Browsing by Subject "GENETIC DIVERSITY"

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  • Wysok, Beata; Wojtacka, Joanna; Hänninen, Marja-Liisa; Kivistö, Rauni (2020)
    Campylobacteriosis is one of the most common causes of bacterial gastroenteritis. However, the clinical course of the illness varies in symptoms and severity. The aim of this study was to characterizeCampylobacter jejuni(34 isolates) andC. coli(9 isolates) from persons with diarrheal and non-diarrheal stools at the time of examination and fecal sampling, in Poland by using whole-genome sequencing (WGS). Multilocus sequence typing (MLST) analysis revealed a high diversity with a total of 20 sequence types (STs) among 26Campylobacterisolates from diarrheic and 13 STs among 17 isolates from non-diarrheic persons. ST-50 and ST-257 were most common in both groups. The phenotypic resistance rate was 74.4% for ciprofloxacin, 67.4% for sulfamethoxazole/trimethoprim, 58.1% for amoxicillin, 48.8% for tetracycline, and 46.5% for ceftriaxone. Only single isolates were resistant to erythromycin, gentamicin, and amoxicillin/clavulanic acid. Overall genotypic resistance toward amoxicillin, fluoroquinolones, tetracyclines, and aminoglycosides was predicted to occur in 93.1, 67.4, 48.8, and 11.6% of the isolates, respectively. None of the isolates showed the presence of theerm(B) gene or mutation in 23S rRNA. Neither was variation found in the important target region in L4 and L22 ribosomal proteins. In regard to the CmeABC efflux pump, a set of variable mutations affecting the regulatory region was noted. AllCampylobacterisolates possessed genes associated with adhesion (cadF,jlpA,porA, andpebA) and invasion (ciaB,pldA, andflaC). The type IV secretion system (T4SS) was found in isolates from both diarrheic (15.4%, CI 95%: 6.1-33.5%) and non-diarrheic (23.5%, CI 95%: 9.6-47.3%) persons. The rates of the presence of cytolethal distending toxincdtABCgene cluster and type VI secretion system (T6SS) were higher inCampylobacterisolates obtained from persons with diarrhea (96.2%, CI 95%: 81.7-99.3% and 26.9%, CI 95%: 13.7-46.1%) compared to isolates from non-diarrheic persons (76.5%, CI 95%: 52.7-90.4% and 11.8%, CI 95%: 3.3-34.3%). The lack of statistically significant differences between two groups in tested virulence factors suggests that individual susceptibility of the host might play more determining role in the disease outcome than characteristics of the infecting strain.
  • Dickson, Laura B.; Jiolle, Davy; Minard, Guillaume; Moltini-Conclois, Isabelle; Volant, Stevenn; Ghozlane, Amine; Bouchier, Christiane; Ayala, Diego; Paupy, Christophe; Moro, Claire Valiente; Lambrechts, Louis (2017)
    Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holo-metabolous insect vector.
  • Chen, Zhi-Hai; Qin, Xin-Cheng; Song, Rui; Shen, Yi; Chen, Xiao-Ping; Wang, Wen; Zhao, Yong-Xiang; Zhang, Jing-Shan; He, Jin-Rong; Li, Ming-Hui; Zhao, Xue-Hua; Liu, De-Wei; Fu, Xiao-Kang; Tian, Di; Li, Xing-Wang; Xu, Jianguo; Plyusnin, Alexander; Holmes, Edward C.; Zhang, Yong-Zhen (2014)
  • Suominen, Saara; Brauer, Verena S.; Rantala-Ylinen, Anne; Sivonen, Kaarina; Hiltunen, Teppo (2017)
    The toxicity of a harmful algal bloom is strongly determined by the relative abundance of non-toxic and toxic genotypes and might therefore be regulated by competition for growth-limiting resources. Here, we studied how the toxic Microcystis aeruginosa strain PCC 7806 and a non-toxic mutant compete for nitrogen and phosphorus under constant and pulsed nutrient supply. Our monoculture and competition experiments show that these closely related genotypes have distinct nutrient physiologies and that they differ in their ability to compete for nitrogen and phosphorus. The toxic wild type won the competition under nitrogen limitation, while the non-toxic mutant dominated under phosphorus limitation. Pulses of both nitrogen and phosphorus increased the dominance of the toxic genotype, which lead to an even faster competitive exclusion of the non-toxic genotype under nitrogen pulses and to coexistence of both genotypes under phosphorus pulses. Our findings indicate that the genotype level dynamics driven by resource competition can be an important factor in determining cyanobacterial bloom toxicity.
  • Kaasalainen, Ulla Susanna; Tuovinen, Veera; Mwachala, Geoffrey; Pellikka, Petri; Rikkinen, Jouko Kalevi (2021)
    Interactions within lichen communities include, in addition to close mutualistic associations between the main partners of specific lichen symbioses, also more elusive relationships between members of a wider symbiotic community. Here, we analyze association patterns of cyanolichen symbionts in the tropical montane forests of Taita Hills, southern Kenya, which is part of the Eastern Afromontane biodiversity hotspot. The cyanolichen specimens analyzed represent 74 mycobiont taxa within the order Peltigerales (Ascomycota), associating with 115 different variants of the photobionts genus Nostoc (Cyanobacteria). Our analysis demonstrates wide sharing of photobionts and reveals the presence of several photobiont-mediated lichen guilds. Over half of all mycobionts share photobionts with other fungal species, often from different genera or even families, while some others are strict specialists and exclusively associate with a single photobiont variant. The most extensive symbiont network involves 24 different fungal species from five genera associating with 38 Nostoc photobionts. The Nostoc photobionts belong to two main groups, the Nephroma-type Nostoc and the Collema/Peltigera-type Nostoc, and nearly all mycobionts associate only with variants of one group. Among the mycobionts, species that produce cephalodia and those without symbiotic propagules tend to be most promiscuous in photobiont choice. The extent of photobiont sharing and the structure of interaction networks differ dramatically between the two major photobiont-mediated guilds, being both more prevalent and nested among Nephroma guild fungi and more compartmentalized among Peltigera guild fungi. This presumably reflects differences in the ecological characteristics and/or requirements of the two main groups of photobionts. The same two groups of Nostoc have previously been identified from many lichens in various lichen-rich ecosystems in different parts of the world, indicating that photobiont sharing between fungal species is an integral part of lichen ecology globally. In many cases, symbiotically dispersing lichens can facilitate the dispersal of sexually reproducing species, promoting establishment and adaptation into new and marginal habitats and thus driving evolutionary diversification.
  • Susi, Hanna; Filloux, Denis; Frilander, Mildco J.; Roumagnac, Philippe; Laine, Anna-Liisa (2019)
    Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Aland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
  • Mull, Nathaniel; Jackson, Reilly; Sironen, Tarja; Forbes, Kristian M. (2020)
    The number of documented American orthohantaviruses has increased significantly over recent decades, but most fundamental research has remained focused on just two of them: Andes virus (ANDV) and Sin Nombre virus (SNV). The majority of American orthohantaviruses are known to cause disease in humans, and most of these pathogenic strains were not described prior to human cases, indicating the importance of understanding all members of the virus clade. In this review, we summarize information on the ecology of under-studied rodent-borne American orthohantaviruses to form general conclusions and highlight important gaps in knowledge. Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. Additionally, few studies have investigated the mechanisms underlying transmission routes and factors affecting the environmental persistence of orthohantaviruses, limiting our understanding of factors driving prevalence fluctuations. As landscapes continue to change, host ranges and human exposure to orthohantaviruses likely will as well. Research on the ecology of neglected orthohantaviruses is necessary for understanding both current and future threats to human health.
  • Vaisanen, Elina; Paloniemi, Minna; Kuisma, Inka; Lithovius, Väinö; Kumar, Arun; Franssila, Rauli; Ahmed, Kamruddin; Delwart, Eric; Vesikari, Timo; Hedman, Klaus; Soderlund-Venermo, Maria (2016)
    Two human parvoviruses were recently discovered by metagenomics in Africa, bufavirus (BuV) in 2012 and tusavirus (TuV) in 2014. These viruses have been studied exclusively by PCR in stool and detected only in patients with diarrhoea, although at low prevalence. Three genotypes of BuV have been identified. We detected, by in-house EIA, BuV1-3 IgG antibodies in 7/228 children (3.1%) and 10/180 adults (5.6%), whereas TuV IgG was found in one child (0.4%). All children and 91% of the adults were Finnish, yet interestingly 3/6 adults of Indian origin were BuV-IgG positive. By competition EIA, no cross-reactivity between the BuVs was detected, indicating that the BuV genotypes represent distinct serotypes. Furthermore, we analysed by BuV qPCR stool and nasal swab samples from 955 children with gastroenteritis, respiratory illness, or both, and found BuV DNA in three stools (0.3%) and for the first time in a nasal swab (0.1%). This is the first study documenting the presence of BuV and TuV antibodies in humans. Although the seroprevalences of both viruses were low in Finland, our results indicate that BuV infections might be widespread in Asia. The BuV-specific humoral immune responses appeared to be strong and long-lasting, pointing to systemic infection in humans.
  • Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Haggstrom, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A. (2013)
  • Pyöriä, Lari; Toppinen, Mari; Mantyla, Elina; Hedman, Lea; Aaltonen, Leena-Maija; Vihinen-Ranta, Maija; Ilmarinen, Taru; Soderlund-Venermo, Maria; Hedman, Klaus; Perdomo, Maria (2017)
    Parvovirus B19 (B19V) DNA persists lifelong in human tissues, but the cell type harbouring it remains unclear. We here explore B19V DNA distribution in B, T and monocyte cell lineages of recently excised tonsillar tissues from 77 individuals with an age range of 2-69 years. We show that B19V DNA is most frequent and abundant among B cells, and within them we find a B19V genotype that vanished from circulation 440 years ago. Since re-infection or re-activation are unlikely with this virus type, this finding supports the maintenance of pathogen-specific humoral immune responses as a consequence of B-cell long-term survival rather than continuous replenishment of the memory pool. Moreover, we demonstrate the mechanism of B19V internalization to be antibody dependent in two B-cell lines as well as in ex vivo isolated tonsillar B cells. This study provides direct evidence for a cell type accountable for B19V DNA tissue persistence.
  • Sasic Zoric, Ljiljana; Stahls, Gunilla; Dan, Mihajla (2019)
    Wolbachia is a widespread bacterial endosymbiont among arthropod species. It influences the reproduction of the host species and also mitochondrial DNA diversity. Until now there were only a few studies that detected Wolbachia infections in hoverflies (Diptera: Syrphidae), and this is the first broader study with the aim of examining the incidence of Wolbachia in the hoverfly genus Merodon. The obtained results indicate an infection rate of 96% and the presence of both Wolbachia supergroup A and B, which are characteristic for most of the infected arthropod species. Additionally, the presence of multiple Wolbachia strains in the Merodon aureus group species was detected and the mitochondrial DNA COI-based relationships of the group are discussed in the light of infection. Finally, we discuss plant-mediated horizontal transmission of Wolbachia strains among the studied hoverfly species.
  • Fitak, Robert Rodgers; Mohandesan, Elmira; Corander, Jukka; Yadamsuren, Adiya; Chuluunbat, Battsetseg; Abdelhadi, Omer; Raziq, Abdul; Nagy, Peter; Walzer, Chris; Faye, Bernard; Burger, Pamela Anna (2020)
    Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack secondary bottlenecks associated with breed development. By re-sequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, here we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pan-domestication set - and overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication. Robert R. Fitak et al. investigate the genetic basis for domestication in camels. They found that the positive selection of candidate domestication genes is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Their work provides insights to the evolutionary history of camels and genetics of domestication.
  • Pino-Bodas, Raquel; Stenroos, Soili (2021)
    The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.
  • Peck, Michael W.; Smith, Theresa J.; Anniballi, Fabrizio; Austin, John W.; Bano, Luca; Bradshaw, Marite; Cuervo, Paula; Cheng, Luisa W.; Derman, Yagmur; Dorner, Brigitte G.; Fisher, Audrey; Hill, Karen K.; Kalb, Suzanne R.; Korkeala, Hannu; Lindström, Miia; Lista, Florigio; Luquez, Carolina; Mazuet, Christelle; Pirazzini, Marco; Popoff, Michel R.; Rossetto, Ornella; Rummel, Andreas; Sesardic, Dorothea; Singh, Bal Ram; Stringer, Sandra C. (2017)
    Botulinum neurotoxins are diverse proteins. They are currently represented by at least seven serotypes and more than 40 subtypes. New clostridial strains that produce novel neurotoxin variants are being identified with increasing frequency, which presents challenges when organizing the nomenclature surrounding these neurotoxins. Worldwide, researchers are faced with the possibility that toxins having identical sequences may be given different designations or novel toxins having unique sequences may be given the same designations on publication. In order to minimize these problems, an ad hoc committee consisting of over 20 researchers in the field of botulinum neurotoxin research was convened to discuss the clarification of the issues involved in botulinum neurotoxin nomenclature. This publication presents a historical overview of the issues and provides guidelines for botulinum neurotoxin subtype nomenclature in the future.
  • Oversti, Sanni; Onkamo, Paivi; Stoljarova, Monika; Budowle, Bruce; Sajantila, Antti; Palo, Jukka U. (2017)
    In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000-5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the 'local' Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the 'immigrant' haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.
  • Nair, Abhilash; Nonaka, Etsuko; van Nouhuys, Saskya (2018)
    Climate change can increase spatial synchrony of population dynamics, leading to large-scale fluctuation that destabilizes communities. High trophic level species such as parasitoids are disproportionally affected because they depend on unstable resources. Most parasitoid wasps have complementary sex determination, producing sterile males when inbred, which can theoretically lead to population extinction via the diploid male vortex (DMV). We examined this process empirically using a hyperparasitoid population inhabiting a spatially structured host population in a large fragmented landscape. Over four years of high host butterfly metapopulation fluctuation, diploid male production by the wasp increased, and effective population size declined precipitously. Our multitrophic spatially structured model shows that host population fluctuation can cause local extinctions of the hyperparasitoid because of the DMV. However, regionally it persists because spatial structure allows for efficient local genetic rescue via balancing selection for rare alleles carried by immigrants. This is, to our knowledge, the first empirically based study of the possibility of the DMV in a natural host–parasitoid system.
  • Teikari, Jonna; Vicentini Popin, Rafael; Hou, Shengwei; Wahlsten, Matti; Hess, Wolfgang R.; Sivonen, Kaarina (2019)
    The Baltic Sea is a shallow basin of brackish water in which the spatial salinity gradient is one of the most important factors contributing to species distribution. The Baltic Sea is infamous for its annual cyanobacterial blooms comprised of Nodularia spumigena, Aphanizomenon spp., and Dolichospermum spp. that cause harm, especially for recreational users. To broaden our knowledge of the cyanobacterial adaptation strategies for brackish water environments, we sequenced the entire genome of Dolichospermum sp. UHCC 0315, a species occurring not only in freshwater environments but also in brackish water. Comparative genomics analyses revealed a close association with Dolichospermum sp. UHCC 0090 isolated from a lake in Finland. The genome closure of Dolichospermum sp. UHCC 0315 unraveled a mixture of two subtypes in the original culture, and subtypes exhibited distinct buoyancy phenotypes. Salinity less than 3 g L−1 NaCl enabled proper growth of Dolichospermum sp. UHCC 0315, whereas growth was arrested at moderate salinity (6 g L−1 NaCl). The concentrations of toxins, microcystins, increased at moderate salinity, whereas RNA sequencing data implied that Dolichospermum remodeled its primary metabolism in unfavorable high salinity. Based on our results, the predicted salinity decrease in the Baltic Sea may favor toxic blooms of Dolichospermum spp.
  • Adamo, Martino; Mammola, Stefano; Noble, Virgile; Mucciarelli, Marco (2020)
    We studied the ecology, distribution, and phylogeography of Tephroseris balbisiana, a rare plant whose range is centered to the South-Western Alps. Our aim was to assess the extent of intraspecific variability within the nominal species and the conservation status of isolated populations. We studied genetic diversity across the whole species range. We analyzed leaf traits, which are distinctive morphological characters within the Tephroseris genus. A clear pattern of genetic variation was found among populations of T. balbisiana, which clustered according to their geographic position. On the contrary, there was a strong overlap in the morphological space of individuals across the species' range, with few peripheral populations diverging in their leaf morphology. Studying habitat suitability by means of species distribution models, we observed that T. balbisiana range is primarily explained by solar radiation and precipitation seasonality. Environmental requirements could explain the genetic and morphological uniformity of T. balbisiana in its core distribution area and justify genetic, morphological, and ecological divergences found among the isolated populations of the Apennines. Our findings emphasize the need to account for the whole diversity of a species, comprising peripheral populations, in order to better estimate its status and to prioritize areas for its conservation.
  • Parratt, Steven R.; Barres, Benoit; Penczykowski, Rachel M.; Laine, Anna-Liisa (2017)
    Predicting and controlling infectious disease epidemics is a major challenge facing the management of agriculture, human and wildlife health. Co-evolutionarily derived patterns of local adaptation among pathogen populations have the potential to generate variation in disease epidemiology; however, studies of local adaptation in disease systems have mostly focused on interactions between competing pathogens or pathogens and their hosts. In nature, parasites and pathogens are also subject to attack by hyperparasitic natural enemies that can severely impact upon their infection dynamics. However, few studies have investigated whether this interaction varies across combinations of pathogen-hyperparasite strains, and whether this influences hyperparasite incidence in natural pathogen populations. Here, we test whether the association between a hyperparasitic fungus, Ampelomyces, and a single powdery mildew host, Podosphaera plantaginis, varies among genotype combinations, and whether this drives hyperparasite incidence in nature. Laboratory inoculation studies reveal that genotype, genotypexgenotype interactions and local adaptation affect hyperparasite infection. However, observations of a natural pathogen metapopulation reveal that spatial rather than genetic factors predict the risk of hyperparasite presence. Our results highlight how sensitive the outcome of biocontrol using hyperparasites is to selection of hyperparasite strains.