Endemic Amphipod Research Articles

THE FIRST ASSESMENT OF THE ANTIOXIDANT POTENTIAL OF ACTINOBACTERIA ASSOSIATED WITH BAIKAL ENDEMIC AMPHIPODS

The study obtained the first materials confirming the hypothesis that actinobacteria associated with Baikal endemic amphipods can be oxyphils and synthesize new natural compounds with antioxidant activity.

Microbial community associated with Baicalian crustacea near gas-oil deepwater discharges

Using scanning electron microscopy we investigated the epibiotic associations of peritrichial sessile ciliates of the Lagenophrys (Ciliophora: Lagenoprydae) and prokaryotes of various morphologies on the surface of endemic amphipods Macropereiopus florii (Dybowsky 1874) and ostracods Candona (Candonidae). We noted biofouling and mineralization in the areas of formation of a bacterial biofilm, which includes Fe, P, and other elements. High-throughput sequencing on the Illumina MiSeq platform showed the presence of such bacterial phyla as Actinobacteria, Gracilibacteria, Cyanobacteria, Proteobacteria, Bacteroidetes in the ostracod microbiome, of which the latter two were dominant. Sequence analysis of the 16S rRNA gene fragment showed epibiotic microorganisms that are related to the colorless sulfur bacteria Thiothrix sp. More than 50% of all sequences were attributed to endosymbiont bacteria of the genus Rickettsia, and the presence of endosymbionts of the genus Ca. Cardinium was shown for the first time for Baikal ostracods.

Spectral sensitivity of the visual system of endemic Baikal amphipods

In this work, we attempted to explore the visual system of Baikal endemic amphipods with behavioral experiments. These data show that a littoral species Eulimnogammarus cyaneus can sense most wavelengths in the human-visible range, while in the case of a deep-water species Ommatogammarus flavus we did not see any response to light.

Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods

The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed.The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated tRNA genes overlooked by using less specific Metazoa-wide models. The application of these models for mt tRNA gene prediction will be useful for the correct annotation of mt genomes of amphipods and probably other crustaceans.

Diet influence on mechanisms of non-specific stress-response in Baikal endemic amphipod species during long-term laboratory exposure

Abstract The purpose of this study was to estimate one of the important aspects of amphipod laboratory culturing — the effect of different types of nutrition on the key biochemical markers widely used in biomonitoring. The study was performed with the Baikal endemic amphipod species Eulimnogammarus verrucosus (Gerstfeldt, 1858), E. cyaneus (Dybowski, 1874), and Gmelinoides fasciatus (Stebbing, 1899). These species are characterized by different ecological properties and evolutionary history. The results of the study demonstrate that a long-term laboratory exposure to different diets has a direct effect on vital and physiological parameters of the species’ adaptation (mortality, weight, protein concentration). Also, feeding imposes its influence on the common stress-markers of oxidative stress (activities of peroxidase, catalase, glutathione S-transferase), and on anaerobic metabolism (activity of lactate dehydrogenase) in Baikal amphipods, and this effect has a species-specific character. The results should be taken into consideration in future ecophysiological experiments performed with amphipods.

Diversity of culturable actinobacteria associated with deepwater endemic amphipods of Lake Baikal and study of their biosynthetic capabilities

Lake Baikal’s ecosystem is among the oldest lacustrine ecosystems on the planet with a diverse and unique flora and fauna. Amphipods (Amphipoda, Crustacea) are one of the most diverse groups among the lake’s invertebrate animals. The lake contains more than 350 species and subspecies of amphipods, and each of these species play a significant role in the lake’s food webs. However, their relationships with microorganisms are poorly investigated, which leaves gaps in understanding the relations between aquatic crustaceans and bacteria. We studied the diversity of a specific group of culturable microorganisms (Actinobacteria), and their possible relations with deepwater endemic amphipods present in Lake Baikal. We found that while 73% of the isolated strains belong to the widely distributed genus of Streptomyces, 27% of the isolates belong to rare genera such as Amycolatopsis, Micromonospora, and Pseudonocardia. Fifty-three percent of the studied strains expressed antibiotic activity against Gram-positive bacteria and possess polyketide synthase (PKS) genes. Thus, Actinobacteria associated with Baikal’s endemic deepwater amphipods might both protect amphipods against pathogenic microorganisms and be an untapped source of new natural products with biosynthetic potential.

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods

BackgroundLake Baikal is one of the oldest freshwater lakes and has constituted a stable environment for millions of years, in stark contrast to small, transient bodies of water in its immediate vicinity. A highly diverse endemic endemic amphipod fauna is found in one, but not the other habitat. We ask here whether differences in stress response can explain the immiscibility barrier between Lake Baikal and non-Baikal faunas. To this end, we conducted exposure experiments to increased temperature and the toxic heavy metal cadmium as stressors.ResultsHere we obtained high-quality de novo transcriptome assemblies, covering mutiple conditions, of three amphipod species, and compared their transcriptomic stress responses. Two of these species, Eulimnogammarus verrucosus and E. cyaneus, are endemic to Lake Baikal, while the Holarctic Gammarus lacustris is a potential invader.ConclusionsBoth Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions.

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species

BackgroundThe ancient Lake Baikal is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies. We determined the genetic diversity within the endemic littoral amphipod species Eulimnogammarus verrucosus, E. cyaneus and E. vittatus and investigated whether within those species genetically separate populations occur across Lake Baikal. Gammarus lacustris from water bodies in the Baikal area was examined for comparison.ResultsGenetic diversities within a species were determined based on fragments of cytochrome c oxidase I (COI) and for E. verrucosus additionally of 18S rDNA. Highly location-specific haplogroups of E. verrucosus and E. vittatus were found at the southern and western shores of Baikal that are separated by the Angara River outflow; E. verrucosus from the eastern shore formed a further, clearly distinct haplotype cluster possibly confined by the Selenga River and Angarskiy Sor deltas. The genetic diversities within these haplogroups were lower than between the different haplogroups. Intraspecific genetic diversities within E. verrucosus and E. vittatus with 13 and 10%, respectively, were similar to interspecies differences indicating the occurrence of cryptic, morphologically highly similar species; for E. verrucosus this was confirmed with 18S rDNA. The haplotypes of E. cyaneus and G. lacustris specimens were with intraspecific genetic distances of 3 and 2%, respectively, more homogeneous indicating no or only recent disruption of gene flow of E. cyaneus across Baikal and recent colonization of water bodies around Baikal by G. lacustris.ConclusionsOur finding of separation of subgroups of Baikal endemic amphipods to different degrees points to a species-specific ability of dispersal across areas with adverse conditions and to potential geographical dispersal barriers in Lake Baikal.

Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods

Heat shock proteins/cognates 70 are chaperones essential for proper protein folding. This protein family comprises inducible members (Hsp70s) with expression triggered by the increased concentration of misfolded proteins due to protein-destabilizing conditions, as well as constitutively expressed cognate members (Hsc70s). Previous works on non-model amphipod species Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, both endemic to Lake Baikal in Eastern Siberia, have only revealed a constitutively expressed form, expression of which was moderately further induced by protein-destabilizing conditions. Here we describe heat-inducible hsp70s in these species. Contrary to the common approach of using sequence similarity with hsp/hsc70 of a wide spectrum of organisms and some characteristic features, such as absence of introns within genes and presence of heat shock elements in their promoter areas, the present study is based on next-generation sequencing for the studied or related species followed by differential expression analysis, quantitative PCR validation and detailed investigation of the predicted polypeptide sequences. This approach allowed us to describe a novel type of hsp70 transcripts that overexpress in response to heat shock. Moreover, we propose diagnostic sequence features of this Hsp70 type for amphipods. Phylogenetic comparisons with different types of Hsp/Hsc70s allowed us to suggest that the hsp/hsc70 gene family in Amphipoda diversified into cognate and heat-inducible paralogs independently from other crustaceans. Thus, the cognate and inducible hsp70 types in distant taxa may not be recognized by sequence similarity.

Hemolymph of Baikal endemic crustacean Eulimnogammarus verrucosus as a source for novel natural products

Event Abstract Back to Event Hemolymph of Baikal endemic crustacean Eulimnogammarus verrucosus as a source for novel natural products Denis Axenov-Gribanov1, 2*, Eugenii Protasov1, Polina Drozdova1, Kseniya Vereshchagina1, Yuliya Lubyaga1, Zhanna Shatilina1 and Maxim Timofeyev1 1 Irkutsk State University, Russia 2 Baikal Research Center, Russia Background Antibiotic resistance and targeted therapy are one of the most important and worldwide issues. Extreme and unusual ecosystems such as Lake Baikal and its inhabitant are considered as potential tools for the discovery of novel natural products with biological activities. The aim of this study was to assess the possibility to use Baikal endemic amphipods as a source for screening of novel natural products. Methods Analysis of hemolymph from an amphipod Eulimnogammarus verrucosus by HPLC-MS was performed for the first time and allowed us to find a number of natural products with new molecular mass values for Baikal endemic macroinvertebrates. Results We identified a compound as chrysin by comparison of MS1, MS2 profiles and molecular masses of natural products registered in Dictionary of Natural Products and MZ-cloud databases. Also, we found a new compound with a mass of 493.80277 Da and a number of antimicrobial peptides circulating in the amphipod hemolymph. Conclusion Thus, we confirmed that the hemolymph of Baikal endemic crustacean E. verrucosus is a source of novel natural products and could have biotechnological value for pharmacy and biomedicine. Acknowledgements This study was carried out with partial financial support of the RSF project (18-74-00018), RFBR project (16-34-60060), projects of the Ministry of Education and Science of the Russian Federation 6.9654.2017/8.9, 6.12738.2018/12.2, 6.12736.2018/12.2, and the Lake Baikal Foundation. Keywords: Baikal, amphipods, endemics, Natural Products, Eulimnogammarus verrucosus Conference: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”, Putrajaya, Malaysia, 3 Dec - 5 Feb, 2019. Presentation Type: Poster Presentation Topic: Infectious diseases Citation: Axenov-Gribanov D, Protasov E, Drozdova P, Vereshchagina K, Lubyaga Y, Shatilina Z and Timofeyev M (2019). Hemolymph of Baikal endemic crustacean Eulimnogammarus verrucosus as a source for novel natural products. Front. Pharmacol. Conference Abstract: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”. doi: 10.3389/conf.fphar.2019.63.00041 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 30 Sep 2018; Published Online: 17 Jan 2019. * Correspondence: Mr. Denis Axenov-Gribanov, Irkutsk State University, Irkutsk, Russia, Denis.axengri@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev Google Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev Google Scholar Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev PubMed Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Long-term physico-chemical and faunal changes in a small, rural South African estuary

The Palmiet Estuary is a small, rural estuary in the Western Cape that only closes briefly during dry summers. The system was previously surveyed during 1979 to 1980 and we repeated the survey in April 2015 (mouth closed) and September 2015 (mouth open). Salinity, temperature, pH and oxygen saturation were measured, and invertebrate and fish faunas surveyed. Physico-chemical characteristics have undergone little directional change, apart from an apparent increase in pH, possibly as a result of changes in land use and application of fertilisers and pesticides in the catchment. Invertebrate species richness increased from 31 to 40 species, despite lower sampling effort in 2015. Most changes were among rare species, or were readily explained by changes in mouth condition and water chemistry. We also confirmed a substantial range extension of the tropical crab, Varuna litterata, rediscovered the locally endemic amphipod, Quadrivisio aviceps, and reported several new distribution records. Gastropods had virtually disappeared from the system, whereas the previously unreported bivalve, Brachidontes virgilae, had become abundant. Overall, fish diversity dropped from 19 to 11 species, but this can largely be ascribed to differ- ences in sampling frequency, season and mouth state. Comparisons of samples from like months showed the fish assemblage to have remained fairly stable, despite changes in inflowing water chemistry and infection of fish by the pathogenic water mould, Aphanomyces invadans. Bird abundance and diversity increased substantially. No alien invertebrate or fish species were recorded. Accordingly, in marked contrast to other smaller estuaries in the region, the Palmiet Estuary has remains in relatively good condition.

The Mechanisms for Genetic Diversity of Baikal Endemic Amphipod Gmelinoides fasciatus: Relationships between the Population Processes and Paleoclimatic History of the Lake

Amphipods of the species Gmelinoides fasciatus are one of the dominant species in the littoral zone community of Lake Baikal. Earlier, on the basis of the analysis of the mitochondrial COX1 gene, four isolated populations within the species range were identified, between which there were no distinct geographical barriers. In the present study, a phylogenetic reconstruction of the evolutionary history of G. fasciatus with the molecular clock hypothesis is carried out. The population divergence time is dated back to the onset of global climate changes on the Pleistocene–Pliocene boundary at 1.8–2.3 Ma. As a result, the estimated substitution rate in the COX1 gene for G. fasciatus was 1.2–2.4% of substitutions per Myr, which corresponded to the values determined for other groups of invertebrates. It was demonstrated that geographical barriers that formed the populations of G. fasciatus periodically appeared and disappeared in the past, resulting from climate changes associated with the periods of global cooling and warming.

Genetic diversity of Microsporidia in the circulatory system of endemic amphipods from different locations and depths of ancient Lake Baikal.

Endemic amphipods (Amphipoda, Crustacea) of the most ancient and large freshwater Lake Baikal (Siberia, Russia) are a highly diverse group comprising >15% of all known species of continental amphipods. The extensive endemic biodiversity of Baikal amphipods provides the unique opportunity to study interactions and possible coevolution of this group and their parasites, such as Microsporidia. In this study, we investigated microsporidian diversity in the circulatory system of 22 endemic species of amphipods inhabiting littoral, sublittoral and deep-water zones in all three basins of Lake Baikal. Using molecular genetic techniques, we found microsporidian DNA in two littoral (Eulimnogammarus verrucosus, Eulimnogammarus cyaneus), two littoral/sublittoral (Pallasea cancellus, Eulimnogammarus marituji) and two sublittoral/deep-water (Acanthogammarus lappaceus longispinus, Acanthogammarus victorii maculosus) endemic species. Twenty sequences of the small subunit ribosomal (SSU) rDNA were obtained from the haemolymph of the six endemic amphipod species sampled from 0–60 m depths at the Southern Lake Baikal’s basin (only the Western shore) and at the Central Baikal. They form clusters with similarity to Enterocytospora, Cucumispora, Dictyocoela, and several unassigned Microsporidia sequences, respectively. Our sequence data show similarity to previously identified microsporidian DNA from inhabitants of both Lake Baikal and other water reservoirs. The results of our study suggest that the genetic diversity of Microsporidia in haemolymph of endemic amphipods from Lake Baikal does not correlate with host species, geographic location or depth factors but is homogeneously diverse.

Investigation of proteome of Baikal endemic amphipod Eulimnogammarus cyaneus (Dybowsky, 1874) using LC-MS

Investigation of proteome of Baikal endemic amphipod Eulimnogammarus cyaneus (Dybowsky, 1874) using LC-MS

Физиологические и биохимические маркеры стресс-ответа эндемичных байкальских амфипод: современное состояние и перспективы исследований

Физиологические и биохимические маркеры стресс-ответа эндемичных байкальских амфипод: современное состояние и перспективы исследований

Accumulation and exchange of parasites during adaptive radiation in an ancient lake

In the ancient Lake Baikal, Russia, amphipod crustaceans have undergone a spectacular adaptive radiation, resulting in a diverse community of species. A survey of microsporidian parasites inhabiting endemic and non-endemic amphipod host species at the margins of Lake Baikal indicates that the endemic amphipods harbour many microsporidian parasite groups associated with amphipods elsewhere in Eurasia. While these parasites may have undergone a degree of adaptive radiation within the lake, there is little evidence of host specificity. Furthermore, a lack of reciprocal monophyly indicates that exchanges of microsporidia between Baikalian and non-Baikalian hosts have occurred frequently in the past and may be ongoing. Conversely, limitations to parasite exchange between Baikalian and non-Baikalian host populations at the margins of the lake are implied by differences in parasite prevalence and lack of shared microsporidian haplotypes between the two host communities. While amphipod hosts have speciated sympatrically within Lake Baikal, the parasites appear instead to have accumulated, moving into the lake from external amphipod populations on multiple occasions to exploit the large and diverse community of endemic amphipods in Lake Baikal.

Crude oil at concentrations considered safe promotes rapid stress-response in Lake Baikal endemic amphipods

The current study evaluated the possible toxic effects of the water-soluble fraction of crude oil on the general cellular stress-response mechanisms of two dominant representatives of Lake Baikal’s littoral community, the endemic amphipod species Eulimnogammarus verrucosus and E. cyaneus. The acute toxicity effects on the cellular stress-response mechanisms of amphipods were studied in the laboratory by exposing amphipods in water from Lake Baikal to addition of a water-soluble fraction of crude oil at concentrations considered safe for the aquatic environment. The present study found that even short-term exposure to a water-soluble fraction of crude oil at concentration of 50 µg/L, established as the threshold limit for fishery and aquaculture water reservoirs in the Russian Federation, directly affected the general stress-response markers HSP70 and lipid peroxidation and significantly changed the activity of antioxidant enzymes in both studied species. This result confirms the high sensitivity of Baikal endemics to crude oil. Thus, it also indicates that established standards and threshold limit values of oil concentrations estimated for ecological monitoring of general water reservoirs cannot be applied directly to the unique Lake Baikal ecosystem.

Bioaccumulation of persistent organic pollutants in the deepest ocean fauna.

The legacy and reach of anthropogenic influence is most clearly evidenced by its impact on the most remote and inaccessible habitats on Earth. Here we identify extraordinary levels of persistent organic pollutants in the endemic amphipod fauna from two of the deepest ocean trenches (>10,000 metres). Contaminant levels were considerably higher than documented for nearby regions of heavy industrialization, indicating bioaccumulation of anthropogenic contamination and inferring that these pollutants are pervasive across the world's oceans and to full ocean depth.

Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection.

Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two nonendemic outgroups, we report a revised phylogeny of this species flock and analyse evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armour and reduction in appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters.

Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia.

Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans. Specifically, we report genome size estimates for 36 species of Baikal amphipods, and examine the relationship between genome size, body size, and the maximum depths at which the amphipods are found in the lake. Genome sizes ranged nearly 8-fold in this sample of amphipod species, from 2.15 to 16.63 pg, and there were significant, positive, phylogenetically corrected relationships between genome size, body size, maximum depth, and diversification rate among these species. Our results suggest that major genomic changes, including transposable element proliferation, have accompanied speciation that was driven by selection for differences in body size and habitat preference in Lake Baikal amphipods.