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Institute of

BD Biodiversity

Project

Microbiom analyses - method development and bioinformatics



Three dimensional visualization of the bacterial diversity from maize rhizospheres – based on the bioinformatic analysis of their phylogenetic relationship of 16S rRNA genes
© Thünen-Institut/BD
Three dimensional visualization of the bacterial diversity from maize rhizospheres – based on the bioinformatic analysis of their phylogenetic relationship of 16S rRNA genes

Development of molecular methods to characterize the soil microbial communities from soils and other natural and technical habitats

The objective of this work is to develop a new methodological repertoire to characterize the diversity and functions of microbial communities and utlize this knowledge for protecting and exploiting these activities for a sustainable use in agroecosystems.

Background and Objective

Microbial activities provide the basis for a sustainable use of agricultural soil, growth promotion and pathogen defence of crops, degradation of organic material and their conversion to high quality fertilizers as well as to produce bioenergy.

All these beneficial activities are provided by collaboratiive efforts of microbial communities. Their single orgnaisms and their interaction within communities, as well as their variability in response to environmental changes are largely unkown.

New molecular methods based on direct analyses of nucleic acids provide a tool to understand such communities and to develop stratiegies to utilize these activities for an ecologically friendly agriculture.

Approach

Method development relates to those independent of cultivating microorganisms on nutrient containing media in the laboratory:

  • Extraction and purification of nucleic acids (DNA, RNA) from environmental samples (soil, groundwater, gut contents, ...)
  • PCR for quantification of microbial groups and genetic profiling von communities 
  • Sequencing of the microbiom from soils and other relevant habitats (compost, biogas reactors, ...)
  • Optimization of bioinformatic tools to analyse large datasets
  • Specific detection methods for beneficial and pathogenic microbial community members, the latter also with the objective to avoid experimental use of animals as much as possible.
  • Connection of structural and functional microbial community analyses by using isotopically labelled nucleic acids, e.g. SIP (stable isotope probing)

Our Research Questions

Examples

  • Who is doing what in a microbial community? Who cooperates, who fights with each other?
  • How variable are the communities, which members are important for function, which members are not important? How does the diversity respond to enviromental changes?

Preliminary Results

Methods were developed to extract DNA and RNA from soil and to characterize the identity and activity of soil microorganisms without the need of cultivation. A genetic profiling technique was developed which allows to study the impact of environmental factors on microbial communities at the scale of a whole agro-ecosystem.

New methods for sequencing metagenomis have been estabilshed, bioinformatic tools are now available

Duration

Permanent task 1.2001 - 2.2024

More Information

Project status: ongoing

Publications

  1. 0

    Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Kong F, Xi M, He Q (2023) Plant invasion threatens coastal blue carbon sequestration. Bull Ecol Soc Am 104(1):e02030, DOI:10.1002/bes2.2030

    https://literatur.thuenen.de/digbib_extern/dn065822.pdf

  2. 1

    Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Wang W, Wang X, Zhao Q, Wen L, Kong F, Xi M, He Q (2022) Habitat-specific responses of soil organic matter decomposition to Spartina alterniflora invasion along China’s coast. Ecol Appl:e2741, DOI:10.1002/eap.2741

  3. 2

    Finn D, Samad MS, Tebbe CC (2022) One-step PCR amplicon sequencing libraries perform better than two-step when assessing soil microbial diversity and community profiles. FEMS Microbiol Lett 369(1):1-9, DOI:10.1093/femsle/fnac079

  4. 3

    Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Wang W, Wang X, Yu L, Zhao Q (2022) Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes. Mol Ecol 31(17):4478-4494, DOI:10.1111/mec.16600

  5. 4

    Finn D, App M, Hertzog LR, Tebbe CC (2022) Reconciling concepts of black queen and tragedy of the commons in simulated bulk soil and rhizosphere prokaryote communities. Frontiers Microbiol 13:969784, DOI:10.3389/fmicb.2022.969784

    https://literatur.thuenen.de/digbib_extern/dn065846.pdf

  6. 5

    Lerner H, Öztürk B, Dohrmann AB, Thomas J, Marchal K, De Mot R, Dehaen W, Tebbe CC, Springael D (2021) DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil. FEMS Microbiol Ecol 97(5):fiab051, DOI:10.1093/femsec/fiab051

  7. 6

    Finn D, Bergk-Pinto B, Hazard C, Nicol G, Tebbe CC, Vogel TM (2021) Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. FEMS Microbiol Ecol 97(5):fiab068, DOI:10.1093/femsec/fiab068

  8. 7

    Szoboszlay M, Tebbe CC (2021) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol Open 10(1):e1144, DOI:10.1002/mbo3.1144

    https://literatur.thuenen.de/digbib_extern/dn064402.pdf

  9. 8

    Schroeder J, Kammann L, Helfrich M, Tebbe CC, Poeplau C (2021) Impact of common sample pre-treatments on key soil microbial properties. Soil Biol Biochem 160:108321, DOI:10.1016/j.soilbio.2021.108321

    https://literatur.thuenen.de/digbib_extern/dn063708.pdf

  10. 9

    Hemkemeyer M, Tebbe CC (2021) Importance of soil primary particles for shaping the diversity and activity of soil microbial communities - Results of a meta-analysis. Verhandl Gesellsch Ökol 50: 128

  11. 10

    Zhang G, Bai J, Tebbe CC, Zhao Q, Jia J, Wang W, Wang X, Yu L (2021) Salinity controls soil microbial community structure and function in coastal estuarine wetlands. Environ Microbiol 23(2):1020-1037, DOI:10.1111/1462-2920.15281

  12. 11

    Geisen S, Hartmann M, Tebbe CC (2021) The European Journal of Soil Biology: A catalyst for soil biodiversity research. Eur J Soil Biol 102:103262, DOI:10.1016/j.ejsobi.2020.103262

  13. 12

    Gao W, Xu J, Zhao J, Zhang H, Ni Y, Zhao B, Tebbe CC, Zhang J, Jia Z (2020) Prokaryotic community assembly after 40 years of soda solonetz restoration by natural grassland and reclaimed farmland. Eur J Soil Biol 100:103213, DOI:10.1016/j.ejsobi.2020.103213

  14. 13

    Hernandez M, Vera-Gargallo B, Calabi-Floody M, King GM, Conrad R, Tebbe CC (2020) Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class ktedonobacteria. Microorganisms 8(12):1880, DOI:10.3390/microorganisms8121880

    https://literatur.thuenen.de/digbib_extern/dn063011.pdf

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