Microbial diversity

Scientific publications - Microbial diversity


Cai, L., Hyde, K.D.

"Ascorhombispora aquatica gen. et sp. nov. from a freshwater habitat in China, and its phylogenetic placement based on molecular data"

Cryptogamie, Mycologie, 28 (4), pp. 291-300. (2007)

Ascorhombispora is a new genus characterised by superficial, dark brown to black perithecial ascomata; bitunicate, swollen saccate asci; and dark brown, 3-septate trapezoid ascospores with a wide septum band. The 28S rDNA and 18S rDNA regions of this fungus were amplified and sequenced. Phylogenetic analysis was conducted in order to infer systematic placement of this fungus. Results show that Ascorhombispora aquatica nests within Pleosporales (Dothidiomycetes, Ascomycota), which corroborate with the morphological prediction. © 2007 Adac.

Borchert, M.S., Nielsen, P., Graeber, I., Kaesler, I., Szewzyk, U., Pape, T., Antranikian, G., Schäfer, T.

"Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6"

International Journal of Systematic and Evolutionary Microbiology, 57 (12), pp. 2888-2893. (2007)

The Gram-positive, alkali- and salt-tolerant marine bacterium strain P203T is described together with its closest phylogenetic neighbour, terrestrial isolate LMG 21005T. Strain P203T was isolated from material from the sponge Plakortis simplex that was obtained from the Sula-Ridge, Norwegian Sea. Strain LMG 21005T was an undescribed strain that was isolated from a church wall mural in Germany. Strains P203T and LMG 21005T were identified as novel alkalitolerant members of the Bacillus rRNA group 6 with a 16S rRNA gene sequence similarity of 99.5 %. The closest described neighbour, Bacillus gibsonii DSM 8722T, showed 99.0% gene sequence similarity with P203T and 98.8% similarity with strain LMG 21005T. Despite the high 16S rRNA gene sequence similarity, DNA-DNA cross-hybridization revealed only 25.8-34.1% similarity amongst the three strains. The DNA G + C contents were 41.1 mol% for strain P203T and 39.6 mol% for strain LMG 21005T. Both strains grew well between pH 7 and pH 11. Strain P203T showed growth at moderate temperatures (from 4 to 30 °C) and in the presence of up to 12 % (w/v) NaCl at pH 9.7, whereas strain LMG 21005T was not salt tolerant (up to 4 % NaCl) and no growth was observed at 4 °C. The major fatty acids of strains P203T, LMG 21005T and the type strain of B. gibsonii were the saturated terminally methyl-branched compounds iso-C15:0 (19.8, 15.6 and 28.0 %, respectively) and anteiso-C15:0 (57.1, 48.6 and 45.2 %, respectively). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains P203T and LMG 21005T from the six related Bacillus species with validly published names and supported the proposal of two novel species, Bacillus plakortidis [type strain P203T (=DSM 19153T=NCIMB 14288T)] and Bacillus murimartini [type strain LMG 21005T (=NCIMB 14102T)]. © 2007 IUMS.

Cai, L., Hyde, K.D.

"Anamorphic fungi from freshwater habitats in China: Dictyosporium tetrasporum and Exserticlava yunnanensis spp. nov., and two new records for Pseudofuscophialis lignicola and Pseudobotrytis terrestris"

Mycoscience, 48 (5), pp. 290-296. (2007)

This article describes two new anamorphic fungi from freshwater habitats, Dictyosporium tetrasporum sp. nov. and Exserticlava yunnanensis sp. nov., based on morphological characters. Both species are illustrated with light micrographs and compared with similar taxa. Pseudofuscophialis lignicola and Pseudobotrytis terrestris are reported as new records from freshwater habitats. © 2007 The Mycological Society of Japan and Springer-Verlag.

Zhao, G., Liu, X., Wu, W.

"Helicosporous hyphomycetes from China"

Fungal Diversity, 26 II, pp. 313-524. (2007)

Morphological studies of anamorphic taxa with helicospores (helicosporous fungi) were carried out based on observation of specimens collected in China and comparisons with descriptions in the literature. After examination of more than 300 freshly collected specimens and 100 herbarium specimens, we conclude that 71 species in 14 genera are presently known in mainland China, including 9 new species and 2 new combinations. The new species are Helicomyces denticulatus G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicosporium dentophorum G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicosporium sympodiophorum G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicoma hainanense G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicoma hyalonema G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicoma latifilum G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicoma scarabaeiforme G.Z. Zhao; Xenosporium latisporum G.Z. Zhao, Xing Z. Liu & W.P. Wu; Xenosporium ovatum G.Z. Zhao, Xing Z. Liu & W.P. Wu. The new combinations are Helicoma fumosum (P. Karst.) G.Z. Zhao, Xing Z. Liu & W.P. Wu; Helicofilia irregularis (P.M. Kirk) G.Z. Zhao, Xing Z. Liu & W.P. Wu. Another three new combinations, Helicoma casuarinae (Matsush.) G.Z. Zhao, Xing Z. Liu & W.P. Wu, Helicoma hyalospora (Rao & D. Rao) G.Z. Zhao, X.Z. Liu & W.P. Wu and Slimacomyces isiola (R.T. Moore) G. Z. Zhao, and a new name, Helicoma palmarum G.Z. Zhao, Xing Z. Liu & W.P. Wu are introduced based on the literature. All species are described, illustrated and discussed. Diagnostic characteristics and keys for most helicosporous genera are provided. Drepanospora is considered to be synonym of Helicosporium and Troposporella and Helicosporina are dealt with as the synonyms of Helicoma. A third group of Xenosporium without secondary conidia was found and four new species are described in this group. Several specimens were unavailable for study and are listed as doubtful records.

Duan, J., Wu, W., Liu, X.Z.

"Dinemasporium (coelomycetes)"

Fungal Diversity, 26 I, pp. 205-218. (2007)

Seven species of the genus Dinemasporium Lév. are described and illustrated, including Dinemasporium asetulum sp. nov., D. fusiforme sp. nov., D. ligongense sp. nov., D. sinense sp. nov. and D. neottiosporioides (Agnihothr.) comb. nov. A key to accepted species in the genus is given. The type specimens for all described new species are kept in the herbarium of W.P. Wu in Novozymes China.

Duan, J., Liu, X., Wu, W.

"Reinstatement of Coleonaema for Coleophoma oleae and notes on Coleophoma"

Fungal Diversity, 26 I, pp. 187-204. (2007)

The development of conidiomata and paraphyses in currently accepted species of Coleophoma is of two types. In both, initials are formed by aggregation of epidermal mycelium and then cells in the upper layer grow upward and become septate. Subsequently, development differs. In C. crateriformis (type species), C. empetri, C. cylindrospora, C. aesculi, C. fusiformis and C. prunicola sp. nov., some hyaline to very pale brown, upwardly growing hyphae with septa only at the base develop from the upper layer of the conidiomatal initials. The apical cells of these hyphae are hyaline, elongated, swollen and with free apices. They develop into paraphyses which persist for a long time and can be seen even in the mature conidiomata. In the second group, which only contains C. oleae and two unnamed collections, the upwardly growing hyphae are pale to dark brown, septate and branched, and anastomose at the apices. They collapse before conidiomata mature, so no paraphyses develop. Based on such differences Coleophoma oleae is reassigned to Coleonaema. Coleophoma prunicola sp. nov. is described and microconidiogenesis is first reported in this genus.

Derekova, A., Sjøholm, C., Mandeva, R., Kambourova, M.

"Anoxybacillus rupiensis sp. Nov., a novel thermophilic bacterium isolated from Rupi basin (Bulgaria)"

Extremophiles, 11 (4), pp. 577-583. (2007)

Three strains of a novel thermophilic, strictly aerobic, Gram-positive, spore-forming hemo-organotrophic bacterium were isolated from three hot springs in the region of Rupi basin, Bulgaria as producers of amylolytic enzymes. Their 16S rRNA gene sequences (first 500 nucleotides) were very similar (99.8%). Strains were able to ferment a wide spectrum of carbohydrates such as sugars, polyols, and polysaccharides like xylan, glycogen and starch. Optimal growth was observed at 55-58°C, and pH at 6.0-6.5. Phylogenetic analysis of the whole 16S rRNA gene sequence clustered the strain R270T with the representatives of the genus Anoxybacillus and with Geobacillus tepidamans. The G + C content of the genomic DNA was 41.7%. DNA-DNA hybridization analysis revealed low homology with the closest relatives (32.0 mol% homology to Geobacillus tepidamans). Fatty acid profile (major fatty acids iso-C15:0 and iso-C17:0) confirmed the affiliation of the strain to the genus Anoxybacillus. On the basis of the data presented here, we propose that strain R270 T, represents a new species of the genus Anoxybacillus for which, we recommend the name Anoxybacillus rupiensis sp. nov. (=DSM 17127T = NBIMCC 8387T). The 16S rRNA gene sequence data of a strain R270 T have been deposited in the EMBL databases under the accession number AJ879076. © 2007 Springer.

Cai, L., Hyde, K.D.

"New species of Clohiesia and Paraniesslia collected from freshwater habitats in China"

Mycoscience, 48 (3), pp. 182-186. (2007)

Two fungi collected from submerged woody debris were found to represent hitherto undescribed species of the ascomycete genera Clohiesia and Paraniesslia. They are described as Clohiesia curvispora sp. nov. and Paraniesslia aquatica sp. nov. based on morphological characters. Clohiesia curvispora is characterized by immersed ascomata under a clypeus, and unitunicate, cylindrical asci containing one-celled, curved, elongate-fusiform ascospores. Paraniesslia aquatica is characterized by small, superficial, setose ascomata, and unitunicate, clavate asci containing verrucose, brown ascospores. Each species is illustrated with light micrographs and compared with similar taxa in this article. © 2007 The Mycological Society of Japan and Springer-Verlag.

Liu, X.Y., Xie, X.G., Duan, J.X.

"Colletotrichum yunnanense sp. nov., a new endophytic species from Buxus sp"

Mycotaxon, 100, pp. 137-144. (2007)

During our study of endophytic fungi from woody plants, an interesting Colletotrichum species was isolated. The morphological characteristics, such as slow growing, cylindrical and large conidia, and irregularly lobed appressoria, plus phylogenetic analysis based on nuclear rDNA sequences indicate that the fungus represents a distinct new species and named as Colletotrichum yunnanense. It is described and illustrated herewith.

Zhang, M., Zhang, T.-Y., Wu, W.-P.

"Taxonomic studies of Helminthosporium from China III. Three new species in guangdong province"

Mycotaxon, 99, pp. 137-142. (2007)

Three new species of the genus Helminthosporium are reported. They are Helminthosporium multiseptatum, Helminthosporium subhyalinum and Helminthosporium constrictum. Type specimens are deposited in the Herbarium of Shandong Agricultural University: Plant Pathology (HSAUP).

De Maré, L., Cimander, C., Elfwing, A., Hagander, P.

"Feeding strategies for E. coli fermentations demanding an enriched environment"

Bioprocess and Biosystems Engineering, 30 (1), pp. 13-25. (2007)

The addition of a carbon nutrient feed to a fed-batch cultivation is often not enough to obtain satisfactory growth and/or production. In some cases, an additional feed with for example supplementary amino acids or complex media is required. This work presents the development of feeding strategies where more than one feed is required and the knowledge of the growth requirements is low. Simulations and cultivations with E. coli are shown using the proposed feed controllers which are based on a probing control concept. The strategies work well and they can be used to shorten the process development phase considerably. © Springer-Verlag 2006.

Shenoy, B.D., Jeewon, R., Wu, W.P., Bhat, D.J., Hyde, K.D.

"Ribosomal and RPB2 DNA sequence analyses suggest that Sporidesmium and morphologically similar genera are polyphyletic"

Mycological Research, 110 (8), pp. 916-928. (2006)

Sporidesmium and morphologically similar dematiaceous, hyphomycetous genera are characterised by holoblastic phragmoconidia produced on proliferating or non-proliferating conidiophores. They include a number of asexual (anamorphic) genera taxonomically segregated from Sporidesmium sensu lato and are similar in having schizolytic conidial secession. The taxonomy of these ubiquitous asexual fungi and their affinities with known Ascomycetes are, however, still obscure. This study incorporates a phylogenetic investigation, based on the LSU nu-rDNA and RNA polymerase II second largest subunit (RPB2) gene sequence, to assess the possible familial placement of Ellisembia, Linkosia, Repetophragma, Sporidesmiella, Sporidesmium and Stanjehughesia, and justify whether anamorphic characters are proper phylogenetic indicators. Phylogenies provide conclusive evidence to suggest that Sporidesmium is not monophyletic and species are phylogenetically distributed in two major ascomycete classes, Dothideomycetes and Sordariomycetes. Morphologies currently used in their classification have undergone convergent evolution and are not phylogenetically reliable. The possible teleomorphic affinities of these anamorphic genera are discussed in light of morphology and molecular data. As these anamorphs, in most cases, are the sole known morph of the holomorph, it is proposed that in the absence of or failure to detect their teleomorphic phase, the anamorph names should be used for the holomorph. © 2006 The British Mycological Society.

Derekova, A., Sjøholm, C., Mandeva, R., Michailova, L., Kambourova, M.

"Biosynthesis of a thermostable gellan lyase by newly isolated and characterized strain of Geobacillus stearothermophilus 98"

Extremophiles, 10 (4), pp. 321-326. (2006)

The thermophilic strain able to degrade gellan was isolated from Bulgarian hot spring. According to its morphological and biochemical properties and by partial sequencing of its 16S rDNA, it was classified as Geobacillus stearothermophilus. It grew in a synthetic medium with gellan as the only carbon source with a specific growth rate of 0.69 h-1 and generation time of 60 min. The strain produced thermostable gellan lyase extracellularly during exponential phase. Its synthesis was inducible; the enzyme was not registered in culture liquid without gellan. The enzyme activity was increased tenfold in conditions of continuous cultivation compared to data from batch fermentations and enzyme productivity was almost sixfold higher. The enzyme showed optimal activity at 75°C in a very large pH area 4-8.5. This enzyme is the first reported thermostable gellan lyase, its residual activity was 100% after 24 h incubation at 60°C and its half-life was 60 min at 70°C. © Springer-Verlag 2006.

Holtze, M.S., Nielsen, P., Ekelund, F., Rasmussen, L.D., Johnsen, K.

"Mercury affects the distribution of culturable species of Pseudomonas in soil"

Applied Soil Ecology, 31 (3), pp. 228-238. (2006)

Pseudomonas bacteria isolated during 52 days on Gould's S1 agar from soil spiked with 0, 3.5 and 15 mg Hg(II) kg soil-1 were characterised to reveal whether mercury affected them differently. Isolates from the treatments with 0 and 15 mg Hg kg-1 were characterised using FT-IR characterisation and subsequent 16S rDNA partial sequencing of representative isolates. To verify the selectivity of Gould's S1 agar and the FT-IR characterisation, all 450 isolates were subjected to the following tests: Gram-determination, catalase and oxidase activity, pigment production on PDA and growth at different temperatures. Furthermore, the isolates were tested for their ability to grow on agar amended with 10 mg Hg kg-1 as an indication of mercury resistance. We found that up to 80% of the isolates in soil amended with 15 mg Hg kg-1 were mercury-resistant, whereas only up to 20% were resistant in the treatments with 0 and 3.5 mg Hg kg-1. We found two groups of Pseudomonas, which probably represent non-described species since they did not group closely with any known species of Pseudomonas in the dendrogram. Hg-enhanced isolates were closely related to P. frederiksbergensis. Furthermore, Hg resistance was almost exclusively restricted to P. frederiksbergensis and P. migulae groups. We conclude that Hg caused a shift in the dominating species of culturable Pseudomonas. © 2005 Elsevier B.V. All rights reserved.

Zhao, G.Z., Wu, W.P., Liu, B., Liu, X.Z.

"Two new species of Xenosporium (Hyphomycetes) lacking secondary conidia"

Nova Hedwigia, 82 (1-2), pp. 127-134. (2006)

Two previously unknown hyphomycetes, assignable to the genus Xenosporium, are reported from China. Xenosporium helicominum, found on decaying wood, and X. tibetanum, found on bamboo, produce conidia characteristic of the genus, but lack the secondary conidia found in most species. The genus Xenosporium was divided into two morphological groups based in the curvature of the conidia. A third group is now needed to accommodate species lacking secondary conidia. This group includes X. latisporum, X. helicominum, X. tibetanum, and X. ovatum. The diagnostic characters of these four species are provided. Type specimens for the two new species are deposited in Wu's mycological herbarium in Novozymes China and the Mycological Herbarium, Institute of Microbiology, Academia Sinica, Beijing (HMAS), respectively. © 2006 J. Cramer in der Gebrüder Borntraeger Verlagsbuchhandlung.

Lydolph, M.C., Jacobsen, J., Arctander, P., Gilbert, M.T.P., Gilichinsky, D.A., Hansen, A.J., Willerslev, E., Lange, L.

"Beringian paleoecology inferred from permafrost-preserved fungal DNA"

Applied and Environmental Microbiology, 71 (2), pp. 1012-1017. (2005)

The diversity of fungi in permanently frozen soil from northeastern Siberia was studied by culture-independent PCR amplification of diverse environmental 18S rRNA genes. Elaborate protocols to avoid contamination during drilling, sampling, and amplification were used. A broad diversity of eukaryotic DNA sequences that were 510 bp long, including sequences of various fungi, plants, and invertebrates, could be obtained reproducibly from samples that were up to 300,000 to 400,000 years old. The sequences revealed that ancient fungal communities included a diversity of cold-adapted yeasts, dark-pigmented fungi, plant-parasitic fungi, and lichen mycobionts. DNA traces of tree-associated macrofungi in a modern tundra sample indicated that there was a shift in fungal diversity following the last ice age and supported recent results showing that there was a severe change in the plant composition in northeastern Siberia during this period. Interestingly, DNA sequences with high homology to sequences of coprophilic and keratinophilic fungi indicated that feces, hair, skin, and nails could have been sources of ancient megafauna DNA recently reported to be present in small amounts of Siberian permafrost sediments.

De Lipthay, J.R., Johnsen, K., Albrechtsen, H.-J., Rosenberg, P., Aamand, J.

"Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations"

FEMS Microbiology Ecology, 49 (1), pp. 59-69. (2004)

An increasing number of herbicides are found in our groundwater environments. This underlines the need for examining the effects of herbicide exposure on the indigenous groundwater microbial communities, as microbial degradation is the major process responsible for the complete removal of most contaminants. We examined the effect of in situ exposure to realistic low concentrations of herbicides on the microbial diversity and community structure of sub-surface sediments from a shallow aquifer near Vejen (Denmark). Three different community analyses were performed: colony morphology typing, sole-carbon source utilisation in Biolog®EcoPlates, and denaturing gradient gel electrophoresis. Cluster analysis demonstrated that the microbial communities of those aquifer sediments that acclimated to the herbicide exposure also had similar community structure. This observation was concurrent for all three community analyses. In contrast, no significant effect was found on the bacterial diversity, except for the culturable fraction where a significantly increased richness and Shannon index was found in the herbicide acclimated sediments. The results of this study show that in situ exposure of sub-surface aquifers to realistic low concentrations of herbicides may alter the overall structure of a natural bacterial community, although significant effects on the genetic diversity and carbon substrate usage cannot be detected. The observed impact was probably due to indirect effects. In future investigations, the inclusion of methods that specifically detect relevant microbial sub-populations and functional genes is therefore recommended. © 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Huber, I., Spanggaard, B., Appel, K.F., Rossen, L., Nielsen, T., Gram, L.

"Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout (Oncorhynchus mykiss, Walbaum)"

Journal of Applied Microbiology, 96 (1), pp. 117-132. (2004)

Aims: To identify the dominant culturable and nonculturable microbiota of rainbow trout intestine. Methods and Results: Microbial density of rainbow trout intestine was estimated by direct microscopic counts (4′,6- diamidino-2-phenylindole, DAPI) and by culturing on tryptone soya agar (TSA). Differential gradient gel electrophoresis analysis of bacterial DNA from intestinal samples, re-amplification of bands and sequence analysis was used to identify the bacteria that dominated samples where aerobic counts were ≤2% of the DAPI counts. 16S rDNA gene sequences of 146 bacterial isolates and three sequences of uncultured bacteria were identified. A set of oligonucleotide probes was constructed and used to detect and enumerate the bacterial community structure of the gastrointestinal tract of rainbow trout by fluorescence in situ hybridization (FISH). Members of the gamma subclass of Proteobacteria (mainly Aeromonas and Enterobacteriaceae) dominated the bacterial population structure. Acinetobacter, Pseudomonas, Shewanella, Plesiomonas and Proteus were also identified together with isolates belonging to the beta subclass of Proteobacteria and Gram-positive bacteria with high and low DNA G + C content. In most samples, the aerobic count (on TSA) was 50-90% of the direct (DAPI) count. A bacterium representing a previously unknown phylogenetic lineage with only 89% 16S rRNA gene sequence similarity to Anaerofilum pentosovorans was detected in intestinal samples where aerobic counts were ≤2% of direct (DAPI) counts. Ten to 75% of the microbial population in samples with low aerobic counts hybridized (FISH) with a probe constructed against this not-yet cultured bacterium. Conclusions: Proteobacteria belonging to the gamma subclass dominated the intestinal microbiota of rainbow trout. However, in some samples the microflora was dominated by uncultivated, presumed anaerobic, microorganisms. The bacterial population structure of rainbow trout intestine, as well as total bacterial counts, varied from fish to fish. Significance and Impact of the Study: Good correlation was seen between cultivation results and in situ analysis, however, a molecular approach was crucial for the identification of organisms uncultivated on TSA.