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

Ear- and hearing-related impact on quality of life in children with cleft palate : development and pretest of a health-related quality of life (HRQOL) instrument

Objectives: To investigate to what extent middle ear problems and associated hearing loss affect quality of life (QoL) of children born with a cleft palate. Methods: Fifty-five children aged between 6 and 18 years, born with non-syndromic cleft palate +/- cleft lip (CP/L) were included. A new health-related quality of life (HRQOL) questionnaire was generated with consideration of the following domains of QoL: communication, hearing loss, physical symptoms, limitation of activities and socio-emotional impact. Results: Major psychosocial problems were not reported in the majority of children as a result of their ear and hearing problems. However, according to their parents, 2 out of 3 children, had difficulty speaking clearly and understandably. These communication problems led to behavioural problems and social isolation in 1 out of 5 children. Scholastic achievement was negatively influenced by two factors: hearing loss and sleep disturbance due to ear problems. Conclusions: To our knowledge this is the first study to quantitatively measure the ear- and hearing-related impact on QoL in children born with CP/L. Large-scale, multicentre studies are needed to further research and expand on the findings of this pilot study

Digital equity: Diversity, inclusion and access for incarcerated students in a digital age

ELearning has been touted as the way in which universities can enable participation by large numbers of students from non-traditional cohorts. There is no doubt that the flexibility of access that eLearning allows makes study accessible for a number of cohorts, including those engaged in full-time work or caring duties. However, cohorts such as incarcerated students and other students without Internet access, are sitting on the wrong side of the digital divide and are increasingly marginalised by the very technology anticipated to overcome their exclusion from study. This paper examines the fundamental issues of equity involved with eLearning, and particularly for incarcerated students. The very issue of access to the Internet is fraught with rates of access varying widely between different sectors of society. This discussion prompts higher education providers to think beyond business-as-usual when speaking of increasing participation in higher education

Digital equity: Diversity, inclusion and access for incarcerated students in a digital age

ELearning has been touted as the way in which universities can enable participation by large numbers of students from non-traditional cohorts. There is no doubt that the flexibility of access that eLearning allows makes study accessible for a number of cohorts, including those engaged in full-time work or caring duties. However, cohorts such as incarcerated students and other students without Internet access, are sitting on the wrong side of the digital divide and are increasingly marginalised by the very technology anticipated to overcome their exclusion from study. This paper examines the fundamental issues of equity involved with eLearning, and particularly for incarcerated students. The very issue of access to the Internet is fraught with rates of access varying widely between different sectors of society. This discussion prompts higher education providers to think beyond business-as-usual when speaking of increasing participation in higher education

Life without a cell membrane: Challenging the specificity of bacterial endophytes within Bryopsis (Bryopsidales, Chlorophyta)

<p>Abstract</p> <p>Background</p> <p>The siphonous green macroalga <it>Bryopsis </it>has some remarkable characteristics. Besides hosting a rich endophytic bacterial flora, <it>Bryopsis </it>also displays extraordinary wound repair and propagation mechanisms. This latter feature includes the formation of protoplasts which can survive in the absence of a cell membrane for several minutes before regenerating into new individuals. This transient 'life without a membrane' state, however, challenges the specificity of the endophytic bacterial communities present and raises the question whether these bacteria are generalists, which are repeatedly acquired from the environment, or if there is some specificity towards the <it>Bryopsis </it>host.</p> <p>Results</p> <p>To answer this question, we examined the temporal stability and the uniqueness of endobiotic bacterial communities within <it>Bryopsis </it>samples from the Mexican west coast after prolonged cultivation. DGGE analysis revealed that <it>Bryopsis </it>endophytic bacterial communities are rather stable and clearly distinct from the epiphytic and surrounding cultivation water bacterial communities. Although these endogenous communities consist of both facultative and obligate bacteria, results suggest that <it>Bryopsis </it>owns some intrinsic mechanisms to selectively maintain and/or attract specific bacteria after repeated wounding events in culture.</p> <p>Conclusions</p> <p>This suggests that <it>Bryopsis </it>algae seem to master transient stages of life without a cell membrane well as they harbor specific - and possibly ecological significant - endophytic bacteria.</p

The increasing significance of digital equity in higher education: An introduction to the Digital equity special issue

Digital equity is a complex and multifaceted concept. It includes not only access to hardware, software, and connectivity to the Internet but also meaningful, high-quality, and culturally relevant content in local languages, and the ability to create, share, and exchange knowledge. Participatory citizenship in the digital era involves the right to access and participate in higher education. Indeed, it is a key civil rights issue of the modern world. This editorial provides the context in which the articles in this special issue are located

Das Weidesystem beeinflusst Schlachtleistung und Fleischqualität von gesömmerten Lämmern

Die Sömmerungsbeiträge für Schafe sind in der Schweiz nach Weidesystem gestaffelt und bei Umtriebsweide höher als bei Standweide. In dieser Studie wurden in einem kontrollierten Alpweideversuch die in diesen beiden Weidesystemen erzielbare Mast- und Schlachtleistung sowie die Fleischqualität verglichen. Hierzu wurden 55 männliche kastrierte Lämmer (36,2±4,2 kg schwer und 27±3 Wochen alt) der Schweizer Rassen Engadinerschaf und Walliser Schwarznasenschaf einer fetten Milchkrautweide und einer Borstgrasweide jeweils mit Standweide- und Umtriebsweidesystem zugeteilt. Von jeder Rasse wurden auf jedem Vegetationstyp und Weidesystem sechs bis sieben Tiere gehalten. Bei Umtriebsweide waren Tageszuwachs, Schlachtausbeute und tendenziell die Fleischigkeit (CH-TAX) bei beiden Rassen höher als bei Standweide. Einen stärkeren Einfluss auf Tageszuwachs und Schlachtgewicht als das Weidesystem hatte jedoch der Vegetationstyp. Im Vergleich zur Standweide waren beim Fleisch vom Umtriebsweidesystem der Garverlust höher und die maximale Scherkraft niedriger. Dies galt aber nur für die Engadinerschafe. Bei den Walliser Schwarznasenschafen war nur die Scherkraft ansatzweise niedriger. Im Hinblick auf die Fleischqualität reagierten die beiden Rassen also unterschiedlich sensibel auf das Weidesystem. Bei den Mast- und Schlachtleistungen hingegen war für beide Rassen die Alplämmermast im Umtriebsweidesystem derjenigen im Standweidesystem vorzuziehe

Who Is in There? Exploration of Endophytic Bacteria within the Siphonous Green Seaweed Bryopsis (Bryopsidales, Chlorophyta)

Associations between marine seaweeds and bacteria are widespread, with endobiotic bacterial-algal interactions being described for over 40 years. Also within the siphonous marine green alga Bryopsis, intracellular bacteria have been visualized by electron microscopy in the early ‘70s, but were up to now never molecularly analyzed. To study this partnership, we examined the presence and phylogenetic diversity of microbial communities within the cytoplasm of two Bryopsis species by combining fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Sequencing results revealed the presence of Arcobacter, Bacteroidetes, Flavobacteriaceae, Mycoplasma, Labrenzia, Phyllobacteriaceae and Xanthomonadaceae species. Although the total diversity of the endobiotic communities was unique to each Bryopsis culture, Bacteroidetes, Mycoplasma, Phyllobacteriaceae, and in particular Flavobacteriaceae bacteria, were detected in several Bryopsis samples collected hundreds of kilometres apart. This suggests that Bryopsis closely associates with well-defined endophytic bacterial communities of which some members possibly maintain an endosymbiotic relationship with the algal host

Epidemic and Nonepidemic Multidrug-Resistant Enterococcus faecium

The epidemiology of vancomycin-resistant Enterococcus faecium (VREF) in Europe is characterized by a large community reservoir. In contrast, nosocomial outbreaks and infections (without a community reservoir) characterize VREF in the United States. Previous studies demonstrated host-specific genogroups and a distinct genetic lineage of VREF associated with hospital outbreaks, characterized by the variant esp-gene and a specific allele-type of the purK housekeeping gene (purK1). We investigated the genetic relatedness of vanA VREF (n=108) and vancomycin-susceptible E. faecium (VSEF) (n=92) from different epidemiologic sources by genotyping, susceptibility testing for ampicillin, sequencing of purK1, and testing for presence of esp. Clusters of VSEF fit well into previously described VREF genogroups, and strong associations were found between VSEF and VREF isolates with resistance to ampicillin, presence of esp, and purK1. Genotypes characterized by presence of esp, purK1, and ampicillin resistance were most frequent among outbreak-associated isolates and almost absent among community surveillance isolates. Vancomycin-resistance was not specifically linked to genogroups. VREF and VSEF from different epidemiologic sources are genetically related; evidence exists for nosocomial selection of a subtype of E. faecium, which has acquired vancomycin-resistance through horizontal transfer