Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

Background: Copper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to primer coverage limitations that can be attributed to their broad taxonomic diversity and enormous nirK sequence divergence. Therefore, we revisited reported analyses on partial NirK sequences using a taxonomically diverse, full-length NirK sequence dataset. Results: Division of NirK sequences into two phylogenetically distinct clades was confirmed, with Clade I mainly comprising Alphaproteobacteria (plus some Gamma- and Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae, Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta and Gamma). Failure of currently available primer sets to target diverse NirK-type denitrifiers in environmental surveys could be attributed to mismatches over the whole length of the primer binding regions including the 3' site, with Clade II sequences containing higher sequence divergence than Clade I sequences. Simultaneous presence of both the denitrification and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers. Conclusion: The previously reported division of NirK into two distinct phylogenetic clades was confirmed using a taxonomically diverse set of full-length NirK sequences. Enormous sequence divergence of nirK gene sequences, probably due to variable nirK evolutionary trajectories, will remain an issue for covering diverse NirK-type denitrifiers in amplicon-based environmental surveys. The potential of a single organism to partition nitrate to either denitrification or dissimilatory nitrate reduction to ammonium appeared to be more widespread than originally anticipated as more than half of all NirK-type denitrifiers were shown to contain both pathways in their genome

Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers

The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6m) with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celenbacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms

Interactions between benthic copepods, bacteria and diatoms promote nitrogen retention in intertidal marine sediments

The present study aims at evaluating the impact of diatoms and copepods on microbial processes mediating nitrate removal in fine-grained intertidal sediments. More specifically, we studied the interactions between copepods, diatoms and bacteria in relation to their effects on nitrate reduction and denitrification. Microcosms containing defaunated marine sediments were subjected to different treatments: an excess of nitrate, copepods, diatoms (Navicula sp.), a combination of copepods and diatoms, and spent medium from copepods. The microcosms were incubated for seven and a half days, after which nutrient concentrations and denitrification potential were measured. Ammonium concentrations were highest in the treatments with copepods or their spent medium, whilst denitrification potential was lowest in these treatments, suggesting that copepods enhance dissimilatory nitrate reduction to ammonium over denitrification. We hypothesize that this is an indirect effect, by providing extra carbon for the bacterial community through the copepods' excretion products, thus changing the C/N ratio in favour of dissimilatory nitrate reduction. Diatoms alone had no effect on the nitrogen fluxes, but they did enhance the effect of copepods, possibly by influencing the quantity and quality of the copepods' excretion products. Our results show that small-scale biological interactions between bacteria, copepods and diatoms can have an important impact on denitrification and hence sediment nitrogen fluxes

The first CCD photometric study of the open cluster NGC 2126

We present the first CCD photometric observations of the northern open cluster NGC 2126. Data were taken on eight nights in February and December 2002 with a total time span of ~57 hours. Almost 1000 individual V-band frames were examined to find short-period variable stars. We discovered six new variable stars, of which one is a promising candidate for an eclipsing binary with a pulsating component. Two stars were classified as delta Scuti stars and one as Algol-type eclipsing binary. Two stars are slow variables with ambiguous classification. From absolute VRI photometry we have estimated the main characteristics of the cluster: m-M=11.0+/-0.5, E(V-I)=0.4+/-0.1, E(V-R)=0.08+/-0.06 (E(B-V)=0.2+/-0.15) and d=1.3+/-0.6 kpc. Cluster membership is suggested for three variable stars from their positions on the colour-magnitude diagram.Comment: 7 pages, 10 figures, accepted for publication in A&

Teaching physics with 670 nm diode lasers—construction of stabilized lasers and lithium cells

We describe the construction and operation of stabilized 670 nm diode lasers for use in undergraduate teaching labs. Because they emit low‐power visible radiation, 670 nm lasers are safe and aesthetically pleasing, and thus are an attractive alternative to near‐infrared diode lasers in the undergraduate laboratory. We also describe the fabrication of a robust and reliable lithium atomic vapor cell, which can be used with the 670 nm diode lasers to perform a variety of atomic physics experiments

Coxiella burnetii in Bulk Tank Milk Samples, United States

Dairy cattle are a primary reservoir of Coxiella burnetii, which causes Q fever. However, no recent nationwide studies have assessed the prevalence and risks of Q fever in dairy cattle. We report ≥94% prevalence in samples of bulk tank milk from U.S. dairy herds tested during the past 3 years

Enumerative Sphere Shaping for Rate Adaptation and Reach Increase in WDM Transmission Systems

The performance of enumerative sphere shaping (ESS), constant composition distribution matching (CCDM), and uniform signalling are compared at the same forward error correction rate. ESS is shown to offer a reach increase of approximately 10% and 22% compared to CCDM and uniform signalling, respectively.Comment: 4 Pages, 4 figure

The OCareCloudS project: toward organizing care through trusted cloud services

The increasing elderly population and the shift from acute to chronic illness makes it difficult to care for people in hospitals and rest homes. Moreover, elderly people, if given a choice, want to stay at home as long as possible. In this article, the methodologies to develop a cloud-based semantic system, offering valuable information and knowledge-based services, are presented. The information and services are related to the different personal living hemispheres of the patient, namely the daily care-related needs, the social needs and the daily life assistance. Ontologies are used to facilitate the integration, analysis, aggregation and efficient use of all the available data in the cloud. By using an interdisciplinary research approach, where user researchers, (ontology) engineers, researchers and domain stakeholders are at the forefront, a platform can be developed of great added value for the patients that want to grow old in their own home and for their caregivers