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Ecology and genomics of microorganisms reducing the greenhouse gas N₂O

examples from the rhizosphere

Graf, Daniel Robert Heinrich (2015). Ecology and genomics of microorganisms reducing the greenhouse gas N₂O. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2015:109
ISBN 978-91-576-8416-5
eISBN 978-91-576-8417-2
[Doctoral thesis]

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Abstract

Nitrous oxide (N₂O) is a potent greenhouse gas and the major ozone depleting substance in the stratosphere. One major source of N₂O is incomplete denitrification, whereas the only known tropospheric sink of N₂O is the microbial enzyme nitrous oxide reductase. Denitrification is defined as the stepwise reduction of nitrite to dinitrogen via nitric oxide and N₂O by facultative anaerobic microorganisms. This thesis aims to elucidate the phylogenetic diversity of the N₂O reductase encoding gene nosZ and its context in microbial genomes in relation to other genes in the denitrification pathway, as well as the relative influence of plants and soil on the activity, abundance and structure of N₂O-reducing communities in the rhizosphere.

Phylogenetic analysis of publicly available nosZ gene sequences revealed that its genetic diversity is divided into two distinct clades termed clade I and clade II, the latter having not been accounted for in previous studies. Newly developed molecular tools revealed that it is abundant in a wide range of environments. Analysis of microbial genomes showed that co-occurrence patterns of nosZ with other denitrification genes were neither randomly distributed among taxonomic units nor among habitats. Many genomes had truncated pathways as organisms possessing nosZII often lacked other genes involved in denitrification, suggesting these organisms may act as N₂O-sinks in the environment. Pot experiments with sunflower and barley indicated a niche differentiation between the two nosZ gene variants, as nosZI showed an affinity for plant roots while nosZII was more abundant in the surrounding soil. However, denitrification and N₂O-production activity in soil were controlled by edaphic factors. Moreover, an intercropping experiment with cocksfoot and lucerne showed that intercropping had a negative influence on nosZII abundances on cocksfoot roots which in conjunction with phylogenetic placement of sequencing reads indicated the presence of organisms with only nosZ lacking a denitrification pathway.

In conclusion, the development of new molecular tools combined with comparative genomic analysis sheds new light on the ecology of biological N₂O reduction in the rhizosphere.

Authors/Creators:Graf, Daniel Robert Heinrich
Title:Ecology and genomics of microorganisms reducing the greenhouse gas N₂O
Subtitle:examples from the rhizosphere
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2015
Depositing date:5 October 2015
Volume:2015:109
Number of Pages:72
Papers/manuscripts:
NumberReferences
IJones, C.M., Graf D.R.H., Bru, D., Philippot, L., Hallin, S. (2013). The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME Journal 7, 417-426.doi:10.1038/ismej.2012.125
IIGraf, D.R.H, Jones, C.M. and Hallin, S. (2014). Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS ONE, 9(12):e114118. doi:10.1371/journal.pone.0114118
IIIGraf, D.R.H, Jones, C.M., Zhao, M. and Hallin, S. Community assembly of N2O-reducing denitrifiers associated with roots include selection and competition with community composition mainly depending on soil type. (manuscript)
IVGraf, D.R.H, Zhao, M., Carlsson, G. Jones, C.M., and Hallin, S. Composition and activity of N2O-reducing communities associated with roots of Medicago sativa and Dactylis glomerata during intercropping. (manuscript)
Place of Publication:Uppsala
Publisher:Department of Microbiology, Swedish University of Agricultural Sciences
Associated Programs and Other Stakeholders:SLU - Agricultural Sciences for Global Development > Land use and climate change
ISBN for printed version:978-91-576-8416-5
ISBN for electronic version:978-91-576-8417-2
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:P Natural resources > P01 Nature conservation and land resources
P Natural resources > P34 Soil biology
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Soil Science
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 405 Other Agricultural Sciences > Environmental Sciences related to Agriculture and Land-use
Agrovoc terms:microorganisms, nitrous oxide, greenhouse gases, oxidoreductases, denitrification, rhizosphere, soil, genes, genetic diversity, genomes, helianthus annuus, hordeum vulgare, medicago sativa, dactylis glomerata, intercropping
Keywords:nitrous oxide, nosZ, nirS, nirK, microbial genomes, community assembly, rhizosphere, intercropping
URN:NBN:urn:nbn:se:slu:epsilon-e-2967
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2967
ID Code:12667
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Microbiology (until 161231)
External funders:Stiftelsen Oscar och Lili Lamms minne
Deposited By: Daniel Graf
Deposited On:05 Oct 2015 11:14
Metadata Last Modified:15 Dec 2015 12:31

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