SSU Gene Research Articles

“Cryptic” group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae

Group-I introns are widespread--though irregularly distributed--in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms.

(Cryptic) sex in the microsporidian Nosema granulosis – Evidence from parasite rDNA and host mitochondrial DNA

Microsporidia are single-celled, intracellular eukaryotes that parasitise a wide range of animals. The Nosema/Vairimorpha group includes some putative asexual species, and asexuality is proposed to have originated multiple times from sexual ancestors. Here, we studied the variation in the ribosomal DNA (rDNA) of 14 isolates of the presumed apomictic and vertically transmitted Nosema granulosis to evaluate its sexual status. The analysed DNA fragment contained a part of the small-subunit ribosomal gene (SSU) and the entire intergenic spacer (IGS). The mitochondrial cox1 gene of the host Gammarus duebeni (Crustacea) was analysed to temporally calibrate the system and to test the expectation of cophylogeny of host and parasite genealogies. Genetic variability of the SSU gene was very low within and between the isolates. In contrast, intraisolate (within a single host) variability of the IGS felt in two categories, because 12 isolates possess a very high IGS genetic diversity and two isolates were almost invariable in the IGS. This difference suggests variable models of rDNA evolution involving birth-and-death and unexpectedly concerted evolution. An alternative explanation could be a likewise unattended mixed infection of host individuals by more than one parasite strain. Despite considerable genetic divergence between associated host mitochondrial haplotypes, some N. granulosis ‘IGS populations’ seem not to belong to different gene pools; the relevant tests failed to show significant differences between populations. A set of recombinant IGS sequences made our data incompatible with the model of a solely maternally inherited, asexual species. In line with recent reports, our study supports the hypothesis that some assumed apomictic Microsporidia did not entirely abstain from the evolutionary advantages of sex. In addition, the presented data indicate that horizontal transmission may occur occasionally. This transmission mode could be a survival strategy of N. granulosis whose host often populates ephemeral habitats.

Dyfrolomycetaceae, a new family in the Dothideomycetes, Ascomycota

A new mangrove fungus collected in Tioman Island, Malaysia, is morphologically similar to marine species of Saccardoella. It also phylogenetically groups with Saccardoella rhizophorae in the Dothideomycetes, based on combined analysis of partial SSU, LSU rRNA and TEF1 gene sequences. The new fungus and S. rhizophorae form a well-supported clade with Acrospermum spp. in the Acrospermaceae. Both species therefore do not belong in Saccardoella, a genus with unitunicate asci. A new genus, Dyfrolomyces, is established to accommodate the new fungus (Dyfrolomyces tiomanensis) while the three marine Saccardoella species (S. mangrovei, S. marinospora, S. rhizophorae) are transferred to the new genus. Dyfrolomyces is characterized by forming a clypeus on substrates, with immersed perithecial ascomata, bitunicate/fissitunicate asci and multi-septate ascospores with/without a sheath. Since D. rhizophorae and D. tiomanensis do not cluster with any known families in the Dothideomycetes, a new family, Dyfrolomycetaceae, is introduced to accommodate the Dyfrolomyces species.

Morphological and molecular characteristics of Homoeostrichus formosana sp. nov. (Dictyotaceae, Phaeophyceae) from Taiwan.

BackgroundIn the marine brown macroalgae, the morphological characters are highly similar between two widely distributed genera, Homoeostrichus and Zonaria (Dictyotaceae), thereby resulting in the difficulty of exploring their hidden biodiversity. Owing to the help of the molecular tools, it is now easy for scientists to objectively describe a new species in nature. In this study, we make a description on the Homoeostrichus formosana sp. nov. from Taiwan, Indo-Pacific Ocean based on the morphological evidence and molecular data.ResultsOur morphological observations revealed that this species has marginal row of apical cells responsible for thallus growth and the thallus with four layers of cells except the marginal regions. The cortical cell lies upon each medullary cell in transverse section, and two cortical cells upon each medullary cell in longitudinal section. Tetrasporangium is developed from cortical cell with stalk cell and singly scattered over the thallus surface, and has no indusia and paraphyses. Molecularly, the phylogenetic trees based on SSU, psaA, psbA, and rbcL gene sequences supported that Homoeostrichus species are closely related to Exallosorus species and clearly separated from each others in addition to Zonaria species.ConclusionsHomoeostrichus formosana sp. nov. can now be clearly distinguished from E. harveyanus and Japanese H. flabellatus.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-13) contains supplementary material, which is available to authorized users.

Gelatinomyces siamensis gen. sp. nov. (Ascomycota, Leotiomycetes, incertae sedis) on bamboo in Thailand.

Gelatinomyces siamensis gen. sp. nov., incertae sedis within Leotiomycetes, the Siamese jelly-ball, is described. The fungus was collected from bamboo culms and branches in Nam Nao National Park, Phetchabun, Thailand. It presents as a ping-pong ball-sized and golf ball-like gelatinous ascostroma. The asci have numerous ascospores, are thick-walled, and arise on discoid apothecia which are aggregated and clustered to form the spherical gelatinous structures. An hyphomycete asexual morph is morphologically somewhat phialophora-like, and produces red pigments. On the basis of phylogenetic analysis based on rRNA, SSU, and LSU gene sequences, the lineage is closest to Collophora rubra. However, ITS sequences place the fungus on a well-separated branch from that fungus, and the morphological and ecological differences exclude it from Collophora.

Equine cryptosporidial infection associated with Cryptosporidium hedgehog genotype in Algeria

Faecal samples from two horse farms in Algeria keeping Arabian, Thoroughbred, and Barb horses were examined for the presence of Cryptosporidium in 2010–2011. A total of 138 faecal samples (16 from a farm keeping 50 animals and 122 from a farm with 267 horses) were screened for Cryptosporidium spp. infection using molecular tools. DNA was extracted from all samples. Nested PCR was performed to amplify fragments of the SSU rDNA and gp60 genes to determine the presence of Cryptosporidium species and genotypes. Sequence analyses of SSU and gp60 genes revealed four animals positive for the presence of subtype XIIIa A22R9 of the Cryptosporidium hedgehog genotype. The infections were not associated with diarrhoea. This study reports, for the first time, the occurrence of Cryptosporidium in Algeria and the first occurrence of the hedgehog genotype in horses. These findings support the potential role of infected horses in sylvatic–domestic transmission of Cryptosporidium.

Bispinodinium angelaceum gen. et sp. nov. (Dinophyceae), a new sand-dwelling dinoflagellate from the seafloor off Mageshima Island, Japan(1).

A new athecate dinoflagellate, Bispinodinium angelaceum N. Yamada et Horiguchi gen. et sp. nov., is described from a sand sample collected on the seafloor at a depth of 36m off Mageshima Island, subtropical Japan. The dinoflagellate is dorsiventrally compressed and axi-symmetric along the sulcus. The morphology resembles that of the genus Amphidinium sensu lato by having a small epicone that is less than one third of the total cell length. However, it has a new type of apical groove, the path of which traces the outline of a magnifying glass. The circular component of this path forms a complete circle in the center of the epicone and the straight "handle" runs from the sulcus to the circular component. Inside the cell, a pair of elongated fibrous structure termed here the "spinoid apparatus" extends from just beneath the circular apical groove to a point near the nucleus. Each of two paired structures consists of at least 10 hyaline fibers and this is a novel structure found in dinoflagellates. Phylogenetic analyses based on the SSU and LSU RNA genes did not show any high bootstrap affinities with currently known athecate dinoflagellates. On the basis of its novel morphological features and molecular signal, we conclude that this dinoflagellate should be described as a new species belonging to a new genus.

The Diversity of the Limnohabitans Genus, an Important Group of Freshwater Bacterioplankton, by Characterization of 35 Isolated Strains

Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology.

Phylogenetic systematics of the Gigasporales

The classification, phylogeny, and evolutionary pathways of the Gigasporales are re-evaluated based on concomitant morphological and molecular phylogenetic analyses. Only Cetraspora was not supported in the morphology-based tree, while Quatunica formed a monophyletic group with its sister genus Dentiscutata. Only a few taxa were not completely supported in the SSU rDNA phylogenetic analyses, namely Dentiscutata and Fuscutata (Dentiscutataceae) and Racocetra and Cetraspora (Racocetraceae). However, all trees generated by the LSU, SSU (rDNA), and β-tubulin genes supported the existence of the families with strong support for all genera represented in the LSU rDNA and β-tubulin analyses. In conclusion, the current classification of the Gigasporales has a strong morphological and molecular congruency.

Bambusicola,a New Genus from Bamboo with Asexual and Sexual Morphs

Bambusicola, gen. nov., is introduced for four new saprobic taxa from culms of bamboos in northern Thailand. One species, chosen as the generic type, has both sexual and asexual morphs, one species has the sexual morph only and two species have the asexual morph only. The four new species, Bambusicola massarinia, B. bambusae, B. irregulispora and B. splendida are illustrated and described. Isolates of each species were sequenced using LSU, SSU and ITS genes and phylogenetic analysis shows the genus to be a distinct clade in the suborder “Massarineae”. Morphological differences between Bambusicola and some related genera are noted. Bambusicola is characterized by small, cone-shaped ascomata, slightly broad and fusiform ascospores and a coelomycete asexual morph with light brown conidia. Bambusicola clusters in Trematosphaeriaceae, but the closeness of this relationship cannot be resolved.

Data Partitions, Bayesian Analysis and Phylogeny of the Zygomycetous Fungal Family Mortierellaceae, Inferred from Nuclear Ribosomal DNA Sequences

Although the fungal order Mortierellales constitutes one of the largest classical groups of Zygomycota, its phylogeny is poorly understood and no modern taxonomic revision is currently available. In the present study, 90 type and reference strains were used to infer a comprehensive phylogeny of Mortierellales from the sequence data of the complete ITS region and the LSU and SSU genes with a special attention to the monophyly of the genus Mortierella. Out of 15 alternative partitioning strategies compared on the basis of Bayes factors, the one with the highest number of partitions was found optimal (with mixture models yielding the best likelihood and tree length values), implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S, and ITS2, loci separately improved model fit significantly as compared to treating all as one and the same partition. Further, within-partition mixture models suggests that not only the SSU, LSU and ITS regions evolve under qualitatively and/or quantitatively different constraints, but that significant heterogeneity can be found within these loci also. The phylogenetic analysis indicated that the genus Mortierella is paraphyletic with respect to the genera Dissophora, Gamsiella and Lobosporangium and the resulting phylogeny contradict previous, morphology-based sectional classification of Mortierella. Based on tree structure and phenotypic traits, we recognize 12 major clades, for which we attempt to summarize phenotypic similarities. M. longicollis is closely related to the outgroup taxon Rhizopus oryzae, suggesting that it belongs to the Mucorales. Our results demonstrate that traits used in previous classifications of the Mortierellales are highly homoplastic and that the Mortierellales is in a need of a reclassification, where new, phylogenetically informative phenotypic traits should be identified, with molecular phylogenies playing a decisive role.

Molecular diversity of Amansieae (Ceramiales, Rhodophyta) from the Hawaiian Islands: a multi‐marker assessment reveals high diversity within Amansia glomerata

SUMMARYSixty‐one Hawaiian algal specimens corresponding to members of the tribe Amansieae (Amansia and Osmundaria) were compared through DNA sequence analysis. Short DNA barcode‐like sequences of mitochondrial cytochrome c oxidase subunit I (COI) and universal plastid amplicon (UPA) markers were obtained for as many of the specimens as possible, and a subset of specimens was also used for amplification and sequencing of the nuclear small‐subunit rRNA (SSU) gene for phylogenetic inference in a broader taxonomic context. Statistical parsimony analysis of the COI and UPA markers for A. glomerata produced relationships among the samples that were largely congruent with each other, although the UPA marker was more conserved. The COI marker yielded three lineages, and nucleotide divergences for these three lineages were intermediate to those typically reported for intraspecific and interspecific comparisons, suggesting that they represent either incipient species or a complex of closely related species. The COI and UPA sequences demonstrated little to no divergence for Osmundaria obtusiloba and the taxon referred to as Amansia fimbrifolia. In contrast, specimens identified as A. daemelii were identical in sequence to lineage 3 sequences of A. glomerata, and it is recommended that this taxon no longer be included in species lists for the Hawaiian flora. Phylogenetic reconstruction based on the SSU gene was largely unresolved, indicating that this marker may be of limited utility for this purpose in this group of algae, but a small amount of nucleotide variation was found for samples of A. glomerata.

A comparative molecular analysis of water‐filled limestone sinkholes in north‐eastern Mexico

Sistema Zacatón in north-eastern Mexico is host to several deep, water-filled, anoxic, karstic sinkholes (cenotes). These cenotes were explored, mapped, and geochemically and microbiologically sampled by the autonomous underwater vehicle deep phreatic thermal explorer (DEPTHX). The community structure of the filterable fraction of the water column and extensive microbial mats that coat the cenote walls was investigated by comparative analysis of small-subunit (SSU) 16S rRNA gene sequences. Full-length Sanger gene sequence analysis revealed novel microbial diversity that included three putative bacterial candidate phyla and three additional groups that showed high intra-clade distance with poorly characterized bacterial candidate phyla. Limited functional gene sequence analysis in these anoxic environments identified genes associated with methanogenesis, sulfate reduction and anaerobic ammonium oxidation. A directed, barcoded amplicon, multiplex pyrosequencing approach was employed to compare ∼100,000 bacterial SSU gene sequences from water column and wall microbial mat samples from five cenotes in Sistema Zacatón. A new, high-resolution sequence distribution profile (SDP) method identified changes in specific phylogenetic types (phylotypes) in microbial mats at varied depths; Mantel tests showed a correlation of the genetic distances between mat communities in two cenotes and the geographic location of each cenote. Community structure profiles from the water column of three neighbouring cenotes showed distinct variation; statistically significant differences in the concentration of geochemical constituents suggest that the variation observed in microbial communities between neighbouring cenotes are due to geochemical variation.

Expression of Divergent LSU rRNA Genes in the Vibrio vulnificus CMCP6 Genome During Both Infection and Non-Pathogenic Stages

The Vibrio vulnificus CMCP6 genome harbors nine copies of divergent large subunit (LSU) rRNA genes that may express and constitute four kinds of LSU rRNA molecules in a single cell. Primer extension analyses showed that these heterogeneous LSU rRNA transcripts are all expressed and assembled into ribosomes during both infection and nonpathogenic stages. Phylogenetic analyses of the internal transcribed spacer between SSU and LSU genes indicated that rRNA operons of V. vulnificus CMCP6 can be clustered into three distinct groups in rRNA genes of closely related Vibrio species. These findings imply that divergent rRNA genes in V. vulnificus CMCP6 resulted from interspecies recombination events in V. species, while the consequences of expression of heterogeneous rRNA molecules are not clear.

Barcoding Amoebae: Comparison of SSU, ITS and COI Genes as Tools for Molecular Identification of Naked Lobose Amoebae

Morphological identification of naked lobose amoebae has always been a problem, hence the development of reliable molecular tools for species distinction is a priority for amoebae systematics. Previous studies based on SSU rDNA sequences provided a backbone for the phylogeny of Amoebozoa but were of little help for the species distinctions in this group. On one hand, the SSU rDNA sequences were rather conserved between closely related species; on the other hand, the intra-strain polymorphism of the SSU gene obscured species identification. In the present study, a 3' fragment of the SSU, a complete ITS1-5.8S-ITS2 block and a 5' fragment of COI gene were cloned and sequenced for six Vannella morphospecies, of which V. simplex was represented by six different isolates. SSU rDNA and ITS were found to be inappropriate for species differentiation, while distinctive and homogenous COI sequences were obtained for each well-defined morphospecies. Moreover, a number of distinct COI genotypes have been identified among V. simplex isolates. This suggests that COI may be a good candidate for DNA barcoding of amoebae, but further studies are necessary to confirm the accurateness of the COI gene as a barcode in other gymnamoebae, and to understand the taxonomic meaning of COI variations.

TRANSIENT TRANSFORMATION OF A CHLORARACHNIOPHYTE ALGA, LOTHARELLA AMOEBIFORMIS (CHLORARACHNIOPHYCEAE), WITH uidA AND egfp REPORTER GENES(1).

A transient genetic transformation system was established for a chlorarachniophyte alga, Lotharella amoebiformis K. Ishida et Y. Hara. We first isolated sequences that contain a putative promoter for a RUBISCO SSU (rbcS) gene and a terminator for another copy of rbcS gene from L.amoebiformis. With those promoter and terminator sequences, we developed two expression vectors, pLaRGus and pLaRGfp, which code uidA and egfp genes, respectively. The cells were then transformed with each vector using a microparticle bombardment system. When the cells were transformed with the pLaRGus, β-glucuronidase (GUS) staining dyed several cells blue. Green fluorescent protein (GFP) fluorescence was observed in the cells transformed with pLaRGfp. The highest transient transformation efficiency, 35 per 2 × 10(7) cells, was detected from the GUS staining. This study demonstrates that two reporter genes are expressed in L.amoebiformis cells when rbcS promoter and terminator are used. The conditions of transformation were also optimized. This is the first report of successful genetic transformation in chlorarachniophyte algae.

ANALYSIS OF ANCIENT DNA FROM FOSSIL CORALLINES (CORALLINALES, RHODOPHYTA)(1).

The field of molecular paleontology has recently made significant contributions to anthropology and biology. Hundreds of ancient DNA studies have been published, but none has targeted fossil coralline algae. Using regions of the SSU gene, we analyzed rDNA from fossil coralline algae of varying ages and states of preservation from Spain, Papua New Guinea (PNG), and the Great Barrier Reef (GBR). Specimens from PNG, GBR, and some localities from Spain did not contain endogenous ancient DNA. Reproducible sequence data were obtained from specimens ∼550 years old from near Cadiz, Spain, and from rocky-shore deposits in Carboneras, Almeria Province of Spain (∼78,000 years before present [YBP]). Based on BLAST searches and a phylogenetic analysis of sequences, an undescribed coralline alga belonging to the Melobesioideae was discovered in the Carboneras material as well as the following coralline genera: Jania, Lithophyllum, Lithothamnion, Mesophyllum, and Phymatolithon. DNA from fleshy brown and red macroalgae was also discovered in the specimens from Carboneras. The coralline algae identified using molecular techniques were in agreement with those based on morphological methods. The identified taxa are common in the present-day southeastern Spain littoral zone. Amino acid racemization, concentration ratios, and specific concentrations failed to show a correlation between biomolecular preservation and PCR amplification success. Results suggest that molecular investigations on fossil algae, although limited by technical difficulties, are feasible. Validity of our results was established using authentication criteria and a self-critical approach to compliance.

An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa

Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.

DNA Taxonomy and the identification of immature insect stages: the true larva of Tauriphila argo (Hagen 1869) (Odonata: Anisoptera: Libellulidae)

For many insect taxa, larval morphology plays a decisive role in various fields like taxonomy, phylogeny or ecology. However, species identification is usually based on imaginal characters and the identification of larvae depends upon an established link to unequivocally identified imagines. This taxonomic correspondence of larvae and imagines is far from being established in many odonate species. We have employed a molecular approach to link larval and adult specimens in Tauriphila argo (Hagen, 1869). The sequenced mt SSU gene fragments of the reared female, supposedly a T. argo female, and a clearly identified male specimen of the species were identical. However, the larva of the reared female clearly differed from the described T. argo larva, previously matched to the species. From this observation, we conclude that the previously described larva of T. argo does not belong to this species because of too many phenotypic differences that far exceed the generally observed intraspecific variation. It can be foreseen that the molecular approach will prove to be effective in identifying unknown larvae in many insect species. Additionally, the discrimination of sibling species or the linkage of allotypes and holotypes will become feasible with this approach.

Role of the ssu and seu genes of Corynebacterium glutamicum ATCC 13032 in utilization of sulfonates and sulfonate esters as sulfur sources.

Corynebacterium glutamicum ATCC 13032 was found to be able to utilize a broad range of sulfonates and sulfonate esters as sulfur sources. The two gene clusters potentially involved in sulfonate utilization, ssuD1CBA and ssuI-seuABC-ssuD2, were identified in the genome of C. glutamicum ATCC 13032 by similarity searches. While the ssu genes encode proteins resembling Ssu proteins from Escherichia coli or Bacillus subtilis, the seu gene products exhibited similarity to the dibenzothiophene-degrading Dsz monooxygenases of Rhodococcus strain IGTS8. Growth tests with the C. glutamicum wild-type and appropriate mutant strains showed that the clustered genes ssuC, ssuB, and ssuA, putatively encoding the components of an ABC-type transporter system, are required for the utilization of aliphatic sulfonates. In C. glutamicum sulfonates are apparently degraded by sulfonatases encoded by ssuD1 and ssuD2. It was also found that the seu genes seuA, seuB, and seuC can effectively replace ssuD1 and ssuD2 for the degradation of sulfonate esters. The utilization of all sulfonates and sulfonate esters tested is dependent on a novel putative reductase encoded by ssuI. Obviously, all monooxygenases encoded by the ssu and seu genes, including SsuD1, SsuD2, SeuA, SeuB, and SeuC, which are reduced flavin mononucleotide dependent according to sequence similarity, have SsuI as an essential component. Using real-time reverse transcription-PCR, the ssu and seu gene cluster was found to be expressed considerably more strongly during growth on sulfonates and sulfonate esters than during growth on sulfate.