Paul, E. A. (ed.) Soil Microbiology, Ecology and Biochemistry (Academic Press, Amsterdam, 2015).
Nannipieri, P. et al. Microbial diversity and soil functions. Eur. J. Soil. Sci. 54, 655–670 (2003).
Kuzyakov, Y. & Blagodatskaya, E. Microbial hotspots and hot moments in soil: concept & review. Soil. Biol. Biochem. 83, 184–199 (2015).
Berg, G. & Smalla, K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol. Ecol. 68, 1–13 (2009).
Bais, H. P., Park, S.-W., Weir, T. L., Callaway, R. M. & Vivanco, J. M. How plants communicate using the underground information superhighway. Trends Plant. Sci. 9, 26–32 (2004).
Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663. https://doi.org/10.1111/1574-6976.12028 (2013).
Praeg, N., Pauli, H. & Illmer, P. Microbial diversity in bulk and rhizosphere soil of Ranunculus glacialis along a high-alpine altitudinal gradient. Front. Microbiol. 10, 1429. https://doi.org/10.3389/fmicb.2019.01429 (2019).
Nacke, H. et al. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE 6, e17000. https://doi.org/10.1371/journal.pone.0017000 (2011).
Jackson, R. B., Solomon, E. I., Canadell, J. G., Cargnello, M. & Field, C. B. Methane removal and atmospheric restoration. Nat. Sustain. 2, 436–438. https://doi.org/10.1038/s41893-019-0299-x (2019).
Ciais, P. et al. Climate Change 2013: The Physical Science Basis. In Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (eds Stocker, T. F. et al.) (Cambridge University Press, Cambridge, 2013).
Adam, P. S., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J. 11, 2407. https://doi.org/10.1038/ismej.2017.122 (2017).
Knief, C. Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front. Microbiol. 6, 1346 (2015).
Hanson, R. S. & Hanson, T. E. Methanotrophic bacteria. Microbiol. Rev. 60, 439–471 (1996).
Op den Camp, H. J. M. et al. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ. Microbiol. Rep. 1, 293–306. https://doi.org/10.1111/j.1758-2229.2009.00022.x (2009).
Knief, C., Lipski, A. & Dunfield, P. F. Diversity and activity of methanotrophic bacteria in different upland soils. Appl. Environ. Microbiol. 69, 6703–6714. https://doi.org/10.1128/AEM.69.11.6703-6714.2003 (2003).
Kolb, S. The quest for atmospheric methane oxidizers in forest soils. Environ. Microbiol. Rep. 1, 336–346 (2009).
Plesa, I. et al. Effects of drought and salinity on European Larch (Larix decidua Mill.) seedlings. Forests 9, 320. https://doi.org/10.3390/f9060320 (2018).
Falk, W., Bachmann-Gigl, U. & Kölling, C. Die Europäische Lärche im Klimawandel. In Beiträge zur Europäischen Lärche (ed. Schmidt, O.) 19–27 (Bayrische Landesanstalt für Wald und Forstwirtschaft, Freising, 2012).
Obojes, N. et al. Water stress limits transpiration and growth of European larch up to the lower subalpine belt in an inner-alpine dry valley. New Phytol. 220, 460–475 (2018).
Wieser, G. (ed.) Trees at Their Upper Limit. Treelife Limitation at the Alpine Timberline (Springer, Dordrecht, 2007).
Dedysh, S. N. et al. Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem. Int. J. Syst. Evol. Microbiol. 65, 3618–3624. https://doi.org/10.1099/ijsem.0.000465 (2015).
Praeg, N., Wagner, A. O. & Illmer, P. Plant species, temperature, and bedrock affect net methane flux out of grassland and forest soils. Plant Soil 410, 193–206 (2017).
Lladó, S., López-Mondéjar, R. & Baldrian, P. Forest soil bacteria: diversity, involvement in ecosystem processes, and response to global change. Microbiol. Mol. Biol. Rev. https://doi.org/10.1128/MMBR.00063-16 (2017).
Urbanová, M., Šnajdr, J. & Baldrian, P. Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees. Soil. Biol. Biochem. 84, 53–64. https://doi.org/10.1016/j.soilbio.2015.02.011 (2015).
Liu, J. et al. Characteristics of bulk and rhizosphere soil microbial community in an ancient Platycladus orientalis forest. Appl. Soil Ecol. 132, 91–98. https://doi.org/10.1016/j.apsoil.2018.08.014 (2018).
Uroz, S. et al. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci. Rep. 6, 27756. https://doi.org/10.1038/srep27756 (2016).
Štursová, M., Bárta, J., Šantrůčková, H. & Baldrian, P. Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiw185 (2016).
Ferrari, B., Winsley, T., Ji, M. & Neilan, B. Insights into the distribution and abundance of the ubiquitous candidatus Saccharibacteria phylum following tag pyrosequencing. Sci. Rep. 4, 3957. https://doi.org/10.1038/srep03957 (2014).
Starr, E. P. et al. Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. Microbiome 6, 122. https://doi.org/10.1186/s40168-018-0499-z (2018).
Brewer, T. E., Handley, K. M., Carini, P., Gilbert, J. A. & Fierer, N. Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’. Nat. Microbiol. 2, 16198. https://doi.org/10.1038/nmicrobiol.2016.198 (2016).
Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A. & Kuramae, E. E. The ecology of acidobacteria: moving beyond genes and genomes. Front. Microbiol. 7, 744. https://doi.org/10.3389/fmicb.2016.00744 (2016).
Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364 (2007).
Johnston-Monje, D., Lundberg, D. S., Lazarovits, G., Reis, V. M. & Raizada, M. N. Bacterial populations in juvenile maize rhizospheres originate from both seed and soil. Plant Soil 405, 337–355. https://doi.org/10.1007/s11104-016-2826-0 (2016).
Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Nat. Acad. Sci. USA 109, 21390–21395. https://doi.org/10.1073/pnas.1215210110 (2012).
Kottke, I. & Oberwinkler, F. Comparative studies on the mycorrhization of Larix decidua and Picea abies by Suillus grevillei. Trees https://doi.org/10.1007/BF00196758 (1988).
Uroz, S., Buée, M., Murat, C., Frey-Klett, P. & Martin, F. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ. Microbiol. Rep. 2, 281–288. https://doi.org/10.1111/j.1758-2229.2009.00117.x (2010).
Mapelli, F. et al. The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence. ISME J. 12, 1188. https://doi.org/10.1038/s41396-017-0026-4 (2018).
Mello, B. L., Alessi, A. M., McQueen-Mason, S., Bruce, N. C. & Polikarpov, I. Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia. Sci. Rep. 6, 38781. https://doi.org/10.1038/srep38781 (2016).
Turnbull, G. A., Morgan, J. A. W., Whipps, J. M. & Saunders, J. R. The role of bacterial motility in the survival and spread of Pseudomonas fluorescens in soil and in the attachment and colonisation of wheat roots. FEMS Microbiol. Ecol. 36, 21–31. https://doi.org/10.1111/j.1574-6941.2001.tb00822.x (2001).
Rees, D. C., Johnson, E. & Lewinson, O. ABC transporters: the power to change. Nat. Rev. Mol. Cell. Biol. 10, 218–227. https://doi.org/10.1038/nrm2646 (2009).
Aronson, E. L., Allison, S. D. & Helliker, B. R. Environmental impacts on the diversity of methane-cycling microbes and their resultant function. Front. Microbiol. 4, 225. https://doi.org/10.3389/fmicb.2013.00225 (2013).
Dalal, R. C., Allen, D. E., Livesley, S. J. & Richards, G. Magnitude and biophysical regulators of methane emission and consumption in the Australian agricultural, forest, and submerged landscapes. A review. Plant Soil 309, 43–76 (2008).
Martins, C. S. C., Nazaries, L., Macdonald, C. A., Anderson, I. C. & Singh, B. K. Water availability and abundance of microbial groups are key determinants of greenhouse gas fluxes in a dryland forest ecosystem. Soil Biol. Biochem. 86, 5–16. https://doi.org/10.1016/j.soilbio.2015.03.012 (2015).
Praeg, N., Schwinghammer, L. & Illmer, P. Larix decidua and additional light affect the methane balance of forest soil and the abundance of methanogenic and methanotrophic microorganisms. FEMS Microbiol Lett. https://doi.org/10.1093/femsle/fnz259 (2020).
Ström, L., Mastepanov, M. & Christensen, T. R. Species-specific effects of vascular plants on carbon turnover and methane emissions from wetlands. Biogeochemistry 75, 65–82 (2005).
Borrel, G. et al. Genome sequence of “Candidatus Methanomassiliicoccus intestinalis” Issoire-Mx1, a third thermoplasmatales-related methanogenic archaeon from human feces. Genome Announc. 1, e004523. https://doi.org/10.1128/genomeA.00453-13 (2013).
Deng, Y., Liu, P. & Conrad, R. Effect of temperature on the microbial community responsible for methane production in alkaline NamCo wetland soil. Soil Biol. Biochem. 132, 69–79. https://doi.org/10.1016/j.soilbio.2019.01.024 (2019).
Söllinger, A. et al. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol. Ecol. 92, 149. https://doi.org/10.1093/femsec/fiv149 (2016).
Berghuis, B. A. et al. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proc. Natl. Acad. Sci. U.S.A. 116, 5037. https://doi.org/10.1073/pnas.1815631116 (2019).
Cai, Y., Zheng, Y., Bodelier, P. L. E., Conrad, R. & Jia, Z. Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat. Commun. 7, 11728 (2016).
Henckel, T., Jäckel, U., Schnell, S. & Conrad, R. Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane. Appl. Environ. Microbiol. 60, 1801–1808 (2000).
Ricke, P., Kolb, S. & Braker, G. Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil. Appl. Environ. Microbiol. 71, 1671–1673. https://doi.org/10.1128/AEM.71.3.1671-1673.2005 (2005).
Pratscher, J., Dumont, M. G. & Conrad, R. Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade. Environ. Microbiol. 13, 2692–2701. https://doi.org/10.1111/j.1462-2920.2011.02537.x (2011).
Cai, Y., Zhou, X., Shi, L. & Jia, Z. Atmospheric methane oxidizers are dominated by upland soil cluster alpha in 20 forest soils of China. Microb. Ecol. 80, 859–871. https://doi.org/10.1007/s00248-020-01570-1 (2020).
Täumer, J. et al. Divergent drivers of the microbial methane sink in temperate forest and grassland soils. Glob. Change Biol. https://doi.org/10.1111/gcb.15430 (2020).
Andreote, F. D. et al. Culture-independent assessment of Rhizobiales-related alphaproteobacteria and the diversity of Methylobacterium in the rhizosphere and rhizoplane of transgenic eucalyptus. Microb. Ecol. 57, 82–93. https://doi.org/10.1007/s00248-008-9405-8 (2009).
Iguchi, H., Yurimoto, H. & Sakai, Y. Interactions of methylotrophs with plants and other heterotrophic bacteria. Microorganisms 3, 137–151. https://doi.org/10.3390/microorganisms3020137 (2015).
Ho, A. et al. Biotic interactions in microbial communities as modulators of biogeochemical processes: methanotrophy as a model system. Front. Microbiol. 7, 1285. https://doi.org/10.3389/fmicb.2016.01285 (2016).
Iguchi, H., Yurimoto, H. & Sakai, Y. Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. Appl. Environ. Microbiol. 77, 8509–8515. https://doi.org/10.1128/AEM.05834-11 (2011).
Veraart, A. J. et al. Living apart together—bacterial volatiles influence methanotrophic growth and activity. ISME J. 12, 1163–1166 (2018).
Karlsson, A. E., Johansson, T. & Bengtson, P. Archaeal abundance in relation to root and fungal exudation rates. FEMS Microbiol. Ecol. 80, 305–311 (2012).
Haichar, F. E. Z. et al. Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2, 1221–1230. https://doi.org/10.1038/ismej.2008.80 (2008).
Tkacz, A., Cheema, J., Chandra, G., Grant, A. & Poole, P. S. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J. 9, 2349–2359. https://doi.org/10.1038/ismej.2015.41 (2015).
Schinner, F. et al. (eds) Methods in Soil Biology (Springer, Berlin, 1996).
Barillot, C. D. C., Sarde, C.-O., Bert, V., Tarnaud, E. & Cochet, N. A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system. Ann. Microbiol. 63, 471–476 (2013).
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Nat. Acad. Sci. U.S.A. 108(Suppl 1), 4516–4522. https://doi.org/10.1073/pnas.1000080107 (2011).
Ihrmark, K. et al. New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol. Ecol. 82, 666–677. https://doi.org/10.1111/j.1574-6941.2012.01437.x (2012).
White, T. J., Bruns, T., Lee, S. & Taylor, J. W. Amplification and direct sequencing of fungal ribosomal RNA Genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications (eds Innis, M. A. et al.) 315–322 (Academic Press, Cambridge, 1990).
Schloss, P. D. et al. Introducing mothur. Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 25, 914–919. https://doi.org/10.1111/2041-210X.12073 (2013).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mah, F. VSEARCH. A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596. https://doi.org/10.1093/nar/gks1219 (2013).
Kõljalg, U. et al. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22, 5271–5277. https://doi.org/10.1111/mec.12481 (2013).
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267. https://doi.org/10.1128/AEM.00062-07 (2007).
Mantel, N. The detection of disease clustering and a generalized regression approach. Can. Res. 27, 209–220 (1967).
Martin, A. P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68, 3673–3682. https://doi.org/10.1128/AEM.68.8.3673-3682.2002 (2002).
Clarke, K. R. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18, 117–143 (1993).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2017). http://www.R-project.org. Accessed 24 Sept 2018.
Oksanen, J. et al. vegan. Community Ecology Package. R package version 2.4–4 (2017). https://CRAN.R-project.org/package=vegan. Accessed 24 Sept 2018.
Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44, W3–W10. https://doi.org/10.1093/nar/gkw343 (2016).
Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16SrRNA marker gene sequences. Nat. Biotechnol. 31, 814–821 (2013).
White, J. R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput. Biol. 5, e1000352. https://doi.org/10.1371/journal.pcbi.1000352 (2009).
Parks, D. H., Tyson, G. W., Hugenholtz, P. & Beiko, R. G. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30, 3123–3124. https://doi.org/10.1093/bioinformatics/btu494 (2014).
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109–D114. https://doi.org/10.1093/nar/gkr988 (2012).
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504. https://doi.org/10.1101/gr.1239303 (2003).
Pratscher, J., Vollmers, J., Wiegand, S., Dumont, M. G. & Kaster, A.-K. Unravelling the identity, metabolic potential and global biogeography of the atmospheric methane-oxidizing upland soil cluster α. Environ. Microbiol. 20, 1016–1029. https://doi.org/10.1111/1462-2920.14036 (2018).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780. https://doi.org/10.1093/molbev/mst010 (2013).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321. https://doi.org/10.1093/sysbio/syq010 (2010).
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