Publications by authors named "Anders Priemé"

31 Publications

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.

ISME J 2021 04 6;15(4):1207-1221. Epub 2021 Jan 6.

Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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http://dx.doi.org/10.1038/s41396-020-00844-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115648PMC
April 2021

Low Turnover of Soil Bacterial rRNA at Low Temperatures.

Front Microbiol 2020 25;11:962. Epub 2020 May 25.

Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.

Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at -4°C, while no degradation was detected at -18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.
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http://dx.doi.org/10.3389/fmicb.2020.00962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261852PMC
May 2020

AgNO Sterilizes Grains of Barley () without Inhibiting Germination-A Necessary Tool for Plant-Microbiome Research.

Plants (Basel) 2020 Mar 17;9(3). Epub 2020 Mar 17.

Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.

To understand and manipulate the interactions between plants and microorganisms, sterile seeds are a necessity. The seed microbiome (inside and surface microorganisms) is unknown for most plant species and seed-borne microorganisms can persist and transfer to the seedling and rhizosphere, thereby obscuring the effects that purposely introduced microorganisms have on plants. This necessitates that these unidentified, seed-borne microorganisms are removed before seeds are used for studies on plant-microbiome interactions. Unfortunately, there is no single, standardized protocol for seed sterilization, hampering progress in experimental plant growth promotion and our study shows that commonly applied sterilization protocols for barley grains using HO, NaClO, and AgNO yielded insufficient sterilization. We therefore developed a sterilization protocol with AgNO by testing several concentrations of AgNO and added two additional steps: Soaking the grains in water before the sterilization and rinsing with salt water (1% (/) NaCl) after the sterilization. The most efficient sterilization protocol was to soak the grains, sterilize with 10% (/) AgNO, and to rinse with salt water. By following those three steps, 97% of the grains had no culturable, viable microorganism after 21 days based on microscopic inspection. The protocol left small quantities of AgNO residue on the grain, maintained germination percentage similar to unsterilized grains, and plant biomass was unaltered. Hence, our protocol using AgNO can be used successfully for experiments on plant-microbiome interactions.
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http://dx.doi.org/10.3390/plants9030372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7154866PMC
March 2020

Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils.

Environ Microbiome 2019 Sep 18;14(1). Epub 2019 Sep 18.

Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark.

Background: Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season.

Results: The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted.

Conclusions: We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.
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http://dx.doi.org/10.1186/s40793-019-0344-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7989089PMC
September 2019

Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil.

ISME J 2019 05 28;13(5):1345-1359. Epub 2019 Jan 28.

Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.

The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from -10 to -2 °C or when freezing from -2 to -10 °C. In contrast, within a few days we observed changes when warming from -2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria-collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.
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http://dx.doi.org/10.1038/s41396-019-0351-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474304PMC
May 2019

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages.

Microbiome 2018 12 13;6(1):223. Epub 2018 Dec 13.

Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.

Background: It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations.

Results: Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition.

Conclusion: Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.
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http://dx.doi.org/10.1186/s40168-018-0606-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292020PMC
December 2018

Catch Crop Residues Stimulate NO Emissions During Spring, Without Affecting the Genetic Potential for Nitrite and NO Reduction.

Front Microbiol 2018 2;9:2629. Epub 2018 Nov 2.

Department of Agroecology, Aarhus University, Tjele, Denmark.

Agricultural soils are a significant source of anthropogenic nitrous oxide (NO) 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 NO emissions were monitored during spring, and soil samples were analyzed for abundances of nitrite reduction ( and ) and NO reduction genes ( clade I and II), and structure of nitrite- and NO-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 depletion associated with residue degradation in organic hotspots. Emissions of NO 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 availability. Both the size and structure of the nitrite- and NO-reducing communities correlated to the difference in NO emissions between years, while there were no consistent effects of management as represented by catch crops or fertilization. It is concluded that NO emissions were constrained by environmental, rather than the genetic potential for nitrite and NO reduction.
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http://dx.doi.org/10.3389/fmicb.2018.02629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225543PMC
November 2018

Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity.

Sci Rep 2017 11 22;7(1):16035. Epub 2017 Nov 22.

Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen K, Denmark.

Future increases in temperature and cloud cover will alter plant growth and decomposition of the large carbon pools stored in Arctic soils. A better understanding of interactions between above- and belowground processes and communities of plants and microorganisms is essential for predicting Arctic ecosystem responses to climate change. We measured ecosystem CO fluxes during the growing season for seven years in a dwarf-shrub tundra in West Greenland manipulated with warming and shading and experiencing a natural larvae outbreak. Vegetation composition, soil fungal community composition, microbial activity, and nutrient availability were analyzed after six years of treatment. Warming and shading altered the plant community, reduced plant CO uptake, and changed fungal community composition. Ecosystem carbon accumulation decreased during the growing season by 61% in shaded plots and 51% in warmed plots. Also, plant recovery was reduced in both manipulations following the larvae outbreak during the fifth treatment year. The reduced plant recovery in manipulated plots following the larvae outbreak suggests that climate change may increase tundra ecosystem sensitivity to disturbances. Also, plant community changes mediated via reduced light and reduced water availability due to increased temperature can strongly lower the carbon sink strength of tundra ecosystems.
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http://dx.doi.org/10.1038/s41598-017-16007-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700064PMC
November 2017

Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation.

Front Microbiol 2017 25;8:1832. Epub 2017 Sep 25.

Microbial Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands.

The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial community composition remains unclear. Here, we used soil microcosm experiments and multiple model disturbances to explore their short-term effect on the recovery of soil microbiota after identical or novel stresses. Soil microcosms were exposed to a heat shock to create an initial effect. Upon initial community recovery (25 days after stress), they were subjected to a second stress, either a heat or a cold shock, and they were monitored for additional 25 days. To carefully verify the bacterial response to the disturbances, we monitored changes in community composition throughout the experiment using 16S rRNA gene transcript amplicon sequencing. The application of a heat shock to soils with or without the initial heat shock resulted in similar successional dynamics, but these dynamics were faster in soils with a prior heat shock. The application of a cold shock had negligible effects on previously undisturbed soils but, in combination with an initial heat shock, caused the largest shift in the community composition. Our findings show that compounded perturbation affects bacterial community recovery by altering community structure and thus, the community's response during succession. By altering dominance patterns, disturbance legacy affects the microbiome's ability to recover from further perturbation within the 25 days studied. Our results highlight the need to consider the soil's disturbance history in the development of soil management practices in order to maintain the system's resilience.
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http://dx.doi.org/10.3389/fmicb.2017.01832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622210PMC
September 2017

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities.

Sci Rep 2017 04 6;7:45691. Epub 2017 Apr 6.

Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.
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http://dx.doi.org/10.1038/srep45691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382530PMC
April 2017

Potential microbial contamination during sampling of permafrost soil assessed by tracers.

Sci Rep 2017 02 23;7:43338. Epub 2017 Feb 23.

Department of Environmental Science, Aarhus University, DK-4000 Roskilde, Denmark.

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.
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http://dx.doi.org/10.1038/srep43338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322388PMC
February 2017

Long-term and realistic global change manipulations had low impact on diversity of soil biota in temperate heathland.

Sci Rep 2017 01 25;7:41388. Epub 2017 Jan 25.

Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark.

In a dry heathland ecosystem we manipulated temperature (warming), precipitation (drought) and atmospheric concentration of CO in a full-factorial experiment in order to investigate changes in below-ground biodiversity as a result of future climate change. We investigated the responses in community diversity of nematodes, enchytraeids, collembolans and oribatid mites at two and eight years of manipulations. We used a structural equation modelling (SEM) approach analyzing the three manipulations, soil moisture and temperature, and seven soil biological and chemical variables. The analysis revealed a persistent and positive effect of elevated CO on litter C:N ratio. After two years of treatment, the fungi to bacteria ratio was increased by warming, and the diversities within oribatid mites, collembolans and nematode groups were all affected by elevated CO mediated through increased litter C:N ratio. After eight years of treatment, however, the CO-increased litter C:N ratio did not influence the diversity in any of the four fauna groups. The number of significant correlations between treatments, food source quality, and soil biota diversities was reduced from six to three after two and eight years, respectively. These results suggest a remarkable resilience within the soil biota against global climate change treatments in the long term.
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http://dx.doi.org/10.1038/srep41388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264592PMC
January 2017

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition.

mSystems 2016 Sep-Oct;1(5). Epub 2016 Oct 18.

National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls and different types of beads for bead beating, facilitating cell lysis. We evaluate DNA concentration, purity, and stability and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate than that in standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from https://dx.doi.org/10.6084/m9.figshare.3475406. Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.
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http://dx.doi.org/10.1128/mSystems.00095-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080404PMC
October 2016

Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure.

FEMS Microbiol Ecol 2016 11 18;92(11). Epub 2016 Aug 18.

Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark.

Copper has been intensively used in industry and agriculture since mid-18(th) century and is currently accumulating in soils. We investigated the diversity of potential active bacteria by 16S rRNA gene transcript amplicon sequencing in a temperate grassland soil subjected to century-long exposure to normal (∼15 mg kg(-1)), high (∼450 mg kg(-1)) or extremely high (∼4500 mg kg(-1)) copper levels. Results showed that bioavailable copper had pronounced impacts on the structure of the transcriptionally active bacterial community, overruling other environmental factors (e.g. season and pH). As copper concentration increased, bacterial richness and evenness were negatively impacted, while distinct communities with an enhanced relative abundance of Nitrospira and Acidobacteria members and a lower representation of Verrucomicrobia, Proteobacteria and Actinobacteria were selected. Our analysis showed the presence of six functional response groups (FRGs), each consisting of bacterial taxa with similar tolerance response to copper. Furthermore, the use of FRGs revealed that specific taxa like the genus Nitrospira and several Acidobacteria groups could accurately predict the copper legacy burden in our system, suggesting a potential promising role as bioindicators of copper contamination in soils.
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http://dx.doi.org/10.1093/femsec/fiw175DOI Listing
November 2016

Enhanced summer warming reduces fungal decomposer diversity and litter mass loss more strongly in dry than in wet tundra.

Glob Chang Biol 2017 01 21;23(1):406-420. Epub 2016 Jun 21.

Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, Copenhagen, 1350, Denmark.

Many Arctic regions are currently experiencing substantial summer and winter climate changes. Litter decomposition is a fundamental component of ecosystem carbon and nutrient cycles, with fungi being among the primary decomposers. To assess the impacts of seasonal climatic changes on litter fungal communities and their functioning, Betula glandulosa leaf litter was surface-incubated in two adjacent low Arctic sites with contrasting soil moisture regimes: dry shrub heath and wet sedge tundra at Disko Island, Greenland. At both sites, we investigated the impacts of factorial combinations of enhanced summer warming (using open-top chambers; OTCs) and deepened snow (using snow fences) on surface litter mass loss, chemistry and fungal decomposer communities after approximately 1 year. Enhanced summer warming significantly restricted litter mass loss by 32% in the dry and 17% in the wet site. Litter moisture content was significantly reduced by summer warming in the dry, but not in the wet site. Likewise, fungal total abundance and diversity were reduced by OTC warming at the dry site, while comparatively modest warming effects were observed in the wet site. These results suggest that increased evapotranspiration in the OTC plots lowered litter moisture content to the point where fungal decomposition activities became inhibited. In contrast, snow addition enhanced fungal abundance in both sites but did not significantly affect litter mass loss rates. Across sites, control plots only shared 15% of their fungal phylotypes, suggesting strong local controls on fungal decomposer community composition. Nevertheless, fungal community functioning (litter decomposition) was negatively affected by warming in both sites. We conclude that although buried soil organic matter decomposition is widely expected to increase with future summer warming, surface litter decay and nutrient turnover rates in both xeric and relatively moist tundra are likely to be significantly restricted by the evaporative drying associated with warmer air temperatures.
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http://dx.doi.org/10.1111/gcb.13362DOI Listing
January 2017

Metagenomes provide valuable comparative information on soil microeukaryotes.

Res Microbiol 2016 Jun 26;167(5):436-50. Epub 2016 Mar 26.

Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark.

Despite the critical ecological roles of microeukaryotes in terrestrial ecosystems, most descriptive studies of soil microbes published so far focused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in public repositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in order to investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factors impacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While most studies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this work represents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure and reference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronounced effect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publicly available metagenome data can provide valuable information on soil microeukaryotes for comparative purposes when handled appropriately, complementing the current view provided by ribosomal amplicon sequencing methods.
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http://dx.doi.org/10.1016/j.resmic.2016.03.003DOI Listing
June 2016

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses.

Front Microbiol 2015 30;6:399. Epub 2015 Apr 30.

Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Department of Biology, University of Copenhagen Copenhagen, Denmark.

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.
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http://dx.doi.org/10.3389/fmicb.2015.00399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415418PMC
May 2015

Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T.

Genome Announc 2013 Dec 5;1(6). Epub 2013 Dec 5.

Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.

Rhodonellum psychrophilum GCM71(T), isolated from the cold and alkaline submarine ikaite columns in the Ikka Fjord in Greenland, displays optimal growth at 5 to 10°C and pH 10. Here, we report the draft genome sequence of this strain, which may provide insight into the mechanisms of adaptation to these extreme conditions.
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http://dx.doi.org/10.1128/genomeA.01014-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853064PMC
December 2013

Extreme emission of n(2)o from tropical wetland soil (pantanal, South america).

Front Microbiol 2012 4;3:433. Epub 2013 Jan 4.

Department of Biology, University of Copenhagen Copenhagen, Denmark.

Nitrous oxide (N(2)O) is an important greenhouse gas and ozone depleter, but the global budget of N(2)O remains unbalanced. Currently, ∼25% of the global N(2)O emission is ascribed to uncultivated tropical soils, but the exact locations and controlling mechanisms are not clear. Here we present the first study of soil N(2)O emission from the Pantanal indicating that this South American wetland may be a significant natural source of N(2)O. At three sites, we repeatedly measured in situ fluxes of N(2)O and sampled porewater nitrate [Formula: see text] during the low water season in 2008 and 2009. In 2010, 10 sites were screened for in situ fluxes of N(2)O and soil [Formula: see text] content. The in situ fluxes of N(2)O were comparable to fluxes from heavily fertilized forests or agricultural soils. An important parameter affecting N(2)O emission rate was precipitation, inducing peak emissions of >3 mmol N(2)O m(-2) day(-1), while the mean daily flux was 0.43 ± 0.03 mmol N(2)O m(-2) day(-1). Over 170 days of the drained period, we estimated non-wetted drained soil to contribute 70.0 mmol N(2)O m(-2), while rain-induced peak events contributed 9.2 mmol N(2)O m(-2), resulting in a total N(2)O emission of 79.2 mmol N(2)O m(-2). At the sites of repeated sampling, the pool of porewater nitrate varied [Formula: see text] with higher concentrations of [Formula: see text] (p < 0.05) found in drained soil than in water-logged soil, indicating dynamic shifts between nitrification and denitrification. In the field, O(2) penetrated the upper 60 cm of drained soil, but was depleted in response to precipitation. Upon experimental wetting the soil showed rapid O(2) depletion followed by N(2)O accumulation and a peak emission of N(2)O [Formula: see text] Assuming that the observed emission of N(2)O from these wetland soils is generally representative to the Pantanal, we suggest that this undisturbed tropical wetland potentially contributes ∼1.7% to the global N(2)O emission budget, a significant single source of N(2)O.
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http://dx.doi.org/10.3389/fmicb.2012.00433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537118PMC
January 2013

Alkalilactibacillus ikkensis, gen. nov., sp. nov., a novel enzyme-producing bacterium from a cold and alkaline environment in Greenland.

Extremophiles 2012 Feb 2. Epub 2012 Feb 2.

Department of Agriculture and Ecology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.

Three novel Gram-positive, endospore-forming bacteria were isolated from a cold and alkaline environment. Phylogenetic analysis showed that the strains were almost identical, and that they were related to Natronobacillus azotifigens 24KS-1(T) (95.8% identity), Paraliobacillus quinghaiensis YIM-C158(T) (95.1%), Paraliobacillus ryukyuensis O15-7(T) (94.5%), and Halolactibacillus miurensis M23-1(T) (93.9%). The isolates produced amylase, α-galactosidase, β-galactosidase, and β-glucuronidase, and showed optimal growth at pH 10, at 20°C, and at 2-8% (w/v) NaCl. Major fatty acids were C(14:0) (10.6-11.6%), anteiso-C(15:0) (25.7-32.7%), C(16:1) ω11c (12.2-16.0%), and C(16:0) (14.0-20.4%). The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and meso-diaminopimelic acid was found in the cell-wall peptidoglycan. The G+C content was 38.4%. DNA-DNA hybridization between strain GCM68(T) and H. miurensis M23-1(T) was 32.4%, while hybridization to N. azotifigens 24KS-1(T), Amphibacillus tropicus Z-7792(T), and Paraliobacillus ryukyuensis O15-7(T) was below 30%. The phylogenetic analysis and G+C content place strain GCM68(T) in relation to species belonging to Bacillus rRNA group 1, but phylogenetic and physiologic data combined with chemotaxonomic analyses support our proposal for a new genus, Alkalilactibacillus, gen. nov., with the novel species Alkalilactibacillus ikkensis, sp. nov. (type strain is GCM68(T) = DSM 19937 = LMG 24405).
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http://dx.doi.org/10.1007/s00792-012-0430-7DOI Listing
February 2012

Triclosan affects the microbial community in simulated sewage-drain-field soil and slows down xenobiotic degradation.

Environ Pollut 2011 Jun 23;159(6):1599-605. Epub 2011 Mar 23.

Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen K, Denmark.

Effects of the common antibacterial agent triclosan on microbial communities and degradation of domestic xenobiotics were studied in simulated sewage-drain-field soil. Cultivable microbial populations decreased 22-fold in the presence of 4 mg kg⁻¹ of triclosan, and triclosan-resistant Pseudomonas strains were strongly enriched. Exposure to triclosan also changed the general metabolic profile (Ecoplate substrate profiling) and the general profile (T-RFLP) of the microbial community. Triclosan degradation was slow at all concentrations tested (0.33-81 mg kg⁻¹) during 50-days of incubation. Mineralization experiments (¹⁴C-tracers) and chemical analyses (LC-MS/MS) showed that the persistence of a linear alkylbenzene sulfonate (LAS) and a common analgesic (ibuprofen) increased with increasing triclosan concentrations (0.16-100 mg kg⁻¹). The largest effect was seen for LAS mineralization which was severely reduced by 0.16 mg kg⁻¹ of triclosan. Our findings indicate that environmentally realistic concentrations of triclosan may affect the efficiency of biodegradation in percolation systems.
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http://dx.doi.org/10.1016/j.envpol.2011.02.052DOI Listing
June 2011

Comparison of aerobic and anaerobic [3H]leucine incorporation assays for determining pollution-induced bacterial community tolerance in copper-polluted, irrigated soils.

Environ Toxicol Chem 2011 Mar 5;30(3):588-95. Epub 2011 Jan 5.

Department of Agriculture and Ecology, University of Copenhagen, Frederiksberg, Denmark.

Pollution-induced community tolerance (PICT) constitutes a sensitive and ecologically relevant impact parameter in ecotoxicology. We report the development and application of a novel anaerobic [(3) H]leucine incorporation assay and its comparison with the conventional aerobic [(3) H]leucine incorporation assay for PICT detection in soil bacterial communities. Selection of bacterial communities was performed over 42 d in bulk soil microcosms (no plants) and in rice (Oryza sativa) rhizosphere soil mesocosms. The following experimental treatments were imposed using a full factorial design: two soil types, two soil water regimes, and four Cu application rates (0, 30, 120, or 280 µg g(-1)). Bacterial communities in bulk soil microcosms exhibited similar Cu tolerance patterns when assessed by aerobic and anaerobic PICT assays, whereas aerobic microorganisms tended to be more strongly selected for Cu tolerance than anaerobic microorganisms in rhizosphere soil. Despite similar levels of water-extractable Cu, bacterial Cu tolerance was significantly higher in acid sulfate soil than in alluvial soil. Copper amendment selected for significant PICT development in soils subjected to alternate wetting and drying, but not in continuously flooded soils. Our results demonstrate that soil bacterial communities subjected to alternate wetting and drying may be more affected by Cu than bacterial communities subjected to continuous flooding. We conclude that the parallel use of anaerobic and aerobic [(3) H]leucine PICT assays constitutes a valuable improvement over existing procedures for PICT detection in irrigated soils and other redox gradient environments such as sediments and wetlands.
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http://dx.doi.org/10.1002/etc.420DOI Listing
March 2011

Investigation of the fate and effects of acetyl cedrene on Capitella teleta and sediment bacterial community.

Ecotoxicology 2010 Aug 26;19(6):1046-58. Epub 2010 Mar 26.

Department of Microbiology, Institute of Biology, Copenhagen University, Sølvgade 83H, 1307 Copenhagen K, Denmark.

The fate of the fragrance material, acetyl cedrene (AC), in sediment was examined in a 16 day laboratory experiment using the sediment microbial community subjected to the following treatments: AC (nominal concentration; 0 and 50 microg g(-1) dw sediment) and macrofaunal worms (with/without Capitella teleta (formerly Capitella sp. I)). Furthermore effects of AC on microbial respiration in the system were determined by examining CO(2) flux. T-RFLP (terminal restriction fragment length polymorphism) was used to analyze PCR (polymerase chain reaction) amplified 16S DNA gene fragments from the sediments to detect changes in the structure and diversity of the bacterial community. In addition, survival of C. teleta in sediment was determined. Lastly, we examined how the interactions between microbes and C. teleta in the sediment affected the above-mentioned parameters. The results showed that there was an interaction between worm treatment and time of sampling on the loss of AC from the sediment. This was caused by AC loss initially being fastest in the sediment with C. teleta present, but at experimental termination there was no significant difference between the two treatments (i.e., with/without worms) in the amount of AC remaining in the sediment. Survival of C. teleta was significantly reduced by AC at experimental termination, but neither microbial respiration nor structure and diversity of the bacterial community were significantly affected.
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http://dx.doi.org/10.1007/s10646-010-0486-zDOI Listing
August 2010

Line probe assay for differentiation within Mycobacterium tuberculosis complex. Evaluation on clinical specimens and isolates including Mycobacterium pinnipedii.

Scand J Infect Dis 2009 ;41(9):635-41

Section for Evolution and Microbiology, Department of Biology, Copenhagen University, Denmark.

A line probe assay (GenoType MTBC) was evaluated for species differentiation within the Mycobacterium tuberculosis complex (MTBC). We included 387 MTBC isolates, 43 IS6110 low-copy MTBC isolates, 28 clinical specimens with varying microscopy grade, and 30 isolates of non-tuberculous mycobacteria. The assay was 100% specific and identified all 387 isolates and 98% of all IS6110 low-copy strains in concordance with the gold standard. The 2% discrepancy was caused by 1 isolate showing a faint restriction fragment length polymorphism (RFLP) pattern. The assay could provide specifies identification in 13 of 19 (68%) microscopy-positive specimens and 0 of 9 microscopy-negative specimens. To our surprise, the probe for M. africanum subtype I reacted with M. pinnipedii. This cross-reaction has not previously been reported. The assay was rapid, easy to perform and directly applicable in highly smear-positive specimens. We predict that the assay will enable enhanced surveillance of species-specific treatment outcome, which may change treatment regimens.
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http://dx.doi.org/10.1080/00365540903127425DOI Listing
March 2010

Different bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marina.

FEMS Microbiol Ecol 2007 Oct 6;62(1):108-17. Epub 2007 Sep 6.

Marine Biological Laboratory, Department of Biology, University of Copenhagen, Helsingør, Denmark.

The bacterial community of Zostera marina-inhabited bulk sediment vs. root-associated bacteria was investigated by terminal restriction fragment length polymorphism and sequencing, and the spatial extension of the oxygen loss from roots was determined by oxygen microsensors. Extensive oxygen loss was found in the tip region of the youngest roots, and most of the rhizoplane of Z. marina roots was thus anoxic. A significant difference between the bacterial communities associated with the roots and bulk sediment was found. No significant differences were found between differently aged root-bundles. Terminal restriction fragments (TRFs) assigned to sulfate-reducing Deltaproteobacteria showed a relative mean distribution of 12% and 23% of the PCR-amplified bacterial community in the bulk-sediment at the two sites, but only contributed <2% to the root-associated communities. TRFs assigned to Epsilonproteobacteria showed a relative mean distribution of between 5% and 11% in the root-associated communities of the youngest root bundle, in contrast to the bulk-sediment where this TRF only contributed <1.3%. TRFs assigned to Actinobacteria and Gammaproteobacteria also seemed important first root-colonizers, whereas TRFs assigned to Deltaproteobacteria became increasingly important in the root-associated community of the older root bundles. The presence of the roots thus apparently selects for a distinct bacterial community, stimulating the growth of potential symbiotic Epsilon- and Gammaproteobacteria and/or inhibiting the growth of sulfate-reducing Deltaproteobacteria.
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http://dx.doi.org/10.1111/j.1574-6941.2007.00373.xDOI Listing
October 2007

Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland.

Int J Syst Evol Microbiol 2006 Dec;56(Pt 12):2887-2892

Department of Ecology, Royal Veterinary and Agricultural University, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71(T) belonged to the family 'Flexibacteraceae' in the phylum Bacteroidetes. Strain GCM71(T), together with five related isolates from ikaite columns, formed a separate cluster with 86-93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71(T) was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA-DNA hybridization between strain GCM71(T) and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71(T) were pH 9.2-10.0, 5 degrees C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90-97 %), with a high abundance of iso-C(17 : 1)omega9c (17.5 %), iso-C(17 : 0) 3-OH (17.5 %) and summed feature 3, comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71(T) (=DSM 17998(T)=LMG 23454(T)) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.
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http://dx.doi.org/10.1099/ijs.0.64450-0DOI Listing
December 2006

Arsukibacterium ikkense gen. nov., sp. nov, a novel alkaliphilic, enzyme-producing gamma-Proteobacterium isolated from a cold and alkaline environment in Greenland.

Syst Appl Microbiol 2007 Apr 21;30(3):197-201. Epub 2006 Jun 21.

Bioneer A/S, Kogle Allé 2, Hørsholm, Denmark.

A novel aerobic, Gram-negative, non-pigmented bacterium, GCM72(T), was isolated from the alkaline, low-saline ikaite columns in the Ikka Fjord, SW Greenland. Strain GCM72(T) is a motile, non-pigmented, amylase- and protease-producing, oxidase-positive, and catalase-negative bacterium, showing optimal growth at pH 9.2-10.0, at 15 degrees C, and at 3% (w/v) NaCl. Major fatty acids were C(12:0) 3-OH (12.2+/-0.1%), C(16:00) (18.0+/-0.1%), C(18:1)omega7c (10.7+/-0.5%), and summed feature 3 comprising C(16:1)omega7c and/or iso-C(15:0) 2-OH (36.3+/-0.7%). Phylogenetic analysis based on 16S rRNA gene sequences showed that isolate GCM72(T) was most closely related to Rheinheimera baltica and Alishewanella fetalis of the gamma-Proteobacteria with a 93% sequence similarity to both. The G+C content of DNA isolated from GCM72(T) was 49.9mol% and DNA-DNA hybridization between GCM72T and R. baltica was 9.5%. Fatty acid analysis and G+C content supports a relationship primarily to R. baltica, but several different features, such as a negative catalase-response and optimal growth at low temperature and high pH, together with the large phylogenetic distance and low DNA similarity to its closest relatives, lead us to propose a new genus, Arsukibacterium, gen. nov., with the new species Arsukibacterium ikkense sp. nov. (type strain is GCM72(T)).
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http://dx.doi.org/10.1016/j.syapm.2006.05.003DOI Listing
April 2007

Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland.

Extremophiles 2006 Dec 13;10(6):551-62. Epub 2006 Jun 13.

Bioneer A/S, Hørsholm, Denmark.

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4 degrees C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.
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http://dx.doi.org/10.1007/s00792-006-0529-9DOI Listing
December 2006

Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments.

FEMS Microbiol Ecol 2004 May;48(2):261-71

Department of Microbiology, Copenhagen University, Sølvgade 83H, Copenhagen K, Denmark.

ABSTRACT Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kgNha(-1)year(-1)) and cattle manure (75 and 150 kgNha(-1)year(-1)) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different. Also, these sites significantly differed from the control plot (no fertilizer treatment), whereas the patterns for low and high N-additions were barely separable from each other. Sequencing and phylogenetic analysis of 54 nirK clones revealed that the major part of the nirK-containing bacteria investigated belonged to a yet uncultivated cluster of denitrifying bacteria.
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http://dx.doi.org/10.1016/j.femsec.2004.02.002DOI Listing
May 2004