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Increased microbial expression of organic nitrogen cycling genes in long-term warmed grassland soils

  • 1.

    Schmidt MWI, Torn MS, Abiven S, Dittmar T, Guggenberger G, Janssens IA, et al. Persistence of soil organic matter as an ecosystem property. Nature. 2011;478:49–56.

    CAS 
    PubMed 

    Google Scholar 

  • 2.

    Bond-Lamberty B, Bailey VL, Chen M, Gough CM, Vargas R. Globally rising soil heterotrophic respiration over recent decades. Nature. 2018;560:80–3.

    CAS 
    PubMed 

    Google Scholar 

  • 3.

    Bradford MA. Thermal adaptation of decomposer communities in warming soils. Front Microbiol. 2013;4:1–16.

    Google Scholar 

  • 4.

    Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, et al. Scientists’ warning to humanity: microorganisms and climate change. Nat Rev Microbiol. 2019;17:569–86.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 5.

    Jansson JK, Hofmockel KS. Soil microbiomes and climate change. Nat Rev Microbiol. 2020;18:35–46.

    CAS 
    PubMed 

    Google Scholar 

  • 6.

    Liu L, Greaver TL. A global perspective on belowground carbon dynamics under nitrogen enrichment. Ecol Lett. 2010;13:819–28.

    PubMed 

    Google Scholar 

  • 7.

    Knicker H. Soil organic N – An under-rated player for C sequestration in soils? Soil Biol Biochem. 2011;43:1118–29.

    CAS 

    Google Scholar 

  • 8.

    Soong JL, Fuchslueger L, Marañon-Jimenez S, Torn MS, Janssens IA, Peñuelas J, et al. Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling. Glob Chang Biol. 2020;26:1953–61.

    Google Scholar 

  • 9.

    Mooshammer M, Wanek W, Hämmerle I, Fuchslueger L, Hofhansl F, Knoltsch A, et al. Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling. Nat Commun. 2014;5:1–7.

    Google Scholar 

  • 10.

    Geisseler D, Horwath WR, Joergensen RG, Ludwig B. Pathways of nitrogen utilization by soil microorganisms – a review. Soil Biol Biochem. 2010;42:2058–67.

    CAS 

    Google Scholar 

  • 11.

    Wang X, Wang C, Cotrufo MF, Sun L, Jiang P, Liu Z, et al. Elevated temperature increases the accumulation of microbial necromass nitrogen in soil via increasing microbial turnover. Glob Chang Biol. 2020;26:5277–89.

    PubMed 

    Google Scholar 

  • 12.

    Simpson AJ, Simpson MJ, Smith E, Kelleher BP. Microbially derived inputs to soil organic matter: Are current estimates too low? Environ Sci Technol. 2007;41:8070–6.

    CAS 
    PubMed 

    Google Scholar 

  • 13.

    Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76.

    CAS 
    PubMed 

    Google Scholar 

  • 14.

    Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, et al. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nat Climate Change. 2018;8:885–9.

    CAS 

    Google Scholar 

  • 15.

    Marañón-Jiménez S, Peñuelas J, Richter A, Sigurdsson BD, Fuchslueger L, Leblans NIW, et al. Coupled carbon and nitrogen losses in response to seven years of chronic warming in subarctic soils. Soil Biol Biochem. 2019;134:152–61.

    Google Scholar 

  • 16.

    Nguyen TTH, Myrold DD, Mueller RS. Distributions of extracellular peptidases across prokaryotic genomes reflect phylogeny and habitat. Front Microbiol. 2019;10:1–14.

    Google Scholar 

  • 17.

    Zimmerman AE, Martiny AC, Allison SD. Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J. 2013;7:1187–99.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 18.

    Beier S, Bertilsson S. Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol. 2013;4:1–12.

    Google Scholar 

  • 19.

    Kielak AM, Cretoiu MS, Semenov AV, Sørensen SJ, Van, Elsas JD. Bacterial chitinolytic communities respond to chitin and pH alteration in soil. Appl Environ Microbiol. 2013;79:263–72.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 20.

    Weintraub MN, Schimel JP. Seasonal protein dynamics in Alaskan arctic tundra soils. Soil Biol Biochem. 2005;37:1469–75.

    CAS 

    Google Scholar 

  • 21.

    Boer VM, De Winde JH, Pronk JT, Piper MDW. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem. 2003;278:3265–74.

    CAS 
    PubMed 

    Google Scholar 

  • 22.

    Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn MMA, Pronk JT, Slijper M, et al. Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol. 2006;2:1–16.

    Google Scholar 

  • 23.

    Silberbach M, Hüser A, Kalinowski J, Pühler A, Walter B, Krämer R, et al. DNA microarray analysis of the nitrogen starvation response of Corynebacterium glutamicum. J Biotechnol. 2005;119:357–67.

    CAS 
    PubMed 

    Google Scholar 

  • 24.

    Merrick MJ, Edwards RA. Nitrogen control in bacteria. Microbiol Rev. 1995;59:604–22.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 25.

    Daebeler A, Abell GCJ, Bodelier PLE, Bodrossy L, Frampton DMF, Hefting MM, et al. Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating. Front Microbiol. 2012;3:1–14.

    Google Scholar 

  • 26.

    Yeager CM, Kornosky JL, Housman DC, Grote EE, Belnap J, Kuske CR. Diazotrophic community structure and function in two successional stages of biological soil crusts from the colorado plateau and Chihuahuan Desert. Appl Environ Microbiol. 2004;70:973–83.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Malik AA, Swenson T, Weihe C, Morrison EW, Martiny JBH, Brodie EL, et al. Drought and plant litter chemistry alter microbial gene expression and metabolite production. ISME J. 2020;14:2236–47.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 28.

    Tveit A, Schwacke R, Svenning MM, Urich T. Organic carbon transformations in high-Arctic peat soils: Key functions and microorganisms. ISME J. 2013;7:299–311.

    CAS 
    PubMed 

    Google Scholar 

  • 29.

    Geisen S, Tveit AT, Clark IM, Richter A, Svenning MM, Bonkowski M, et al. Metatranscriptomic census of active protists in soils. ISME J. 2015;9:2178–90.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 30.

    Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE. 2008;3:1–13.

    Google Scholar 

  • 31.

    Kallenbach CM, Frey SD, Grandy AS. Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat Commun. 2016;7:1–10.

    Google Scholar 

  • 32.

    Walker TWN, Janssens IA, Weedon JT, Sigurdsson BD, Richter A, Peñuelas J, et al. A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem. Nat Ecol Evol. 2020;4:101–8.

    PubMed 

    Google Scholar 

  • 33.

    Sigurdsson BD, Wallander H, Gunnarsdóttir GE, Richter A, Sigurðsson P, Leblans NIW, et al. Geothermal ecosystems as natural climate change experiments: the ForHot research site in Iceland as a case study. Icelandic Agric Sci. 2016;29:53–71.

    Google Scholar 

  • 34.

    Söllinger A, Séneca J, Dahl MB, Prommer J, Verbruggen E, Sigurdsson BD, et al. Downregulation of the microbial protein biosynthesis machinery in response to weeks, years and decades of soil warming. 2021 Research Square preprint. https://doi.org/10.21203/rs.3.rs-132190/v2

  • 35.

    Leblans N. Natural gradients in temperature and nitrogen: Iceland represents a unique environment to clarify long-term global change effects on carbon dynamics. Joint doctoral dissertation. Antwerp University and Agricultural University of Iceland, Reykjavik, Iceland; 2016:1–229.

  • 36.

    Angel R, Claus P, Conrad R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J. 2012;6:847–62.

    CAS 
    PubMed 

    Google Scholar 

  • 37.

    Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:5–11.

    Google Scholar 

  • 38.

    Gillespie CS. Fitting heavy tailed distributions: the poweRlaw Package. J Stat Softw. 2015;64:1–16.

    Google Scholar 

  • 39.

    El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2018;47:427–32.

    Google Scholar 

  • 40.

    Eddy SR. Accelerated profile HMM searches. PLOS Comput Biol. 2011;7:e1002195.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 41.

    Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.

    CAS 
    PubMed 

    Google Scholar 

  • 42.

    Bendtsen JD, Kiemer L, Fausbøll A, Brunak S. Non-classical protein secretion in bacteria. BMC Microbiol. 2005;5:1–13.

    Google Scholar 

  • 43.

    Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26:1608–15.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 44.

    Orsi WD. MetaProt: an integrated database of predicted proteins for improved annotation of metaomic datasets. Open Data LMU. 2020. https://doi.org/10.5282/ubm/data.183

  • 45.

    Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2013;42:490–5.

    Google Scholar 

  • 46.

    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59–60.

    PubMed 

    Google Scholar 

  • 47.

    Oksanen AJ, Blanchet FG, Kindt R, Legen- P, Minchin PR, Hara RBO, et al. vegan: Community Ecology Package. 2019. https://cran.r-project.org/package=vegan

  • 48.

    Lê S, Josse J, Husson F. FactoMineR: an R package for multivariate analysis. J Stat Softw. 2008;25:1–18.

    Google Scholar 

  • 49.

    Kolde R. pheatmap: pretty heatmaps. 2019. https://cran.r-project.org/package=pheatmap

  • 50.

    Noll L, Zhang S, Zheng Q, Hu Y, Wanek W. Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content. Soil Biol Biochem. 2019;133:37–49.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 51.

    Schimel JP, Bennett J. Nitrogen mineralization: challenges of a changing paradigm. Ecology. 2004;85:591–602.

    Google Scholar 

  • 52.

    Wild B, Ambus P, Reinsch S, Richter A. Resistance of soil protein depolymerization rates to eight years of elevated CO2, warming, and summer drought in a temperate heathland. Biogeochemistry. 2018;140:255–67.

    CAS 

    Google Scholar 

  • 53.

    Wanek W, Mooshammer M, Blöchl A, Hanreich A, Richter A. Determination of gross rates of amino acid production and immobilization in decomposing leaf litter by a novel 15N isotope pool dilution technique. Soil Biol Biochem. 2010;42:1293–302.

    CAS 

    Google Scholar 

  • 54.

    Liang C, Schimel JP, Jastrow JD. The importance of anabolism in microbial control over soil carbon storage. Nat Microbiol. 2017;2:1–6.

    Google Scholar 

  • 55.

    Vranova V, Rejsek K, Formanek P. Proteolytic activity in soil: a review. Appl Soil Ecol. 2013;70:23–32.

    Google Scholar 

  • 56.

    Schimel JP, Weintraub MN. The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model. Soil Biol Biochem. 2003;35:549–63.

    CAS 

    Google Scholar 

  • 57.

    Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: The database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 2014;42:503–9.

    Google Scholar 

  • 58.

    Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev. 2008;32:259–86.

    CAS 
    PubMed 

    Google Scholar 

  • 59.

    Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell wall hydrolases in bacteria: Insight on the diversity of cell wall amidases, glycosidases and peptidases toward peptidoglycan. Front Microbiol. 2019;10:1–27.

    Google Scholar 

  • 60.

    Donhauser J, Qi W, Bergk-Pinto B, Frey B. High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils. Glob Chang Biol. 2020;27:1365–86.

  • 61.

    Vollmer W, Blanot D, De Pedro MA. Peptidoglycan structure and architecture. FEMS Microbiology Reviews. 2008;32:149–67.

    CAS 
    PubMed 

    Google Scholar 

  • 62.

    Semchenko M, Leff JW, Lozano YM, Saar S, Davison J, Wilkinson A, et al. Fungal diversity regulates plant-soil feedbacks in temperate grassland. Science Adv. 2018;4.

  • 63.

    Saary P, Mitchell AL, Finn RD. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis. Genome Biol. 2020;21:244.

    PubMed 
    PubMed Central 

    Google Scholar 


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