Articles | Volume 8, issue 1
https://doi.org/10.5194/soil-8-163-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-8-163-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| 
11 Mar 2022
Original research article |
| 11 Mar 2022
| 11 Mar 2022
Pairing litter decomposition with microbial community structures using the Tea Bag Index (TBI)
Anne Daebeler
CORRESPONDING AUTHOR
Soil & Water Research Infrastructure (SoWa), Biology Centre CAS,
České Budějovice, Czechia
Centre for Microbiology and Environmental
Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
Eva Petrová
Soil & Water Research Infrastructure (SoWa), Biology Centre CAS,
České Budějovice, Czechia
Elena Kinz
Open Science – Life Sciences in Dialogue, Vienna, Austria
Susanne Grausenburger
Federal College for Viticulture and Fruit Growing, Klosterneuburg,
Austria
Helene Berthold
Institute for Seed and Propagating Material, Phytosanitary Service and
Apiculture, Department for Seed Testing, Austrian Agency for Health and Food
Safety (AGES), Vienna, Austria
Taru Sandén
Institute for Sustainable Plant Production, Department for Soil Health
and Plant Nutrition, Austrian Agency for Health and Food Safety (AGES),
Vienna, Austria
Soil & Water Research Infrastructure (SoWa), Biology Centre CAS,
České Budějovice, Czechia
Institute of Soil Biology, Biology Centre CAS, České
Budějovice, Czechia
A full list of authors appears at the end of the paper.
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Studies on how microbes use C in soils typically assume oxic conditions but often overlook anaerobic processes and extracellular metabolite release. We examined how O2 and Fe content affect C mineralisation in forest soils by tracking 13C flow into biomass, CO2, metabolites, and active microbes under oxic and anoxic conditions. Results showed that anoxic conditions preserved C longer, especially in high-Fe soils. We conclude that microbial exudates play a role in anoxic C stabilisation.
Julia Fohrafellner, Maximilian Lippl, Armin Bajraktarevic, Andreas Baumgarten, Heide Spiegel, Robert Körner, and Taru Sandén
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2025-426, https://doi.org/10.5194/essd-2025-426, 2025
Preprint under review for ESSD
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The first openly accessible Austrian near-infrared (NIR) Soil Spectral Library was developed, including over 2100 samples covering all Austrian environmental zones. The prediction of soil properties via partial least square regression showed potential, but the accuracy was insufficient compared to routine laboratory analyses. We encourage using the open Library as a foundation for further spectral analysis and modelling and we support future soil health assessments via spectroscopy.
Jörg Schnecker, Theresa Böckle, Julia Horak, Victoria Martin, Taru Sandén, and Heide Spiegel
SOIL, 10, 521–531, https://doi.org/10.5194/soil-10-521-2024, https://doi.org/10.5194/soil-10-521-2024, 2024
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Microbial processes are driving the formation and decomposition of soil organic matter. In contrast to respiration and growth, microbial death rates currently lack distinct methods to be determined. Here, we propose a new approach to measure microbial death rates. This new approach to determine microbial death rates as well as dynamics of intracellular and extracellular DNA separately will help to improve concepts and models of C dynamics in soils in the future.
Maria Regina Gmach, Martin Anders Bolinder, Lorenzo Menichetti, Thomas Kätterer, Heide Spiegel, Olle Åkesson, Jürgen Kurt Friedel, Andreas Surböck, Agnes Schweinzer, and Taru Sandén
SOIL, 10, 407–423, https://doi.org/10.5194/soil-10-407-2024, https://doi.org/10.5194/soil-10-407-2024, 2024
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We evaluated the effect of soil management practices on decomposition at 29 sites (13 in Sweden and 16 in Austria) using long-term field experiments with the Tea Bag Index (TBI) approach. We found that the decomposition rate (k) and stabilization factor (S) were mainly governed by climatic conditions. In general, organic and mineral fertilization increased k and S, and reduced tillage increased S. Edaphic factors also affected k and S.
Talia Gabay, Eva Petrova, Osnat Gillor, Yaron Ziv, and Roey Angel
SOIL, 9, 231–242, https://doi.org/10.5194/soil-9-231-2023, https://doi.org/10.5194/soil-9-231-2023, 2023
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This paper evaluates bacterial growth in biocrusts after a large-scale mining disturbance in a hyperarid desert, using a stable isotope probing assay.
We discovered that biocrust bacteria from both natural and post-mining plots resumed photosynthetic activity but did not grow following hydration. Our paper provides insights into the effects of a large-scale disturbance (mining) on biocrusts and their response to hydration, with implications for biocrust restoration practices in Zin mines.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
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Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Cited articles
Albright, M. B. N. and Martiny, J. B. H.: Dispersal alters bacterial diversity and
composition in a natural community, ISME J., 12, 296–299,
https://doi.org/10.1038/ismej.2017.161, 2018.
Albright, M. B. N., Chase, A. B., and Martiny, J. B. H.: Experimental
Evidence that Stochasticity Contributes to Bacterial Composition and
Functioning in a Decomposer Community, mBio, 10, e00568-19, https://doi.org/10.1128/mBio.00568-19, 2019.
Aleklett, K., Ohlsson, P., Bengtsson, M., and Hammer, E. C.: Fungal foraging
behaviour and hyphal space exploration in micro-structured Soil Chips,
ISME J., 15, 1782–1793, https://doi.org/10.1038/s41396-020-00886-7, 2021.
Allison, S. D., Wallenstein, M. D., and Bradford, M. A.: Soil-carbon response
to warming dependent on microbial physiology, Nat. Geosci., 3,
336–340, https://doi.org/10.1038/ngeo846, 2010.
Allison, S. D., Lu, Y., Weihe, C., Goulden, M. L., Martiny, A. C., Treseder,
K. K., and Martiny, J. B. H.: Microbial abundance and composition influence
litter decomposition response to environmental change, Ecology, 94,
714–725, https://doi.org/10.1890/12-1243.1, 2013.
Aneja, M. K., Sharma, S., Fleischmann, F., Stich, S., Heller, W., Bahnweg,
G., Munch, J. C., and Schloter, M.: Microbial Colonization of Beech and
Spruce LitterInfluence of Decomposition Site and Plant Litter Species on the
Diversity of Microbial Community, Microb. Ecol., 52, 127–135,
https://doi.org/10.1007/s00248-006-9006-3, 2006.
Angel, R.: General Bacteria and Archaea 16S-rRNA (515Fmod-806Rmod) for
Illumina Amplicon Sequencing V.4, protocols.io [data set], https://doi.org/10.17504/protocols.io.bsxanfie,
2021.
Angel, R.: roey-angel/TeaTime4Schools: First release – EGU SOIL (V1.0), Zenodo [code], https://doi.org/10.5281/zenodo.6340082, 2022.
Bailey, V. L., Fansler, S. J., Stegen, J. C., and McCue, L. A.: Linking
microbial community structure to β-glucosidic function in soil
aggregates, ISME J, 7, 2044–2053, 2013.
Benjamini, Y. and Hochberg, Y.: Controlling the False Discovery Rate: A
Practical and Powerful Approach to Multiple Testing, J. Roy.
Stat. Soc. B, 57, 289–300,
https://doi.org/10.1111/j.2517-6161.1995.tb02031.x, 1995.
Boddy, L.: Interspecific combative interactions between wood-decaying
basidiomycetes, FEMS Microbiol. Ecol., 31, 185–194,
https://doi.org/10.1111/j.1574-6941.2000.tb00683.x, 2000.
Bray, S. R., Kitajima, K., and Mack, M. C.: Temporal dynamics of microbial
communities on decomposing leaf litter of 10 plant species in relation to
decomposition rate, Soil Biol. Biochem., 49, 30–37,
https://doi.org/10.1016/j.soilbio.2012.02.009, 2012.
Buchholz, J., Querner, P., Paredes, D., Bauer, T., Strauss, P., Guernion,
M., Scimia, J., Cluzeau, D., Burel, F., Kratschmer, S., Winter, S.,
Potthoff, M., and Zaller, J. G.: Soil biota in vineyards are more influenced
by plants and soil quality than by tillage intensity or the surrounding
landscape, Sci. Rep.-UK, 7, 17445, https://doi.org/10.1038/s41598-017-17601-w, 2017.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J.
A., and Holmes, S. P.: DADA2: High-resolution sample inference from Illumina
amplicon data, Nat. Meth., 13, 581–583, https://doi.org/10.1038/nmeth.3869,
2016.
Chen, T., Nomura, K., Wang, X., Sohrabi, R., Xu, J., Yao, L., Paasch, B. C.,
Ma, L., Kremer, J., Cheng, Y., Zhang, L., Wang, N., Wang, E., Xin, X.-F., and
He, S. Y.: A plant genetic network for preventing dysbiosis in the
phyllosphere, Nature, 580, 653–657, https://doi.org/10.1038/s41586-020-2185-0,
2020.
Cotrufo, M. F., Wallenstein, M. D., Boot, C. M., Denef, K., and Paul, E.: The
Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant
litter decomposition with soil organic matter stabilization: do labile plant
inputs form stable soil organic matter?, Glob. Change Biol., 19,
988–995, https://doi.org/10.1111/gcb.12113, 2013.
Daebeler, A., Bodelier, P. L. E., Yan, Z., Hefting, M. M., Jia, Z., and
Laanbroek, H. J.: Interactions between Thaumarchaea Nitrospira and
methanotrophs modulate autotrophic nitrification in volcanic grassland soil,
ISME J., 8, 2397–2410, https://doi.org/10.1038/ismej.2014.81, 2014.
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., and Callahan, B. J.: Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data, Microbiome, 6, 226, https://doi.org/10.1186/s40168-018-0605-2, 2018.
de Boer, W. and van der Wal, A.: Chapter 8 Interactions between saprotrophic basidiomycetes and bacteria, in: British Mycological Society Symposia Series, Vol. 28, edited by: Boddy, L., Frankland, J. C., and van West, P., Academic Press, 143–153, https://doi.org/10.1016/S0275-0287(08)80010-0, 2008.
de Boer, W., Folman, L. B., Summerbell, R. C., and Boddy, L.: Living in a
fungal world: impact of fungi on soil bacterial niche development, FEMS
Microbiol. Rev., 29, 795–811, https://doi.org/10.1016/j.femsre.2004.11.005,
2005.
du Plessis, L., Rose, S. H., and van Zyl, W. H.: Exploring improved
endoglucanase expression in Saccharomyces cerevisiae strains, Appl.
Microbiol. Biot., 86, 1503–1511,
https://doi.org/10.1007/s00253-009-2403-z, 2009.
Elumeeva, T. G., Onipchenko, V. G., Akhmetzhanova, A. A., Makarov, M. I., and
Keuskamp, J. A.: Stabilization versus decomposition in alpine ecosystems of
the Northwestern Caucasus: The results of a tea bag burial experiment,
J. Mt. Sci., 15, 1633–1641,
https://doi.org/10.1007/s11629-018-4960-z, 2018.
Falkowski, P. G., Fenchel, T., and Delong, E. F.: The Microbial Engines That
Drive Earths Biogeochemical Cycles, Science, 320, 1034–1039,
https://doi.org/10.1126/science.1153213, 2008.
Faust, K. and Raes, J.: Microbial interactions: from networks to models,
Nat. Rev. Microbiol., 10, 538–550, https://doi.org/10.1038/nrmicro2832, 2012.
Fernandes, A. D., Macklaim, J. M., Linn, T. G., Reid, G., and Gloor, G. B.:
ANOVA-like differential expression (ALDEx) analysis for mixed population
RNA-Seq, PLoS One, 8, e67019, https://doi.org/10.1371/journal.pone.0067019, 2013.
Freschet, G. T., Weedon, J. T., Aerts, R., van Hal, J. R., and Cornelissen,
J. H. C.: Interspecific differences in wood decay rates: insights from a new
short-term method to study long-term wood decomposition, J. Ecol.,
100, 161–170, https://doi.org/10.1111/j.1365-2745.2011.01896.x, 2011.
Garbeva, P., Hordijk, C., Gerards, S., and de Boer, W.: Volatile-mediated
interactions between phylogenetically different soil bacteria, Front.
Microbiol., 5, 289, https://doi.org/10.3389/fmicb.2014.00289, 2014.
Gardes, M. and Bruns, T. D.: ITS primers with enhanced specificity for
basidiomycetes–application to the identification of mycorrhizae and rusts,
Mol. Ecol., 2, 113–118, 1993.
Glassman, S. I., Weihe, C., Li, J., Albright, M. B. N., Looby, C. I.,
Martiny, A. C., Treseder, K. K., Allison, S. D., and Martiny, J. B. H.:
Decomposition responses to climate depend on microbial community
composition, P. Natl. Acad. Sci. USA, 115,
11994–11999, https://doi.org/10.1073/pnas.1811269115, 2018.
Graham, E. B., Knelman, J. E., Schindlbacher, A., Siciliano, S., Breulmann,
M., Yannarell, A., Beman, J. M., Abell, G., Philippot, L., Prosser, J.,
Foulquier, A., Yuste, J. C., Glanville, H. C., Jones, D. L., Angel, R.,
Salminen, J., Newton, R. J., Bürgmann, H., Ingram, L. J., Hamer, U.,
Siljanen, H. M. P., Peltoniemi, K., Potthast, K., Bañeras, L., Hartmann,
M., Banerjee, S., Yu, R.-Q., Nogaro, G., Richter, A., Koranda, M., Castle,
S. C., Goberna, M., Song, B., Chatterjee, A., Nunes, O. C., Lopes, A. R.,
Cao, Y., Kaisermann, A., Hallin, S., Strickland, M. S., Garcia-Pausas, J.,
Barba, J., Kang, H., Isobe, K., Papaspyrou, S., Pastorelli, R., Lagomarsino,
A., Lindström, E. S., Basiliko, N., and Nemergut, D. R.: Microbes as
Engines of Ecosystem Function: When Does Community Structure Enhance
Predictions of Ecosystem Processes?, Front. Microbiol., 7, 214,
https://doi.org/10.3389/fmicb.2016.00214, 2016.
Guo, T., Zhang, Q., Ai, C., Liang, G., He, P., Lei, Q., and Zhou, W.:
Analysis of microbial utilization of rice straw in paddy soil using a
DNA-SIP approach, Soil Sci. Soc. Am. J., 84, 99–114,
https://doi.org/10.1002/saj2.20019, 2020.
Ho, A., Angel, R., Veraart, A. J., Daebeler, A., Jia, Z., Kim, S. Y.,
Kerckhof, F.-M., Boon, N., and Bodelier, P. L. E.: 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.
Hoppe, B., Purahong, W., Wubet, T., Kahl, T., Bauhus, J., Arnstadt, T.,
Hofrichter, M., Buscot, F., and Krüger, D.: Linking molecular
deadwood-inhabiting fungal diversity and community dynamics to ecosystem
functions and processes in Central European forests, Fungal Divers.,
77, 367–379, https://doi.org/10.1007/s13225-015-0341-x, 2015.
Horn, H. S.: Measurement of Overlap in Comparative Ecological Studies,
Am. Nat., 100, 419–424, https://doi.org/10.1086/282436, 1966.
Jackson, C. A., Couger, M. B., Prabhakaran, M., Ramachandriya, K. D.,
Canaan, P., and Fathepure, B. Z.: Isolation and characterization
ofRhizobiumsp. strain YS-1r that degrades lignin in plant biomass, J. Appl. Microbiol., 122, 940–952, https://doi.org/10.1111/jam.13401, 2017.
Jiménez, D. J., Korenblum, E., and van Elsas, J. D.: Novel multispecies
microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural
bioconversion, Appl. Microbiol. Biot., 98, 2789–2803,
https://doi.org/10.1007/s00253-013-5253-7, 2013.
Jiménez, D. J., Dini-Andreote, F., and van Elsas, J.: Metataxonomic
profiling and prediction of functional behaviour of wheat straw degrading
microbial consortia, Biotechnol. Biofuels, 7, 92,
https://doi.org/10.1186/1754-6834-7-92, 2014.
Kandeler, E.: Bestimmung der N-Mineralisation im anaeroben
Brutversuch, in: Bodenbiologische Arbeitsmethoden, 2nd Edn., 160–161, edited by: Schinner, F., Öhlinger, R., Kandeler, E., and Margesin, R., Springer Verlag,
Berling, Heidelberg, Germany, 1993.
Keeney, D. R.: Nitrogen availability indices, in: Methods of Soil Analysis. Part II, 2nd
Edn., edited by: Page, A. L.,
Millet, R. H., and Keeney, D. R., Agronomy Monograph No. 9, 711–730, American
Society of Agronomy, Madison, USA, 1982.
Keuskamp, J. A., Dingemans, B. J. J., Lehtinen, T., Sarneel, J. M., and
Hefting, M. M.: Tea Bag Index: a novel approach to collect uniform
decomposition data across ecosystems, Meth.
Ecol. Evol., 4, 1070–1075, https://doi.org/10.1111/2041-210x.12097, 2013.
Kirschbaum, M. U. F.: The temperature dependence of soil organic matter
decomposition and the effect of global warming on soil organic C storage,
Soil Biol. Biochem., 27, 753–760,
https://doi.org/10.1016/0038-0717(94)00242-s, 1995.
Knorr, K., Jørgensen, L. N., and Nicolaisen, M.: Fungicides have complex
effects on the wheat phyllosphere mycobiome, PLOS
ONE, 14, e0213176, https://doi.org/10.1371/journal.pone.0213176, 2019.
Koga, S., Ogawa, J., Choi, Y.-M., and Shimizu, S.: Novel bacterial peroxidase
without catalase activity from Flavobacterium meningosepticum: purification
and characterization, Biochim. Biophys. Acta, 1435, 117–126,
https://doi.org/10.1016/s0167-4838(99)00190-9, 1999.
Lennon, J. T. and Jones, S. E.: Microbial seed banks: the ecological and
evolutionary implications of dormancy, Nat. Rev. Microbiol., 9, 119–130, 2011.
Lenth, R. V.: emmeans: Estimated Marginal Means, aka Least-Squares Means, https://CRAN.R-project.org/package=emmeans (last access: 9 March 2022), 2021.
Liang, C., Schimel, J. P., and Jastrow, J. D.: The importance of anabolism in
microbial control over soil carbon storage, Nat. Microbiol., 2, 17105,
https://doi.org/10.1038/nmicrobiol.2017.105, 2017.
López, M. J., Nichols, N. N., Dien, B. S., Moreno, J., and Bothast, R.
J.: Isolation of microorganisms for biological detoxification of
lignocellulosic hydrolysates, Appl. Microbiol. Biotechnol., 64,
125–131, https://doi.org/10.1007/s00253-003-1401-9, 2004.
Lynd, L. R., Weimer, P. J., van, Z. W. H., and Pretorius, I. S.: Microbial
cellulose utilization: fundamentals and biotechnology, Microbiol. Mol. Biol.
Rev., 66, 506–577, 2002.
Maron, P.-A., Sarr, A., Kaisermann, A., Lévêque, J., Mathieu, O., Guigue, J., Karimi, B., Bernard, L., Dequiedt, S., Terrat, S., Chabbi, A., and Ranjard, L.: High microbial diversity promotes soil ecosystem functioning, Appl. Environ. Microb., 84, e02738-17, https://doi.org/10.1128/AEM.02738-17, 2018.
Martin, M.: Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, 17, 10–12, https://doi.org/10.14806/ej.17.1.200, 2011.
Martinez, D., Berka, R. M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S. E., Chapman, J., Chertkov, O., Coutinho, P. M., Cullen, D., Danchin, E. G. J., Grigoriev, I. V., Harris, P., Jackson, M., Kubicek, C. P., Han, C. S., Ho, I., Larrondo, L. F., de Leon, A. L., Magnuson, J. K., Merino, S., Misra, M., Nelson, B., Putnam, N., Robbertse, B., Salamov, A. A., Schmoll, M., Terry, A., Thayer, N., Westerholm-Parvinen, A., Schoch, C. L., Yao, J., Barabote, R., Barbote, R., Nelson, M. A., Detter, C., Bruce, D., Kuske, C. R., Xie, G., Richardson, P., Rokhsar, D. S., Lucas, S. M., Rubin, E. M., Dunn-Coleman, N., Ward, M., and Brettin, T. S.: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nat. Biotechnol., 26, 553–560, https://doi.org/10.1038/nbt1403, 2008.
Mathieu, Y., Gelhaye, E., Dumarçay, S., Gérardin, P., Harvengt, L.,
and Buée, M.: Selection and validation of enzymatic activities as
functional markers in wood biotechnology and fungal ecology, J.
Microbiol. Meth., 92, 157–163, https://doi.org/10.1016/j.mimet.2012.11.017,
2013.
Matsuyama, H., Katoh, H., Ohkushi, T., Satoh, A., Kawahara, K., and Yumoto,
I.: Sphingobacterium kitahiroshimense sp. nov. isolated from soil,
Int. J. Syst. Evol. Micr., 58,
1576–1579, https://doi.org/10.1099/ijs.0.65791-0, 2008.
McBride, M. J., Xie, G., Martens, E. C., Lapidus, A., Henrissat, B., Rhodes,
R. G., Goltsman, E., Wang, W., Xu, J., Hunnicutt, D. W., Staroscik, A. M.,
Hoover, T. R., Cheng, Y.-Q., and Stein, J. L.: Novel Features of the
Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as
Revealed by Genome Sequence Analysis, Appl. Environ.
Microbiol., 75, 6864–6875, https://doi.org/10.1128/aem.01495-09, 2009.
McGuire, K. L. and Treseder, K. K.: Microbial communities and their
relevance for ecosystem models: Decomposition as a case study, Soil Biol.
Biochem., 42, 529–535, https://doi.org/10.1016/j.soilbio.2009.11.016, 2010.
McMurdie, P. J. and Holmes, S.: phyloseq: An R Package for Reproducible
Interactive Analysis and Graphics of Microbiome Census Data, PLoS ONE, 8, e61217, https://doi.org/10.1371/journal.pone.0061217, 2013.
Mcardle, B. and Anderson, M.: Fitting Multivariate Models to Community Data:
A Comment on Distance-Based Redundancy Analysis, Ecology, 82, 290–297,
https://doi.org/10.1890/0012-9658(2001)082[0290:fmmtcd]2.0.co;2, 2001.
Naqib, A., Poggi, S., and Green, S. J.: Deconstructing the polymerase chain reaction II: an improved workflow and effects on artifact formation and primer degeneracy, PeerJ, 7, e7121, https://doi.org/10.7717/peerj.7121, 2019.
NCBI: Teabag microbiome – Klosterneuburg Targeted loci environmental, NCBI [data set, sample], https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA765214, last access: 9 March 2022.
Newsham, K. K., Garnett, M. H., Robinson, C. H., and Cox, F.: Discrete taxa
of saprotrophic fungi respire different ages of carbon from Antarctic soils,
Sci. Rep.-UK, 8, 7866, https://doi.org/10.1038/s41598-018-25877-9, 2018.
Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., Bengtsson-Palme, J.,
Jeppesen, T. S., Schigel, D., Kennedy, P., Picard, K., Glöckner, F. O.,
Tedersoo, L., Saar, I., Kõljalg, U., and Abarenkov, K.: The UNITE
database for molecular identification of fungi: handling dark taxa and
parallel taxonomic classifications, Nucleic Acids Research, 47,
D259–D264, https://doi.org/10.1093/nar/gky1022, 2018.
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P.,
McGlinn, D., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P.,
Stevens, M. H. H., Szoecs, E., and Wagner, H.: Vegan: Community Ecology
Package, https://CRAN.R-project.org/package=vegan (last access: 9 March 2022), 2018.
Parks, D. H., Tyson, G. W., Hugenholtz, P., and Beiko, R. G.: STAMP:
statistical analysis of taxonomic and functional profiles, Bioinformatics,
30, 3123–3124, https://doi.org/10.1093/bioinformatics/btu494, 2014.
Pioli, S., Sarneel, J., Thomas, H. J. D., Domene, X., Andrés, P.,
Hefting, M., Reitz, T., Laudon, H., Sandén, T., Piscová, V., Aurela,
M., and Brusetti, L.: Linking plant litter microbial diversity to
microhabitat conditions environmental gradients and litter mass loss:
Insights from a European study using standard litter bags, Soil Biol.
Biochem., 144, 107778, https://doi.org/10.1016/j.soilbio.2020.107778, 2020.
Prescott, C. E.: Litter decomposition: what controls it and how can we alter
it to sequester more carbon in forest soils?, Biogeochemistry, 101,
133–149, https://doi.org/10.1007/s10533-010-9439-0, 2010.
Purahong, W., Wubet, T., Lentendu, G., Schloter, M., Pecyna, M. J.,
Kapturska, D., Hofrichter, M., Krüger, D., and Buscot, F.: Life in leaf
litter: novel insights into community dynamics of bacteria and fungi during
litter decomposition, Mol. Ecol., 25, 4059–4074,
https://doi.org/10.1111/mec.13739, 2016.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,
Peplies, J., and Glöckner, F. O.: 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, 2012.
R Core Team: R: A Language and Environment for Statistical Computing,
http://www.R-project.org/ (last access: 28
June 2021), 2020.
Sandén, T., Spiegel, H., Wenng, H., Schwarz, M., and Sarneel, J. M.:
Learning Science during Teatime: Using a Citizen Science Approach to Collect
Data on Litter Decomposition in Sweden and Austria, Sustainability, 12,
7745, https://doi.org/10.3390/su12187745, 2020.
Sandén, T., Wawra, A., Berthold, H., Miloczki, J., Schweinzer, A.,
Gschmeidler, B., Spiegel, H., Debeljak, M., and Trajanov, A.:
TeaTime4Schools: Using Data Mining Techniques to Model Litter Decomposition
in Austrian Urban School Soils, Front. Ecol. Evol., 9, 703794,
https://doi.org/10.3389/fevo.2021.703794, 2021.
Sarneel, J. M., Sundqvist, M. K., Molau, U., Björkman, M. P., and
Alatalo, J. M.: Decomposition rate and stabilization across six tundra
vegetation types exposed to >20 years of warming, Sci.
Total Environ., 724, 138304,
https://doi.org/10.1016/j.scitotenv.2020.138304, 2020.
Schmidt, M. W. I., Torn, M. S., Abiven, S., Dittmar, T., Guggenberger, G.,
Janssens, I. A., Kleber, M., Kogel-Knabner, I., Lehmann, J., Manning, D. A.
C., Nannipieri, P., Rasse, D. P., Weiner, S., and Trumbore, S. E.:
Persistence of soil organic matter as an ecosystem property, Nature, 478,
49–56, 2011.
Talbot, J. M. and Treseder, K. K.: Dishing the dirt on carbon cycling,
Nat. Clim. Change, 1, 144–146, https://doi.org/10.1038/nclimate1125, 2011.
Talbot, J. M. and Treseder, K. K.: Interactions among lignin cellulose, and
nitrogen drive litter chemistrydecay relationships, Ecology, 93,
345–354, https://doi.org/10.1890/11-0843.1, 2012.
Talia, P., Sede, S. M., Campos, E., Rorig, M., Principi, D., Tosto, D.,
Hopp, H. E., Grasso, D., and Cataldi, A.: Biodiversity characterization of
cellulolytic bacteria present on native Chaco soil by comparison of
ribosomal RNA genes, Res. Microbiol., 163, 221–232,
https://doi.org/10.1016/j.resmic.2011.12.001, 2012.
MGnify: Who eats the tough stuff DNA stable isotope probing (SIP) of bacteria and fungi degrading 13C-labelled lignin and cellulose in forest soils, Sampling event dataset, GBIF.org [data set], https://doi.org/10.15468/cewp3n, 2020.
Tatzber, M., Schlatter, N., Baumgarten, A., Dersch, G., Körner, R.,
Lehtinen, T., … Spiegel, H.: KMnO4 determination of active carbon
for laboratory routines: three long-term field experiments in Austria, Soil
Res., 53, 190–204, https://doi.org/10.1071/SR14200, 2015.
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey,
K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G.,
Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y.,
González, A., Morton, J. T., Mirarab, S., Zech, X. Z., Jiang, L.,
Haroon, M. F., Kanbar, J., Zhu, Q., Jin, S. S., Kosciolek, T., Bokulich, N.
A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M.,
Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J.
A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D.,
Jansson, J. K., Gilbert, J. A., and Knight, R.: A communal catalogue reveals
Earth's multiscale microbial diversity, Nature, 551, 457–463, 2017.
Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., and Knight, R.: Improved bacterial 16S rRNA gene (v4 and v4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys, mSystems, 1, e00009-15, https://doi.org/10.1128/mSystems.00009-15, 2016.
Wang, Y., Liu, Q., Yan, L., Gao, Y., Wang, Y., and Wang, W.: A novel lignin
degradation bacterial consortium for efficient pulping, Bioresource
Technol., 139, 113–119, https://doi.org/10.1016/j.biortech.2013.04.033, 2013.
Wei, H., Ma, R., Zhang, J., Saleem, M., Liu, Z., Shan, X., Yang, J., and
Xiang, H.: Crop-litter type determines the structure and function of
litter-decomposing microbial communities under acid rain conditions, Sci. Total Environ., 713, 136600, https://doi.org/10.1016/j.scitotenv.2020.136600,
2020.
Wickham, H.: ggplot2: Elegant Graphics for Data Analysis, Springer-Verlag, New York, USA, ISBN 978-3-319-24277-4, 2016.
Wieder, W. R., Grandy, A. S., Kallenbach, C. M., and Bonan, G. B.: Integrating microbial physiology and physio-chemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, Biogeosciences, 11, 3899–3917, https://doi.org/10.5194/bg-11-3899-2014, 2014.
Wilhelm, R. C., Singh, R., Eltis, L. D., and Mohn, W. W.: Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing, ISME J., 13, 413–429, https://doi.org/10.1038/s41396-018-0279-6, 2019.
Wilpiszeski, R. L., Aufrecht, J. A., Retterer, S. T., Sullivan, M. B., Graham, D. E., Pierce, E. M., Zablocki, O. D., Palumbo, A. V., and Elias, D. A.: Soil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scales, Appl. Environ. Microb., 85, e00324-19, https://doi.org/10.1128/AEM.00324-19, 2019.
Anjos, L., Gaistardo, C., Deckers, J., Dondeyne, S., Eberhardt, E., Gerasimova, M., Harms, B., Jones, A., Krasilnikov, P., Reinsch, T., Vargas, R., and Zhang, G.: World reference base for soil resources 2014 International soil classification system for naming soils and creating legends for soil maps, 3rd ed., edited by: Schad, P., Van Huyssteen, C., and Micheli, E., FAO, Rome (Italy), ISBN 978-92-5-108369-7, 2015.
Yan, J., Wang, L., Hu, Y., Tsang, Y. F., Zhang, Y., Wu, J., Fu, X., and Sun,
Y.: Plant litter composition selects different soil microbial structures and
in turn drives different litter decomposition pattern and soil carbon
sequestration capability, Geoderma, 319, 194–203,
https://doi.org/10.1016/j.geoderma.2018.01.009, 2018.
Yuste, J. C., Peñuelas, J., Estiarte, M., Garcia-Mas, J., Mattana, S.,
Ogaya, R., Pujol, M., and Sardans, J.: Drought-resistant fungi control soil
organic matter decomposition and its response to temperature, Glob. Change
Biol., 17, 1475–1486, https://doi.org/10.1111/j.1365-2486.2010.02300.x, 2010.
Zheng, H., Yang, T., Bao, Y., He, P., Yang, K., Mei, X., Wei, Z., Xu, Y.,
Shen, Q., and Banerjee, S.: Network analysis and subsequent culturing reveal
keystone taxa involved in microbial litter decomposition dynamics, Soil
Biol. Biochem., 157, 108230, https://doi.org/10.1016/j.soilbio.2021.108230,
2021.
Short summary
In this citizen science project, we combined a standardised litter bag method (Tea Bag Index) with microbiome analysis of bacteria and fungi colonising the teabags to gain a holistic understanding of the carbon degradation dynamics in temperate European soils. Our method focuses only on the active part of the soil microbiome. The results show that about one-third of the prokaryotes and one-fifth of the fungal species (ASVs) in the soil were enriched in response to the presence of fresh OM.
In this citizen science project, we combined a standardised litter bag method (Tea Bag Index)...
