RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

Improving the framework for assessment of ecological change in the Arctic: A circumpolar synthesis of freshwater biodiversity

1. Climate warming and subsequent landscape transformations result in rapid ecological change in Arctic freshwaters. Here we provide a synthesis of the diversity of benthic diatoms, plankton, macrophytes, macroinvertebrates, and fish in Arctic freshwaters.2. We developed a multi-organism measure of alpha diversity to characterise circumpolar spatial patterns and their environmental correlates, and we assessed ecoregion-level beta diversity for all organism groups across the Arctic.3. Alpha diversity was lowest at high latitudes and elevations and where dispersal barriers exist. Diversity was positively related to temperature, and both temperature and connectivity limited diversity on high latitude islands. Beta diversity was highly variable among ecoregions for most organism groups, ranging from 0 (complete similarity) to 1 (complete dissimilarity). The high degree of dissimilarity within many ecoregions illustrates the uniqueness of many Arctic freshwater communities.4. Northward range expansion of freshwater taxa into Arctic regions may lead to increased competition for cold-stenothermic and cold-adapted species, and ultimately lead to the extinction of unique Arctic species. Societal responses to predicted impacts include: (1) actions to improve detection of changes (e.g., harmonised monitoring, remote sensing) and engagement with Arctic residents and Indigenous Peoples; and (2) actions to reduce the impact of unwanted changes (e.g., reductions of CO2 emissions, action against the spread of invasive species).5. Current Arctic freshwater monitoring shows large gaps in spatial coverage, while time series data are scarce. Arctic countries should develop an intensified, long-term monitoring programme with routine reporting. Such an approach will allow detection of long-term changes in water quality, biodiversity, and ecosystem services of Arctic freshwaters

First circumpolar assessment of Arctic freshwater phytoplankton and zooplankton diversity : Spatial patterns and environmental factors

Arctic freshwaters are facing multiple environmental pressures, including rapid climate change and increasing land-use activities. Freshwater plankton assemblages are expected to reflect the effects of these stressors through shifts in species distributions and changes to biodiversity. These changes may occur rapidly due to the short generation times and high dispersal capabilities of both phyto- and zooplankton. Spatial patterns and contemporary trends in plankton diversity throughout the circumpolar region were assessed using data from more than 300 lakes in the U.S.A. (Alaska), Canada, Greenland, Iceland, the Faroe Islands, Norway, Sweden, Finland, and Russia. The main objectives of this study were: (1) to assess spatial patterns of plankton diversity focusing on pelagic communities; (2) to assess dominant component of beta diversity (turnover or nestedness); (3) to identify which environmental factors best explain diversity; and (4) to provide recommendations for future monitoring and assessment of freshwater plankton communities across the Arctic region. Phytoplankton and crustacean zooplankton diversity varied substantially across the Arctic and was positively related to summer air temperature. However, for zooplankton, the positive correlation between summer temperature and species numbers decreased with increasing latitude. Taxonomic richness was lower in the high Arctic compared to the sub- and low Arctic for zooplankton but this pattern was less clear for phytoplankton. Fennoscandia and inland regions of Russia represented hotspots for, respectively, phytoplankton and zooplankton diversity, whereas isolated regions had lower taxonomic richness. Ecoregions with high alpha diversity generally also had high beta diversity, and turnover was the most important component of beta diversity in all ecoregions. For both phytoplankton and zooplankton, climatic variables were the most important environmental factors influencing diversity patterns, consistent with previous studies that examined shorter temperature gradients. However, barriers to dispersal may have also played a role in limiting diversity on islands. A better understanding of how diversity patterns are determined by colonisation history, environmental variables, and biotic interactions requires more monitoring data with locations dispersed evenly across the circumpolar Arctic. Furthermore, the importance of turnover in regional diversity patterns indicates that more extensive sampling is required to fully characterise the species pool of Arctic lakes.Peer reviewe

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes ∼11 500 candidate binding sites for ∼400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes

Figure 4 in Fauna of microcrustaceans (Cladocera: Copepoda) of shallow freshwater ecosystems of Wrangel Island (Russian Far East)

Figure 4. Dendrogram for hierarchical clustering (group average) of faunas of different arctic regions.Published as part of Novichkova, Anna A. & Chertoprud, Elena S., 2015, Fauna of microcrustaceans (Cladocera: Copepoda) of shallow freshwater ecosystems of Wrangel Island (Russian Far East), pp. 2955-2968 in Journal of Natural History 49 (45) on page 2962, DOI: 10.1080/00222933.2015.1056269, http://zenodo.org/record/400237

Crustaceans in the Meiobenthos and Plankton of the Thermokarst Lakes and Polygonal Ponds in the Lena River Delta (Northern Yakutia, Russia): Species Composition and Factors Regulating Assemblage Structures

Information about invertebrates in the low-flow water bodies of northeastern Siberia is far from complete. In particular, little is known about crustaceans—one of the main components of meiobenthic and zooplanktonic communities. An open question is which environmental factors significantly affect the crustaceans in different taxonomic and ecological groups? Based on the data collected on the zooplankton and meiobenthos in the tundra ponds in the southern part of the Lena River Delta, analysis of the crustacean taxocene structure was performed. In total, 59 crustacean species and taxa were found. Five of these are new for the region. The species richness was higher in the large thermokarst lakes than in the small water bodies, and the abundance was higher in small polygonal ponds than in the other water bodies. Variations in the Cladocera assemblages were mainly affected by the annual differences in the water temperature; non-harpacticoid copepods were generally determined by hydrochemical factors; and for Harpacticoida, the macrophyte composition was significant. Three types of the crustacean assemblages characteristic of different stages of tundra lake development were distinguished. The hypothesis that the formation of crustacean taxocenes in the Lena River Delta is mainly determined by two types of ecological filters, temperature and local features of the water body, was confirmed

Compositionı characteristics and long-term variability of the freshwater microcrustacean fauna of the Faroe Islands

Chertoprud, Anna A. Novichkova ı Elena S., Azovsky, Andrey I. (2019): Compositionı characteristics and long-term variability of the freshwater microcrustacean fauna of the Faroe Islands. Journal of Natural History 53 (39): 2449-2465, DOI: 10.1080/00222933.2019.170458

New and previously known species of Copepoda and Cladocera (Crustacea) from Svalbard, Norway – who are they and where do they come from?

Arctic landscapes are characterised by an immense number of fresh and brackish water habitats – lakes, ponds and puddles. Due to a rather harsh environment, there is a limited number of species inhabiting these ecosystems. Recent climate-driven regime shifts impact and change Arctic biological communities. New species may appear, and existing communities may become supressed or even disappear, depending on how ongoing changes match their ecological needs. This study provides data on presently existing and probably recently arrived fresh and brackish water microcrustacean species in the Norwegian High Arctic - Svalbard archipelago. The study focused on two taxonomic groups, Cladocera and Copepoda and altogether we found seven taxa new for Svalbard: Alona werestschagini, Polyphemus pediculus, Diaptomus sp., Diacyclops abyssicola, Nitokra spinipes, Epactophanes richardi and Geeopsis incisipes. Compared with an existing overview for the area, our study increased the number of species by more than 20 %, and some of the new species have never been found that far north. Finally, we present a complete and critically updated revised species list of fresh and brackish water cladocerans and copepods for Svalbard.publishedVersio

FREMONEC: Effect of climate change and related stressors on fresh and brackish water ecosystems in Svalbard. A Norwegian and Russian joint scientific project

Dimante-Deimantovica, I., Chertoprud, M., Chertoprud, E., Christoffersen, K.S., Novichkova, A. & Walseng, B. 2015. FREMONEC: Effect of climate change and related stressors on fresh and brackish water ecosystems in Svalbard. A Norwegian and Russian joint scientific project. - NINA Report 1218. 40 pp. This report summarizes the results of the Russian-Norwegian collaboration project FREMONEC which was established as part of POLRES (Polar Research sub-program NORRUSS) with the aim to stimulate bilateral cooperation on polar research. Researchers from The Norwegian Insti-tute for Nature Research and M. V. Lomonosov Moscow State University have studied the effects of climate change and related stressors on fresh and brackish water habitats, by using inverte-brates as biological quality elements. Both partners were involved in preparing the study design, as well as participating in meetings, fieldwork (2014 and 2015) and analyzing/reporting of col-lected material. Altogether, 75 localities in Isfjorden and Kongsfjorden areas, including both lotic and lentic waters, were sampled. pH varied between 6.2 and 9.5 and conductivity from < 0,01 to ˃ 10000 μS/cm. In general, biodiversity was low, especially when we compare Svalbard with other areas in the high and low Arctic. Still this survey revealed 6 microcrustacean taxa new to Svalbard: Polyphemus pediculus, Diaptomidae sp., Diacyclops abyssicola, Epactophanes rich-ardi, Nitokra spinipes and Geeopsis incisipes. Most likely, some of these newcomers are directly or indirectly linked to the recent climate warming (obtained results were compared with old liter-ature data). For macrozoobenthos it seemed that the origin of habitat, temperature, substrate type and water velocity were of importance. The number of crustaceans increased with the age of the localities (distance to the retreating glacier). For instance, the youngest habitats close to the glacier had the lowest number of copepod species and no cladocerans. The fauna in ‘urban’ ponds near human settlements did not differ from non-urban habitats. In the urban ponds, birds seem to be a more important factor than anthropogenic activities, contributing to diversity. As part of this project, one bachelor and one PhD student completed their theses. The network building between Norwegian and Russian research groups, which has included thematic areas relevant for both countries, has been a positive experience for both partners. Further, new knowledge on Svalbard’s biodiversity might give a contribution to future Arctic Freshwater Biodi-versity Monitoring activities and to the implementation of integrated and sustainable Arctic fresh-water ecosystems management. Because of FREMONEC, new collaboration projects and dis-semination activities have also been initiated (projects NORUSVA and BRANTA-DULCIS)

Assemblages of Meiobenthic and Planktonic Microcrustaceans (Cladocera and Copepoda) from Small Water Bodies of Mountain Subarctic (Putorana Plateau, Middle Siberia)

The Putorana Plateau (Krasnoyarsk Territory, Russia) is one of the largest mountainous regions of subarctic Eurasia. Studies of aquatic ecosystems of this are far from complete. In particular, microcrustaceans (Cladocera и Copepoda) of the Putorana Plateau are poorly investigated, although they are one of the main components of meiobenthic and zooplanktonic communities and a target for monitoring of the anthropogenic influence and climate change. An open question is a biogeographical status of the crustacean fauna of the plateau. Additionally, it is unknown which environmental factors significantly affect benthic and planktonic crustacean assemblages? Based on the samples collected in tundra and forest tundra ponds in the western and central parts of the plateau, analysis of the composition of crustacean fauna and factors regulating the assemblage structure was performed. In total, 36 Cladocera and 24 Copepoda species were found. Of these, 23 taxa are new for the region, and four are new to science. Species richness of Copepoda is higher in the central part and on the western slopes of the plateau than in foothills, while number of the Cladocera species in contrast decreases in mountainous areas. Variations in meiobenthic assemblages are due to the research area, type of water supply and less affected by altitude above sea level. For planktonic assemblages the size of the water body and, to a lesser degree, by macrophytes species composition was significant. Almost 12.8% of microcrustacean species of the Putorana Plateau can be attributed to glacial relics. Crustacean fauna of the Putorana Plateau has a high species richness and distinguishes significantly from the fauna of both western and eastern regions of the Arctic. The specifics of faunal composition of the region are connected to the climatic features of Middle Siberia and the retaining of the Pleistocene fauna in some glacial refugia