Aims Brassicaceae cover crops can be used to suppress soil-borne pathogens. The aim was to invest... more Aims Brassicaceae cover crops can be used to suppress soil-borne pathogens. The aim was to investigate the effect of different brassicas with different glucosinolate profiles on the development of Aphanomyces pea root rot in subsequent pea plants, and the genetic potential of free-living N 2 -fixing bacteria and ammonia oxidising bacteria (AOB) and archaea (AOA) performing key soil ecosystem services. Methods The Brassicaceae species Brassica juncea and Sinapis alba and non-Brassicaceae species Secale cereale were grown for 11-weeks in Aphanomyces euteiches infested soil at low and high nitrogen (N) fertiliser doses. After removing both shoots and roots of the cover crops, peas were grown as a bioassay to evaluate Aphanomyces pea root rot development. Soil was sampled before harvesting the cover crops and at the end of the bioassay. Volatile compounds were collected in the root-soil environment before harvesting the Brassicaceae cover crops to determine the concentration of isothiocyanates. The abundance of genes involved in N 2 -fixing bacteria and ammonia oxidation in AOA and AOB were assessed. Results Pea root rot disease severity was reduced in Brassicaceae grown soil at the high N fertiliser dose. This was associated with increased growth of the cover crops. The growth of Brassicaceae did not suppress the abundance of N-cycling microbial communities, but rather increased the AOB at the end of the bioassay, most likely due to increased N availability. The disease suppressive effect was higher with S. alba than with B. juncea, and this coincided with a more diverse composition and higher concentration of aliphatic ITCs released from S. alba roots. Fewer nodules were formed after the Brassicaceae crops, especially Sinapis alba. Conclusions Brassicaceae cover crops, particularly S. alba, can be used to control soil-borne pathogens without major side effects on the genetic potential of beneficial soil microorganisms involved in N cycling. However, less nodule formation after brassicas indicates an effect on rhizobium activity.
Microorganisms drive biogeochemical processes, but linking these processes to real changes in 27 ... more Microorganisms drive biogeochemical processes, but linking these processes to real changes in 27 microbial communities under field conditions is not trivial. Here, we present a model-based 28 approach to estimate independent contributions of microbial community shifts to ecosystem 29 properties. The approach was tested empirically, using denitrification potential as our model 30 process, in a spatial survey of arable land encompassing a range of edaphic conditions and two 31 agricultural production systems. Soil nitrate was the most important single predictor of 32 denitrification potential (ΔAIC c = 20.29); however, the inclusion of biotic variables 33 (particularly the evenness and size of denitrifier communities [ΔAIC c = 12.02], and the 34 abundance of one denitrifier genotype [ΔAIC c = 18.04]) had a substantial effect on model 35 precision, comparable to the inclusion of abiotic variables (R 2 biotic = 0.28, R 2 abiotic = 0.50, R 2 biotic 36 + abiotic = 0.76). This approach provides a valuable tool for explicitly linking microbial 37 communities to ecosystem functioning. By making this link, we have demonstrated that 38 including aspects of microbial community structure and diversity in biogeochemical models can 39 improve predictions of nutrient cycling in ecosystems and enhance our understanding of 40 ecosystem functionality. 41 42 keywords: ecosystem services, functional diversity, model selection, multimodel inference, 43 nitrogen cycling 44 45 46 47 48 49 50 Microorganisms are dominant components in the functioning of all ecological systems, and 51
ABSTRACT The objective of the present study was to use a test system for clustering and character... more ABSTRACT The objective of the present study was to use a test system for clustering and characterizing the bacterial populations in five wastewater infiltration systems ranging in size from 12 m2 to 1960 m2 (corresponding to the demand for 4–500 population equivalents). From each system two sand samples were taken and from each sample 88 bacterial isolates were collected. Every isolate was exposed to 52 physiological and biochemical tests. The resulting 880 objects × 52 variable data matrix was subjected to principal components analysis (PCA). After a variable reduction the PCA model revealed a scattered bacteria pattern (score plot) in parts of the sand filters expected to have high loading rates of wastewater, e.g. at the inlet of the filters. This indicates that a diverse bacterial population had developed in response to the carbon and energy source in the wastewater. In contrast to this pattern a more narrow bacteria pattern had developed in low loaded parts of the sand filter. The most important variables explaining the structure of the microbial biofilm at high wastewater load were the ability to ferment sugars and the capacity to sustain different pH levels. The potential to ammonify and grow on nutrient broth was also an important feature. In conclusion, the bacterial test system together with PCA seems to be a useful tool to evaluate the function of a bacterial sand-filter ecosystem.
Using consensus regions in gene sequences encoding the two forms of nitrite reductase (Nir), a ke... more Using consensus regions in gene sequences encoding the two forms of nitrite reductase (Nir), a key enzyme in the denitrification pathway, we designed two sets of PCR primers to amplify cd1- and Cu-nir. The primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. Sequence relationships of nir genes were also established. The cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in the six published sequences. Likewise, the Cu primers amplified a 473-bp region in seven of the eight published Cu-nir sequences. Together, the two sets of PCR primers amplified nir genes in nine species within four genera, as well as in four of the seven sludge isolates. The primers did not amplify genes of nondenitrifying strains. The Cu primers amplified the expected fragment in all 13 sludge samples, but cd1-nir fragments were only obtained in five samples. PCR products of the expected s...
Aims Brassicaceae cover crops can be used to suppress soil-borne pathogens. The aim was to invest... more Aims Brassicaceae cover crops can be used to suppress soil-borne pathogens. The aim was to investigate the effect of different brassicas with different glucosinolate profiles on the development of Aphanomyces pea root rot in subsequent pea plants, and the genetic potential of free-living N 2 -fixing bacteria and ammonia oxidising bacteria (AOB) and archaea (AOA) performing key soil ecosystem services. Methods The Brassicaceae species Brassica juncea and Sinapis alba and non-Brassicaceae species Secale cereale were grown for 11-weeks in Aphanomyces euteiches infested soil at low and high nitrogen (N) fertiliser doses. After removing both shoots and roots of the cover crops, peas were grown as a bioassay to evaluate Aphanomyces pea root rot development. Soil was sampled before harvesting the cover crops and at the end of the bioassay. Volatile compounds were collected in the root-soil environment before harvesting the Brassicaceae cover crops to determine the concentration of isothiocyanates. The abundance of genes involved in N 2 -fixing bacteria and ammonia oxidation in AOA and AOB were assessed. Results Pea root rot disease severity was reduced in Brassicaceae grown soil at the high N fertiliser dose. This was associated with increased growth of the cover crops. The growth of Brassicaceae did not suppress the abundance of N-cycling microbial communities, but rather increased the AOB at the end of the bioassay, most likely due to increased N availability. The disease suppressive effect was higher with S. alba than with B. juncea, and this coincided with a more diverse composition and higher concentration of aliphatic ITCs released from S. alba roots. Fewer nodules were formed after the Brassicaceae crops, especially Sinapis alba. Conclusions Brassicaceae cover crops, particularly S. alba, can be used to control soil-borne pathogens without major side effects on the genetic potential of beneficial soil microorganisms involved in N cycling. However, less nodule formation after brassicas indicates an effect on rhizobium activity.
Microorganisms drive biogeochemical processes, but linking these processes to real changes in 27 ... more Microorganisms drive biogeochemical processes, but linking these processes to real changes in 27 microbial communities under field conditions is not trivial. Here, we present a model-based 28 approach to estimate independent contributions of microbial community shifts to ecosystem 29 properties. The approach was tested empirically, using denitrification potential as our model 30 process, in a spatial survey of arable land encompassing a range of edaphic conditions and two 31 agricultural production systems. Soil nitrate was the most important single predictor of 32 denitrification potential (ΔAIC c = 20.29); however, the inclusion of biotic variables 33 (particularly the evenness and size of denitrifier communities [ΔAIC c = 12.02], and the 34 abundance of one denitrifier genotype [ΔAIC c = 18.04]) had a substantial effect on model 35 precision, comparable to the inclusion of abiotic variables (R 2 biotic = 0.28, R 2 abiotic = 0.50, R 2 biotic 36 + abiotic = 0.76). This approach provides a valuable tool for explicitly linking microbial 37 communities to ecosystem functioning. By making this link, we have demonstrated that 38 including aspects of microbial community structure and diversity in biogeochemical models can 39 improve predictions of nutrient cycling in ecosystems and enhance our understanding of 40 ecosystem functionality. 41 42 keywords: ecosystem services, functional diversity, model selection, multimodel inference, 43 nitrogen cycling 44 45 46 47 48 49 50 Microorganisms are dominant components in the functioning of all ecological systems, and 51
ABSTRACT The objective of the present study was to use a test system for clustering and character... more ABSTRACT The objective of the present study was to use a test system for clustering and characterizing the bacterial populations in five wastewater infiltration systems ranging in size from 12 m2 to 1960 m2 (corresponding to the demand for 4–500 population equivalents). From each system two sand samples were taken and from each sample 88 bacterial isolates were collected. Every isolate was exposed to 52 physiological and biochemical tests. The resulting 880 objects × 52 variable data matrix was subjected to principal components analysis (PCA). After a variable reduction the PCA model revealed a scattered bacteria pattern (score plot) in parts of the sand filters expected to have high loading rates of wastewater, e.g. at the inlet of the filters. This indicates that a diverse bacterial population had developed in response to the carbon and energy source in the wastewater. In contrast to this pattern a more narrow bacteria pattern had developed in low loaded parts of the sand filter. The most important variables explaining the structure of the microbial biofilm at high wastewater load were the ability to ferment sugars and the capacity to sustain different pH levels. The potential to ammonify and grow on nutrient broth was also an important feature. In conclusion, the bacterial test system together with PCA seems to be a useful tool to evaluate the function of a bacterial sand-filter ecosystem.
Using consensus regions in gene sequences encoding the two forms of nitrite reductase (Nir), a ke... more Using consensus regions in gene sequences encoding the two forms of nitrite reductase (Nir), a key enzyme in the denitrification pathway, we designed two sets of PCR primers to amplify cd1- and Cu-nir. The primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. Sequence relationships of nir genes were also established. The cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in the six published sequences. Likewise, the Cu primers amplified a 473-bp region in seven of the eight published Cu-nir sequences. Together, the two sets of PCR primers amplified nir genes in nine species within four genera, as well as in four of the seven sludge isolates. The primers did not amplify genes of nondenitrifying strains. The Cu primers amplified the expected fragment in all 13 sludge samples, but cd1-nir fragments were only obtained in five samples. PCR products of the expected s...
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Papers by Sara Hallin