S. G. Livanov

Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks

Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species), Rickettsia (I. persulcatus and D. reticulatus) and Francisella (D. reticulatus). B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilum and Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002). Between-sex variation was confirmed by PERMANOVA testing in I. persulcatus (p = 0.042) and I. pavlovskyi (p = 0.042) ticks. Our study indicated that 16S metagenomic profiling could be used for rapid assessment of the occurrence of medically important bacteria in tick populations inhabiting different natural biotopes and therefore the epidemic danger of studied foci.

Detection and genetic characterization of a wide range of infectious agents in Ixodes pavlovskyi ticks in Western Siberia, Russia

BackgroundThe Ixodes pavlovskyi tick species, a member of the I. persulcatus/I. ricinus group, was discovered in the middle of the 20th century in the Russian Far East. Limited data have been reported on the detection of infectious agents in this tick species. The aim of this study was to investigate the prevalence and genetic variability of a wide range of infectious agents in I. pavlovskyi ticks collected in their traditional and recently invaded habitats, the Altai Mountains and Novosibirsk Province, respectively, which are both located within the Western Siberian part of the I. pavlovskyi distribution area.ResultsThis study reports the novel discovery of Borrelia bavariensis, Rickettsia helvetica, R. heilongjiangensis, R. raoultii, “Candidatus Rickettsia tarasevichiae”, Anaplasma phagocytophilum, Ehrlichia muris, “Candidatus Neoehrlichia mikurensis” and Babesia microti in I. pavlovskyi ticks. In addition, we confirmed the previous identification of B. afzelii, B. garinii and B. miyamotoi, as well as tick-borne encephalitis and Kemerovo viruses in this tick species. The prevalence and some genetic characteristics of all of the tested agents were compared with those found in I. persulcatus ticks that were collected at the same time in the same locations, where these tick species occur in sympatry. It was shown that the prevalence and genotypes of many of the identified pathogens did not significantly differ between I. pavlovskyi and I. persulcatus ticks. However, I. pavlovskyi ticks were significantly more often infected by B. garinii and less often by B. bavariensis, B. afzelii, “Ca. R. tarasevichiae”, and E. muris than I. persulcatus ticks in both studied regions. Moreover, new genetic variants of B. burgdorferi (sensu lato) and Rickettsia spp. as well as tick-borne encephalitis and Kemerovo viruses were found in both I. pavlovskyi and I. persulcatus ticks.ConclusionAlmost all pathogens that were previously detected in I. persulcatus ticks were identified in I. pavlovskyi ticks; however, the distribution of species belonging to the B. burgdorferi (sensu lato) complex, the genus Rickettsia, and the family Anaplasmataceae was different between the two tick species. Several new genetic variants of viral and bacterial agents were identified in I. pavlovskyi and I. persulcatus ticks.

Erratum to: Genetic diversity of Ixodes pavlovskyi and I. persulcatus (Acari: Ixodidae) from the sympatric zone in the south of Western Siberia and Kazakhstan

The most epidemiologically significant tick species in Siberia involved in transmission of a large number of pathogens causing human infectious diseases is Ixodes persulcatus. Ixodes pavlovskyi, being more active, also poses epidemiological threats. These tick species share morphology, activity seasons and geographic distribution range. In this paper, we characterize the geographic and genetic structures of I. persulcatus and I. pavlovskyi populations inhabiting the southern part of Western Siberia (Russia and Kazakhstan)—the western part of I. pavlovskyi distribution range. The data are based on six distinct Ixodes tick populations. Analysis of the concatenated mitochondrial marker sequences (16S rRNA and COI) and the nuclear sequence (ITS2) showed genetic polymorphisms in both I. persulcatus and I. pavlovskyi ticks inhabiting the sympatric zone. We could not determine the phylogeographic structure of I. pavlovskyi populations whereas for I. persulcatus significant within-region variance was shown. Notably, the abundance of I. persulcatus ticks negatively correlates with nucleotide and haplotype diversity in the concatenated sequence of mitochondrial gene (16S rRNA and COI) fragments. This is the first description of the genetic polymorphism of I. persulcatus and I. pavlovskyi ticks coexisting in a sympatric zone based on analysis of mitochondrial and nuclear markers.

Distribution of the Ticks Ixodes persulcatus and Ixodes pavlovskyi on the Boundary of the Forest and Forest-Steppe Zones in the Ob Region

Surveys of ixodoid ticks were performed in Novosibirsk Province (Novosibirsk and Toguchin Districts) and in the vicinity of Akademgorodok (Novosibirsk) in 2009–2010. The abundance and distribution of ticks were assessed in 8 types of habitats. Ixodes persulcatus (Schulze, 1930) was collected by flagging in Novosibirsk and Toguchin Districts, with the highest densities of 19 ind./km being observed in habitats with small-leaved trees. Three species of ticks: Ixodes persulcatus, I. pavlovskyi (subspecies I. pavlovskyi occidentalis Filip. et Pan., 1998), and Dermacentor reticulatus (Fabricius, 1794) were recorded in a recreational forest of Akademgorodok. A high abundance (22 ind./km) of I. pavlovskyi was observed in pine forests subjected to considerable recreational load. The abundance of I. persulcatus was the highest in aspen-birch and birch-aspen forests. D. reticulatus was captured in pine forests and fallow lands, its abundance varying from 0.2 to 2 ind./km.

Occurrence and genetic variability of Kemerovo virus in Ixodes ticks from different regions of Western Siberia, Russia and Kazakhstan.

Kemerovo virus (KEMV), a member of the Reoviridae family, Orbivirus genus, is transmitted by Ixodes ticks and can cause aseptic meningitis and meningoencephalitis. Recently, this virus was observed in certain provinces of European part of Russia, Ural, and Western and Eastern Siberia. However, the occurrence and genetic diversity of KEMV in Western Siberia remain poorly studied. Therefore, the aim of this work was to investigate the prevalence and genetic variability of KEMV in Ixodes ticks from Western Siberia. A total of 1958 Ixodes persulcatus, I. pavlovskyi ticks and their hybrids from Novosibirsk and Omsk provinces, Altai Republic (Russia) and East Kazakhstan province (Kazakhstan) were analyzed for the presence of KEMV and tick-borne encephalitis virus (TBEV) RNA. It was observed that the KEMV distribution area in Western Siberia was wider than originally thought and included Northern and Northeastern Altai in addition to the Omsk and Novosibirsk provinces. For the first time, this virus was found in Kazakhstan. The occurrence of KEMV was statistically lower than TBEV in most locations in Western Siberia. KEMV was found both in I. persulcatus and I. pavlovskyi ticks and in their hybrids. Notably, KEMV variants observed in the 2010s were genetically different from those isolated in the 1960s, which indicated the ongoing process of evolution of the Kemerovo virus group. Moreover, the possibility of reassortment for KEMV was demonstrated for the first time.

Seasonal changes in populations of Ixodes persulcatus and I. pavlovskyi on the border between the forest and forest-steppe zones of the Ob region

The seasonality of epidemic and epizootic processes of tick-borne encephalitis (TBE) and borreliosis among the populations of Ixodes persulcatus and Ixodes pavlovskyi ticks was studied. The study was carried out in 2011–2012 on the flatland part of Toguchin and in the vicinities of Akademgorodok in Novosibirsk, on the border between the forest and forest-steppe zones of the Ob region. The results obtained for I. persulcatus did not contradict the previously published studies. The starting point and peak of mass activity of I. pavlovskyi ticks were registered later (the last ten days of May) than that of I. persulcatus ticks. Seasonal variations in the physiological age of I. pavlovskyi ticks were similar to that of I. persulcatus ticks. The only exception to this was detected in the last ten days of April when young specimens prevailed in the population of I. pavlovsky ticks in contrast to the I. persulcatus population. The large influence of I. persulcatus on the circulation of TBE was shown, as well as the influence of I. pavlovskyi on the spreading of Borrelia burgdorferi s.l.

Ecological and molecular genetic features of Ixodes persulcatus and I. pavlovskyi ticks in Southern West Siberia

Ixodiae ticks have been counted and sampled in six distant locations within the Altai-Sayan Mountain Area and northern forest steppe in 2012. In total, 1829 individuals of I. persulcatus and 719 of I. pavlovskyi ticks were collected by flagging. I. persulcatus is found in all six examined locations and I. pavlovskyi is found in Western Altai, Northeastern Altai, and Northern Altai, as well as in forest parks near Akademgorodok of Novosibirsk. In total, 16S rRNA and COI sequences have been determined in 144 and 164 I. persulcatus individuals, as well as in 60 and 55 I. pavlovskyi. Selectively equivalent mutant forms are present in I. pavlovskyi populations of Northeastern Altai and Northern Altai. The hydrothermal regime in the forest parks near Novosibirsk is optimal for the I. pavlovskyi ticks. These ticks have recently colonized the forest parks near Novosibirsk and therefore are genetically close to I. pavloskyi from the Altai–Sayan Mountain Area populations.

Spatial organization of summer bird assemblages in the Northern Urals

The spatial heterogeneity of bird assemblages has been evaluated based on the results of transect bird counts taken in different areas of the Northern Urals from June 1 to July 15 in 1966 to 2005. On the whole, 154 bird species were recorded over the routes extending for about 3000 km. A total of 126 variants of bird assemblages were included in calculations. Using multidimensional factor analysis, a hierarchical classification of these assemblages has been constructed, and basic environmental factors having an effect on their structure have been revealed. The results show that the spatial organization of bird assemblages in the Northern Urals is most similar to that in the Northeastern Altai.

Spatial Bird Distribution in North Urals in First Half of Summer

Проанализированы результаты маршрутных учетов птиц, проведенных на территории Северного Урала в первой половине лета (1.06–15.07) и в целом охватывающих период с 1966 по 2005 г. Суммарная протяженность маршрутов составила около 3000 км. Всего использовано 126 исходных вариантов населения птиц. По результатам многомерного факторного анализа для 154 зарегистрированных видов выявлены особенности их пространственного предпочтения и составлена иерархическая классификация. Классификация показала, что 3% птиц этой уральской провинции предпочитают горные тундры, 49% — преимущественно обитают в лесах, 18% — тяготеют к застроенным территориям, 31% — это виды водно-болотных экосистем. Проведен сравнительный анализ с аналогичными классификациями по другим регионам. Из-за отсутствия обширных открытых сельскохозяйственных ландшафтов на Северном Урале, в отличие от Среднего Урала, не представлен соответствующий им комплекс видов, а водно-болотная группа, наоборот, выглядит явно представительней. По характеру распределения видов птиц Северный Урал значимо отличается от Среднего Урала и в целом ближе к алтайским провинциям, среди которых особенно близок к наиболее лесной из них — СевероВосточной. Ключевые слова: птицы, учеты, распределение, виды, Урал, классификация, факторный анализ. Results of route counts of the birds spent in territory of North Urals Mountains in first half of summer (1.06– 15.07) and, in whole, are analyzed, covering the period with 1966 for 2005. Total extent of routes has made about 3000 km. In total 126 initial variants of the bird communities are used. By results of the multidimensional factorial analysis for 154 registered species features of their spatial preference are revealed and hierarchical classification is made. Comparisons to similar classifications by another regions are spent. Classification showed that 3% of the birds of this Ural provinces prefer the mountain tundra, 49% from it’s, mostly live in forests, 18% of the birds gravitate to the urbanized territories and 31% is a species of wetland ecosystems. A comparative analysis with similar classifications in other regions revealed the following. Due to the lack of extensive open agricultural landscapes in the Northern Urals, in contrast to the Medium, not the complex species, water and wetlands group, on the contrary, a lot more. By the nature of the distribution of bird species North Ural significantly differs from the average and, in General, the closer to the Altai provinces, among which are especially close to the forest of them — the North-East province.