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| 2. |
- Cederlund, Harald, et al.
(author)
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Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla
- 2014
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In: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 84, s. 62-68
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Journal article (peer-reviewed)abstract
- Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatments. We hypothesized that the long-term treatments had created distinctly different ecological niches for soil bacteria, suitable for either fast-growing copiotrophic bacteria, or slow-growing oligotrophic bacteria. Based on terminal-restriction fragment length polymorphism of the 16S rRNA genes from the total soil bacterial community and taxa-specific quantitative real-time PCR of seven different groups, all treatments significantly affected the community structure, but nitrogen fertilization was the most important driver for changes in the relative abundances of the studied taxa. According to an indicator species analysis, the changes were largely explained by the decline in the relative abundances of Acidobacteria, Gemmatimonadetes and Verrucomicrobia with nitrogen fertilization. Conditions more favourable for copiotrophic life strategies were indicated in these plots by the decreased metabolic quotient, i.e. the ratio between basal respiration rate and soil biomass. Apart from the Alphaproteobacteria that were significantly associated with peat, no taxa were indicative of organic amendment in general. However, several significant indicators of both peat and straw were identified among the terminal restriction fragments suggesting that changes induced by the organic amendments were mainly manifested at a lower taxonomical level. Our findings strengthen the proposition that certain higher bacterial taxa adapt in an ecologically coherent way in response to changes induced by fertilization. (C) 2014 Elsevier B.V. All rights reserved.
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| 3. |
- Wessén, Ella, et al.
(author)
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Abundance of archaeal and bacterial ammonia oxidizers - Possible bioindicator for soil monitoring
- 2011
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In: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 11, s. 1696-1698
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Journal article (peer-reviewed)abstract
- Many soil functions are driven by soil microorganisms and they have therefore been identified as appropriate indicators for monitoring of soil status. Genetic profiling of the bacterial ammonia oxidizing community was recently top-scored as soil biological indicator (Ritz et al., 2009). However, ammonia oxidation is not only performed by bacteria, but also ammonia oxidizing archaea. Based on the suggested niche differentiation between these two groups and findings that they are susceptible to environmental change in soil ecosystems at varying scales, we suggest that the abundance of these two communities rather than community profiling of the ammonia oxidizing bacteria could serve as a relevant and cost-effective bioindicator for soil monitoring. (C) 2011 Elsevier Ltd. All rights reserved.
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| 4. |
- Wessén, Ella, et al.
(author)
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Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management
- 2010
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 42, s. 1759-1765
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Journal article (peer-reviewed)abstract
- Little is known about abundances of the major bacterial taxa in agricultural soils and how they are affected by fertilization or other agricultural practices. Our aim was to determine the abundance and relative distribution of several bacterial phyla and one class, as well as the archaeal and crenarchaeal communities, and how they were affected by different fertilization regimes to examine whether specific responses of microorganisms could be identified at these high taxonomic ranks. We used real-time PCR with taxa specific primers to quantify the abundance of the Actinobacteria, Acidobacteria, Bacteriodetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Alphaproteobacteria and Crenarchaeota, as well as of the total bacteria and total archaea in soil sampled in 2002 and 2007 from a long term experimental field site subjected to six different fertilization regimes since 1956. The fertilization had affected soil pH, carbon and nitrogen, in addition to the C:N ratio. The total abundances of each taxon were affected in similar ways by the imposed treatments. By contrast, the relative abundance of certain taxa responded differently to the same fertilizer, with some taxa increasing while others decreased. Significant treatment effects were observed for the relative abundance of Alphaproteobacteria, Firmicutes, Verrucomicrobia and the Crenarchaeota and soil pH was the main driver for the observed differences. Differences between sampling years were also observed for the relative abundance of the Actinobacteria and the Bacteroidetes. Altogether, our results showed that agricultural practices can impact bacterial and archaeal phyla and classes in soil differently, which is consistent with recent work suggesting ecological coherence of members of bacterial clades at high taxonomic ranks. (C) 2010 Elsevier Ltd. All rights reserved.
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| 5. |
- Wessén, Ella
(author)
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Niche differentiation of ammonia oxidizing bacteria and archaea in managed soils
- 2011
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Doctoral thesis (other academic/artistic)abstract
- Soils offer humanity a multitude of ecosystem services, including production of food and clean drinking water, and many such services are driven by soil microbial communities. However, human activities are constantly affecting soil ecosystems through altered land use or various management strategies, and thereby influence microbial communities and their functions. Human activities also result in increasing amounts of nitrogen entering terrestrial ecosystems, which modifies the global nitrogen cycle. This can lead to a number of negative environmental effects such as increased amounts of nitrous oxide (N2O) being emitted to the atmosphere or nitrate (NO3-) being leached from soils to surrounding water bodies, causing eutrophication. This thesis explores how indigenous soil bacterial and archaeal communities are affected in managed soils, with emphasis on ammonia oxidizing bacteria (AOB) and archaea (AOA). The objectives were to identify specific environmental drivers for AOB and AOA and to evaluate how potential changes might affect their activity. Long-term application of various fertilizer regimes on an agricultural soil was found to alter the total abundance of targeted bacterial and archaeal phyla and classes in similar ways, although different taxa-specific responses were observed for the relative abundance of certain phyla/classes. Long-term organic and fertilizer amendments also affected the ammonia-oxidizing community. The AOA appeared to be functionally more important in the nitrification process than the AOB at the studied field site. Also, the AOA dominated in abundance except under certain conditions, when the AOB dominated, suggesting niche differentiation between the two groups. Studies on a drained forested peat soil revealed that the AOB were numerically superior to the AOA, and that AOB and AOA community structures and AOB abundance exhibited temporal variation. Furthermore, a spatially focused study on an agricultural soil revealed contrasting spatial patterns between the AOB and AOA with regard to both abundance and structure, which correlated differently to soil properties. This too indicates niche differentiation between the two ammonia oxidizing groups and there were also indications that the AOA were the drivers of nitrate leaching from the studied agro-ecosystem. In conclusion, the AOB and AOA communities clearly respond to different management strategies. Based on current knowledge, it is suggested that the size of the AOB and AOA communities could serve as a good bioindicator when monitoring soil status.
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| 6. |
- Wessén, Ella, et al.
(author)
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Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management
- 2010
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In: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 45, s. 193-200
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Journal article (peer-reviewed)abstract
- Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and potentially cover a broader range of habitats. (C) 2010 Elsevier B.V. All rights reserved.
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| 7. |
- Wessén, Ella, et al.
(author)
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Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning
- 2011
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In: Isme Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 5:7, s. 1213-1225
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Journal article (peer-reviewed)abstract
- Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers. The ISME Journal (2011) 5, 1213-1225; doi:10.1038/ismej.2010.206; published online 13 January 2011 Subject Category: microbial ecology and functional diversity of natural habitats
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