TY  - JOUR
AB  - Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
AU  - Viver, T.*
AU  - Conrad, R.E.*
AU  - Lucio, M.
AU  - Harir, M.
AU  - Urdiain, M.*
AU  - Gago, J.F.*
AU  - Suárez-Suárez, A.*
AU  - Bustos-Caparros, E.*
AU  - Sanchez-Martinez, R.*
AU  - Mayol, E.*
AU  - Fassetta, F.*
AU  - Pang, J.*
AU  - Mădălin Gridan, I.*
AU  - Venter, S.*
AU  - Santos, F.*
AU  - Baxter, B.*
AU  - Llames, M.E.*
AU  - Cristea, A.*
AU  - Banciu, H.L.*
AU  - Hedlund, B.P.*
AU  - Stott, M.B.*
AU  - Kämpfer, P.*
AU  - Amann, R.*
AU  - Schmitt-Kopplin, P.
AU  - Konstantinidis, K.T.*
AU  - Rosselló-Mora, R.*
C1  - 67664
C2  - 53971
CY  - Hackerbrucke 6, 80335 Munich, Germany
TI  - Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.
JO  - Syst. Appl. Microbiol.
VL  - 46
IS  - 3
PB  - Elsevier Gmbh
PY  - 2023
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - Nitrate-dependent iron oxidation was discovered in 1996 and has been reported from various environments ever since. To date, despite the widespread nature of this process, all attempts to cultivate chemolithoautotrophic nitrate-dependent iron oxidizers have been unsuccessful. The present study was focused on understanding the influence of natural chelating agents of iron, like humic substances, on the culturability, activity, and enumeration, of these microorganisms. Pure culture studies conducted with Thiobacillus denitrificans showed a constant increase in cell mass with a corresponding nitrate-dependent iron oxidation activity only when Fe(II) was provided together with humic substances, compared to no growth in control incubations without humic substances. The presence of a relatively strong chelating agent, such as EDTA, inhibited the growth of Thiobacillus denitrificans. It was concluded that complex formation between humic substances and iron was required for chemolithoautotrophic nitrate-dependent iron oxidation. Most probable number enumerations showed that numbers of chemolithoautotrophic nitrate-dependent iron-oxidizing bacteria were one to three orders of magnitude higher in the presence of humic substances compared to media without. Similar results were obtained when potential nitrate-dependent iron oxidation activity was determined in soil samples. In summary, this study showed that humic substances significantly enhanced the growth and activity of autotrophic nitrate-dependent iron-oxidizing microorganisms, probably by chelation of iron.
AU  - Kanaparthi, D.
AU  - Conrad, R.*
C1  - 47310
C2  - 39243
SP  - 184-188
TI  - Role of humic substances in promoting autotrophic growth in nitrate-dependent iron-oxidizing bacteria.
JO  - Syst. Appl. Microbiol.
VL  - 38
IS  - 3
PY  - 2015
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - For microorganisms that play an important role in bioremediation, the adaptation to swift changes in the availability of various substrates is a key for survival. The iron-reducing bacterium Geobacter metallireducens was hypothesized to repress utilization of less preferred substrates in the presence of high concentrations of easily degradable compounds. In our experiments, acetate and ethanol were preferred over benzoate, but benzoate was co-consumed with toluene and butyrate. To reveal overall physiological changes caused by different single substrates and a mixture of acetate plus benzoate, a nano-liquid chromatography-tandem mass spectrometry-based proteomic approach (nano-LC-MS/MS) was performed using label-free quantification. Significant differential expression during growth on different substrates was observed for 155 out of 1477 proteins. The benzoyl-CoA pathway was found to be subjected to incomplete repression during exponential growth on acetate in the presence of benzoate and on butyrate as a single substrate. Peripheral pathways of toluene, ethanol, and butyrate degradation were highly expressed only during growth on the corresponding substrates. However, low expression of these pathways was detected in all other tested conditions. Therefore, G. metallireducens seems to lack strong carbon catabolite repression under high substrate concentrations, which might be advantageous for survival in habitats rich in fatty acids and aromatic hydrocarbons.
AU  - Marozava, S.
AU  - Röling, W.F.*
AU  - Seifert, J.*
AU  - Küffner, R.
AU  - von Bergen, M.*
AU  - Meckenstock, R.U.
C1  - 31077
C2  - 34137
CY  - Jena
SP  - 277-286
TI  - Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part I. Batch cultivation with excess of carbon sources.
JO  - Syst. Appl. Microbiol.
VL  - 37
IS  - 4
PB  - Elsevier Gmbh, Urban & Fischer Verlag
PY  - 2014
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - The strict anaerobe Geobacter metallireducens was cultivated in retentostats under acetate and acetate plus benzoate limitation in the presence of Fe(III) citrate in order to investigate its physiology under close to natural conditions. Growth rates below 0.003h(-1) were achieved in the course of cultivation. A nano-liquid chromatography-tandem mass spectrometry-based proteomic approach (nano-LC-MS/MS) with subsequent label-free quantification was performed on proteins extracted from cells sampled at different time points during retentostat cultivation. Proteins detected at low (0.002h(-1)) and high (0.06h(-1)) growth rates were compared between corresponding growth conditions (acetate or acetate plus benzoate). Carbon limitation significantly increased the abundances of several catabolic proteins involved in the degradation of substrates not present in the medium (ethanol, butyrate, fatty acids, and aromatic compounds). Growth rate-specific physiology was reflected in the changed abundances of energy-, chemotaxis-, oxidative stress-, and transport-related proteins. Mimicking natural conditions by extremely slow bacterial growth allowed to show how G. metallireducens optimized its physiology in order to survive in its natural habitats, since it was prepared to consume several carbon sources simultaneously and to withstand various environmental stresses.
AU  - Marozava, S.
AU  - Röling, W.F.*
AU  - Seifert, J.*
AU  - Küffner, R.
AU  - von Bergen, M.*
AU  - Meckenstock, R.U.
C1  - 31080
C2  - 34133
CY  - Jena
SP  - 287-295
TI  - Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part II. Mimicking environmental conditions during cultivation in retentostats.
JO  - Syst. Appl. Microbiol.
VL  - 37
IS  - 4
PB  - Elsevier Gmbh, Urban & Fischer Verlag
PY  - 2014
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated CT348(T), isolated from the ectorhizosphere of an organic olive tree in Spain and characterised as an efficient plant growth promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best in a temperature range of 5-35°C, at pH 5.0-8.0 and with 0-1% (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The DNA G+C content of the novel strain was 38.2mol%. The strain contained a polyamine pattern with sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15:0, C17:1ω9c, iso-C17:0 3-OH and iso-C15:0 2-OH. The main polar lipids were phosphatidylethanolamine and several unidentified lipids and aminolipids. The 16S rRNA gene showed 92.2-97.8% sequence identity with the members of the genus Chyseobacterium. Based on the phenotypic traits and DNA-DNA hybridizations with the type strains of the most closely related species, the isolate is shown to represent a novel species, Chyseobacterium oleae, type strain CT348(T) (=DSM 25575 =CCUG 63020). Emended descriptions of the genus Chryseobacterium and C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense are also proposed.
AU  - Montero-Calasanz, M.D.*
AU  - Göker, M.*
AU  - Rohde, M.*
AU  - Spröer, C.*
AU  - Schumann, P.*
AU  - Busse, H.J.*
AU  - Schmid, M.
AU  - Klenk, H.P.*
AU  - Tindall, B.J.*
AU  - Camacho, M.*
C1  - 31501
C2  - 34513
CY  - Jena
SP  - 342-350
TI  - Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense.
JO  - Syst. Appl. Microbiol.
VL  - 37
IS  - 5
PB  - Elsevier Gmbh, Urban & Fischer Verlag
PY  - 2014
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - Two novel Pseudomonas strains were isolated from groundwater sediment samples. The strains showed resistance against the antibiotics tetracycline, cephalothin, nisin, vancomycin. Nalidixic acid, erythromycin, lincomycin, and penicillin and grew at temperatures between 15 and 37 degrees C and pH values from 4 to 10 with a maximum at pH 7 to 10. The 16S ribosomal RNA gene sequences and the substrate spectrum of the isolates revealed that the two strains belonged to the Pseudomonas fluorescens group. The supernatants of both strains had an antibiotic effect against Gram-positive bacteria and one Gram-negative strain. The effective substance was produced under standard cultivation conditions without special inducer molecules or special medium composition. The antibiotically active compound was identified as pseudomonic acid A by off-line high performance liquid chromatography (HPLC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The measurement on ultra performance liquid chromatography (UPLC, UV-vis detection) confirmed the determination of pseudomonic acid A which was produced by both strains at 1.7-3.5 mg/l. Our findings indicate that the ability to produce the antibiotic pseudomonic acid A (Mupirocin) is more spread among the pseudomonads then anticipated from the only producer known so far.
AU  - Fritz, E.
AU  - Fekete, A.
AU  - Lintelmann, J.
AU  - Schmitt-Kopplin, P.
AU  - Meckenstock, R.U.
C1  - 907
C2  - 25831
SP  - 56-64
TI  - Isolation of two Pseudomonas strains producing pseudomonic acid A.
JO  - Syst. Appl. Microbiol.
VL  - 32
IS  - 1
PB  - Elsevier
PY  - 2009
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - The genetic diversity and phylogenetic interrelationships among 106 Ochrobactrum strains (O. anthropi: 72, O. intermedium: 22, O. tritici: 5, O. oryzae: 2, O. grignonense: 2, O. gallinifaecis: 1, O. lupini: 2), the type strains of the eight Brucella species and other closely related taxa were studied by recA and rrs gene (16S rRNA) comparative sequence analysis. Both markers correctly delineated the various Ochrobactrum species; however, resolution at the subspecies level was considerably higher in the recA gene-based approach. Phylogenetic analyses using neighbor-joining, parsimony, and maximum likelihood algorithms generated trees with similar topologies but the overall branching order, and also the order of the subclades, were not stable in either assay, which could be explained by generally high recA and rrs sequence similarities. Ochrobactrum and Pseudochrobactrum formed separate clades distinct from other Alphaproteobacteria with Bartonella, Agrobacterium, and Rhizobium as the closest relatives. O. gallinifaecis was the most distinct member, when compared to the type species O. anthropi, with rrs and recA similarities of 96.2% and 81.4%. Brucella species were indistinguishable, exhibiting high rrs and recA gene similarities of 98.6% and 85.5% compared with Ochrobactrum intermedium. At the protein level, all RecA sequences among the various Ochrobactrum species and between Ochrobactrum and Brucella were highly similar with only a few amino acid substitutions. O. anthropi and O. tritici were indistinguishable by means of their RecA proteins. A set of initially biochemically classified strains did not cluster within their assigned species and they either grouped within other known species or grouped as potential novel Ochrobactrum species. In further investigations, these strains were reclassified and described as novel species. In summary, Ochrobactrum is a highly diverse genus comprising several novel species. We recommend recA- in addition to rrs gene-analysis for correct species allocation and subtyping of novel Ochrobactrum isolates.
AU  - Scholz, H.C.*
AU  - Al Dahouk, S.*
AU  - Tomaso, H.*
AU  - Neubauer, H.*
AU  - Witte, A.*
AU  - Schloter, M.
AU  - Kämpfer, P.*
AU  - Falsen, E.*
AU  - Pfeffer, M.*
AU  - Engel, M.
C1  - 3797
C2  - 25166
SP  - 1-16
TI  - Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis.
JO  - Syst. Appl. Microbiol.
VL  - 31
IS  - 1
PB  - Elsevier
PY  - 2008
SN  - 0723-2020
ER  - 

TY  - JOUR
AU  - Lebuhn, M.
AU  - Bathe, S.*
AU  - Achouak, W.*
AU  - Hartmann, A.
AU  - Heulin, T.*
AU  - Schloter, M.
C1  - 3412
C2  - 23565
SP  - 265-275
TI  - Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species.
JO  - Syst. Appl. Microbiol.
VL  - 29
PY  - 2006
SN  - 0723-2020
ER  - 

TY  - JOUR
AU  - Lehner, A.*
AU  - Riedel, K.*
AU  - Rattei, T.*
AU  - Ruepp, A.
AU  - Frishman, D.*
AU  - Breeuwer, P.*
AU  - Diep, B.*
AU  - Eberl, L.*
AU  - Stephan, R.*
C1  - 3847
C2  - 24111
SP  - 609-625
TI  - Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism.
JO  - Syst. Appl. Microbiol.
VL  - 29
PY  - 2006
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - The genus Listeria contains the two pathogenic species Listeria monocytogenes and Listeria ivanovii and the four apparently apathogenic species Listeria innocua, Listeria seeligeri, Listeria welshimeri, and Listeria grayi. Pathogenicity of the former two species is enabled by an approximately 9 kb virulence gene cluster which is also present in a modified form in L. seeligeri. For all Listeria species, the sequence of the virulence gene cluster locus and its flanking regions was either determined in this study or assembled from public databases. Furthermore, some virulence-associated internalin loci were compared among the six species. Phylogenetic analyses were performed on a data set containing the sequences of prs, ldh, vclA, and vclB (all directly flanking the virulence gene cluster), as well as the iap gene and the 16S and 23S-rRNA coding genes which are located at different sites in the listerial chromosomes. L. grayi represents the deepest branch within the genus. The remaining five species form two groupings which have a high bootstrap support and which are consistently found by using different treeing methods. One lineage represents L. monocytogenes and L. innocua, while the other contains L. welshimeri, L. ivanovii and L. seeligeri, with L. welshimeri forming the deepest branch. Based on this perception, we tried to reconstruct the evolution of the virulence gene cluster. Since no traces of lateral gene transfer events could be detected the most parsimonious scenario is that the virulence gene cluster was present in the common ancestor of L. monocytogenes, L. innocua, L. ivanovii, L. seeligeri and L. welshimeri and that the pathogenic capability has been lost in two separate events represented by L. innocua and L. welshimeri. This hypothesis is also supported by the location of the putative deletion breakpoints of the virulence gene cluster within L. innocua and L. welshimeri.
AU  - Schmid, M.W.
AU  - Ng, E.Y.*
AU  - Lampidis, R.*
AU  - Emmerth, M.*
AU  - Walcher, M.*
AU  - Kreft, J.*
AU  - Goebel, W.*
AU  - Wagner, M.*
AU  - Schleifer, K.H.*
C1  - 22941
C2  - 31067
SP  - 1-18
TI  - Evolutionary history of the genus Listeria and its virulence genes.
JO  - Syst. Appl. Microbiol.
VL  - 28
IS  - 1
PB  - Elsevier
PY  - 2005
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - The genera Azospirillum, Skermanella and Rhodocista form a phylogenetic subgroup within the alfa subclass of Proteobacteria. Based on comparative 16S rRNA sequence analysis a nested set of new oligonucleotide probes was designed. It comprises probes for the whole genus cluster Azospirillum-Skermanella-Rhodocista, for the Azospirilli subcluster I including A. lipoferum, A. doebereinerae, A. largimobile, A. brasilense and A. halopraeferens, for the Azospirilli subcluster II including A. amazonense, A. irakense and the genus Skermanella, for the genus Rhodocista as well as for all Azospirilli species or species cluster. The new probes allow a fast and reliable in situ identification of bacteria belonging to the Azospirillum-Skermanella-Rhodocista-cluster at different phylogenetic levels. The specificity of the new probes was tested with 56 strains of the Azospirillum-Rhodocista-Skermanella-cluster and selected reference cells from other genera by hybridising with the complete probe set. In addition, applications of the fluorescently labelled probes for in situ identification of isolates and for the in situ localisation of A. brasilense on maize roots were demonstrated using confocal laser scanning microscopy.
AU  - Stoffels, M.
AU  - Castellanos, T.*
AU  - Hartmann, A.
C1  - 23014
C2  - 31114
SP  - 83-97
TI  - Design and application of new 16S rRNA-targeted oligonucleotide probes for the Azospirillum-Skermanella-Rhodocista-cluster.
JO  - Syst. Appl. Microbiol.
VL  - 24
IS  - 1
PB  - Urban & Fischer Verl.
PY  - 2001
SN  - 0723-2020
ER  - 

TY  - JOUR
AB  - Gram-negative filamentous bacteria are commonly observed in activated sludge and contribute to poor settlement of activated sludge flocs in secondary sedimentation tanks, a problem referred to as activated sludge bulking. However, the standard morphological identification system is of limited value for a high resolution, rapid monitoring of these bacteria. Therefore, specific 16S rRNA-targeted oligonucleotide probes were developed for Haliscomenobacter spp., Sphaerotilus spp., Leptothrix spp., Thiothrix spp., Leucothrix mucor and bacteria of the Eikelboom type 021N. Probe specificities were evaluated by nonisotopic dot blot hybridization to 145 reference strains representing a diverse collection of taxa. In situ hybridization with fluorescent probe derivatives was combined with scanning confocal laser microscopy (SCLM) for analyzing the three dimensional localization of the filaments inside the sludge flocs. Filaments could be localized even in the center of fixed flocs at a high resolution undisturbed by problems like autofluorescence.
AU  - Wagner, M.*
AU  - Amann, R.*
AU  - Kämpfer, P.*
AU  - Aßmus, B.
AU  - Hartmann, A.
AU  - Hutzler, P.
AU  - Springer, N.*
AU  - Schleifer, K.-H.*
C1  - 23200
C2  - 31483
SP  - 405-417
TI  - Identification and in situ detection of gram-negative filamentous bacteria in activated sludge.
JO  - Syst. Appl. Microbiol.
VL  - 17
IS  - 3
PB  - Elsevier
PY  - 1994
SN  - 0723-2020
ER  - 

TY  - JOUR
AU  - Hwang, B.K.
AU  - de Cock, A.W.A.M.
AU  - Bahnweg, G.
AU  - Prell, H.H.
AU  - Heitefuss, R.
C1  - 20518
C2  - 13728
TI  - Restriction Fragment Length Polymorphisms of Mitochondrial DNA Among Phytophthora capsici Isolates from Pepper (Capsicum annuum).
JO  - Syst. Appl. Microbiol.
PY  - 1991
SN  - 0723-2020
ER  - 

TY  - JOUR
AU  - Laaser, G.
AU  - Möller, E.
AU  - Jahnke, K.-D.
AU  - Bahnweg, G.
AU  - Prillinger, H.
AU  - Prell, H.H.
C1  - 18624
C2  - 11179
TI  - Ribosomal DNA Restriction Fragment Analysis as a Taxonomic Tool in Separating Physiologically Similar Basidiomycetous Yeasts.
JO  - Syst. Appl. Microbiol.
PY  - 1989
SN  - 0723-2020
ER  -