Canfield, D. E., Glazer, A. N. & Falkowski, P. G. The evolution and future of Earth’s nitrogen cycle. Science 330, 192–196 (2010).
Heffer, P. & Prud’ homme, M. Global nitrogen fertiliser demand and supply: trend, current level and outlook. In Proceedings of the 2016 International Nitrogen Initiative Conference, “Solutions to Improve Nitrogen Use Efficiency for the World”. Melbourne, Australia 4–8 (2016).
Liu, C., Watanabe, M. & Wang, Q. Changes in nitrogen budgets and nitrogen use efficiency in the agroecosystems of the Changjiang river basin between 1980 and 2000. Nutr. Cycl. Agroecosyst. 80, 19–37 (2007).
Masuda, Y., Matsumoto, T., Isobe, K. & Senoo, K. Denitrification in paddy soil as a cooperative process of different nitrogen oxide reducers, revealed by metatranscriptomic analysis of denitrification-induced soil microcosm. Soil Sci. Plant. Nutr. 65, 342–345 (2019).
Opdyke, M. R., Ostrom, N. E. & Ostrom, P. H. Evidence for the predominance of denitrification as a source of N2O in temperate agricultural soils based on isotopologue measurements. Glob. Biogeochem. Cycles 23, GB4018 (2009).
Stein, L. Y. The long-term relationship between microbial metabolism and greenhouse gases. Trends Microbiol. 28, 500–511 (2020).
Cai, Y., Zheng, Y., Bodelier, P. L., Conrad, R. & Jia, Z. Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat. Commun. 7, 11728 (2016).
Raghoebarsing, A. A. et al. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440, 918–921 (2006).
Ettwig, K. F. et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464, 543–548 (2010).
Shen, L.-D. et al. Activity, abundance and community composition of nitrite-dependent methanotrophs in response to fertilization in paddy soils. Appl. Soil Ecol. 166, 103987 (2021).
Hui, C. et al. Depth-specific distribution and diversity of nitrite-dependent anaerobic ammonium and methane-oxidizing bacteria in upland-cropping soil under different fertilizer treatments. Appl. Soil Ecol. 113, 117–126 (2017).
Conrad, R. Microbial ecology of methanogens and methanotrophs. Adv. Agron. 96, 1–63 (2007).
Kirk, G. J. D. Rice root properties for internal aeration and efficient nutrient acquisition in submerged soil. New. Phytol. 159, 185–194 (2003).
Wang, J. et al. Denitrifying anaerobic methane oxidation: a previously overlooked methane sink in intertidal zone. Environ. Sci. Technol. 53, 203–212 (2019).
Roland, F. A. E., Darchambeau, F., Morana, C., Bouillon, S. & Borges, A. V. Emission and oxidation of methane in a meromictic, eutrophic and temperate lake (Dendre, Belgium). Chemosphere 168, 756–764 (2017).
Lu, J. J. et al. Simultaneous enhancement of nitrate removal flux and methane utilization efficiency in MBFR for aerobic methane oxidation coupled to denitrification by using an innovative scalable double-layer membrane. Water Res. 194, 116936 (2021).
Hao, Q. et al. Methylobacter couples methane oxidation and N2O production in hypoxic wetland soil. Soil Biol. Biochem. 175, 108863 (2022).
Chistoserdova, L. & Kalyuzhnaya, M. G. Current trends in methylotrophy. Trends Microbiol. 26, 703–714 (2018).
He, R. et al. Metabolic flexibility of aerobic methanotrophs under anoxic conditions in arctic lake sediments. ISME J. 16, 78–90 (2022).
Strong, P. J., Xie, S. & Clarke, W. P. Methane as a resource: can the methanotrophs add value? Environ. Sci. Technol. 49, 4001–4018 (2015).
Knowles, R. Denitrifiers associated with methanotrophs and their potential impact on the nitrogen cycle. Ecol. Eng. 24, 441–446 (2005).
Sun, F. Y. et al. Aerobic methane oxidation coupled to denitrification in a membrane biofilm reactor: treatment performance and the effect of oxygen ventilation. Bioresour. Technol. 145, 2–9 (2013).
Zhu, J. et al. Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: a review. Water Res. 90, 203–215 (2016).
Kits, K. D., Klotz, M. G. & Stein, L. Y. Methane oxidation coupled to nitrate reduction under hypoxia by the gammaproteobacterium methylomonas denitrificans, sp. Nov. Type strain FJG1. Environ. Microbiol. 17, 3219–3232 (2015).
Yao, Z. et al. A 3-year record of N2O and CH4 emissions from a sandy loam paddy during rice seasons as affected by different nitrogen application rates. Agr. Ecosyst. Environ. 152, 1–9 (2012).
Bai, X., Zhang, H., Chen, F., Sun, G. & Li, Y. Tillage effects on CH4 and N2O emission from double cropping paddy field. Trans. CSAE 26, 282–289 (2010).
Costa, C. et al. Denitrification with methane as electron donor in oxygen-limited bioreactors. Appl. Microbiol. Biot. 53, 754–762 (2000).
Kalyuzhnaya, M. G. et al. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat. Commun. 4, 2785 (2013).
Zhang, M., Daraz, U., Sun, Q., Chen, P. & Wei, X. Denitrifier abundance and community composition linked to denitrification potential in river sediments. Environ. Sci. Pollut. Res. 28, 51928–51939 (2021).
Tsiknia, M., Paranychianakis, N. V., Varouchakis, E. A. & Nikolaidis, N. P. Environmental drivers of the distribution of nitrogen functional genes at a watershed scale. FEMS Microbiol. Ecol. 91, fiv052 (2015).
Chen, H., Liu, S., Liu, T., Yuan, Z. G. & Guo, J. H. Efficient nitrate removal from synthetic groundwater via in situ utilization of short-chain fatty acids from methane bioconversion. Chem. Eng. J. 393, 124594 (2020).
Kim, I. T. et al. Development of a combined aerobic–anoxic and methane oxidation bioreactor system using mixed methanotrophs and biogas for wastewater denitrification. Water 11, 1377 (2019).
Shi, L.-D. et al. Coupled anaerobic methane oxidation and reductive arsenic mobilization in wetland soils. Nat. Geosci. 13, 799–805 (2020).
Dumbrell, A. J., Nelson, M., Helgason, T., Dytham, C. & Fitter, A. H. Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J. 4, 337–345 (2010).
Brune, A., Frenzel, P. & Cypionka, H. Life at the oxic–anoxic interface: microbial activities and adaptations. FEMS Microbiol. Rev. 24, 691–710 (2000).
Modin, O., Fukushi, K. & Yamamoto, K. Denitrification with methane as external carbon source. Water Res. 41, 2726–2738 (2007).
Zuo, Y., Xing, D., Regan, J. M. & Logan, B. E. Isolation of the exoelectrogenic bacterium Ochrobactrum anthropi YZ-1 by using a U-tube microbial fuel cell. Appl. Environ. Microbiol. 74, 3130–3137 (2008).
Zimmermann, J. et al. The functional repertoire contained within the native microbiota of the model nematode caenorhabditis elegans. ISME J. 14, 26–38 (2020).
de Graaff, D. R., van Loosdrecht, M. C. M. & Pronk, M. Stable granulation of seawater-adapted aerobic granular sludge with filamentous thiothrix bacteria. Water Res. 175, 115683 (2020).
Liu, D. et al. Research on microbial structures, functions and metabolic pathways in an advanced denitrification system coupled with aerobic methane oxidation based on metagenomics. Bioresour. Technol. 332, 125047 (2021).
Yun, H. et al. Enhanced biotransformation of triclocarban by ochrobactrum sp. Tcc-1 under anoxic nitrate respiration conditions. Curr. Microbiol. 74, 491–498 (2017).
Pang, Y. & Wang, J. Various electron donors for biological nitrate removal: a review. Sci. Total Environ. 794, 148699 (2021).
Joe-Wong, C. & Maher, K. A model for kinetic isotope fractionation during redox reactions. Geochim. Cosmochim. Acta 269, 661–677 (2020).
Tieszen, L. L. & Boutton, T. W. Stable Isotopes in Ecological Research 167–195 (Springer, 1989).
Xu, X., Wu, W., Li, X., Zhao, C. & Qin, Y. Metagenomics coupled with thermodynamic analysis revealed a potential way to improve the nitrogen removal efficiency of the aerobic methane oxidation coupled to denitrification process under the hypoxic condition. Sci. Total Environ. 912, 168953 (2024).
Yuan, C.-Y. et al. Management of biofilm by an innovative layer-structured membrane for membrane biofilm reactor (MBfR) to efficient methane oxidation coupled to denitrification (AME-D). Water Res. 251, 121107 (2024).
Peng, Y. et al. Unimodal response of soil methane consumption to increasing nitrogen additions. Environ. Sci. Technol. 53, 4150–4160 (2019).
Lee, J. et al. Attenuation of methane oxidation by nitrogen availability in arctic tundra soils. Environ. Sci. Technol. 269, 661–677 (2023).
Stein, L. Y. & Klotz, M. G. Nitrifying and denitrifying pathways of methanotrophic bacteria. Biochem. Soc. Trans. 39, 1826–1831 (2011).
Jaftha, J. B., Strijdom, B. W. & Steyn, P. L. Characterization of pigmented methylotrophic bacteria which nodulate lotononis bainesii. Syst. Appl. Microbiol. 25, 440–449 (2002).
Kanukollu, S. et al. Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species. Environ. Microbiome 17, 35 (2022).
Blagodatskaya, Е & Kuzyakov, Y. Mechanisms of real and apparent priming effects and their dependence on soil microbial biomass and community structure: critical review. Biol. Fert. Soils 45, 115–131 (2008).
Steenbergh, A. K., Meima, M. M., Kamst, M. & Bodelier, P. L. Biphasic kinetics of a methanotrophic community is a combination of growth and increased activity per cell. FEMS Microbiol. Ecol. 71, 12–22 (2009).
Su, X. et al. Estuarine plastisphere as an overlooked source of N2O production. Nat. Commun. 13, 3884 (2022).
Su, X., Chen, Y., Wang, Y., Yang, X. & He, Q. Impacts of chlorothalonil on denitrification and N2O emission in riparian sediments: microbial metabolism mechanism. Water Res. 148, 188–197 (2019).
Conrad, R., Frenzel, P. & Cohen, Y. Methane emission from hypersaline microbial mats: lack of aerobic methane oxidation activity. FEMS Microbiol. Ecol. 16, 297–305 (1995).
Börjesson, G., Sundh, I., Tunlid, A., Frostegård, Å. & Svensson, B. H. Microbial oxidation of CH4 at high partial pressures in an organic landfill cover soil under different moisture regimes. FEMS Microbiol. Ecol. 26, 207–217 (1998).
Walkley, A. A critical examination of a rapid method for determining organic carbon in soils—effect of variations in digestion conditions and of inorganic soil constituents. Soil Sci. 63, 251–264 (1947).
Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 19, 703–707 (1987).
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).
Magoc, T. & Salzberg, S. L. Flash: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
Müller, C., Stevens, R., Laughlin, R., Azam, F. & Ottow, J. The nitrification inhibitor DMPP had no effect on denitrifying enzyme activity. Soil Biol. Biochem. 34, 1825–1827 (2002).
Huang, T. et al. Ammonia-oxidation as an engine to generate nitrous oxide in an intensively managed calcareous fluvo-aquic soil. Sci. Rep. 4, 3950 (2014).
Florio, A., Maienza, A., Dell’Abate, M. T., Stazi, S. R. & Benedetti, A. Changes in the activity and abundance of the soil microbial community in response to the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP). J. Soils Sediment. 16, 2687–2697 (2016).
Bozal-Leorri, A., González-Murua, C., Marino, D., Aparicio-Tejo, P. M. & Corrochano-Monsalve, M. Assessing the efficiency of dimethylpyrazole-based nitrification inhibitors under elevated CO2 conditions. Geoderma 400, 115160 (2021).
Whittenbury, R., Phillips, K. & Wilkinson, J. Enrichment, isolation and some properties of methane-utilizing bacteria. Microbiology 61, 205–218 (1970).
Dedysh, S. N. et al. Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiol. Ecol. 43, 299–308 (2003).
Chang, J. et al. Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers. Appl. Environ. Microbiol. 87, 2301–2320 (2020).
Lu, X. et al. Methylmercury uptake and degradation by methanotrophs. Sci. Adv. 3, e1700041 (2017).
He, R. et al. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments. ISME J. 6, 1937–1948 (2012).
Lee, S. et al. Methane-derived carbon flows into host-virus networks at different trophic levels in soil. Proc. Natl Acad. Sci. USA 118, e2105124118 (2021).
Wigley, K. et al. RNA stable isotope probing and high‐throughput sequencing to identify active microbial community members in a methane‐driven denitrifying biofilm. J. Appl. Microbiol. 132, 1526–1542 (2022).
Lide, D. R. & Frederikse, H. CRC Handbook of Chemistry and Physics (CRC Press, Inc, 1995).
Shi, L.-D. et al. Methane-dependent selenate reduction by a bacterial consortium. ISME J. 15, 1–10 (2021).
Dumont, M. G. & Murrell, J. C. Stable isotope probing—linking microbial identity to function. Nat. Rev. Microbiol. 3, 499–504 (2005).
Videvall, E., Strandh, M., Engelbrecht, A., Cloete, S. & Cornwallis, C. K. Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for gut microbiomes. mSystems 2, e00132–00117 (2017).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Murdock, S. A. & Juniper, S. K. Capturing compositional variation in denitrifying communities: a multiple-primer approach that includes Epsilonproteobacteria. Appl. Environ. Microbiol. 83, e02753–e02816 (2017).
Li, C. et al. Global co-occurrence of methanogenic archaea and methanotrophic bacteria in microcystis aggregates. Environ. Microbiol. 23, 6503–6519 (2021).
Wang, Z. et al. Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments. Methods Ecol. Evol. 13, 1976–1989 (2022).
Liu, Y. R. et al. Unraveling microbial communities associated with methylmercury production in paddy soils. Environ. Sci. Technol. 52, 13110–13118 (2018).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 11, 1–11 (2010).
Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peer J. 3, e1165 (2015).
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Uritskiy, G. V., DiRuggiero, J. & Taylor, J. Metawrap—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018).
Parks, D. H. et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat. Biotechnol. 38, 1079–1086 (2020).
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., Parks, D. H. & Hancock, J. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36, 1925–1927 (2020).
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).
Hua, Z. S. et al. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring archaea. Nat. Commun. 10, 4574 (2019).
Zhou, Z., Tran, P. Q., Kieft, K. & Anantharaman, K. Genome diversification in globally distributed novel marine proteobacteria is linked to environmental adaptation. ISME J. 14, 2060–2077 (2020).
Walsh, A. M., Macori, G., Kilcawley, K. N. & Cotter, P. D. Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nat. Food 1, 500–510 (2020).
Stewart, R. D. et al. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nat. Biotechnol. 37, 953–961 (2019).
Jain, C., Rodriguez, R. L., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ani analysis of 90k prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009).
Aramaki, T. et al. KoFamkoala: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).
de Crécy-Lagard, V., Graf, D. R. H., Jones, C. M. & Hallin, S. Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS ONE 9, e114118 (2014).
Arora, J. et al. The functional evolution of termite gut microbiota. Microbiome 10, 78 (2022).
Fan, L. et al. Presence and role of viruses in anaerobic digestion of food waste under environmental variability. Microbiome 11, 170 (2023).
Martinez-Perez, C. et al. Phylogenetically and functionally diverse microorganisms reside under the ross ice shelf. Nat. Commun. 13, 117 (2022).
Millard, P. et al. IsoCor: isotope correction for high-resolution MS labeling experiments. Bioinformatics 35, 4484–4487 (2019).
Stone, M. M., DeForest, J. L. & Plante, A. F. Changes in extracellular enzyme activity and microbial community structure with soil depth at the luquillo critical zone observatory. Soil Biol. Biochem. 75, 237–247 (2014).
Delgadobaquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).
Grace, J. B. Structural Equation Modeling and Natural Systems, Vol. 8, 368–369 (Cambridge University Press, 2006).
Bastian, M., Heymann, S. & Jacomy, M. in Proceedings of the Third International Conference on Weblogs and Social Media, ICWSM 2009, San Jose, California, USA, May 17-20, 361–362 (2009).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 15, 550 (2014).
Source link
