Exposure to Environmental Radionuclides Associates With Tissue-Specific Impacts on Telomerase Expression and Telomere Length

Telomeres, the protective structures at the ends of chromosomes, can be shortened when individuals are exposed to stress. In some species, the enzyme telomerase is expressed in adult somatic tissues, and potentially protects or lengthens telomeres. Telomeres can be damaged by ionizing radiation and oxidative stress, although the effect of chronic exposure to elevated levels of radiation on telomere maintenance is unknown for natural populations. We quantified telomerase expression and telomere length (TL) in different tissues of the bank vole Myodes glareolus, collected from the Chernobyl Exclusion Zone, an environment heterogeneously contaminated with radionuclides, and from uncontaminated control sites elsewhere in Ukraine. Inhabiting the Chernobyl Exclusion Zone was associated with reduced TL in the liver and testis, and upregulation of telomerase in brain and liver. Thus upregulation of telomerase does not appear to associate with longer telomeres but may reflect protective functions other than telomere maintenance or an attempt to maintain shorter telomeres in a stressful environment. Tissue specific differences in the rate of telomere attrition and apparent radiosensitivity weaken the intra-individual correlation in telomere length among tissues in voles exposed to radionuclides. Our data show that ionizing radiation alters telomere homeostasis in wild animal populations in tissue specific ways

Compensatory IgM to the Rescue: Patients with Selective IgA Deficiency Have Increased Natural IgM Antibodies to MAA-LDL and No Changes in Oral Microbiota

IgA is the most abundant Ab in the human body. However, most patients with selective IgA deficiency (SIgAD) are asymptomatic. IgM, and to lesser extent IgG Abs, are generally presumed to compensate for the lack of IgA in SIgAD by multiplying and adopting functions of IgA. We used data from the Northern Finland Birth Cohort 1966 to investigate whether SIgAD patients have differences in levels of natural Abs to oxidized epitopes compared with 20 randomly selected healthy controls. First, we screened the saliva and serum samples from the Northern Finland Birth Cohort 1966 cohort (n 5 1610) for IgA concentration. We detected five IgA-deficient subjects, yielding a prevalence of 0.3%, which is consistent with the general prevalence of 0.25% in the Finnish population. To detect natural Abs, we used malondialdehyde acetaldehyde–low-density lipoprotein (MAA–LDL), an Ag known to bind natural Abs. In this study, we show that natural secretory IgM and IgG Abs to MAA–DL were significantly increased in subjects with SIgAD. Given that secretory IgA is an important part of mucosal immune defense and that, in the gut microbiota, dysbiosis with SIgAD patients has been observed, we characterized the oral bacterial microbiota of the subjects with and without SIgAD using high-throughput 16S rRNA gene sequencing. We found no significant alterations in diversity and composition of the oral microbiota in subjects with SIgAD. Our data suggest that increased levels of secretory natural Abs in patients with SIgAD could be a compensatory mechanism, providing alternative first-line defense against infections and adjusting mucosal milieu to maintain a healthy oral microbiota. ImmunoHorizons, 2021, 5: 170–181.Peer reviewe

A boom‐or‐bust approach — the ‘Glass Cannon’ hypothesis in host microbiomes

In Focus: Dunphy, CM, Vollmer, SV, Gouhier, TC. (2021) Host–microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations. Journal of Animal Ecology, 90, 1044–1057. The importance of symbiotic microbial communities for the functioning of animal hosts is now well‐documented; however, the interactions between host microbiomes and stress are less well‐understood. Dunphy et al. used a common garden experiment to show that host–microbiomes vary in their resilience across different coral species. The authors then used mathematical modelling to provide novel evidence that species with microbiomes that are regulated by host processes are robust to perturbation from stressors, but that robustness comes at a higher cost to the host. Conversely, species with microbiomes that are regulated by microbial processes are generally much more resilient and cheaper to support, but when disrupted by external stressors, the communities break down entirely—these latter species are termed ‘glass cannons’. This novel hypothesis has important implications for how host microbiomes function in a rapidly changing world that exposes animal hosts to multiple biotic and abiotic perturbations

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

The effects of exposure to radionuclide contamination on microbiota of wild mammals

Abstract All animals host diverse microbial communities (bacteria, fungi, viruses, known as the microbiota) that inhabit external and internal surfaces of the host. Host-associated microbiota provide essential services to their hosts, such as provision of nutrients, protection against pathogens, and toxic compounds. As changes in the microbiota composition can impact delivery of these functions and thus host health, it is important to understand processes that shape host-associated microbiota. In this thesis, I assess the impacts of environmental contamination on the gut and skin microbiota (bacteria) of small mammals inhabiting areas affected by radionuclides derived from the Chernobyl (Ukraine) and Fukushima (Japan) nuclear accidents. I used marker gene sequencing and field studies to test (I) the effects of exposure to radionuclide contamination on the gut and (II) skin microbiota of the bank vole, Myodes glareolus. By conducting a capture-mark-recapture study, I tested (III) the effects of radiation exposure on the temporal dynamics of the bank vole gut microbiota. I also sampled two pairs of mouse species (Apodemus flavicollis, A. sylvaticus, A. speciosus, A. argenteus) that occur in sympatry in Chernobyl and Fukushima, to quantify (IV) the general influence of radiation exposure on the gut microbiota of rodents. These data indicate that chronic exposure to radionuclide contamination alters bank vole gut microbiota composition, yet has little notable impact on community composition of the skin microbiota: skin and gut microbiota thus respond to different environmental cues. Longitudinal data indicate that radiation exposure can constrain natural, temporal changes in the bank vole gut microbiota, which is potentially a sign of chronic stress. Also, I show that radiation exposure elicits comparable responses in the gut microbiota of different species of rodents, although host lifestyle can modulate the effects of exposure to radiation on gut microbiota composition. As such, exposure to environmental contaminants has clear potential to alter wildlife microbiota community composition. Given that the microbiota are pivotal to host health, it is important to quantify any microbiota changes in response to diverse anthropogenic disturbances if we are to understand the significance of host-environment interactions in a rapidly changing world.Tiivistelmä Eläinten mikrobiomi koostuu sen sisällä ja ulkopinnalla elävistä bakteeri-, sieni- ja virusyhteisöistä. Mikrobiomi tuottaa isäntäeliölle olennaisia ravinteita, sekä suojaa taudinaiheuttajia ja myrkyllisiä yhdisteitä vastaan. Koska muutokset mikrobiyhteisöissä voivat vaikuttaa isännän terveyteen, on tärkeää tutkia mikrobiomia muokkaavia tekijöitä. Väitöskirjassani tutkin saastuneen elinympäristön vaikutuksia suoliston ja ihon mikrobiomeihin (bakteerien yhteisöihin) pikkunisäkkäillä Tšernobylin (Ukraina) ja Fukushiman (Japani) ydinvoimalaonnettomuusalueilla. Laajoissa kenttätutkimuksissa selvitin ionisoivalle säteilylle altistumisen vaikutuksia metsämyyrän (Myodes glareolus) (I) suoliston ja (II) ihon mikrobiomeihin. Tutkin myös (III) säteilyaltistuksen vaikutusta ajallisiin muutoksiin metsämyyrän suolistomikrobiomissa pyynti-takaisinpyyntimenetelmällä. Lisäksi tutkin (IV) säteilyaltistuksen vaikutuksia laajemmin jyrsijöiden suolistomikrobiomiin käyttäen sympatrisia hiirilajeja Tšernobylissä (Apodemus flavicollis ja A. sylvaticus) sekä Fukushimassa (A. speciosus ja A. argenteus). Tulosteni mukaan pitkäaikainen altistuminen ympäristön säteilylle muokkaa metsämyyrien suolistomikrobiomin koostumusta, mutta ei vaikuta merkittävästi ihon mikrobiomiin, osoittaen että ihon ja suoliston mikrobiomeihin vaikuttavat erilaiset ympäristötekijät. Säteilyaltistus voi myös rajoittaa metsämyyräyksilöiden suolistomikrobiomissa tapahtuvia luonnollisia ajallisia muutoksia, mahdollisesti johtuen pitkäaikaisesta stressialtistuksesta. Lisäksi osoitan, että ympäristösäteilylle altistumisen vaikutukset suolistomikrobiomiin ovat samankaltaisia eri jyrsijälajeilla, mutta mikrobiomiin vaikuttavat myös lajien väliset erot elintavoissa. Tutkimukseni siis osoitti, että ympäristön saasteet voivat muokata luonnonvaraisten eläinten mikrobiomien koostumusta. Isäntäeliön ja sen ympäristön vuorovaikutus voi oleellisesti vaikuttaa eläinyksilöiden ja niiden populaatioiden terveyteen ja edelleen niiden kykyyn vastata ihmisen aiheuttamiin ympäristömuutoksiin

Skin and gut microbiomes of a wild mammal respond to different environmental cues

Abstract Background: Animal skin and gut microbiomes are important components of host fitness. However, the processes that shape the microbiomes of wildlife are poorly understood, particularly with regard to exposure to environmental contaminants. We used 16S rRNA amplicon sequencing to quantify how exposure to radionuclides impacts the skin and gut microbiota of a small mammal, the bank vole Myodes glareolus, inhabiting areas within and outside the Chernobyl Exclusion Zone (CEZ), Ukraine. Results: Skin microbiomes of male bank voles were more diverse than females. However, the most pronounced differences in skin microbiomes occurred at a larger spatial scale, with higher alpha diversity in the skin microbiomes of bank voles from areas within the CEZ, whether contaminated by radionuclides or not, than in the skin microbiomes of animals from uncontaminated locations outside the CEZ, near Kyiv. Similarly, irrespective of the level of radionuclide contamination, skin microbiome communities (beta diversity) showed greater similarities within the CEZ, than to the areas near Kyiv. Hence, bank vole skin microbiome communities are structured more by geography than the level of soil radionuclides. This pattern presents a contrast with bank vole gut microbiota, where microbiomes could be strikingly similar among distant (~ 80 km of separation), uncontaminated locations, and where differences in microbiome community structure were associated with the level of radioactivity. We also found that the level of (dis)similarity between the skin and gut microbiome communities from the same individuals was contingent on the potential for exposure to radionuclides. Conclusions: Bank vole skin and gut microbiomes have distinct responses to similar environmental cues and thus are structured at different spatial scales. Our study shows how exposure to environmental pollution can affect the relationship between a mammalian host’s skin and gut microbial communities, potentially homogenising the microbiomes in habitats affected by pollution

Two Hundred and Fifty-Four Metagenome-Assembled Bacterial Genomes From the Bank Vole Gut Microbiota

Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota

Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents.peerReviewe

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota.

Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents

Does intraspecific variation in rDNA copy number affect analysis of microbial communities?

Abstract Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to profile microbial communities. However, the rDNA is dynamic and can exhibit substantial interspecific and intraspecific variation in copy number in prokaryotes and, especially, in microbial eukaryotes. As change in rDNA copy number is a common response to environmental change, rDNA copy number is not necessarily a property of a species. Variation in rDNA copy number, especially the capacity for large intraspecific changes driven by external cues, complicates analyses of rDNA amplicon sequence data. We highlight the need to (i) interpret amplicon sequence data in light of possible interspecific and intraspecific variation, and (ii) examine the potential plasticity in rDNA copy number as an important ecological factor to better understand how microbial communities are structured in heterogeneous environments