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Comamonas: Relationship to Aquaspirillum Aquaticum, E

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INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1991, p. 427-444 Vol. 41, No. 3 0020-7713/91/030427- 18$02 .OO/O Copyright 0 1991, International Union of Microbiological Societies Polyphasic Taxonomic Study of the Emended Genus Comamonas: Relationship to Aquaspirillum aquaticum, E. Falsen Group 10, and Other Clinical Isolates A. WILLEMS,l B. POT,l E. FALSEN,2 P. VANDAMME,' M. GILLIS,l* K. KERSTERS,l AND J. DE LEY' Laboratorium voor Microbiologie en Microbiele Genetica, Rijksuniversiteit, B-9000 Ghent, Belgium, and Culture Collection, Department of Clinical Bacteriology, University of Goteborg, S-413 46 Goteborg, Sweden2 We used DNA-rRNA hybridization, DNA base composition, polyacrylamide gel electrophoresis of whole-cell proteins, DNA-DNA hybridization, numerical analysis of phenotypic features, and immunotyping to study the taxonomy of the genus Comamonas. The relationships of this genus to Aquaspirillum aquaticum and a group of clinical isolates (E. Falsen group 10 [EF lo]) were studied. Our DNA and rRNA hybridization results indicate that the genus Comamonas consists of at least the following five genotypic groups: (i) Comamonas acidovoruns, (ii) Comamonas fesfosferoni,(iii) Comamonas ferrigena, (iv) A. aquaticum and a number of EF 10 strains, and (v) other EF 10 strains, several unnamed clinical isolates, and some misnamed strains of Pseudomonas alcaligenes and Pseudomonas pseudoalcaligenes subsp. pseudoalcaligenes. The existence of these five groups was confirmed by the results of immunotyping and protein gel electrophoresis. A numerical analysis of morpho- logical, auxanographic, and biochemical data for the same organisms revealed the existence of three large phena. Two of these phena (C. acidovorans and C. tesfosferoni)correspond to two of the genotypic groups. The third phenon contains strains belonging to the other three genotypic groups, including most EF 10 strains and the type strains of C. ferrigena and A. aquaticum. The strains belonging to the third phenon were all incorporated into C. ferrigena, and we propose that the use of the name Aquaspirillum aquaticum should be discontinued. Emended descriptions of the genus Comamonas and C. ferrigena are presented. De Vos et al. (9) revived the genus Comamonas and its [Pseudomonas alcaligenes] CUETM 25-3, and a number of type species, Comamonas terrigena, in a study in which unidentified clinical isolates from the Culture Collection of they performed DNA-rRNA and DNA-DNA hybridization the University of Goteborg (CCUG), Goteborg Sweden; 33 experiments, immunotyping experiments, gel electrophore- of the unidentified clinical strains were previously grouped sis of total cellular proteins, and a numerical analysis of by using serological techniques (10) and are referred to as E. phenotypic features. C. terrigena was shown to form a Falsen group 10 (EF 10) (11). separate taxon within the acidovorans rRNA complex in rRNA superfamily I11 (i.e., the beta subclass of the Proteo- bacteria [37]). This species can be differentiated phenotypi- MATERIALS AND METHODS cally from its nearest neighbors, such as [Pseudomonas] acidovorans and [Pseudomonas]testosteroni (9); the latter Bacterial strains. The strains which we used are listed in two species are generically misnamed according to present Table 1. Most of these strains were grown on nutrient agar phylogenetic data (misnamed taxa are enclosed in brackets). (0.1% [wthol] beef extract, 0.2% [wt/vol] yeast extract, On the basis of the results of studies in which several 0.5% [wthol] NaCl, 0.5% [wt/vol] peptone, 2% [wt/vol] Aquaspirillum techniques were used, Tamaoka et al. (38) later transferred agar; pH 7.4); the exceptions were strains of Leptothrix cholodnii, Rubrivivax gelatinosus, Xy- [Pseudomonas]acidovorans and [Pseudomonas]testoster- spp., and lophilus ampelinus, oni to the genus Comamonas as Comamonas acidovorans which were grown on the media de- and Comamonas testosteroni, respectively. For a more scribed previously (44). Most strains were grown at 28°C; the detailed review of the history of the genus Cornamonas see exceptions were X. ampelinus NCPPB 2217T (T = type [Aquaspirillum] references 9 and 42. strain), which was grown at 24"C, and psychrophilum In this paper we describe the results of a study of the IF0 13611T, which was grown at 18°C. genus Comamonas in which we performed DNA-rRNA and Morphological and biochemical characteristics. We used DNA-DNA hybridization experiments, determined DNA the methods described by De Vos et al. (9) to determine base compositions, and conducted immunotyping experi- morphological and biochemical characteristics. Nitrite re- ments, a numerical analysis of morphological, physiological, duction was tested as described by Rossau et al. (34). and biochemical characteristics, and a numerical analysis of Carbon substrate assimilation tests. API galleries (API protein gel electrophoretic patterns. On the basis of serolog- 50CH, API 50A0, and API 50AA; API System S.A., Mon- ical results and results of routine phenotypic analyses, a talieu-Vercieu, France) were used to test the assimilation of number of strains seemed to be highly related to the genus 147 organic compounds as sole carbon sources. The exper- Comamonas. These strains included [Pseudomonas imental procedure which we used has been described previ- pseudoalcaligenes] CUETM 85-15 and CUETM 85-24, ously (19). Numerical analysis of phenotypic characteristics. The re- sults of auxanographic and biochemical tests for 79 Coma- monas or possible Comamonas strains and 23 reference * Corresponding author. strains belonging to the acidovorans rRNA complex were 427 428 WILLEMS ET AL. INT. J. SYST.BACTERIOL. TABLE 1. Strains used ~~ Other Source, place, and year Name Strain" strain designation(s) of isolation Assigned to C. acidovorans Comamonas acidovorans Stanier 14T LMG 1226T, ATCC 15668T, Soil enriched with acetamide, Delft, The Nether- CCUG 14481T (= LMG lands. 1926 6031T = LMG 8911T), CCUG 12692T (= LMG 8910T) C. acidovorans ATCC 9355tlb LMG 1801tl,b CCUG 1822 Soil enriched with indole C. acidovorans ATCC 15005 LMG 1802, CCUG 15338 Soil C. acidovorans ATCC 17406 LMG 1790, CCUG 15340 Soil enriched with p-hydroxybenzoate C. acidovorans ATCC 17476 LMG 1791, CCUG 15337 Great Britain C. acidovorans CCUG 274B LMG 7098 Urine, 60-yr-old male, Goteborg, Sweden, 1968 C. acidovorans CCUG 536tlb LMG 5931tl,b NCTC 9991 Pharyngeal swab (received as Comamonas perco- lans) C. acidovorans CCUG 727 LMG 5932, CIP 60.78, Pharyngeal biopsy specimen ATCC 17439 C. acidovorans CCUG 1686 LMG 7099 Sludge, enrichment on testosterone, Goteborg, Sweden, 1972 C. acidovorans CCUG 1711 LMG 7100 Pus, Goteborg, Sweden, 1972 C. acidovorans CCUG 2861 LMG 8926, ATCC 11299a, Colony variant of strain ATCC 11299 NCIB 9289 C. acidovorans CCUG 10545 LMG 7101 Tap water, Goteborg, Sweden, 1981 C. acidovorans CCUG 10726B LMG 7102 Contact lens, Goteborg, Sweden, 1981 C. acidovorans CCUG 15835 LMG 7103 Eye of newborn boy, Goteborg, Sweden, 1984 C. acidovorans CCUG 18325 LMG 8912 Tap water, Goteborg, Sweden, 1986 C. acidovorans CCUG 18417 LMG 7185 Industry water C. acidovorans CCUG 21074 LMG 8914 Urine, Goteborg, Sweden, 1987 C. acidovorans CCUG 23474 LMG 9146 Urine, Goteborg, Sweden, 1988 [Bordetella bronchiseptica] LRA 147.04.76 LMG 2842 Unknown [Achromobacter cystinovorum] NCIB 4854 LMG 1795, CCUG 2485 Soil, Nottingham, Great Britain, before 1936 Assigned to C. testosteroni Comamonas testosteroni NCTC 10698= LMG 1786T, CCUG 1426T, Soil, Berkeley, Calif. ATCC 11996T C. testosteroni ATCC 17407 LMG 1787, CCUG 15341 Soil enriched with anthranilate C. testosteroni ATCC 17409 LMG 1788, CCUG 15339 Soil enriched with kynurenate, Berkeley, Calif., 1963 C. testosteroni ATCC 17510tlb LMG 1789tl,b CCUG 14480 Soil enriched with poly-P-hydroxybutyrate, Berkeley, Calif., 1961 C. testosteroni ATCC 17510t2' LMG 1789t2,' CCUG 14480 Soil enriched with poly-P-hydroxybutyrate, Berkeley, Calif., 1961 C. testosteroni CCUG 178A LMG 7104 Pus, Goteborg, Sweden, 1968 C. testosteroni CCUG 1135 LMG 5933 Kidney, 26-yr-old woman, Goteborg, Sweden, 1971 C. testosteroni CCUG 1689 LMG 9290 Mud enriched with testosterone, Goteborg, Swe- den, 1972 C. testosteroni CCUG 4381 LMG 7105 Urine, Heidelberg, Federal Republic of Germany, 1975 C. testosteroni CCUG 12941 LMG 9386 Bronchial aspirate, United States, 1982 C. testosteroni CCUG 14479 LMG 7106, ATCC 15667 Delft, The Netherlands EF 10 CCUG 13889 LMG 6140, LRA 57.3.76 Unknown (received as Pseudomonas testosteroni) Assigned to C. terrigena Group 1' Comamonas terrigena NCIB 8193T LMG 1253T, CCUG 2MT Hay infusion filtrate, United States (= LMG 5929T), CCUG 15327T, ATCC 8461T C. terrigena NCIB 2581 LMG 1249, CCUG 2474 Soil C. terrigena NCIB 2582 LMG 1251, CCUG 2475, Soil ATCC 14636 C. terrigena CCUG 12940 LMG 5520, G-4425 Blood, 1982 EF 10 CCUG 4470 LMG 6164 Buccal cavity, man, Heidelberg, Federal Republic of Germany, 1975 Unidentified CCUG 17736 LMG 6733 Horse blood, Sweden, 1985 Group 2 [Aquaspirillum aquaticum] ATCC 11330T LMG 2370T, CCUG 1739ST Fresh water EF 10 CCUG 1192 LMG 5937 Clinical laboratory, University of California, Los Angeles (received as P. alcaligenes) EF 10 CCUG 2632tlb LMG 6162tl' Metal-cutting fluid, Goteborg, Sweden, 1973 EF 10 CCUG 8404 LMG 6163 Human, Heidelberg, Federal Republic of Ger- many, 1979 Continued on following page VOL.41, 1991 COMAMONAS TAXONOMY 429 TABLE 1-Continued ~~ strain Name Strain“ Other Source, place, and year designation(s1 of isolation EF 10 CCUG 9672 LMG 6015, LMG 9569 Human, Heidelberg, Federal Republic of Germany,
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  • Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P

    Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P

    www.nature.com/scientificreports OPEN Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P. Garay3, Jose Manuel Martí3 Accepted: 17 November 2015 & Manuel Porcar1,2 Published: 16 December 2015 We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. There is a growing interest on disentangling the complexity of microbial interactions in order to both optimize reactions performed by natural consortia and to pave the way towards the development of synthetic consor- tia with improved biotechnological properties1,2. Despite the enormous amount of metagenomic data on both natural and artificial microbial ecosystems, bacterial consortia are not necessarily deduced from those data. In fact, the flexibility of the bacterial interactions, the lack of replicated assays and/or biases associated with differ- ent DNA isolation technologies and taxonomic bioinformatics tools hamper the clear identification of bacterial consortia. We propose here a holistic approach aiming at identifying bacterial interactions in laboratory-selected microbial complex cultures. The method requires multi-replicated taxonomic data on independent subcultures, and high-throughput sequencing-based taxonomic data. From this data matrix, randomness of replicates can be verified, linear correlations can be visualized and interactions can emerge from statistical correlations.