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Margarida Soares


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Fungal and bacterial contributions to decomposition in terrestrial and aquatic ecosystems


  • Margarida Soares

Summary, in English

Microbial decomposers process a great majority of net primary production in the biosphere and regulate carbon (C) and nutrient cycling. Microbial communities are extremely diverse and often disregarded from global C-cycling models, but one strategy to overcome this challenge is to focus on the major decomposer groups: fungi and bacteria. These groups have distinct life strategies and are differently affected by environmental factors. During microbial decomposition of organic matter (OM), the fraction of C assimilated into microbial growth or used in cell maintenance and respiration is defined as microbial carbon-use efficiency (CUE). Since soils represent a large C pool with a critical role in regulating atmospheric CO2 concentrations, CUE is a key parameter central to understanding the soil C-cycle and its feedback to environmental change.
In this thesis I compared the bacterial and fungal contributions to decomposition by developing conversion factors to measure microbial growth in units of C. I estimated CUE and studied the influence of environmental factors on the fungal-to-bacterial ratio (F:B) and how that affects CUE. This was applied to a survey of field sites and verified in laboratory microcosms. CUE was higher in sites with low F:B ratio, and within field sites higher CUE was associated to lower F:B in high fertility soils. However, in microcosms, higher CUE was a result of low F:B in low mineral N and high pH soils, with no effect of OM quality. This indicated that CUE was also regulated by another component of soil fertility other than mineral N, pH or OM availability, and I suggest that plant community traits such as litter and rhizosphere inputs might influence F:B ratio and CUE. I also investigated the effect of long and short term-stress on CUE in a subartic region. CUE was unaffected by increasing metal concentrations along a gradient of long-term contamination. Fungi were overall less affected by heavy metal pollution than bacteria but F:B and CUE were unrelated. In experimental microcosms I tested the effect of short-term stress with heavy metals in both soils previously exposed to stress and unexposed soils. CUE decreased only in unexposed soils, but by the end of the experimental period previously stressed soils exposed to heavy metals had higher CUE than unexposed soils because adapted microbial decomposers could allocate more resources to growth than to maintenance and survival.
The differences between fungal and bacterial decomposition of plant litter in aquatic and terrestrial systems were explored in a boreal catchment forest site, where litter bags were installed in soils and adjacent streams. F:B ratios were higher in litter decomposing in streams than in soils but overall mass loss was higher in soils. Litter decomposition was explored with IR spectroscopy and litter changes in terms of chemical functional groups (carbohydrate and aromatic compound loss) were fundamentally different between systems.
The effect of a labile C source on litter decomposing in aquatic systems was tested in laboratory microcosms. I investigated the priming effect - increased mineralization of native OM in response to a external labile C source- on biofilms growth in plant litter. In these systems the spatial proximity between photosynthetic algae and microbial decomposers allows for products of metabolisms to be exchanged. I found that labile C of photosynthetic algae origin did not affect the decomposition of plant litter in terms of mass loss but increased the fungal removal of N from plant litter.
In conclusion, microbial growth rates in C units and CUE can now be estimated in natural environments. This thesis provides a deeper understanding of the fungal and bacterial contributions to decomposition in different systems, and how F:B and CUE are regulated by environmental factors.


  • BECC: Biodiversity and Ecosystem services in a Changing Climate
  • Microbial Ecology

Publishing year




Document type



Department of Biology, Lund University


  • Ecology


  • Fungi
  • bacteria
  • microbial carbon use efficiency
  • litter decomposition
  • priming effect
  • heavy metal stress



Research group

  • Microbial Ecology


  • Johannes Rousk
  • Emma Kritzberg


  • ISBN: 978-91-7895-106-2
  • ISBN: 978-91-7895-105-5

Defence date

24 May 2019

Defence time


Defence place

Lecture hall “Blå hallen”, the Ecology building, Sölvegatan 37, Lund


  • David Kirchman (Professor)