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In this study, we describe Halamphora vantushpaensis sp. nov., a newly identified diatom species found in the highly alkaline Lake Van in Eastern Turkey (Türkiye). This new species is characterized morphologically by light and scanning electron microscopy, performed on both wild and cultivated samples. Two monoclonal cultures were submitted to a genome-skimming approach, giving access to the complete sequence of their nuclear rRNA cluster of genes, mitochondrial and plastid genomes. Both strains were highly similar from the genomic point of view, with few mutations noted, although in organellar genomes some of them concerned protein coding genes and were non-silent. Also, the group II intron in the mitochondrial cox1 gene was found to display a relatively high number of polymorphisms. The plastome also distinguishes itself from other Halamphora spp. by the extension of its inverted repeat at the expense of the two single copy regions of the genome. Maximum likelihood molecular phylogeny inferred from a concatenated three genes dataset (18S, psbC and rbcL) positions this species within the K clade, which is known to contain hypersaline to freshwater species.

Climate change and nutrient enrichment are increasing the frequency of algal blooms, with sometimes significant impacts on coastal ecosystems. Haslea ostrearia blooms have been documented in oyster ponds and are not harmful, yet their effects in open environments remain underexplored. Marennine, a blue pigment produced by H. ostrearia, can display a range of biological properties in laboratory conditions, including antibacterial and allelopathic properties. Other blue Haslea species, forming blooms, synthesize bioactive marennine-like pigments. This study aims to understand if and how these blooms could affect the underlying community of microorganisms living in the biofilms. Morphological and molecular techniques were used to assess community dynamics during bloom events. Our findings indicate that blue Haslea blooms do not significantly alter the diatom or bacterial populations. However, they are paired with enhanced alpha diversity in the microbial communities. These observations suggest a complex interaction between bloom events and microbial dynamics. Additionally, this study expands our understanding of the bioactive properties of marennine-like pigments and their ecological roles, suggesting new avenues for biotechnological applications. This work underscores the importance of further research into the environmental and biological implications of blue Haslea blooms.

ABSTRACT Since 2013, we have undertaken a detailed study of terrestrial flatworms (Geoplanidae) introduced into mainland France (including Corsica). Around ten species have been listed, mapped, and often characterized molecularly. These species include, in alphabetical order, Bipalium kewense, Caenoplana coerulea, Caenoplana decolorata, Caenoplana variegata, Diversibipalium multilineatum, Marionfyfea adventor, Obama nungara, Parakontikia ventrolineata, Platydemus manokwari, and Vermiviatum covidum. Outside of mainland France, we also studied species from the French islands of the Caribbean (Guadeloupe, Martinique), Réunion and Mayotte in the Indian Ocean, as well as New Caledonia, French Polynesia, and Wallis and Futuna in the Pacific. Two new species have been described. The major invasive species in mainland France are Obama nungara, present in two thirds of the country, Caenoplana variegata, and Parakontikia ventrolineata (especially in Brittany). Bipalium kewense and Diversibipalium multilineatum are mainly present in the southwest region of the French Atlantic coast. The origins of invasive species in France are varied and include Argentina (Obama nungara), Australia (Caenoplana variegata and Parakontikia ventrolineata), and Southeast Asia (Bipaliinae). We have characterized and published the complete mitogenomes of 12 species, with unexpected results, such as the very long cox2 gene in Rhynchodeminae. The phylogenies built on the genes of the mitogenomes generally confirm the previous classifications of the subfamilies of Geoplanidae, and individualize the three subfamilies Rhynchodeminae, Geoplaninae, and Bipaliinae. We emphasize the importance of citizen science for obtaining data, and the importance of good communication with the public to obtain significant engagement towards citizen science.

Specimens of a flat and dark brown land planarian were found in a plant nursery in North Carolina, USA in 2020. On the basis of examination of photographs of the live specimens only, the specimens were considered as belonging to Obama nungara, a species originally from South America, which has now invaded a large part of Europe. Unexpectedly, a molecular analysis revealed that the specimens did not belong to this species, neither to the genus Obama. We then undertook its histological study, which finally confirmed that the species is a member of the genus Amaga: the species is herein described as a new species, Amaga pseudobama n. sp. The species has been found in three locations in North Carolina and some infested plants were from Georgia. We reinvestigated specimens collected in Florida in 2015 and found that they also belong to this species. Citizen science observations suggest its presence in other states. Therefore, it is likely that A. pseudobama has already invaded a part of south-east USA and that the invasion took place more than ten years ago. The complete 14,909 bp long mitochondrial genome was obtained. The mitogenome is colinear with those of other Geoplanidae and it was possible to find and annotate a tRNA-Thr, which has been reported missing in several geoplanids. Amaga pseudobama shares with other Geoplaninae the presence of alternative start codons in three protein-coding genes of its mitogenome. The availability of this new genome helped us to improve our annotations of the ND3 gene, for which an ATT start codon is now suggested. Also, the sequence of the ATP6 gene raised questions concerning the use of genetic code 9 to translate the protein-coding genes of Geoplanidae, as the whole translated protein would not contain a single methionine residue when using this code. Two maximum likelihood phylogenies were obtained from genomic data. The first one was based on concatenated alignments of the partial 28S, Elongation Factor 1-alpha (EF1) and cox1 genes. The second was obtained from a concatenated alignment of the mitochondrial proteins. Both strictly discriminate A. pseudobama from O. nungara and instead associate it with Amaga expatria. We note that the nine species currently accepted within Amaga can be separated into two groups, one with extrabulbar prostatic apparatus, including the type species A. amagensis, and one with intrabulbar prostatic apparatus, including the new species A. pseudobama. This suggests that species of the latter group should be separated from Amaga and constitute a new genus. This finding again illustrates the possible emergence of new invasive species in regions naturally devoid of large land planarians, such as North America. Amaga pseudobama thus deserves to be monitored in the USA, although its superficial resemblance to O. nungara and Geoplana arkalabamensis will complicate the use of photographs obtained from citizen science. Our molecular information provides tools for this monitoring.

Abstract Using a combination of short- and long-reads sequencing, we were able to sequence the complete mitochondrial genome of the invasive ‘New Zealand flatworm’ Arthurdendyus triangulatus (Geoplanidae, Rhynchodeminae, Caenoplanini) and its two complete paralogous nuclear rRNA gene clusters. The mitogenome has a total length of 20,309 bp and contains repetitions that includes two types of tandem-repeats that could not be solved by short-reads sequencing. We also sequenced for the first time the mitogenomes of four species of Caenoplana (Caenoplanini). A maximum likelihood phylogeny associated A. triangulatus with the other Caenoplanini but Parakontikia ventrolineata and Australopacifica atrata were rejected from the Caenoplanini and associated instead with the Rhynchodemini, with Platydemus manokwari. It was found that the mitogenomes of all species of the subfamily Rhynchodeminae share several unusual structural features, including a very long cox2 gene. This is the first time that the complete paralogous rRNA clusters, which differ in length, sequence and seemingly number of copies, were obtained for a Geoplanidae.

The current article describes Navicula vanseea sp. nov., a new species of diatom from Lake Van, a highly alkaline lake in Eastern Anatolia (Türkiye). The description is based on light and scanning electron microscopy performed on two monoclonal cultures. The complete nuclear rRNA clusters and plastid genomes have been sequenced for these two strains and the complete mitogenome for one of them. The plastome of both strains shows the probable loss of a functional ycf35 gene. They also exhibit two IB4 group I introns in their rrl, each encoding for a putative LAGLIDADG homing endonuclease, with the first L1917 IB4 intron reported amongst diatoms. The Maximum Likelihood phylogeny inferred from a concatenated alignment of 18S, rbcL and psbC distinguishes N. vanseea sp. nov. from the morphologically similar species Navicula cincta and Navicula microdigitoradiata.

The Clarion-Clipperton Zone (CCZ) in the tropical East Pacific is a region of interest for deep-sea mining due to its underwater deposits of polymetallic nodules containing economically important metals such as nickel, copper, and cobalt. It is also a region of extensive baseline studies aiming to describe the state of the environment, including the biodiversity of the benthic fauna. An abundant component of the abyssal plain ecosystem consists of sessile fauna which encrusts polymetallic nodules and are vulnerable to potential impacts arising from exploitation activities, particularly removal of substrate. Therefore, this fauna is often considered to have key species whose genetic connectivity should be studied to assess their ecological resilience. One such species is Abyssoprimnoa gemina Cairns, 2015, a deep-sea coral from the CCZ whose presence in the Interoceanmetal Joint Organization (IOM) claim area has been confirmed during samplings. In this study, we used next-generation sequencing (NGS) to obtain the 18S nuclear rRNA gene and the complete mitochondrial genome of A. gemina from IOM exploration area. The mitogenome is 18,825 bp long and encodes for 14 protein coding genes, 2 rRNAs, and a single tRNA. The two phylogeny reconstructions derived from these data confirm previous studies and display A. gemina within a highly supported cluster of seven species whose mitogenomes are all colinear and of comparable size. This study also demonstrates the suitability of NGS for DNA barcoding of the benthic megafauna of the CCZ, which could become part of the IOM protocol for the assessment of population diversity and genetic connectivity in its claim area.

Craspedostauros E.J. Cox is a diatom genus comprising 17 taxa reported from various regions of the world. While many species of Craspedostauros are epibiontic, the taxa have variable ecological preferences. In this study we formally describe Craspedostauros nazmii sp. nov., an epilithic species discovered along the Turkish Black Sea Coast, based on light and scanning electron microscopy. Craspedostauros nazmii sp. nov. is characterized by valves that are lanceolate to narrowly lanceolate, slightly constricted near the apices with uniseriate, parallel throughout the whole valve, transapical striae and and the presence of an apical silica flap. The areolae are distributed over the valve face and the mantle. The differences and similarities between C. nazmii sp. nov. and established species of Craspedostauros are discussed. Based on shape and morphometrics, the most similar species is Craspedostauros capensis, but it is easily distinguished from C. nazmii sp. nov. by its lack of an apical silica flap.

IntroductionThere is little information on evolutionarily ancient eukaryotes, which are often referred to as basal eukaryotes, in Arctic waters. Despite earlier studies being conducted in the Russian White Sea, only few have been reported.MethodsFollowing a shotgun sequence survey of diatom cultures from Sugluk Inlet off the Hudson Strait in Northern Québec, we obtained the complete mitochondrial genome and the operon of nuclear ribosomal RNA genes from a strain that matches that of Ancyromonas sigmoides (Kent, 1881).ResultsThe sequence of the mitogenome retrieved was 41,889 bp in length and encoded 38 protein-coding genes, 5 non-conserved open-reading frames, and 2 rRNA and 24 tRNA genes. The mitogenome has retained sdh2 and sdh3, two genes of the succinate dehydrogenase complex, which are sometimes found among basal eukaryotes but seemingly missing among the Malawimonadidae, a lineage sister to Ancyromonadida in some phylogenies. The phylogeny inferred from the 18S rRNA gene associated A. sigmoides from Sugluk Inlet with several other strains originating from the Arctic. The study also unveiled the presence of a metagenomic sequence ascribed to bacteria in GenBank, but it was clearly a mitochondrial genome with a gene content highly similar to that of A. sigmoides, including the non-conserved open-reading frames.DiscussionAfter re-annotation, a phylogeny was inferred from mitochondrial protein sequences, and it strongly associated A. sigmoides with the misidentified organism, with the two being possibly conspecific or sibling species as they are more similar to one another than to species of the genus Malawimonas. Overall our phylogeny showed that the ice associated ancryomonads were clearly distinct from more southerly strains.

We determined the complete mitogenome sequence of the bioluminescent fish Malacosteus niger using long-read sequencing technologies. The 21,263 bp mitogenome features a complex structure with two copies of a 1198-bp inverted-repeat and a region of 2616-bp containing alternating copies of 16 and 26 bp repeat elements. Whole mitogenome phylogenies inferred from both nucleotide and amino-acid datasets place M. niger among Melanostomiinae. The need for additional complete mitogenome sequences from the subfamily Malacosteinae is discussed.

Abstract The complete chloroplast genome of Secale cereale ssp. segetale (Zhuk.) Roshev. (Poaceae: Triticeae) was sequenced and analyzed to better use its genetic resources to enrich rye and wheat breeding. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other complete chloroplast genomes of the five Secale species, and multigene phylogeny. As a result of the study, it was determined that the chloroplast genome is 137,042 base pair (bp) long and contains 137 genes, including 113 unique genes and 24 genes which are duplicated in the IRs. Moreover, a total of 29 SSRs were detected in the Secale cereale ssp. segetale chloroplast genome. The phylogenetic analysis showed that Secale cereale ssp. segetale appeared to share the highest degree of similarity with S. cereale and S. strictum. Intraspecific diversity has been observed between the published chloroplast genome sequences of S. cereale ssp. segetale. The genome can be accessed on GenBank with the accession number (OL688773).

Abstract The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56′41.4′′N, 24°48′44.6′′E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński & Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.

We sequenced the complete mitochondrial genome of the flatworm Australopacifica atrata. The species, originally described from New South Wales, Australia, has been found in various locations in the British Isles, New Zealand and in the United States of America; it is thus potentially invasive. The genome is 16513 bp long, encodes for 12 protein coding genes, two ribosomal RNA genes and 20 tRNA genes, and is completely colinear with the other two available Rhynchodeminae. In addition, it shares with them some unusual characters discriminating them from members of the other subfamilies of Geoplanidae, the most noticeable being the extra length of its cox2 gene. The data allow a reliable multigene phylogeny to be derived, and also provide a means of accurate biomonitoring of possible invasiveness by A. atrata.

Background and aims – Kützing separated the genus Achnanthidium from the genus Achnanthes based on two species: Achnanthes minutissima and Achnanthidium microcephalum. These two genera were distinguished by the presence of stalks in the Achnanthes genus and their absence in Achnanthidium. Before electron microscopy, the difference between Achnanthes and Achnanthidium was not clear, especially in Achnanthidium minustissimum sensu lato. The aim of the study is to describe three new species of Achnanthidium from Lake Salda. Material and methods – Lake Salda is located in southwestern Anatolia, in Turkey. The diatoms were collected seasonally from four stations in the lake between 2016 and 2020, from different substrata (epipelic, epiphytic, and epilithic). Key results – Three new species belonging to the genus Achnanthidium have been found in Lake Salda, Turkey. Based on the morphological observations, all new taxa are part of the Achnanthidium minutissimum complex. Achnanthidium barlasii sp. nov. and A. dumlupinarii sp. nov. show a high degree of similarity to each other, but can be separated based on valve outline and a denser areolation, especially in striae close to the apices of the raphe valve. Both species can be distinguished from A. minutissimum based on more separate apices and less elliptic valves. In the case of A. dumlupinarii sp. nov., large specimens show slight undulations of the valve, which is a unique feature. Achnanthidium anatolicum sp. nov. is the most characteristic based on its valve width, broadly rounded valve apices, and almost straight valves in girdle view. All newly described Achnanthidium species can be found in lentic environments, with alkaline water and high calcium ion content. Conclusion – The newly described taxa occurred in the unique habitat of a soda lake. The environment of the lake is highly alkaline, rich in magnesium and calcium, and derived from limestone and dolomitic limestone rocks.

In this study, samples were collected from the Java Sea coasts, from the South China Sea in Hainan Island coasts and Quảng Yên region and Rú Chá mangrove near Hue in Central Vietnam. In studied samples a total of eight Luticola species have been observed. Three of the taxa studied are described herein as species new to science – Luticola orientalis sp. nov., L. cribriareolata sp. nov. and L. halongiana sp. nov. Under light microscopy (LM) L. orientalis sp. nov. and L. cribriareolata sp. nov. are similar with rhombic-lanceolate to rhombic/ elliptic-lanceolate to elliptic valve shapes and narrowly rounded apices. Both species can be easily distinguished by stria density (higher density in L. orientalis). Under SEM L. cribriareolata is characterized by cribrate areola occlusions, a character thus far observed only in three established species. The remaining species of the whole genus known thus far are characterized by hymenate areola. Similar morphology Luticola species have been observed from tropical mangrove forests from Madagascar but they all can be easily distinguished based on the lack of grooves in the central area. The third species – L. halongiana sp. nov. has rhombic-elliptic to rhombic-lanceolate valves with broadly rounded to slightly protracted apices in larger specimens. This species has a relatively broad central area. Also unique among brackish-water Luticola is the small, rounded stigma positioned almost midway between the valve center and valve margin. In the habitats from which the new species are described we also identified five established Luticola taxa including, L. belawanensis, L. celebesica, L. inserata, L. seposita and L. tropica. For those species we provide detailed SEM characteristics of valve ultrastructure, as well as the range of environmental conditions and geographic distribution within the study area.

Haslea ostrearia represents the model species of blue diatoms, a cluster of benthic marine species all belonging to the genus Haslea, noticeable for producing a blue pigment called marennine famous for its greening activity on the gills of bivalves but also for its potential in biotechnology. The exact distribution of H. ostrearia is unknown. It has been long considered a cosmopolitan diatom, but recent studies provided evidence for cryptic diversity and the existence of several other blue species, some of them inhabiting places where diatoms described as H. ostrearia had previously been observed. Recently, a marine diatom with blue tips was isolated into clonal culture from a plankton net sample from Kei Mouth on the Indian Ocean coast of South Africa. It was identified as H. ostrearia through a combination of LM/SEM microscopy and molecular analysis. This constitutes the first established record of this species from South Africa and the Indian Ocean and the second record for the southern hemisphere. Molecular barcoding clearly discriminated the South African strain from an Australian strain and cox1 based molecular phylogeny associated it instead with strains from the French Atlantic Coast, raising questions about the dispersal of this species. The complete mitochondrial and plastid genomes were compared to those of Haslea nusantara and Haslea silbo. Multigene phylogenies performed with all protein-coding genes of the plastome and the mitogenome associated H. ostrearia with H. silbo. In addition, complete sequences of circular plasmids were obtained and one of them showed an important conservation with a plasmid found in H. silbo.

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.

The current article focuses on the morphological and molecular characterization of the often inconspicuous genus Amicula. This recently erected genus from brackish and marine sediments was monotypic but here we describe two new tropical species: Amicula micronesica sp. nov. and Amicula vermiculata sp. nov. Once considered an incertae sedis genus regarding its higher rank taxonomy, its position among the family Diploneidaceae is proposed here by molecular phylogenetics. The complete plastid and mitochondrial genomes of Amicula micronesica sp. nov. are also presented here. It appears that the 177614-bp long mitogenome is the biggest yet recorded among stramenopiles, due to its invasion by 57 introns. Moreover, it utilizes the genetic code 4 for translation instead of the code 1 usually found among diatoms.

We sequenced the chloroplast genome of Poterioochromonas malhamensis (Pringsheim) R.A.Andersen strain SZCZR2049, which originates from Van Lake in Turkey. This genome is 133,923 bp long, and like those currently available for six phototrophic chrysophytes, it displays a long, gene-rich inverted repeat and a very short single-copy region. Compared to its chrysophyte counterparts, the P. malhamensis inverted repeat differs noticeably in gene content and the whole genome is missing 11 protein-coding genes. The maximum likelihood phylogeny inferred from concatenated protein-coding genes positioned P. malhamensis among the chrysophytes sensu lato as sister to the clade containing the Synurales (Synurophyceae) and Chromulinales (Chrysophyceae).

The focus of this study was to determine the mating type of Schizostauron trachyderma and examine the relationship between cell size (life cycle), lipid droplet size, and lipid content among diatoms with similar cell dimensions. To accomplish that, we have chosen monoclonal cultures of two closely related diatom species, namely S. trachyderma and S. rawaii. In a series of experiments, we successfully induced sexual reproduction within S. trachyderma strains to reconstruct the whole cell cycle involving cells of the maximum (initial cells) and minimum viable size for a given species. The mating-type and sexual reproduction stages were described and documented. A unique experimental setting involved initial cell isolation and their lipid droplet examination using flow cytometry and confocal microscopy after Nile Red staining. The results of the series of experiments indicate correlations between cell size, the number of neutral lipids per cell, and the size of lipid droplets, suggesting that cell capacity for lipid accumulation is dependent on their position in the life cycle.

Background New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. Methods Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium “black”, and the morphology of a species previously reported as Diversibipalium “blue”. Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. Results The new species Humbertium covidum n. sp. (syn: Diversibipalium “black” of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium “blue” of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position. Conclusion Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.

We report the complete chloroplast genome of the MED1 strain of Nephroselmis pyriformis from the Eastern Mediterranean Sea. At 111,026 bp, this genome is smaller and more compact than those of Nephroselmis olivacea and Nephroselmis astigmatica, and in contrast to the latter taxa, its inverted repeat contains no complete protein-coding genes. It encodes 3 rRNAs, 33 tRNAs and 94 proteins. Maximum likelihood analysis of a concatenated set of chloroplast genes from green algae belonging to deep-diverging lineages positioned the three Nephroselmis species in a strongly supported clade in which N. pyriformis is sister to N. astigmatica.

In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.

Background and aims – The present study aims to describe a new species of pennate blue diatom from the genus Haslea, H. nusantara sp. nov., collected from Semak Daun Island, the Seribu Archipelago, in Indonesian marine waters.Methods – Assessment for species identification was conducted using light microscopy, Scanning Electron Microscopy and molecular techniques. The morphological characteristics of H. nusantara have been described, illustrated and compared to other morphologically similar blue Haslea taxa, distributed worldwide. Additionally, molecular characterization was achieved by sequencing plastidial and mitochondrial genomes.Key results – This new species, named Haslea nusantara, cannot be discriminated by its morphology (stria density) but it is characterized by its gene sequences (rbcL chloroplast gene and cox1 mitochondrial gene). Moreover, it differentiates from other blue Haslea species by the presence of a thin central bar, which has been previously reported in non-blue species like H. pseudostrearia. The complete mitochondrion (36,288 basepairs, bp) and plastid (120,448 bp) genomes of H. nusantara were sequenced and the gene arrangements were compared with other diatom genomes. Phylogeny analyses established using rbcL indicated that H. nusantara is included in the blue Haslea cluster and close to a blue Haslea sp. found in Canary Islands (H. silbo sp. ined.).Conclusions – All investigations carried out in this study show that H. nusantara is a new blue-pigmented species, which belongs to the blue Haslea clade, with an exceptional geographic distribution in the Southern Hemisphere.

Background and aims – The diatom genus Simonsenia has been considered for some time a minor taxon, limited in its distribution to fresh and slightly brackish waters. Recently, knowledge of its diversity and geographic distribution has been enhanced with new species described from brackish-marine waters of the southern Iberian Peninsula and from inland freshwaters of South China, and here we report novel Simonsenia from fully marine waters.Methods – New isolates of Simonsenia species were obtained from marine waters, the littoral zone of the Korean Yellow Sea coast and the Gulf of Mexico in Corpus Christi (Texas), and documented in LM, SEM and with DNA sequence data (plastid-encoded rbcL and psbC). Phylogenetic trees of raphid diatoms were constructed to assess the relationships of the new species and of the genus as a whole.Key results and conclusions – Two novel species of Simonsenia (S. eileencoxiae and S. paucistriata) are described and a further putative taxon is characterized morphologically. The molecular phylogeny of the new Simonsenia species and previously sequenced species supports both the monophyly of the genus and its place within the Bacillariaceae. The Simonsenia clade clusters with clades composed of Cylindrotheca, Denticula and some Nitzschia spp. (including N. amphibia, N. frustulum, N. inconspicua). Hence Simonsenia is firmly positioned within the Bacillariaceae by molecular phylogenies, confirming its position within this group based on the possession of a canal raphe and its ultrastructure, and rejecting its classification within the Surirellaceae. Morphological data from the new Simonsenia species is typical for the genus, with a “simonsenioid” canal raphe type supported over the valve face with fenestral braces, alar canals connecting the canal raphe with the cell lumen, and the presence of fenestrae between the alar canals externally. Our results indicate unequivocally that the biogeography and the biodiversity of Simonsenia remain highly underestimated.

We describe the new species Gomphonemopsis sieminskae from brackish waters of the East China Sea littoral near Ningbo, China. Two diatom strains isolated from Ulva sp. were successfully grown, then analyzed by light (LM) and scanning electron (SEM) microscopy. The new species is compared to known Gomphonemopsis species, and similarities to G. pseudoexigua and G. obscurum are emphasized. Although the size metric data overlap and the external views are fairly similar, the two taxa differ in their valve interior. Molecular barcoding strongly discriminated G. sieminskae from G. cf. exigua, while rbcL gene-based phylogeny showed G. sieminskae to be sister to Phaeodactylum tricornutum. In this respect our results confirm the recent discovery, based on molecular data, that Gomphonemopsis is a close-relative taxon to Phaeodactylum, and place it in Phaeodactylaceae instead of Rhoicospheniaceae as inferred solely from morphology.

A water sample was obtained from an arheic oasis in the deep Sahara Desert, the Gueltates Afilal in Tamanrasset (Algeria). Five diatom strains were isolated, cultivated and identified as Tryblionella apiculata, Nitzschia supralitorea, Fistulifera saprophila, Navicula veneta and Thalassiosira pseudonana using a combination of scanning electron microscopy and next generation sequencing. The diatoms identified are opportunistic and cosmopolitan species with known tolerances to organic pollution and variations in salinities, often found in meso- and polysaprobic zones in Europe. Their complete organellar genomes have been sequenced and some exhibit features never observed among diatoms before. To our knowledge this is the first time that living specimens of diatoms from the deep Sahara are identified using modern taxonomical tools in the frame of a study which also demonstrates the possibility to cultivate such material in laboratories for further experiments on biogeography and bioindication. Our study also suggests that European identification keys can be effective when employed on diatoms from the Sahara.

The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.

Background The land flatworm Amaga expatria Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since. Methods On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA. Results We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.

The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).

We report the chloroplast genome sequence of Nanofrustulum shiloi, a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp N. shiloi genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, psbY is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloroplast ORFs found in other diatom species. The genome features a single intron, a group II intron in petB. Phylogenomic analysis identified N. shiloi at a basal position within the araphid 2 clade.

We sequenced the complete mitogenome of the invasive flatworm Parakontikia ventrolineata (Platyhelminthes, order Tricladida, family Geoplanidae). The genome is 17,210 bp long, and displays common unusual characteristics shared with Platydemus manokwari, such as its colinearity, an overlap between ND4L and ND4 genes and an unusually long cox2 genes. Both Parakontikia and Platydemus are members of the subfamily Rhynchodeminae and their close relationships are supported by the maximum likelihood phylogeny inferred from the protein-coding genes.

We sequenced the complete mitogenome of the invasive flatworm Platydemus manokwari (Tricladida order, Geoplanidae family). This 19,959-bp genome contains 36 genes and is almost colinear with the mitogenomes of the two other species previously sampled from the Geoplanidae, Bipalium kewense and Obama nungara, both of which feature an extra tRNA gene. A single P. manokwari gene, encoding tRNA-Cys, is rearranged compared to its orthologs in the latter flatworms. Another distinctive trait of P. manokwari is the unusually large cox2 gene. In the phylogeny inferred from 12 proteins, P. manokwari formed a strongly supported clade with B. kewense and O. nungara.

We sequenced the complete mitogenome of a specimen of Cymbiola nobilis (Neogastropoda, Volutidae) from Phú Quốc Island in Vietnam. The mitogenome of this predatory sea snail is 16,314-bp long and comprises the typical set of genes encoding 13 proteins, 2 rRNAs, and 22 tRNAs. It features a complex control region that contains two copies of an inverted repeat sequence separated by an AT-rich region, a characteristic previously observed in a few other gastropods. Phylogenetic analysis based on all protein-coding genes revealed that the Volutidae form a strongly supported clade.

We sequenced the complete mitogenome of the red chut-chut snail Cerithidea obtusa, from the Cần Giờ mangrove in Vietnam. The mitogenome is 15,708 bp long. It is colinear with the mitogenomes of other members of the superfamily Cerithioidea, and the maximum-likelihood phylogeny obtained with the cox1, cox2 and cox3 genes of several Caenogastropoda associated all Cerithioidea together inside a strongly supported clade.

Specimens of a new species of blue diatoms from the genus Haslea Simonsen were discovered in geographically distant sampling sites, first in the Canary Archipelago, then North Carolina, Gulf of Naples, the Croatian South Adriatic Sea, and Turkish coast of the Eastern Mediterranean Sea. An exhaustive characterization of these specimens, using a combined morphological and genomic approach led to the conclusion that they belong to a single new to science cosmopolitan species, Haslea silbo sp. nov. A preliminary characterization of its blue pigment shows similarities to marennine produced by Haslea ostrearia, as evidenced by UV–visible spectrophotometry and Raman spectrometry. Life cycle stages including auxosporulation were also observed, providing data on the cardinal points of this species. For the two most geographically distant populations (North Carolina and East Mediterranean), complete mitochondrial and plastid genomes were sequenced. The mitogenomes of both strains share a rare atp6 pseudogene, but the number, nature, and positions of the group II introns inside its cox1 gene differ between the two populations. There are also two pairs of genes fused in single ORFs. The plastid genomes are characterized by large regions of recombination with plasmid DNA, which are in both cases located between the ycf35 and psbA genes, but whose content differs between the strains. The two sequenced strains hosts three plasmids coding for putative serine recombinase protein whose sequences are compared, and four out of six of these plasmids were highly conserved.

We sequenced the complete mitogenome of a Baltic Sea specimen of the invasive bivalve Rangia cuneata. The mitogenome is 18,993 bp long and encodes 13 proteins, 2 rRNAs, and 22 tRNAs. A large intergenic region between ND6 and ND2 contains an open reading frame that may originate from duplication of ND2. The R. cuneata mitogenome is rearranged in gene order relative to previously sequenced mitogenomes of Mactroidea.

We obtained the complete mitogenome of Proschkinia sp. strain SZCZR1824, a strain belonging to a poorly known diatom genus with no previous molecular data. This genome is 48,863 bp long, with two group I introns in rnl and three group II introns in cox1. Using mitogenomic data, Proschkinia sp. was recovered with Fistulifera solaris, far distant from Navicula and Nitzschia, two genera with which Proschkinia has sometimes been associated based on morphology.

We sequenced the complete mitogenome of Marenzelleria neglecta, a non-indigenous polychaete of the Baltic Sea originating from North America. This is the first complete mitogenome made available for the family Spionidae. The genome is 15,339 bp with a gene order identical to the generic order of the Pleistoannelida. The multigene maximum likelihood phylogeny, based on all protein-coding genes, weakly resolved the position of M. neglecta, as it tended to asssociate it with species representing the basal lineage of Annelids. This result underlines the need for more mitogenomes of Spionidae in order to improve the accuracy of their phylogeny.

We sequenced the chloroplast genome of Skeletonema pseudocostatum clone SZCZ 1832 from Algeria. The genome is 127,013 bp long. The inverted repeat region is 18,240 bp long and the order of the genes it encodes appeared as highly conserved when compared with other Thalassiosirales. The maximum likelihood phylogeny also evidenced the belonging of S. pseudocostatum within the Thalassiosirales. This chloroplastic genome is so far the first made available for the cosmopolitan and ecologically important genus Skeletonema.

We determined the sequence of the complete mitogenome of Bipalium kewense, an invasive land flatworm with worldwide distribution. All 37 genes encoded on this 15,666-bp genome reside on the same DNA strand. Phylogenomic analyses of mitochondrial proteins from taxa of the order Tricladida associated B. kewense with another invasive species of land planarians (Obama sp.).

In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.

We obtained the mitogenome sequence of a Black Sea isolate of the kinetoplastid Bodo saltans. This sequence consists of two contigs totaling 24,925 bp and encodes ten protein-coding genes, one conserved ORF and one rRNA gene. Alignment of the Black Sea mitogenome with the limited sequence data currently available in public databases for another strain of B. saltans revealed significant genetic divergence between the two isolates. Maximum likelihood phylogenetic inference clearly resolved the Bodonidae from the Trypanosomatidae.

The complete mitochondrial genome of the oyster Crassostrea belcheri from the Cần Giò’ mangrove in Vietnam has been sequenced. It consists of a circular DNA molecule of 21020 base pairs (bp), coding for 12 proteins, 20 transfer RNAs, and two ribosomal RNAs. Like the mitogenomes of Crassostrea iredalei and Crassostrea sp. DB1, it contains a non-coding region and two ORFs. The C. belcheri mitogenome provides information that could improve the molecular phylogeny of Asian oysters and be useful to the development of oyster aquaculture in South East Asia.

The search for novel compounds of marine origin has increased in the last decades for their application in various areas such as pharmaceutical, human or animal nutrition, cosmetics or bioenergy. In this context of blue technology development, microalgae are of particular interest due to their immense biodiversity and their relatively simple growth needs. In this review, we discuss about the promising use of microalgae and microalgal compounds as sources of natural antibiotics against human pathogens but also about their potential to limit microbial infections in aquaculture. An alternative to conventional antibiotics is needed as the microbial resistance to these drugs is increasing in humans and animals. Furthermore, using natural antibiotics for livestock could meet the consumer demand to avoid chemicals in food, would support a sustainable aquaculture and present the advantage of being environmentally friendly. Using natural and renewable microalgal compounds is still in its early days, but considering the important research development and rapid improvement in culture, extraction and purification processes, the valorization of microalgae will surely extend in the future.