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Herberich E.,Ludwig Maximilians University of Munich | Sikorski J.,Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH | Hothorn T.,Ludwig Maximilians University of Munich
PLoS ONE | Year: 2010

Investigating differences between means of more than two groups or experimental conditions is a routine research question addressed in biology. In order to assess differences statistically, multiple comparison procedures are applied. The most prominent procedures of this type, the Dunnett and Tukey-Kramer test, control the probability of reporting at least one false positive result when the data are normally distributed and when the sample sizes and variances do not differ between groups. All three assumptions are non-realistic in biological research and any violation leads to an increased number of reported false positive results. Based on a general statistical framework for simultaneous inference and robust covariance estimators we propose a new statistical multiple comparison procedure for assessing multiple means. In contrast to the Dunnett or Tukey-Kramer tests, no assumptions regarding the distribution, sample sizes or variance homogeneity are necessary. The performance of the new procedure is assessed by means of its familywise error rate and power under different distributions. The practical merits are demonstrated by a reanalysis of fatty acid phenotypes of the bacterium Bacillus simplex from the "Evolution Canyons" I and II in Israel. The simulation results show that even under severely varying variances, the procedure controls the number of false positive findings very well. Thus, the here presented procedure works well under biologically realistic scenarios of unbalanced group sizes, non-normality and heteroscedasticity. © 2010 Herberich et al. Source

Cummings D.E.,Point Loma Nazarene University | Zimmerman A.E.,University of California at Irvine | Spring S.,Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Geomicrobiology Journal | Year: 2010

We analyzed PCR-amplified 16S rRNA genes from native and Fe(III)-enriched surface sediments of a major tidal channel in the Tijuana River Estuary, California, USA. Clones from native sediments were most closely affiliated with photosynthetic taxa (Cyanobacteria, Chloroflexi, and Halochromatium) and microorganisms known to reduce (Desulfatibacillus, Desulfobacterium, and Desulfuromusa) or oxidize (Microcoleus, Phormidium, and Halochromatium) various sulfur species, reflective of the fluctuating redox conditions in the tidal zone. Fe(III) was rapidly reduced in anaerobic microcosms amended with 2-line ferrihydrite, with or without the sulfate reduction inhibitor sodium molybdate. The addition of ferrihydrite without molybdate caused a major shift in community structure to a dominance of the Fe(III)-reducing genus Shewanella, while at the same time the sulfate-reducing and sulfide-oxidizing populations were replaced by taxa known to cycle elemental sulfur. Sediments amended with both ferrihydrite and molybdate were again populated by Shewanella clones, but also numerically important were clones most similar to Marinobacterium, Pseudomonas, and Bacillus, suggesting a role for these taxa in Fe(III) reduction in marine habitats. © Taylor & Francis Group, LLC. Source

In a recent publication the name Solimonadaceae Losey et al. 2013 has been proposed as a replacement name for the family name Sinobacteraceae Zhou et al. 2008. This course of action contravenes the current Code governing the nomenclature of prokaryotes, making Solimonadaceae Losey et al. 2013 an illegitimate name that neither has claim to priority nor can be used as a correct name. Closer examination of publications dealing with the taxonomy of members of the genera Solimonas and Sinobacter and the placement of these taxa at the rank of family and order reveal problems associated with the application of the family names Sinobacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and the order names Lysobacterales Christensen and Cook 1978 (Approved Lists 1980) and Xanthomonadales Saddler and Bradbury 2005. © 2014 IUMS. Source

Xing K.,Xuzhou Normal University | Bian G.-K.,Xuzhou Normal University | Qin S.,Xuzhou Normal University | Klenk H.-P.,Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH | And 4 more authors.
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2012

A novel actinomycete, designated strain KLBMP 1111 T, was isolated from the root of the oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China. Strain KLBMP 1111 T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Kibdelosporangium, with the highest similarity to Kibdelosporangium aridum subsp. aridum DSM 43828 T (98.8%), K. aridum subsp. largum DSM 44150 T (98.1%) and Kibdelosporangium philippinense DSM 44226 T (98.1%). The organism produced sporangium-like structures, the typical morphological characteristic of the genus Kibdelosporangium. The chemotaxonomic properties of this strain were also consistent with those of the genus Kibdelosporangium: the peptidoglycan contained meso-diaminopimelic acid; the predominant menaquinone was MK-9(H 4); phospholipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol and an unknown phospholipid; iso-C 16:0, C 16:0, anteiso-C 15:0 and iso-C 15:0 as the predominant cellular fatty acids and the G+C content was 67.2 mol%. DNA-DNA hybridization values between strain KLBMP 1111 T and the three Kibdelosporangium species were less than 50%. This strain had the ability to produce a siderophore, utilized 1-aminocyclopropane-1-carboxylic acid (ACC) as sole source of nitrogen and possessed ACC deaminase enzyme. Based on genotypic and phenotypic data, strain KLBMP 1111 T represents a novel species in the genus Kibdelosporangium. We propose the name Kibdelosporangium phytohabitans sp. nov. for this species. The type strain is the strain KLBMP 1111 T (=KCTC 19775 T = CCTCC AA 2010001 T). © 2011 Springer Science+Business Media B.V. Source

Tindall B.J.,Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
International Journal of Systematic and Evolutionary Microbiology | Year: 2015

The wording of Rule 15 as originally published in the 1975 and 1990 revisions of the International Code of Nomenclature of Bacteria with regard to the definition of nomenclatural types was not clearly expressed and was modified by the Judicial Commission in 2008. However, there is a difference between the wording as proposed and that accepted. On reflection there is justification for re-examining both the proposed and the accepted wording. © 2015 IUMS. Source

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