellular interactions that take place in this important bloom-forming organism during variable nutrient conditions and highlight a potential unknown molecular mechanism that may drive Microcystis blooms and evolution.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
Change history
23 September 2013
This article has been corrected since Advance Online Publication and a corrigendum is also printed in this issue
References
Abraham P, Adams R, Giannone RJ, Kalluri U, Ranjan P, Erickson B et al. (2011). Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res 11: 449–460.
Alikhan N-F, Petty N, Ben Zakour N, Beatson S . (2011). BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12: 402.
Baggerly KA, Deng L, Morris JS, Aldaz CM . (2003). Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19: 1477–1483.
Bao W, Jurka J . (2013). Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. Mobile DNA 4: 12.
Berman T . (1970). Alkaline phosphatases and phosphorus availability in Lake Kinneret. Limnol Oceanogr 15: 663–674.
Berman T, Béchemin C, Maestrini SY . (1999). Release of ammonium and urea from dissolved organic nitrogen in aquatic ecosystems. Aquat Microb Ecol 16: 295–302.
Chao L, Vargas C, Spear BB, Cox EC . (1983). Transposable elements as mutator genes in evolution. Nature 303: 633–635.
Christiansen G, Molitor C, Philmus B, Kurmayer R . (2008). Nontoxic strains of cyanobacteria are the result of major gene deletion events induced by a transposable element. Mol Biol Evol 25: 1695–1704.
Clasquin MF, Melamud E, Rabinowitz JD . (2012). LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr Protoc Bioinformatics 14.11.1–14.11.23.
Davis T, Harke MJ, Marcoval MA, Goleski J, Orano-Dawson C, Berry DL et al. (2010). Effects of nitrogenous compounds and phosphorus on the growth of toxic and non-toxic strains of Microcystis during cyanobacterial blooms. Aquat Microb Ecol 61: 149–162.
DeBruyn JM, Leigh-Bell JA, McKay RML, Bourbonniere RA, Wilhelm SW . (2004). Microbial distributions and the impact of phosphorus on bacterial activity in Lake Erie. J Great Lak Res 30: 166–183.
Dillies M-A, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N et al. (2013). A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 14: 671–683.
Dodds WK, Bouska WW, Eitzmann JL, Pilger TJ, Pitts KL, Riley AJ et al. (2008). Eutrophication of U.S. freshwaters: analysis of potential economic damages. Environ Sci Tech 43: 12–19.
Dolman AM, Rücker J, Pick FR, Fastner J, Rohrlack T, Mischke U et al. (2012). Cyanobacteria and cyanotoxins: the influence of nitrogen versus phosphorus. PLoS One 7: e38757.
Donald DB, Bogard MJ, Finlay K, Leavitt PR . (2011). Comparative effects of urea, ammonium, and nitrate on phytoplankton abundance, community composition, and toxicity in hypereutrophic freshwaters. Limnol Oceanogr 56: 2161–2175.
Downing JA, Watson SB, McCauley E . (2001). Predicting cyanobacteria dominance in lakes. Can J Fish Aquat Sci 58: 1905–1908.
Frangeul L, Quillardet P, Castets A-M, Humbert J-F, Matthijs H, Cortez D et al. (2008). Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium. BMC Genomics 9: 274.
Gibert I, Barbé J, Casadesús J . (1990). Distribution of insertion sequence IS200 in Salmonella and Shigella. J Gen Microbiol 136: 2555–2560.
Glibert P, Harrison J, Heil C, Seitzinger S . (2006). Escalating worldwide use of urea – a global change contributing to coastal eutrophication. Biogeochemistry 77: 441–463.
Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV et al. (2011). Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci USA 108: 4352–4357.
Harke M, Berry D, Ammerman J, Gobler C . (2012). Molecular response of the bloom-forming cyanobacterium, Microcystis aeruginosa, to phosphorus limitation. Microb Ecol 63: 188–198.
Harke M, Gobler C . (2013). Global transcriptional responses of the toxic cyanobacterium, Microcystis aeruginosa, to nitrogen stress, phosphorus stress, and growth on organic matter. PLoS One 8: e69834.
Healey FP, Hendzel LL . (1979). Indicators of phosphorus and nitrogen deficiency in five algae in culture. J Fish Res Board Can 36: 1364–1369.
Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, Bench SR et al. (2009). In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. ISME J 3: 618–631.
Hotto AM, Satchwell MF, Berry DL, Gobler CJ, Boyer GL . (2008). Spatial and temporal diversity of microcystins and microcystin-producing genotypes in Oneida Lake, NY. Harmful Algae 7: 671–681.
Humbert J-F, Barbe V, Latifi A, Gugger M, Calteau A, Coursin T et al. (2013). A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. PLoS One 8: e70747.
Ichimura T . (1971). Sexual cell division and conjugation-papilla formation in sexual reproduction of Closterium stringosum. Proceedings of the 7th International Seaweed Symposium, 1971., Sappora, Japan.
Ishida K, Welker M, Christiansen G, Cadel-Six S, Bouchier C, Dittmann E et al. (2009). Plasticity and evolution of aeruginosin biosynthesis in cyanobacteria. Appl Environ Microbiol 75: 2017–2026.
Ivanikova NV, McKay RML, Bullerjahn GS, Sterner RW . (2007). Nitrate utilization by phytoplankton in Lake Superior is impaired by nutrient (P, Fe) availability and season light limitation - a cyanobacterial bioreporter study. J Phycol 43: 475–484.
Jäger D, Sharma CM, Thomsen J, Ehlers C, Vogel J, Schmitz RA . (2009). Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci USA 106: 21878–21882.
Kaneko T, Nakajima N, Okamoto S, Suzuki I, Tanabe Y, Tamaoki M et al. (2007). Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843. DNA Res 14: 247–256.
Kleiner M, Young JC, Shah M, VerBerkmoes NC, Dubilier N . (2013). Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts. mBio 4: e00223–13.
Lin S, Haas S, Zemojtel T, Xiao P, Vingron M, Li R . (2011). Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. Gene 473: 139–149.
Lu WY, Clasquin MF, Melamud E, Amador-Noguez D, Caudy AA, Rabinowitz JD . (2010). Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone Orbitrap mass spectrometer. Anal Chem 82: 3212–3221.
Mackerras AH, Smith GD . (1986). Urease activity of the cyanobacterium Anabaena cylindrica. J Gen Microbiol 132: 2749–2752.
McClintock B . (1950). The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36: 344–355.
Melamud E, Vastag L, Rabinowitz JD . (2010). Metabolomic analysis and visualization engine for LC-MS data. Anal Chem 82: 9818–9826.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B . (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth 5: 621–628.
Myklestad S, Sakshaug E . (1983). Alkaline phosphatase activity of Skeletonema costatum populations in the Trondheimsfjord. J Plank Res 5: 557–564.
Nausch M . (1998). Alkaline phosphatase activities and the relationship to inorganic phosphate in the Pomeranian Bight (southern Baltic Sea). Aquat Microb Ecol 16: 87–94.
Neddermann K, Nausch M . (2004). Effects of organic and inorganic nitrogen compounds on the activity of bacterial alkaline phosphatase. Aquat Ecol 38: 475–484.
Paerl HW, Xu H, McCarthy MJ, Zhu G, Qin B, Li Y et al. (2011). Controlling harmful cyanobacterial blooms in a hyper-eutrophic lake (Lake Taihu, China): the need for a dual nutrient (N & P) management strategy. Water Res 45: 1973–1983.
Paterson M, Schindler D, Hecky R, Findlay D . (2011). Comment: Lake 227 shows clearly that controlling inputs of nitrogen will not reduce or prevent eutrophication of lakes. Limnol Oceanogr 56: 1545–1547.
Purvina S, Bechemin C, Balode M, Verite C, Arnaud C, Maerstrini SY . (2010). Release of available nitrogen from river-discharged dissolved organic matter by heterotrophic bacteria associated with the cyanobacterium Microcystis aeruginosa. Estonian J Ecol 59: 184–196.
Ram RJ, VerBerkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC et al. (2005). Community proteomics of a natural microbial biofilm. Science 308: 1915–1920.
Rinta-Kanto JM, Konopko EA, DeBruyn JM, Bourbonniere RA, Boyer GL, Wilhelm SW . (2009). Lake Erie Microcystis: relationship between microcystin production, dynamics of genotypes and environmental parameters in a large lake. Harmful Algae 8: 665–673.
Schindler DW . (1977). Evolution of phosphorus limitation in lakes. Science 195: 260–262.
Schmitz-Esser S, Penz T, Spang A, Horn M . (2011). A bacterial genome in transition - an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus. BMC Evol Biol 11: 270.
Scott JT, McCarthy MJ . (2010). Nitrogen fixation may not balance the nitrogen pool in lakes over timescales relevant to eutrophication management. Limnol Oceanogr 55: 1265–1270.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C . (2012). Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Meth 9: 811–814.
Shen H, Song L . (2007). Comparative studies on physiological responses to phosphorus in two phenotypes of bloom-forming Microcystis. Hydrobiologia 592: 475–486.
Slotkin RK, Martienssen R . (2007). Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272–285.
Spura J, Christian Reimer L, Wieloch P, Schreiber K, Buchinger S, Schomburg D . (2009). A method for enzyme quenching in microbial metabolome analysis successfully applied to gram-positive and gram-negative bacteria and yeast. Anal Biochem 394: 192–201.
Steglich C, Lindell D, Futschik M, Rector T, Steen R, Chisholm S . (2010). Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus. Genome Biol 11: R54.
Straub C, Quillardet P, Vergalli J, de Marsac NT, Humbert J-F . (2011). A day in the life of Microcystis aeruginosa strain PCC 7806 as revealed by a transcriptomic analysis. PLoS One 6: e16208.
Vézie C, Rapala J, Vaitomaa J, Seitsonen J, Sivonen K . (2002). Effect of nitrogen and phosphorus on growth of toxic and nontoxic Microcystis strains and on intracellular microcystin concentrations. Microb Ecol 43: 443–454.
Wang H, Sivonen K, Rouhiainen L, Fewer D, Lyra C, Rantala-Ylinen A et al. (2012). Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90. BMC Genomics 13: 613.
Welschmeyer NA . (1994). Fluorometric analysis of chlorophyll-a in the presence of chlorophyll-B and pheopigments. Limnol Oceanogr 39: 1985–1992.
Wilhelm SW, DeBruyn JM, Gillor O, Twiss MR, Livingston K, Bourbonniere RA et al. (2003). Effect of phosphorus amendments on present day plankton communities in pelagic Lake Erie. Aquat Microb Ecol 32: 275–285.
Wurch LL, Haley ST, Orchard ED, Gobler CJ, Dyhrman ST . (2011). Nutrient-regulated transcriptional responses in the brown tide-forming alga Aureococcus anophagefferens. Environ Microbiol 13: 468–481.
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP . (2006). Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5: 2339–2347.
Acknowledgements
We thank Dr GL Boyer, Dr LJ Hauser, Dr NC VerBerkmoes, Dr RL Hettich, Dr GS Bullerjahn and Dr RML McKay for support and meaningful ideas and discussion. We also thank Shafer Belisle, Chad Effler and Justine Schmidt for their assistance. This project was supported by grants from the National Science Foundation (IOS 0841918 and DEB 1240870 to SWW; and OCE 1233964 and OCE 1208784 to SRC) and a UT/ORNL Science Alliance JDRD award to SWW. MMS was supported by a Wallace-Dean fellowship from the University of Tennessee.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Additional information
Supplementary Information accompanies this paper on The ISME Journal website
Supplementary information
Rights and permissions
About this article
Cite this article
Steffen, M., Dearth, S., Dill, B. et al. Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis. ISME J 8, 2080–2092 (2014). https://doi.org/10.1038/ismej.2014.78
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/ismej.2014.78
Keywords
This article is cited by
-
Using a separation method to study the intra-colony cellular response in cyanobacterium Microcystis
Journal of Applied Phycology (2024)
-
Response of Microcystis aeruginosa FACHB-905 to different nutrient ratios and changes in phosphorus chemistry
Journal of Oceanology and Limnology (2018)
-
High abundance and expression of transposases in bacteria from the Baltic Sea
The ISME Journal (2017)
-
Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production
Standards in Genomic Sciences (2016)
-
Daily transcriptome changes reveal the role of nitrogen in controlling microcystin synthesis and nutrient transport in the toxic cyanobacterium, Microcystis aeruginosa
BMC Genomics (2015)
