Spatial distribution and species composition of prosthecate bacteria in Lake Baĭkal

From the water column of Lake Baikal, several strains of prosthecate bacteria belonging to the genera Caulobacter and Brevundimonas were isolated. In this article, the methods applied for their isolation and cell number determination are described; the occurrence frequency and spatial distribution of these microorganisms in the lake are demonstrated. Characterization of the species composition of cultivable and uncultivable prosthecate bacteria was carried out using the methods of traditional and molecular microbiology, respectively. A comparative phylogenetic analysis of the DNA sequences of uncultivable bacteria, which showed homology to the members of the alpha subclass of proteobacteria, was carried out. It was demonstrated that the lake water column is inhabited by uncultivable alpha-proteobacteria of uncertain phylogenetic affinity, in addition to representatives of the species Caulobacter vibrioides and C. leidyi, which were detected by traditional microbiological methods.     

Seasonal Changes in the Structure of the Anoxygenic Phototrophic Bacterial Community in Lake Mogilnoe,a Relict Lake on Kil'din Island in the Barents Sea

An anaerobic phototrophic bacterial community in Lake Mogilnoe, a relict lake on Kil'din Island in the Barents Sea, was studied in June 1999 and September 2001. Irrespective of the season, the upper layer of the anaerobic zone of this lake had a specific species composition of sulfur phototrophic bacteria, which were dominated by the brown-colored green sulfur bacterium Chlorobium phaeovibrioides. The maximum number of sulfur phototrophic bacteria was observed in June 1999 at a depth of 9 m, which corresponded to a concentration of bacteriochlorophyll (Bchl) e equal to 4.6 mg/l. In September 2001, the maximum concentration of this pigment (3.4 mg/l) was found at a depth of 10 m. In both seasons, the concentration of Bchl a did not exceed 3 μg/l. Purple sulfur bacteria were low in number, which can be explained by their poor adaptation to the hydrochemical and optical conditions of the Lake Mogilnoe water. In June 1999, the water contained a considerable number of Pelodictyon phaeum microcolonies and Prosthecochloris phaeoasteroides cell chains, which was not the case in September 2001. A 16S rDNA-based phylogenetic analysis of pure cultures of phototrophic bacteria isolated from the lake water confirmed that the bacterial community is dominated by Chl. phaeovibrioides and showed the presence of three minor species, Thiocystis gelatinosa, Thiocapsa sp., and Thiorhodococcus sp., the last of which is specific to Lake Mogilnoe.     

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.     

A cellulose-decomposing bacterial association

The structure of a cellulose-decomposing bacterial association was described using phenotypic and phylogenetic characteristics. Based on their morphological, physiological, and biochemical characteristics, the bacteria isolated from the association were identified as Sporocytophaga sp., Xanthomonas sp, and Pseudomonas sp. The phylogenetic analysis based on comparison of 16S rRNA gene fragments obtained from the association revealed six bacterial species belonging to the clusters of Alcaligenes sp., Ochrobactrum sp., Sphingomonas sp., Achromobacter sp., Pseudomonas sp., and Flexibacteriaceae (Sporocytophaga).     

Genotypic characterization of Lactic acid bacteria in gut microbiome of freshwater fish

The present study focused on identification and genotypic characterization of Lactic acid bacteria (LAB) in the intestine of freshwater fish. 76 strains of LAB were isolated and identified by 16S rRNA gene sequences and hsp60 gene sequences as different strains of Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus fermentum, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus brevis, Lactobacillus reuteri, Lactobacillus salivarius, Pediococcus pentosaceus, Pediococcus acidilactici, Weissella paramesenteroides, Weissella cibaria, Enterococcus faecium, and Enterococcus durans. The hsp60 gene showed a higher level of sequence variation among the isolates examined, with lower interspecies sequence similarity providing more resolutions at the species level than the 16S rRNA gene. Phylogenetic tree derived from hsp60 gene sequences with higher bootstrap values at the nodal branches was more consistent as compared to phylogenetic tree constructed from 16S rRNA gene sequences. Closely related species L. plantarum and L. pentosus as well as species L. delbrueckii subsp. bulgaricus and L. fermentum were segregated in different cluster in hsp60 phylogenetic tree whereas such a distribution was not apparent in 16S rRNA phylogenetic tree. In silico restriction analysis revealed a high level of polymorphism within hsp60 gene sequences. Restriction pattern with enzymes AgsI and MseI in hsp60 gene sequences allowed differentiation of all the species including closely related species L. plantarum and L. pentosus, E. faecium and E. durans. In general, hsp60 gene with higher evolutionary divergence proved to be a better phylogenetic marker for the group LAB.     

Obligate gut symbiotic association in the sloe bug <Emphasis Type="Italic">Dolycoris baccarum</Emphasis> (Hemiptera: Pentatomidae)

A number of phytophagous stinkbugs are associated with specific bacterial symbionts in their alimentary tracts. The sloe bug Dolycoris baccarum (Linnaeus), a notorious pest of diverse crops, possesses a number of sac-like tissues, called crypts, in a posterior section of the midgut, wherein a specific bacterial symbiont colonizes. Here we characterized the symbiotic bacterium of D. baccarum by histological analysis, molecular phylogeny, and diagnostic PCR with a specific primer set. The cloning and sequencing analyses of bacterial 16S rRNA genes and fluorescent in situ hybridization demonstrated that the sloe bug is associated with a single species of Gammaproteobacteria in the midgut crypts. Molecular phylogenetic analysis strongly suggested that the symbiont should be placed in the genus Pantoea of the Enterobacteriaceae. Diagnostic PCR and egg surface sterilization with formalin indicated the stinkbug vertically transmits the Pantoea symbiont via egg-smearing. The sterilization-produced aposymbiotic nymphs showed high mortality and no insects reached adulthood. In addition, the Pantoea symbiont was uncultivable outside the insect host, indicating an obligate and intimate host-symbiont association.     

<Emphasis Type="Italic">Metarhizium bibionidarum</Emphasis> and <Emphasis Type="Italic">M. purpureogenum</Emphasis>: new species from Japan

Two new species of Metarhizium, M. bibionidarum and M. purpureogenum are described from Japan. Metarhizium bibionidarum is the phylogenetic sister species of M. pemphigi and a member of the M. flavoviride species complex. It is distinguished morphologically from M. pemphigi by its larger conidia. The species is based on a collection of an infected March fly larva (Diptera: Bibionidae) but is also known to occur on fruit beetle (Coleoptera: Scarabaeidae) encountered in France. Metarhizium purpureogenum was isolated from soil by plating and insect baiting methods and represents a unique phylogenetic lineage placed outside the M. anisopliae and M. flavoviride species complexes. Three isolates of M. purpureogenum excreted a distinctive red-purple pigment into agar medium when co-cultured with M. robertsii or Aspergillus oryzae.     

Molecular phylogenetic analysis of key <Emphasis Type="Italic">Jatropha</Emphasis> species inferred from nrDNA ITS and chloroplast (<Emphasis Type="Italic">trn</Emphasis>L-F and <Emphasis Type="Italic">rbc</Emphasis>L) sequences

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS+trnL-F+rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.     

Phylogenetic Relationships within <Emphasis Type="Italic">Phyllophaga</Emphasis> Harris (sensu <Emphasis Type="Italic">lato</Emphasis>) (Coleoptera: Melolonthidae,Melolonthinae) with Emphasis on <Emphasis Type="Italic">Listrochelus</Emphasis> Blanchard

As partial results of a long-term project for the revision of the supraspecific classification of the American Melolonthini, using phylogenetic methods, interesting information on the relationships between the subgeneric groups of Phyllophaga Harris proposed by Saylor were obtained. The genus Listrochelus was described by Blanchard in 1851. However, in 1940, Saylor reduced it as a subgenus of Phyllophaga. The objective of the present study is to confirm the monophyly of Listrochelus by means of a phylogenetic analysis. A total of 132 species were analyzed; 31 species of them belong to Listrochelus, 76 are from other groups of Phyllophaga, and 25 species are from the outgroup. A morphological matrix with 281 characters was codified. A traditional search with 1000 iterations was performed in TNT. Branch support was investigated using the bootstrap method. Parsimony analysis resulted in ten equally parsimonious trees. The topology obtained in the strict consensus tree shows that the limits of Listrochelus are very clear (bootstrap 99%), supported by five synapomorphies and a combination of eight character states that are not exclusive to the group. Based on the hypothesis obtained, the restitution of the genus Listrochelus is proposed.     

Specific features of ecology of chars of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> (Salmonidae) from the basin of Lake Kronotskoe (Kamchatka) according to parasitological data

A parasitological study was performed of chars of the genus Salvelinus inhabiting Lake Kronotskoe (Kamchatka Peninsula)—S. malma, S. albus, S. schmidtii, and S. kronocius, as well as of juvenile Salvelinus spp. Twenty-three species of parasites, including six species new for the lake, Hennequya zschokkei, Protteocephalus longicollis, Diphyllobothrium dendriticum, Crepidostomum sp., Echinorhynchus salmonis, and Paracanthobdella livanowi, were found. With consideration of published data, in chars of this water body, 28 species of parasites were recorded, including seven species (N. cf. pungitius, B. luciopercae, Crepidostomum sp., Cr. fausti, Cr. cf. cooperi, Eubothrium crassium, and Proteocephalus sp.), whose presence or species identification in the lake ecosystem need confirmation. Two species (N. rutili and Diphyllobothrium sp.) are removed from the list. Parasites common for all species of chars were revealed. They include Myxobolus arcticus, E. salvelini, D. ditretum, Crepidostotum sp., Cr. farionis, Cr. metoecus, Cystidicola farionis, Cucullanus truttae, Philonema oncorhynchi, and Salmincola carpionis. Cluster analysis of the fauna of parasites of different species of chars demonstrated considerable differences in infestation, which indicates differences between them in preference for food items and occupied biotopes and thereby supports the ecological differentiation of chars in the basin of Lake Kronotskoe. S. albus and S. kronocius are most similar in parasitofauna, which is determined by their predation; S. malma as a benthophage is infected by the same species of parasites, but considerably less intensively. Extremely high indices of population numbers of some parasite species are considered as a manifestation of the Krebs cycle in parasites under the conditions of an isolated lake.     

Diversity and succession of pelagic microorganism communities in a newly restored Illinois River floodplain lake

Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, ‘isolation-with-migration’ models indicated that divergence between the two Altolamprologus species was recent (67–142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.     

Testing two contrasting evolutionary patterns in ancient lakes: species flock versus species scatter in valvatid gastropods of Lake Ohrid

Ancient lakes have long been recognized as “hot spots of evolution” and “evolutionary theatres” and they have significantly contributed to a better understanding of speciation and radiation processes in space and time. Yet, phylogenetic relationships of many ancient lake taxa, particularly invertebrate groups, are still unresolved. Also, the lack of robust morphological, anatomical, and phylogeographical data has largely prevented a rigorous testing of evolutionary hypotheses. For the freshwater gastropod genus Valvata—a group with a high degree of endemism in several ancient lakes—different evolutionary scenarios are suggested for different ancient lakes. Lake Baikal, for example, is inhabited by several endemic Valvata taxa that presumably do not form a monophyletic group. For such an evolutionary pattern, the term ancient lake species scatter is introduced here. In contrast, for the Balkan Lake Ohrid, workers previously suggested the presence of a monophyletic group of endemic Valvata species, that is, an ancient lake species flock. Sequence data of the mitochondrial cytochrome oxidase c subunit I gene (COI) from worldwide taxa, with a strong emphasis on Balkan species, are here used to test whether the putative Ohrid Valvata endemics represent an ancient lake species flock and to study patterns of speciation both on the Ohrid and the Balkan scale. The study reveals three distinct clades of endemic Valvata in Lake Ohrid. Monophyly of these taxa, however, is rejected, and they therefore do not represent an ancient lake species flock, but rather an ancient lake species scatter. Also, in contrast to many other gastropod groups in Lake Ohrid, the valvatids apparently did not radiate. Many Valvata taxa in ancient lakes are characterized by enhanced levels of shell complexity. However, it remains unclear whether these patterns are associated with ancient lake environments per se. It is here suggested that similarities in shell structure between North American and Balkan taxa might simply be due to convergent evolution.     

Revision of the taxonomic status of the genus <Emphasis Type="Italic">Gloeoporus</Emphasis> (Polyporales,Basidiomycota) reveals two new species

Gloeoporus Mont. is characterized by an easily separated gelatinous hymenophore and a continuous hymenium over the pore mouth. Recent molecular taxonomic and phylogenetic research showed that morphological grouping of Gloeoporus is polyphyletic. The lack of comprehensive phylogenetic studies of Gloeoporus exacerbates confusion in determining the taxonomic position of the genus. To delimit the genus Gloeoporus, we performed multi-locus phylogenetic analysis using the internal transcribed spacer (ITS) region, the nuclear large subunit ribosomal DNA (LSU), and the second-largest subunit of RNA polymerase II (rpb2). The phylogenetic analyses revealed that current delimitation of Gloeoporus is not monophyletic. Gloeoporus s.s. includes mostly clamped species lacking cystidia. Some species of Gloeoporus featuring simple septa and cystidia are proposed to be renamed to Meruliopsis. Two new species of Gloeoporus were also observed and they are named Gloeoporus africanus and Gloeoporus orientalis.     

Taxonomic and phylogenetic studies reveal a new species from <Emphasis Type="Italic">Funalia gallica</Emphasis> complex (Polyporales,Basidiomycota)

Taxonomic and phylogenetic studies of the Funalia gallica species complex and its related species were carried out. The phylogenetic analyses were based on datasets of either combined ITS, nrLSU and RPB2 sequences or single ITS sequences. The results reveal that at least four strongly hispid to strigose Funalia species can be recognised, i.e. the cosmopolitan F. trogii, Eurasian F. gallica, North American “F. gallica” and a new species F. subgallica discovered from tropical China. Morphologically, F. subgallica is characterised by its strongly hispid to strigose pileal surface, large pores (1–3 per mm) and basidiospores (11–15?×?4–5 μm).     

Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

Background

Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of eucalyptus in China) in approximately 17 genera. However, very limited information of Cosmoscartini is available except for some scattered taxonomic studies. Even less is known about its phylogenetic relationship, especially among closely related genera or species. In this study, the detailed comparative genomic and phylogenetic analyses were performed on nine newly sequenced mitochondrial genomes (mitogenomes) of Cosmoscartini, with the purpose of exploring the taxonomic status of the previously defined genus Okiscarta and some closely related species within the genus Cosmoscarta.

Results

Mitogenomes of Cosmoscartini display similar genomic characters in terms of gene arrangement, nucleotide composition, codon usage and overlapping regions. However, there are also many differences in intergenic spacers, mismatches of tRNAs, and the control region. Additionally, the secondary structures of rRNAs within Cercopidae are inferred for the first time.Based on comparative genomic (especially for the substitution pattern of tRNA secondary structure) and phylogenetic analyses, the representative species of Okiscarta uchidae possesses similar structures with other Cosmoscarta species and is placed consistently in Cosmoscarta. Although Cosmoscarta bimacula is difficult to be distinguished from Cosmoscarta bispecularis by traditional morphological methods, evidence from mitogenomes highly support the relationships of (C. bimacula?+?Cosmoscarta rubroscutellata)?+?(C. bispecularis?+?Cosmoscarta sp.).

Conclusions

This study presents mitogenomes of nine Cosmoscartini species and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae. It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels. Sequencing more mitogenomes at various taxonomic levels will also improve our understanding of mitogenomic evolution and phylogeny in Cercopidae.

     

The high diversity of <Emphasis Type="Italic">Lotus corniculatus</Emphasis> endosymbionts in soils of northwest Spain

The diversity of rhizobia that establish symbiosis with Lotus corniculatus has scarcely been studied. Several species of Mesorhizobium are endosymbionts of this legume, including Mesorhizobium loti, the type species of this genus. We analysed the genetic diversity of strains nodulating Lotus corniculatus in Northwest Spain and ten different RAPD patterns were identified among 22 isolates. The phylogenetic analysis of the 16S rRNA gene showed that the isolated strains belong to four divergent phylogenetic groups within the genus Mesorhizobium. These phylogenetic groups are widely distributed worldwide and the strains nodulate L. corniculatus in several countries of Europe, America and Asia. Three of the groups include the currently described Mesorhizobium species M. loti, M. erdmanii and M. jarvisii which are L. corniculatus endosymbionts. An analysis of the recA and atpD genes showed that our strains belong to several clusters, one of them very closely related to M. jarvisii and the remanining ones phylogenetically divergent from all currently described Mesorhizobium species. Some of these clusters include L. corniculatus nodulating strains isolated in Europe, America and Asia, although the recA and atpD genes have been sequenced in only a few L. corniculatus endosymbionts. The results of this study revealed great phylogenetic diversity of strains nodulating L. corniculatus, allowing us to predict that even more diversity will be discovered as further ecosystems are investigated.     

Molecular taxonomy and morphological characterization reveal new species and new host records of <Emphasis Type="Italic">Torula</Emphasis> species (Torulaceae,Pleosporales)

Four new species and two new host records of Torula (Torulaceae, Pleosporales) are described and illustrated from herbaceous litter collected in Italy and Thailand. The new species possess colony, conidiophore and conidial characteristics that fit within the generic concept of Torula. Detailed morphological observations clearly demarcate four of these from extant species and are hence described as new (Torula chiangmaiensis sp. nov., Torula pluriseptata sp. nov., Torula chromolaenae sp. nov., Torula mackenziei sp. nov.). Details of asexual morphs are described, and justifications for establishing these new species are provided. The nuclear are sequenced ribosomal RNA genes as well as protein coding genes to infer phylogenetic relationships and discuss phylogenetic affinities with morphologically similar species. Our morphological distinction is further supported by phylogenetic discrimination. In particular, phylogenies depict a close relationship of Torula chiangmaiensis and T. pluriseptata to T. hollandica, while T. chromolaenae and T. mackenziei constitute an independent phylogenetic lineage basal to T. herbarum and T. ficus. Torula ficus and T. masonii are also described and their phylogeny investigated as new host records from Bidens pilosa and Iris germanica, respectively.