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Extent and limitations of functional redundancy among bacterial communities towards dissolved organic matter
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Description
Abstract [en]

One of the key processes in the carbon cycle on our planet is the degradation of dissolved organic matter (DOM) in aquatic environments. The use of organic matter by bacteria links energy from DOM to higher trophic levels of the ecosystem when bacteria are consumed by other organisms. This is referred to as the microbial loop. In this thesis I examined if the communities were functionally redundant in their ability to utilize organic matter, or if variation in bacterial composition and richness is of importance. To test this overarching question several experiments were conducted that include methods such as illumina sequencing of the 16S rRNA gene for taxonomic identification of bacterial communities, flow cytometry to follow the growth of communities and spectroscopic measurement to describe the composition of the organic matter pool. Initially we demonstrated how to optimally sterilize organic matter for experimental studies in order to preserve its natural complexity. In further experiments we found that bacterial communities are redundant in their utilization of organic matter and can maintain optimal performance towards a range of organic matter pools. Related to this we found that pre-adaptation to organic matter played a small role as communities performed equally well regardless of their environmental history. We saw a small effect of richness and composition of bacterial communities on the efficiency of organic matter use, but conclude that this is of minor importance relative to abiotic factors. Still, we also show that organic matter can put strong selection pressure on bacterial communities with regards to richness and composition. Additionally we found that the supply rate of a carbon compound greatly influenced the energy utilization of the compound, i.e. a higher growth rate can be maintained if substrate is delivered in pulses relative to a continuous flow. Finally we conclude that the variation in bacterial communities is unlikely to have a major influence on carbon cycling in boreal lakes, but to enable a finer understanding, the genetics underlying the carbon utilization needs to be further explored. 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. , 41 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1578
Keyword [en]
Dissolved organic matter, BCC, biodiversity, functional redundancy
National Category
Natural Sciences
Research subject
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-331772ISBN: 978-91-513-0112-9 (print)OAI: oai:DiVA.org:uu-331772DiVA: diva2:1150094
Public defence
2017-12-01, Friessalen, Norbyvägen 18, Uppsala, 09:00 (English)
Opponent
Supervisors
Available from: 2017-11-08 Created: 2017-10-17 Last updated: 2017-11-08Bibliographically approved
List of papers
1. Effects of sterilization on composition and bacterial utilization of dissolved organic carbon
Open this publication in new window or tab >>Effects of sterilization on composition and bacterial utilization of dissolved organic carbon
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Sterilization of dissolved organic carbon (DOC) is an essential step in research on interactions between DOC and organisms, for example where the effect of different microbial communities on DOC is studied or vice versa. Few studies have, however, gone beyond acknowledging that sterilization of DOC influences its characteristics. Here we aimed to provide further knowledge that enables scientists to better tailor their sterilization methods to their research question. To meet this aim, we conducted a sterilization experiment with DOC from 4 boreal lakes treated with 4 sterilization methods, 2 filtrations (0.2 µm, 0.1 µm) and 2 autoclaving approaches (single autoclaving and double with intermediate pH adjustment). Quantity and spectroscopic properties of DOC were compared before and after sterilization and DOC was further tested as a substrate for bacterial growth. We found that the filtration methods better preserved the qualities of DOC, particularly the 0.2 µm filtration. On the contrary, autoclaving caused major inconsistent shifts in both qualitative and quantitative measurements of DOC as well as an increase of the maximum abundance of bacteria in growth experiments. Nonetheless, there remains a trade-off between retaining the quality of DOC and achieving sterile conditions. Therefore, the sterilization method of choice should be guided by the scientific question at hand.    

Keyword
sterilization, autoclave, filtration, dissolved organic carbon, excitation emission matrices, parallel factor analysis
National Category
Biological Sciences
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-331676 (URN)
Available from: 2017-10-16 Created: 2017-10-16 Last updated: 2017-10-23
2. Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors
Open this publication in new window or tab >>Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Aquatic environments are typically not homogenous, but characterized by changing substrate concentration gradients and nutrient patches. This heterogeneity in substrate availability creates a multitude of niches allowing bacteria with different substrate utilization strategies to hypothetically coexist even when competing for the same substrate. To study the impact of heterogeneous distribution of organic substrates on bacterioplankton, bioreactors with freshwater bacterial communities were fed artificial freshwater medium with acetate supplied either continuously or in pulses. After a month-long incubation, bacterial biomass and community-level substrate uptake rates were twice as high in the pulsed treatment compared to the continuously fed reactors even if the same total amount of acetate was supplied to both treatments. The composition of the bacterial communities emerging in the two treatments differed significantly with specific taxa overrepresented in the respective treatments. The higher estimated growth yield in cultures that received pulsed substrate inputs, imply that such conditions enable bacteria to use resources more efficiently for biomass production. This finding agrees with established concepts of basal maintenance energy requirements and high energetic costs to assimilate substrates at low concentration. Our results further imply that degradation of organic matter is influenced by temporal and spatial heterogeneity in substrate availability. 

National Category
Biological Sciences
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-331692 (URN)
Available from: 2017-10-17 Created: 2017-10-17 Last updated: 2017-10-23
3. Response and effect interactions between bacterial communities and organic matter
Open this publication in new window or tab >>Response and effect interactions between bacterial communities and organic matter
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The interaction between bacteria and dissolved organic matter (DOM) is crucial for the global carbon cycling. Despite decades of research there are, however, few consistent patterns regarding the relationship between bacterial diversity and community composition and DOM. Here we hypothesized that one reason for such inconsistences among studies is that bacterial communities can adapt to a DOM source over time, whereby a change in the functioning of a community can be, at least partly, decoupled from its composition and diversity. To test this idea we performed a reciprocal transplant experiment with medium (i.e. DOM source) and bacterial communities from two boreal lakes. In this experiment the two communities were allowed to adapt to their indigenous and their foreign source of DOM over 42 days. Bacterial community composition (BCC) was measured throughout the experiment. In addition we measured the capacity of the communities to use DOM, in repeated short (5 days) separated bioassays. The results show a response of bacterial community composition to the DOM sources which was influenced by the origin of the community. In contrast, we could not show an effect of BCC on DOM-processing and functional performance. Indeed, communities of different origin processed the two DOM sources equally well even at the beginning of the experiment. This work demonstrates that the DOM pool can be a strong selective force for BCC but not vice versa. 

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-331696 (URN)
Available from: 2017-10-17 Created: 2017-10-17 Last updated: 2017-10-23
4. The relative importance of richness and BCC for DOC degradation
Open this publication in new window or tab >>The relative importance of richness and BCC for DOC degradation
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The importance of biodiversity has been of primary interest for ecologist the last 20 years, giving rise to biodiversity ecosystem function (BEF) studies. Within the traditional field of ecology reoccurring patterns have emerged but within microbial ecology the importance of species richness for functioning is still poorly understood with few consistent patterns. In this study we examined the effect of species richness for dissolved organic matter degradation in lakes. This was examined within a smaller span of species richness compared to what is typically in microbial BEF experiments. Bacterial communities of reduced species richness were exposed to a range of DOC environments to test if reduced richness changed the functioning of communities and if the effect was similar among DOC environments. This was conducted in a full factorial design of 3 levels, with 6 dilutions, 5 media and 3 inocula resulting in 90 treatments. Overall, richness and community composition appeared to have effects on DOC degradation, but these effects were minor compared to the variation caused by the different DOC sources. Further, the importance of species richness varied among media and, thus, the chemical complexity of the environment influenced the biodiversity-ecosystem functioning relationship. 

National Category
Biological Sciences
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-331693 (URN)
Available from: 2017-10-17 Created: 2017-10-17 Last updated: 2017-10-23

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