Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica

Abby, S. S., Kerou, M., & Schleper, C. (2020). Ancestral reconstructions decipher major adaptations of ammonia-oxidizing archaea upon radiation into moderate terrestrial and marine environments. mBio 11, e02371-20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ahlgren, N. A., Chen, Y., Needham, D. M., Parada, A. E., Sachdeva, R., Trinh, V., Chen, T., & Fuhrman, J. A. (2017). Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environmental Microbiology, 19, 2434–2452.

Article  CAS  PubMed  Google Scholar 

Alcaman-Arias, M. E., Cifuentes-Anticevic, J., Díez, B., Testa, G., Troncoso, M., Bello, E., & Farías, L. (2022). Surface ammonia-oxidizer abundance during the late summer in the West Antarctic coastal system. Frontiers in Microbiology, 13, 821902.

Article  PubMed  PubMed Central  Google Scholar 

Alicea, I., Marvin, J. S., Miklos, A. E., Ellington, A. D., Looger, L. L., & Schreiter, E. R. (2011). Structure of the Escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors. Journal of Molecular Biology, 414, 356–369.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alonso-Sáez, L., Sánchez, O., Gasol, J. M., Balagué, V., & Pedrós-Alio, C. (2008). Winter-to-summer changes in the composition and single-cell activity of near-surface Arctic prokaryotes. Environmental Microbiology, 10, 2444–2454.

Article  PubMed  Google Scholar 

Alonso-Sáez, L., Waller, A. S., Mende, D. R., Bakker, K., Farnelid, H., Yager, P. L., Lovejoy, C., Tremblay, J. É., Potvin, M., et al. (2012). Role for urea in nitrification by polar marine Archaea. Proceedings of the National Academy of Sciences of the USA, 109, 17989–17994.

Article  PubMed  PubMed Central  Google Scholar 

Arp, D. J., & Stein, L. Y. (2003). Metabolism of inorganic N compounds by ammonia-oxidizing bacteria. Critical Reviews in Biochemistry and Molecular Biology, 38, 471–495.

Article  CAS  PubMed  Google Scholar 

Arrigo, K. R., Lowry, K. E., & van Dijken, G. L. (2012). Annual changes in sea ice and phytoplankton in polynyas of the Amundsen Sea, Antarctica. Deep Sea Research Part II: Topical Studies in Oceanography, 71–76, 5–15.

Article  Google Scholar 

Arrigo, K. R., Robinson, D. H., Worthen, D. L., Dunbar, R. B., DiTullio, G. R., VanWoert, M., & Lizotte, M. P. (1999). Phytoplankton community structure and the drawdown of nutrients and CO2 in the Southern Ocean. Science, 283, 365–367.

Article  CAS  PubMed  Google Scholar 

Arrigo, K. R., & van Dijken, G. L. (2003). Phytoplankton dynamics within 37 Antarctic coastal polynya systems. Journal of Geophysical Research, 108, 3271.

Article  Google Scholar 

Baker, B. J., Lesniewski, R. A., & Dick, G. J. (2012). Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. The ISME Journal, 6, 2269–2279.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bayer, B., Hansman, R. L., Bittner, M. J., Noriega-Ortega, B. E., Niggemann, J., Dittmar, T., & Herndl, G. J. (2019). Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environmental Microbiology, 21, 4062–4075.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berube, P. M., & Stahl, D. A. (2012). The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. Journal of Bacteriology, 194, 3448–3456.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bryant, D. M., Johnson, K., DiTommaso, T., Tickle, T., Couger, M. B., Payzin-Dogru, D., Lee, T. J., Leigh, N. D., Kuo, T. H., Davis, F. G., et al. (2017). A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Reports, 18, 762–776.

Article  CAS  PubMed  Google Scholar 

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421.

Article  PubMed  PubMed Central  Google Scholar 

Carini, P., Dupont, C. L., & Santoro, A. E. (2018). Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environmental Microbiology, 20, 2112–2124.

Article  CAS  PubMed  Google Scholar 

Chícharo, M. A., & Chícharo, L. (2008). RNA:DNA ratio and other nucleic acid derived indices in marine ecology. International Journal of Molecular Sciences, 9, 1453–1471.

Article  PubMed  PubMed Central  Google Scholar 

Church, M. J., DeLong, E. F., Ducklow, H. W., Karner, M. B., Preston, C. M., & Karl, D. M. (2003). Abundance and distribution of planktonic Archaea and Bacteria in the waters west of the Antarctic Peninsula. Limnology and Oceanography, 48, 1893–1902.

Article  Google Scholar 

DeLong, E. F., Wu, K. Y., Prézelin, B. B., & Jovine, R. V. M. (1994). High abundance of Archaea in Antarctic marine picoplankton. Nature, 371, 695–697.

Article  CAS  PubMed  Google Scholar 

Ducklow, H. W., Baker, K., Martinson, D. G., Quetin, L. B., Ross, R. M., Smith, R. C., Stammerjohn, S. E., Vernet, M., & Fraser, W. (2007). Marine pelagic ecosystems: The West Antarctic Peninsula. Philosophical Transactions of the Royal Society B: Biological Sciences, 362, 67–94.

Article  Google Scholar 

Ducklow, H. W., Wilson, S. E., Post, A. F., Stammerjohn, S. E., Erickson, M., Lee, S., Lowry, K. E., Sherrell, R. M., & Yager, P. L. (2015). Particle flux on the continental shelf in the Amundsen Sea Polynya and Western Antarctic Peninsula. Elementa Science of the Anthropocene, 3, 000046.

Article  Google Scholar 

Eddy, S. R. (2011). Accelerated profile HMM searches. PLoS Computational Biology, 7, e1002195.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., et al. (2016). The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Research, 44, D279–D285.

Article  CAS  PubMed  Google Scholar 

Fouilland, E., Gosselin, M., Rivkin, R. B., Vasseur, C., & Mostajir, B. (2007). Nitrogen uptake by heterotrophic bacteria and phytoplankton in Arctic surface waters. Journal of Plankton Research, 29, 369–376.

Article  CAS  Google Scholar 

Gifford, S. M., Sharma, S., Booth, M., & Moran, M. A. (2013). Expression patterns reveal niche diversification in a marine microbial assemblage. The ISME Journal, 7, 281–298.

Article  CAS  PubMed  Google Scholar 

Gifford, S. M., Sharma, S., Rinta-Kanto, J. M., & Moran, M. A. (2011). Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. The ISME Journal, 5, 461–472.

Article  PubMed  Google Scholar 

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644–652.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grzymski, J. J., Riesenfeld, C. S., Williams, T. J., Dussaq, A. M., Ducklow, H., Erickson, M., Cavicchioli, R., & Murray, A. E. (2012). A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters. The ISME Journal, 6, 1901–1915.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haas, B., Papanicolaou, A., & Yassour, M. (2017). TransDecoder. https://github.com/TransDecoder/TransDecoder.

Heal, K. R., Qin, W., Ribalet, F., Bertagnolli, A. D., Coyote-Maestas, W., Hmelo, L. R., Moffett, J. W., Devol, A. H., Armbrust, E. V., Stahl, D. A., et al. (2017). Two distinct pools of B12 analogs reveal community interdependencies in the ocean. Proceedings of the National Academy of Sciences of the United States of America, 114, 364–369.

Article  CAS  PubMed  Google Scholar 

Herfort, L., Schouten, S., Abbas, B., Veldhuis, M. J. W., Coolen, M. J. L., Wuchter, C., Boon, J. P., Herndl, G. J., & Sinninghe Damsté, J. S. (2007). Variations in spatial and temporal distribution of archaea in the North Sea in relation to environmental variables. FEMS Microbiology Ecology, 62, 242–257.

Article  CAS  PubMed  Google Scholar 

Hodgskiss, L. H., Melcher, M., Kerou, M., Chen, W., Ponce-Toledo, R. I., Savvides, S. N., Wienkoop, S., Hartl, M., & Schleper, C. (2023). Unexpected complexity of the ammonia monooxygenase in archaea. The ISME Journal, 17, 588–599.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hollibaugh, J. T., Gifford, S., Sharma, S., Bano, N., & Moran, M. A. (2011). Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. The ISME Journal, 5, 866–878.

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