Gábor M. Kovács

Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia)

Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksár tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68T and TAGA27T was supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68T and TAGA27T is 69.4 and 69.6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925T and Kocuria rhizophila, type strain DSM 11926T.

The dark side is not fastidious--dark septate endophytic fungi of native and invasive plants of semiarid sandy areas.

Dark septate endophytic (DSE) fungi represent a frequent root-colonizing fungal group common in environments with strong abiotic stress, such as (semi)arid ecosystems. This work aimed to study the DSE fungi colonizing the plants of semiarid sandy grasslands with wood steppe patches on the Great Hungarian Plain. As we may assume that fungi colonizing both invasive and native species are generalists, root associated fungi (RAF) were isolated from eight native and three invasive plant species. The nrDNA sequences of the isolates were used for identification. To confirm that the fungi were endophytes an artificial inoculation system was used to test the isolates: we considered a fungus as DSE if it colonized the roots without causing a negative effect on the plant and formed microsclerotia in the roots. According to the analyses of the ITS sequence of nrDNA the 296 isolates clustered into 41 groups. We found that 14 of these 41 groups were DSE, representing approximately 60% of the isolates. The main DSE groups were generalist and showed no specificity to area or season and colonized both native and invasive species, demonstrating that exotic plants are capable of using the root endophytic fungi of the invaded areas. The DSE community of the region shows high similarity to those found in arid grasslands of North America. Taking into account a previous hypothesis about the common root colonizers of those grasslands and our results reported here, we hypothesize that plants of (semi)arid grasslands share common dominant members of the DSE fungal community on a global scale.

Morphologic, Host Specificity, and Molecular Characterization of a Hungarian Cryptosporidium meleagridis Isolate

ABSTRACT This study was undertaken in order to characterizeCryptosporidium meleagridis isolated from a turkey in Hungary and to compare the morphologies, host specificities, organ locations, and small-subunit RNA (SSU rRNA) gene sequences of this organism and other Cryptosporidium species. The phenotypic differences between C. meleagridis andCryptosporidium parvum Hungarian calf isolate (zoonotic genotype) oocysts were small, although they were statistically significant. Oocysts of C. meleagridis were successfully passaged in turkeys and were transmitted from turkeys to immunosuppressed mice and from mice to chickens. The location ofC. meleagridis was the small intestine, like the location of C. parvum. A comparison of sequence data for the variable region of the SSU rRNA gene of C. meleagridisisolated from turkeys with other Cryptosporidium sequence data in the GenBank database revealed that the Hungarian C. meleagridis sequence is identical to a C. meleagridissequence recently described for a North Carolina isolate. Thus,C. meleagridis is a distinct species that occurs worldwide and has a broad host range, like the C. parvum zoonotic strain (also called the calf or bovine strain) andCryptosporidium felis. Because birds are susceptible toC. meleagridis and to some zoonotic strains of C. parvum, these animals may play an active role in contamination of surface waters not only with Cryptosporidium baileyi but also with C. parvum-like parasites.

Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences

• Estimation of the proportion of undescribed fungal taxa is an issue that has remained unresolved for many decades. Several very different estimates have been published, and the relative contributions of traditional taxonomic and next-generation sequencing (NGS) techniques to species discovery have also been called into question recently. • Here, we addressed the question of what proportion of hitherto unidentifiable molecular operational taxonomic units (MOTUs) have already been described but not sequenced, and how many of them represent truly undescribed lineages. We accomplished this by modeling the effects of increasing type strain sequencing effort on the number of identifiable MOTUs of the widespread soil fungus Mortierella. • We found a nearly linear relationship between the number of type strains sequenced and the number of identifiable MOTUs. Using this relationship, we made predictions about the total number of Mortierella species and found that it was very close to the number of described species in Mortierella. • These results suggest that the unusually high number of unidentifiable MOTUs in environmental sequencing projects can be, at least in some fungal groups, ascribed to a lag in type strain and specimen sequencing rather than to a high number of undescribed species.

Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts

Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms arose early in fungal evolution and became dominant independently in multiple clades, most likely via parallel diversification of Zn-cluster transcription factors, a fungal-specific family involved in regulating yeast-filamentous switches. Our results imply that convergent evolution can happen by the repeated deployment of a conserved genetic toolkit for the same function in distinct clades via regulatory evolution. We suggest that this mechanism might be a common source of evolutionary convergence even at large time scales.

Schineria larvae gen. nov., sp. nov., isolated from the 1st and 2nd larval stages of Wohlfahrtia magnifica (Diptera: Sarcophagidae).

Four bacterial strains were isolated from the fly larvae of an obligate parasitic fly, Wohlfahrtia magnifica (Diptera: Sarcophagidae). These isolates were characterized by a polyphasic approach and represent a new lineage of gamma-Proteobacteria as their closest relative is Xylella fastidiosa (87.1% 16S rDNA similarity). The four strains are identical at the 16S rDNA level, the level of similarity between them, based on DNA-DNA hybridization, is high (97.8-102.5%) and they are similar in their physiological and biochemical characteristics, although they differ in their utilization of different sole carbon sources. All produce chitinase. They are obligately aerobic: no growth is detected under anaerobic conditions, even in the presence of NO3- as terminal electron acceptor. Their predominant respiratory quinone is Q-8. The G+C content of their DNA is 42 mol%. Their cell membrane contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and two unknown polar lipids. Their main fatty acids are C18:1, C16:0 and C14:0. To accommodate these bacteria, a new genus, Schineria gen. nov., with the type species Schineria larvae sp. nov., is proposed.

Molecular study of arbuscular mycorrhizal fungi colonizing the sporophyte of the eusporangiate rattlesnake fern (Botrychium virginianum, Ophioglossaceae)

The arbuscular mycorrhizal (AM) fungi colonizing the sporophytes of the eusporangiate rattlesnake fern (Botrychium virginianum, Ophioglossaceae) in its Hungarian population were investigated in the present study. Different regions of the nrRNA gene complex were analyzed using two different primer sets. These produced similar results for the detected AM fungi phylotypes. Several AM fungal lineages were associated with sporophytes of B. virginianum. Phylogenetic analyses of different partial small subunit datasets grouped one lineage into the Gigasporaceae, showing similarities with Scutellospora sequences. In addition to unidentified Scutellospora phylotypes, it is possible that S. gregaria also colonized the fern. Several AM fungal phylotypes colonizing the sporophytes grouped into Glomus group A. They did not form distinct clades but grouped with sequences of AM fungi with different geographic and host origins. One main lineage clustered into the widespread G. fasciculatum/G. intraradices group and one into the subgroup GlGrAc, while others had no affinity to the subgroups of Glomus group A. As AM fungal phylotypes associated with B. virginianum seem to belong to widespread AM fungal taxa and show no specificity to this fern, we suppose that the previously described special anatomy of AM of B. virginianum is determined by the plant.

Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi.

Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.

Diversity of Alkaliphilic and Alkalitolerant Bacteria Cultivated from Decomposing Reed Rhizomes in a Hungarian Soda Lake

Bacterial communities associated with decomposing rhizomes of Phragmites australis were investigated in Lake Fertő (Neusiedlersee, Hungary). Alkaliphilic and alkalitolerant strains were isolated on cellulose-containing alkaline medium spread with dilutions of scrapings taken from the surface of the decaying plant material. Fifty-one strains were grouped by numerical analysis based on physiological tests and BIOLOG sole carbon source utilization data. The strains identified by 16S rDNA sequence comparisons included members of low G+C Gram positives (Marinibacillus marinus, Bacillus cereus, and Exiguobacterium aurantiacum), high G+C Gram positives (Nesterenkonia halobia and Dietzia natronolimnea), α-proteobacteria (Pannonibacter phragmitetus), and γ-proteobacteria (Pseudomonas pseudoalcaligenes and Halomonas venusta). Most of the strains were characterized by aerobic chemoorganotrophic respiratory metabolism and utilized several different carbon sources, although no direct cellulolytic activity was observed. Results of the pH and salt tolerance tests revealed optimuma in most cases at pH 11 and at the presence of 2.5–5% NaCl. These bacteria probably occupy niches in the aerobic, alkaline, water-influenced environments on the decomposing reed surfaces.

Imaia, a new truffle genus to accommodate Terfezia gigantea.

Originally described from Japan by Sanshi Imai in 1933, the hypogeous ascomycete Terfezia gigantea was subsequently discovered in the Appalachian Mountains of the USA. Morphological, electron microscopic, and phylogenetic studies of specimens collected in both regions revealed that, despite this huge geographic disjunction, (1) the Japanese and Appalachian specimens are remarkably similar both in morphology and the sampled rDNA sequences, (2) the species unambiguously falls into the Morchellaceae and is separated from the genus Terfezia in the Pezizaceae, (3) its spores are much larger than those of Terfezia spp. and are enclosed in a unique, electron-semitransparent, amorphous epispore that appears to be permeated with minute, meandering strands or canals. In addition to the molecular phylogenetic results, the numerous nuclei in ascospores, the dome shaped, striate ascus septal plugs and the long cylindric Woronin bodies also strengthen the family assignment to the Morchellaceae. Moreover, the species occurs in moist, temperate forests as opposed to the xeric to arid habitats of other Terfezia spp. We propose the new, monotypic genus Imaia to accommodate the species.