Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing

A recent investigation of bacterioplankton communities in the German Bight towards the end of a diatomdominated spring phytoplankton bloom revealed pronounced successions of distinct bacterial clades. A combination of metagenomics and metaproteomics indicated that these clades had distinct substrate spectra and consumed different algal substrates. In this study we re-analyzed samples from the initial study by total community RNA (metatranscriptomics) and 16S rRNA gene amplicon sequencing. This complementary approach provided new insights into the community composition and expressed genes as well as the assessment of metabolic activity levels of distinct clades. Flavobacteria (genera Ulvibacter, Formosa, and Polaribacter), Alphaproteobacteria (SARI 1 clade and Rhodobacteraceae) and Gammaproteobacteria (genus Reinekea and SAR92 dade) were the most abundant taxa. Mapping of the metatranscriptome data on assembled and taxonomically classified metagenome data of the same samples substantiated that Formosa and Polaribacter acted as major algal polymer degraders, whereas Rhodobacteraceae and Reinekea spp. exhibited less specialized substrate spectra. In addition, we found that members of the Rhodobacteraceae and SAR92 clade showed high metabolic activity levels, which suggests that these clades played a more important role during the bloom event as indicated by their in situ abundances. (c) 2014 The Authors. Published by Elsevier B.V

How to make large, void free dust clusters in dusty plasma under microgravity

Collections of micrometer sized solid particles immersed in plamsa are used to mimic many systems from solid state and fluid physics, due to their strong electrostatic interaction, their large inertia, and the fact that they are large enough to be visualized with ordinary optics. On Earth, gravity restricts the so called dusty plasma systems to thin, two-dimensional layers, unless special experimental geometries are used, involving heated or cooled electrons, and/or the use of dielectric materials.In micro-gravity experiments, the formation of a dust-free void breaks the isotropy of three-dimensional dusty plasma systems. In order to do real three-dimensional experiments, this void has somehow to be closed. In this paper, we use a fully self-consistent fluid model to study the closure of a void in a micro-gravity experiment, by lowering the driving potential. The analysis goes beyond the simple description of the virtual void, which describes the formation of a void without taking the dust into account. We show that self-organization plays an important role in void formation and void closure, which also allows a reversed scheme, where a discharge is run at low driving potentials and small batches of dust are added. No hysteresis is found this way. Finally, we compare our results to recent experiments and find good agreement,but only when we do not take charge-exchange collisions into account

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Pink‐ and orange‐pigmented Planctomycetes produce saproxanthin‐type carotenoids including a rare C45 carotenoid

Planctomycetes, are ubiquitous and environmentally important Gram-negative aquatic bacteria with key roles in global carbon and nitrogen cycles. Many planctomycetal species have a pink or orange colour and have been suggested to produce carotenoids. Potential applications as food colorants or anti-oxidants have been proposed. Hitherto, the planctomycetal metabolism is largely unexplored and the strain pigmentation has not been identified. For a holistic view on the complex planctomycetal physiology we analyzed carotenoid profiles of the pink-pigmented strain Rhodopirellula rubra LF2T and of the orange strain Rubinisphaera brasiliensis Gr7. During LC-MS/MS analysis of culture extracts we were able to identify three saproxanthin-type carotenoids including a rare C45 carotenoid. These compounds, saproxanthin, dehydroflexixanthin and 2’-isopentenyldehydrosaproxanthin, derive from the common carotenoid precursor lycopene and are characterized by related end groups, namely a 3-hydroxylated β-carotene-like cyclohexene ring as one end group and simple hydration on the other end of the molecule. Based on the observed molecule structure we present putative pathways for their biosynthesis. Results support Planctomycetes as a promising, yet mostly untapped source of carotenoids

Evaluation and optimization of PCR primers for selective and quantitative detection of marine ANME subclusters involved in sulfate-dependent anaerobic methane oxidation

Since the discovery that anaerobic methanotrophic archaea (ANME) are involved in the anaerobic oxidation of methane coupled to sulfate reduction in marine sediments, different primers and probes specifically targeting the 16S rRNA gene of these archaea have been developed. Microbial investigation of the different ANME subtypes (ANME-1; ANME-2a, b, and c; and ANME-3) was mainly done in sediments where specific subtypes of ANME were highly enriched and methanogenic cell numbers were low. In different sediments with higher archaeal diversity and abundance, it is important that primers and probes targeting different ANME subtypes are very specific and do not detect other ANME subtypes or methanogens that are also present. In this study, primers and probes that were regularly used in AOM studies were tested in silico on coverage and specificity. Most of the previously developed primers and probes were not specific for the ANME subtypes, thereby not reflecting the actual ANME population in complex samples. Selected primers that showed good coverage and high specificity for the subclades ANME-1, ANME-2a/b, and ANME-2c were thoroughly validated using quantitative polymerase chain reaction (qPCR). From these qPCR tests, only certain combinations seemed suitable for selective amplification. After optimization of these primer sets, we obtained valid primer combinations for the selective detection and quantification of ANME-1, ANME-2a/b, and ANME-2c in samples where different ANME subtypes and possibly methanogens could be present. As a result of this work, we propose a standard workflow to facilitate selection of suitable primers for qPCR experiments on novel environmental samples.This research is supported by the Dutch Technology Foundation STW (project 10711), which is part of the Netherlands Organization for Scientific Research (NWO), and which is partly funded by the Ministry of Economic Affairs. Research of AJMS is supported by ERC grant (project 323009). Research of PHATand AJMS is supported by the SIAM Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO).info:eu-repo/semantics/publishedVersio

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

Ovine footrot is a highly prevalent bacterial disease caused by Dichelobacter nodosus and characterised by the separation of the hoof horn from the underlying skin. The role of innate immune molecules and other bacterial communities in the development of footrot lesions remains unclear. This study shows a significant association between the high expression of IL1β and high D. nodosus load in footrot samples. Investigation of the microbial population identified distinct bacterial populations in the different disease stages and also depending on the level of inflammation. Treponema (34%), Mycoplasma (29%) and Porphyromonas (15%) were the most abundant genera associated with high levels of inflammation in footrot. In contrast, Acinetobacter (25%), Corynebacteria (17%) and Flavobacterium (17%) were the most abundant genera associated with high levels of inflammation in healthy feet. This demonstrates for the first time there is a distinct microbial community associated with footrot and high cytokine expression

Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability

Aims: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). Methods: Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues. Results: Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants. Conclusions: Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture

Maternal Risk of Breeding Failure Remained Low throughout the Demographic Transitions in Fertility and Age at First Reproduction in Finland

Radical declines in fertility and postponement of first reproduction during the recent human demographic transitions have posed a challenge to interpreting human behaviour in evolutionary terms. This challenge has stemmed from insufficient evolutionary insight into individual reproductive decision-making and the rarity of datasets recording individual long-term reproductive success throughout the transitions. We use such data from about 2,000 Finnish mothers (first births: 1880s to 1970s) to show that changes in the maternal risk of breeding failure (no offspring raised to adulthood) underlay shifts in both fertility and first reproduction. With steady improvements in offspring survival, the expected fertility required to satisfy a low risk of breeding failure became lower and observed maternal fertility subsequently declined through an earlier age at last reproduction. Postponement of the age at first reproduction began when this risk approximated zero–even for mothers starting reproduction late. Interestingly, despite vastly differing fertility rates at different stages of the transitions, the number of offspring successfully raised to breeding per mother remained relatively constant over the period. Our results stress the importance of assessing the long-term success of reproductive strategies by including measures of offspring quality and suggest that avoidance of breeding failure may explain several key features of recent life-history shifts in industrialized societies

Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins

High-fat (HF) diets are thought to disrupt the profile of the gut microbiota in a manner that may contribute to the neuroinflammation and neurobehavioral changes observed in obesity. Accordingly, we hypothesize that by preventing HF-diet induced dysbiosis it is possible to prevent neuroinflammation and the consequent neurological disorders. Anthocyanins are flavonoids found in berries that exhibit anti-neuroinflammatory properties in the context of obesity. Here, we demonstrate that the blackberry anthocyanin-rich extract (BE) can modulate gut microbiota composition and counteract some of the features of HF-diet induced dysbiosis. In addition, we show that the modifications in gut microbial environment are partially linked with the anti-neuroinflammatory properties of BE. Through fecal metabolome analysis, we unravel the mechanism by which BE participates in the bilateral communication between the gut and the brain. BE alters host tryptophan metabolism, increasing the production of the neuroprotective metabolite kynurenic acid. These findings strongly suggest that dietary manipulation of the gut microbiota with anthocyanins can attenuate the neurologic complications of obesity, thus expanding the classification of psychobiotics to anthocyanins

Phenotypic, cytogenetic and spike fertility characterization of a population of male-sterile triticale

Triticale (X Triticosecale Wittmack) is a good cereal for production of flour and feed. A segregating population of triticale was developed from a male-sterile (MS) plant. To determine whether this new source of male sterility in triticale is appropriate for use in breeding programs the expression of the male sterility phenotype was characterized through spike fertility, meiotic behavior, and pollen. Controlled crosses between male-sterile plants and control varieties male-fertile (MF) of triticale were also conducted, and cytological analyses were performed in the F2 and backcross plants. Plants with male-sterile phenotypes displayed reduced spike fertility when compared to plants with male-fertile phenotypes. Compared to male-fertile plants, male-sterile plants exhibited a lower percentage of normal meiotic cells, a reduced meiotic index and reduced pollen viability. The F2 plants had improved pollen fertility when compared to the male-sterile population; however there were no corresponding improvements in the percentage of normal meiotic cells or in the meiotic index. A single generation of backcrosses resulted in an improved meiotic index and increased pollen viability. However, no changes in the percentage of normal meiotic cells were observed. Meiotic instability, which was shown to be inheritable, was the likely cause of male sterility. Therefore, the use of this population in triticale breeding was considered to be inappropriate because it could promote or contribute to the maintenance of meiotic instability, which is commonly observed in this species