Diversity and dynamics of Archaea in an activated sludge wastewater treatment plant

ABSTRACT: BACKGROUND: The activated sludge process is one of the most widely used methods for treatment of wastewater and the microbial community composition in the sludge is important for the process operation. While the bacterial communities have been characterized in various activated sludge systems little is known about archaeal communities in activated sludge. The diversity and dynamics of the Archaea community in a full-scale activated sludge wastewater treatment plant were investigated by fluorescence in situ hybridization, terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes. RESULTS: The Archaea community was specialized and dominated by Methanosaeta-like species. During a 15 month period major changes in the community composition were only observed twice despite seasonal variations in environmental and operating conditions. Water temperature appeared to be the process parameter that affected the community composition the most. Several terminal restriction fragments also showed strong correlations with sludge properties and effluent water properties. The Archaea were estimated to make up 1.6-% of total cell numbers in the activated sludge and were present both as single cells and colonies of varying sizes. CONCLUSIONS: The results presented here show that Archaea can constitute a constant and integral part of the activated sludge and that it can therefore be useful to include Archaea in future studies of microbial communities in activated sludge.     

Blue Carbon Storage in Tropical Seagrass Meadows Relates to Carbonate Stock Dynamics,Plant–Sediment Processes,and Landscape Context: Insights from the Western Indian Ocean

Globally, seagrass ecosystems are considered major blue carbon sinks and thus indirect contributors to climate change mitigation. Quantitative estimates and multi-scale appraisals of sources that underlie long-term storage of sedimentary carbon are vital for understanding coastal carbon dynamics. Across a tropical–subtropical coastal continuum in the Western Indian Ocean, we estimated organic (C_org) and inorganic (C_carb) carbon stocks in seagrass sediment. Quantified levels and variability of the two carbon stocks were evaluated with regard to the relative importance of environmental attributes in terms of plant–sediment properties and landscape configuration. The explored seagrass habitats encompassed low to moderate levels of sedimentary C_org (ranging from 0.20 to 1.44% on average depending on species- and site-specific variability) but higher than unvegetated areas (ranging from 0.09 to 0.33% depending on site-specific variability), suggesting that some of the seagrass areas (at tropical Zanzibar in particular) are potentially important as carbon sinks. The amount of sedimentary inorganic carbon as carbonate (C_carb) clearly corresponded to C_org levels, and as carbonates may represent a carbon source, this could diminish the strength of seagrass sediments as carbon sinks in the region. Partial least squares modelling indicated that variations in sedimentary C_org and C_carb stocks in seagrass habitats were primarily predicted by sediment density (indicating a negative relationship with the content of carbon stocks) and landscape configuration (indicating a positive effect of seagrass meadow area, relative to the area of other major coastal habitats, on carbon stocks), while seagrass structural complexity also contributed, though to a lesser extent, to model performance. The findings suggest that accurate carbon sink assessments require an understanding of plant–sediment processes as well as better knowledge of how sedimentary carbon dynamics are driven by cross-habitat links and sink–source relationships in a scale-dependent landscape context, which should be a priority for carbon sink conservation.     

High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe

Background  

Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture.     

Design and synthesis of 2'-anilino-4,4'-bipyridines as selective inhibitors of c-Jun N-terminal kinase-3

The design and synthesis of a new series of c-Jun N-terminal kinase-3 (JNK3) inhibitors with selectivity against JNK1 are reported. The novel series of substituted 2'-anilino-4,4'-bipyridines were designed based on a combination of hits from high throughput screening and X-ray crystal structure information of compounds crystallized into the JNK3 ATP binding active site.     

A comparison of growing season indices for the Greater Baltic Area

Predictions of the effects of global warming suggest that climate change may have large impacts on ecosystems. The length of the growing season is predicted to increase in response to increasing global temperatures. The object of this study was to evaluate different indices used for calculating the thermal growing season for the Greater Baltic Area (GBA). We included established indices of growing season start, end and length, as well as new and modified indices. Based on the results, the GBA can be divided into a maritime western part and a more continental eastern part, with the western part reacting more sensitively to the use of different indices. The eastern part is more stable, but even here the index-to-index differences are large. It was found that including or excluding a frost criterion had a significant influence on the initiation of the growing season in the western, maritime, parts of the GBA. Frost has not the same importance for the end of the growing season. However, some end indices can result in a “never ending” growing season. When looking at twentieth century trends in growing season parameters, it was found that, when averaged over the whole GBA, there was little difference in trends depending on the indices used. The general mean trend in the GBA for the twentieth century discloses an earlier onset of c. 12 days, a delayed end of c. 8 days and consequently a lengthening of the growing season of about 20 days.     

Accommodation of hydroxyl groups and their hydrogen bond system in a hydrocarbon matrix

From data of sisingle crystal analysis of 12-D-hydroxyoctadecanoic acid methyl ester principles for the incorporation of hydroxyl groups into a hydrocarbon chain matrix can be deduced. In the crystalline compound infinite hydrogen bond systems are accommodated in an orthorhombic perpendicular (O) chain arrangement. The O hydrocarbon subcell is expanded towards a hexagonal packing pattern, allowing more space and optimal geometry for the hydrogen bond system. The arrangement of the bond system in the O subcell requires that hydrogen bonded carbon chains carry alternatingly hydroxyl roups with opposite configuration. For the enantiomeric compound this requirement is met by a head to tail packing of molecules in a single layer arrangement. The corresponding racemates on the other hand pack head to head in double layers as confirmed by X-ray powder and IR studies. In monolayers both enantiomers and racemates behave identicalyy. The hydrogen bonding of the hydroxyl groups apparently leads to the formation of lipid clusters, in which the geometric conditions for both a close packing of hydrocarbon chains and the formation of an extensive hydrogen bond system do not exist.     

A novel inositol-containing glycosphingolipid isolated from human peripheral nerve

An inositol-phosphate-containing glycosphingolipid, not reported earlier, was isolated from human cauda equina. Structural characterization showed the glycosphingolipid to be inosital-phosphoryl-2(3) galactosylceramide. The concentration varied between 25 and 30 nmol/g fresh tissue.     

Tools for T-RFLP data analysis using Excel

Background

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is no consensus on how T-RFLP data should be treated and analyzed before comparisons between samples are made, and several different approaches have been proposed in the literature. The analysis of T-RFLP data can be cumbersome and time-consuming, and for large datasets manual data analysis is not feasible. The currently available tools for automated T-RFLP analysis, although valuable, offer little flexibility, and few, if any, options regarding what methods to use. To enable comparisons and combinations of different data treatment methods an analysis template and an extensive collection of macros for T-RFLP data analysis using Microsoft Excel were developed.

Results

The Tools for T-RFLP data analysis template provides procedures for the analysis of large T-RFLP datasets including application of a noise baseline threshold and setting of the analysis range, normalization and alignment of replicate profiles, generation of consensus profiles, normalization and alignment of consensus profiles and final analysis of the samples including calculation of association coefficients and diversity index. The procedures are designed so that in all analysis steps, from the initial preparation of the data to the final comparison of the samples, there are various different options available. The parameters regarding analysis range, noise baseline, T-RF alignment and generation of consensus profiles are all given by the user and several different methods are available for normalization of the T-RF profiles. In each step, the user can also choose to base the calculations on either peak height data or peak area data.

Conclusions

The Tools for T-RFLP data analysis template enables an objective and flexible analysis of large T-RFLP datasets in a widely used spreadsheet application.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0361-7) contains supplementary material, which is available to authorized users.