| 1. |
- Beier, Sara, et al.
(författare)
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Global Phylogeography of Chitinase Genes in Aquatic Metagenomes
- 2011
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 77:3, s. 1101-1106
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Tidskriftsartikel (refereegranskat)abstract
- Phylogeny-based analysis of chitinase and 16S rRNA genes from metagenomic data suggests that salinity is a major driver for the distribution of both chitinolytic and total bacterial communities in aquatic systems. Additionally, more acidic chitinase proteins were observed with increasing salinity. Congruent habitat separation was further observed for both genes according to latitude and proximity to the coastline. However, comparison of chitinase and 16S rRNA genes extracted from different geographic locations showed little congruence in distribution. There was no indication that dispersal limited the global distribution of either gene.
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| 2. |
- Alsterberg, Christian, 1982, et al.
(författare)
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Habitat diversity and ecosystem multifunctionality-The importance of direct and indirect effects
- 2017
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 3:2
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Tidskriftsartikel (refereegranskat)abstract
- Ecosystems worldwide are facing habitat homogenization due to human activities. Although it is commonly proposed that such habitat homogenization can have negative repercussions for ecosystem functioning, this question has yet to receive explicit scientific attention. We expand on the framework for evaluating the functional consequences of bio-diversity loss by scaling up from the level of species to the level of the entire habitats. Just as species diversity generally fosters ecosystem functioning through positive interspecies interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and through exchange of material and energy across habitats. We show that experimental ecosystems comprised of a diversity of habitats show higher levels of multiple ecosystem functions than ecosystems with low habitat diversity. Our results demonstrate that the effect of habitat diversity on multifunctionality varies with season; it has direct effects on ecosystem functioning in summer and indirect effects, via changes in species diversity, in autumn, but no effect in spring. We propose that joint consideration of habitat diversity and species diversity will prove valuable for both environmental management and basic research.
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| 3. |
- Andersson, Björn, 1985, et al.
(författare)
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Nitrogen fixation in shallow-water sediments: Spatial distribution and controlling factors
- 2014
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 59:6, s. 1932-1944
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogenase activity (NA) in shallow-water (< 1 m) sediments was investigated at 60 randomly selected sites along a 150 km stretch on the brackish-water Swedish west coast, without targeting any specific type of sediments, such as microbial mats. Benthic nitrogen (N) fixation and diazotrophs (nifH genes) were found at all sites, regardless of the presence of cyanobacterial or microbial mats. The majority of sites showed N fixation rates between 0.03 and 1 mmol N m−2 d−1. These rates were similar to those of benthic denitrification previously measured in the area. Maximum rates up to 3.4 mmol N m−2 d−1 were measured. A structural equation model was used to investigate direct and indirect effects of biogeochemical and physical factors on NA. Number of nifH genes had the largest direct positive influence on NA, whereas increasing wave exposure had an indirect negative effect on NA through its influence on the diazotrophic abundance. Increased salinity, previously been shown to suppress NA in coastal waters, was found to directly stimulate benthic N fixation, likely by generating favorable conditions for diazotrophic sulfate-reducing bacteria. Our field data confirmed previously observed negative effects of dissolved inorganic nitrogen on NA, which have so far mainly been experimentally studied. Both NA rates and the number of nifH genes correlated positively with pore-water dissolved inorganic phosphorus concentrations. These findings show that the potential for N fixation in illuminated sediments can be considerable, stretching beyond cyanobacterial mats, being controlled by complex interactions between biotic and abiotic factors.
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| 4. |
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| 5. |
- Andert, Janet, et al.
(författare)
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Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil
- 2011
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 17, s. 1497-1504
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of inoculated C58 population in the soils was in the same range as the indigenous nosZ community. However, in two of the three soils, the increase in potential denitrification in inoculated microcosms compared with the noninoculated microcosms was higher than the increase in N2O emissions. This suggests that the indigenous denitrifier community was capable of acting as a sink for the N2O produced by A. tumefaciens. The relative amount of N2O emitted also increased in two soils with the number of inoculated C58 cells, establishing a direct causal link between the denitrifier community composition and potential N2O emissions by manipulating the proportion of denitrifiers having the nosZ gene. However, the number of denitrifiers which do not possess a nitrous oxide reductase might not be as important for N2O emissions in soils having a high N2O uptake capacity compared with those with lower. In conclusion, we provide a proof of principle that the inability of some denitrifiers to synthesize the nitrous oxide reductase can influence the nature of the denitrification end products, indicating that the extent of the reduction of N2O to N-2 by the denitrifying community can have a genetic basis.
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| 6. |
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| 7. |
- Andert, Janet, et al.
(författare)
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Temporal Changes in Methane Oxidizing and Denitrifying Communities and Their Activities in a Drained Peat Soil
- 2012
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Ingår i: Wetlands. - : Springer Science and Business Media LLC. - 0277-5212 .- 1943-6246. ; 32, s. 1047-1055
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Tidskriftsartikel (refereegranskat)abstract
- Northern peat soils are both sources and sinks of the greenhouse gases nitrous oxide (N2O) and methane (CH4). These fluxes are regulated by the activity of microbial communities. Temporal, spatial and depth related differences in potential activity and composition of the denitrifier and methanotrophic bacterial communities were compared between winter and summer in relation to in situ fluxes of N2O and CH4 from a drained and forested peat land in Sweden. The composition of the genetic pool of these guilds was assessed using terminal fragment length polymorphism analysis of signature genes in the denitrification and methane oxidation pathways, respectively. The composition of the communities was similar throughout the soil profile, although both denitrification and methane oxidation rates decreased with soil depth. The potential methane oxidation rates were significantly correlated to soil N content, and , indicating a nitrogen induced stimulation of methane oxidation capacity. The site was a source of N2O and a small sink for CH4, and although the fluxes did not vary significantly over time, both the methane oxidizing and denitrifier community composition exhibited temporal patterns. Differences in the composition of the methanotrophic community reflected that the peat site shifted from a summer to a winter community. The denitrifiers exhibited a similar trend, but also differed significantly between the sampling occasions during summer, as well as between locations at the site. The latter was explained by differences in soil pH. It was only the differences in the methane oxidizer community composition that correlated with its corresponding potential activity, which implies a higher degree of functional redundancy within the denitrifier community.
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| 8. |
- Bommarco, Riccardo, et al.
(författare)
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Exploiting ecosystem services in agriculture for increased food security
- 2018
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Ingår i: Global Food Security. - : Elsevier BV. - 2211-9124. ; 17, s. 57-63
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Forskningsöversikt (refereegranskat)abstract
- Despite contributing to economy and food security, Ecosystem Services (ES) are still not fully exploited in agriculture. Instead, external inputs have been used to boost yields, while exacting costs on public goods. Ecological intensification capitalizes on ecosystem services to enhance and stabilize production and reduce the need for external inputs, while sparing the environment. Of particular relevance are biodiversity-based ES connected to soil fertility, pest control and pollination. Ecological intensification is applicable in all regions, but for food security purposes, particular attention should be dedicated to implement it as ecological enhancement in regions with wide yield gaps, coinciding with poor food security. Diversified cropping system show promise to create win-win situations. Knowledge on ecology and socio-economy of ES will be needed, and agricultural research and innovation need to heed to resource use efficiency, production stability, minimal environmental impact, buffering of extreme events and adaptation to local conditions.
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| 9. |
- Bonilla Rosso, German, et al.
(författare)
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Design and evaluation of primers targeting genes encoding NO-forming nitrite reductases: implications for ecological inference of denitrifying communities
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The detection of NO-forming nitrite reductase genes (nir) has become the standard when studying denitrifying communities in the environment, despite well-known amplification biases in available primers. We review the performance of 35 published and 121 newly designed primers targeting the nirS and nirK genes, against sequences from complete genomes and 47 metagenomes from three major habitats where denitrification is important. There were no optimal universal primer pairs for either gene, although published primers targeting nirS displayed up to 75% coverage. The alternative is clade-specific primers, which show a trade-off between coverage and specificity. The test against metagenomic datasets showed a distinct performance of primers across habitats. The implications of clade-specific nir primers choice and their performance for ecological inference when used for quantitative estimates and in sequenced-based community ecology studies are discussed and our phylogenomic primer evaluation can be used as a reference along with their environmental specificity as a guide for primer selection. Based on our results, we also propose a general framework for primer evaluation that emphasizes the testing of coverage and phylogenetic range using full-length sequences from complete genomes, as well as accounting for environmental range using metagenomes. This framework serves as a guideline to simplify primer performance comparisons while explicitly addressing the limitations and biases of the primers evaluated.
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| 10. |
- Bösch, Yvonne, et al.
(författare)
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Distribution and Environmental Drivers of Fungal Denitrifiers in Global Soils
- 2023
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Ingår i: Microbiology Spectrum. - 2165-0497. ; 11, s. e00061-23
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Tidskriftsartikel (refereegranskat)abstract
- The microbial process of denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase, and thereby are sources of N2O. Still, their diversity, global distribution, and environmental determinants, as well as their relative importance, compared to bacterial and archaeal denitrifiers, remain unresolved. Employing a phylogenetically informed approach to analyze 1,980 global soil and rhizosphere metagenomes for the denitrification marker gene nirK, which codes for the copper dependent nitrite reductase in denitrification, we show that fungal denitrifiers are sparse, yet cosmopolitan and that they are dominated by saprotrophs and pathogens. Few showed biome-specific distribution patterns, although members of the Fusarium oxysporum species complex, which are known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands, but they were most abundant in forest soils when normalized to metagenome size. Nevertheless, the overwhelming dominance of bacterial and archaeal denitrifiers suggests a much lower fungal contribution to N2O emissions than was previously estimated. In relative terms, they could play a role in soils that are characterized by a high carbon to nitrogen ratio and a low pH, especially in the tundra as well as in boreal and temperate coniferous forests. Because global warming predicts the proliferation of fungal pathogens, the prevalence of potential plant pathogens among fungal denitrifiers and the cosmopolitan distribution of these organisms suggest that fungal denitrifier abundance may increase in terrestrial ecosystems.IMPORTANCE Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed. Here, we probed a massive amount of DNA sequences and corresponding soil data from a large number of samples that represented the major soil environments for a broad understanding of fungal denitrifier diversity at the global scale. We show that fungal denitrifiers are predominantly cosmopolitan saprotrophs and opportunistic pathogens. Fungal denitrifiers constituted, on average, 1% of the total denitrifier community. This suggests that earlier estimations of fungal denitrifier abundance, and, thereby, it is also likely that the contributions of fungal denitrifiers to N2O emissions have been overestimated. Nevertheless, with many fungal denitrifiers being plant pathogens, they could become increasingly relevant, as soilborne pathogenic fungi are predicted to increase with ongoing climate change.Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed.
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| 11. |
- Bösch, Yvonne, et al.
(författare)
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Minimizing tillage modifies fungal denitrifier communities, increases denitrification rates and enhances the genetic potential for fungal, relative to bacterial, denitrification
- 2022
-
Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 170
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Tidskriftsartikel (refereegranskat)abstract
- Nitrous oxide (N2O) emissions from arable soils are predominantly caused by denitrifying microbes, of which fungal denitrifiers are of particular interest, as fungi, in contrast to bacteria, terminate denitrification with N2O. Reduced tillage has been shown to increase gaseous nitrogen losses from soil, but knowledge of how varying tillage regimes and associated soil physical and chemical alterations affect fungal denitrifiers is limited. Based on results from a long-term (>40 years) tillage experiment, we show that non-inversion tillage resulted in increased potential denitrification activity in the upper soil layers, compared to annual or occasional (every 4-5 years) conventional inversion tillage. Using sequence-corrected abundance of the fungal nirK gene, we further identified an increased genetic potential for fungal denitrification, compared to that caused by bacteria, with decreasing tillage intensity. Differences in the composition and diversity of the fungal nirK community imply that different tillage regimes select for distinct fungal denitrifiers with differing functional capabilities and lifestyles, predominantly by altering carbon and nitrogen related niches. Our findings suggest that the creation of organic hotspots through stratification by non-inversion tillage increases the diversity and abundance of fungal denitrifier communities and modifies their composition, and thus their overall relevance for N2O production by denitrification, in arable soils.
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| 12. |
- Castaño, Carles, et al.
(författare)
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Contrasting plant–soil–microbial feedbacks stabilize vegetation types and uncouple topsoil C and N stocks across a subarctic–alpine landscape
- 2023
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Ingår i: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 238:6, s. 2621-2633
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Tidskriftsartikel (refereegranskat)abstract
- Global vegetation regimes vary in belowground carbon (C) and nitrogen (N) dynamics. However, disentangling large-scale climatic controls from the effects of intrinsic plant–soil–microbial feedbacks on belowground processes is challenging. In local gradients with similar pedo-climatic conditions, effects of plant–microbial feedbacks may be isolated from large-scale drivers. Across a subarctic–alpine mosaic of historic grazing fields and surrounding heath and birch forest, we evaluated whether vegetation-specific plant–microbial feedbacks involved contrasting N cycling characteristics and C and N stocks in the organic topsoil. We sequenced soil fungi, quantified functional genes within the inorganic N cycle, and measured 15N natural abundance. In grassland soils, large N stocks and low C : N ratios associated with fungal saprotrophs, archaeal ammonia oxidizers, and bacteria capable of respiratory ammonification, indicating maintained inorganic N cycling a century after abandoned reindeer grazing. Toward forest and heath, increasing abundance of mycorrhizal fungi co-occurred with transition to organic N cycling. However, ectomycorrhizal fungal decomposers correlated with small soil N and C stocks in forest, while root-associated ascomycetes associated with small N but large C stocks in heath, uncoupling C and N storage across vegetation types. We propose that contrasting, positive plant–microbial feedbacks stabilize vegetation trajectories, resulting in diverging soil C : N ratios at the landscape scale.
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| 13. |
- Cederlund, Harald, et al.
(författare)
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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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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 84, s. 62-68
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Tidskriftsartikel (refereegranskat)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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| 14. |
- Choudhury, Maidul, et al.
(författare)
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Disentangling the roles of plant functional diversity and plaint traits in regulating plant nitrogen accumulation and denitrification in freshwaters
- 2022
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 36, s. 921-932
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Tidskriftsartikel (refereegranskat)abstract
- 1. There is a growing recognition that functional measures of diversity, based on quantification of functionally important species traits, are useful for explaining variation in ecosystem processes. However, the mechanisms linking functional diversity to different processes remain poorly understood, hindering development of a predictive framework for ecosystem functioning based on species traits.2. The current understanding of how the functional traits of aquatic plants (macrophytes) affect nitrogen (N) cycling by regulating microbial communities and their activity in freshwater habitats is particularly limited. Denitrifying bacteria are typically associated with the roots of both aquatic and terrestrial plants and denitrification is the main cause of loss of N from ecosystems. Disentangling the interplay between plants and microbial denitrifiers is key to understanding variation in rates of denitrification from local to landscape scales.3. In a mesocosm experiment, we varied the species richness (monocultures or two-species mixtures) and composition of macrophytes. We quantified effects of both macrophyte functional diversity, quantified as functional trait dissimilarity, and functional trait composition, quantified as community weighted mean trait values, on N removal in wetlands. We used structural equation modelling to disentangle the direct and indirect influences of traits on N accumulation in plant biomass, denitrification activity and abundance of key bacterial denitrification genes (nirS and nirK).4. Both functional diversity and functional trait composition regulated N removal, explaining 70%-94% variation in the underlying ecosystem processes. Increased macrophyte functional diversity increased plant N accumulation, and indirectly enhanced denitrification by increasing denitrification gene abundance. Among traits, greater plant relative growth rates, specific leaf area and above-ground biomass increased plant N accumulation. Denitrification activity increased with increasing below-ground biomass but decreased with increasing root diameter.5. These findings improve our understanding of N removal in freshwater wetlands dominated by macrophytes, and have broad ecological implications for wetland management targeting enhanced ecosystem services. Our results highlight the potential for optimizing denitrification and plant N accumulation in wetlands and thereby improving water purification by increasing macrophyte functional diversity and ensuring the presence of key traits in macrophyte assemblages.
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| 15. |
- Choudhury, Maidul, et al.
(författare)
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Importance of plant species for nitrogen removal using constructed floating wetlands in a cold climate
- 2019
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Ingår i: Ecological Engineering. - : Elsevier BV. - 0925-8574 .- 1872-6992. ; 138, s. 126-132
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Tidskriftsartikel (refereegranskat)abstract
- Constructed floating wetlands (CFWs) have been tested in different climatic regions and aquatic habitat types for nitrogen (N) removal from surface water, but there is limited knowledge about their applicability for N removal in cold climate regions. Most CFWs studies are conducted at the micro- or mesocosm scale, while the application of CFWs at in situ is rare. Moreover, most CFWs studies have focused on plant N accumulation without considering macrophyte root-associated denitrification as a possible N removal pathway. Here, we study the N removal potential of CFWs through N accumulation by macrophytes and potential denitrification activity (PDA) associated with plants. At a mining area in the sub-arctic region of Sweden receiving N-rich mine effluents, we tested the concept of CFWs and evaluated the performance of six native, emerging macrophyte species planted in CFWs. The CFWs were deployed in two types of systems: in situ in the recipient lake, subjected to ambient N concentrations, and CFWs placed in water-side "eco-tanks", subjected to higher N concentrations. We showed that macrophyte establishment in CFWs is feasible under cold climatic conditions, both in situ and eco-tanks. The standing biomass of macrophytes, bulk N accumulation in plant biomass and PDA in mesocosms were 0.54-2.25 kg m(-2), 7.56-24.75 mg N m(-2) d(-1) and 31.82-2250.77 mg N2O-N m(-2) d(-1), respectively. In the recipient, the variation was larger and the values were higher (standing biomass, 0.37-6.74 kg m(-2); bulk N accumulation, 8.09-106.93 mg N m(-2) d(-1); PDA, 11.89-8446.15 mg N m(-2) d(-1)). Macrophyte root-associated denitrification was the main N removal pathway in the CFWs. Given the demonstrated applicability of CFWs and the high denitrification rates that can be obtained, future studies should focus on designing CFWs to enhance denitrification as this process leads to permanent removal of N from the water phase.
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| 16. |
- Choudhury, Maidul, et al.
(författare)
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Mixtures of macrophyte growth forms promote nitrogen cycling in wetlands
- 2018
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 635, s. 1436-1443
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Tidskriftsartikel (refereegranskat)abstract
- The importance of aquatic plant diversity in regulating nutrient cycling in wetlands remains poorly understood. We investigated how variation in macrophyte growth form (emerging, submerged and bryophyte) combinations and species mixtures affect nitrogen (N) removal from the water and N accumulation in plant biomass. We conducted a wetland mesocosm experiment for 100 days during July-September 2015. Twelve species were grown in mono- and in two-species mixed cultures for a total of 32 single and two-growth form combinations. Nitrogen removal from the water was quantified on three occasions during the experiment, while N accumulation in plant biomass was determined following termination of the experiment. The number of species and growth forms present increased N removal and accumulation. The growth form combinations of emerging and bryophyte species showed the highest N accumulation and N removal from water, followed by combinations of emerging species. By contrast, submerged species growing in the presence of emerging or other submerged species showed the lowest levels of N accumulation and N removal. Temporal variation in N removal also differed among growth form combinations: N removal was highest for emerging-bryophyte combinations in July, but peaked for the emerging-submerged and emerging-bryophyte combinations in August. Indeed, the occurrence of complementarity among macrophyte species, particularly in combinations of bryophyte and emerging species, enhanced N removal and uptake during the entire growing season. Our study highlights the importance of bryophytes, which have been neglected in research on nutrient cycling in wetlands, for aquatic N cycling, especially given their worldwide distribution across biomes. Overall, our findings point towards the potential important role of the diversity of macrophyte growth forms in regulating key ecosystem processes related to N cycling in wetlands. (C) 2018 Elsevier B.V. All rights reserved.
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| 17. |
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| 18. |
- Ek, Anders, et al.
(författare)
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Slaughterhouse waste co-digestion - Experiences from 15 years of full-scale operation
- 2011
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Ingår i: World Renewable Energy Congress - Sweden 8-13 May, 2011. - Linköping : Linköping University Electronic Press. - 9789173930703 ; , s. 64-71
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Konferensbidrag (refereegranskat)abstract
- At Tekniska Verken in Linköping AB (TVAB) there is a long time experience of handling and producing biogas from large volumes of slaughterhouse waste. Experiences from research and development and plant operations have lead to the implementation of several process improving technological/biological solutions. We can in this paper describe how the improvements have had several positive effects on the process, including energy savings, better odor control, higher gas quality, increased organic loading rates and higher biogas production with maintained process stability. In addition, it is described how much of the process stability in anaerobic digestion of slaughter house waste relates to the plant operation, which allow the microbiological consortia to adapt to the substrate. Since digestion of proteinaceous substrates like slaughterhouse waste lead to high ammonia loads, special requirements in ammonia tolerance are placed on the microbiota of the anaerobic digestion. Biochemical assays revealed that the main route for methane production proceed through syntrophic acetate oxidation, which require longer retention times than methane production by acetoclastic methanogens. Thus, the long retention time of the plant, accomplished by a low dilution of the substrate, is a vital component of the process stability when treating high protein substrates like slaughterhouse waste.
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| 19. |
- Engelbrecht Clemmensen, Karina, et al.
(författare)
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A tipping point in carbon storage when forest expands into tundra is related to mycorrhizal recycling of nitrogen
- 2021
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 24, s. 1193-1204
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Tidskriftsartikel (refereegranskat)abstract
- Tundra ecosystems are global belowground sinks for atmospheric CO2. Ongoing warming-induced encroachment by shrubs and trees risks turning this sink into a CO2 source, resulting in a positive feedback on climate warming. To advance mechanistic understanding of how shifts in mycorrhizal types affect long-term carbon (C) and nitrogen (N) stocks, we studied small-scale soil depth profiles of fungal communities and C-N dynamics across a subarctic-alpine forest-heath vegetation gradient. Belowground organic stocks decreased abruptly at the transition from heath to forest, linked to the presence of certain tree-associated ectomycorrhizal fungi that contribute to decomposition when mining N from organic matter. In contrast, ericoid mycorrhizal plants and fungi were associated with organic matter accumulation and slow decomposition. If climatic controls on arctic-alpine forest lines are relaxed, increased decomposition will likely outbalance increased plant productivity, decreasing the overall C sink capacity of displaced tundra.
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| 20. |
- Enwall, Karin, et al.
(författare)
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Comparison of T-RFLP and DGGE techniques to assess denitrifier community composition in soil
- 2009
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Ingår i: Letters in Applied Microbiology. - 0266-8254 .- 1472-765X. ; 48, s. 145-148
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Tidskriftsartikel (refereegranskat)abstract
- Terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) and subsequent statistical analysis were compared with assess denitrifier community composition in agricultural soil based on the nosZ gene, encoding the nitrous oxide reductase. Analysis of binary or relative abundance-based metric and semi-metric distance matrices provided similar results for DGGE, but not for T-RFLP. Moreover, DGGE had a higher resolution than T-RFLP and binary data was better for discriminating between samples.
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| 21. |
- Enwall, Karin, et al.
(författare)
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Long-Term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil
- 2007
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 39:1, s. 106-115
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Tidskriftsartikel (refereegranskat)abstract
- To explore long-term impact of organic and inorganic fertilizers on microbial communities, we targeted both the total bacterial community and the autotrophic ammonia oxidizing bacteria (AOB) in soil from six treatments at an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, unfertilized and unfertilized without crops. All plots, except the bare fallows, were cropped with maize. Effects on activity were assessed by measuring the basal respiration and substrate induced respiration (SIR) rates, and the potential activity of the AOB. To determine the bacterial community composition, 16S rRNA genes were used to fingerprint total soil communities by terminal restriction fragment length polymorphism analysis and AOB communities by denaturing gradient gel electrophoresis. The fertilization regimes had clear effects on both activity and composition of the soil communities. Basal respiration and r, which was kinetically derived as the exponentially growing fraction of the SIR-response, correlated well with the soil organic C content (r=0.93 and 0.66, respectively). Soil pH ranged from 3.97 to 6.26 in the treatments and was found to be an important factor influencing all microbial activities. pH correlated negatively with the ratio between basal respiration and SIR (r=0.90), indicating a decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass in the most acid soils with pH 3.97 and 4.68 ((NH4)2SO4 and sewage sludge fertilized plots, respectively). The lowest SIR and ammonia oxidation rates were also found in these treatments. In addition, these treatments exhibited individually different community fingerprints, showing that pH affected the composition of AOB and total bacterial communities. The manure fertilized plots harbored the most diverse AOB community and the pattern was linked to a high potential ammonia oxidation activity. Thus, the AOB community composition appeared to be more strongly linked to the activity than the total bacterial communities were, likely explained by physiological differences in the populations present.
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| 22. |
- Enwall, Karin, et al.
(författare)
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Soil Resources Influence Spatial Patterns of Denitrifying Communities at Scales Compatible with Land Management
- 2010
-
Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 76, s. 2243-2250
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Tidskriftsartikel (refereegranskat)abstract
- Knowing spatial patterns of functional microbial guilds can increase our understanding of the relationships between microbial community ecology and ecosystem functions. Using geostatistical modeling to map spatial patterns, we explored the distribution of the community structure, size, and activity of one functional group in N cycling, the denitrifiers, in relation to 23 soil parameters over a 44-ha farm divided into one organic and one integrated crop production system. The denitrifiers were targeted by the nirS and nirK genes that encode the two mutually exclusive types of nitrite reductases, the cd(1) heme-type and copper reductases, respectively. The spatial pattern of the denitrification activity genes was reflected by the maps of the abundances of nir genes. For the community structure, only the maps of the nirS community were related to the activity. The activity was correlated with nitrate and dissolved organic nitrogen and carbon, whereas the gene pools for denitrification, in terms of size and composition, were influenced by the soil structure. For the nirS community, pH and soil nutrients were also important in shaping the community. The only unique parameter related to the nirK community was the soil Cu content. However, the spatial pattern of the nirK denitrifiers corresponded to the division of the farm into the two cropping systems. The different community patterns, together with the spatial distribution of the nirS/nirK abundance ratio, suggest habitat selection on the nirS-and nirK-type denitrifiers. Our findings constitute a first step in identifying niches for denitrifiers at scales relevant to land management.
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| 23. |
- Graf, Daniel, et al.
(författare)
-
Assembly of root-associated N₂O-reducing communities of annual crops is governed by selection for nosZ Glade I over Glade II
- 2022
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 98
-
Tidskriftsartikel (refereegranskat)abstract
- The rhizosphere is a hotspot for denitrification. The nitrous oxide (N₂O) reductase among denitrifiers and nondenitrifying N₂O reducers is the only known N₂O sink in the biosphere. We hypothesized that the composition of root-associated N₂O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N₂O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N₂O availability, determined as potential N₂O production rates, but for sunflower no N₂O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N₂O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N₂O.
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| 24. |
- Graf, Daniel, et al.
(författare)
-
Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions
- 2014
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the importance of community structure for N2O emissions.
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| 25. |
- Graf, Daniel, et al.
(författare)
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Lucerne (Medicago sativa) alters N2O-reducing communities associated with cocksfoot (Dactylis glomerata) roots and promotes N2O production in intercropping in a greenhouse experiment
- 2019
-
Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 137
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Tidskriftsartikel (refereegranskat)abstract
- Lower emissions of the greenhouse gas nitrous oxide (N2O) are generally observed from intercropped compared to sole cropped systems. This could be due to better N-use efficiency, but differences in microbial communities establishing in the rhizosphere may also play a role as the only known biological sink for N2O is its reduction to nitrogen gas (N-2) by bacteria and archaea that possess the nosZ gene encoding the N2O reductase. Nitrous oxide reducing communities can be divided into two clades, I and II, and their relative abundance and diversity may have important consequences for N2O emissions. Here, we examine how intercropping with a legume (Medicago sativa, "lucerne") and a grass (Dactylis glomerata, "cocksfoot") species, compared to sole cropping of each species, affects the N2O emission potential, and the structure and abundance of root-associated N2O-reducing microbial communities. In a rhizobox experiment, we show that intercropping resulted in higher total shoot biomass compared to sole cropping. Further, N2O production rates were significantly higher in intercropped cocksfoot roots compared to sole cropping of either species. This coincided with lower abundances of nosZ Glade II communities in intercropped compared to sole cropped cocksfoot roots, suggesting that these organisms likely act as a N2O sink. Phylogenetic placement of sequencing reads placed root-associated nosZ Glade II reads close to Ignavibacteria and Opitutaceae, which harbour non-denitrifying N2O reducers with the genetic capacity to also perform dissimilatory nitrate reduction to ammonium (DNRA). We observed a shift in the composition of the cocksfoot root-associated nosZI communities towards incomplete denitrifiers terminating with N2O in intercropped roots. Overall, we hypothesize that such alterations of plant-microbe and/or microbe-microbe interactions contributed to the higher potential N2O emission rate observed in intercropped cocksfoot roots. Understanding the nature of these interactions would represent an important step forward for the design of management practices that minimize N2O emissions.
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| 26. |
- Graf, Daniel, et al.
(författare)
-
Soil type overrides plant effect on genetic and enzymatic N2O production potential in arable soils
- 2016
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 100, s. 125-128
-
Tidskriftsartikel (refereegranskat)abstract
- Nitrous oxide (N2O) is a potent greenhouse gas mainly produced by incomplete denitrification in agricultural soils. The rhizosphere is a hot spot for denitrification and this study aimed to discern the relative importance of soil type and crop on the genetic N2O production and reduction potential in soil and root associated communities in relation to denitrification activity. Based on a pot experiment with two agricultural soils planted with barley or sunflower, we showed that the effect of soil type overrode that of crop on both genetic and enzymatic potential. We also demonstrate niche differentiation between the nitrous oxide reductase genes nosZI and nosZII, with clade I dominating in the root-associated community and clade II in the soil. (C) 2016 Elsevier Ltd. All rights reserved.
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| 27. |
- Graham, Emily B., et al.
(författare)
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Microbes as Engines of Ecosystem Function : When Does Community Structure Enhance Predictions of Ecosystem Processes?
- 2016
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.
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| 28. |
- Granhall, Ulf, et al.
(författare)
-
Bacterial community diversity in paper mills processing recycled paper
- 2010
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Ingår i: Journal of Industrial Microbiology & Biotechnology. - : Oxford University Press (OUP). - 1367-5435 .- 1476-5535. ; 37:10, s. 1061-1069
-
Tidskriftsartikel (refereegranskat)abstract
- Paper mills processing recycled paper suffer from biofouling causing roblems both in the mill and final product. The total bacterial ommunity composition and identification of specific taxa in the process ater and biofilms at the stock preparation and paper machine areas in a ill with recycled paper pulp was described by using a DNA-based pproach. Process water in a similar mill was also analyzed to nvestigate if general trends can be found between mills and over time. acterial community profiles, analyzed by terminal-restriction fragment ength polymorphism (T-RFLP), in process water showed that the dominant eaks in the profiles were similar between the two mills, although the verall composition was unique for each mill. When comparing process ater and biofilm at different locations within one of the mills, we bserved a separation according to location and sample type, with the iofilm from the paper machine being most different. 16S rRNA gene clone ibraries were generated and 404 clones were screened by RFLP analysis. rouping of RFLP patterns confirmed that the biofilm from the paper achine was most different. A total of 99 clones representing all RFLP atterns were analyzed, resulting in sequences recovered from nine acterial phyla, including two candidate phyla. Bacteroidetes epresented 45% and Actinobacteria 23% of all the clones. Sequences with imilarity to organisms implicated in biofouling, like Chryseobacterium pp. and Brevundimonas spp., were recovered from all samples even though he mill had no process problems during sampling, suggesting that they re part of the natural paper mill community. Moreover, many sequences howed little homology to as yet uncultivated bacteria implying that aper mills are interesting for isolation of new organisms, as well as or bioprospecting.
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| 29. |
- Gärdenäs, Annemieke, et al.
(författare)
-
Knowledge gaps in soil carbon and nitrogen interactions - From molecular to global scale
- 2011
-
Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 43, s. 702-717
-
Tidskriftsartikel (refereegranskat)abstract
- The objective of this review was to identify, address and rank knowledge gaps in our understanding of five major soil C and N interactions across a range of scales – from molecular to global. The studied five soil C and N interactions are: i) N controls on the soil emissions of greenhouse gases, ii) plant utilisation of organic N, iii) impact of rhizosphere priming on C and N cycling, iv) impact of black N on the stabilisation of soil organic matter (SOM) and v) representation of fractions of SOM in simulation models. We ranked the identified knowledge gaps according to the importance we attached to them for functional descriptions of soil–climate interactions at the global scale, for instance in general circulation models (GCMs). Both the direct and indirect influences on soil–climate interactions were included. We found that the level of understanding declined as the scale increased from molecular to global for four of the five topics. By contrast, the knowledge level for SOM simulation models appeared to be highest when considered at the ecosystem scale. The largest discrepancy between knowledge level and importance was found at the global modelling scale. We concluded that a reliable quantification of greenhouse gas emissions at the ecosystem scale is of utmost importance for improving soil–climate representation in GCMs. We see as key questions the identification of the role of different N species for the temperature sensitivity of SOM decomposition rates and its consequences for plant available N
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| 30. |
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| 31. |
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| 32. |
- Hallberg, Lukas, et al.
(författare)
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Catchment controls of denitrification and nitrous oxide production rates in headwater remediated agricultural streams
- 2022
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 838
-
Tidskriftsartikel (refereegranskat)abstract
- Heavily modified headwater streams and open ditches carry high nitrogen loads from agricultural soils that sustain eutrophication and poor water quality in downstream aquatic ecosystems. To remediate agricultural streams and reduce the export of nitrate (NO3-), phosphorus and suspended sediments, two-stage ditches with constructed floodplains can be implemented as countermeasures. By extending hydrological connectivity between the stream channel and riparian corridor within constructed floodplains, these remediated ditches enhance the removal of NO3- via the microbial denitrification process. Ten remediated ditches were paired with upstream trapezoidal ditches in Sweden across different soils and land uses to measure the capacity for denitrification and nitrous oxide (N2O) production and yields under denitrifying conditions in stream and floodplain sediments. To examine the controls for denitrification, water quality was monitored monthly and flow discharge continuously along reaches. Floodplain sediments accounted for 33% of total denitrification capacity of remediated ditches, primarily controlled by inundation and stream NO3- concentrations. Despite reductions in flow-weighted NO3- concentrations along reaches, NW removal in remediated ditches via denitrification can be masked by inputs of NW-rich groundwaters, typical of intensively managed agricultural landscapes. Although N2O production rates were 50 % lower in floodplains compared to the stream, remediated ditches emitted more N2O than conventional trapezoidal ditches. Higher denitrification rates and reductions of N2O proportions were predicted by catchments with loamy soils, higher proportions of agricultural land use and lower floodplain elevations. For realizing enhanced NO3- removal from floodplains and avoiding increased N2O emissions, soil type, land use and the design of floodplains need to be considered when implementing remediated streams. Further, we stress the need for assessing the impact of stream remediation in the context of broader catchment processes, to determine the overall potential for improving water quality.
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| 33. |
- Hallberg, Lukas, et al.
(författare)
-
Trade-offs between nitrogen and phosphorus removal with floodplain remediation in agricultural streams
- 2024
-
Ingår i: Water Research. - 0043-1354. ; 258
-
Tidskriftsartikel (refereegranskat)abstract
- To improve water quality and reduce instream erosion, floodplain remediation along agricultural streams can provide multiple ecosystem services through biogeochemical and fluvial processes. During floodplain inundation, longer water residence time and periodic anoxic conditions can lead to increased nitrogen (N) removal through denitrification but also mobilization of phosphorus (P), impeding overall water quality improvements. To investigate the capacity for N and P processing in remediated streams, we measured potential denitrification and nitrous oxide production and yields together with potential P desorption and P fractions in floodplain and stream sediments in ten catchments in Sweden. Sediment P desorption was measured as equilibrium P concentration, using P isotherm incubations. Denitrification rates were measured with the acetylene inhibition method. Sediment nutrient process rates were combined with hydrochemical monitoring along remediated streams and their paired upstream control reaches of trapezoidal shape to determine the impact of floodplains on water quality. The correlation between floodplain denitrification rates and P desorption (r = 0.53, p = 0.02) revealed a trade-off between soluble reactive P (SRP) and nitrate removal, driven by stream water connectivity to floodplains. Nitrous oxide production was not affected by differences in P processing, but nitrous oxide yields decreased with higher denitrification and P desorption. The release of SRP from floodplains (0.03 ± 0.41 mg P kg−1 day−1) was significantly lower than from trapezoidal stream banks (0.38 ± 0.37 mg P kg−1 day−1), predicted by long-term SRP concentrations in stream water and floodplain inundation frequency. The overall impact of SRP release from floodplains on stream SRP concentrations in remediated reaches was limited. However, the remediated reaches showing increased stream SRP concentrations were also frequently inundated and had higher labile P content and coarse soil texture in floodplain sediments. To fully realize the potential for water quality improvements with constructed floodplains in agricultural streams, the promotion of denitrification through increased inundation should be balanced against the risk of P release from sediments, particularly in streams with high SRP inputs.
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| 34. |
- Hallin, Sara
(författare)
-
Abundance, activity and structure of denitrifier communities in phototrophic river biofilms (River Garonne, France)
- 2013
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Ingår i: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 716, s. 177-187
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Tidskriftsartikel (refereegranskat)abstract
- Phototrophic river biofilms are microbial assemblages involved in in-stream processes. For a better understanding of N-cycling, the denitrifier community abundance, activity and structure were monitored in natural biofilm assemblages, in two sites exhibiting contrasting nutrient concentrations during a 1-year period. The denitrifier abundance, estimated by quantification of the nirS, nirK and nosZ genes, correlated to biofilm biomass and total bacterial counts. Site-related differences in denitrification activity were observed and the rates were significantly correlated with the nosZ gene copy numbers and biofilm biomass. The denitrifier community structure, assessed by PCR-DGGE of nosZ, differed between sites with only minor differences between sampling occasions, and correlated with the total bacterial community structure. Altogether, these findings suggest that nutrient loading, especially nitrogen, affect both denitrifier community structure and activity.
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| 35. |
- Hallin, Sara
(författare)
-
Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae
- 2012
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 78, s. 318-325
-
Tidskriftsartikel (refereegranskat)abstract
- Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for 0. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions.
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| 36. |
- Hallin, Sara, et al.
(författare)
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Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts
- 2022
-
Ingår i: Nature ecology & evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 6, s. 1145-1154
-
Tidskriftsartikel (refereegranskat)abstract
- Combining field data and greenhouse experiments, the authors show how agricultural management practices like fungicide applications can affect the degree to which arbuscular mycorrhizal fungi in the soil provision phosphorus to plants.Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope P-33 from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring P-33 and transferred 64% more P-33 to plants compared with AMF in cropland soils. Fungicide application best explained hyphal P-33 transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced P-33 uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.
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| 37. |
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| 38. |
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| 39. |
- Hallin, Sara
(författare)
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Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe
- 2024
-
Ingår i: Nature Communications. - 2041-1723. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.How arable farming affects soil fungal biogeography is poorly understood. Here, the authors find that prevalent fungal groups become more abundant, whereas rare groups become fewer or absent in arable lands across Europe, suggesting a biotic homogenization due to arable farming.
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| 40. |
- Hallin, Sara, et al.
(författare)
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Catch Crop Residues Stimulate N2O Emissions During Spring, Without Affecting the Genetic Potential for Nitrite and N2O Reduction
- 2018
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- Agricultural soils are a significant source of anthropogenic nitrous oxide (N2O) emissions, because of fertilizer application and decomposition of crop residues. We studied interactions between nitrogen (N) amendments and soil conditions in a 2-year field experiment with or without catch crop incorporation before seeding of spring barley, and with or without application of N in the form of digested liquid manure or mineral N fertilizer. Weather conditions, soil inorganic N dynamics, and N2O emissions were monitored during spring, and soil samples were analyzed for abundances of nitrite reduction (nirK and nirS) and N2O reduction genes (nosZ clade I and II), and structure of nitrite- and N2O-reducing communities. Fertilization significantly enhanced soil mineral N accumulation compared to treatments with catch crop residues as the only N source. Nitrous oxide emissions, in contrast, were stimulated in rotations with catch crop residue incorporation, probably as a result of concurrent net N mineralization, and O-2 depletion associated with residue degradation in organic hotspots. Emissions of N2O from digested manure were low in both years, while emissions from mineral N fertilizer were nearly absent in the first year, but comparable to emissions from catch crop residues in the second year with higher precipitation and delayed plant N uptake. Higher gene abundances, as well as shifts in community structure, were also observed in the second year, which were significantly correlated to NO3- availability. Both the size and structure of the nitrite- and N2O-reducing communities correlated to the difference in N2O emissions between years, while there were no consistent effects of management as represented by catch crops or fertilization. It is concluded that N2O emissions were constrained by environmental, rather than the genetic potential for nitrite and N2O reduction.
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| 41. |
- Hallin, Sara, et al.
(författare)
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Denitrification rates in lake sediments of mountains affected by high atmospheric nitrogen deposition
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- During the last decades, atmospheric nitrogen loading in mountain ranges of the Northern Hemisphere has increased substantially, resulting in high nitrate concentrations in many lakes. Yet, how increased nitrogen has affected denitrification, a key process for nitrogen removal, is poorly understood. We measured actual and potential (nitrate and carbon amended) denitrification rates in sediments of several lake types and habitats in the Pyrenees during the ice-free season. Actual denitrification rates ranged from 0 to 9 mu mol N2O m(-2) h(-1) (mean, 1.5 +/- 1.6 SD), whereas potential rates were about 10times higher. The highest actual rates occurred in warmer sediments with more nitrate available in the overlying water. Consequently, littoral habitats showed, on average, 3-fold higher rates than the deep zone. The highest denitrification potentials were found in more productive lakes located at relatively low altitude and small catchments, with warmer sediments, high relative abundance of denitrification nitrite reductase genes, and sulphate-rich waters. We conclude that increased nitrogen deposition has resulted in elevated denitrification rates, but not sufficiently to compensate for the atmospheric nitrogen loading in most of the highly oligotrophic lakes. However, there is potential for high rates, especially in the more productive lakes and landscape features largely govern this.
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| 42. |
- Hallin, Sara
(författare)
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Emergent Macrophytes Act Selectively on Ammonia-Oxidizing Bacteria and Archaea
- 2012
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 78, s. 6352-6356
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Tidskriftsartikel (refereegranskat)abstract
- Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favoring enrichment of AOB.
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| 43. |
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| 44. |
- Hallin, Sara
(författare)
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Genetic potential for N2O emissions from the sediment of a free water surface constructed wetland
- 2011
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Ingår i: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 45, s. 5621-5632
-
Tidskriftsartikel (refereegranskat)abstract
- Removal of nitrogen is a key aspect in the functioning of constructed wetlands. However, incomplete denitrification may result in the net emission of the greenhouse gas nitrous oxide (N2O) resulting in an undesired effect of a system supposed to provide an ecosystem service. In this work we evaluated the genetic potential for N2O emissions in relation to the presence or absence of Phragmites and Typha in a free water surface constructed wetland (FWS-CW), since vegetation, through the increase in organic matter due to litter degradation, may significantly affect the denitrification capacity in planted areas. Quantitative real-time PCR analyses of genes in the denitrification pathway indicating capacity to produce or reduce N2O were conducted at periods of different water discharge. Genetic potential for N2O emissions was estimated from the relative abundances of all denitrification genes and nitrous oxide reductase encoding genes (nosZ). nosZ abundance was invariably lower than the other denitrifying genes (down to 100 fold), and differences increased significantly during periods of high nitrate loads in the CW suggesting a higher genetic potential for N2O emissions. This situation coincided with lower nitrogen removal efficiencies in the treatment cell. The presence and the type of vegetation, mainly due to changes in the sediment carbon and nitrogen content, correlated negatively to the ratio between nitrate and nitrite reducers and positively to the ratio between nitrite and nitrous oxide reducers. These results suggest that the potential for nitrous oxide emissions is higher in vegetated sediments. (C) 2011 Elsevier Ltd. All rights reserved.
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| 45. |
- Hallin, Sara, et al.
(författare)
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Genomics and Ecology of Novel N2O-Reducing Microorganisms
- 2018
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Ingår i: Trends in Microbiology. - : Elsevier BV. - 0966-842X .- 1878-4380. ; 26, s. 43 - 55
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Forskningsöversikt (refereegranskat)abstract
- Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N2O) to harmless dinitrogen gas are receiving increased attention due to increasing N2O emissions (and our need to mitigate climate change) and to recent discoveries of novel N2O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N2O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N2O reducers, which could be N2O sinks without major contribution to N2O formation. We review the recent advances about fundamental understanding of the genomics, physiology, and ecology of N2O reducers and the importance of these findings for curbing N2O emissions.
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| 46. |
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| 47. |
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| 48. |
- Hallin, Sara, et al.
(författare)
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Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity
- 2022
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Ingår i: Environmental Microbiome. - : Springer Science and Business Media LLC. - 2524-6372. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.
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| 49. |
- Hallin, Sara
(författare)
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nir gene-based co-occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire
- 2021
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23, s. 239-251
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Tidskriftsartikel (refereegranskat)abstract
- Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co-existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co-existence of denitrifiers across multiple assemblages by using nir gene-based co-occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co-occurrence patterns. Bacteria with the same nir co-occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co-occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance.
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| 50. |
- Hallin, Sara, et al.
(författare)
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Potential denitrification rates are spatially linked to colonization patterns of nosZ genotypes in an alluvial wetland
- 2015
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Ingår i: Ecological Engineering. - : Elsevier BV. - 0925-8574 .- 1872-6992. ; 80, s. 191-197
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Tidskriftsartikel (refereegranskat)abstract
- Through denitrification, attached bacterial communities reduce water nitrogen loads during transport from land to river. In an in situ colonization experiment, spatial and temporal dynamics in composition of bacterial communities and denitrification activity were studied in bacterial biofilms in an alluvial aquifer. Mesh bags with glass beads were installed in different wells in an alluvial aquifer affected by surface water fluxes from an adjacent river and biofilms were sampled throughout the 15-month experiment. By combining structural (PCR-DGGE using nosZ genes) and functional (Denitrification Enzyme Activity measurements) descriptors, the denitrifiers community structure of biofilms and their functional responses were studied. Denitrifiers bacterial community composition developed on beads linked to denitrification capability were correlated with the modeled load of dissolved organic carbon coming from the river and dissolved oxygen concentration, which were set by the river channel water flow through the aquifer. (C) 2015 Elsevier B.V. All rights reserved.
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