Publications by authors named "Elena Kupriyanova"

40 Publications

Laminatubus (Serpulidae, Annelida) from eastern Pacific hydrothermal vents and methane seeps, with description of two new species.

Zootaxa 2021 Jan 20;4915(1):zootaxa.4915.1.1. Epub 2021 Jan 20.

Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla CA, 92093-0202, USA.

The bathyal serpulid Laminatubus alvini ten Hove Zibrowius, 1986 was described from the periphery of hydrothermal vents of the Galapagos Rift and has been recorded from other vent communities of the East Pacific Rise (EPR). Here we assessed the biodiversity of serpulids collected from eastern Pacific hydrothermal vents and methane seeps using DNA sequences and morphology. Laminatubus alvini showed little genetic variation over a wide geographic range from the Alarcon Rise vents in southern Gulf of California (~23°N), to at least a point at 38°S on the EPR. Specimens from several methane seeps off Costa Rica and the Gulf of California (Mexico) differed markedly from those of Laminatubus alvini on DNA sequence data and in having seven thoracic chaetigers and lacking Spirobranchus-type special collar chaetae, thus fitting the diagnosis of Neovermilia. However, phylogenetic analysis of molecular data showed that L. alvini and the seep specimens form a well-supported clade. Moreover, among the seep specimens there was minimally a ~7% distance in mitochondrial cytochrome b sequences between a shallow-water (1000 m) seep clade restricted to Costa Rica and a deep-water clade (1800 m) from Costa Rica to Gulf of California. We describe the seep taxa here as morphologically indistinguishable L. paulbrooksi n. sp. and L. joycebrooksae n. sp.
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http://dx.doi.org/10.11646/zootaxa.4915.1.1DOI Listing
January 2021

Annelids of the eastern Australian abyss collected by the 2017 RV 'Investigator' voyage.

Zookeys 2021 24;1020:1-198. Epub 2021 Feb 24.

South China Sea Environmental Monitoring Centre, State Oceanic Administration, Guangzhou, China.

In Australia, the deep-water (bathyal and abyssal) benthic invertebrate fauna is poorly known in comparison with that of shallow (subtidal and shelf) habitats. Benthic fauna from the deep eastern Australian margin was sampled systematically for the first time during 2017 RV 'Investigator' voyage 'Sampling the Abyss'. Box core, Brenke sledge, and beam trawl samples were collected at one-degree intervals from Tasmania, 42°S, to southern Queensland, 24°S, from 900 to 4800 m depth. Annelids collected were identified by taxonomic experts on individual families around the world. A complete list of all identified species is presented, accompanied with brief morphological diagnoses, taxonomic remarks, and colour images. A total of more than 6000 annelid specimens consisting of 50 families (47 Polychaeta, one Echiura, two Sipuncula) and 214 species were recovered. Twenty-seven species were given valid names, 45 were assigned the qualifier cf., 87 the qualifier sp., and 55 species were considered new to science. Geographical ranges of 16 morphospecies extended along the eastern Australian margin to the Great Australian Bight, South Australia; however, these ranges need to be confirmed with genetic data. This work providing critical baseline biodiversity data on an important group of benthic invertebrates from a virtually unknown region of the world's ocean will act as a springboard for future taxonomic and biogeographic studies in the area.
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http://dx.doi.org/10.3897/zookeys.1020.57921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930015PMC
February 2021

Mitochondrial genome of (Gmelin, 1791) (Sabellida: Sabellidae).

Mitochondrial DNA B Resour 2021 Feb 11;6(2):499-501. Epub 2021 Feb 11.

Australian Museum Research Institute, Australian Museum, Sydney, Australia.

We report the mitochondrial genome of , an invasive Mediterranean sabellid introduced to Australia and New Zealand. The mitogenome is 15,581 bp long and consists of 38 genes, including 13 protein coding genes, two rRNA genes, and 23 tRNA genes. It shows deviations from the putative annelid ground pattern, such as gene order re-arrangements and regions encoding on the negative strand. It is, however, very different from the mitogenome of the closely related serpulid, . Phylogenetic analyses of the mitochondrial genes support a sister relationship of and .
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http://dx.doi.org/10.1080/23802359.2021.1872431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889199PMC
February 2021

Another blow to the conserved gene order in Annelida: Evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides.

Mol Phylogenet Evol 2021 Jul 19;160:107124. Epub 2021 Feb 19.

Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia. Electronic address:

Mitochondrial genomes are frequently applied in phylogenetic and evolutionary studies across metazoans, yet they are still poorly represented in many groups of invertebrates, including annelids. Here, we report ten mitochondrial genomes from the annelid genus Hydroides (Serpulidae) and compare them with all available annelid mitogenomes. We detected all 13 protein coding genes in Hydroides spp., including the atp8 which was reported as a missing gene in the Christmas Tree worm Spirobranchus giganteus, another annelid of the family Serpulidae. All available mitochondrial genomes of Hydroides show a highly positive GC skew combined with a highly negative AT skew - a feature consistent with that found only in the mitogenome of S. giganteus. In addition, amino acid sequences of the 13 protein-coding genes showed a high genetic distance between the Hydroides clade and S. giganteus, suggesting a fast rate of mitochondrial sequence evolution in Serpulidae. The gene order of protein-coding genes within Hydroides exhibited extensive rearrangements at species level, and were different from the arrangement patterns of other annelids, including S. giganteus. Phylogenetic analyses based on protein-coding genes recovered Hydroides as a monophyletic group sister to Spirobranchus with a long branch, and sister to the fan worm Sabellidae. Yet the Serpulidae + Sabellidae clade was unexpectedly grouped with Sipuncula, suggesting that mitochondrial genomes alone are insufficient to resolve the phylogenetic position of Serpulidae within Annelida due to its high base substitution rates. Overall, our study revealed a high variability in the gene order arrangement of mitochondrial genomes within Serpulidae, provided evidence to question the conserved pattern of the mitochondrial gene order in Annelida and called for caution when applying mitochondrial genes to infer their phylogenetic relationships.
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http://dx.doi.org/10.1016/j.ympev.2021.107124DOI Listing
July 2021

Two new species of Sabellariidae (Annelida, Polychaeta) from the abyss of eastern Australia.

Zootaxa 2020 Aug 3;4821(3):zootaxa.4821.3.4. Epub 2020 Aug 3.

South China Sea Environmental Monitoring Center, State Oceanic Administration, 155 Xingangxi Road, Guangzhou, P. R. China Australian Museum Research Institute, Australian Museum, 1, William Street, 2010, New South Wales, Australia. Department of Biological Sciences, Macquarie University, North Ryde 2109, Australia..

In May-June 2017 an expedition on board RV 'Investigator' sampled benthic communities along the lower slope and abyss of eastern Australia from off Tasmania to the Coral Sea. Over 200 sabellariid specimens of the genera Phalacrostemma and Gesaia were collected during the voyage and deposited in the Australian Museum. Here we describe two new species Gesaia csiro n. sp. (4414-4436 m) and Phalacrostemma timoharai n. sp. (1013-1093 m). We did not formally describe another species of Phalacrostemma due to poor condition of the single specimen. Gesaia csiro n. sp. is the first record of the genus from Australian waters (only a planktonic larva attributed to the genus has previously been recorded), and it can be distinguished from other congeners by the smooth surface of inner paleae, distal thecae of outer paleae with long, irregular and expanded distal fringe and circled distal margin. Phalacrostemma timoharai n. sp. differs from congeners by the following combination of characters: presence of the buccal flap, absence of tentacular filament, 18-22 pairs of outer paleae, two pairs of neuropodial cirri on first thoracic segment, and only one pair of lateral lobes on second thoracic segment. Morphological descriptions are accompanied by mitochondrial cytochrome c oxidase subunit 1 (COI) and ribosomal (16S, 18S and 28S) sequence data. A key to all Australian species of sabellariids is given.
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http://dx.doi.org/10.11646/zootaxa.4821.3.4DOI Listing
August 2020

Alcohol stress on cyanobacterial membranes: New insights revealed by transcriptomics.

Gene 2021 Jan 1;764:145055. Epub 2020 Sep 1.

Department of Molecular Biosystems, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Science, Botanicheskaya str., 35, Moscow 127276, Russian Federation.

Cyanobacteria are model photosynthetic prokaryotic organisms often used in biotechnology to produce biofuels including alcohols. The effect of alcohols on cyanobacterial cell physiology and specifically on membrane fluidity is poorly understood. Previous research on various primary aliphatic alcohols found that alcohols with a short hydrocarbon chain (C-C) do not affect expression of genes related to membrane physical state. In addition, less water-soluble alcohols with a hydrocarbon chain longer than C are found to have a reduced ability to reach cellular membranes hence do not drastically change membrane physical state or induce expression of stress-responsive genes. Therefore, hexan-1-ol (C) is suggested to have the most profound effect on cyanobacterial membrane physical state. Here, we studied the effects of hexan-1-ol on the cyanobacterium Synechocystis sp. PCC 6803 transcriptome. The transcriptome data obtained is compared to the previously reported analysis of gene expression induced by benzyl alcohol and butan-1-ol. The set of genes whose expression is induced after exposure to all three studied alcohols is identified. The expression under alcohol stress for several general stress response operons is analyzed, and examples of antisense interactions of RNA are investigated.
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http://dx.doi.org/10.1016/j.gene.2020.145055DOI Listing
January 2021

A new species of the Spirobranchus kraussii-complex (Annelida, Serpulidae) from the Persian Gulf and Gulf of Oman.

Zootaxa 2020 Mar 9;4748(3):zootaxa.4748.3.1. Epub 2020 Mar 9.

Department of Animal Biology, School of Biology, College of Sciences, University of Tehran, Tehran, Iran..

A recent study (Simon et al. 2019) confirmed that Spirobranchus kraussii is neither a widely distributed tropical species of Indo-Pacific origin nor a Lessepsian migrant to the Mediterranean, but a large complex of species, some of which might be indeed invasive. Thus, a common intertidal gregarious serpulid, previously attributed to S. kraussii in the Persian Gulf and Gulf of Oman, is described herein as Spirobranchus sinuspersicus sp. nov., using a combination of morphological and molecular data. The new species differs from S. kraussii by smaller size, fewer abdominal chaetigers, arrangement of abdominal chaetae and shape of opercular endplate talon. Results of phylogenetic analyses of a dataset combining 18S nucleotide and Cyt-b amino-acid sequences of S. sinuspersicus sp. nov. and Spirobranchus spp. available from GenBank supported monophyly of S. kraussii complex (including S. cariniferus) nested within Spirobranchus and thus, provided molecular support for synonymy of Pomatoleios with Spirobranchus proposed based on morphological criteria. The new species forms a well-supported clade with (S. kraussii (sp. 2 Hawaii + sp. 3 Australia)) clade, which in turn forms a clade with Spirobranchus sp.1 from temperate Japan, while S. cariniferus from New Zealand forms a basal grade. Evidence of substitution saturation of Cyt-b nucleotide sequences suggests that using translated amino-acid sequences to exclude non-informative substitutions should provide a better phylogenetic resolution for the genus Spirobranchus. Further studies are required to determine the invasive status of S. sinuspersicus sp. nov. as well as taxonomic and invasive status of S. cf. kraussii populations from the Mediterranean Sea, Suez Bay, Pakistan, India, Sri Lanka, Philippines, Singapore, and Panama.
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http://dx.doi.org/10.11646/zootaxa.4748.3.1DOI Listing
March 2020

A revision of the genus Petta Malmgren, 1866 (Annelida: Pectinariidae), with two new species from deep waters of southeastern Australia, and comments on phylogeny of the family.

Zootaxa 2019 Jun 10;4614(2):zootaxa.4614.2.3. Epub 2019 Jun 10.

South China Sea Environmental Monitoring Center, State Oceanic Administration, 155 Xingangxi Road, Guangzhou, P. R. China Australian Museum Research Institute, Australian Museum, 1, William Street, 2010, New South Wales, Australia Department of Biological Sciences, Macquarie University, North Ryde 2109, Australia.

Petta Malmgren, 1866 is a small and poorly known genus of the annelid family Pectinariidae Quatrefages, 1866. Prior to this study, the genus comprised four species P. pusilla Malmgren, 1866 (type locality Gullmarsfjord, west coast of Sweden), P. assimilis McIntosh, 1885 (type locality between Prince Edward and Kerguelen Island, southern Indian Ocean), P. pellucida (Ehlers, 1887) (type locality Santarem Channel between Cay Sal Bank and Bahamas, Caribbean Sea) and P. tenuis Caullery, 1944 (type locality Sulu, Philippines, tropical Pacific Ocean), the two last ones were known only from the original description. We revised the genus by re-examining the types and providing updated illustrated re-descriptions of its species, except for P. assimilis of which the type material has been lost. Commonly used morphological characters of the genus are expanded to also include new ones such as the presence of pair of lateral ear-shaped lobes adjacent to dorsal base of cephalic veil, pair of ventral lappets on segment 1, pair of dorso-lateral pads on segment 5, large basal hump on branchiae, and a rounded anterior peg with a blunt tip and a longitudinal row of two major teeth on uncini. The type species P. pusilla is recognised as having four lappets on the anterior margins of cephalic veil and a large lower lip posterior to buccal cavity. Two species P. investigatoris n. sp. and P. williamsonae n. sp. are described from deep water off the coast of southeastern Australia and represent the first records of this genus in Australian waters. A phylogenetic position of one new species was assessed in the framework of a phylogeny based on a fragment of the mitochondrial cytochrome oxidase I gene (mtCOI). An updated taxonomic key to Pectinariidae genera and all species of Petta is given.
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http://dx.doi.org/10.11646/zootaxa.4614.2.3DOI Listing
June 2019

A new species of the sanguinea-group Quatrefages, 1866 (Annelida: Eunicidae: Marphysa) from the Philippines.

Zootaxa 2019 Sep 24;4674(2):zootaxa.4674.2.7. Epub 2019 Sep 24.

Museum and Art Gallery Northern Territory, GPO Box 4646, Darwin NT 0801, Australia..

A new species of the Marphysa sanguinea group, M. iloiloensis n. sp. (Annelida: Eunicida: Eunicidae), is described from the Marine Annelids Hatchery of the Southeast Asian Fisheries Development Center, Aquaculture Department (SEAFDEC- AQD), Iloilo Province, Philippines. It represents the first record of this group in the Philippines. The new species is most similar morphologically to M. hongkongensa Wang, Zhang Qiu, 2018, but can be distinguished from it by having fewer branchial filaments, a pair of faint eyes (absent in M. hongkongensa), and in slight differences in jaw morphology and chaetation. The embryos of the new species develop inside a jelly cocoon attached to the entrance of the adult burrow; this is the first time that egg-containing cocoons have been found in any species of the sanguinea-group. Phylogenetic analysis based on the mitochondrial gene cytochrome c oxidase subunit I (COI) revealed that Marphysa iloiloensis n. sp. is genetically distinct from all other analysed Marphysa species and forms a sister group to M. hongkongensa. A revised identification key to members of the sanguinea-group in Southeast Asia is provided.
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http://dx.doi.org/10.11646/zootaxa.4674.2.7DOI Listing
September 2019

The formation of human populations in South and Central Asia.

Science 2019 09;365(6457)

Earth Institute, University College Dublin, Dublin 4, Ireland.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
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http://dx.doi.org/10.1126/science.aat7487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619PMC
September 2019

Draft Genome Sequences of a Putative Prokaryotic Consortium (IPPAS B-1204) Consisting of a Cyanobacterium ( sp.) and an Alphaproteobacterium ( sp.).

Microbiol Resour Announc 2019 Apr 11;8(15). Epub 2019 Apr 11.

K. A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia.

A new presumably simple consortium of a sp. and a sp. was isolated from Tolbo Lake in Mongolia. The draft genome sequences of both species are reported. The consortium has been deposited in the Collection of Microalgae and Cyanobacteria of the Institute of Plant Physiology, Moscow, Russia, under the accession number IPPAS B-1204.
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http://dx.doi.org/10.1128/MRA.01637-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460039PMC
April 2019

Highly active extracellular α-class carbonic anhydrase of Cyanothece sp. ATCC 51142.

Biochimie 2019 May 18;160:200-209. Epub 2019 Mar 18.

К.А. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, 127276, Russia.

Here, for the first time, we report the presence of highly active extracellular carbonic anhydrase (CA) of α-class in cyanobacterial cells. The enzyme activity was confirmed both in vivo in intact cells and in vitro, using the recombinant protein. CA activity in intact cells of Cyanothece sp. ATCC 51142 reached ∼0.6 Wilbur-Anderson units (WAU) per 1 mg of total cell protein, and it was inhibited by a specific CAs inhibitor, ethoxyzolamide. The genes cce_4328 (ecaA) and cce_0871 (ecaB), encoding two potential extracellular CAs of Cyanothece have been cloned, and the corresponding proteins EcaA and EcaB, representing CAs of α- and β-class, respectively, have been heterologously expressed in Escherichia coli. High specific activity (∼1.1 × 10 WAU per 1 mg of target protein) was detected for the recombinant EcaA only. The presence of EcaA in the outer cellular layers of Cyanothece was confirmed by immunological analysis with antibodies raised against the recombinant protein. The absence of redox regulation of EcaA activity indicates that this protein does not possess a disulfide bond essential for some α-class CAs. The content and activity of EcaA in a fraction of periplasmic proteins was higher in Cyanothece cells grown at ambient concentration of CO (0.04%) compared to those grown at an elevated CO concentration (1.7%). At the same time, the level of ecaA gene mRNA varied insignificantly in response to changes in CO supply. Our results indicate that EcaA is responsible for CA activity of intact Cyanothece cells and point to its possible physiological role under low-CO conditions.
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http://dx.doi.org/10.1016/j.biochi.2019.03.009DOI Listing
May 2019

Developmental studies provide new insights into the evolution of sense organs in Sabellariidae (Annelida).

BMC Evol Biol 2018 10 4;18(1):149. Epub 2018 Oct 4.

Biology Department, University of the Balearic Islands, Department of Biology, Ctra. Valldemossa, Palma de Mallorca, Balearic Islands, Spain.

Background: Sabellarids, also known as honeycomb or sandcastle worms, when building their tubes, produce chemical signals (free fatty acids) that are responsible for larval settlement and the formation of three-dimensional aggregations. The larval palps and the dorsal hump (becoming the median organ in adults) are presumed to participate in such a substrate selection during settlement. Notably, the sabellariid median organ is an apparently unique organ among annelids that has been attributed with a sensory function and perhaps with some affinities to the nuchal organs of other polychaetes. Nevertheless, detailed investigations of this prominent character complex including ultrastructural examinations are lacking so far.

Results: Our comprehensive investigations provide data about the anterior sensory organs in Sabellariidae and inform about their transformation during pelagic larval development. We used a comparative approach including immunostaining with subsequent confocal laser scanning microscopy (clsm), histological sections as well as electron microscopy in a range of larval and adult stages of two sabellariid species. We find that the neuronal innervation as well as the ultrastructure of the sabellariid ciliary structures along the median organ are highly comparable with that of nuchal organs known from other polychaetes. Furthermore, the myoinhibitory protein (MIP) - a protein known to be also involved into chemo-sensation - was detected in the region of the larval median organ. Moreover, we reveal the presence of an unusual type of photoreceptor as part of the median organ in Idanthyrsus australiensis with a corrugated sensory membrane ultrastructure unlike those observed in the segmental ocelli of other polychaetes.

Conclusions: We are describing for the first time the nuchal organ-like structures in different developmental stages of two species of Sabellariidae. The external morphology, neuronal innervation, developmental fate and ultrastructure of the newly-discovered median organ-based ciliary pits are comparable with the characteristics known for annelid nuchal organs and therefore indicate a homology of both sensory complexes. The presence of myoinhibitory peptide (MIP) in the respective region supports such a hypothesis and exhibits the possibility of an involvement of the entire sabellariid median organ complex, and in particular the prominent ciliated pits, in chemo-sensation.
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http://dx.doi.org/10.1186/s12862-018-1263-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172725PMC
October 2018

Barcoding and multi-locus phylogeography of the globally distributed calcareous tubeworm genus Hydroides Gunnerus, 1768 (Annelida, Polychaeta, Serpulidae).

Mol Phylogenet Evol 2018 10 12;127:732-745. Epub 2018 Jun 12.

Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia. Electronic address:

Hydroides is a large and diverse group of calcareous tubeworms (Serpulidae, Annelida) recognised by a distinctive but variable two-tiered operculum. Despite considerable research using several species of Hydroides as models in ecological and biofouling studies, phylogenetic and biogeographic relationships within the genus are still poorly understood. Using combined mitochondrial (COI, cytochrome b) and nuclear (18S, 28S and ITS) gene markers for 284 individuals of 45 morphospecies of Hydroides, we investigated the global phylogenetic and biogeographic relationships within the genus. Phylogenetic topologies were well supported and indicated high genetic diversity within Hydroides, revealing potential cryptic species. Present results also include the first COI barcoding data enabling rapid and effective species identification of Hydroides on a global scale. Phylogenetic relationships within Hydroides were more concordant with geographical distributions than morphological similarity of their opercula. Molecular divergence estimates suggested the origin and subsequent diversification in the western Tethys Sea followed by a shift of the historical centre of diversity from the Indo-Mediterranean region to the central Indo-Pacific during the last 50 million years. Further studies on population genetics of species consisting of multiple lineages would provide a better understanding on the status of potential cryptic species. Furthermore, paleogeographic studies based on fossil Hydroides tubes would provide evidence to test this biogeographic hypothesis.
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http://dx.doi.org/10.1016/j.ympev.2018.06.021DOI Listing
October 2018

Two new species of Marphysa Quatrefages, 1865 (Polychaeta: Eunicida: Eunicidae) from northern coast of China and redescription for Marphysa orientalis Treadwell, 1936.

Zootaxa 2018 Jan 31;4377(2):191-215. Epub 2018 Jan 31.

Ocean University of China, 5 Yushan Road, Qingdao, China The Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia.

Two new species of Marphysa Quatrefages, 1865 (Polychaeta: Eunicida: Eunicidae), M. bulla n. sp. and M. maxidenticulata n. sp., are described from the northern coast of China with comments on the usefulness of pectinate chaetae to separate species. A redescription of Marphysa orientalis Treadwell, 1936 originally described from China is given. The genus Marphysa is widely collected for bait for recreational fishermen and anglers in China and is also exported to Australia and Japan, yet the number of species involved or their native distribution are currently unknown. It is critical that aquaculture programs know which species they are attempting to breed and their native distributional ranges. A key to all described species of Marphysa from China, including two new species described in this paper is given.
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http://dx.doi.org/10.11646/zootaxa.4377.2.3DOI Listing
January 2018

Putative extracellular α-class carbonic anhydrase, EcaA, of Synechococcus elongatus PCC 7942 is an active enzyme: a sequel to an old story.

Microbiology (Reading) 2018 04 27;164(4):576-586. Epub 2018 Feb 27.

Laboratory of Cell Regulation, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow 127276, Russia.

Carbonic anhydrase (CA) EcaA of Synechococcus elongatus PCC 7942 was previously characterized as a putative extracellular α-class CA, however, its activity was never verified. Here we show that EcaA possesses specific CA activity, which is inhibited by ethoxyzolamide. An active EcaA was expressed in heterologous bacterial system, which supports the formation of disulfide bonds, as a full-length protein (EcaA+L) and as a mature protein that lacks a leader peptide (EcaA-L). EcaA-L exhibited higher specific activity compared to EcaA+L. The recombinant EcaA, expressed in a bacterial system that does not support optimal disulfide bond formation, exhibited extremely low activity. This activity, however, could be enhanced by the thiol-oxidizing agent, diamide; while a disulfide bond-reducing agent, dithiothreitol, further inactivated the enzyme. Intact E. coli cells that overexpress EcaA+L possess a small amount of processed protein, EcaA-L, whereas the bulk of the full-length protein resides in the cytosol. This may indicate poor recognition of the EcaA leader peptide by protein export systems. S. elongatus possessed a relatively low level of ecaA mRNA, which varied insignificantly in response to changes in CO2 supply. However, the presence of protein in the cells is not obvious. This points to the physiological insignificance of EcaA in S. elongatus, at least under the applied experimental conditions.
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http://dx.doi.org/10.1099/mic.0.000634DOI Listing
April 2018

Draft Genome Sequences of Two Thermotolerant Cyanobacterial Strains Isolated from Hot Springs.

Genome Announc 2018 Feb 1;6(5). Epub 2018 Feb 1.

Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia.

We report here two draft cyanobacterial genome sequences, those of IPPAS B-1201, isolated from a hot spring in the Turgen Gorge (Kazakhstan), and the uncharacterized cyanobacterium IPPAS B1203, isolated from a hot spring in Karlovy Vary (Czech Republic). These two strains were deposited at the Collection of Microalgae (IPPAS) of the Timiryazev Institute of Plant Physiology.
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http://dx.doi.org/10.1128/genomeA.01548-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794950PMC
February 2018

sp. n. (Annelida, Sabellidae) from Okinawa and Ogasawara, Japan, with notes on its ecology.

Zookeys 2017 7(660):1-16. Epub 2017 Mar 7.

Marine Invertebrates, Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney NSW 2010, Australia.

The polychaete (Sabellidae) is described from Okinawa and Ogasawara, south Japan, where it was found living embedded in a dead skeleton of the coral sp. The new species is characterized by the presence of a pigmented sub-distal swelling on the tips of the crown radioles, a unique feature among species of the genus. Besides, its collar chaetae have an L-shape orientation, and the dorsal basal flanges of the branchial lobes are long and have a dorsal joint.
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http://dx.doi.org/10.3897/zookeys.660.11228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549527PMC
March 2017

Gunnerus, 1768 (Annelida, Serpulidae) is feminine: a nomenclatural checklist of updated names.

Zookeys 2017 3(642):1-52. Epub 2017 Jan 3.

Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia; Department of Biological Science, Macquarie University, Sydney, NSW, Australia.

As a service to taxonomists and ecologists using names in the well-known and species-rich ship-fouling serpulid genus we present an update of all 107 non-synonymised scientific names, with additional information on nomenclature, original names, etymologies, and type localities derived from original literature, and in accord with the World Register of Marine Species (WoRMS) database. An update is needed because the gender of genus has from 1 January 2000 reverted to the original feminine, due to a change in the wording of International Code of Zoological Nomenclature which was overlooked at that time, and is contrary to the usage in practice of as masculine which had started about 1992, although Code-required from the 1960s. We match 31 further original names of current WoRMS subjective junior synonyms to each non-synonymised name, and also report on the world distribution of the genus as illustrated by type localities of the valid names. We include notes on seven . The correct rendering is given of six names that have been altered for gender agreement for the first time herein. replaces junior homonym Pillai, 1971. Currently there are 41 non-synonymised species-group names in which should be gender invariant, and 23 names which would only change if moved to a neuter genus; the remaining 43 names are fully gender variable. Place-names (23), and personal names (16) make up more than a third (36%) of the species names, with most of the remainder (68) being descriptive of species character states, usually of operculum morphology (54). All species, except (63°N), have type localities in shallow-water coastal locations in temperate to tropical waters below latitude 44°, with the highest number of new species (54) from the adjoining Western Pacific and Indian Ocean areas. The other concentration of new species (31) are those first found on the Pacific and Atlantic coasts of North America and in the Caribbean.
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http://dx.doi.org/10.3897/zookeys.642.10443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240528PMC
January 2017

Polyphasic characterization of the thermotolerant cyanobacterium Desertifilum sp. strain IPPAS B-1220.

FEMS Microbiol Lett 2017 02;364(4)

Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia.

A cyanobacterial strain from Lake Shar-Nuur, a freshwater lake in Mongolia, was isolated and characterized by a polyphasic approach. According to the 16S ribosomal RNA gene sequence, this strain (IPPAS B-1220) belongs to a newly described genus Desertifilum. In general, strains of Desertifilum maintain their genetic stability, as seen from the analysis of the 16S rRNA gene and 16S-23S rRNA internal transcribed spacer sequences from strains collected at distant locations. The newly discovered strain is characterized by an unusual fatty acid composition (16:1Δ7 and 16:2Δ7,10). Analysis of its draft genomic sequence reveals the presence of six genes for the acyl-lipid desaturases: two Δ9-desaturases, desC1 and desC2; two Δ12-desaturases, desA1 and desA2; one desaturase of unknown specificity, desX; and one gene for the bacillary-type desaturase, desG, which supposedly encodes an ω9-desaturase. A scheme for a fatty acid desaturation pathway that describes the biosynthesis of 16:1Δ7 and 16:2Δ7,10 fatty acids in Desertifilum is proposed.
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http://dx.doi.org/10.1093/femsle/fnx027DOI Listing
February 2017

Draft Genome Sequence of Cyanobacterium sp. Strain IPPAS B-1200 with a Unique Fatty Acid Composition.

Genome Announc 2016 Nov 17;4(6). Epub 2016 Nov 17.

Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia

Here, we report the draft genome of Cyanobacterium sp. IPPAS strain B-1200, isolated from Lake Balkhash, Kazakhstan, and characterized by the unique fatty acid composition of its membrane lipids, which are enriched with myristic and myristoleic acids. The approximate genome size is 3.4 Mb, and the predicted number of coding sequences is 3,119.
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http://dx.doi.org/10.1128/genomeA.01306-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114388PMC
November 2016

Draft Genome Sequence of the Thermotolerant Cyanobacterium Desertifilum sp. IPPAS B-1220.

Genome Announc 2016 Nov 17;4(6). Epub 2016 Nov 17.

Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia.

Here, we report the draft genome of the filamentous cyanobacterium Desertifilum sp. strain IPPAS B-1220, isolated from Lake Shar-Nuur, Mongolia. The genome of 6.1 Mb codes for 5,113 genes. Genome mining revealed 10 clusters for the synthesis of bioactive compounds (nonribosomal peptides, polyketides, bacteriocins, and lantipeptides) with potential biotechnological or medical importance.
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http://dx.doi.org/10.1128/genomeA.01304-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114386PMC
November 2016

The complete genome of a cyanobacterium from a soda lake reveals the presence of the components of CO-concentrating mechanism.

Photosynth Res 2016 Dec 23;130(1-3):151-165. Epub 2016 Feb 23.

Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276.

At present geological epoch, the carbon concentrating mechanism (CCM) of cyanobacteria represents the obligatory tool for adaptation to low content of CO in the atmosphere and for the maintenance of sufficient photosynthetic activity. Functional CCM was found in modern cyanobacteria from different ecological niches. However, the presence of such mechanism in species that inhabit soda lakes is not obvious due to high content of inorganic carbon (C ) in the environment. Here we analyze CCM components that have been identified by sequencing of the whole genome of the alkaliphilic cyanobacterium Microcoleus sp. IPPAS B-353. The composition of the CCM components of Microcoleus is similar to that of 'model' β-cyanobacteria, freshwater and marine Synechococcus or Synechocystis spp. However, CahB1 protein of Microcoleus, which is the homolog of CcaA, the carboxysomal β-type carbonic anhydrase (CA) of β-cyanobacteria, appeared to be the only active CA located in cell envelopes. The conservative regions of CcmM, CahG (a homolog of archeal γ-CAs, Cam/CamH), and ChpX of Microcoleus possess single amino acid substitutions that may cause a lack of CA activities. Unlike model cyanobacteria, Microcoleus induces only one BicA-type bicarbonate transporter in response to C limitation. The differences in the appearance of CCM components and in their characteristics between alkaliphilic Microcoleus and freshwater or marine cyanobacteria are described. The possible reasons for the maintenance of CCM components in cyanobacteria, which permanently live at high concentrations of C in soda lakes, are discussed.
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http://dx.doi.org/10.1007/s11120-016-0235-0DOI Listing
December 2016

Synechocystis mutants defective in manganese uptake regulatory system, ManSR, are hypersensitive to strong light.

Photosynth Res 2016 Dec 31;130(1-3):11-17. Epub 2015 Dec 31.

Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, Russia, 127276.

High affinity transport of manganese ions (Mn) in cyanobacteria is carried by an ABC-type transporter, encoded by the mntCAB operon, which is derepressed by the deficiency of Mn. Transcription of this operon is negatively regulated by the two-component system consisting of a sensory histidine kinase ManS and DNA-binding response regulator ManR. In this study, we examined two Synechocystis mutants, defective in ManS and ManR. These mutants were unable to grow on high concentrations of manganese. Furthermore, they were sensitive to high light intensity and unable to recover after short-term photoinhibition. Under standard illumination and Mn concentration, mutant cells revealed the elevated levels of transcripts of genes involved in the formation of Photosystem II (psbA, psbD, psbC, pap-operon). This finding suggests that, in mutant cells, the PSII is sensitive to high concentrations of Mn even at relatively low light intensity.
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http://dx.doi.org/10.1007/s11120-015-0214-xDOI Listing
December 2016

Sabellaria jeramae, a new species (Annelida: Polychaeta: Sabellariidae) from the shallow waters of Malaysia, with a note on the ecological traits of reefs.

Zootaxa 2015 Dec 7;4052(5):555-68. Epub 2015 Dec 7.

Environmental and Life Sciences Programme, Universiti Brunei Darussalam, BE1410 Gadong, Negara Brunei Darussalam; Email: unknown.

A new species of the genus Sabellaria Lamarck, 1818 (Annelida: Polychaeta: Sabellariidae) is described from the intertidal zone of Jeram, Selangor, Malaysia. Sabellaria jeramae n. sp. is a gregarious species that constructs large reefs several hundreds of meters long and 50-200 m wide. The new species is distinguished from other congeners by the character combination of the presence of a single kind of middle paleae with conspicuous morphology, and outer paleae with long frayed teeth. Morphological features of the species are described and compared to those of all congeneric species. We also compare the reef structure and geographical distribution of the new species to those of the members of the family Sabellariidae around the world, demonstrating the ecological traits of the reefs.
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http://dx.doi.org/10.11646/zootaxa.4052.5.3DOI Listing
December 2015

Deep-sea serpulids (Annelida: Polychaeta) in tetragonal tubes: on a tube convergence path from the Mesozoic to Recent.

Zootaxa 2015 Nov 18;4044(2):151-200. Epub 2015 Nov 18.

Geological Institute of Russian Academy of Sciences, 7 Pyzhevski Lane, Moscow, 119017, Russia.; Email:

Serpulids typically build cylindrical calcareous tubes attached to hard substrates. Until now, only three serpulid species inhabiting free-lying polygonal tubes were reported from the deep sea: Spirodiscus grimaldii Fauvel, 1909 with quadrangular spirally coiled tubes, Bathyditrupa hovei Kupriyanova, 1993a with quadrangular tusk-shaped tubes, and Ditrupa groenlandica McIntosh, 1877 with octagonal tusk-shaped tubes. Similar free-lying tubes with tetragonal cross-section, both coiled and tusk-shaped, are described from shallow-water Mesozoic deposits as Nogrobs de Montfort, 1808, Tetraserpula Parsch, 1956, Tetraditrupa Regenhardt, 1961, Glandifera Regenhardt, 1961 and Tubulostium Stoliczka, 1868. We have revised deep-sea serpulids with tetragonal (and secondary octagonal) tubes and compared their tube ultrastructures and mineralogies with those of morphologically similar fossils. Revision of the Recent material has revealed six species in five genera: Spirodiscus grimaldii, S. groenlandicus comb. nov., Bathyditrupa hovei, Bathyvermilia gregrousei sp. nov., Hyalopomatus dieteri sp. nov. and Zibrovermilia zibrowii gen. et sp. nov. Comparisons showed significant ultrastructural and mineralogical differences between Recent and Mesozoic species. Similar tetragonal tube morphology of the Recent forms appears to be a result of convergence due to adaptation to similar soft-sediment habitats of the deep sea. None of Recent genera should be synonymised with any fossil genus, and the genus Spirodiscus Fauvel, 1909, previously synonymised with fossil Nogrobs, should be re-instated. However, a huge stratigraphic gap (66 Myr) between the earliest known fossil tetragonal tubes and their Recent counterparts still allows the possibility that such essentially different structures is a result of ultrastructural evolution, a hypothesis that could be verified by discovery and further study of Caenozoic material.
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http://dx.doi.org/10.11646/zootaxa.4044.2.1DOI Listing
November 2015

Serpulidae (Annelida) of Lizard Island, Great Barrier Reef, Australia.

Zootaxa 2015 Sep 18;4019:275-353. Epub 2015 Sep 18.

Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla CA, 92093-0202, USA.; Email:

Serpulidae are obligatory sedentary polychaetes inhabiting calcareous tubes that are most common in subtropical and tropical areas of the world. This paper describes serpulid polychaetes collected from Lizard Island, Great Barrier Reef, Australia in 1983-2013 and deposited in Australian museums and overseas. In total, 17 serpulid genera were recorded, but although the study deals with 44 nominal taxa, the exact number of species remains unclear because a number of genera (i.e., Salmacina, Protula, Serpula, Spirobranchus, and Vermiliopsis) need world-wide revisions. Some species described herein are commonly found in the waters around Lizard Island, but had not previously been formally reported. A new species of Hydroides (H. lirs) and two new species of Semivermilia (S. annehoggettae and S. lylevaili) are described. A taxonomic key to all taxa found at Lizard Island is provided.
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http://dx.doi.org/10.11646/zootaxa.4019.1.13DOI Listing
September 2015

Polychaetes and allies of Lizard Island.

Zootaxa 2015 Sep 18;4019:5-6. Epub 2015 Sep 18.

Australian Museum Research Institute, Australian Museum, 6 College Street, Sydney, NSW, 2010, Australia.; Email: unknown.

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http://dx.doi.org/10.11646/zootaxa.4019.1.3DOI Listing
September 2015

Revision of the genus Hydroides (Annelida: Serpulidae) from Australia.

Zootaxa 2015 Sep 1;4009:1-99. Epub 2015 Sep 1.

Australian Museum Research Institute, Australian Museum, 6 College Street, Sydney, NSW, 2010, Australia; Email:

Hydroides Gunnerus, 1768 is the largest and one of the economically most important genera of calcareous tubeworms (Serpulidae, Annelida) that includes a number of notorious fouling and bioinvading species. Although the representatives of the genus are typically found in shallow waters of tropical and subtropical areas worldwide, the species composition of the genus in Australia has never been revised. We conducted the first detailed regional taxonomic revision of Hydroides species based both on the historical collections from Australian museums (Australian Museum, Museum Victoria, South Australian Museum, Western Australian Museum, Queensland Museum, and Museum and Art Gallery of Northern Territory) and newly collected material from New South Wales, Victoria, Queensland, Northern Territory, and Western Australia. In total, 25 species are currently considered valid in Australia, including three new species: H. amri n. sp. from NSW, SA, and Vic (previously referred to as H. cf. brachyacantha), as well as H. glasbyi n. sp. and H. qiui n. sp., both from NT, and two new records of H. furcifera and H. multispinosa for Australia. We have synonymised H. spiratubus with H. albiceps, and H. spiculitubus with H. tambalagamensis in this study. The status of the taxon H. cf. recta remains undecided. An identification key and diagnoses accompanied by original high-quality photographs for all species recorded in Australia are provided. Application of molecular genetics is needed to resolve the status of some problematic species.
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http://dx.doi.org/10.11646/zootaxa.4009.1.1DOI Listing
September 2015

Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353.

J Biol Chem 2015 Nov 24;290(47):28502-28514. Epub 2015 Sep 24.

Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea.

Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found.
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http://dx.doi.org/10.1074/jbc.M115.669150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653706PMC
November 2015