Phylogenetic in situ/ex situ analysis of a sulfur mat microbial community from a thermal sulfide spring in the north Caucasus

A phylogenetic in situ/ex situ analysis of a sulfur mat formed by colorless filamentous sulfur bacteria in a thermal sulfide spring (northern spur of the main Caucasian ridge) was carried out. Nine phylotypes were revealed in the mat. Thiothrix sp. and Sphaerotilus sp. were the dominant phylotypes (66.3% and 26.3%, respectively). The 16S rRNA gene nucleotide sequence of Sphaerotilus sp. phylotype from the clone library was identical to the sequences of the seven Sphaerotilus strains isolated from the same source. A very high degree of similarity of Sphaerotilus strains revealed by ERIC-PCR fingerprints indicated little or no population diversity of this species in the mat. Thiothrix phylotype from the clone library and two Thiothrix strains isolated from the same mat sample differed in one to three nucleotides of 16S rRNA genes; this is an indication of this organism’s population variability in the mat. 16S rRNA genes of the strains and clones of Thiothrix sp. exhibited the highest similarity (ca. 99%) with Thiothrix unzii; the strains and clones of Sphaerotilus had 99% similarity with the type species Sphaerotilus natans (the only species of this genus) and therefore can be assigned to this species. The minor seven components belong to the phylotypes from the Proteobacteria (3%), as well as the Chlorobia, Cyanobacteria, Clostridia, and Bacteroidetes phylogenetic groups, each of them constituting not more than 1%. Intracellular accumulation of elemental sulfur by Sphaerotilus similar to other filamentous sulfur bacteria was demonstrated for the first time (both in the population of the sulfur spring and in cultures with sulfide). Although mass growth of Sphaerotilus and Thiothrix is typical of bacterial populations of anthropogenic ecosystems (the activated sludge of treatment facilities), stable communities of these bacteria have not been previously found in the sulfur mats or “threads” of natural sulfide springs.     

Long-term changes in forest composition and diversity following early logging (1919–1923) and the decline of American chestnut (<Emphasis Type="Italic">Castanea dentata</Emphasis>)

Chestnut blight fungus (Endothia parasitica [Murr.] P.J. And. &; H.W. And.)) is a classic example of an invasive species, which severely damaged populations of its host, Castanea dentata, and had widespread and long-term impacts on eastern North American forests. Concurrently, forests were further disturbed by lumbering, which was common across the region from the mid 1800s to the early 1900s. In 1926, local infestations of chestnut blight were reported in the Coweeta Basin, Southern Appalachian Mountains of North Carolina. We used permanent plot inventories of the Basin (first sampled in 1934 and twice afterward in 1969–72 and 1988–93) to describe the distribution of species along a complex environmental gradient. Specifically, we asked: How does vegetation change over approximately 60 years following logging and the demise of C. dentata? Does the association between vegetation and environment determine the pattern of species distributions through time? Which species replaced C. dentata across this complex environmental gradient? We used nonmetric multidimensional scaling ordination and multiresponse permutation procedure for the analyses of the inventory periods. In 1934, C. dentata was the most important species in the Coweeta Basin. It was present in 98% of the plots and contributed 22% of the total density and 36% of the total basal area. Diversity increased significantly over time and was attributed to an increase in evenness of species distribution. The canopy dominant, C. dentata, was replaced by more than one species across the environmental gradient. Importance values of Quercus prinus, Acer rubrum, Cornus florida, Tsuga canadensis, and Oxydendrum arboreum increased by 2–5% across the basin following the decline of C. dentata. Tsuga canadensis increased in abundance and distribution, especially near streams across elevations. Liriodendron tulipifera replaced C. dentata in moist coves, which have low terrain shape and high organic matter content. In contrast, Q. prinus and A. rubrum were ubiquitous, much like C. dentata before the chestnut blight becoming dominant or co-dominant species across all environmental conditions.     

Population demographics and trade-offs to reproduction of an invasive and noninvasive species of <Emphasis Type="Italic">Rubus</Emphasis>

Do trade-offs between growth and reproduction differ between an invasive and noninvasive plant species and how do such trade-offs relate to population demographics? To help address these questions, we compared demographics for an invasive plant species, Rubus discolor, with a noninvasive congener, R. ursinus, in several populations of varying density. Removal of floral buds from reproductive canes increased the size of juvenile canes that arose from clonal sprouting in R. ursinus, suggesting a trade-off between current reproduction and growth. Removal of floral buds had no effect on growth of R. discolor. R. ursinus displayed trade-offs between reproduction (sexual and vegetative) and future growth based on negative correlations between leaf area production and both clonal sprouting and seedling production during the previous year. R. discolor did not exhibit these trade-offs. Both species had high population growth rates in low-density populations, but exhibited little or no growth in high-density populations. A life table response experiment was used to determine the underlying cause for the effect of density on population growth. For R. ursinus, lack of population growth in high-density populations was due primarily to increased mortality of clonally sprouting canes, while for R. discolor, it was due to decreased clonal cane production. Elasticity analysis revealed that clonal growth was more important than sexual reproduction for population growth of both species. However, elasticity values for sexual reproduction in R. discolor were greater in high- than low-density populations. This suggests an increased reliance on sexual reproduction in populations that had reached stable sizes, which could increase the capacity of R. discolor to disperse to new sites. Elasticity analyses were also used to simulate the efficacy of various control strategies for R. discolor. Control of this species could be attained by reducing clonal production within existing populations while reducing seed production to limit establishment of new populations.     

Ticks collected on birds in the state of São Paulo,Brazil

The present study reports a collection of Amblyomma spp. ticks in birds from several areas of the state of São Paulo, Brazil. A total of 568 tick specimens (404 larvae, 164 nymphs) were collected from 261 bird specimens. From these ticks, 204 (36%) specimens (94 larvae, 110 nymphs) were reared to the adult stage, being identified as Amblyomma longirostre (94 larvae, 90 nymphs), Amblyomma calcaratum (13 nymphs), Amblyomma nodosum (2 nymphs), and Amblyomma cajennense (5 nymphs). Additionally, 39 larvae reared to the nymphal stage and 8 nymphs that died before reaching the adult stage were identified as A. longirostre according to peculiar characters inherent to the nymphal stage of this species: scutum elongate, and hypostome pointed. The remaining 271 larvae and 46 nymphs were identified as Amblyomma sp. Ticks were collected from 51 species of birds distributed in 22 bird families and 6 orders. The order Passeriformes constituted the vast majority of the records, comprising 253 (97%) out of the 261 infested birds. Subadults of A. longirostre were identified from 35 species of Passeriformes, comprising 11 families (Cardinalidae, Dendrocolaptidae, Fringillidae, Furnariidae, Parulidae, Pipridae, Thamnophilidae, Thraupidae, Turdidae, Tyrannidae, and Vireonidae), and from 1 species of a non-passerine bird, a puffbird (Bucconidae). Subadults of A. calcaratum were identified from 5 species of Passeriformes, comprising 5 families (Cardinalinae, Conopophagidae, Pipridae, Thamnophilidae and Turdidae). Subadults of A. nodosum were identified from 2 species of Passeriformes, comprising two bird families (Thamnophilidae and Pipridae). Subadults of A. cajennense were identified from 2 species of non-passerine birds, belonging to 2 different orders (Ciconiiformes: Threskiornithidae, and Gruiformes: Cariamidae). Birds were usually infested by few ticks (mean infestation of 2.2 ticks per bird; range: 1–16). Currently, 82 bird species are known to be infested by immature stages of A. longirostre, with the vast majority [74 (90%)] being Passeriformes. Our results showed that Passeriformes seems to be primary hosts for subadult stages of A. longirostre, A. calcaratum, and A. nodosum. However, arboreal passerine birds seem to be the most important hosts for A. longirostre whereas ground-feeding passerine birds seem to be the most important for both A. calcaratum and A. nodosum. In contrast, the parasitism of birds by subadults of A. cajennense has been restricted to non-passerine birds.     

Delineating species for conservation using mitochondrial sequence data: the taxonomic status of two problematic <Emphasis Type="Italic">Bombus</Emphasis> species (Hymenoptera: Apidae)

Across Western Europe and North America, many bumblebee species are currently undergoing drastic declines in their abundance and ranges, primarily as a result of habitat fragmentation. In contrast, a smaller number of species are seemingly unaffected by this and remain common. The UK Biodiversity Action Plan-designated Bombus ruderatus belongs to the former group while B. hortorum belongs to the latter. These two species are sympatric and remarkably similar in morphology. There are no diagnostic characters for workers and male genitalia are illustrated with the same diagram in standard keys. Isolated records of putative B. ruderatus occur amongst a mass of records for B. hortorum. This raises two important issues: first, are B. ruderatus and B. hortorum ‘good’ species? Second, if they are, can the uncertainty over their identification be resolved? We present COII and cytochrome b mtDNA sequence data from these and other Bombus species. Molecular data and coat colour characters are in concordance and confirm that B. ruderatus and B. hortorum should be regarded as separate species (although coat colour alone is an unreliable diagnostic character for many individuals). Confirmation of the specific status of B. ruderatus allows the work on the conservation of this species to continue.     

Molecular genetic characterization of the yeast <Emphasis Type="Italic">Lachancea kluyveri</Emphasis>

A comparative study of Lachancea kluyveri strains isolated in Europe, North America, Japan, and the Russian Far East was performed using restriction analysis, sequencing of non-coding rDNA regions, molecular karyotyping, and the phylogenetic analysis of the α-galactosidase MEL genes. This study showed a close genetic relatedness of these L. kluyveri strains. The chromosomal DNAs of the L. kluyveri strains were found to range in size from 980 to 3100 kb. The haploid number of chromosomes is equal to eight. The IGS2 restriction patterns and single nucleotide substitutions in the ITS1/ITS2 rDNA region correlate neither with geographic origin nor with the source of the strains. The L. kluyveri strains isolated from different sources have a high degree of homology (79–100%) of their MEL genes. The phylogenetic analysis of all of the known α-galactosidases in the “Saccharomyces” clade showed that the MEL genes of the yeasts L. kluyveri, L. cidri, Saccharomyces cerevisiae, S. paradoxus, S. bayanus, and S. mikatae are species specific.     

Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences

Aciculosporium and Heteroepichloë (Clavicipitaceae) are characteristic bambusicolous fungi in east Asia. In this study, we examined their intergeneric relationships based on the ALDH1-1 gene, which encodes a member of the aldehyde dehydrogenase family. In the clavicipitaceous fungi examined in this study, the nucleotide sequence of the third exon of ALDH1-1 (Exon-3) is 889 bp in length and has no insertion/deletion. A phylogenetic tree based on Exon-3 indicated that the clavicipitaceous fungi could be divided into two large groups: Cordyceps, Nomuraea, and Ustilaginoidea species formed a paraphyletic group, and the other grass biotrophic species formed a monophyletic group. This monophyletic group was further divided into three groups with high bootstrap support: i.e., species with Neotyphodium anamorphs (e.g., Epichloë), species with Ephelis anamorphs (e.g., Heteroepichloë), and Aciculosporium-Claviceps species. We discuss the relationships among Aciculosporium, Heteroepichloë, and other clavicipitaceous fungi.     

Chromosomal differentiation of the sibling species <Emphasis Type="Italic">Pichia membranifaciens</Emphasis> and <Emphasis Type="Italic">Pichia manshurica</Emphasis>

The molecular karyotyping analysis of 21 strains within the taxonomic complex Pichia membranifaciens allowed the sibling species P. membranifaciens and P. manshurica, as well as P. deserticola and P. punctispora, to be differentiated. Heterogeneity of the species P. membranifaciens at the variety level is discussed.     

Antirestriction and antimodification activities of T7 Ocr: Effects of amino acid substitutions in the interface

The T7 antirestriction protein Ocr, encoded by 0.3 (ocr), specifically inhibits ATP-dependent type I restriction-modification systems. T7 0.3 (ocr) was cloned in pUC18. Ocr inhibited both restriction and modification activities of the type I restriction-modification system (EcoKI) in Escherichia coli K12. The Ocr F53D A57E mutant was obtained and proved to inhibit only restriction activity of EcoKI. The 0.3 (ocr) and Photorhabdus luminescens luxCDABE genes were cloned in pZ-series vectors with the P _ltetO-1 promoter, strongly controlled by the TetR repressor. The bioluminescence intensity and luciferase content varied up to 5000-fold in E. coli K12 MG1655Z1 tetR⁺ (pZE21-luxCDABE) cells, depending on the environmental concentration of the inductor anhydrotetracycline. The antirestriction activity of Ocr and Ocr F53D A57E was studied as a function of their concentration in the cell. The dissociation constant K _d, characterizing the binding with EcoKI, differed 1000-fold between Ocr and Ocr F53D A57E (10^?10 M versus 10^?7 M).     

Taxonomic relations of three flounder species of the subfamily pleuronectinae of the sea of Japan

The taxonomic relations of two flatfish genera, Pseudopleuronectes and Liopsetta were examined for the species Ps. yokohamae, L. obscura and L. pinnifasciata with the use of morphometry and lateral line system structure analysis. Ps. yokohamae and L. obscura were found to be very similar in the majority of plastic and meristic characters and in the arrangement of the lateral line sensory canals on the head. Our findings confirmed the recent suggestions of a close relationship between Ps. yokohamae and L. obscura and provided a solid argument for the transfer of L. obscura from the genus Liopsetta to the genus Pseudopleuronectes.     

Search for genes influencing the maintenance of the [<Emphasis Type="Italic">ISP</Emphasis><Superscript>+</Superscript>] prion-like antisuppressor determinant in yeast with the use of an insertion gene library

The prion-like determinant [ISP ⁺] manifests itself as an antisuppressor of certain sup35 mutations. To establish that [ISP ⁺] is indeed a new yeast prion, it is necessary to identify the gene that codes for the protein whose prion form is [ISP ⁺]. Analysis of the transformants obtained by transformation of an [ISP ⁺] strain with an insertion gene library revealed three genes controlling the [ISP ⁺] maintenance: UPF1, UPF2, and SFP1. SFP1 codes for a potentially prionogenic protein, which is enriched in Asn and Gln residues, and is thereby the most likely candidate for the [ISP ⁺] structural gene. UPF1 and UPF2 code for components of nonsense-mediated mRNA decay. The [ISP ⁺] elimination caused by UPF1 and UPF2 inactivation was reversible, and Upf1p and Upf2p were not functionally related to phosphatase Ppz1p, which influences the [ISP ⁺] manifestation. Possible mechanisms sustaining the influence of UPF1 and UPF2 on [ISP ⁺] maintenance are discussed.     

Abundance,distribution, and territory areas of rock-dwelling Lake Tanganyika cichlid fish species

Lake Tanganyika, the second-oldest and second-deepest lake in the world, harbors an impressive cichlid fish fauna counting about 250 endemic species that are characterized by a great level of ecological, morphological, and behavioral specialization. This study describes and compares cichlid fish communities at two rocky shores with differential human impact in the south of Lake Tanganyika. Species inventories and depth-dependent abundances were elaborated. About 41 and 46 sympatric cichlid species were recorded in the two study sites, respectively. Variabilichromis moorii was the most abundant species (29–60% of total number of fishes), followed by Aulonocranus dewindti (3–19%), Tropheus moorii (12%), Ophthalmotilapia ventralis (4–10%), Eretmodus cyanostictus (6–11%), and Cyathopharynx furcifer (0.01–9%). All other species had abundances below 5%. It further emerged that large cichlids such as Petrochromis species, Cyathopharynx furcifer, and Lobochilotes labiatus were very rare at one location, with frequencies of 0.55% or less. Territorial sizes of three particularly abundant species, Variabilichromis moorii, Aulonocranus dewindti, and Tropheus moorii, were assessed by behavioral observations. We distinguished between territorial core areas and total defended area, yielding average core areas between 0.4 (V. moorii) and 1.6 m² (T. moorii), and total defended areas averaging for each species between 1.6 (V. moorii) and 5.0 m² (A. dewindti) with no significant differences between the two study sites. The data on individual densities are also relevant for evolutionary studies, in that they allow more accurate calculations of effective population sizes.     

Free-living nematodes of the genus <Emphasis Type="Italic">Alaimella</Emphasis> Cobb 1920 (Nematoda: Leptolaimidae): A description of <Emphasis Type="Italic">A. macramphis</Emphasis> sp. n. from the White Sea and a revision of the genus

Alaimella cincta Cobb 1920 and Alaimella macramphis sp. n. are described and illustrated. Both the species were first recorded for the White Sea in northern Russia. A. cincta occurs in the shells of the agglutinated foraminiferan Reophax curtus, as well as freely in bottom sediments. A. macramphis sp. n. is described from a single male sampled from bottom sediments. A. macramphis sp. n. is distinguished from two previously known species of Alaimella (A. cincta Cobb 1920 and A. truncate Cobb 1920) by having a longer body, longer cephalic setae, and a wide amphid equal to the respective body diameter. The new species also differs from A. truncate by the distinct striation of the cuticular annulations. The Alaimella species are additionally characterized by having a posterior glandular widening of the esophagus. An emended diagnosis of the genus Alaimella Cobb 1920 and a key for species identification are provided.     

Molecular identification key based on PCR/RFLP for three polychaete sibling species of the genus <Emphasis Type="Italic">Marenzelleria</Emphasis>, and the species’ current distribution in the Baltic Sea

Studies of Marenzelleria species were often hampered by identification uncertainties when using morphological characters only. A newly developed PCR/RFLP protocol allows a more efficient discrimination of the three species Marenzelleria viridis, Marenzelleria neglecta and Marenzelleria arctia currently known for the Baltic Sea. The protocol is based on PCR amplification of two mitochondrial DNA gene segments (16S, COI) followed by digestion with restriction enzymes. As it is faster and cheaper than PCR/sequencing protocols used so far, the protocol is recommended for large-scale analyses. The markers allow an undoubted determination of species irrespective of life stage or condition of the worms in the samples. The protocol was validated on about 950 specimens sampled at more than 30 sites of the Baltic and the North Sea, and on specimens from populations of the North American east coast. Besides this test we used mitochondrial DNA sequences (16S, COI, Cytb) and starch gel electrophoresis to further investigate the distribution of the three Marenzelleria species in the Baltic Sea. The results show that M. viridis (formerly genetic type I or M. cf. wireni) occurred in the Öresund area, in the south western as well as in the eastern Baltic Sea, where it is found sympatric with M. neglecta. Allozyme electrophoresis indicated an introduction by range expansion from the North Sea. The second species, M. arctia, was only found in the northern Baltic Sea, where it sometimes occurred sympatric with M. neglecta or M. viridis. For Baltic M. arctia, the most probable way of introduction is by ship ballast water from the European Arctic. There is an urgent need for a new genetic analysis of all Marenzelleria populations of the Baltic Sea to unravel the current distribution of the three species.     

Relationships among several species of the subfamily Gymnelinae (Zoarcidae) inferred from mitochondrial DNA sequence analysis

Nucleotide sequences of the mtDNA COI and cytochrome b genes were determined in Magadanichthys skopetsi, a member of the new monotypic genus Magadanichthys, endemic to the northern coast of the Sea of Okhotsk. Comparison of this species with other representatives of the subfamily Gymnelinae (family Zoarcidae) revealed high genetic similarity of M. skopetsi to Hadropareia middendorffii and considerable differences between these species and Gymnelopsis ochotensis.     

Efficacy of bacterial seed treatments for the control of <Emphasis Type="Italic">Fusarium verticillioides</Emphasis> in maize

Maize colonization by the phytopathogenic fungi Fusarium verticillioides leads to economical and food quality losses and also implicates potential health risks. In order to control this fungal species different strategies are being considered. In the present work we investigated the in situ effects of the use of two in vitro proven bacterial biological control agents against Fusarium verticillioides, using maize seedlings grown in greenhouse conditions. The treatment of maize seeds with Fusarium verticillioides 10⁷ spores ml^?1 negatively affected the length of the stem and the weight of the root systems of resultant seedlings, and also reduced the numbers of non-rhizospheric organisms with ammonification and nitrification activities. The addition of Bacillus amyloliquefaciens or Microbacterium oleovorans, at a concentration of 10⁹ colony forming units ml^?1, to the seeds significantly reduced Fusarium verticillioides count at the root inner tissues of resultant seedlings. When testing the impact of bacterial treatments on soil populations, no alterations with respect to control numbers of organisms with nitrification, ammonification or cellulolytic potentials were observed. Culturable bacterial richness and diversity calculated at the rhizoplane and root inner tissues of maize seedlings neither changed in bacterized treatments when compared to control treatment. Our study showed that the Fusarium verticillioides in vitro proven antagonists, Bacillus amyloliquefaciens and Microbacterium oleovorans (at 10⁹ colony forming units ml^?1), were also effective at greenhouse conditions without causing major changes in culturable rhizospheric and endophytic microbial richness and diversity.     

Interactions of Algae within the Community of <Emphasis Type="Italic">Gracilaria gracilis</Emphasis> (Rhodophyta)

Interactions among the unattached red alga Gracilaria gracilis, the dominant species of an algal community, and associated algal species Chaetomorpha linum, Enteromorpha prolifera f. prolifera, and Polysiphonia sp. were studied during and after an algal bloom. It was shown that during their bloom the associated algae Enteromorpha and Polysiphonia sp. significantly decreased the photosynthetic rate of G. gracilis but did not affect its growth rate. It is suggested that the inhibition of Gracilaria gracilis photosynthesis is connected to the impact of extracellular metabolites excreted by Chaetomorpha linum, Enteromorpha prolifera f. prolifera, and Polysiphonia sp. In laboratory experiments, the photosynthetic rate of the associated species was enhanced in the presence of Gracilaria. However, no significant alterations were observed in the content of chlorophyll a, growth, and the dark respiration rates of associated algae when they were kept together with Gracilaria. It was suggested that allelopathic interactions observed among algal species during the formation of the monospecific Gracilaria community, as well as during algal blooms, are not determinative.