Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A (2019)
Genes 10(6): 424.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA 4.25 MB
URL
DOI
URN
urn:nbn:de:0070-pub-29359236
Autor*in
Nelkner, JohannaUniBi; Henke, ChristianUniBi; Lin, Timo Wentong; Pätzold, Wiebke; Hassa, JuliaUniBi ; Jaenicke, Sebastian; Grosch, Rita; Pühler, AlfredUniBi ; Sczyrba, AlexanderUniBi ; Schlüter, AndreasUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Computational Metagenomics
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Abstract / Bemerkung
To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe–plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant–growth–promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.
Erscheinungsjahr
2019
Zeitschriftentitel
Genes
Band
10
Ausgabe
6
Art.-Nr.
424
Urheberrecht / Lizenzen
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0)
ISSN
2073-4425
eISSN
2073-4425
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2935923

Zitieren

Nelkner J, Henke C, Lin TW, et al. Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes. 2019;10(6): 424.
Nelkner, J., Henke, C., Lin, T. W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., et al. (2019). Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes, 10(6), 424. https://doi.org/10.3390/genes10060424
Nelkner, Johanna, Henke, Christian, Lin, Timo Wentong, Pätzold, Wiebke, Hassa, Julia, Jaenicke, Sebastian, Grosch, Rita, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. 2019. “Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes”. Genes 10 (6): 424.
Nelkner, J., Henke, C., Lin, T. W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A., and Schlüter, A. (2019). Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes 10:424.
Nelkner, J., et al., 2019. Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes, 10(6): 424.
J. Nelkner, et al., “Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes”, Genes, vol. 10, 2019, : 424.
Nelkner, J., Henke, C., Lin, T.W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A., Schlüter, A.: Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes. 10, : 424 (2019).
Nelkner, Johanna, Henke, Christian, Lin, Timo Wentong, Pätzold, Wiebke, Hassa, Julia, Jaenicke, Sebastian, Grosch, Rita, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes”. Genes 10.6 (2019): 424.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):
cc_by_4_0
https://creativecommons.org/licenses/by/4.0/deed.de
https://creativecommons.org/licenses/by/4.0/legalcode.de
Volltext(e)
Name
4.25 MB
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-06-04T09:38:00Z
MD5 Prüfsumme
9e822fa8bfadb0b0871792bcb3b3eb66


Link(s) zu Volltext(en)
URL
https://doi.org/10.3390/genes10060424
Access Level
Restricted Closed Access

1 Zitation in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures.
Alves RJE, Kerou M, Zappe A, Bittner R, Abby SS, Schmidt HA, Pfeifer K, Schleper C., Front Microbiol 10(), 2019
PMID: 31379764

124 References

Daten bereitgestellt von Europe PubMed Central.

LUCAS Soil, the largest expandable soil dataset for Europe: a review
Orgiazzi A, C. Ballabio , P. Panagos , A. Jones , O. FernA¡ndeza€Ugalde ., European journal of soil science. 69(1), 2018
PMID: IND605885223
Functions of Soil for Society and the Environment
Blum W.E.H.., 2005
Agricultural intensification and ecosystem properties.
Matson PA, Parton WJ, Power AG, Swift MJ., Science 277(5325), 1997
PMID: 20662149
Global food security, biodiversity conservation and the future of agricultural intensification
Tscharntke T, Clough Y, Wanger TC, Jackson L, Motzke I, Perfecto I, Vandermeer J, Whitbread A., Biol. Conserv. 151(1), 2012
PMID: IND44727234
Biodiversity is associated with indicators of soil ecosystem functions over a landscape gradient of agricultural intensification
Culman S.W., Young-Mathews A., Hollander A.D., Ferris H., Sánchez-Moreno S., O’Geen A.T., Jackson L.E.., 2010
Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness.
Garbeva P, van Veen JA, van Elsas JD., Annu Rev Phytopathol 42(), 2004
PMID: 15283667
Microbial diversity and function in soil: from genes to ecosystems.
Torsvik V, Ovreas L., Curr. Opin. Microbiol. 5(3), 2002
PMID: 12057676
Empirical and theoretical bacterial diversity in four Arizona soils.
Dunbar J, Barns SM, Ticknor LO, Kuske CR., Appl. Environ. Microbiol. 68(6), 2002
PMID: 12039765
Comparative metagenomics of microbial communities.
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM., Science 308(5721), 2005
PMID: 15845853
Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.
Cretoiu MS, Korthals GW, Visser JH, van Elsas JD., Appl. Environ. Microbiol. 79(17), 2013
PMID: 23811512
Soil suppressiveness to fusarium disease: shifts in root microbiome associated with reduction of pathogen root colonization.
Klein E, Ofek M, Katan J, Minz D, Gamliel A., Phytopathology 103(1), 2013
PMID: 22950737
Impact of Green Manure and Vermicompost on Soil Suppressiveness, Soil Microbial Populations, and Plant Growth in Conditions of Organic Agriculture of Northern Temperate Climate
Grantina-Ievina L., Nikolajeva V., Rostoks N., Skrabule I., Zarina L., Pogulis A., Ievinsh G.., 2015
Metagenomic analysis of microbial community and function involved in cd-contaminated soil.
Feng G, Xie T, Wang X, Bai J, Tang L, Zhao H, Wei W, Wang M, Zhao Y., BMC Microbiol. 18(1), 2018
PMID: 29439665
Deciphering the rhizosphere microbiome for disease-suppressive bacteria.
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM., Science 332(6033), 2011
PMID: 21551032
Soil microbial activity and crop sustainability in a long-term experiment with three soil-tillage and two crop-rotation systems
Hungria Mariangela, Franchini JulioCezar, Brandao-Junior Osvaldino, Kaschuk Glaciela, Souza RosineiAparecida., Agric., Ecosyst. Environ., Appl. Soil Ecol. 42(3), 2009
PMID: IND44230051
Organic inputs, tillage and rotation practices influence soil health and suppressiveness to soilborne pests and pathogens of ginger
Stirling G.R., Smith M.K., Smith J.P., Stirling A.M., Hamill S.D.., 2012
Community composition and population genetics of insect pathogenic fungi in the genus Metarhizium from soils of a long-term agricultural research system.
Kepler RM, Ugine TA, Maul JE, Cavigelli MA, Rehner SA., Environ. Microbiol. 17(8), 2015
PMID: 25627647
Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla
Cederlund H, Christopher M. Jones , Ella Wessen , Jaanis Juhanson , Karin Enwall , Laurent Philippot , Mikael Pell , Sara Hallin ., Agric., Ecosyst. Environ., Appl. Soil Ecol. 84(), 2014
PMID: IND605356313
Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.
Gomez Exposito R, de Bruijn I, Postma J, Raaijmakers JM., Front Microbiol 8(), 2017
PMID: 29326674
Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules.
Banik JJ, Brady SF., Curr. Opin. Microbiol. 13(5), 2010
PMID: 20884282
Metagenomics: A guide from sampling to data analysis
Thomas T., Gilbert J., Meyer F.., 2014
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.
Scholz MB, Lo CC, Chain PS., Curr. Opin. Biotechnol. 23(1), 2011
PMID: 22154470
Metagenomics and novel gene discovery: promise and potential for novel therapeutics.
Culligan EP, Sleator RD, Marchesi JR, Hill C., Virulence 5(3), 2013
PMID: 24317337
Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.
Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, Schluter A, Schellenberg I., PLoS ONE 13(4), 2018
PMID: 29621291
Long-term effects of tillage on stratification and plant availability of phosphate and potassium in a loess chernozem
Deubel A., Hofmann B., Orzessek D.., 2011
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Flexible metagenome analysis using the MGX framework.
Jaenicke S, Albaum SP, Blumenkamp P, Linke B, Stoye J, Goesmann A., Microbiome 6(1), 2018
PMID: 29690922
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Li D, Liu CM, Luo R, Sadakane K, Lam TW., Bioinformatics 31(10), 2015
PMID: 25609793
Gene and translation initiation site prediction in metagenomic sequences.
Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC., Bioinformatics 28(17), 2012
PMID: 22796954
Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH., Nat. Methods 12(1), 2014
PMID: 25402007
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
Huson DH, Beier S, Flade I, Gorska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R., PLoS Comput. Biol. 12(6), 2016
PMID: 27327495
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
Kang DD, Froula J, Egan R, Wang Z., PeerJ 3(), 2015
PMID: 26336640
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.
Wu YW, Simmons BA, Singer SW., Bioinformatics 32(4), 2015
PMID: 26515820
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.
Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF., Nat Microbiol 3(7), 2018
PMID: 29807988
Bioinformatics for NGS-based metagenomics and the application to biogas research.
Junemann S, Kleinbolting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schluter A, Goesmann A, Sczyrba A, Stoye J., J. Biotechnol. 261(), 2017
PMID: 28823476
A proposal for a standardized bacterial taxonomy based on genome phylogeny
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P, Hugenholtz P., 2018
PMID: PPR19266
The RAST Server: rapid annotations using subsystems technology.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O., BMC Genomics 9(), 2008
PMID: 18261238
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y., Nucleic Acids Res. 46(W1), 2018
PMID: 29771380
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH., Nucleic Acids Res. 43(W1), 2015
PMID: 25948579
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.
Blin K, Kim HU, Medema MH, Weber T., Brief. Bioinformatics (), 2017
PMID: 29112695
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.
Kanehisa M, Sato Y, Morishima K., J. Mol. Biol. 428(4), 2015
PMID: 26585406
Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.
Zakrzewski M, Proietti C, Ellis JJ, Hasan S, Brion MJ, Berger B, Krause L., Bioinformatics 33(5), 2017
PMID: 28025202
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies.
Segata N, Huttenhower C., PLoS ONE 6(9), 2011
PMID: 21931822
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL., Genome Biol. 15(3), 2014
PMID: 24580807
Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments.
Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, Brown CT, Giongo A, Drew JC, Sayavedra-Soto LA, Arp DJ, Camargo FA, Daroub SH, Clark IM, McGrath SP, Hirsch PR, Triplett EW., Front Microbiol 4(), 2013
PMID: 23641242
The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica.
Ganzert L, Lipski A, Hubberten HW, Wagner D., FEMS Microbiol. Ecol. 76(3), 2011
PMID: 21314705
Embracing the unknown: disentangling the complexities of the soil microbiome.
Fierer N., Nat. Rev. Microbiol. 15(10), 2017
PMID: 28824177
Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents.
Beneduzi A, Ambrosini A, Passaglia LM., Genet. Mol. Biol. 35(4 (suppl)), 2012
PMID: 23411488
Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture.
Berg G., Appl. Microbiol. Biotechnol. 84(1), 2009
PMID: 19568745
Plant growth promoting bacteria: role in soil improvement, abiotic and biotic stress management of crops.
Majeed A, Muhammad Z, Ahmad H., Plant Cell Rep. 37(12), 2018
PMID: 30178214
Plant growth-promoting bacteria as inoculants in agricultural soils.
Souza Rd, Ambrosini A, Passaglia LM., Genet. Mol. Biol. 38(4), 2015
PMID: 26537605
Connecting microbial capabilities with the soil and plant health: Options for agricultural sustainability
Sahu P.K., Singh D.P., Prabha R., Meena K.K., Abhilash P.., 2018
A review of the effects of soil organisms on plant hormone signalling pathways
Puga-Freitas R., Blouin M.., 2015
Chernozem. From concept to classification: A review
Vysloužilová B., Ertlen D., Schwartz D., Šefrna L.., 2016
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.
Hassa J, Maus I, Off S, Puhler A, Scherer P, Klocke M, Schluter A., Appl. Microbiol. Biotechnol. 102(12), 2018
PMID: 29713790
Tackling soil diversity with the assembly of large, complex metagenomes.
Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT., Proc. Natl. Acad. Sci. U.S.A. 111(13), 2014
PMID: 24632729
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.
Lin HH, Liao YC., Sci Rep 6(), 2016
PMID: 27067514
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.
Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, Pande D, Zaeri P, Silva GGZ, Thompson F, Edwards RA, Dinsdale EA., BMC Genomics 18(1), 2017
PMID: 29183281
Recovering complete and draft population genomes from metagenome datasets.
Sangwan N, Xia F, Gilbert JA., Microbiome 4(), 2016
PMID: 26951112
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jorgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvociute M, Hansen LH, Sorensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Goker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC., Nat. Methods 14(11), 2017
PMID: 28967888
The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A., Nucleic Acids Res. 44(D1), 2015
PMID: 26673716
New approach for understanding genome variations in KEGG.
Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M., Nucleic Acids Res. 47(D1), 2019
PMID: 30321428
Structure and functions of the bacterial microbiota of plants.
Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, Schulze-Lefert P., Annu Rev Plant Biol 64(), 2013
PMID: 23373698
Nitric oxide: the versatility of an extensive signal molecule.
Lamattina L, Garcia-Mata C, Graziano M, Pagnussat G., Annu Rev Plant Biol 54(), 2003
PMID: 14502987
Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria
Rodríguez H., Fraga R., Gonzalez T., Bashan Y.., 2006
Biochar of animal origin: a sustainable solution to the global problem of high‐grade rock phosphate scarcity?
Vassilev N, Martos E, Mendes G, Martos V, Vassileva M., J. Sci. Food Agric. 93(8), 2013
PMID: IND500663103
Bacteria with ACC deaminase can promote plant growth and help to feed the world.
Glick BR., Microbiol. Res. 169(1), 2013
PMID: 24095256
The multifactorial basis for plant health promotion by plant-associated bacteria.
Kim YC, Leveau J, McSpadden Gardener BB, Pierson EA, Pierson LS 3rd, Ryu CM., Appl. Environ. Microbiol. 77(5), 2011
PMID: 21216911
Auxin-Gibberellin Interactions and Their Role in Plant Growth.
Ross JJ, O'Neill DP, Wolbang CM, Symons GM, Reid JB., J. Plant Growth Regul. 20(4), 2001
PMID: 11986760
Microbial volatiles as plant growth inducers.
Fincheira P, Quiroz A., Microbiol. Res. 208(), 2018
PMID: 29551213
Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere.
Kai M, Effmert U, Piechulla B., Front Microbiol 7(), 2016
PMID: 26903987
Recent developments in the isolation, biological function, biosynthesis, and synthesis of phenazine natural products.
Guttenberger N, Blankenfeldt W, Breinbauer R., Bioorg. Med. Chem. 25(22), 2017
PMID: 28094222
New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase.
Vekeman B, Kerckhof FM, Cremers G, de Vos P, Vandamme P, Boon N, Op den Camp HJ, Heylen K., Environ. Microbiol. 18(12), 2016
PMID: 27501305
Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria.
Iguchi H, Yurimoto H, Sakai Y., Microorganisms 3(2), 2015
PMID: 27682083
Current Trends in Methylotrophy.
Chistoserdova L, Kalyuzhnaya MG., Trends Microbiol. 26(8), 2018
PMID: 29471983
Methylotrophic bacteria in sustainable agriculture.
Kumar M, Tomar RS, Lade H, Paul D., World J. Microbiol. Biotechnol. 32(7), 2016
PMID: 27263015
Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia.
Garrido-Oter R, Nakano RT, Dombrowski N, Ma KW; AgBiome Team, McHardy AC, Schulze-Lefert P., Cell Host Microbe 24(1), 2018
PMID: 30001518
Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plants.
Costa R, Salles JF, Berg G, Smalla K., Environ. Microbiol. 8(12), 2006
PMID: 17107555
Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth.
Khan AL, Waqas M, Kang SM, Al-Harrasi A, Hussain J, Al-Rawahi A, Al-Khiziri S, Ullah I, Ali L, Jung HY, Lee IJ., J. Microbiol. 52(8), 2014
PMID: 24994010
Bacterial synthesis of biodegradable polyhydroxyalkanoates.
Verlinden RA, Hill DJ, Kenward MA, Williams CD, Radecka I., J. Appl. Microbiol. 102(6), 2007
PMID: 17578408
RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots.
Pankievicz VC, Camilios-Neto D, Bonato P, Balsanelli E, Tadra-Sfeir MZ, Faoro H, Chubatsu LS, Donatti L, Wajnberg G, Passetti F, Monteiro RA, Pedrosa FO, Souza EM., Plant Mol. Biol. 90(6), 2016
PMID: 26801330

Reuben S., Bhinu V.S., Swarup S.., 2008
Siderophores: More than Stealing Iron.
Behnsen J, Raffatellu M., MBio 7(6), 2016
PMID: 27935843
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.
Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA., Cell 158(2), 2014
PMID: 25036635
Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids.
Schoner TA, Gassel S, Osawa A, Tobias NJ, Okuno Y, Sakakibara Y, Shindo K, Sandmann G, Bode HB., Chembiochem 17(3), 2016
PMID: 26629877
Bacteriocins and the assembly of natural Pseudomonas fluorescens populations.
Bruce JB, West SA, Griffin AS., J. Evol. Biol. 30(2), 2016
PMID: 28000957
Volatile affairs in microbial interactions.
Schmidt R, Cordovez V, de Boer W, Raaijmakers J, Garbeva P., ISME J 9(11), 2015
PMID: 26023873
The quorum sensing molecule N-acyl homoserine lactone produced by Acinetobacter baumannii displays antibacterial and anticancer properties.
John J, Saranathan R, Adigopula LN, Thamodharan V, Singh SP, Lakshmi TP, CharanTej MA, Rao RS, Krishna R, Rao HS, Prashanth K., Biofouling 32(9), 2016
PMID: 27643959
Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens.
Biggins JB, Ternei MA, Brady SF., J. Am. Chem. Soc. 134(32), 2012
PMID: 22765305
Recent advances in genome-based polyketide discovery.
Helfrich EJ, Reiter S, Piel J., Curr. Opin. Biotechnol. 29(), 2014
PMID: 24762576
Isoprenoid biosynthesis via 1-deoxy-D-xylulose 5-phosphate/2-C-methyl-D-erythritol 4-phosphate (DOXP/MEP) pathway.
Wanke M, Skorupinska-Tudek K, Swiezewska E., Acta Biochim. Pol. 48(3), 2001
PMID: 11833775
Nitric oxide as a key component in hormone-regulated processes.
Simontacchi M, Garcia-Mata C, Bartoli CG, Santa-Maria GE, Lamattina L., Plant Cell Rep. 32(6), 2013
PMID: 23584547
Biodegradable plastic agricultural mulches and key features of microbial degradation.
Brodhagen M, Peyron M, Miles C, Inglis DA., Appl. Microbiol. Biotechnol. 99(3), 2014
PMID: 25487893
Ecology of Bacillaceae
Mandic-Mulec I., Stefanic P., van J.D.., 2015
Chance and Necessity in Bacillus subtilis Development
Mirouze N., Dubnau D.., 2016
Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.
Ransom-Jones E, McCarthy AJ, Haldenby S, Doonan J, McDonald JE., mSphere 2(4), 2017
PMID: 28776044
Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems.
Lopez-Mondejar R, Zuhlke D, Becher D, Riedel K, Baldrian P., Sci Rep 6(), 2016
PMID: 27125755
Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family.
Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, Taguchi H., J. Biol. Chem. 292(18), 2017
PMID: 28270506
Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β-1,2-Glucooligosaccharides from Parabacteroides distasonis.
Shimizu H, Nakajima M, Miyanaga A, Takahashi Y, Tanaka N, Kobayashi K, Sugimoto N, Nakai H, Taguchi H., Biochemistry 57(26), 2018
PMID: 29763309
Rhizosphere microbiome structure alters to enable wilt resistance in tomato.
Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, Lee PA, Choi SY, Seo M, Lee HJ, Jung EJ, Park H, Roy N, Kim H, Lee MM, Rubin EM, Lee SW, Kim JF., Nat. Biotechnol. (), 2018
PMID: 30295674
Terpene Production by Bacteria and its Involvement in Plant Growth Promotion, Stress Alleviation, and Yield Increase
Piccoli P., Bottini R.., 2013
Type III polyketide synthases in natural product biosynthesis.
Yu D, Xu F, Zeng J, Zhan J., IUBMB Life 64(4), 2012
PMID: 22362498
Type III polyketide synthases in microorganisms.
Katsuyama Y, Ohnishi Y., Meth. Enzymol. 515(), 2012
PMID: 22999182
The Ecology of Acidobacteria: Moving beyond Genes and Genomes.
Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE., Front Microbiol 7(), 2016
PMID: 27303369
Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments.
Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D., Environ. Microbiol. 20(3), 2018
PMID: 29327410
Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria.
Kielak AM, Cipriano MA, Kuramae EE., Arch. Microbiol. 198(10), 2016
PMID: 27339258
The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology.
Pester M, Schleper C, Wagner M., Curr. Opin. Microbiol. 14(3), 2011
PMID: 21546306
Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil.
Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C., Proc. Natl. Acad. Sci. U.S.A. 108(20), 2011
PMID: 21525411
Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples.
Offre P, Nicol GW, Prosser JI., Environ Microbiol Rep 3(2), 2010
PMID: 23761257
Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?
Nicol GW, Schleper C., Trends Microbiol. 14(5), 2006
PMID: 16603359
Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation.
Konneke M, Schubert DM, Brown PC, Hugler M, Standfest S, Schwander T, Schada von Borzyskowski L, Erb TJ, Stahl DA, Berg IA., Proc. Natl. Acad. Sci. U.S.A. 111(22), 2014
PMID: 24843170
A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea.
Berg IA, Kockelkorn D, Buckel W, Fuchs G., Science 318(5857), 2007
PMID: 18079405
Isolation of acetic, propionic and butyric acid-forming bacteria from biogas plants.
Cibis KG, Gneipel A, Konig H., J. Biotechnol. 220(), 2016
PMID: 26779817
Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees.
Muller H, Berg C, Landa BB, Auerbach A, Moissl-Eichinger C, Berg G., Front Microbiol 6(), 2015
PMID: 25784898
Gibberellin biosynthesis and its regulation.
Hedden P, Thomas SG., Biochem. J. 444(1), 2012
PMID: 22533671
The GH130 Family of Mannoside Phosphorylases Contains Glycoside Hydrolases That Target β-1,2-Mannosidic Linkages in Candida Mannan.
Cuskin F, Basle A, Ladeveze S, Day AM, Gilbert HJ, Davies GJ, Potocki-Veronese G, Lowe EC., J. Biol. Chem. 290(41), 2015
PMID: 26286752
Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects.
Hong JK, Cho JC., PLoS ONE 10(8), 2015
PMID: 26241328
Phylogenetic diversity of Acidobacteria in a former agricultural soil.
Kielak A, Pijl AS, van Veen JA, Kowalchuk GA., ISME J 3(3), 2008
PMID: 19020558
Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce.
Schreiter S, Ding GC, Heuer H, Neumann G, Sandmann M, Grosch R, Kropf S, Smalla K., Front Microbiol 5(), 2014
PMID: 24782839
Comparison of nitrogen removal and microbial properties in solid-phase denitrification systems for water purification with various pretreated lignocellulosic carriers.
Feng L, Chen K, Han D, Zhao J, Lu Y, Yang G, Mu J, Zhao X., Bioresour. Technol. 224(), 2016
PMID: 27843089
A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera.
Gupta RS, Son J, Oren A., Antonie Van Leeuwenhoek 112(4), 2018
PMID: 30392177
Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association.
Torres-Cortes G, Ghignone S, Bonfante P, Schußler A., Proc. Natl. Acad. Sci. U.S.A. 112(25), 2015
PMID: 25964335
Arbuscular mycorrhizal fungi as mediators of ecosystem responses to nitrogen deposition: A trait‐based predictive framework
Treseder KK, Edith B. Allen , Louise M. Egerton‐Warburton , Miranda M. Hart , John N. Klironomos , Hafiz Maherali , Leho Tedersoo ., J. Ecol. 106(2), 2018
PMID: IND605892974
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap.
Metsalu T, Vilo J., Nucleic Acids Res. 43(W1), 2015
PMID: 25969447
Material in PUB:
Dissertation, die diesen PUB Eintrag enthält
Metagenomic analyses of microbial communities from agricultural soils for an environmentally sustainable crop production
Nelkner J (2023)
Bielefeld: Universität Bielefeld.
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 31163637
PubMed | Europe PMC

Suchen in

Google Scholar