The Revised Road Map to theManual

Abstract

The Second Edition of Bergey's Manual of Systematic Bacteriology (the “Systematics” ) represents a major departure from the First Edition, as well as from the Eighth and Ninth Editions of the Bergey's Manual of Determinative Bacteriology (the ‘Determinative” ), in that the organization of the content follows a phylogenetic framework based on analyses of the nucleotide sequence of the ribosomal small‐subunit RNA, rather than one based on phenotypic characters. The connection between systematics and evolution is pervasive but not logically necessary: purely phenetic taxonomies have been widely used in bacteriology; for many bacteriologists, the current “best practice” in bacterial systematics is polyphasic taxonomy, in which both phenotypic and genotypic information are used. Each volume of this edition will have an updated “road map” chapter (at the current rate of description of new taxa, the number of new genera validly published between the first volume and the fifth and last could number well over 500). A related strategy using genomic information for evolutionary studies has been to produce trees based on the presence or absence of orthologous genes in the genomes being analyzed. As new data become available, more precise placement is likely to occur. Higher taxa and genera that have been moved are listed in Table 2, along with the reasons for these moves. While we believe that the current taxonomy is a better reflection of reality than previous versions, we expect that further changes will be made as we work our way through the subsequent volumes and plan for future editions of the Systematics .

Screening and identification of newly isolated Pseudomonas sp. for biodegrading the textile azo dye C.I. Procion Red H‐3B

“…The bacteria that are able to decolourize textile azo dye were identified from several aspects including morphology characters and biochemical analysis as described in Bergey’s manual of determinative bacteriology (Garrity et al . 2005). The following biochemical tests, that is, Indole, Methyl Red, Voges‐Proskauer test, Citrate, Catalase, Oxidase, Nitrate Reduction test, Hydrolysis of Casein, Starch, Urea and Gelatin were performed.…”

ISOLATION, PURIFICATION AND CHARACTERIZATION OF A BACTERIOCIN WITH BROAD SPECTRUM ACTIVITY FROM Lactococcus lactis JC10 FROM PERISHABLE PAPAYA FRUIT

“…Preliminary identification was based on its morphological and biochemical characteristics in addition to its carbohydrate fermentation profile following Bergey's Manual of Systematic Bacteriology (Garrity et al, 2005). Finally it was characterized according to its 16S rDNA sequence analysis.…”

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

“…Using a novel approach to both fix the derived coordinates and overlay subsets of sequences based on assigned names, we were able to quickly identify areas of disagreement between the existing nomenclature and the phylogenetic model. Scree plots revealed that the first three dimensions in the derived coordinate system accounted for Ͼ90% of the total variance, indicating the reliability of the projections (34,35). PCA also provided a unique view of the topology of bacterial and archaeal domains, which has remained remarkably stable, robust, and resistant to perturbation by different alignments, different implementations of PCA, or an almost 3-fold increase in the number of validly named species.…”

“…Historically, our approach (6,(34)(35)(36) to reconciling nomenclature and 16S rRNA phylogeny was to employ methods from the field exploratory data analysis (37,38). Rather than relying on phylogenetic trees, which either lacked resolution when collapsed or were too unwieldy when viewed in full (Ͼ10,000 nodes), we applied principal-component analysis (PCA) to the 16S rRNA sequence data.…”