Nitrogen-fixing cyanobacterium <Emphasis Type="Italic">Trichormus variabilis</Emphasis> of the Lake Baikal phytoplankton

A new filamentous cyanobacterial strain BAC 9610 was isolated from the lake Baikal pelagial. Data obtained by light, scanning, and transmission electron microscopy, along with 16S rRNA gene sequence analysis, allowed the bacterium identification as Trichormus variabilis, previously known as Anabaena variabilis. Trichormus is a cyanobacterial genus not presented in the list of Baikal plankton algae; A. variabilis also hasn’t been previously detected in Baikal phytoplankton. T. variabilis nitrogen fixation ability was demonstrated. The gene responsible for nitrogen fixation, nifH, was identified by PCR and was partially sequenced. No hepatotoxin synthesis genes were revealed in the strain.     

Detection and Genetic Characterization of Bacteria of the Genus <Emphasis Type="Italic">Pseudomonas</Emphasis> from Microbial Communities of Lake Baikal

The genus Pseudomonas is one of the most diverse and ecologically important groups of bacteria. Numerous representatives of the genus are found in microbial communities of all natural environments, including those closely associated with plants and animals. This ubiquitous distribution determines a necessity of their physiological and genetic adaptations. Molecular methods revealed that bacteria of the genus Pseudomonas were predominant in ulcerative lesions on the skin of Baikal yellowfin Cottocomephorus grewingkii (Dybowski, 1874). According to ribosomal phylogeny, cultivated Pseudomonas spp. isolated from both ulcerative lesions and the water column of Lake Baikal were grouped into the intrageneric cluster IG P. fluorescens. The topology of the phylogenetic tree based on the gene for outer membrane porin OprF generally coincided with that based on the 16S rRNA genes at the intrageneric level; however, it reflected ecological features of the strains of the genus Pseudomonas at the subgroup level. Screening of pathogenicity determinants detected the oprL, ecfX, fliC, and algD genes in the genomes of Pseudomonas spp. isolated from the ulcerative lesions of fish, whereas oprL and gyrB genes were determined in the strains isolated from the water column.     

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains,Buryat Republic)

High-throughput sequencing was used for comparative analysis of microbial communities of the water and mat from the Hoito-Gol mesothermal mineral sulfide spring (Eastern Sayan Mountains, Buryat Republic). Activity of microbial communities was determined. While both spring biotopes were dominated by members of three bacterial phyla—Proteobacteria, Bacteroidetes, and Firmicutes—they differed drastically in the composition of predominant phylotypes (at the genus level). In the water, the organisms widespread in aquatic environments were predominant, mostly aerobic chemoorganotrophs of the genera Acinetobacter, Pedobacter, and Flavobacterium. In the microbial mat, the organisms actively involved in the sulfur cycle predominated, including sulfur-reducing bacteria Sulfurospirillum, sulfate-reducing deltaproteobacteria, sulfuroxidizing chemoautotrophic bacteria, anoxygenic phototrophic bacteria of the phyla Chloroflexi and Chlorobi, as well as purple bacteria belonging to the α-, ß-, and γ-Proteobacteria. Microbial mats of the spring exhibited higher phylogenetic diversity compared to high-temperature mats containing photosynthetic microorganisms.     

Biodiversity and Activity of the Microbial Community in the Kotelnikovsky Hot Springs (Lake Baikal)

Complex microbiological and chemical analyses of water and bacterial mats were performed in the Kotelnikovsky Hot Springs (Lake Baikal). Transmission electron microscopy demonstrated that short rods about 1.2–2 μm in diameter predominated in the natural microbial community. Scanning electron microscopy coupled with chemical analysis revealed a characteristic P peak in the bacteria-like mineral particles, which suggests their biogenic origin. Most strains of the thermophilic microorganisms were gram-positive spore-forming rods and can be assigned to the genus Bacillus. Assays for potential enzyme activity demonstrated that most of the strains tested were active at high temperature. The data obtained suggest high activity of the bacterial community in situ and its particular role in the functioning of the hydrothermal ecosystem. __________ Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 6, 2005, pp. 664–671. Original Russian Text Copyright ? 2005 by Bel'kova, Parfenova, Suslova, Ahn, Tazaki.     

A metagenomic assessment of the bacteria associated with <Emphasis Type="Italic">Lucilia sericata</Emphasis> and <Emphasis Type="Italic">Lucilia cuprina</Emphasis> (<Emphasis Type="Italic">Diptera: Calliphoridae</Emphasis>)

Lucilia Robineau-Desvoidy (Diptera: Calliphoridae) is a blow fly genus of forensic, medical, veterinary, and agricultural importance. This genus is also famous because of its beneficial uses in maggot debridement therapy (MDT). Although the genus is of considerable economic importance, our knowledge about microbes associated with these flies and how these bacteria are horizontally and trans-generationally transmitted is limited. In this study, we characterized bacteria associated with different life stages of Lucilia sericata (Meigen) and Lucilia cuprina (Wiedemann) and in the salivary gland of L. sericata by using 16S rDNA 454 pyrosequencing. Bacteria associated with the salivary gland of L. sericata were also characterized using light and transmission electron microscopy (TEM). Results from this study suggest that the majority of bacteria associated with these flies belong to phyla Proteobacteria, Firmicutes, and Bacteroidetes, and most bacteria are maintained intragenerationally, with a considerable degree of turnover from generation to generation. In both species, second-generation eggs exhibited the highest bacterial phylum diversity (20 % genetic distance) than other life stages. The Lucilia sister species shared the majority of their classified genera. Of the shared bacterial genera, Providencia, Ignatzschineria, Lactobacillus, Lactococcus, Vagococcus, Morganella, and Myroides were present at relatively high abundances. Lactobacillus, Proteus, Diaphorobacter, and Morganella were the dominant bacterial genera associated with a survey of the salivary gland of L. sericata. TEM analysis showed a sparse distribution of both Gram-positive and Gram-negative bacteria in the salivary gland of L. sericata. There was more evidence for horizontal transmission of bacteria than there was for trans-generational inheritance. Several pathogenic genera were either amplified or reduced by the larval feeding on decomposing liver as a resource. Overall, this study provides information on bacterial communities associated with different life stages of Lucilia and their horizontal and trans-generational transmission, which may help in the development of better vector-borne disease management and MDT methods.     

Use of specific PCR primers for the study of sulfate-reducing bacteria diversity in microbial mats of Ebro Delta,Spain

Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Sulfate-reducing bacteria (SRB) play a key role in sulfur and nutrient recycling in these ecosystems. In this work, specific primers for 16S rRNA encoding gene, previously described, were used to study the diversity of SRB in microbial mats of the Ebro Delta. We confirm that this method is reliable to identify the diversity of SRB in these ecosystems. However, some mismatches in obtained sequences had been observed in our system and must be taken under consideration. Various genera of SRB in Ebro Delta microbial mats were identified, such as Desulfonema, Desulfatitalea, Desulfosalsimonas, Desulfoccocus, and Desulfovibrio. The diversity observed in our samples is very similar to previously reported in other microbial mats communities.     

The effect of bloom of filamentous green algae on the reproduction of yellowfin sculpin <Emphasis Type="Italic">Cottocomephorus grewingkii</Emphasis> (Dybowski, 1874) (Cottoidae) during ecological crisis in Lake Baikal

In shallow water areas of open Lake Baikal, filamentous green alga of the genus Spirogyra grows abundantly. Together with alga of the genus Ulothrix, it forms algal mats. According to our observations from 2010 to 2013, the spawning habitat conditions for the yellowfin sculpin Cottocomephorus grewingkii (Dybowski, 1874) (Cottidae) proved to be significantly disturbed in the littoral zone of Listvennichnyi Bay (southern Baikal), which, in turn, reduced the number of egg layings. With a 100% projective cover of the floor and a high density of green filamentous algae, the shallow-water stony substrate becomes completely inaccessible for spawning of the August population.     

Colorless sulfur bacteria <Emphasis Type="Italic">Thioploca</Emphasis> from different sites in Lake Baikal

The colorless sulfur bacteria Thioploca spp. found in Lake Baikal are probably a marker for the influx of subterranean mineralized fluids. Bacteria act as a biological filter; by consuming sulfide in their metabolism, they detoxicate it and maintain the purity of Lake Baikal’s water. The bacteria were investigated by various techniques. According to analysis of the 16S rRNA gene fragment, Thioploca sp. from Frolikha Bay, Baikal belongs to the clade of freshwater species found in Lake Biwa and Lake Constance; it is most closely related to Thioploca ingrica.     

Microbial community of freshwater sponges in Lake Baikal

The microbial community of Baikal sponges has been studied in five species belonging to the genera Swartschewskia, Baicalospongia, and Lubomirskia of the endemic family Lubomirskiidae. The results show that the total numbers of bacteria and bacterioplankton production have an effect on the growth of L. baicalensis body. Bacteria of the genera Pseudomonas, Bacillus, Micrococcus, Sarcina, Flavobacterium, Arthrobacter, and Acinetobacter living in the sponges are representatives of the Baikal bacterioplankton. Actinomycetes of the genera Streptomyces and Micromonospora are a permanent component of the cultivable sponge microbial community. The numbers and enzyme activities of heterotrophic, oligotrophic, and psychrophilic bacteria isolated from different sponge species and from the ambient water in autumn and in winter have been estimated.     

Study of ectoparasitism of ultramicrobacteria of the genus <Emphasis Type="Italic">Kaistia</Emphasis>, strains NF1 and NF3 by electron and fluorescence microscopy

Transmission electron and fluorescence microscopy was used to study the character of the interaction of free-living ultramicrobacterial (UMB) strains NF1 and NF3, affiliated with the genus Kaistia, and seven species of gram-positive and gram-negative heterotrophic bacteria. Strains NF1 and NF3 were found to exhibit parasitic activity against gram-positive Bacillus subtilis and gram-negative Acidovorax delafildii. UMB cells are tightly attached to the envelopes of the victim cells and induce their lysis, thus demonstrating the features of typical ectoparasitism. The selectivity of parasitism of the studied UMB to the victim bacteria has been shown: only two soil microorganisms of the seven test objects, B. subtilis ATCC 6633 and an aerobic gramnegative bacterium A. delafildii 39, were found to be sensitive to UMB attack. Other bacteria (Micrococcus luteus VKM Ac-2230, Staphylococcus aureus 209-P, Pseudomonas putida BS394, Escherichia coli C 600, and Pantoea agglomerans ATCC 27155) were not attacked by UMB. It was established for the first time that free-living UMB may be facultative parasites not only of phototrophic bacteria, as we have previously demonstrated [1], but of heterotrophic bacteria as well. The UMB under study seem to play an important role in the regulation of the quantity of microorganisms and in the functioning of microbial communities in some natural ecotopes.     

Phylogenetic Diversity of the Sulfur Cycle Bacteria in the Bottom Sediments of the Chersonesus Bay

The Black Sea is the largest meromictic basin, in the bottom sediments of which a powerful biogenic process of sulfide production occurs. The goal of the present work was to obtain data on phylogenetic diversity of the sulfur cycle microorganisms (sulfate-reducing and sulfur-oxidizing bacteria) in the Black Sea coastal gas-saturated bottom sediments. The samples were collected in the Chersonesus (Blue) Bay near Sevastopol from whitish bacterial mats of sulfurettes, and from the upper layer of the nearby seabed. Using DNA isolated from the native samples and obtained enrichment cultures, PCR analysis was performed with oligonucleotide primers specific to the fragments of the 16S rRNA genes of the main subgroups of sulfatereducing bacteria (SRB) and to the fragments of the dsrB gene (both reductive and oxidative types), encoding the β-subunit of dissimilatory (bi)sulfite reductase, the key enzyme in the sulfur cycle, inherent in both sulfate- reducing and sulfur-oxidizing microorganisms. The presence of 16S rRNA gene fragments specific to the genera Desulfobacterium, Desulfobacter, Desulfococcus–Desulfonema–Desulfosarcina, and Desulfovibrio–Desulfomicrobium was detected in the DNA samples isolated from coastal bottom bacterial mats. Usage of denaturing gradient gel electrophoresis (DGGE) with subsequent sequencing of reamplified dsrB gene fragments revealed that according to deduced amino acid sequences encoded by the dsrB gene (reductive type), SRB from the coastal gas-saturated bottom sediments of the Black Sea had the highest homology (92?99%) with the dsrB gene of cultured SRB belonging to the genera Desulfovibrio, Desulfatitalea, Desulfobacter, and Desulfobacterium, as well as with uncultured SRB strains from various marine habitats, such as bottom sediments of the Northern and Japanese seas. Deduced amino acid sequences encoded by the oxidative dsrB gene had the highest homology (90?99%) with the relevant sequences of the genera Thiocapsa, Thiobaca, Thioflavicoccus, and Thiorhodococcus.     

Identification of two cyanobacterial strains isolated from the Kotel’nikovskii hot spring of the Baikal rift

Two cyanobacterial strains, Pseudanabaena sp. 0411 and Synechococcus sp. 0431, were isolated from a sample collected in the Kotel’nikovskii hot spring of the Baikal rift. According to the results of light and transmission electron microscopy, as well as of the phylogenetic analysis of the 16S rRNA gene, these cyanobacteria were classified as Pseudanabaena sp. nov. and Synechococcus bigranulatus Skuja. The constructed phylogenetic tree shows that the studied strains are positioned in the clades of cyanobacteria isolated from hydrothermal vents of Asia and New Zealand, separately from marine and freshwater members of these genera, including those isolated from Lake Baikal.     

Bacterial communities during the period of massive under-ice dinoflagellate development in Lake Baikal

Taxonomic diversity of Lake Baikal bacteria during the period of massive under-ice development of dinoflagellate Gymnodinium baicalense was studied. During the ice-covered period in 2013, both the abundance and biomass of G. baicalense were several orders of magnitude higher than the values for previous years, the maximum values were 8.9 × 10⁶ cells/L and 405 g/m³, respectively. The taxonomic structure of bacterial communities was determined using the data obtained by 454 pyrosequencing (Roche) with Mothur 1.19.0. Predominance of three phyla was revealed: Bacteroidetes, Proteobacteria, and Actinobacteria. Massive dinoflagellate development resulted in a considerable decrease in the richness and diversity of bacterial communities compared to the results of the earlier long-term studies.     

New host species and new distribution areas of <Emphasis Type="Italic">Salmincola lavaretus</Emphasis> (Copepoda: Lernaeopodidae): A parasite of coregonid fishes of Siberia

Data on the infestation of certain fish species by the parasitic copepod Salmincola lavaretus are presented for the first time. The infested fish species included Bauntovsky whitefish (Coregonus baunti), an endemic species from the Maloye and Bolshoye Kapylyushi lakes; Siberian whitefish (C. pidschian) and Siberian cisco (C. sardinella) from Bolshoye Kapylyushi Lake and Baunt Lake, which belong to the Tsypo-Tsypikan lake system (the Lena River basin, Transbaikalia); and Teletsky whitefish (C. lavaretus natio smitti) from Teletskoe Lake (the Ob River basin). Previously, S. lavaretus had been described as a parasite of Baikal omul (C. migratorius) and Baikal whitefish (C. baicalensis) from Baikal. The taxons of S. longimanus complex (S. longimanus, S. l. sibirica, S. svetlanovi, and S. lavaretus)—parasites of nasal fossae of grayling and coregonid fishes—were registered in the lakes of the Lake Baikal basin (Lake Baikal and Khovsgol Lake), the Lena River, the Yenisei and the Ob rivers (the largest rivers of the Arctic zoogeographic province), and the Kobdo River (the Western Mongolian province). It was assumed that S. longimanus complex is more widely distributed in the water bodies of the Arctic zoogeographic province of the Palearctic.     

Diatoms (Bacillariophyceae) associated with free-drifting Antarctic icebergs: taxonomy and distribution

Free-drifting Antarctic icebergs can alter the phytoplankton in surrounding waters. In addition, diatom mats live attached to the submerged walls of the icebergs. In this study we describe a diverse diatom community associated with these mats and an atypical planktonic community in waters affected by icebergs. Samples were collected in the winter of 2008 and fall of 2009 from Antarctic icebergs and their adjacent waters, utilizing a remote operated vehicle and plankton nets, respectively, and subsequently analyzed using light and electron microscopy. Thalassioneis signyensis, dominant species growing on the icebergs’ flanks, provided substrate for other diatoms, mainly Synedropsis lata var. angustata, Synedropsis recta, Fragilaria cf. islandica var. adeliae, Attheya gaussii, Navicula cf. perminuta, Amphora sp. and Nitzschia spp. New morphological characteristics are given for S. lata var. angustata, S. recta and A. gaussii. We report also Biddulphia alternans and Coscinodiscus concinnus for the first time in Antarctic waters. Similar to sea ice algae, the term sympagic is used to describe the habitat of these diatom communities. A particular planktonic community is also found close to icebergs, including diatoms known to have a benthic, epiphytic, sympagic or freshwater habitat: Amphora sp., B. alternans, Cocconeis spp., Delphineis minutissima, Licmophora gracilis, Luticola cf. australomutica, Opephora sp., Pinnularia spp., Plagiogramma sp., Psammodictyon panduriforme var. minor, Pseudogomphonema kamtschaticum, Rhaphoneis amphiceros, S. recta and T. signyensis. Our results support the hypothesis that species associated with icebergs exchange freely with plankton, ice shelves and sea ice, suggesting that icebergs can act as physical agents to transport and distribute organisms in between these habitats.     

Taxonomic significance of pollen morphology for species delimitation in <Emphasis Type="Italic">Psidium</Emphasis> (Myrtaceae)

Previous studies reported Psidium as one of the most difficult genera to delimit within the American Myrtaceae. Even though palynology has improved the taxonomy of Angiosperms, information about the usefulness of pollen morphology for taxonomic purposes in Myrtaceae remains contradictory. Here, we investigate the significance of pollen morphology for Psidium taxonomy with specific focus on its usefulness for determining species groups of taxonomic significance. Pollen traits observed by light and scanning electron microscopy were quantified and examined using cluster and ordination analyses. Average size of pollen grains was visualized by boxplots. Pollen grains of Psidium are isopolar, oblate, peroblate or oblate-spheroidal, 3-syncolporate or 4-syncolporate. The sexine ornamentation is rugulate, granulate or spinulose-granulate and differs between the mesocolpium and apocolpium. Cluster analysis revealed four distinct groups: Psidium cauliflorum (G1) and Psidium oligospermum (G3) as single-species groups; Psidium brownianum, P. oblongatum, P. ovale, P. sartorianum, P. guajava, Psidium sp. 1, Psidium sp. 2 (G2), and Psidium cattleianum, P. longipetiolatum, P. guineense, P. myrtoides (G4). Supported by ordination analysis, three traits better explained these groups: type of exine ornamentation, size of P-EV and pollen shape. The used approach efficiently distinguished related species, as well as explained species groups of taxonomic significance suggesting pollen morphology to be a significant source of information for taxonomic studies in Psidium.     

<Emphasis Type="Italic">Entransia</Emphasis> and <Emphasis Type="Italic">Hormidiella</Emphasis>, sister lineages of <Emphasis Type="Italic">Klebsormidium</Emphasis> (Streptophyta), respond differently to light,temperature, and desiccation stress

The green-algal class Klebsormidiophyceae (Streptophyta), which occurs worldwide, comprises the genera Klebsormidium, Interfilum, Entransia, and Hormidiella. Ecophysiological research has so far focused on the first two genera because they are abundant in biological soil crust communities. The present study investigated the photosynthetic performances of Hormidiella attenuata and two strains of Entransia fimbriata under light, temperature, and desiccation stress. Their ultrastructure was compared using transmission electron microscopy. The two Entransia strains showed similar physiological responses. They used light more efficiently than Hormidiella, as indicated by higher oxygen production and relative electron transport rate under low light conditions, lower light saturation and compensation points, and higher maximum oxygen production during light saturation. Their requirement for low light levels explains the restriction of Entransia to dim limnetic habitats. In contrast, Hormidiella, which prefers drier soil habitats, responded to light gradients similarly to other aero-terrestrial green algae. Compared to Entransia, Hormidiella was less affected by short-term desiccation, and rehydration allowed full recovery of the photosynthetic performance. Nevertheless, both strains of Entransia coped with low water availability better than other freshwater algae. Photosynthetic oxygen production in relation to respiratory consumption was higher in low temperatures (Entransia: 5 °C, Hormidiella: 10 °C) and the ratio decreased with increasing temperatures. Hormidiella exhibited conspicuous triangular spaces in the cell wall corners, which were filled either with undulating cell wall material or with various inclusions. These structures are commonly seen in various members of Klebsormidiophyceae. The data revealed significant differences between Hormidiella and Entransia, but appropriate adaptations to their respective habitats.     

The taxonomic composition,characteristics, and neurotoxic activities of ribbon worm-associated bacteria from the Sea of Japan

The taxonomic composition of bacteria associated with two species of tetrodotoxin-bearing (TTX-bearing) (Hubrechtella juliae and Lineus alborostratus) and two species of non-TTX-bearing (Quasitetrastemma stimpsoni and Malacobdella grossa) ribbon worms collected from the Peter the Great Bay of Sea of Japan was studied. Bacterial isolates were identified using 16S rRNA gene sequencing and phenotypic characteristics. Thirty-eight strains of heterotrophic bacteria from the eight genera: Pseudoalteromonas, Shewanella, Ruegeria, Pseudomonas, Defluviicoccus, Vibrio, Alteromonas, and Bacillus, were isolated and characterized. γ-Proteobacteria dominated among the associated microflora of nemerteans (76.3% of the total number of isolates). Sensitivity analysis of 38 strains to antibiotics of various classes revealed multiple resistance to three or more antibiotics in all of the studied isolates. The 15 bacterial strains isolated in the study exhibited antimicrobial activities against at least one of five indicator microorganisms, most of which corresponded to the Pseudoalteromonas genus. Screening of the TTX-producing bacteria was performed using confocal laserscanning microscopy and polyclonal antibodies. A TTX-producing strain, Pseudoalteromonas sp., was found in the nemertean H. juliae. A correlation between the presence of TTX-positive microflora and the toxicity of nemerteans was determined.