Abstract
An analysis of the microbial metabolism is fundamental to understanding globally important element transformations. One culture-independent approach to deduce those prokaryotic metabolic functions is to analyze metatranscriptomes. Unfortunately, since mRNA is extremely labile, it is unclear whether the abundance patterns detected in nature are vulnerable to considerable modification in situ simply due to sampling procedures. Exemplified on comparisons of metatranscriptomes retrieved from pelagic suboxic zones of the central Baltic Sea (70–120 m depth), earlier identified as areas of high aerobic ammonium oxidation activity, and quantification of specific transcripts in them, we show that different sampling techniques significantly influence the relative abundance of transcripts presumably diagnostic of the habitat. In situ fixation using our newly developed automatic flow injection sampler resulted in an abundance of thaumarchaeal ammonia monooxygenase transcripts that was up to 30-fold higher than that detected in samples obtained using standard oceanographic sampling systems. By contrast, the abundance of transcripts indicative of cellular stress was significantly greater in non-fixed samples. Thus, the importance of in situ fixation in the reliable evaluation of distinct microbial activities in the ecosystem based on metatranscriptomics is obvious. In consequence, our data indicate that the significance of thaumarchaeota to aerobic ammonium oxidation could yet have been considerably underestimated. Taken these results, this could in general also be the case in attempts aimed at an unbiased gene expression analysis of areas below the epipelagic zone, which cover 90% of the world's oceans.
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Amann RI, Ludwig W, Schleifer KH . (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143–169.
Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R et al. (2006). Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol 188: 6739–6756.
Belasco J . (1993). Control of Messenger RNA Stability. Academic Press: San Diego, pp 3–11.
Brady A, Salzberg SL . (2009). Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 6: 673–676.
Brettar I, Rheinheimer G . (1991). Denitrification in the central Baltic: evidence for H2S-oxidation as motor of denitrification at the oxic-anoxic interface. Mar Ecol Prog Ser 77: 157–169.
Chin-Leo G, Kirchman DL . (1988). Estimating bacterial production in marine waters from the simultaneous incorporation of thymidine and leucine. Appl Environ Microbiol 54: 1934–1939.
Church MJ, Wai B, Karl DM, DeLong EF . (2010). Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol 12: 679–688.
Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG, Sinninghe Damste JS . (2007). Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environ Microbiol 9: 1001–1016.
Créach V, Baudoux A-C, Bertru G, Rouzic BL . (2003). Direct estimate of active bacteria: CTC use and limitations. J Microbiol Methods 52: 19–28.
DeLong EF . (2009). The microbial ocean from genomes to biomes. Nature 459: 200–206.
Deutscher MP . (2006). Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res 34: 659–666.
Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W . (2009). Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33: 855–869.
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB . (2005). Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683–14688.
Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW et al. (2008). Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805–3810.
Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA. . (2010). Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J 5: 461–472.
Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P et al. (2008). Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3: e3042.
Grasshoff K, Erhardt M, Kremling K . (1983). Methods of Seawater Analysis, vol. 2. Verlag Chemie Weinheim: New York.
Grote J. (2009). Physiology, ecology, and genomics of facultative chemoautotrophic Epsilonproteobacteria in marine pelagic redoxclines . PhD thesis, University of Rostock, Germany.
Grote J, Labrenz M, Pfeiffer B, Jost G, Jürgens K . (2007). Quantitative distribution of Epsilonproteobacteria and a specific Sulfurimonas subgroup in pelagic redoxclines of the central Baltic Sea. Appl Environ Microbiol 73: 7155–7161.
Hollibaugh JT, Gifford SM, Sharma S, Bano N, Moran MA . (2010). Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. ISME J 5: 866–878.
Khodursky AB, Bernstein JA, Peter BJ, Rhodius V, Wendisch VF, Zimmer DP . (2003). Escherichia coli spotted double-strand DNA microarrays. In: Brownstein MJ, Khodursky AB (eds). Functional Genomics. Humana Press Inc.: Totowa, pp 61–78.
Labrenz M, Jost G, Jürgens K . (2007). Distribution of abundant prokaryotic organisms in the water column of the central Baltic Sea with an oxic-anoxic interface. Aquat Microb Ecol 46: 177–190.
Labrenz M, Sintes E, Toetzke F, Zumsteg A, Herndl GJ, Seidler M et al. (2010). Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea. ISME J 4: 1496–1508.
Lam P, Jensen MM, Lavik G, McGinnis DF, Müller B, Schubert CJ et al. (2007). Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proc Natl Acad Sci USA 104: 7104–7109.
Lin X, Wakeham SG, Putnam IF, Astor YM, Scranton MI, Chistoserdov AY et al. (2006). Comparison of vertical distributions of prokaryotic assemblages in the anoxic Cariaco Basin and Black Sea by use of fluorescence in situ hybridization. Appl Environ Microbiol 72: 2679–2690.
Little JW, Edmiston SH, Pacelli LZ, Mount DW . (1980). Cleavage of the Escherichia coli lexA protein by the recA protease. Proc Natl Acad Sci USA 77: 3225–3229.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
Masín M, Zdun A, Ston-Egiert J, Nausch M, Labrenz M, Moulisová V et al. (2006). Seasonal changes and diversity of aerobic anoxygenic phototrophs in the Baltic Sea. Aquat Microb Ecol 45: 247–254.
Meyer F, Paarmann D, D′Souza M, Olson R, Glass EM, Kubal M et al. (2008). The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
Moran MA. (2009). Metatranscriptomics: Eavesdropping on complex microbial communities. Microbe 4: 329–335.
Pace NR . (1997). A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA . (2009). Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11: 1358–1375.
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.
Strady E, Pohl C, Yakushev EV, Krüger S, Hennings U . (2008). PUMP-CTD-System for trace metal sampling with a high vertical resolution. A test in the Gotland Basin, Baltic Sea. Chemosphere 70: 1309–1319.
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC . (2008). Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3: e2527.
Vetriani C, Tran HV, Kerkhof LJ . (2003). Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Appl Environ Microbiol 69: 6481–6488.
Wartman WB . (1960). Leitfaden der Mikroskopischen Technik. Arch Intern Med 106: 739.
Walker CB, De la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ et al. (2010). Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107: 8818–8823.
Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P et al. (2006). Archaeal nitrification in the ocean. Proc Natl Acad Sci USA 103: 12317–12322.
Acknowledgements
We thank the captains and the crews of the RV Poseidon and RV Maria S Merian. We are very grateful to Hanno Teeling (MPI Bremen) for providing fruitful discussion and Thomas Schott for support on metatranscriptomic analyses. This study was funded by the WGL-pact project ‘REAL’ (Leibniz Association) to KJ.
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Feike, J., Jürgens, K., Hollibaugh, J. et al. Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system. ISME J 6, 461–470 (2012). https://doi.org/10.1038/ismej.2011.94
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DOI: https://doi.org/10.1038/ismej.2011.94
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