Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. Acknowledgements We would like to thank Dr Robert Griffith/CEH for providing DNA from soil samples and Dr Anthony Travis for his help with BioLinux. Sequencing was performed in NERC platform in Liverpool. CG-R was funded by a NERC fellowship NE/J019151/1. CQ was funded by a MRC fellowship (MR/M50161X/1) as part of the cloud infrastructure for microbial genomics consortium (MR/L015080/1).Peer reviewedPublisher PD

A PRECISE, LOW-COST RTK GNSS SYSTEM FOR UAV APPLICATIONS

High accuracy with real-time positioning of moving objects has been considered a standard task of engineering geodesy for 10 to 15 years. An absolute positioning accuracy of 1–3 cm is generally possible worldwide and is further used in many areas of machine guidance (machine control and guidance), and farming (precision farming) as well as for various special applications (e.g. railway trolley, mining, etc.). The cost of the measuring instruments required for the use of geodetic L1/L2 receivers with a local reference station amounts to approximately USD 30,000 to 50,000. Therefore, dual frequency RTK GNSS receivers are not used in the mass market. Affordable GPS/GNSS modules have already reached the mass market in various areas such as mobile phones, car navigation, the leisure industry, etc. Kinematic real-time positioning applications with centimetre or decimetre levels could also evolve into a mass product. In order for this to happen, the costs for such systems must lie between USD 1,000 to 2,000. What exactly low-cost means is determined by the precise specifications of the given individual application. Several university studies in geodesy focus on the approach of high-accuracy positioning by means of single frequency receivers for static applications [e.g. GLABSCH et. al. 2009, SCHWIEGER and GLÄSER 2005, ALKAN 2010, REALINI et. al. 2010, KORTH and HOFMANN 2011]. Although intelligent approaches have been developed that compute a trajectory in the post-processing mode [REALINI et. al., 2010], at present, there are only a very few GNSS Low-Cost Systems that enable real-time processing. This approach to precise position determination by means of the computation of static raw data with single frequency receivers is currently being explored in a research project at the Beuth Hochschule für Technik Berlin – and is being further developed for kinematic applications. The project is embedded in the European Social Fund. It is a follow-up project in the area of static positioning with single GNSS frequency receivers [KORTH and HOFMANN, 2011]

Soil pH and plant diversity drive co-occurrence patterns of ammonia and nitrite oxidizer in soils from forest ecosystems.

In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acidic sites with low availability of ammonia, would reduce the abundance of nitrite-oxidizing bacteria (NOB). To detect shifts in co-occurrence patterns, the abundance of key players was measured at 50 forest plots with coniferous respectively deciduous vegetation and different soil pH levels in the region Schwäbische Alb (Germany). We found ammonia-oxidizing archaea (AOA) and Nitrospira-like NOB (NS) to be dominating in numbers over their counterparts across all forest types. AOA co-occurred mostly with NS, while bacterial ammonia oxidizers (AOB) were correlated with Nitrobacter-like NOB (NB). Co-occurrence patterns changed from tight significant relationships of all ammonia and nitrite oxidizers in deciduous forests to a significant relationship of AOB and NB in coniferous forests, where AOA abundance was reduced. Surprisingly, no co-occurrence structures between ammonia and nitrite oxidizers could be determined at acidic sites, although abundances were correlated to the respective nitrogen pools. This raises the question whether interactions with heterotrophic nitrifiers may occur, which needs to be addressed in future studies

Drivers for ammonia-oxidation along a land-use gradient in grassland soils.

In this study, drivers for ammonia-oxidation and the related microbial communities (ammonia-oxidizing bacteria and archaea) were investigated in grassland soils on the local as well as on the regional scale focusing on the role of land-use intensity (LUI). To this end, 150 sites from three distinct regions across Germany were selected, covering the whole range of LUI levels (from natural grasslands up to intensive managed meadows). Furthermore, the role of contrasting soil types was analyzed in one of the regions (high vs low organic matter content) for ammonia-oxidation. We revealed a significant increase in potential nitrification rates and abundance of ammonia-oxidizing microbes at two sites on the local level from extensively to intensively managed sites, which indicates that the response pattern of ammonia-oxidizing microbes in grassland soils is likely triggered to a large extent by LUI. However at a third site, where two different soil types were investigated, no correlation between LUI and potential nitrification rates was observed, and only a site-specific effect was apparent. At this site, on the one hand the specific soil type (Histosol) and the related continuous nutrient mobilization from the former peat matrix, as well as the high groundwater level, which could induce a high abundance of methane- oxidizing microbes in the top soil, may be of greater importance as a driver for potential nitrification rates and abundance of ammonia- oxidizing microbes than LUI. On the other hand, the mineral soils of this site were characterized by extreme water shortage, which may also explain the lack of potential nitrification and the abundance of ammonia-oxidizing bacteria and archaea. Thus any extrapolation of local data to regional predictions must be made with care, as factors other than LUI may be of importance if the nitrification potential of a soil is to be described

Nitrification inhibitors mitigate N₂O emissions more effectively under straw-induced conditions favoring denitrification.

The application of reactive nitrogen (N) in the form of synthetic/organic fertilizers plays a central role in supporting a larger human population, but also contributes to global warming through the emission of nitrous oxide (N2O). The use of nitrification inhibitors (NIs) has repeatedly been shown to minimize N2O emissions; however, their effectiveness in reducing N2O emissions varies greatly under different environmental conditions. A better understanding of how and to what extent NIs can mitigate fertilizer-related soil-borne N2O emissions under a range of different conditions is required. In the present study, we carried out a soil incubation experiment in a fully automated continuous-flow incubation system under conditions favoring either nitrification- or denitrification-derived N2O emissions. Additionally, the abundance of AOB amoA, and AOA amoA genes was quantified and N2O isotopic signatures were analyzed. We mixed a common NI (PIADIN®) with mineral fertilizer (ammonium sulfate) and examined the N2O mitigation potential of the NI in a fertilized sandy soil (low denitrification potential) and a sandy soil mixed with wheat straw (high denitrification potential) at 70% water holding capacity (WHC). In non-NI treatments, the addition of straw led to a drastic increase of CO2 and N2O emissions compared to the non-straw-amended soils, suggesting stimulated microbial activity and higher denitrification rate. The NI reduced N2O emissions in the straw-amended treatment by 41%, whereas in the treatment without straw this was only 17%. With the combination of N2O isotopic signatures and functional gene abundances, fungal denitrification was considered to be the major process contributing to the higher N2O fluxes specifically in straw-amended soils. Overall, our study indicated that NI can be used as an effective method for mitigating N2O emissions in cropland specifically when the denitrification potential is high, e.g. in moist N-fertilized and straw-amended soils

A High Precision Information Retrieval Method for WiQA

7th Workshop of the Cross-Language Evaluation Forum, CLEF 2006, Alicante, Spain, September 20-22, 2006, Revised Selected PapersThis paper presents Wolverhampton University’s participation in the WiQA competition. The method chosen for this task combines a high precision, but low recall information retrieval approach with a greedy sentence ranking algorithm. The high precision retrieval is ensured by querying the search engine with the exact topic, in this way obtaining only sentences which contain the topic. In one of the runs, the set of retrieved sentences is expanded using coreferential relations between sentences. The greedy algorithm used for ranking selects one sentence at a time, always the one which adds most information to the set of sentences without repeating the existing information too much. The evaluation revealed that it achieves a performance similar to other systems participating in the competition and that the run which uses coreference obtains the highest MRR score among all the participants

Paraphrase Substitution for Recognizing Textual Entailment

We describe a method for recognizing textual entailment that uses the length of the longest common subsequence (LCS) between two texts as its decision criterion. Rather than requiring strict word matching in the common subsequences, we perform a flexible match using automatically generated paraphrases. We find that the use of paraphrases over strict word matches represents an average F-measure improvement from 0.22 to 0.36 on the CLEF 2006 Answer Validation Exercise for 7 languages

In vivo fate mapping and expression analysis reveals molecular hallmarks of prospectively isolated adult neural stem cells.

Until now, limitations in the ability to enrich adult NSCs (aNSCs) have hampered meaningful analysis of these cells at the transcriptome level. Here we show via a split-Cre technology that coincident activity of the hGFAP and prominin1 promoters is a hallmark of aNSCs in vivo. Sorting of cells from the adult mouse subependymal zone (SEZ) based on their expression of GFAP and prominin1 isolates all self-renewing, multipotent stem cells at high purity. Comparison of the transcriptome of these purified aNSCs to parenchymal nonneurogenic astrocytes and other SEZ cells reveals aNSC hallmarks, including neuronal lineage priming and the importance of cilia- and Ca-dependent signaling pathways. Inducible deletion of the ciliary protein IFT88 in aNSCs validates the role of ciliary function in aNSCs. Our work reveals candidate molecular regulators for unique features of aNSCs and facilitates future selective analysis of aNSCs in other functional contexts, such as aging and injury

Spatial interaction of archaeal ammonia-oxidizers and nitrite-oxidizing bacteria in an unfertilized grassland soil.

Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m2. Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation