The archaeal community in sediments of freshwater lakes of north-east Antarctic Peninsula: Structure and diversity
Vol.14,No.1(2024)
This research represents the first attempt to study the structure and diversity of the archaeal and methanogenic archaeal community in selected lakes around the Czech polar station J.G. Mendel on James Ross Island (JRI), Antarctica. Sediment samples from a total of 19 of JRI and the nearby Vega Island and Long Island, were analyzed using 16S rRNA and mcrA genes sequencing and real-time qPCR. Contrary to the sequences retrieved by 16S rRNA analysis, many more reads belonging to methanogens were found with mcrA gene sequencing. Generally, archaea represented only a small proportion (0–8.8%) of the total prokaryotic community. With the exception of lakes in the Solorina Valley and Lagoons Mesa area and Lake Esmeralda on Vega Island, methanogenic archaea made up a small proportion of the archaea present in most lakes. The genera Methanothrix and Methanosarcina were identified as the predominant methanogenic representatives in the lake samples. Sequences of representatives belonging to Methanothermobacter sp. and Methanomassiliicoccales and a high proportion of sequences belonging to Methanoperedens-like archaea, methanotrophs that associate anaerobic methane oxidation with denitrification, were recorded for the first time in Antarctica. It is also the first time that the presence of the genus Methanobacterium has been detected to such a large extent. Generally, sequences of the methanogens which might be involved in all three pathways of methane production were found in our samples, indicating the broad metabolic potential of the methanogens present. Individual lakes from one area shared much higher similarity in their methanogenic diversity with the lakes from another area rather than with the lakes within the same area, suggesting that a lake location is probably not the main factor influencing the diversity of the methanogens. Indeed, archaeal and methanogenic community structure and mcrA gene copy numbers varied even within a single lake, suggesting that more sampling within a single lake, preferably at different times of the year, will be necessary in the future for more comprehensive information. Although this is an initial study, our research unambiguously provides evidence that the lakes of the JRI and surrounding islands may be potential sources of new archaeal species or metabolic pathways.
Archaea; methanogens; Antarctica; James Ross Island; NGS; lake sediments; biodiversity
Achberger, A. M., Christner, B. C., Michaud, A. B., Priscu, J. C., Skidmore, M. L., Vick-Majors, T. J. and the WISSARD Science Team (2016): Microbial community structure of subglacial Lake Whillans, West Antarctica. Frontiers in Microbiology, 7: 1-13.
Barbier, B. A., Dziduch, I., Liebner, S., Ganzert, L., Lantuit, H., Pollard, W. and Wagner, D. (2012): Methane-cycling communities in a permafrost-affected soil on Herschel Island, Western Canadian Arctic: Active layer profiling of mcrA and pmoA genes. FEMS Microbiology Ecology, 82: 287-302.
Björck, S., Olsson, S., Ellis-Evans, C., Håkansson, H., Humlum, O. and Lirio, J. M. (1996): Late holocene palaeoclimatic records from lake sediments on James Ross Island, Antarctica. Palaeogeography, Palaeoclimatology, Palaeoecology, 121: 195-220.
Bowman, J. P., McCammon, S. A., Gibson, J. A. E., Robertson, L. and Nichols, P. D. (2003): Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments. Applied and Environmental Microbiology, 69: 2448-2462.
Bowman, J. P., McCammon, S. A., Rea, S. M. and McMeekin, T. A. (2000): The microbial composition of three limnologically disparate hypersaline Antarctic lakes. FEMS Microbiology Letters, 183: 81-88.
Bray, J. R., Curtis, J. T. (1957): An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs, 27: 325-349.
Bulínová, M., Kohler, T. J., Kavan, J., Van de Vijver, B., Nývlt, D., Nedbalová, L., Coria, S. H., Lirio, J. M. and Kopalová, K. (2020): Comparison of diatom paleo-assemblages with adjacent limno-terrestrial communities on Vega Island, Antarctic Peninsula. Water, 12: 1340.
Callahan, B. J., Sankaran, K., Fukuyama, J. A., McMurdie, P. J. and Holmes, S. P. (2016): Bioconductor workflow for microbiome data analysis: From raw reads to community analyses. F1000 Research, 5: 1492. doi: 10.12688/f1000research.8986.2
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., Taylor, R. C., Williams, K. H. and Banfield, J. F. (2015): Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Current Biology, 25: 690-701.
Cavicchioli, R. (2006): Cold-adapted archaea. Nature Reviews. Microbiology, 4: 331-343. doi: 10.1038/nrmicro1390
Cavicchioli, R. (2015): Microbial ecology of Antarctic aquatic systems. Nature Reviews. Microbiology, 13: 691-706.
Chaya, A., Kurosawa, N., Kawamata, A., Kosugi, M. and Imura, S. (2019): Community structures of bacteria, archaea, and eukaryotic microbes in the freshwater glacier lake Yukidori-Ike in Langhovde, East Antarctica. Diversity, 11: 105. doi: 10.3390/d11070105
Conrad, R. (2020): Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: A mini review. Pedosphere, 30: 25-39. doi: 10.1016/S1002-0160(18)60052-9
Conrad, R., Claus, P. (2005): Contribution of methanol to the production of methane and its 13C-isotopic signature in anoxic rice field soil. Biogeochemistry, 73: 381-393.
Coufalík, P., Prochazková, P., Zvěřina, O., Trnková, K., Skácelová, K., Nývlt, D. and Komárek, J. (2016): Freshwater mineral nitrogen and essential elements in autotrophs in James Ross Island, West Antarctica. Polish Polar Research, 37: 477-491. doi: 10.1515/popore-2016-0025
Cui, M., Ma, A., Qi, H., Zhuang, X. and Zhuang, G. (2015): Anaerobic oxidation of methane: An “active” microbial process. Microbiologyopen, 4: 1-11. doi: 10.1002/mbo3.232
Denman, S. E., Tomkins, N. W., McSweeney, C. S. (2007): Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiology Ecology, 62: 313-322.
Ding, J., Ding, Z. W., Fu, L., Lu, Y. Z., Cheng, S. H. and Zeng, R. J. (2015): New primers for detecting and quantifying denitrifying anaerobic methane oxidation archaea in different ecological niches. Applied Microbiology and Biotechnology, 99: 9805-9812. doi: 10.1007/s00253-015-6893-6
Ding, J., Zeng, R. J. (2021): Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea. The Science of the Total Environment, 757: 143928. doi: 10.1016/j.scitotenv.2020.143928
Doytchinov, V. V., Dimov, S. G. (2022): Microbial community composition of the Antarctic ecosystems: Review of the bacteria, fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. Life (Basel), 12(6): 916. doi: 10.3390/life12060916
Dridi, B., Fardeau, M. L., Ollivier, B., Raoult, D. and Drancourt, M. (2012): Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. International Journal of Systematic and Evolutionary Microbiology, 62: 1902-1907. doi: 10.1099/ijs.0.033712-0
Ellis-Evans, J. C. (1984): Methane in maritime Antarctic freshwater lakes. Polar Biology, 3: 63-71. doi: 10.1007/BF00258149
Engel, Z., Nývlt, D., Láska, K. (2012): Ice thickness, areal and volumetric changes of Davies Dome and Whisky Glacier (James Ross Island, Antarctic Peninsula) in 1979-2006. Journal of Glaciology, 58: 904-914. doi: 10.3189/2012JoG11J156
Franzmann, P. D., Liu, Y., Balkwill, D. L., Aldrich, H. C., Conway de Macario, E. and Boone, D. R. (1997): Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica. International Journal of Systematic Bacteriology, 47: 1068-1072. doi: 10.1099/00207713-47-4-1068
Friedrich, M. W. (2005): Methyl-Coenzyme M reductase genes: Unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea. Methods in Enzymology, 397: 428-442.
Garcia, J. L., Patel, B. K. C. and Ollivier, B. (2000): Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea. Anaerobe, 6: 205-226.
Grodnitskaya, I. D., Trusova, M. Y., Syrtsov, S. N. and Koroban, N. V. (2018): Structure of microbial communities of peat soils in two bogs in Siberian tundra and forest zones. Microbiology, 87: 89-102.
Gründger, F., Carrier, V., Svenning. M. M., Panieri, G., Vonnahme, T. R., Klasek, S. and Niemann, H. (2019): Methane-fuelled biofilms predominantly composed of methanotrophic ANME-1 in Arctic gas hydrate-related sediments. Scientific Reports, 9(1): 9725. doi: 10.1038/ s41598-019-46209-5
Guerrero-Cruz, S., Cremers, G., van Alen, T. A., Op den Camp, H. J. M., Jetten, M. S. M., Rasigraf, O. and Vaksmaa, A. (2018): Response of the Anaerobic Methanotroph “Candidatus Methanoperedens nitroreducens” to Oxygen Stress. Applied and Environmental Microbiology, 84(24): e01832-18. doi: 10.1128/AEM.01832-18
Gugliandolo, C., Michaud, L., Lo Giudice, A., Lentini, V., Rochera, C., Camacho, A. and Maugeri, T. L. (2016): Prokaryotic community in lacustrine sediments of Byers Peninsula (Livingston Island, Maritime Antarctica). Microbial Ecology, 71: 387-400. doi: 10.1007/ s00248-015-0666-8
Haroon, M. F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P., Yuan, Z. and Tyson, G. W. (2013): Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500: 567-570. doi: 10.1038/nature12375
Hrbáček, F., Kňažková, M., Nývlt, D., Láska, K., Mueller, C. W. and Ondruch, J. (2017): Active layer monitoring at CALM-S site near J.G. Mendel Station, James Ross Island, Eastern Antarctic Peninsula. Science of the Total Environment, 601-602: 987-997.
Ji, Y., Liu, P., Conrad, R. (2018): Response of fermenting bacterial and methanogenic archaeal communities in paddy soil to progressing rice straw degradation. Soil Biology and Biochemistry, 124: 70-80. doi: 10.1016/j.soilbio.2018.05.029
Juottonen, H., Fontaine, L., Wurzbacher, C., Drakare, S., Peura, S. and Eiler, A. (2020): Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly. Environmental Microbiology, 22: 3158-3171. doi: 10.1111/1462-2920.15058
Karr, E. A., Ng, J. M., Belchik, S. M., Sattley, W. M., Madigan, M. T. and Achenbach, L. A. (2006): Biodiversity of methanogenic and other Archaea in the permanently frozen Lake Fryxell, Antarctica. Applied and Environmental Microbiology, 72: 1663-1666. doi: 10.1128/AEM.72.2.1663-1666.2006
Kollár, J., Kopalová, K., Kavan, J., Vrbická, K., Nývlt, D., Nedbalová, L., Stibal, M. and Kohler, T. J. (2023): Recently formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts. FEMS Microbiology Ecology, 99: 1-15.
Komárek, J., Elster, J., Komárek, O. (2008): Diversity of the cyanobacterial microflora of the northern part of James Ross Island, NW Weddell Sea, Antarctica. Polar Biology, 31: 853-865.
Komárek, J., Nedbalová, L., Hauer, T. (2012): Phylogenetic position and taxonomy of three heterocytous cyanobacteria dominating the littoral of deglaciated lakes, James Ross Island, Antarctica. Polar Biology, 35: 759-774.
Kopalová, K., Nedbalová, L., Nývlt, D., Elster, J. and Vijver, B.V. (2013): Diversity, ecology and biogeography of the freshwater diatom communities from Ulu Peninsula (James Ross Island, NE Antarctic Peninsula). Polar Biology, 36: 933-948.
Kopalová, K., Soukup, J., Kohler, T. J., Román, M., Coria, S. H., Vignoni, P. A., Lecomte, K. L., Nedbalová, L., Nývlt, D. and Lirio, J. M. (2019): Habitat controls on limno-terrestrial diatom communities of Clearwater Mesa, James Ross Island, Maritime Antarctica. Polar Biology, 42: 1595-1613.
Kurosawa, N., Sato, S., Kawarabayasi, Y., Imura, S. and Naganuma, T. (2010): Archaeal and bacterial community structures in the anoxic sediment of Antarctic meromictic lake Nurume-Ike. Polar Science, 4: 421-429. doi: 10.1016/j.polar.2010.04.002
Laskar, F., Das Purkayastha, S., Sen, A., Bhattacharya, M. K. and Misra, B. B. (2018): Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems. Journal of Basic Microbiology, 58: 101-119. doi: 10.1002/jobm.201700341
Lavergne, C., Aguilar-Muňoz, Calle, N., Thalasso, F., Astorga-España, M. S., Sepulveda-Jauregui, A., Martinez-Cruz, K., Gandois, L., Mansilla, A., Chamy, R., Barret, M. and Cabrol, L. (2021): Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems. Environment International, 154: 106575.
Laybourn-Parry, J., Pearce, D. A. (2007): The biodiversity and ecology of Antarctic lakes: Models for evolution. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 362: 2273-2289. doi: 10.1098/rstb.2006.1945
Lecomte, K. L, Vignoni, P. A., Córdoba, F. E., Chaparro, M. A., Chaparro, M. A., Kopalová, K., Gargiulo, J. D., Lirio, J. M., Irurzun, M. A. and Böhnel, H. N. (2016): Hydrological systems from the Antarctic Peninsula under climate change: James Ross archipelago as study case. Environmental Earth Sciences, 75: 1-20. doi: 10.1007/s12665-016-5406-y
Li, M., Wei, G., Shi, W., Sun, Z., Li, H., Wang, X. and Gao, Z. (2018): Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary. Scientific Reports, 8(1): 1584. doi: 10.1038/s41598-018-20044-6
Li, W., Guan, W., Chen, H., Liao, B., Hu, J., Peng, C., Rui, J., Tian, J., Zhu, D. and He, Y. (2016): Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China. Journal of Soils and Sediments, 16: 1995-2004.
Liu, X., Li, M., Castelle, C. J., Probst, A. J., Zhou, Z., Pan, J., Liu, Y., Banfield, J. F. and Gu, J. (2018): Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome, 6: 1-16.
Liu, Y., Whitman, W. B. (2008): Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Annals of the New York Academy of Sciences, 1125: 171-189.
Lovley, D. R., Klug, M. J. (1983): Methanogenesis from methanol and methylamines and acetogenesis from hydrogen and carbon dioxide in the sediments of a eutrophic lake. Applied and Environmental Microbiology, 45: 1310-1315.
Lu, S., Liu, X., Liu, C., Cheng, G., Zhou, R. and Li, Y. (2021): A review of ammonia-oxidizing Archaea and anaerobic ammonia-oxidizing bacteria in the aquaculture pond environment in China. Frontiers in Microbiology, 12: 3554.
Ma, H., Yan, W., Xiao, X., Shi, G., Li, Y., Sun, B., Dou, Y. and Zhang, Y. (2018): Ex situ culturing experiments revealed psychrophilic hydrogentrophic methanogenesis being the potential dominant methane-producing pathway in subglacial sediment in Larsemann Hills, Antarctic. Frontiers in Microbiology, 9: 237.
Matheus Carnevali, P. B., Rohrssen, M. R., Williams, M. R., Michaud, A. B., Adams, H., Berisford, S., Love, G. D., Priscu, J. C., Rassuchine, O., Hand, K. P. and Murray, A. E. (2015): Methane sources in arctic thermokarst lake sediments on the North Slope of Alaska. Geobiology, 13: 181-197. doi: 10.1111/gbi.12124
McMurdie, P. J., Holmes, S. (2013): Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PloS One, 8(4), e61217. doi: 10.1371/journal.pone.0061217
Michaud, L., Caruso, C., Mangano, S., Interdonato, F., Bruni, V. and Lo Giudice, A. (2012): Predominance of Flavobacterium, Pseudomonas, and Polaromonas within the prokaryotic community of freshwater shallow lakes in the northern Victoria Land, East Antarctica. FEMS Microbiology Ecology, 82: 391-404. doi: 10.1111/j.1574-6941.2012.01394.x
Mickol, R. L., Laird, S. K. and Kral, T. A. (2018): Non-psychrophilic methanogens capable of growth following long-term extreme temperature changes, with application to mars. Microorganisms, 6(2), 34. doi: 10.3390/microorganisms6020034
Moreno, L., Silva-Busso, A., López-Martínez, J., Durán-Valsero, J. J., Martínez-Navarrete, C., Cuchí, J. A. and Ermolin, E. (2012): Hydrogeochemical characteristics at Cape Lamb, Vega Island, Antarctic Peninsula. Antarctic Science, 24: 591-607. doi: 10.1017/ S0954102012000478
Mulyukin, A. L., Demkina, E. V., Manucharova, N. A., Akimov, V. N., Andersen, D., McKay, C. and Gal'chenko, V. F. (2014): The prokaryotic community of subglacial bottom sediments of Antarctic Lake Untersee: Detection by cultural and direct microscopic techniques. Microbiology, 83: 77-84. doi: 10.1134/S0026261714020143
Nedbalová, L., Nývlt, D., Kopáček, J., Šobr, M. and Elster, J. (2013): Freshwater lakes of Ulu Peninsula, James Ross Island, north-east Antarctic Peninsula: Origin, geomorphology and physical and chemical limnology. Antarctic Science, 25: 358-372. doi: 10.1017/ S0954102012000934
Nedbalová, L., Nývlt, D., Lirio, J. M., Kavan, J. and Elster, J. (2017): Current distribution of Branchinecta gaini on James Ross Island and Vega Island. Antarctic Science, 29: 341-342. doi: 10.1017/S0954102017000128
Niemann, H., Fischer, D., Graffe, D., Knittel, K., Montiel, A., Heilmayer, O., Nöthen, K., Pape, T., Kasten, S., Bohrmann, G., Boetius, A. and Gutt, J (2009): Biogeochemistry of a low-activity cold seep in the Larsen B area, western Weddell Sea, Antarctica. Biogeosciences, 6: 2383-2395. doi: 10.5194/bg-6-2383-2009
Ortiz-Alvarez, R., Casamayor, E. O. (2016): High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes. Environmental Microbiology Reports, 8: 210-217. doi: 10.1111/1758-2229. 12370
Paul, K., Nonoh, J. O., Mikulski, L. and Brune, A. (2012): “Methanoplasmatales,” thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Applied and Environmental Microbiology, 78: 8245-8253. doi: 10.1128/AEM.02193-12
Pearce, D. A., Galand, P. E. (2009): Microbial biodiversity and biogeography. In: F. Vincent Warwick, Johanna Laybourn-Parry (eds): Polar lakes and rivers: Limnology of Arctic and Antarctic aquatic ecosystems (Oxford 2008; online edn, Oxford Academic), doi: 10.1093/acprof:oso/9780199213887.003.0012
Pester, M., Schleper, C. and Wagner, M. (2011): The Thaumarchaeota: An emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology, 14: 300-306. doi: 10.1016/j.mib.2011.04.00
Pichler, M., Coskun, Ö. K., Ortega-Arbulú, A. S., Conci, N., Wörheide, G., Vargas, S. and Orsi, W. D. (2018): A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform. MicrobiologyOpen, 7(6): e00611. doi: 10.1002/mbo3.611
Píšková, A., Roman, M., Bulínová, M., Pokorný, M., Sanderson, D., Cresswell, A., Lirio, J. M., Coria, S. H., Nedbalová, L., Lami, A., Musazzi, S., Van de Vijver, B., Nývlt, D. and Kopalová, K. (2019): Late-Holocene palaeoenvironmental changes at Lake Esmeralda (Vega Island, Antarctic Peninsula) based on a multi-proxy analysis of laminated lake sediment. Holocene, 29: 1155-1175. doi: 10.1177/0959683619838033
Pociecha, A., Dumont, H. J. (2008): Life cycle of Boeckella poppei Mrazek and Branchinecta gaini Daday (King George Island, South Shetlands). Polar Biology, 31: 245-248.
Purdy, K. J., Nedwell, D. B. and Embley, T. M. (2003): Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting antarctic sediments. Applied and Environmental Microbiology, 69: 3181-3191. doi: 10.1128/AEM.69.6.3181-3191.2003
Raghoebarsing, A. A., Pol, A., Van De Pas-Schoonen, K. T., Smolders, A. J., Ettwig, K. F., Rijpstra, W. I., Schouten, S., Damsté, J. S., Op den Camp, H. J., Jetten, M. S. and Strous, M. (2006): A microbial consortium couples anaerobic methane oxidation to denitrification. Nature, 440 (7086): 918-921. doi: 10.1038/nature04617
Rivkina, E., Shcherbakova, V., Laurinavichius, K., Petrovskaya, L., Krivushin, K., Kraev, G., Pecheritsina, S. and Gilichinsky, D. (2007): Biogeochemistry of methane and methanogenic archaea in permafrost. FEMS Microbiology Ecology, 61: 1-15. doi: 10.1111/j.1574-6941.2007.00315.x
Roman, M., Nedbalová, L., Kohler, T. J., Lirio, J. M., Coria, S. H., Kopáček, J., Vignoni, P. A., Kopalová, K., Lecomte, K. L., Elster, J. and Nývlt, D. (2019): Lacustrine systems of Clearwater Mesa (James Ross Island, north-eastern Antarctic Peninsula): Geomorphological setting and limnological characterization. Antarctic Science, 31: 169-188. doi: 10.1017/S095410201900017
Ruiz-Fernández, J., Oliva, M., Nývlt, D., Cannone, N., García-Hernández, C., Guglielmin, M., Hrbáček, F., Roman, M., Fernández, S., López-Martínez, J. and Antoniades, D. (2019): Patterns of spatio-temporal paraglacial response in the Antarctic Peninsula region and associated ecological implications. Earth-Science Reviews, 192: 379-402.
Santoro, A. E., Buchwald, C., McIlvin, M. R. and Casciotti, K. L. (2011): Isotopic signature of N2O produced by marine ammonia-oxidizing archaea. Science (New York), 333: 1282-1285. doi: 10.1126/science.1208239
Savvichev, A., Rusanov, I., Dvornikov, Y., Kadnikov, V., Kallistova, A., Veslopolova, E., Chetverova, A., Leibman, M., Sigalevich, P. A., Pimenov, N., Ravin, N. and Khomutov, A. (2021): The water column of the Yamal tundra lakes as a microbial filter preventing methane emission. Biogeosciences, 18: 2791-2807. doi: 10.5194/bg-18-2791-2021
Shivaji, S., Kumari, K., Kishore, K. H., Pindi, P. K., Rao, P. S., Radha Srinivas, T. N., Asthana, R. and Ravindra, R. (2011): Vertical distribution of bacteria in a lake sediment from Antarctica by culture-independent and culture-dependent approaches. Research in Microbiology, 162(2): 191-203. doi: 10.1016/j.resmic.2010.09.020
Schleper, C., Nicol, G. W. (2010): Ammonia-oxidising archaea-physiology, ecology and evolution. Advances in Microbial Physiology, 57: 1-41. doi: 10.1016/B978-0-12-381045-8.00001-1
Schliep, K. P. (2011): Phangorn: Phylogenetic analysis in R. Bioinformatics, 27: 592-593.
Siddiqui, K. S., Williams, T. J., Wilkins, D., Yau, S., Allen, M. A., Brown, M. V., Lauro, F. M. and Cavicchioli, R. (2013): Psychrophiles. Annual Review of Earth and Planetary Sciences, 41: 87-115. doi: 10.1146/annurev-earth-040610-133514
Sjöling, S., Cowan, D. A. (2003): High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica. Extremophiles, 7: 275e282.
Skácelová, K., Barták, M., Coufalík, P., Nývlt, D. and Trnková, K. (2013): Biodiversity of freshwater algae and cyanobacteria on deglaciated northern part of James Ross Island, Antarctica. A preliminary study. Czech Polar Reports, 3: 93-106. doi: 10.5817/CPR2013-2-12
Söllinger, A., Schwab, C., Weinmaier, T., Loy, A., Tveit, A. T., Schleper, C. and Urich, T. (2016): Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat. FEMS Microbiology Ecology, 92(1): fiv149. doi: 10.1093/femsec/fiv149
Steinberg, L. M., Regan, J. M. (2008): Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Applied and Environmental Microbiology, 74: 6663-6671. doi: 10.1128/AEM.00553-08
Steinberg, L. M, Regan, J. M. (2009): mcrA-targeted real-time quantitative PCR method to examine methanogen communities. Applied and Environmental Microbiology, 75: 4435-4442. doi: 10.1128/AEM.02858-08
Stieglmeier, M., Mooshammer, M., Kitzler, B., Wanek, W., Zechmeister-Boltenstern, S., Richter, A. and Schleper, C. (2014): Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME Journal, 8: 1135-1146. doi: 10.1038/ismej.2013.220
Tang, C., Madigan, M. T. and Lanoil, B. (2013): Bacterial and archaeal diversity in sediments of west Lake Bonney, McMurdo Dry Valleys, Antarctica. Applied and Environmental Microbiology, 79(3): 1034-1038. doi: 10.1128/AEM.02336-12
Tóth, E., Toumi, M., Farkas, R., Takáts, K., Somodi, C. and Ács, É. (2020): Insight into the hidden bacterial diversity of Lake Balaton, Hungary. Biologia Futura, 71: 383-391. doi: 10.1007/s42977-020-00040-6
Váczi, P., Hájek, J. (2013): Annual water temperature courses in two contrasting lakes at James Ross Island, Antarctica. Czech Polar Reports, 3: 213-219. doi: 10.5817/CPR2013-2-22
Vaksmaa, A., Jetten, M. S. M., Ettwig, K. F. and Lüke, C. (2017): McrA primers for the detection and quantification of the anaerobic archaeal methanotroph “Candidatus Methanoperedens nitroreducens”. Applied Microbiology and Biotechnology, 101: 1631-1641. doi: 10.1007/s00253-016-8065-8
Vick-Majors, T. J., Priscu, J. C. and Amaral-Zettler, L. A. (2014): Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes. ISME Journal, 8(4): 778-789. doi: 10.1038/ismej.2013.190
Wang, G., Watanabe, T., Jin, J., Liu, X., Kimura, M. and Asakawa, S. (2010): Methanogenic archaeal communities in paddy field soils in north-east China as evaluated by PCR-DGGE, sequencing and real-time PCR analyses. Soil Science & Plant Nutrition, 56: 831-838. doi: 10.1111/j.1747-0765.2010.00521.x
Wang, X., Wang, C., Bao, L. and Xie, S. (2014): Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils. Applied Microbiology and Biotechnology, 98: 1883-1892. doi: 10.1007/s00253-013-5174-5
Wang, Y., Cui, H., Su, X., Wei, S., Zhu, Y., Lu, Z., Pang, S., Liu, H., Zhang, S. and Hou, W. (2020): Diversity and distribution of methanogenic community between two typical alpine ecosystems on the Qinghai–Tibetan plateau. Current Microbiology, 77: 1061-1069. doi: 10.1007/s00284-020-01891-x
Wang, Y., Wegener, G., Ruff, S. E. and Wang, F. (2021): Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea. Environmental Microbiology, 23: 530-541. doi: 10.1111/1462-2920.15057
Whitman, W. B., Bowen, T. L. and Boone, D. R. (2014): The methanogenic bacteria. The Prokaryotes: Other Major Lineages of Bacteria and The Archaea. Vol 9783642389. Springer, Berlin, Heidelberg, pp. 123–163.
Wilkins, D., Lu, X. Y., Shen, Z., Chen, J. and Lee, P. K. (2015): Pyrosequencing of mcrA and Archaeal 16S rRNA genes reveals diversity and substrate preferences of methanogen communities in anaerobic digesters. Applied and Environmental Microbiology, 81(2): 604-613.
Wilkins, D., Yau, S., Williams, T. J., Allen, M. A., Brown, M. V., DeMaere, M. Z., Lauro, F. M. and Cavicchioli, R. (2013): Key microbial drivers in Antarctic aquatic environments. FEMS Microbiology Reviews, 37: 303-335. doi: 10.1111/1574-6976.12007
Williams, T. J., Lauro, F. M., Ertan, H., Burg, D. W., Poljak, A., Raftery, M. J. and Cavicchioli, R. (2011): Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°C to 28°C) using multiplex quantitative proteomics. Environmental Microbiology, 13: 2186-2203. doi: 10.1111/j.1462-2920.2011.02467.x
Yang, Y., Chen, J., Tong, T., Xie, S. and Liu, Y. (2020): Influences of eutrophication on methanogenesis pathways and methanogenic microbial community structures in freshwater lakes. Environmental Pollution (Barking, Essex: 1987), 260: 114106. doi: 10.1016/j.envpol. 2020.114106
Zvěřina, O., Coufalík, P., Barták, M., Petrov, M. and Komárek, J. (2017): The contents and distributions of cadmium, mercury, and lead in Usnea antarctica lichens from Solorina Valley, James Ross Island (Antarctica). Environmental Monitoring and Assessment, 190(1): 13. doi: 10.1007/s10661-017-6397-1
Web sources / Other sources
[1] Wickham, H., Chang, W., Henry, L., Takahashi K., Wilke C., Woo K., Yutani H., Dunnington D. and Brandt T. (2021): ggplot2: Create elegant data visualisations using the grammar of graphics.
[2] Czech Geological Survey (2009). James Ross Island - Northern Part. Topographic map 1 : 25 000. First edition. Praha, Czech Geological Survey. ISBN 978-80-7075-734-5.
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