van Mantgem PJ, Stephenson NL, Byrne JC, Daniels LD, Franklin JF, Fule PZ, et al. Widespread increase of tree mortality rates in the western United States. Science. 2009;323:521–4.
Allen CD, Macalady AK, Chenchouni H, Bachelet D, McDowell N, Vennetier M, et al. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. For Ecol Manag. 2010;259:660–84.
Carnicer J, Coll M, Ninyerola M, Pons X, Sanchez G, Penuelas J. Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought. Proc Natl Acad Sci USA. 2011;108:1474–8.
Brown N, Vanguelova E, Parnell S, Broadmeadow S, Denman S. Predisposition of forests to biotic disturbance: predicting the distribution of Acute Oak Decline using environmental factors. For Ecol Manag. 2018;407:145–54.
Denman S, Doonan J, Ransom-Jones E, Broberg M, Plummer S, Kirk S, et al. Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline. ISME J. 2017. https://doi.org/10.1038/ismej.2017.170.
Denman S, Barrett G, Kirk SA, McDonald JE, Coetzee MPA. Identification of Armillaria species on oak in Britain: implications for Oak Health. Forestry. 2017;90:148–61.
Martınez-Vilalta J, Lloret F, Breshears DD. Drought-induced forest decline: causes, scope and implications. Biol Lett. 2012;8:689–91.
McDowell NG, Ryan MG, Zeppel MJB, Tissue DT. Improving our knowledge of drought-induced forest mortality through experiments, observations, and modeling. N. Phytologist. 2013;200:289–93.
Thomas FM, Blank R, Hartmann G. Abiotic and biotic factors and their interactions as causes of oak decline in central Europe. Pathol. 2002;32:277–307.
Niinemets Ü. Responses of forest trees to single and multiple environmental stresses from seedlings to mature plants: past stress history, stress interactions, tolerance and acclimation. Ecol Manag. 2010;260:1623–39.
Amoroso MM, Daniels LD, Larson BC. Temporal patterns of radial growth in declining Austrocedrus chilensis forests in Northern Patagonia: the use of treerings as an indicator of forest decline. Ecol Manag. 2012;265:62–70.
Bansal S, Hallsby G, Löfvenius MO, Nilsson MC. Synergistic, additive and antagonistic impacts of drought on herbivory on Pinus sylvestris: leaf, tissue and whole-plant responses and recovery. Tree Physiol. 2013;33:451–63.
Whyte G, Howard K, Hardy GEStJ, Burgess T. The Tree Decline Recovery Seesaw; a conceptual model of the decline and recovery of drought stressed plantation trees. For Ecol Manag. 2016;370:102–13.
Calder JA, Kirkpatrick JB. Climate change and other factors influencing the decline of the Tasmanian cider gum (Eucalyptus gunnii). Australian J Botany. 2008;56. https://doi.org/10.1071/BT08105.
Avila JM, Gallardo A, Ibáñez B, Gómez‐Aparicio L. Quercus suber dieback alters soil respiration and nutrient availability in Mediterranean forests. J Ecol. 2016;104:1441–52.
Crawford N. Nitrate: nutrient and signal for plant growth. Plant Cell. 1995;7:859–68.
Lovett GM, Arthur MA, Weathers KC, Griffin JM. Long-term changes in forest carbon and nitrogen cycling caused by an introduced pest/pathogen complex. Ecosystems. 2010;13:1188–1200.
Throop H, Lerdau MT. Effects of nitrogen deposition on insect herbivory: Implications for community and ecosystem processes. Ecosystems. 2004;7:109–33.
Thomas FM, Ahlers U. Effects of excess nitrogen on frost hardiness and freezing injury of above-ground tissue in young oaks (Quercus petraea and Q. robur). N. Phytologist. 1999;144:73–83.
Hardham AR. The cell biology behind Phytophthora pathogenicity. Australas Plant Pathol. 2001;30:91–98.
Brown N, Jeger M, Kirk S, Xu X, Denman S. Spatial and temporal patterns in symptom expression within eight woodlands affected by acute Oak Decline. For Ecol Manag. 2016;360:97–109.
Scarlett K, Guest DI, Daniel R. Elevated soil nitrogen increases the severity of dieback due to Phytophthora cinnamomi. Australas Plant Pathol. 2013;42:155–62.
Yao H, Bowman D, Shi W. Seasonal variations in soil microbial biomass and activity in warm and cool season turfgrass systems. Soil Biol Biochem. 2011;43:1536–43.
Prosser JI, Nicol GW. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol. 2008;10:2931–41.
Prosser JI, Nicol GW. Archaeal and bacterial ammonia oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 2012;20:523–31.
Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W. Environmental factors shaping the ecological niches of ammonia‐oxidizing archaea. FEMS Microbiol Rev. 2009;33:855–69.
Hink L, Lycus P, Gubry-Rangin C, Frostgard A, Nicol GW, Prosser JI, et al. Kinetics of NH3‐oxidation, NO‐turnover, N2O‐production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environ Microbiol. 2017;19:4882–96.
Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, et al. Niche specialization of terrestrial archaeal ammonia oxidisers. Proc Natl Acad Sci. 2011;108:21206–11.
Leininger S, Schloter UT, Schwark I, Qi J, Nicol GW, Prosser JI, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature. 2006;442:806–9.
Gubry-Rangin C, Nicol GW, Prosser JI. Archaea rather than bacterial control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol. 2010;74:566–74.
Verhamme DT, Prosser JI, Nicol GW. Ammonia concentration determines differential growth of ammonia oxidizing archaeal and bacteria in soil microcosms. ISME J. 2011;5:1067–71.
Di HJ, Cameron KC, Shen J-P, Winefield CS, O’Callaghan M, Bowatte S, et al. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol. 2010;72:386–94.
Hink L, Gubry-Rangin C, Nicol GW, Prosser J. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J. 2018;12:1084–93.
Clark D, McKew B, Dong L, Leung G, Dumbrell AJ, Stott A, et al. Mineralization and nitrification: archaea dominate ammonia-oxidising communities in grassland soils. Soil Biol Biochem. 2020;143:107725.
Delgado-Baquerizo M, Maestre FT, Eldridge DJ, Singh BK. Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients. Front Microbiol. 2016;7:505.
Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature. 2009;461:976–9.
Barta J, Tahovska K, Santruckova H, Oulehle F. Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching. Sci Rep Nat. 2017;7:9738.
Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012;6:1007–17. https://doi.org/10.1038/ismej.2011.159.
Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology. 2010;91:3463–70. https://doi.org/10.1890/10-0426.1.
Cranfield University 2020. The Soils Guide. www.landis.org.uk. UK; Cranfield University.
G Kerr, J Haufe. Thinning practice. A Silvicultural Guide. Bristol: Forestry Commission; 2011;1:54.
Cools N, De Vos B Sampling and Analysis of Soil. In: Manual on methods and criteria for harmonized sampling, assessment, monitoring and analysis of the effects of air pollution on forests. Hamburg: UNECE, ICP Forests; 2010, pp. 208.
MAFF. Code of good agricultural practice for the protection of soil. London, UK: Ministry of Agriculture, Fisheries and Food; 1993.
Li J, Nedwell DB, Beddow J, Dumbrell AJ, McKew BA, Thorpe EL, et al. amoA gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria (AOB) not archaea (AOA) dominate N cycling in the Colne estuary, UK. Appl Environ Microbiol. 2015;81:159–65.
Beddow J, Stolpe B, Cole PA, Lead JR, Sapp M, Lyons BP, et al. Nanosilver inhibits nitrification and reduces ammonia-oxidizing bacterial but not archaeal amoA gene abundance in estuarine sediments. Environ Microbiol. 2017;19:500–10.
Tourna M, Freitag TE, Nicol GW, Prosser JI. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol. 2008;10:1357–64.
Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol. 1997;63:4704–12.
Throbäck IN, Enwall K, Jarvis A, Hallin S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol. 2004;49:401–17.
Braker G, Fesefeldt A, Witzel KP. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol. 1998;64:3769–75.
Henry S, Bru D, Stres B, Hallet S, Philippot L. Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ Genes in Soils. Appl Environ Microbiol. 2006;72:5181–9.
Herlemann D, Labrenz M, Jürgens K, Bertilsson S, Waniek J, Andersson A. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5:1571–9.
Raskin L, Stromley JM, Rittmann BE, Stahl DA. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol. 1994;60:1232–40.
Stahl DA, Amann R Development and application of nucleic acid probes. In: Nucleic acid techniques in bacterial systematics. Stackebrandt, E, Goodfellow M, editors. Chichester, UK: John Wiley & Sons Ltd; 1991. pp. 205–48.
Dumbrell AJ, Ferguson RMW, Clark DR. Microbial community analysis by single-amplicon high-throughput next generation sequencing: Data analysis—from raw output to ecology. In: McGenity T, Timmis K, Nogales B, editors. Hydrocarbon and Lipid Microbiology Protocols. Berlin, Heidelberg: Springer Protocols Handbooks. Springer; 2016. 155–206.
Joshi NA, Fass JN Sickle: A Sliding-Window, Adaptive, Quality-Based Trimming Tool for FastQ Files 2011; (Version 1.33).
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013;20:714–37.
Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics SP. 2013;14:S7.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4. https://doi.org/10.7717/peerj.2584.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;16:2194–200.
Wang Q, Quensen JF, Fish JA, Lee TK, Sun Y, Tiedje JM, et al. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. MBio. 2013;4:e00592–13.
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;16:5261–7.
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;5:1792–7.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;12:2725–9.
Fish J, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, et al. FunGene: the functional gene pipeline and repository. Front Microbiol. 2013;4:291.
Altschul S, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.
Lefcheck J. PIECEWISESEM: Piecewise structural equation modelling in R for ecology, evolution, and systematics. Methods Ecol Evol. 2016;7:573–9.
Shipley B. A new inferential test for path models based on directed acyclic graphs. Struct Equ Modeling. 2000;7:206–18.
Grace JB. Structural Equation Modelling and Natural Systems. New York, NY: Cambridge University Press; 2006.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. Vegan: Community Ecology Package. R package Version. 2017;2:4–3.
Leininger Wang Y, Naumann U, Wright S, Warton D. Mvabund—an R package for model‐based analysis of multivariate abundance data. Methods Ecol Evolution. 2012;3:471–4.
Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci USA. 2011;108:15892–7.
Hu H, Zhang L, Dai Y, et al. pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing. J Soils Sediment. 2013;13:1439–49.
Hu BL, Liu S, Wang W, Shen LD, Lou LP, Liu WP, et al. pH-dominated niche segregation of ammonia-oxidising microorganisms in Chinese agricultural soils. FEMS Microbiol Ecol. 2014;90:290–9. https://doi.org/10.1111/1574-6941.12391.
Hu H, Zhang L, Yuan C, Zheng Y, Wang J, Chen D, et al. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors. Front Microbiol. 2015;6:938.
Delgado-Baquerizo M, Gallardo A, Wallenstein MD, Maestre FT. Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea. FEMS Microbiol Ecol. 2013;13:273–82.
Eldridge DJ, Beecham G, Grace J. Do shrubs reduce the adverse effects of grazing on soil properties? Ecohydrology. 2015;8:1503–13.
Berdugo M, Soliveres S, Maestre FT. Vascular plants and biocrusts modulate how abiotic factors affect wetting and drying events in drylands. Ecosystems. 2014;17:1242–56.
Köhler S, Levia DF, Jungkunst HF, Gerold G. An In Situ Method to Measure and Map Bark pH. J Wood Chem Technol. 2015;35:438–49.
Matschonat G, Falkengren-Grerup U. Recovery of soil pH, Cation-exchange Capacity and the Saturation of Exchange Sites from Stemflow-induced Soil Acidification in Three Swedish Beech (Fagus sylvatica L.) Forests. Scand J For Res. 2000;15:39–48.
Wang Y, Uchida Y, Shimomura U, Akiyama H, Hayatsu M. Responses of denitrifying bacterial communities to short-term waterlogging of soils. Sci Rep. 2017;7:803.
Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, et al. Ammonia-oxidizing Archaea show more distinct biogeographic distribution patterns than ammonia-oxidizing bacteria across the black soil zone of Northeast China. Front Microbiol. 2018;9:171.
Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X, et al. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biol Biochem. 2013;57:204–11.
Nicol GW, Leininger S, Schleper C, Prosser JI. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol. 2008;10:2966–78.
Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010;4:1340–51.
Yuan YL, Si GC, Wang J, Luo TX, Zhang GX. Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau. FEMS Microbiol Ecol. 2014;87:121–32.
Kaiser k, Wemheuer B, Korolkow V, Wemheuer F, Nacke H, Schöning I, et al. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Sci Rep. 2017;7:9738.
Meaden S, Metcalf CJE, Koskella B. The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur). Environ Microbiol Rep. 2016;8:649–58.
Patra AK, Abbadie L, Clays-Josserand A, Degrange V, Grayston SJ, Guillaumaud N, et al. Effects of management regime and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils. Environ Microbiol. 2006;8:1005–16.
Bremer C, Braker G, Matthies D, Beierkuhnlein C, Conrad R. Plant presence and species combination, but not diversity, influence denitrifier activity and the composition of nirK-type denitrifier communities in grassland soil. FEMS Microbiol Ecol. 2009;70:377–87.
Source: Ecology - nature.com
