The Richness of Prokaryotic Diversity: There Must Be a Species Somewhere

The rapidly increasing number of potentially novel species, combined with the methodologically laborious polyphasic approach used in bacterial systematics, makes identification and, consequently, the description of novel taxa a highly demanding discipline. The number of new descriptions of about 200 species a year can apparently not be expanded significantly but new isolation procedures and renewed interest in working with bacteria rather than with DNA clones provide microbiologists with a broad range of different pheno- and genotypes. It seems obvious that some of the worldwide acknowledged techniques will not be continued but the question which methods will be used in the future is still open. At present, DNA-DNA reassociation is the final arbiter for the taxon »species«, but the limitations of these techniques, which are subject to significant errors, are well known. On the other side of the range of molecular techniques stands a whole genome sequencing that demonstrates the evolutionary events which lead to differences in DNA, such as point mutations, insertions and deletions, DNA acquisition and loss, recombination, gene loss and formation of pseudogenes. Each of these evolutionary events has an effect on DNA-DNA reassociation similarity, which, however, cannot be tested by the reassociation approaches used. Further, DNA pairing does not allow the establishment of a cumulative database because the hybridization parameters change from laboratory to laboratory and reference organisms need to be included in each experiment. This communication reports on the development of ideas that may change the paradigm of the present concept of artificial, arbitrary and pragmatic species into a species definition, driven by insights into population genetics

Culturable aerobic bacteria from the upstream region of a karst water rivulet

The composition of 681 aerobic and heterotrophic strains that were isolated on two different media was assessed at four sampling points along a ~300 m stretch of a karst water rivulet. Based on partial sequence analysis of 16S rRNA genes, members of 35 genera were identified; however, only a few species dominated as their representatives were repeatedly isolated at different sampling sites. Determination of the phylum affiliation showed that the isolates included members of Bacteriodetes (especially the genus Flavobacterium) and Proteobacteria (mainly Pseudomonas and Stenotrophomonas). MALDI-TOF analysis and/or similarities of partial sequences of flavobacterial strains resulted in the generation of almost complete 16S rRNA gene sequences for 100 isolates, about 60 of which may represent novel phylospecies. The number as well as the intra-phylum distribution of the isolates changed with distance from the discharge site. While phylogenetically restricted at the spring, diversity increased at downstream sampling sites

Isolation and Characterization of a Novel As(V)-Reducing Bacterium: Implications for Arsenic Mobilization and the Genus \u3ci\u3eDesulfitobacterium\u3c/i\u3e

Dissimilatory arsenate-reducing bacteria have been implicated in the mobilization of arsenic from arsenic-enriched sediments. An As(V)-reducing bacterium, designated strain GBFH, was isolated from arsenic-contaminated sediments of Lake Coeur d\u27Alene, Idaho. Strain GBFH couples the oxidation of formate to the reduction of As(V) when formate is supplied as the sole carbon source and electron donor. Additionally, strain GBFH is capable of reducing As(V), Fe(III), Se(VI), Mn(IV) and a variety of oxidized sulfur species. 16S ribosomal DNA sequence comparisons reveal that strain GBFH is closely related to Desulfitobacterium hafniense DCB-2T and Desulfitobacterium frappieri PCP-1T. Comparative physiology demonstrates that D. hafniense and D. frappieri, known for reductively dechlorinating chlorophenols, are also capable of toxic metal or metalloid respiration. DNA-DNA hybridization and comparative physiological studies suggest that D. hafniense, D. frappieri, and strain GBFH should be united into one species. The isolation of an Fe(III)- and As(V)-reducing bacterium from Lake Coeur d\u27Alene suggests a mechanism for arsenic mobilization in these contaminated sediments while the discovery of metal or metalloid respiration in the genus Desulfitobacterium has implications for environments cocontaminated with arsenious and chlorophenolic compounds

Microbial genomic taxonomy

A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups

The recently proposed species Aeromonas sharmana sp. nov., isolate GPTSA-6T, is not a member of the genus Aeromonas

A new species of the genus Aeromonas, Aeromonas sharmana sp. nov., was recently described on the basis of a single isolate, strain GPTSA-6T, obtained from a warm spring in India. The description of this new species included biochemical characterization, antibiotic susceptibility, cellular fatty-acid profiles, and 16S rRNA gene sequencing, but not DNADNA hybridization data. In the present article, phylogenetic analysis (branch distances in the tree and nucleotide signatures) of the 16S rRNA of isolate GPTSA-6T, together with certain phenotypic characteristics of the isolate reported in the earlier description, clearly indicate that this microorganism does not belong to the genus Aeromonas as known to date, although it falls within the radiation of the family Aeromonadaceae. Emendation from the List of Prokaryotic Names with Standing in Nomenclature is consequently proposed. [Int Microbiol 2007; 10(1):61-64

Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training

A survey of European Microbial Biological Resource Centers and their users provided an overview on Microbiology education and training. The results identified future increases in demand despite several shortcomings and gaps in the current offer. Urgent adjustments are needed to match users' needs, integrate innovative programs, and adopt new technologies

Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres

Through their long history of public service, diverse microbial Biological Resource Centres (mBRCs) have made myriad contributions to society and science. They have enabled the maintenance of specimens isolated before antibiotics, made available strains showing the development and change of pathogenicity toward animals, humans and plants, and have maintained and provided reference strains to ensure quality and reproducibility of science. However, this has not been achieved without considerable financial commitment. Different collections have unique histories and their support is often tied to their origins. However many collections have grown to serve large constituencies and need to develop novel funding mechanisms. Moreover, several international initiatives have described mBRCs as a factor in economic development and have led to the increased professionalism among mBRCs.Peer Reviewe

Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science

Despite recommendations to release microbial resources to the community post-publication, the reality is far from satisfying. A workshop discussed the need for a coordinated and effective deposition policy for 'key' microbial strains and proposes a set of criteria to facilitate their deposition into public service collections. The majority of authors either contacted directly or during submission of manuscripts to several international, mainly European bacteriology journals agreed to this set of 'key strain' criteria and to the voluntarily deposition of resources into public resource centres.The authors thank additional members of the 2011 Braunschweig workshop: Jorg Overmann, Esperanza Garay-Auban, Peter Kampfer, Yohan Lecuona, James I Prosser, Ramon Rosello-Mora, Karl-Heinz Schleifer, and Kornelia Smalla. The workshop was an initiative of the European Consortium of Microbial Resource Centres (EMbaRC), supported by the European Commission's Seventh Framework Programme (FP7, 2007-2013), Research Infrastructures action, under the grant agreement No. FP7-228310. This communication received funding from the European Union's Seventh Framework Programme for Research, Technological Development and Demonstration under grant agreement no 312251. Additionally, thanks go to all those attending the February 2014 MIRRI Heads of Collections meeting who participated in the discussions, including some of those above plus Pedro Crous, Edward Moore, Oleg Stupar, Chantal Bizet, Dominique Clermont, Rosa Aznar, Paul Devos, and Anna Misiewicz

UV-radiation-induced formation of DNA bipyrimidine photoproducts in Bacillus subtilis endospores and their repair during germination

The spore photoproduct (SP) is the main DNA lesion after UV-C irradiation, and its repair is crucial for the resistance of spores to UV. The aims of the present study were to assess the formation and repair of bipyrimidine photoproducts in spore DNA of various Bacillus subtilis strains using a sensitive HPLC tandem mass spectrometry assay. Strains deficient in nucleotide excision repair, spore photoproduct lyase, homologous recombination (recA), and with wild-type repair capability were investigated. Additionally, one strain deficient in the formation of major small, acid-soluble spore proteins (SASPs) was tested. In all SASP wild-type strains, UV-C irradiation generated almost exclusively SP (>95 %) but also a few by-photoproducts. In the major SASP-deficient strain, SP and by-photoproducts were generated in equal quantities. The status of the UV-induced bipyrimidine photoproducts was determined at different stages of spore germination. After a germination time of 60 min, >75% of the SP was repaired in wild-type strains and in the SASP-deficient strain, while half of the photoinduced SP was removed in the recA-deficient strain. SP-lyase-deficient spores repaired < 20% of the SP produced. Thus, SP lyase, with respect to nucleotide excision repair, has a remarkable impact on the removal of SP upon spore germination. [Int Microbiol 2007; 10(1):39-46

Phenotypic, genotypic, and phylogenetic discrepancies to differentiate Aeromonas salmonicida from Aeromonas bestiarum

The taxonomy of the “Aeromonas hydrophila” complex (comprising the species A. hydrophila, A. bestiarum, A. salmonicida, and A. popoffii) has been controversial, particularly the relationship between the two relevant fish pathogens A. salmonicidaand A. bestiarum. In fact, none of the biochemical tests evaluated in the present study were able to separate these two species. One hundred and sixteen strains belonging to the four species of this complex were identified by 16S rDNA restriction fragment length polymorphism (RFLP). Sequencing of the 16S rDNA and cluster analysis of the 16S–23S intergenic spacer region (ISR)-RFLP in selected strains of A. salmonicida and A. bestiarum indicated that the two species may share extremely conserved ribosomal operons and demonstrated that, due to an extremely high degree of sequence conservation, 16S rDNA cannot be used to differentiate these two closely related species. Moreover, DNA–DNA hybridization similarity between the type strains of A. salmonicida subsp. salmonicida and A. bestiarum was 75.6 %, suggesting that they may represent a single taxon. However, a clear phylogenetic divergence between A. salmonicida and A. bestiarum was ascertained from an analysis based on gyrB and rpoD gene sequences, which provided evidence of a lack of congruence of the results obtained from 16S rDNA, 16S–23S ISR-RFLP, DNA–DNA pairing, and biochemical profiles.[Int Microbiol 2005; 8(4):259-269