Existence and distribution of novel phylotypes of Nitrospira in water columnsof the South China Sea

iScience - Tập 25 - Trang 104895 - 2022
Wei Sun1,2,3, Lijing Jiao2,3, Jiapeng Wu2,3, Jiaqi Ye2,3, Mingken Wei1, Yiguo Hong2,3
1Guangdong University of Petrochemical Technology, Maoming 525000, P.R.China
2Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou 510006, P.R. China
3Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China

Tài liệu tham khảo

Alawi, 2007, Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic, ISME J., 1, 256, 10.1038/ismej.2007.34 Alawi, 2009, Temperature influences the population structure of nitrite-oxidizing bacteria in activated sludge, Environ. Microbiol. Rep., 1, 184, 10.1111/j.1758-2229.2009.00029.x Alonso, 2003, Short-term toxicity of ammonia, nitrite, and nitrate to the aquatic snail Potamopyrgus antipodarum (Hydrobiidae, Mollusca), Bull. Environ. Contam. Toxicol., 70, 1006, 10.1007/s00128-003-0082-5 Altmann, 2003, In situ distribution and activity of nitrifying bacteria in freshwater sediment, Environ. Microbiol., 5, 798, 10.1046/j.1469-2920.2003.00469.x Bayer, 2021, Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions, ISME J., 15, 1025, 10.1038/s41396-020-00828-3 Bartelme, 2017, Freshwater recirculating aquaculture system operations drive biofilter bacterial community shifts around a stable nitrifying consortium of ammonia-oxidizing archaea and comammox Nitrospira, Front. Microbiol., 8, 101, 10.3389/fmicb.2017.00101 Nowka, 2015, Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages, FEMS. Microbiol. Ecol., 91, 10.1093/femsec/fiu031 Breider, 2019, Response of N2O production rate to ocean acidification in the western North Pacific, Nat. Clim. Chang., 9, 954, 10.1038/s41558-019-0605-7 Camargo, 2005, Nitrate toxicity to aquatic animals: a review with new data for freshwater invertebrates, Chemosphere, 58, 1255, 10.1016/j.chemosphere.2004.10.044 Cébron, 2005, Nitrobacter and Nitrospira genera as representatives of nitrite-oxidizing bacteria: detection, quantification and growth along the lower seine river (France), Water. Res., 39, 4979, 10.1016/j.watres.2005.10.006 Chen, 2014, Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the south China sea revealed by amplification of both 16s rrna and pmoa genes, Appl. Microbiol. Biotechnol., 98, 5685, 10.1007/s00253-014-5733-4 Chen, 2015, Existence of novel phylotypes of nitrite-dependent anaerobic methane-oxidizing bacteria in surface and subsurface sediments of the south China sea, Geomicrobiol. J., 32, 1, 10.1080/01490451.2014.917742 Chen, 2021, Nitrite cycle indicated by dual isotopes in the northern South China Sea, J. Geophys. Res. Biogeosci., 126 Daims, 2001, In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants, Appl. Environ. Microbiol., 67, 5273, 10.1128/AEM.67.11.5273-5284.2001 Daims, 2015, Complete nitrification by Nitrospira bacteria, Nature, 528, 504, 10.1038/nature16461 Daims, 2016, A new perspective on microbes formerly known as nitrite-oxidizing bacteria, Trends. Microbiol., 24, 699, 10.1016/j.tim.2016.05.004 Daryabor, 2016, Dynamics of the water circulations in the southern South China Sea and its seasonal transports, PLoS One, 11, 10.1371/journal.pone.0158415 Duan, 2012, A study of the mixed layer of the South China Sea based on the multiple linear regression, Acta Oceanol. Sin., 31, 19, 10.1007/s13131-012-0250-8 Ehrich, 1995, A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship, Arch. Microbiol., 164, 16, 10.1007/BF02568729 Fan, 2015, Hydrodynamic design of deep ocean water discharge for the creation of a nutrient-rich plume in the South China Sea, Ocean Engineering, 108, 356, 10.1016/j.oceaneng.2015.08.006 Fitzgerald, 2015, Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen, Water. Res., 70, 38, 10.1016/j.watres.2014.11.041 Füssel, 2012, Nitrite oxidation in the Namibian oxygen minimum zone, ISME J., 6, 1200, 10.1038/ismej.2011.178 Fujitani, 2014, Isolation of sublineage I Nitrospira by a novel cultivation strategy, Environ. Microbiol., 16, 3030, 10.1111/1462-2920.12248 Fujitani, 2020, Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions, FEMS. Microbiol. Lett., 367, fnaa025, 10.1093/femsle/fnaa025 Guan, 2017, A fast sodium hypobromite oxidation method for the sequential determination of ammonia nitrogen in small volume, Ecol. Sci., 36, 42 Gruber, 2018, The marine nitrogen cycle: overview and challenges, 1 Gruber-Dorninger, 2015, Functionally relevant diversity of closely related Nitrospira in activated sludge, ISME J., 9, 643, 10.1038/ismej.2014.156 Hiraoka, 2020, Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments, ISME J., 14, 740, 10.1038/s41396-019-0564-z Hong, 2020, New primers, taxonomic database and cut-off value for processing nxrB gene high-throughput sequencing data by MOTHUR, J. Microbiol. Methods., 173, 10.1016/j.mimet.2020.105939 Hong, 2021, Shifts in the abundance and community composition of particle-associated and free-living Nitrospira across physicochemical gradients in the Pearl River Estuary, Estuaries Coast., 44, 1931, 10.1007/s12237-021-00909-2 Hou, 2018, Niche differentiation of ammonia and nitrite oxidizers along a salinity gradient from the Pearl River estuary to the South China Sea, Biogeosciences, 15, 5169, 10.5194/bg-15-5169-2018 Keuter, 2011, Relevance of Nitrospira for nitrite oxidation in a marine recirculation aquaculture system and physiological features of a Nitrospira marina-like isolate, Environ. Microbiol., 13, 2536, 10.1111/j.1462-2920.2011.02525.x Koch, 2014, Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation, Science, 345, 1052, 10.1126/science.1256985 Koch, 2015, Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira, Proc. Natl. Acad. Sci. USA, 112, 11371, 10.1073/pnas.1506533112 Kits, 2017, Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle, Nature, 549, 269, 10.1038/nature23679 Kruse, 2013, The nitrite-oxidizing community in activated sludge from a municipal wastewater treatment plant determined by fatty acid methyl ester-stable isotope probing, Syst. Appl. Microbiol., 36, 517, 10.1016/j.syapm.2013.06.007 Kumar, 2016, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 33, 1870, 10.1093/molbev/msw054 Lebedeva, 2010, Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring, FEMS. Microbiol. Ecol., 75, 195, 10.1111/j.1574-6941.2010.01006.x Li, 2020, Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils, Soil. Biol. Biochem., 149, 10.1016/j.soilbio.2020.107925 Liu, 2020, Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China, Sci. Total. Environ., 742, 10.1016/j.scitotenv.2020.140456 Liu, 2020, Comammox nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers, ISME J., 14, 2488, 10.1038/s41396-020-0701-8 Lücker, 2010, A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria, Proc. Natl. Acad. Sci. USA, 107, 13479, 10.1073/pnas.1003860107 Maixner, 2006, Nitrite concentration influences the population structure of Nitrospira-like bacteria, Environ. Microbiol., 8, 1487, 10.1111/j.1462-2920.2006.01033.x Mao, 2020, Spatio-temporal variations in the abundance and community structure of nitrospira in a tropical bay, Curr. Microbiol., 77, 3492, 10.1007/s00284-020-02193-y Morton, 2002, South China sea, Mar. Pollut. Bull., 42, 1236, 10.1016/S0025-326X(01)00240-5 Mehrani, 2020, The occurrence and role of Nitrospira in nitrogen removal systems, Bioresour. Technol., 303, 10.1016/j.biortech.2020.122936 Noble, 2017, Coastal sources, sinks and strong organic complexation of dissolved cobalt within the US North Atlantic GEOTRACES transect GA03, Biogeosciences, 14, 2715, 10.5194/bg-14-2715-2017 Nowka, 2015, Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages. FEMS microbial, FEMS. Microbiol. Ecol., 91, fiu031, 10.1093/femsec/fiu031 Ngugi, 2016, Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines, ISME J., 10, 1383, 10.1038/ismej.2015.214 Nunoura, 2015, Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth, Proc. Natl. Acad. Sci. USA, 112, E1230, 10.1073/pnas.1421816112 Pachiadaki, 2017, Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation, Science, 358, 1046, 10.1126/science.aan8260 Pester, 2014, NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira, Environ. Microbiol., 16, 3055, 10.1111/1462-2920.12300 Pjevac, 2017, AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment, Front. Microbiol., 8, 1508, 10.3389/fmicb.2017.01508 Prosser, 2020, Nitrous oxide production by ammonia oxidizers: physiological diversity, niche differentiation and potential mitigation strategies, Glob. Chang. Biol., 26, 103, 10.1111/gcb.14877 Sakoula, 2018, The draft genome sequence of “Nitrospira lenta” strain BS10, a nitrite oxidizing bacterium isolated from activated sludge, Stand. Genomic Sci., 13, 32, 10.1186/s40793-018-0338-7 Sañudo-Wilhelmy, 2014, The role of B vitamins in marine biogeochemistry, Ann. Rev. Mar. Sci, 6, 339, 10.1146/annurev-marine-120710-100912 Saito, 2005, Production of cobalt binding ligands in a Synechococcus feature at the Costa Rica upwelling dome, Limnol. Oceanogr., 50, 279, 10.4319/lo.2005.50.1.0279 Sato, 2019, Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism, Commun. Biol., 2, 179, 10.1038/s42003-019-0418-2 Schloss, 2020, Reintroducing mothur: 10 years later, Appl. Environ. Microbiol., 86, 10.1128/AEM.02343-19 Shelton, 2019, Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics, ISME J., 13, 789, 10.1038/s41396-018-0304-9 Siripong, 2007, Diversity study of nitrifying bacteria in full-scale municipal wastewater treatment plants, Water. Res., 41, 1110, 10.1016/j.watres.2006.11.050 Spieck, 2006, Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge, Environ. Microbiol., 8, 405, 10.1111/j.1462-2920.2005.00905.x Spieck, 2011, Cultivation, growth physiology, and chemotaxonomy of nitrite-oxidizing bacteria, Methods. Enzymol., 486, 109, 10.1016/B978-0-12-381294-0.00005-5 Sun, 2021, Niche adaptation strategies of different clades of comammox Nitrospira in the Yangtze Estuary, Int. Biodeterior. Biodegradation, 164, 10.1016/j.ibiod.2021.105286 Sun, 2022, Distribution, diversity, and abundance of nitrite oxidizing bacteria in the subterranean estuary of the Daya bay, Front. Mar. Sci., 9 Tsai, 2002, Acute toxicity of nitrate on Penaeus monodon juveniles at different salinity levels, Aquaculture, 213, 163, 10.1016/S0044-8486(02)00023-6 ter Braak, 2018 Ushiki, 2013, Isolation of Nitrospira belonging to sublineage II from a wastewater treatment plant, Microbes Environ., 28, 346, 10.1264/jsme2.ME13042 Ushiki, 2017, Nitrite oxidation kinetics of two Nitrospira strains: the quest for competition and ecological niche differentiation, J. Biosci. Bioeng., 123, 581, 10.1016/j.jbiosc.2016.12.016 Ushiki, 2018, Genomic analysis of two phylogenetically distinct Nitrospira species reveals their genomic plasticity and functional diversity, Front. Microbiol., 8, 2637, 10.3389/fmicb.2017.02637 Vanparys, 2007, The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis, Syst. Appl. Microbiol., 30, 297, 10.1016/j.syapm.2006.11.006 van Kessel, 2015, Complete nitrification by a single microorganism, Nature, 528, 555, 10.1038/nature16459 Wagner, 2002, Microbial life in terrestrial permafrost: methanogenesis and nitrification in gelisols as potentials for exobiological process, p143–159 Watson, 1971, Characteristics of two marine nitrite oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus mobilis nov, Arch. Mikrobiol., 77, 203, 10.1007/BF00408114 Watson, 1986, Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium, Arch. Microbiol., 144, 1, 10.1007/BF00454947 Wegen, 2019, Low temperature and neutral pH define“Candidatus Nitrotoga sp.” as a competitive nitrite oxidizer in coculture with Nitrospira defluvii, Appl. Environ. Microbiol., 85, 10.1128/AEM.02569-18 Wertz, 2008, Development and application of a PCR-denaturing gradient gel electrophoresis tool to study the diversity of Nitrobacter-like nxrA sequences in soil, FEMS Microbiol. Ecol., 63, 261, 10.1111/j.1574-6941.2007.00416.x Wu, 2016, A rapid and high-throughput microplate spectrophotometric method for field measurement of nitrate in seawater and freshwater, Sci. Rep., 6 Xu, 2008, Bacterial diversity in deep-sea sediment from northeastern Pacific Ocean, Acta. Ecol. Sin., 28, 479, 10.1016/S1872-2032(08)60026-8 Zhang, 2020, Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean, Proc. Natl. Acad. Sci. USA, 117, 4823, 10.1073/pnas.1912367117 Zhao, 2021, Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata, Sci. Total. Environ., 795, 10.1016/j.scitotenv.2021.148768 Zimmerman, 1985, Use of an improved statistical method for group comparisons to study effects of prairie fire, Ecology, 66, 606, 10.2307/1940409