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  • Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-27
    Raul Munoz; Hanno Teeling; Rudolf Amann; Ramon Rosselló-Móra

    To date, the phylum Bacteroidetes comprises more than 1500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.

    更新日期:2020-01-27
  • High-throughput cultivation of heterotrophic bacteria during a spring phytoplankton bloom in the North Sea
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-27
    Carlota Alejandre-Colomo; Jens Harder; Bernhard M. Fuchs; Ramon Rosselló-Móra; Rudolf Amann

    On-going studies of phytoplankton-bacterioplankton interactions at the long-term ecological research site Helgoland Roads have indicated that many of the heterotrophic bacterial taxa have not yet been cultivated. A high-throughput approach combining whole cell matrix-assisted laser desorption ionization - time of flight mass spectroscopy with 16S rRNA gene sequencing was applied to the spring bloom of 2016. Aiming at an assessment of cultivability during a spring bloom, cultivation on solid marine media had to be used since dilution to extinction would not have been feasible for a high-throughput approach, as performed in this study. A total of 5,023 isolates were obtained from nine weekly samples on eight different solid media between the early-bloom and post-bloom periods. Most of the 4,136 strains identified affiliated with Bacteroidetes (13.3%), Gammaproteobacteria (26.9%), Alphaproteobacteria (40.6%) and Actinobacteria (6.7%). Of the 271 operational phylogenetic units (OPUs) identified, 13 are likely to represent novel genera and 143 novel species. A comparison with 16S rRNA gene tag data indicated that most of the isolates were rather rare in surface waters, with the exception of five OPUs affiliating with Rhodobacteraceae, Polaribacter, Psychromonas and Pseudoalteromonas. The effort yielded many novel isolates, yet most of the abundant heterotrophic bacteria still remained elusive. The large strain collection obtained will not only provide insights into the succession of the cultivable fraction of the bacterioplankton, but also enable fine-tuned taxonomic and physiological follow-up studies for improving our knowledge on heterotrophic bacteria in North Sea waters.

    更新日期:2020-01-27
  • The first crenarchaeon capable of growth by anaerobic carbon monoxide oxidation coupled with H2 production
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-25
    Tatiana V. Kochetkova; Andrei V. Mardanov; Tatyana G. Sokolova; Elizaveta A. Bonch-Osmolovskaya; Ilya V. Kublanov; Vadim V. Kevbrin; Alexey V. Beletsky; Nikolay V. Ravin; Alexander V. Lebedinsky

    The ability to grow by anaerobic CO oxidation with production of H2 from water is known for some thermophilic bacteria, most of which belong to Firmicutes, as well as for a few hyperthermophilic Euryarchaeota isolated from deep-sea hydrothermal habitats. A hyperthermophilic, neutrophilic, anaerobic filamentous archaeon (strain 1505 = VKM B-3180 = KCTC 15798) was isolated from a terrestrial hot spring in Kamchatka (Russia) in the presence of 30% CO in the gas phase. Strain 1505 could grow lithotrophically using carbon monoxide as the energy source with the production of hydrogen according to the equation CO + H2O -> CO2 + H2; mixotrophically on CO plus glucose; and organotrophically on peptone, yeast extract, glucose, sucrose, or Avicel. The genome of strain 1505 was sequenced and assembled into a single chromosome. Based on 16S rRNA gene sequence analysis and in silico genome-genome hybridization, this organism was shown to be closely related to the ‘Thermofilum adornatum’ species. In the genome of Thermofilum sp. strain 1505, a gene cluster (TCARB_0867-TCARB_0879) was found that included genes of anaerobic (Ni,Fe-containing) carbon monoxide dehydrogenase and genes of energy-converting hydrogenase ([Ni,Fe]-CODH–ECH gene cluster). Compared to the [Ni,Fe]-CODH–ECH gene clusters occurring in the sequenced genomes of other H2-producing carboxydotrophs, the [Ni,Fe]-CODH–ECH gene cluster of Thermofilum sp. strain 1505 presented a novel type of gene organization. The results of the study provided the first evidence of anaerobic CO oxidation coupled with H2 production performed by a crenarchaeon, as well as the first documented case of lithotrophic growth of a Thermofilaceae representative.

    更新日期:2020-01-26
  • 更新日期:2020-01-26
  • Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-22
    Archana Yadav; Javier Vilcáez; Ibrahim F. Farag; Britny Johnson; Katherine Mueller; Noha H. Youssef; Mostafa S. Elshahed

    We report on the characterization of a novel genomic assembly (ARYD3) recovered from formation water (17.6% salinity) and crude oil enrichment amended by isolated soy proteins (0.2%), and incubated for 100 days under anaerobic conditions at 50 °C. Phylogenetic and phylogenomic analysis demonstrated that the ARYD3 is unaffiliated with all currently described bacterial phyla and candidate phyla, as evident by the low AAI (34.7%), shared gene content (19.4%), and 78.9% 16S rRNA gene sequence similarity to Halothiobacillus neapolitanus, its closest cultured relative. Genomic characterization predicts a slow-growing, non-spore forming, and non-motile Gram-negative rod. Adaptation to high salinity is potentially mediated by the production of the compatible solutes cyclic 2,3-diphosphoglycerate (cDPG), α-glucosylglycerate, as well as the uptake of glycine betaine. Metabolically, the genome encodes primarily aminolytic capabilities for a wide range of amino acids and peptides. Interestingly, evidence of propionate degradation to succinate via methyl-malonyl CoA was identified, suggesting possible capability for syntrophic propionate degradation. Analysis of ARYD3 global distribution patterns identified its occurrence in a very small fraction of Earth Microbiome Project datasets examined (318/27068), where it consistently represented an extremely rare fraction (maximum 0.28%, average 0.004%) of the overall community. We propose the Candidatus name Mcinerneyibacterium aminivorans gen. nov, sp. nov. for ARYD3T, with the genome serving as the type material for the novel family Mcinerneyibacteriaceae fam. nov., order Mcinerneyibacteriales ord. nov., class Mcinerneyibacteria class nov., and phylum Mcinerneyibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number VSIX00000000.

    更新日期:2020-01-22
  • Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-22
    Michał Kalita; Wanda Małek; Teresa A. Coutinho

    In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89T and Bradyrhizobium valentinum LmjM3T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89T, Bradyrhizobium valentinum LmjM3T and Bradyrhizobium retamae Ro19T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.

    更新日期:2020-01-22
  • Serratia nevei sp. nov. and Serratia bockelmannii sp. nov., isolated from fresh produce in Germany and reclassification of Serratia marcescens subsp. sakuensis Ajithkumar et al. 2003 as a later heterotypic synonym of Serratia marcescens subsp. Marcescens
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-22
    Gyu-Sung Cho; Maria Stein; Erik Brinks; Jana Rathje; Woojung Lee; Soo Hwan Suh; Charles M.A.P. Franz

    Fifteen enterobacterial strains were isolated from fresh produce. The 16S rRNA gene sequences indicated that these belong to Serratia, with twelve strains showing 99.57 % to 99.93 % and three strains showing 99.86-100 % 16S rRNA gene sequence similarity with Serratia marcescens and Serratia nematodiphila as nearest neighbors, respectively. Further comparative multi locus sequence analyses, as well as phylogenomic comparisons, revealed that 6 of the 15 strains were well-separated from their nearest neighbors and formed two clearly distinct taxa. Strains S2, S9, S10 and S15T were urease-positive, while strains S3T and S13 were urease-negative. Average nucleotide identity and digital DNA-DNA hybridization comparisons of representative strains S3T and S15T with type strains of S. marcescens, S. nematodiphila and S. ureilytica indicated that these shared less than 96 % and 70 % homology, respectively. Major fatty acids of strains S3T and S15T included C16:0, C16:1 ω7c/C16:1 ω6c, C17:0 Cyclo and C18:1 ω6c /C18:1 ω7c. The mol % G + C of genomic DNA of strain S15T was 59.49 % and of strain S3T was 59.04. These results support the description of two novel species, Serratia nevei and Serratia bockelmannii, with strains S15T (=LMG 31536T =DSM 110085T) and S3T (=LMG 31535T =DSM 110152T) as type strains, respectively. Although Serratia marcescens subsp. sakuensis was previously described to form spores, spores could not be determined in this study. As spore formation was the only differential characteristic of this subspecies, S. marcescens subsp. sakuensis is a later heterotypic synonym of Serratia marcescens.

    更新日期:2020-01-22
  • Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-07
    Luisa Caroline Ferraz Helene; Graham O’Hara; Mariangela Hungria

    Bradyrhizobium are N2-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.

    更新日期:2020-01-07
  • Survival of Brenneria goodwinii and Gibbsiella quercinecans, Associated with Acute Oak Decline, in Rainwater and Forest Soil
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2020-01-03
    Bethany J. Pettifor; James Doonan; Sandra Denman; James E. McDonald
    更新日期:2020-01-04
  • Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-12-23
    Patrycja Golinska; Maria del Carmen Montero-Calasanz; Magdalena Świecimska; Adnan Yaramis; Jose M. Igual; Alan T. Bull; Michael Goodfellow

    A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H4), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9% similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6T and M. italicus BC 501T were 90.9% and 42.3%, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6T (=DSM 107535T =PCM 3004T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.

    更新日期:2019-12-23
  • Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-12-19
    Svetlana N. Dedysh; Irina S. Kulichevskaya; Alexey V. Beletsky; Anastasia A. Ivanova; W. Irene C. Rijpstra; Jaap S. Sinninghe Damsté; Andrey V. Mardanov; Nikolai V. Ravin

    Pirellula-like planctomycetes are ubiquitous aquatic bacteria, which are often detected in anoxic or micro-oxic habitats. By contrast, the taxonomically described representatives of these bacteria, with very few exceptions, are strict aerobes. Here, we report the isolation and characterization of the facultatively anaerobic planctomycete, strain P X 69T, which was isolated from a boreal lake. Its 16S rRNA gene sequence is affiliated with the Pirellula-related Pir4 clade, which is dominated by environmental sequences retrieved from a variety of low-oxygen habitats. Strain P X 69T was represented by ellipsoidal cells that multiplied by budding and grew on sugars, some polysaccharides and glycerol. Anaerobic growth occurred by means of fermentation. Strain P X 69T grew at pH 5.5-7.5 and at temperatures between 10 and 30 °C. The major fatty acids were C18:1ω9c, C16:0 and C16:1ω7c; the major intact polar lipid was dimethylphosphatidylethanolamine. The complete genome of strain P X 69T was 6.92 Mb in size; DNA G + C content was 61.7 mol%. Among characterized planctomycetes, the highest 16S rRNA gene similarity (90.4%) was observed with ‘Bythopirellula goksoyri’ Pr1d, a planctomycete from deep-sea sediments. We propose to classify P X 69T as a novel genus and species, Lacipirellula parvula gen. nov., sp. nov.; the type strain is strain P X 69T (=KCTC 72398T = CECT 9826T =VKM B-3335T). This genus is placed in a novel family, Lacipirellulaceae fam. nov., which belongs to the order Pirellulales ord. nov. Based on the results of comparative genome analysis, we also suggest establishment of the orders Gemmatales ord. nov. and Isosphaerales ord. nov. as well as an emendation of the order Planctomycetales.

    更新日期:2019-12-19
  • Genotypic and symbiotic diversity of native rhizobia nodulating red pea (Lathyrus cicera L) in Tunisia
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-12-16
    Gritli Takwa; Walid Ellouze; Chihaoui Saif-Allah; Barhoumi Fathi; Ridha Mhamdi; Bacem Mnasri

    Nodulation and genetic diversity of native rhizobia nodulating Lathyrus cicera plants grown in 24 cultivated and marginal soils collected from northern and central Tunisia were studied. L. cicera plants were nodulated and showed the presence of native rhizobia in 21 soils. A total of 196 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. The sequence analysis of the rrs and two housekeeping genes (recA and thrC) from 36 representative isolates identified Rhizobium laguerreae as the dominant (53%) rhizobia nodulating L. cicera. To the best of our knowledge, this is the first time that this species has been reported among wild populations of the rhizobia-nodulating Lathyrus genus. Twenty-five percent of the isolates were identified as R. leguminosarum and isolates LS11.5, LS11.7 and LS8.8 clustered with Ensifer meliloti. Interestingly, five isolates (LS20.3, LS18.3, LS19.10, LS1.2 and LS21.20) were segregated from R. laguerreae and clustered as a separate clade. These isolates possibly belong to new species. According to nodC and nodA phylogeny, strains of R. laguerreae and R. leguminosarum harbored the symbiotic genes of symbiovar viciae and clustered in three different clades showing heterogeneity within the symbiovar. Strains of E. meliloti harbored symbiotic genes of Clade V and induced inefficient nodules.

    更新日期:2019-12-17
  • Vibrio taketomensis sp. nov. by genome taxonomy
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-12-10
    Mami Tanaka, Bi Hongyu, Chunqi Jiang, Sayaka Mino, Pedro Milet Meirelles, Fabiano Thompson, Bruno Gomez-Gil, Tomoo Sawabe

    Two novel strains C4III282T and C4III291 were isolated from seawater collected a site off the Taketomi coral reef. Phylogenetic analysis based on the 16S rRNA sequences revealed that the two strains belong to the genus Vibrio. MLSA using eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) showed that C4III282T and C4III291 are closely related to the members of the Ponticus clade, namely Vibrio panuliri JCM 19500T, Vibrio ponticus DSM 16217T, and “Vibrio rhodolitus” G98. ANI and in silico DDH values with members of the Ponticus clade were 77.6-78.7% and 22.2-23.1, respectively. The name Vibrio taketomensis sp. nov. is proposed with C4III282T (CAIM 1928T = DSM 106943T = JCM 33434T) as the type strain.

    更新日期:2019-12-11
  • Mycoplasma nasistruthionis sp. nov. and Mycoplasma struthionis sp. nov. isolated from ostriches with respiratory disease
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-12-09
    Joachim Spergser, Annelise Botes, Tyron Nel, Werner Ruppitsch, Sarah Lepuschitz, Stefan Langer, Sally Ries, Nora Dinhopl, Michael Szostak, Igor Loncaric, Hans-Jürgen Busse

    Twelve Mycoplasma (M.) strains isolated from the nose, the trachea, and the lung of ostriches (Struthio camelus) displaying respiratory disease were investigated. Analysis of 16S rRNA gene sequences placed five of these strains within the M. synoviae cluster, and seven strains within the M. hominis cluster of genus Mycoplasma, which was further confirmed by analyses of the 16S-23S rRNA intergenic spacer region, and partial rpoB gene and amino acid sequences. Genomic information as well as phenotypic features obtained by matrix-assisted laser desorption ionization time of flight (MALDI-ToF) mass spectrometry analysis and serological reactions indicated that the strains examined are representatives of two hitherto unclassified species of genus Mycoplasma, for which the names Mycoplasma nasistruthionis sp. nov., with type strain 2F1AT (= ATCC BAA-1893T = DSM 22456T), and Mycoplasma struthionis sp. nov., with type strain 237IAT (= ATCC BAA-1890T = DSM 22453T), are proposed.

    更新日期:2019-12-11
  • History and current taxonomic status of genus Agrobacterium
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-29
    José David Flores-Félix, Esther Menéndez, Alvaro Peix, Paula García-Fraile, Encarna Velázquez

    The genus Agrobacterium was created a century ago by Conn who included it in the family Rhizobiaceae together with the genus Rhizobium. Initially, the genus Agrobacterium contained the non-pathogenic species Agrobacterium radiobacter and the plant pathogenic species Agrobacterium tumefaciens and Agrobacterium rhizogenes. At the end of the past century two new pathogenic species, Agrobacterium rubi and Agrobacterium vitis, were added to the genus. Already in the present century these species plus Agrobacterium larrymoorei were reclassified into genus Rhizobium. This reclassification was controversial and for a time both genus names were used when new species were described. Few years ago, after a taxonomic revision based on genomic data, the old species A. rhizogenes was maintained in the genus Rhizobium, the old species A. vitis was transferred to the genus Allorhizobium and several Rhizobium species were transferred to the genus Agrobacterium, which currently contains 14 species including the old species A. radiobacter, A. tumefaciens, A. rubi and A. larrymoorei. Most of these species are able to produce tumours in different plants, nevertheless the genus Agrobacterium also encompasses non-pathogenic species, one species able to nodulate legumes and one human pathogenic species. Taking into account that the species affiliations to five Agrobacterium genomospecies have not been determined yet, an increase in the number of species within this genus is expected in the near future.

    更新日期:2019-11-30
  • High taxonomic diversity of Micromonospora strains isolated from Medicago sativa nodules in Western Spain and Australia
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-22
    Pilar Martínez-Hidalgo, José David Flores-Félix, Encarna Velázquez, Lambert Brau, Martha E. Trujillo, Eustoquio Martínez-Molina

    The genus Micromonospora has been found in nodules of several legumes and some new species of this genus were isolated from these plant organs. In this study we analysed the taxonomic diversity of Micromonospora strains isolated from alfalfa nodules in Spain and Australia on the basis of three phylogenetic markers, the rrs and gyrB genes and 16S-23S intergenic spacer (ITS). The genome analysis of selected strains representative of different clusters or lineages found after rrs, gyrB and ITS analyses confirmed the results obtained with these phylogenetic markers. They showed that the analysed strains belong to at least 18 Micromonospora species including previously described ones, such as Micromonospora noduli, Micromonospora ureilytica, Micromonospora taraxaci, Micromonospora zamorensis, Micromonospora aurantiaca and Micromonospora tulbaghiae. Most of these strains belong to undescribed species of Micromonospora showing the high taxonomic diversity of strains from this genus inhabiting alfalfa nodules. Although Micromonospora strains are not able to induce the formation of these nodules, and it seems that they do not contribute to fix atmospheric nitrogen, they could play a role related with the mechanisms of plant growth promotion and pathogen protection presented by Micromonospora strains isolated from legume nodules.

    更新日期:2019-11-22
  • Ecological and functional capabilities of an uncultured Kordia sp
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-22
    M. Royo-Llonch, P. Sánchez, J.M. González, C. Pedrós-Alió, S.G. Acinas

    Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species was described, which included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche seemed to be particles of phytoplanktonic origin. It could attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.

    更新日期:2019-11-22
  • Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-22
    María Julia Estrella, María Florencia Fontana, Liz Marjory Cumpa Velásquez, Gonzalo Arturo Torres Tejerizo, Luis Diambra, Lars Hestbjerg Hansen, Mariano Pistorio, Analía Inés Sannazzaro

    Three symbiotic nitrogen-fixing bacteria (BD68T, BD66 and BD73) isolated from root nodules of Lotus tenuis in lowland soils of the Flooding Pampa (Argentina), previously classified as members of the Mesorhizobium genus, were characterized in this study. Phylogenetic analysis of their 16S rRNA gene sequences showed a close relationship to M. japonicum MAFF 303099T, M. erdmanii USDA 3471T, M. opportunistum WSM 2975T, M. jarvisii ATCC 33669T and M. huakuii LMG 14107T, with sequence identities of 99.78% - 100%. Multilocus sequence analysis of other housekeeping genes revealed that the three isolates belonged to a phylogenetically distinct clade within the genus Mesorhizobium. Strain BD68T was designated as the group representative and its genome was fully sequenced. The average nucleotide identity and in silico DNA-DNA hybridization comparisons between BD68T and the most related type strains showed values below the accepted threshold for species discrimination. Phenotypic and chemotaxonomic features were also studied. Based on these results, BD68T, BD66 and BD73 could be considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium intechi sp. nov. is hereby proposed. The type strain of this species is BD68T (= CECT 9304T = LMG 30179T).

    更新日期:2019-11-22
  • Halomonas borealis sp. nov. and Halomonas niordiana sp. nov., two new species isolated from seawater
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-17
    Ana L. Diéguez, Sabela Balboa, Jesús L. Romalde

    Two Gram-negative strains obtained from tank water in a scallop hatchery in Norway, were phenotypically and genotypically characterized in order to clarify their taxonomic position. On the basis of 16S rRNA gene sequence analysis, these isolates, ATF 5.2T and ATF 5.4T, were included in the genus Halomonas, being their closest relatives H. smyrnensis and H. taeanensis, with similarities of 98.9% and 97.7%, respectively. Sequence analysis of the housekeeping genes atpA, ftsZ, gyrA, gyrB, mreB, rpoB, rpoD, rpoE, rpoH, rpoN and rpoS clearly differentiated the isolates from the currently described Halomonas species, and the phylogenetic analysis using concatenated sequences of these genes located them in two robust and independent branches. DNA–DNA hybridization (eDDH) percentage, together with Average Nucleotide Identity (ANI), were calculated using the complete genome sequences of the strains, and demonstrate that the isolates constitute two new species of Halomonas, for which the names of Halomonas borealis sp. nov. and Halomonas niordiana sp. nov. are proposed, with type strains ATF 5.2T (=CECT 9780T = LMG 31367T) and ATF 5.4T (= CECT 9779T = LMG 31227T), respectively.

    更新日期:2019-11-18
  • The Mimosoid tree Leucaena leucocephala can be nodulated by the symbiovar genistearum of Bradyrhizobium canariense
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-16
    Martha Helena Ramírez-Bahena, José David Flores-Félix, Encarna Velázquez, Álvaro Peix

    Leucaena leucocephala is a Mimosoid legume tree indigenous to America that has spread to other continents, although it is not still present in some European countries such as Portugal. Nevertheless, we found that this legume can be nodulated in this country by slow-growing rhizobial strains which were identified as Bradyrhizobium canariense trough the analysis of the core genes recA and glnII. The analysis of the symbiotic gene nodC showed that these strains belong to the symbiovar genistearum, which commonly nodulates Genistoid legumes. Although two strains nodulating L. leucocephala in China and Brazil were classified within the genus Bradyrhizobium, they belong to undescribed species and to the symbiovars glycinearum and tropici, respectively. Therefore, we report here for the first time the ability of L. leucocephala to establish symbiosis with strains of B. canariense sv genistearum confirming the high promiscuity of L. leucocephala, that allows it to establish symbiosis with rhizobia native to different continents increasing its invasiveness potential.

    更新日期:2019-11-18
  • Corynebacterium sanguinis sp. nov., a clinical and environmental associated corynebacterium
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-11-14
    Daniel Jaén-Luchoro, Lucia Gonzales-Siles, Roger Karlsson, Liselott Svensson-Stadler, Kent Molin, Sofia Cardew, Susanne Jensie-Markopolous, Maria Ohlén, Elisabeth Inganäs, Susann Skovbjerg, Brian J. Tindall, Edward R.B. Moore

    Clinical and environmental-associated strains (n = 17), genotypically related to Corynebacterium spp., yet distinct from any species of the genus Corynebacterium with validly published names, have been isolated during the last 20 years and tentatively identified as C. sanguinis, although the combination, “C. sanguinis” was never validly published. The comprehensive genotypic and phenotypic characterisations and genomic analyses in this study support the proposal for recognising the species within the genus Corynebacterium, for which the name, Corynebacterium sanguinis sp. nov., is reaffirmed and proposed. Strains of C. sanguinis are Gram-positive, non-motile, non-spore-forming, short, pleomorphic and coryneform bacilli, growing aerobically, with CO2. They contain mycolic acids, major respiratory menaquinones, MK-8 (II-H2) and MK-9(II-H2), and polar lipids, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, glycolipids and a novel lipid that remains to be characterised and identified. Strains of C. sanguinis are genotypically most similar to C. lipophiliflavum, with 16S rRNA gene sequence similarities of 98.3% and rpoB sequence similarities of 94.9 to 95.2%. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were able to clearly differentiate C. sanguinis from the most closely-related species. The genome size of C. sanguinis is 2.28 to 2.37 Mbp with 65.1 to 65.5 mol% G + C content. A total of 2,202 to 2,318 ORFs were predicted, comprising 2,141 to 2,251 protein-encoding genes. The type strain is CCUG 58655T (= CCM 8873T = NCTC 1428T).

    更新日期:2019-11-14
  • 更新日期:2019-11-01
  • Corrigendum to "Natronobiforma cellulositropha gen. nov., sp. nov., a novel haloalkaliphilic member of the family Natrialbaceae (class Halobacteria) from hypersaline alkaline lakes" [Syst. Appl. Microbiol. 41 (2018) 355-362].
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2018-12-16
    Dimitry Y Sorokin,Tatiana V Khijniak,Nadezhda A Kostrikina,Alexander G Elcheninov,Stepan V Toshchakov,Nicole J Bale,Jaap S Sinninghe Damsté,Ilya V Kublanov

    更新日期:2019-11-01
  • Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2019-10-23
    Milan Čanković,Jurica Žučko,Iris Dupčić Radić,Ivica Janeković,Ines Petrić,Irena Ciglenečki,Gavin Collins

    Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.

    更新日期:2019-11-01
  • Characterization of Desulfomicrobium salsuginis sp. nov. and Desulfomicrobium aestuarii sp. nov., two new sulfate-reducing bacteria isolated from the Adour estuary (French Atlantic coast) with specific mercury methylation potentials.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2008-05-03
    M Dias,J C Salvado,M Monperrus,P Caumette,D Amouroux,R Duran,R Guyoneaud

    Three strains of sulfate-reducing bacteria (ADR21, ADR26 and ADR28) were isolated from Adour estuary sediments (French South Atlantic coast). Cells of these isolates were rod-shaped, motile and stained Gram-negative. The 16S rRNA and dsrAB genes sequence analyses indicated that these three strains belonged to the genus Desulfomicrobium within the delta Proteobacteria, with Desulfomicrobium escambiense strain DSM10707T as their closest relative. According to phenotypic characteristics, strains ADR21 and ADR28 could be considered as members of the same species. The relatedness values, based on DNA-DNA hybridization studies, between strains ADR21/DSM10707T, ADR26/DSM10707T and ADR21/ADR26 ranged between 30.6-40.8%, 45.2-43.0% and 19.0-26.4%, respectively. Strains ADR21 and ADR28 grew well on lactate, fumarate, malate, formate, ethanol and H2/acetate in the presence of sulfate as an electron acceptor. Thiosulfate, nitrate, fumarate and DMSO were alternative electron acceptors. Malate was well fermented but pyruvate and fumarate only poorly. Strain ADR26 could not grow on ethanol or fumarate and was unable to use DMSO or fumarate as electron acceptors. The three new strains exhibited differences compared to the type strain of D. escambiense, such as temperature optima, substrate utilization and mercury methylation capacities. On the basis of both genetic and phenotypic evidences, strain ADR21 is proposed as the type strain of the species Desulfomicrobium salsuginis sp. nov., and strain ADR26 as the type strain of the species Desulfomicrobium aestuarii sp. nov.

    更新日期:2019-11-01
  • Lactobacillus harbinensis sp. nov., consisted of strains isolated from traditional fermented vegetables 'Suan cai' in Harbin, Northeastern China and Lactobacillus perolens DSM 12745.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-11-03
    Mari Miyamoto,Yasuyuki Seto,Dong Hai Hao,Tamaki Teshima,Yan Bo Sun,Toshihide Kabuki,Li Bing Yao,Hadjime Nakajima

    Taxonomical analysis of two genetically distinguished Lactobacillus strains isolated from traditional Chinese fermented vegetables 'Suan cai' was performed. They formed L-lactate from glucose, were facultatively heterofermentative, and had a DNA G+C content of 53-54mol%. They fermented D- and L-arabinose. They produced lactate, ethanol and acetate from gluconate at a molar ratio of 1.1:0.4:0.7. Phylogenetic analysis of 16S rDNA revealed that the two strains were closely related to L. perolens. DNA-DNA hybridization analysis revealed that the two strains were different from L. perolens type strain DSM 12744 and formed a separate cluster with L. perolens DSM 12745. G + C molar content of DNA of the former is 51%, whereas those of the latter strains were in the range of 53-54%. Based on the results, we propose that the new species be named L. harbinensis sp. nov. and that L. perolens DSM 12745 be reclassified as L. harbinensis DSM 12745. The type strain of L. harbinensis DSM 16991T (= AHU 1762T = SBT 10908T).

    更新日期:2019-11-01
  • Stappia alba sp. nov., isolated from Mediterranean oysters.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-11-03
    Maria J Pujalte,M Carmen Macián,David R Arahal,Esperanza Garay

    Three bacterial strains isolated from oysters recovered at the Spanish Mediterranean coast have been phenotypically and genetically characterized. The results of the phylogenetic analysis based on almost complete 16S rDNA sequences clustered all three strains together with 99.9% average sequence similarity and situated them in the neighbourhood of the genera Stappia, Roseibium and Pannonibacter, Stappia aggregata being their closest neighbour with sequence similarities between 98.8% and 98.9%. DNA-DNA hybridization experiments using DNA of strains 5OM6T and S. aggregata CECT 4269T as reference DNAs confirmed the independent status at species level of the oyster isolates. Phenotypically, they can be distinguished from the closest relatives by the ionic requirements, growth temperatures and use of carbon compounds. We propose these oyster strains constitute a new species of Stappia, for which the name Stappia alba sp. nov. has been chosen, and strain 5OM6T (= CECT 5095T = CIP 108402T) as its type strain.

    更新日期:2019-11-01
  • Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-09-15
    Chantal Fernandes,Fred A Rainey,M Fernanda Nobre,Isabel Pinhal,Fátima Folhas,Milton S da Costa

    Several yellowish-pigmented bacteria with an optimum growth temperature of about 30 degrees C, were recovered from the source (borehole) of bottled mineral water in the Serra da Estrela in Eastern Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strains S-94T , S-97, S-99 and S-92 indicated that these organisms represent a new species of the Betaproteobacteria that is not closely related to any other known species. The major fatty acids of the strains are 16:1 omega7c and 16:0. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. The new strains only assimilated organic acids, glycine and alanine. Casamino acids and a mixture of all natural amino acids are not used as sole carbon and nitrogen sources; these are used as nitrogen source in the presence of organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we are of the opinion that strains S-94T, S-97, S-99 and S-92 represent a new species of a novel genus for which we propose the name Herminiimonas fonticola gen. nov., sp. nov.

    更新日期:2019-11-01
  • PCR detection assays for the trichothecene-producing species Fusarium graminearum, Fusarium culmorum, Fusarium poae, Fusarium equiseti and Fusarium sporotrichioides.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-08-18
    Miguel Jurado,Covadonga Vázquez,Belén Patiño,M Teresa González-Jaén

    Contamination of small-grain cereals with the fungal species Fusarium graminearum, F. culmorum, F. poae, F. sporotrichioides and F. equiseti is an important source of trichothecenes, Zearalenone and other mycotoxins which cause serious diseases in human and animals. Additionally, these species contribute to Fusarium Head Blight, a disease which produces important losses in cereal yield. Early detection and control of these Fusarium species is crucial to prevent toxins entering the food chain and a useful tool in disease management practices. We describe the development of specific PCR assays to F. graminearum, F. culmorum, F. poae, F. sporotrichioides and F. equiseti using DNA from pure fungal cultures as well as from naturally infected wheat seeds, using in this case a rapid and easy protocol for DNA isolation. The specific primers were designed on the basis of IGS sequences (Intergenic Spacer of rDNA), a multicopy region in the genome that permits to enhance the sensitivity of the assay in comparison with PCR assays based on single-copy sequences.

    更新日期:2019-11-01
  • Molecular detection and isolation from antarctica of methylotrophic bacteria able to grow with methylated sulfur compounds.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-08-18
    S Azra Moosvi,Ian R McDonald,David A Pearce,Donovan P Kelly,Ann P Wood

    This study is the first demonstration that a diverse facultatively methylotrophic microbiota exists in some Antarctic locations. PCR amplification of genes diagnostic for methylotrophs was carried out with bacterial DNA isolated from 14 soil and sediment samples from ten locations on Signy Island, South Orkney Islands, Antarctica. Genes encoding the mxaF of methanol dehydrogenase, the fdxA for Afipia ferredoxin, the msmA of methanesulfonate monooxygenase, and the 16S rRNA gene of Methylobacterium were detected in all samples tested. The mxaF gene sequences corresponded to those of Hyphomicrobium, Methylobacterium, and Methylomonas. Over 30 pure cultures of methylotrophs were isolated on methanesulfonate, dimethylsulfone, or dimethylsulfide from ten Signy Island lakes. Some were identified from 16S rRNA gene sequences (and morphology) as Hyphomicrobium species, strains of Afipia felis, and a methylotrophic Flavobacterium strain. Antarctic environments thus contain diverse methylotrophic bacteria, growing on various C1-substrates, including C1-sulfur compounds.

    更新日期:2019-11-01
  • Diverse rhizobia associated with woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the temperate zone of China.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-08-13
    Jie Liu,En Tao Wang,Wen Xin Chen

    Fifty-nine bacterial isolates from root nodules of the woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the central and eastern regions of China were characterized with phenotypic analysis, PCR-based 16S and 23S rRNA gene RFLP, Box PCR and 16S rRNA gene sequencing. Seven main phena were defined in numerical taxonomy, which corresponded to distinct groups within the genera Agrobacterium, Bradyrhizobium, Mesorhizobium and Rhizobium in 16S and 23S rRNA gene PCR-RFLP. The phylogenetic relationships of the 16S rRNA genes supported the grouping results of PCR-RFLP. Most of the isolates from Amorpha fruticosa were classified into two groups closely related to Mesorhizobium amorphae. Seventeen of the 21 isolates from Wisteria sinensis were identified as two groups related to Rhizobium and Agrobacterium. Six out of 10 isolates from Cercis racemosa were identified as a group related to Bradyrhizobium. Our results indicated that each of the investigated legumes nodulated mainly with one or two rhizobial groups, although isolates from different plants intermingled in some small bacterial groups. In addition, correlation between geographic origin and grouping results was found in the isolates from Amorpha fruticosa. These results revealed that the symbiotic bacteria might have been selected by both the legume hosts and the geographic factors.

    更新日期:2019-11-01
  • Molecular characterisation of Xanthomonas strains isolated from aroids in Mauritius.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-07-07
    M H R Khoodoo,F Sahin,M F Donmez,Y Jaufeerally Fakim

    Mauritius is one of the largest world producers of Anthurium cut flowers but outbreaks of bacterial blight have never been reported on the island. This work was about the characterisation and identification of bacterial strains isolated from Anthurium andreanum, Dieffenbachia maculata and Aglaonema simplex in Mauritius. Fifteen strains, that showed the morphological properties of Xanthomonas on conventional media, were tested on two semi-selective media (Esculin-trehalose and cellobiose-starch). ELISA tests using a panel of monoclonal antibodies were carried out and three out of 15 strains reacted with a Xanthomonas-specific monoclonal antibody (MAb XII). Analysis using four sets of ribosomal primers revealed that the same three Mauritius strains shared conserved PCR products with reference xanthomonads including virulent strains of Xanthomonas axonopodis pv. dieffenbachiae (Xad). BIOLOG tests and the Sherlock Microbial Identification system (MIDI) identified these three new strains at the species level as X. axonopodis. The complementary tests that were carried out clearly confirmed that the three strains are xanthomonads and, moreover, a DNA probe which showed specificity to Xad strains suggested that the three Mauritius strains are non-virulent forms of the pathogen causing Anthurium blight.

    更新日期:2019-11-01
  • Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-07-07
    Igor Tiago,Vítor Mendes,Carlos Pires,Paula V Morais,António Verśsimo

    A Gram-negative bacterium designated AC-49T was isolated from an alkaline groundwater with a pH 11.4. This organism formed rod-shaped cells, was strictly aerobic, catalase and oxidase positive, with an optimum growth temperature of 35 degrees C and an optimum pH value of 8.0. Strain AC-49T assimilated primarily amino acids and some Krebs cycle metabolites, did not use sugars for growth. The organism did not grow on L-phenylalanine or antipyrin. The G+ C content of DNA was 66.9 mol%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relatives of strain AC-49T were Phenylobacterium lituiforme and Phenylobacterium immobile, indicating that the organism is a member of the order Caulobacterales of the Alphaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-49T, represents a novel species of the genus Phenylobacterium for which we propose the name Phenylobacterium falsum sp. nov.

    更新日期:2019-11-01
  • Natural association of Gluconacetobacter diazotrophicus and diazotrophic Acetobacter peroxydans with wetland rice.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-05-20
    Ramachandran Muthukumarasamy,Ilse Cleenwerck,Gopalakrishnan Revathi,Muthaiyan Vadivelu,D Janssens,B Hoste,Kang Ui Gum,Ki-Do Park,Cho Young Son,Tongmin Sa,Jesus Caballero-Mellado

    The family Acetobacteraceae currently includes three known nitrogen-fixing species, Gluconacetobacter diazotrophicus, G. johannae and G. azotocaptans. In the present study, acetic acid-producing nitrogen-fixing bacteria were isolated from four different wetland rice varieties cultivated in the state of Tamilnadu, India. Most of these isolates were identified as G. diazotrophicus on the basis of their phenotypic characteristics and PCR assays using specific primers for that species. Based on 16S rDNA partial sequence analysis and DNA: DNA reassociation experiments the remaining isolates were identified as Acetobacter peroxydans, another species of the Acetobacteraceae family, thus far never reported as diazotrophic. The presence of nifH genes in A. peroxydans was confirmed by PCR amplification with nifH specific primers. Scope for the findings: This is the first report of the occurrence and association of N2-fixing Gluconacetobacter diazotrophicus and Acetobacter peroxydans with wetland rice varieties. This is the first report of diazotrophic nature of A. peroxydans.

    更新日期:2019-11-01
  • Unity in organisation and regulation of catabolic operons in Lactobacillus plantarum, Lactococcus lactis and Listeria monocytogenes.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-05-20
    Ulrika Andersson,Douwe Molenaar,Peter Rådström,Willem M de Vos

    Global regulatory circuits together with more specific local regulators play a notable role when cells are adapting to environmental changes. Lactococcus lactis is a lactic acid bacterium abundant in nature fermenting most mono- and disaccharides. Comparative genomics analysis of the operons encoding the proteins and enzymes crucial for catabolism of lactose, maltose and threhalose revealed an obvious unity in operon organisation . The local regulator of each operon was located in a divergent transcriptional direction to the rest of the operon including the transport protein-encoding genes. Furthermore, in all three operons a catabolite responsive element (CRE) site was detected inbetween the gene encoding the local regulator and one of the genes encoding a sugar transport protein. It is evident that regardless of type of transport system and catabolic enzymes acting upon lactose, maltose and trehalose, respectively, Lc. lactis shows unity in both operon organisation and regulation of these catabolic operons. This knowledge was further extended to other catabolic operons in Lc. lactis and the two related bacteria Lactobacillus plantarum and Listeria monocytogenes. Thirty-nine catabolic operons responsible for degradation of sugars and sugar alcohols in Lc. lactis, Lb. plantarum and L. monocytogenes were investigated and the majority of those possessed the same organisation as the lactose, maltose and trehalose operons of Lc. lactis. Though, the frequency of CRE sites and their location varied among the bacteria. Both Lc. lactis and Lb. plantarum showed CRE sites in direct proximity to genes coding for proteins responsible for sugar uptake. However, in L. monocytogenes CRE sites were not frequently found and not in the vicinity of genes encoding transport proteins, suggesting a more local mode of regulation of the catabolic operons found and/or the use of inducer control in this bacterium.

    更新日期:2019-11-01
  • Carnobacterium divergens and Carnobacterium maltaromaticum as spoilers or protective cultures in meat and seafood: phenotypic and genotypic characterization.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-04-16
    Birgit Groth Laursen,Lene Bay,Ilse Cleenwerck,Marc Vancanneyt,Jean Swings,Paw Dalgaard,Jørgen J Leisner

    Carnobacterium, a genus of lactic acid bacteria, frequently dominate the microflora of chilled vacuum- or modified atmosphere-packed meat and seafood. In this study Carnobacterium isolates were characterized by phenotypic and molecular methods in order to investigate the association of species and intra-species groups with distinct kinds of meat and seafood. Of 120 test strains, 50 originated from meat (beef and pork products, including 44 strains isolated during this study and 6 strains obtained from culture collections) and 52 from seafoods (cod, halibut, salmon, shrimps and roe products). In addition, 9 reference strains of Carnobacterium spp from other sources than meat and fish and 9 reference strains of lactic acid bacteria belonging to other genera than Carnobacterium were included. Numerical taxonomy relying on classical biochemical reactions, carbohydrate fermentation and inhibition tests (temperature, salt, pH, chemical preservatives, antibiotics, bacteriocins), SDS-PAGE electrophoresis of whole cell proteins, plasmid profiling, intergenic spacer region (ISR) analysis and examination of amplified-fragment length polymorphism (AFLP) were employed to characterize the strains. The numerical taxonomic approach divided the carnobacteria strains into 24 groups that shared less than 89% similarity. These groups were identified as Carnobacterium divergens with one major cluster (40 strains) and 7 branches of one to four strains, Carnobacterium maltaromaticum (previous C. piscicola) with one major cluster (37 strains) and 9 branches of one to four strains and Carnobacterium mobile (three branches consisting in total of 4 strains). Branches consisting of references strains of the remaining Carnobacterium spp. were separated from clusters and branches of C. divergens, C. maltaromaticum and C. mobile. Isolates from the main clusters of C. divergens and C. maltaromaticum were found both in fresh and lightly preserved meat and seafood products. High phenotypic intra-species variability was observed for C. divergens and C. maltaromaticum but despite this heterogeneity in phenotypic traits a reliable identification to species levels was obtained by SDS-PAGE electrophoresis of whole cell proteins and by ISR based on 16S-23S rDNA intergenic spacer region polymorphism. With AFLP, two distinct clusters were observed for C. divergens but only one for C. maltaromaticum. The two C. divergens clusters were not identical to any of the clusters observed by numerical taxonomy. A limited number of C. divergens and C. maltaromaticum isolates possessed a biopreservative potential due to their production of bacteriocins with a wide inhibition spectrum. This study serves as a base-line for further investigations on the potential role of species of Carnobacterium in foods where they predominate the spoilage microflora.

    更新日期:2019-11-01
  • Geobacillus jurassicus sp. nov., a new thermophilic bacterium isolated from a high-temperature petroleum reservoir, and the validation of the Geobacillus species.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2005-02-16
    Tamara N Nazina,Diana Sh Sokolova,Alexander A Grigoryan,Nataliya M Shestakova,Ekaterina M Mikhailova,Andrei B Poltaraus,Tatiyana P Tourova,Anatolii M Lysenko,George A Osipov,Sergey S Belyaev

    Four thermophilic, spore-forming bacterial strains, DS1(T), DS2, 46 and 49, were isolated from the high-temperature Dagang oilfield, located in China. The strains were identified by using the polyphasic taxonomy approach. These were aerobic, gram-positive, rod-shaped, moderately thermophilic (with an optimum growth temperature of 60-65 degrees C), chemoorganotrophic bacteria capable of growing on various sugars, carboxylic acids and crude oil. Two strains, DS1(T) and DS2, were capable of growing on individual saturated hydrocarbons. The G + C content of the DNA of strains DS1(T) and DS2 was 54.5 and 53.8 mol%, respectively. The phylogenetic analysis of the 16S rDNA of strains DS1(T) and DS2 showed that they form a separate cluster within the genus Geobacillus. The cellular fatty acids of the isolates were dominated by iso-15:0, iso-16:0 and iso-17:0 acids, which are the typical fatty acids of bacteria from the genus Geobacillus. The DNA-DNA hybridization study and the comparative analysis of the morphological and chemotaxonomic characteristics of strains DS1(T) and DS2 showed that they differ from the previously described Geobacillus species and belong to a new species, which was called Geobacillus jurassicus. DS1(T) (=VKM B2301(T), = DSM 15726(T)) is the type strain of this species. According to both DNA-DNA reassociation studies and 16S rDNA sequence analysis, two other strains, 46 and 49, were assigned to the species G. stearothermophilus. In this paper, we provide evidence that the new combinations G. stearothermophilus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans may be considered to be valid.

    更新日期:2019-11-01
  • Mycobacterium fluoranthenivorans sp. nov., a fluoranthene and aflatoxin B1 degrading bacterium from contaminated soil of a former coal gas plant.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-12-23
    D Hormisch,I Brost,G W Kohring,F Giffhorn,R M Kroppenstedt,E Stackebrandt,P Färber,W H Holzapfel

    Mycobacterium strain FA4T was isolated with fluoranthene as the single carbon source from soil of a former coal gas plant, polluted with polycyclic aromatic hydrocarbons. The physiological properties, fatty acid pattern, and the 16S ribosomal RNA gene sequence indicated membership to the genus Mycobacterium, but were different from all type strains of Mycobacterium species. Based on comparative 16S rRNA gene sequence analyses strain FA4T could be assigned to the Mycobacterium neoaurum taxon showing 98% sequence similarity to M. diernhoferi as its closest neighbour. The occurrence of epoxymycolate in the cell wall differentiates FA4 from all members of this taxon which synthesize wax-ester mycolates in addition to alpha-mycolates. Strain FA4T is able to degrade aflatoxin B1. This biological attribute might be useful in biological detoxification processes of foods and feeds. From the investigated characteristics it is concluded that strain FA4T represents a new species, for which we propose the name Mycobacterium fluoranthenivorans sp. nov. The type strain of Mycobacterium fluoranthenivorans is FA4T (DSM 44556T = CIP 108203T).

    更新日期:2019-11-01
  • Rhodovarius lipocyclicus gen. nov. sp. nov., a new genus of the alpha-1 subclass of the Proteobacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-10-20
    Peter Kämpfer,Hans-Jürgen Busse,Ramon Rosséllo-Mora,Eva Kjellin,Enevold Falsen

    A bacterial strain (CCUG 44693T) was recovered during an industrial hygiene control. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that it represents a new lineage in the alpha-1 subclass of the Proteobacteria, with the highest sequence similarity of 93.3% to the type strain of Muricoccus roseus. In the polyamine pattern spermidine was the predominant compound. The polar lipid profile consisted of the major lipids phosphatidyl ethanolamine, phosphatidyl dimethylethanolamine, phosphatidyl glycerol, phosphatidyl cholin and an unknown amino lipid. The major respiratory quinone was a ubiquinone Q-10 and the major whole cell fatty acids were 19:0 cyclo omega8c and 18:1 omega7c. The isolate also contained 18:1 2-OH and other fatty acids typical for members of the alpha-1 subclass of the Proteobacteria in addition to 10:0 2-OH in low amounts, not detected in members of closely related genera. The strain grew heterotrophically and strictly aerobically and formed red-colored colonies on tryptone soy agar. Bacteriochlorophyll a could not be detected by direct spectrophotometric analyses of aerobically grown cells. On the basis of the phylogenetic analyses, chemotaxonomic and biochemical characteristics, we propose that strain CCUG 44693T (CIP 108310T) represents a new genus of the alpha-1 subclass of the Proteobacteria for which we propose the name Rhodovarius lipocyclicus gen. nov. sp. nov.

    更新日期:2019-11-01
  • Technological and molecular diversity of Lactobacillus plantarum strains isolated from naturally fermented sourdoughs.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-09-17
    Olimpia Pepe,Giuseppe Blaiotta,Marilena Anastasio,Giancarlo Moschetti,Danilo Ercolini,Francesco Villani

    Thirty Lactobacillus (L.) plantarum strains, isolated from sourdough, were identified by biochemical tests as well as 16S rDNA sequencing and differentiated on the basis of technological properties, such as amylase, protease, phytase and antirope activities. These properties were shown to be widely differing among the strains, indicating a significant technological diversity. Genetic differentiation was achieved by restriction endonuclease analysis-pulsed field gel electrophoresis (REA-PFGE) that allowed the L. plantarum strains to be divided into 10 different genomic groups. Moreover, 32 different starters were employed in dough making experiments; each starter consisted of a single strain of L. plantarum associated with a maltose positive or a maltose negative yeast. The technological properties of the doughs were greatly influenced by the type of strain included in the starter. The time of leavening and the acidification activities detected in the dough were enhanced by the presence of L. plantarum strains. The bacterial and yeast contents and fermentation properties were statistically treated by principal component analysis (PCA), which allowed the discrimination of different typologies of dough. The study of the peculiar characteristics of different strains of L. plantarum is fundamental for a better understanding of their potential in affecting the nutritional value, quality and stability of the baked goods. L. plantarum strains are able to differentially influence the dough quality when employed as starters.

    更新日期:2019-11-01
  • A genomic perspective on the relationship between the Aquificales and the epsilon-Proteobacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-06-25
    Tom Coenye,Peter Vandamme

    The goal of this study was to determine to what extent the Aquificales are related to the epsilon-Proteobacteria. The genome sequence of several members of this group as well as the genome sequence of Aquifex aeolicus are available. In this study we used information extracted from those whole-genome sequences to gain further insights into the relationships between these organisms, including the fraction of shared putative orthologous protein-encoding genes, dinucleotide relative abundance values and the sequences of the 16S rRNA gene and 20 housekeeping genes. The results of our analyses show that it is not straightforward to come to a consistent picture of the phylogenetic position of the order Aquificales but our data clearly show that there is no particularly close relationship between A. aeolicus and the epsilon-Proteobacteria as (i) they do not share more genes with each other than do other distantly related organisms and (ii) they do not share significant sequence similarity in many macromolecules. In addition, there is considerable evidence that confirms the placement of the Aquificales near the root of the bacterial tree.

    更新日期:2019-11-01
  • Nocardia alba sp.nov., a novel actinomycete strain isolated from soil in China.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-06-25
    Wen-Jun Li,Yi Jiang,Reiner M Kroppenstedt,Li-Hua Xu,Cheng-Lin Jiang

    A novel actinomycete strain, designated YIM 30243T, was isolated from a soil sample in Yunnan Province, China. Based on the results of phenotypic and genotypic characteristics, strain YIM 30243T should be assigned to a new species of the genus Nocardia, for which the name Nocardia alba sp. nov. is proposed. The type strain is YIM 30243T (= CCTCC AA001030T = DSM 44684T).

    更新日期:2019-11-01
  • Xylella fastidiosa subspecies: X. fastidiosa subsp. [correction] fastidiosa [correction] subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-06-25
    Norman W Schaad,Elena Postnikova,George Lacy,M'Barek Fatmi,Chung-Jan Chang

    Xylella fastidiosa, a fastidious bacterium causing disease in over 100 plant species, is classified as a single species, although genetic studies support multiple taxons. To determine the taxonomic relatedness among strains of X. fastidiosa, we conducted DNA-DNA relatedness assays and sequenced the 16S-23S intergenic spacer (ITS) region using 26 strains from 10 hosts. Under stringent conditions (Tm -15 degrees C), the DNA relatedness for most X. fastidiosa strains was *70%. However, at high stringency (Tm -8 degrees C), three distinct genotypes (A, B, and C) were revealed. Taxon A included strains from cultivated grape, alfalfa, almond (two), and maple, interrelated by 85% (mean); taxon B included strains from peach, elm, plum, pigeon grape, sycamore, and almond (one), interrelated by 84%; and taxon C included only strains from citrus, interrelated by 87%. The mean reciprocal relatedness between taxons A and B, A and C, and B and C, were 58, 41, and 45%, respectively. ITS results also indicated the same grouping; taxons A and B, A and C, and B and C had identities of 98.7, 97.9, and 99.2%, respectively. Previous and present phenotypic data supports the molecular data. Taxon A strains grow faster on Pierce's disease agar medium whereas B and C strains grow more slowly. Taxon B and C strains are susceptible to penicillin and resistant to carbenicillin whereas A strains are opposite. Each taxon can be differentiated serologically as well as by structural proteins. We propose taxons A, B, and C be named X. fastidiosa subsp. fastidiosa [correction] subsp. nov, subsp. multiplex, subsp. nov., and subsp. pauca, subsp. nov., respectively. The type strains of the subspecies are subsp. fastidiosa [correction] ICPB 50025 (= ATTC 35879T and ICMP 15197), subsp. multiplex ICPB 50039 (= ATTC 35871 and ICMP 15199), and subsp. pauca ICPB 50031 (= ICMP 15198).

    更新日期:2019-11-01
  • Hydrolysis of oligofructoses by the recombinant beta-fructofuranosidase from Bifidobacterium lactis.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-06-25
    Carolina Janer,Lukas M Rohr,Carmen Peláez,Maryse Laloi,Valentine Cleusix,Teresa Requena,Leo Meile

    The ability of the beta-fructofuranosidase (EC 3.2.1.26) from Bifidobacterium lactis DSM 10140T to cleave a variety of fructooligosaccharides was characterised. We identified its gene on a cloned chromosomal DNA fragment by sequence similarity (69% identity) to the putative CscA protein encoded in the Bifidobacterium longum genome. The deduced amino acid sequence of 532 residues (59.4 kDa) appeared to be identical to the beta-fructofuranosidase from the same strain recently described by Ehrmann et al. (Curr. Microbiol. 2003, 46, 391-397). However, the characterisation of the heterologously expressed enzyme showed several discrepancies to the referred study. First, the B. lactis beta-fructofuranosidase gene was found to have 41% identity with CscA from E. coli in contrast to the 16% reported, therefore it was assigned to as CscA protein instead of BfrA. Second, we observed only low activity of the enzyme towards sucrose (6%) instead of the 100% previously reported. Instead, we measured highest activity (100%) of the enzyme with the oligofructose Raftilose as a substrate compared with the inulin of low degree of polymerisation Raftiline LS (29%) and the highly polymerised Raftiline HP (10%). Altogether, the enzyme showed high affinity to terminal beta(2-1) glycosyl linkages between fructose moieties. The Km values obtained for Raftilose, Raftiline LS and sucrose were 0.12, 7.08 and 8.37 mM, respectively, and V(max) values for the conversion to fructose were calculated to be 5, 21 and 17 micromol/min per mg of protein, respectively. Growth of B. lactis was supported by fructans of low degree of polymerisation (Raftilose and Raftiline LS), whereas we observed no growth with highly polymerised inulin (Raftiline HP).

    更新日期:2019-11-01
  • Functional and safety aspects of Enterococci isolated from different Spanish foods.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-04-01
    Nabil Ben Omar,Araceli Castro,Rosario Lucas,Hikmate Abriouel,Nuha M K Yousif,Charles M A P Franz,Wilhelm H Holzapfel,Rubén Pérez-Pulido,Magdalena Martínez-Cañamero,Antonio Gálvez

    The incidence and diversity of enterococci in retail food samples of meat, dairy and vegetable origin was investigated. Enterococci were present, at concentrations of 10(1) to 10(4) CFU/g. Fifty selected isolates from food samples grouped in two separate clusters by RAPD analysis. Cluster G1 (72% of the isolates) contained the E. faecium CECT 410T type strain, and also showed a high degree of genetic diversity. Cluster G2 (28% of the isolates) contained the E. faecalis CECT 481T type strain and was genetically more homogeneous. Virulence traits (haemolysin, gelatinase or DNAse activities, or the presence of structural genes cylL, ace, asal and esp) were not detected. All isolates were sensitive to the antibiotics ampicillin, penicillin, gentamicin, streptomycin and chloramphenicol. A high pecentage of isolates were resistant to erythromycin and rifampicin. Many isolates showed intermediate sensitivity to several antibiotics (tetracycline, ciprofloxacin, levofloxacin, or quinupristin/dalfopristin). Vancomycin and teicoplanin resistance was detected in one strain, but vanA, vanB, vanC1, vanC2 or vanC3 genes were not detected. Many of the isolates showed functional properties of food or health relevance. Production of antimicrobial substances was detected in 17 of the isolates, and 14 of them carried structural genes for enterocins A, B and/or P.

    更新日期:2019-11-01
  • Genotypic analyses of lactobacilli with a range of tannase activities isolated from human feces and fermented foods.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-04-01
    Yosuke Nishitani,Eiki Sasaki,Tomohiko Fujisawa,Ro Osawa

    A total of 77 tannase producing lactobacilli strains isolated from human feces or fermented foods were examined for their genotypic profiles and intensities of tannase production. With a PCR-based assay targeting recA gene, all strains except one isolate were assigned to either Lactobacillus plantarum, L. paraplantarum, or L. pentosus whereas a 16/23S rDNA targeted PCR-based assay identified all except 6 isolates (inclusive of the above one isolate) as one of the closely related species. Subsequent DNA/DNA hybridization assays revealed that these 6 exceptional isolates showed low homology (between 1.2% and 55.8% relative DNA binding) against type strains of the three species. Supplemental carbohydrate fermentation profiles on the 6 isolates indicated that two of them were identified as L. acidophilus, one as Pediococcus acidilactici, one as P. pentosaceus, and two remained unidentifiable. The evidence suggests that the 16/23S rDNA targeted PCR assay can be used as a reliable identification tool for the closely related lactobacilli, and that the tannase gene is widely distributed within members of the Lactobacillaceae family. Meanwhile, a randomly amplified polymorphism DNA (RAPD) analysis revealed that all except 8 isolates were well allocated in 4 major RAPD clusters, though not species specific, consisting of two L. plantarum predominant clusters, one L. paraplantarum predominant, and one L. pentosus predominant. The RAPD patterns of the 8 non-clustered isolates, which consisted of the 6 unidentifiable isolates and 2 isolates identified as L. pentosus, were <40% similarity to those belonging to the 4 clusters. A quantitative assay of the tannase activities showed that there was a marked variation in the activities among the strains, which did not correlate with either species identification or clustering by RAPD.

    更新日期:2019-11-01
  • Balneomonas flocculans gen. nov., sp. nov., a new cellulose-producing member of the alpha-2 subclass of Proteobacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2004-03-30
    Minoru Takeda,Ichiro Suzuki,Jun-Ichi Koizumi

    A new bacterial strain capable of producing cellulose was isolated from a hot spring. The isolate was Gram-negative, aerobic, and rod-shaped. The optimum temperature for growth was 40-45 degrees C. Methanol, glucose and other common carbohydrates were not utilized as sole growth substrates. Thiosulfate was not oxidized. The G+C content of the DNA was determined to be 64.0 mol%. Comparative 16S rDNA analysis indicated that Bosea thiooxidans and some strains of the genus Methylobacterium were the nearest relatives. The isolate can be distinguished from these relatives by its defectiveness in methanol utilization and thiosulfate oxidation. On the basis of its phenotypic properties and phylogeny, it is proposed that the isolate be designated Balneomonas flocculans gen. nov., sp. nov. The type strain is TFBT (= JCM 11936T, = KCTC 12101T, = IAM 15034T, = ATCC BAA-817T).

    更新日期:2019-11-01
  • Erratum to "First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarod is sp. nov" [Syst. Appl. Microbiol. 42 (2019) 457-467].
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : null
    Ana S Ramírez,Orestes M Vega-Orellana,Tomeu Viver,José B Poveda,Rubén S Rosales,Carlos G Poveda,Joachim Spergser,Michael P Szostak,M José Caballero,Lorenzo Ressel,Janet M Bradbury,M Mar Tavío,Smruthi Karthikeyan,Rudolf Amann,Konstantinos T Konstantinidis,Ramon Rosselló-Móra

    更新日期:2019-11-01
  • Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-12-12
    Markus Schmid,Kerry Walsh,Rick Webb,W Irene C Rijpstra,Katinka van de Pas-Schoonen,Mark Jan Verbruggen,Thomas Hill,Bruce Moffett,John Fuerst,Stefan Schouten,Jaap S Sinninghe Damsté,James Harris,Phil Shaw,Mike Jetten,Marc Strous

    Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus "Scalindua brodae" and "Scalindua wagneri" considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus "Scalindua sorokinii", was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.

    更新日期:2019-11-01
  • Cry29A and Cry30A: two novel delta-endotoxins isolated from Bacillus thuringiensis serovar medellin.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-12-12
    Victor Juárez-Pérez,Manuel Porcar,Sergio Orduz,Armelle Delécluse

    Two novel crystal protein genes from a highly mosquitocidal Bacillus thuringiensis serovar medellin strain were cloned and sequenced. The corresponding proteins, Cry29A and Cry30A, were nontoxic when tested individually against the mosquito species bioassayed (Aedes aegypti, Culex pipiens and Anopheles stephensi). However, Cry29A synergized the toxicity of Cry11Bb against Aedes aegypti by a four-fold factor.

    更新日期:2019-11-01
  • Tepidimonas aquatica sp. nov., a new slightly thermophilic beta-proteobacterium isolated from a hot water tank.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-10-08
    Mariana Freitas,Fred A Rainey,M Fernanda Nobre,Armando J D Silvestre,Milton S da Costa

    A bacterial isolate, with an optimum growth temperature of about 50 degrees C, was recovered from a domestic hot water tank in Coimbra. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain CLN-1T is a member of the beta-Proteobacteria and represents a new species of the genus Tepidimonas. The major fatty acids of strain CLN-1T are 16:0, 17:0 cyclo and 16:1 omega7c. Ubiquinone 8 is the major respiratory quinone, the major polar lipids are phosphatidylethanolamine, and phosphatidylglycerol. The new isolate is aerobic and facultatively chemolithoheterotrophic. Thiosulfate and tetrathionate are oxidized to sulfate in the presence of a metabolizable carbon source. Strain CLN-1T grows on amino acids and organic acids, but this organism does not assimilate carbohydrates. Glycerol is the only polyol assimilated. Resinic acids, namely abietic acid, dehydroabietic acid and isopimaric acid are not degraded. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strain CLN-1T represents a new species for which we offer the name Tepidimonas aquatica.

    更新日期:2019-11-01
  • Cloning, sequence analysis and expression of the F1F0-ATPase beta-subunit from wine lactic acid bacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-10-08
    Martin Sievers,Christina Uermösi,Marc Fehlmann,Sibylle Krieger

    The nucleotide sequences of the genes encoding the F1F0-ATPase beta-subunit from Oenococcus oeni, Leuconostoc mesenteroides subsp. mesenteroides, Pediococcus damnosus, Pediococcus parvulus, Lactobacillus brevis and Lactobacillus hilgardii were determined. Their deduced amino acid sequences showed homology values of 79-98%. Data from the alignment and ATPase tree indicated that O. oeni and L. mesenteroides subsp. mesenteroides formed a group well-separated from P. damnosus and P. parvulus and from the group comprises L. brevis and L. hilgardii. The N-terminus of the F1F0-ATPase beta-subunit of O. oeni contains a stretch of additional 38 amino acid residues. The catalytic site of the ATPase beta-subunit of the investigated strains is characterized by the two conserved motifs GGAGVGKT and GERTRE. The amplified atpD coding sequences were inserted into the pCRT7/CT-TOPO vector using TA-cloning strategy and transformed in Escherichia coli. SDS-PAGE and Western blot analyses confirmed that O. oeni has an ATPase beta-subunit protein which is larger in size than the corresponding molecules from the investigated strains.

    更新日期:2019-11-01
  • Thermomonas hydrothermalis sp. nov., a new slightly thermophilic gamma-proteobacterium isolated from a hot spring in central Portugal.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-05-16
    Marta P Alves,Fred A Rainey,M Fernanda Nobre,Milton S da Costa

    Several non-pigmented bacterial isolates, with an optimum growth temperature of about 50 degrees C, were recovered from the hot spring at São Gemil in Central Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strain SGM-6T indicated that this organism represents a new species of the gamma-subclass of the Proteobacteria that is closely related to the newly described slightly thermophilic species Thermomonas haemolytica. The major fatty acids of strains SGM-6T and SGM-7 are C15:0 iso, C16:0 iso, C11:0 iso and C11:0 iso 3OH. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. Strain SGM-6T only assimilated D-glucose, D-maltose, D-cellobiose, D-furanose, L-glutamate, L-glutamine, L-lysine, L-proline, L-ornithine, acetate, L-glutamic acid and pyruvate of sixty-five carbon sources tested. Strain SGM-7 also assimilates L-serine, but does not assimilate L-ornithine. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strains SGM-6T and SGM-7 represent a new species most closely related to Thermomonas haemolytica for which we propose the name Thermomonas hydrothermalis.

    更新日期:2019-11-01
  • Teichococcus ludipueritiae gen. nov. sp. nov., and Muricoccus roseus gen. nov. sp. nov. representing two new genera of the alpha-1 subclass of the Proteobacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-05-16
    Peter Kämpfer,Maria A Andersson,Udo Jäckel,Mirja Salkinoja-Salonen

    Two bacterial isolates (170/96T and 173/96T) were recovered from the indoor building materials of a children's day care center. Phylogenetic analyses using the 16S rRNA gene sequences of both isolates indicated they both represent new lineages in the alpha-1-subclass of the Proteobacteria, with the highest sequence similarities of 93.7% and 93.6%, respectively to the type strain of Paracraurococcus ruber. When directly compared both isolates showed a 93.4% sequence similarity of their 16S rRNAs. The major respiratory quinone in both strains was a ubiquinone with 10 isoprenoid units and the major whole cell fatty acid of both strains was 18:1 omega7c. Both isolates also contained 18:1 2-OH and other fatty acids typical for members of the alpha-1 subclass of the Proteobacteria. Both strains were heterotrophic and strictly aerobic and formed slightly red-colored colonies on tryptone soy agar. Bacteriochlorophyll a could not be detected by direct spectrophotometric analyses of aerobically grown cells. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strains 170/96T and 173/96T represent two new genera and new species of the alpha-1 subclass of the Proteobacteria for which we propose the names Teichococcus ludipueritiae gen. nov. sp. nov., and Muricoccus roseus gen. nov. sp. nov., respectively.

    更新日期:2019-11-01
  • Virulence factors in food, clinical and reference Enterococci: A common trait in the genus?
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-05-16
    Teresa Semedo,Margarida Almeida Santos,Maria Fátima Silva Lopes,José J Figueiredo Marques,Maria Teresa Barreto Crespo,Rogério Tenreiro

    The occurrence of several virulence traits (cytolysin, adhesins and hydrolytic enzymes) was investigated in a collection of 164 enterococci, including food and clinical isolates (from human and veterinary origin), as well as type and reference strains from 20 enterococcal species. Up to fifteen different cyl genotypes were found, as well as silent cyl genes. The occurrence of the cyl operon and haemolytic potential seems to be widespread in the genus. A significant association of this virulent trait with clinical isolates was found (p < 0.05). High levels of incidence were also observed for genes encoding surface adhesins (esp, efaA(fs), efaA(fm)), agg and gelE, irrespectively of species allocation and origin of strains. Although gelE behaves as silent in the majority of the strains, gelatinase activity predominates in clinical isolates, whereas lipase and DNase were mainly detected in food isolates pointing to their minor role as virulence determinants. No hyaluronidase activity was detected for all strains. Numerical hierarchic data analysis grouped the strains in three main clusters, two of them including a total of 50 strains with low number of virulence determinants (from 2 to 7) and the other with 114 strains with a high virulence potential (up to 12 determinants). No statistical association was found between virulence clusters and species allocation (p > 0.10), strongly suggesting that virulence determinants are a common trait in the genus Enterococcus. Clinical strains seem to be significantly associated with high virulence potential, whereas food, commensal and environmental strains harbour fewer virulence determinants (p < 0.01). A high level of relative diversity in virulence patterns was observed (Shannon's index varies from 0.95 to 1.0 among clusters), reinforcing the strain-specific nature of the association of virulence factors. Although a low risk seems to be associated with the use of enterococci in long-established artisanal cheeses, screening of virulence traits and their cross-synergies must be performed, particularly for commercial starters, probiotic strains and products to be used by high risk population groups.

    更新日期:2019-11-01
  • Enumeration of thermophilic Bacillus species in composts and identification with a Random Amplification Polymorphic DNA (RAPD) protocol.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2003-02-14
    Yunqiao C Zhang,Ron S Ronimus,Nicola Turner,Yi Zhang,Hugh W Morgan

    The thermophilic microbial flora of general garden and domestic wastes composts, derived from thermogenic, post-thermogenic and maturation phases, was analysed using spore and total plate counts in combination with an optimised RAPD protocol. A total of 459 isolates were recovered obtained at 55 degrees C, and another 56 at 70 degrees C using tryptic soy-starch agar plates, with near-equal numbers being derived from total plate counts or spore preparations. The isolates were obtained from 11 compost samples and were assigned to eighteen different RAPD fingerprint types, with 76.1% of these ultimately being positively assigned by their RAPD profiles to just 2 species including Bacillus thermodenitrificans and B. licheniformis. Viable cell numbers ranged from 1.4 to 150 x 10(6) colony forming units per gram compost (wet weight), with the highest two counts being from 2 week and 4 week old compost samples with temperatures of 70 degrees C and 55 degrees C, respectively. B. thermodenitrificans was a dominant isolate (representing more than 50% of isolates from total plate counts) in 7 of the 11 individual compost total plate count samples between 30 degrees C to 73 degrees C, and accounted for 68.9% of all isolates overall. Another relatively common Bacillus species that was identified with RAPDs in significant numbers included B. licheniformis (7.2% of all isolates and dominant isolate in 1 sample). Three other relatively common RAPD profiles could not be identified by comparison with known species in a RAPD profile database but were tentatively identified using 16S rDNA sequence comparisons. These were B. sporothermodurans (4.9% of all isolates and dominant in 1 sample), B. thermosphaericus (7.4% and dominant in 1 sample) and Terrabacter tumescens (5.0%). Overall, based on the vegetative and spore count results and the subsequent RAPD-based identification, the data strongly support a significant role for B. thermodenitrificans in the composting process, and casts doubt on the notion that B. stearothermophilus sensu strictu (DSMZ 22) is a prominent member within compost ecology.

    更新日期:2019-11-01
  • Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2002-10-02
    Albin Alfreider,Carsten Vogt,Wolfgang Babel

    A molecular approach based on the construction of 16S ribosomal DNA clone libraries was used to investigate the microbial diversity of an underground in situ reactor system filled with the original aquifer sediments. After chemical steady state was reached in the monochlorobenzene concentration between the original inflowing groundwater and the reactor outflow, samples from different reactor locations and from inflowing and outflowing groundwater were taken for DNA extraction. Small-subunit rRNA genes were PCR-amplified with primers specific for Bacteria, subsequently cloned and screened for variation by restriction fragment length polymorphism (RFLP). A total of 87 bacterial 16S rDNA genes were sequenced and subjected to phylogenetic analysis. The original groundwater was found to be dominated by a bacterial consortium affiliated with various members of the class of Proteobacteria, by phylotypes not affiliated with currently recognized bacterial phyla, and also by sporulating and non-sporulating sulfate-reducing bacteria. The most occurring clone types obtained from the sediment samples of the reactor were related to the beta-Proteobacteria, dominated by sequences almost identical to the widespread bacterium Alcaligenes faecalis, to low G+C gram-positive bacteria and to Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans) within the gamma subclass of Proteobacteria in the upper reactor sector. Although bacterial phylotypes originating from the groundwater outflow of the reactors also grouped within different subdivisions of Proteobacteria and low G+C gram-positive bacteria, most of the 16S rDNA sequences were not associated with the sequence types observed in the reactor samples. Our results suggest that the different environments were inhabited by distinct microbial communities in respect to their taxonomic diversity, particular pronounced between sediment attached microbial communities from the reactor samples and free-living bacteria from the groundwater in- and outflow.

    更新日期:2019-11-01
  • Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the alpha-1 subclass of the Proteobacteria.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2002-10-02
    Susana Alarico,Fred A Rainey,Nuno Empadinhas,Peter Schumann,M Fernanda Nobre,Milton S da Costa

    A bacterial isolate, with an optimum growth temperature of about 50 degrees C, was recovered from the hot spring at Egerszalók in Hungary. Phylogenetic analyses using the 16S rRNA gene sequence of strain H-8T indicated that the new organism represented a new genus and species of alpha-1 subclass of the Proteobacteria. The major fatty acids of strain H-8T are 16:0, 18:1 omega7c; the rare fatty acid 19:0 20H cyclo 11,12 is also present. Ubiquinone 9 is the major respiratory quinone, the polar lipids are phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The new isolate forms red-colored colonies, flocculates in liquid media, is heterotrophic and strictly aerobic. Thiosulfate is oxidized to sulfate, but an increase in biomass could not be measured because of the flocculating behavior. Bacteriochloropyll a was detected by direct spectrophotometric analysis when the organism was grown at 30 degrees C, but could not be detected after growth at 50 degrees C. pufL and pufM genes were present. Heterotrophic growth of strain H-8T occurs on a few carbohydrates, amino acids and organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strain H-8T represents a new genus and a new species most closely related to Roseococcus thiosulfatophilus for which we propose the name Rubritepida flocculans.

    更新日期:2019-11-01
  • Molecular characterization of ochratoxin A producing strains of the genus Penicillium.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2002-06-28
    Gemma Castella,Thomas Ostenfeld Larsen,Javier Cabanes,Holger Schmidt,Alessandro Alboresi,Ludwig Niessen,Paul Färber,Rolf Geisen

    Sixty-six strains classified as P. verrucosum based on morphological criteria were characterized by molecular methods like RAPD, AFLP and ITS sequencing. Two groups could be identified by RAPD and AFLP analyses. The two RAPD as well as the two AFLP groups were completely coincidental. Strains in the two groups differed in their ability to produce ochratoxin A, with group I containing mainly high producing strains, and group II containing moderate to non-producing strains. The strains from group I originate from foods, such as cheeses and meat products, while the strains from group II originate from plants. The ribosomal ITS1-5.8S-ITS2 sequences were similar, except for two single nucleotide exchanges in several strains of each group. A chemotaxonomical analysis of some of the strains identified differences between the groups in secondary metabolite production. Strains from group I possessed the chemotype of P. nordicum and strains from group II that of P. verrucosum. The differences at the RAPD and AFLP level, which parallel the chemotypic differences, are consistent with the recent reclassification of ochratoxin A producing penicillia to be either P. verrucosum or P. nordicum. The homolgy between the ITS sequences however indicates phylogenetic relationship between the two species.

    更新日期:2019-11-01
  • Study of the first hours of microvinification by the use of osmotic stress-response genes as probes.
    Syst. Appl. Microbiol. (IF 2.808) Pub Date : 2002-06-28
    Roberto Pérez-Torrado,Purificación Carrasco,Agustín Aranda,José Gimeno-Alcañiz,José E Pérez-Ortín,Emilia Matallana,Marcel Lí del Olmo

    When yeast cells are inoculated into grape must for vinification they find stress conditions because of osmolarity, which is due to very high sugar concentration, and pH lower than 4. In this work an analysis of the expression of three osmotic stress induced genes (GPD1, HSP12 and HSP104) under microvinification conditions is shown as a way to probe those stress situations and the regulatory mechanisms that control them. The results indicate that during the first hours of microvinification there is an increase in the GPDI mRNA levels with a maximum about one hour after inoculation, and a decrease in the amount of HSP12 and HSP104 mRNAs, although with differences between them. The RNA steady-state levels of all the genes considered, and in some cases the microvinification progress are significantly affected by the composition of the must (pH, nature of the osmotic agent and carbon source). These results point out the importance of the control of these parameters and the yeast molecular response during the first hours of vinification for an accurate winemaking process.

    更新日期:2019-11-01
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