Publications using SIP in Ecology


Nweze JE, S Gupta, MM Salcher, V Šustr, T Horváthová, R Angel. 2024.
Cellulose fermentation by the gut microbiota is likely not essential for the nutrition of millipedes.

Poulsen JS, WV Macêdo, T Bonde, JL Nielsen. 2023.
Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics.
Biotechnology for Biofuels and Bioproducts 16: 183.

Hartmann M, C Herzog, I Brunner, B Stierli, F Meyer, N Buchmann, B Frey. 2023.
Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition.
Frontiers in Microbiology 14: 1267270.

Bonin P, A Portas, J Hardy, S Guasco, TS Bianchi, ND Ward, JF Rontani. 2023.
Biological mechanisms underlying priming of vascular plant material in the presence of diatoms.
Aquatic Microbial Ecology 89: 99-117.

Štursová M, R López-Mondéjar, P Baldrian. 2023.
Investigating the bacterial and fungal communities involved in dead biomass degradation in forest soils.
In: Martin F, S Uroz, eds. Methods in Molecular Biology, Microbial Environmental Genomics (MEG). Volume 2605: 157-168. Springer, NY.

Fu Y, Y Luo, C Tang, Y Li, G Guggenberger, J Xu. 2022.
Microbial utilization of simple and complex carbon compounds in a temperate forest soil.
Soil Biology and Biochemistry 173: 108785.

Martinović T, T Mašínová, R López-Mondéjar, J Jansa, M Štursová, R Starke, P Baldrian. 2022.
Microbial utilization of simple and complex carbon compounds in a temperate forest soil.
Soil Biology and Biochemistry 173: 108786.

Miao Y, Y Lin, Z Chen, H Zheng, Y Niu, Y Kuzyakov, D Liu, W Ding. 2022.
Fungal key players of cellulose utilization: Microbial networks in aggregates of long-term fertilized soils disentangled using 13C-DNA-stable isotope probing.
Science of the Total Environment 832: 155051.

Poulsen JS, N de Jonge, WV Macêdo, FR Dalby, A Feilberg, JL Nielsen. 2022.
Characterisation of cellulose-degrading organisms in an anaerobic digester.
Bioresource Technology 351: 126933.

Dang C, JGV Walkup, BA Hungate, RB Franklin, E Schwartz, EM Morrissey. 2022.
Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria.
Environmental Microbiology 24: 357–369.

Raczka NC. 2021.
Mycorrhizal type dictates soil microbial diversity and function and the integrated root-microbial response to water stress in temperate forests.
PhD Thesis. West Virginia University.

Raczka N, J Piñeiro, MM Tfaily, MS Lipton, RK Chu, L Pasa-Tolic, E Morrissey, E Brzostek. 2021.
Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil.
NATURE – Scientific Reports 11: 19320.

López-Mondéjar R, V Tlăskál, T Vĕtrovský, M Štursová, R Toscan, U Nunes da Rocha, P Baldrian. 2020.
Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil.
Soil Biology and Biochemistry 148: 107875.

Yu J, MJ Pavia, LM Deem, SE Crow, JL Deenik, CR Penton. 2020.
DNA-Stable isotope probing shotgun metagenomics reveals the resilience of active microbial communities to biochar amendment in oxisol soil.
Frontiers in Microbiology 11: 587972.

Ogata EM. 2020.
Anthropogenic influences on bacterial assemblages in stream anthropogenic influences on bacterial assemblages in stream biofilms.
PhD Thesis. Utah State University.

Yu J. 2020.
Characterization of tropical agricultural soil microbiomes after biochar amendment.
PhD Thesis. Arizona State University.

Shridar B. 2020.
Microbes in the limelight: liming alters microbial communities, reducing decomposition in northern hardwood forest soils.
PhD Thesis. Cornell University.

Vieira S, J Sikorski, A Gebala, RS Boeddinghaus, S Marhan, T Rennert, E Kandeler, J Overmann. 2020.
Bacterial colonization of minerals in grassland soils is selective and highly dynamic.
Environmental Microbiology 22: 917–933.

Liles MR, Kloepper J. 2020.
Use of pectin or pectin-related saccharides to enhance efficacy of plant growth-promoting rhizobacteria (pgpr) strains for promoting growth and health in plants and animals.
United States Patent Application 20200009200 A1.

Koechli C, AN Campbell, C Pepe-Ranney, DH Buckley. 2019.
Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing.
Soil Biology and Biochemistry 130: 150-158.

Lemmel F. 2019.
Diversités taxonomique et fonctionnelle des communautés microbiennes en lien avec le cycle du carbone dans un gradient de sols multi-contaminés.
PhD Thesis. Université de Lorraine.

Siles JA, T Cajthaml, J Frouz, R Margesin. 2019.
Assessment of soil microbial communities involved in cellulose utilization at two contrasting Alpine forest sites.
Soil Biology and Biochemistry 129: 13-16.

Li Z, Q Yao, X Guo, A Crits-Christoph, MA Mayes, W Judson Hervey IV, SL Lebeis, JF Banfield, GB Hurst, RL Hettich, C Pan. 2019.
Genome-resolved proteomic Stable Isotope Probing of soil microbial communities using 13CO2 and 13C-methanol.
Frontiers in Microbiology 10: 2706.

Wieczorek AS, O Schmidt, A Chatzinotas, M von Bergen, A Gorissen, S Kolb. 2019.
Ecological functions of agricultural soil bacteria and microeukaryotes in chitin degradation – a case study.
Frontiers in Microbiology 10: 1293.

Taubert M, J Stähly, S Kolb, K Küsel. 2019.
Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation.
PLoS ONE 14: e0212937.

Kaplan H, S Ratering, P Felix-Henningsen, S Schnell. 2019.
Stability of in situ immobilization of trace metals with different amendments revealed by microbial 13C-labelled wheat root decomposition and efflux-mediated metal resistance of soil bacteria.
Science of The Total Environment  659: 1082-1089.

Maarastawi SA, Frindte K, Geer R, Kröber E, Knief C. 2018.
Temporal dynamics and compartment specific rice straw degradation in bulk soil and the rhizosphere of maize.
Soil Biology and Biochemistry 127: 200-212.

Wieczorek A. 2018.
Trophic interactions of a chitin-degrading microbiome of an aerated agricultural soil.
PhD Thesis. University of Bayreuth.

López-Mondéjar R, V Brabcová, M Štursová, A Davidová, J Jansa, T Cajthaml, P Baldrian. 2018.
Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling.
NATURE – The ISME Journal 12: 1768–1778.

Alonso-Pernas P, S Bartram, EM Arias-Cordero, AL Novoselov, L Halty-deLeon, Y Shao, W Boland. 2017.
In vivo isotopic labeling of symbiotic bacteria involved in cellulose degradation and nitrogen recycling within the gut of the forest cockchafer (Melolontha hippocastani).
Frontiers in Microbiology 10: 1970.

Herzog CP. 2017.
Growth and decay of Scots pine roots.
PhD Thesis. ETH Zürich.

Wilhelm RC, E Cardenas, H Leung, K Maas, M Hartmann, A Hahn, S Hallam, WW Mohn. 2017.
Data Descriptor: A metagenomics survey of forest soil microbial communities more than a decade after timber harvesting.
NATURE Scientific Data 4: 170092.

Cheng L, N Zhang, M Yuan, J Xiao, Y Qin, Y Deng, Q Tu, K Xue, JD Van Nostrand, L Wu, Z He, X Zhou, MB Leigh, KT Konstantinidis, EAG Schuur, Y Luo, JM Tiedje, J Zhou. 2017.
Warming enhances old organic carbon decomposition through altering functional microbial communities.
NATURE – The ISME Journal 11: 18251835.

Kramer S, D Dibbern, J Moll, M Huenninghaus, R Koller, D Krueger, S Marhan, T Urich, T Wubet, M Bonkowski, F Buscot, T Lueders, E Kandeler. 2016.
Resource partitioning between bacteria, fungi and protists in the detritusphere of an agricultural soil.
Frontiers in Microbiology 7: 1524.

Rime T, M Hartmann, B Stierli, AM Anesio, B Frey. 2016.
Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields.
Soil Biology and Biochemistry 98: 30-41.

Vetrovský T, M Štursová, P Baldrian. 2016.
Fungal communities in soils: Soil organic matter degradation.
Methods in Molecular Biology (Microbial Environmental Genomics (MEG)) 1399: 89-100.

Leung HTC, KR Maas, RC Wilhelm, WW Mohn. 2016.
Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils.
NATURE – The ISME Journal 10: 363-375.

Torres Bocero IF. 2015.
Dynamics of carbon in degraded semiarid soils: effects of organic amendments and associated soil microbial communities.
PhD Thesis. University of Murcia.

Dibbern D. 2014.
Key prokaryotic populations contributing to carbon flow in an agricultural soil food web.
PhD Thesis. Technical University München.

Darjany LE, CR Whitcraft, JG Dillon. 2014.
Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing.
Frontiers in Microbiology 5: 263.

Schmidt O, MA Horn, S Kolb, HL Drake. 2014.
Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil.
Environmental Microbiology 17: 720-734.

Strasser F. 2014.
Investigating complex carbon degradation in a beech forest soil and first insights into the application of single-cell methods to detect active microorganisms in soil systems.
MsC Thesis. University of Vienna.

Leung H. 2014.
Long-term effects of timber harvesting on cellulolytic microbial communities in North American coniferous forest soils.
MsC Thesis. University of British Columbia.

Torres IF, F Bastida, T Hernández, P Bombach, HH Richnow, C García. 2014.
The role of lignin and cellulose in the carbon-cycling of degraded soils under semiarid climate and their relation to microbial biomass.
Soil Biology and Biochemistry 75: 152-160.

Chatzinotas A, S Schellenberger, K Glaser, S Kolb. 2013.
Assimilation of Cellulose-Derived Carbon by Microeukaryotes in Oxic and Anoxic Slurries of an Aerated Soil.
Applied and Environmental Microbiology 79: 5777-5781.

Semenov AV, MC Pereira e Silva, A Szturc-Koetsier, H Schmitt, J Falcão Salles, JD van Elsas. 2012.
Impact of incorporated fresh 13C potato tissues on the bacterial and fungal community composition of soil.
Soil Biology and Biochemistry 49: 88-95.

Štursová M, L Žifčáková, MB Leigh, R Burgess, P Baldrian. 2012.
Cellulose utilisation in forest litter and soil: identification of bacterial and fungal decomposers.
FEMS Microbiology Ecology 80: 735-746.

Kiers TE, M Duhamel, Y Beesetty, JA Mensah, O Franken, E Verbruggen, CR Fellbaum, GA Kowalchuk, MM Hart, A Bago, TM Palmer, SA West, P Vandenkoornhuyse, J Jansa, H Bücking. 2011. (see Applications)
Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis.
SCIENCE 333: 880-882.

Taylor DL, IC Herriott, KE Stone, JW McFarland, MG Booth, MB Leigh. 2010.
Structure and resilience of fungal communities in Alaskan boreal forest soils.
Canadian Journal of Forest Research 40: 1288–1301.

Bastias BA, IA Anderson, J Ignacio-Castro, PI Parkin, JI Prosser, JWG Cairney. 2009.
Influence of repeated prescribed burning on incorporation of 13C from cellulose by forest soil fungi as determined by RNA stable isotope probing. (see Applications)
Soil Biology and Biochemistry 41: 467-472.