104,699 research outputs found
Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches
No full textTo understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases inChloroflexisequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effect
The evolution of bacterial genome assemblies - where do we need to go next?
No full textAltermann E, Tegetmeyer H, Chanyi RM. The evolution of bacterial genome assemblies - where do we need to go next? Microbiome Research Reports. 2022;1(3): 15.Genome sequencing has fundamentally changed our ability to decipher and understand the genetic blueprint of life and how it changes over time in response to environmental and evolutionary pressures. The pace of sequencing is still increasing in response to advances in technologies, paving the way from sequenced genes to genomes to metagenomes to metagenome-assembled genomes (MAGs). Our ability to interrogate increasingly complex microbial communities through metagenomes and MAGs is opening up a tantalizing future where we may be able to delve deeper into the mechanisms and genetic responses emerging over time. In the near future, we will be able to detect MAG assembly variations within strains originating from diverging sub-populations, and one of the emerging challenges will be to capture these variations in a biologically relevant way. Here, we present a brief overview of sequencing technologies and the current state of metagenome assemblies to suggest the need to develop new data formats that can capture the genetic variations within strains and communities, which previously remained invisible due to sequencing technology limitations. © The Author(s) 2022
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Microbial nitrate respiration - Genes, enzymes and environmental distribution
No full textKraft B, Strous M, Tegetmeyer H. Microbial nitrate respiration - Genes, enzymes and environmental distribution. Journal of Biotechnology. 2011;155(1):104-117.Nitrate is a key node in the network of the assimilatory and respiratory nitrogen pathways. As one of the 'fixed' forms of nitrogen, nitrate plays an essential role in both nature and industry. For bacteria, it is both a nitrogen source and an electron acceptor. In agriculture and wastewater treatment, nitrate respiration by microorganisms is an important issue with respect to economics, greenhouse gas emission and public health. Several microbial processes compete for nitrate: denitrification, dissimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. In this review we provide an up to date overview of the organisms, genes and enzymes involved in nitrate respiration. We also address the molecular detection of these processes in nature. We show that despite rapid progress in the experimental and genomic analyses of pure cultures, knowledge on the mechanism of nitrate reduction in natural ecosystems is still largely lacking. (C) 2011 Elsevier B. V. All rights reserved
An isogenic Actinobacillus pleuropneumoniae AasP mutant exhibits altered biofilm formation but retains virulence.
No full textTegetmeyer H, Fricke K, Baltes N. An isogenic Actinobacillus pleuropneumoniae AasP mutant exhibits altered biofilm formation but retains virulence. Veterinary Microbiology. 2009;137(3-4):392-396.AasP, an autotransporter serine protease of Actinobacillus pleuropneumoniae, has been shown to be expressed in necrotic porcine lung tissue. Based on the hypothesis that AasP might play an important role in A. pleuropneumoniae adhesion and virulence by processing other surface-associated proteins, the predicted catalytic site of AasP was deleted and the isogenic mutant, AP76DeltaaasP, was compared to the wild-type strain in a biofilm assay as well as an aerosol infection model. AP76DeltaaasP showed increased adherence compared to the wild-type strain under standard culturing conditions as well as under NAD restriction. No significant differences between AP76 wild-type and AP76DeltaaasP were observed upon experimental infection of pigs, indicating that AasP does not play a crucial role in A. pleuropneumoniae virulence
On site analysis of bacterial communities of the ultra-oligotrophic South Pacific Gyre.
No full textReintjes G, Tegetmeyer H, Burgisser M, et al. On site analysis of bacterial communities of the ultra-oligotrophic South Pacific Gyre. Applied and environmental microbiology. 2019;85(14): UNSP e00184-19.The South Pacific Gyre (SPG) covers 10% of the ocean's surface and is often regarded as a marine biological desert. To gain an on-site overview of the remote, ultra-oligotrophic microbial community of the SPG we developed a novel on-board analysis pipeline, which combines next-generation sequencing with fluorescence in situ hybridisation and automated cell enumeration. We tested the pipeline during the SO245 "UltraPac" cruise from Chile to New Zealand and found that the overall microbial community of the SPG was highly similar to that of other oceanic gyres. The SPG was dominated by 20 major bacterial clades, including SAR11, SAR116, AEGEAN-169 marine group, SAR86, Prochlorococcus, SAR324, SAR406, and SAR202. Most of the bacterial clades showed a strong vertical (20 m - 5000 m), but only a weak longitudinal (80°W - 160°W), distribution pattern. Surprisingly, in the central gyre Prochlorococcus, the dominant photosynthetic organism, had only low cellular abundances in the upper waters (20 - 80 m) and were more frequent around the 1% irradiance zone (100 - 150 m). Instead, the surface waters of the central gyre were dominated by SAR11, SAR86, and SAR116 clades known to harbour light-driven proton pumps. The alphaproteobacterial AEGEAN-169 marine-group was particularly abundant in the surface waters of the central gyre indicating a potentially interesting adaptation to ultraoligotrophic waters and high solar irradiance. In the future, the newly developed community analysis pipeline will allow for on-site insights into a microbial community within 35 hours of sampling, which will permit more targeted sampling efforts and hypothesis-driven research.ImportanceThe South Pacific Gyre is due to its vast size and remoteness one of the least studied oceanic regions on earth. However, both remote sensing and in situ measurements indicated that the activity of its microbial community contributes significantly to global biogeochemical cycles. Presented here is an unparalleled investigation of the microbial community of the SPG from 20 - 5000 m depth covering a geographic distance of 7000 km. This insight was achieved through the development of a novel on-board analysis pipeline, which combines next-generation sequencing with fluorescence in situ hybridisation and automated cell enumeration. The pipeline is well comparable to on-shore systems based on the Illumina platforms and yields microbial community data in less than 35 hours after sampling. Going forward the ability to gain on-site knowledge of a remote microbial community will permit hypothesis-driven research, through the generation of novel scientific questions and subsequent additional targeted sampling efforts. Copyright © 2019 American Society for Microbiology
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
The construction of Karen Karnak: The multi-author-function
No full textThis thesis is situated within the comparatively recent developments of Web 2.0 and the emergence of interactive WikiMedia, and explores the mode of authorship within a Read/Write culture compared to that of a Read/Only tradition. The hypothesis of this study is that the role of the audience has become merged with the author, and as such, represents new functions and attributes, distinct from a more conventional concept of authorship, in which the roles of audience and author are more separate. Read/Write and participatory culture, as defined by this study, is focused on collaboration, and includes the influences of D.I.Y. culture, Open-Source practices and the production of text by multiple authors. Multi-authorship presents a re-thinking of several concepts which support the notion of the individual author, since the focus of multi-authorship is not on attribution and ownership of a finished text, but on the continued malleability of a text. Modes of multi-authorship, demonstrated in the use of the pseudonyms Alan Smithee and Karen Eliot, represent declarative authors whose names signify multiple origins, whilst concurrently indicating a distinct body of work. The function of these names form an important context to this study, since primary research involves the construction of an experimental mode of multi-authorship utilising WikiMedia technology and the interaction of thirty nine participants, who are invited to create a body of work under the collective pseudonym Karen Karnak. The data generated by this experiment is analysed using aspects of Michel Foucault's author-function to identify and determine power structures inherent in the WikiMedia context. The interplay of power structures, including concepts such as identity, ownership and the body of work, affect the resulting mode of authorship and contribute to the construction of Karen Karnak, suggesting further areas of research into the emerging multi-author
Contribution of Information and Communication Technology (ICT) in Country’S H-Index
No full textThe aim of this study is to examine the effect of Information and Communication Technology (ICT) development on country’s scientific ranking as measured by H-index. Moreover, this study applies ICT development sub-indices including ICT Use, ICT Access and ICT skill to find the distinct effect of these sub-indices on country’s H-index. To this purpose, required data for the panel of 14 Middle East countries over the period 1995 to 2009 is collected. Findings of the current study show that ICT development increases the H-index of the sample countries. The results also indicate that ICT Use and ICT Skill sub-indices positively contribute to higher H-index but the effect of ICT access on country’s H-index is not clear
- …
