Algal taxonomy: a road to nowhere?

Hidden diversity in high-latitude Southern Hemisphere environments: Reinstatement of the genus Rama and description of Vandenhoekia gen. nov. (Cladophoraceae, Ulvophyceae, Chlorophyta), two highly variable genera

The continental coasts and remote islands in the high-latitude Southern Hemisphere, including the subantarctic region, are characterized by many endemic species, high abundance of taxa, and intermediate levels of biodiversity. The macroalgal flora of these locations has received relatively little attention. Filamentous green algae are prolific in the intertidal of southern islands, but the taxonomy, distribution, and evolutionary history of these taxa are yet to be fully explored, mostly due to the difficulty of access to some of these locations. In this study, we examined specimens of the order Cladophorales from various locations in the high-latitude Southern Hemisphere including the subantarctic (the Auckland Islands, Bounty Islands, Campbell Island, Macquarie Island, and Kerguelen Islands), as well as mainland New Zealand, the Chatham Islands, Chile, and Tasmania. The analyses of the rDNA sequences of the samples revealed the existence of two new clades in a phylogeny of the Cladophoraceae. One of these clades is described as the novel genus Vandenhoekia gen. nov., which contains three species that are branched or unbranched. The amended genus Rama is reinstated to accommodate the other clade, and contains four species, including the Northern Hemisphere "Cladophora rupestris." In Rama both branched and unbranched morphologies are found. It is remarkable that gross morphology is not a predictor for generic affiliations in these algae. This study illustrates that much can still be learned about diversity in the Cladophorales and highlights the importance of new collections, especially in novel locations.

Applying an internal transcribed spacer as a single molecular marker to differentiate between Tetraselmis and Chlorella species

In the realm of applied phycology, algal physiology, and biochemistry publications, the absence of proper identification and documentation of microalgae is a common concern. This poses a significant challenge for non-specialists who struggle to identify numerous eukaryotic microalgae. However, a promising solution lies in employing an appropriate DNA barcoding technique and establishing comprehensive databases of reference sequences. To address this issue, we conducted a study focusing on the molecular characterization and strain identification of Tetraselmis and Chlorella species, utilizing the internal transcribed spacer (ITS) barcode approach. By analyzing the full nuclear ITS region through the Sanger sequencing approach, we obtained ITS barcodes that were subsequently compared with other ITS sequences of various Tetraselmis and Chlorella species. To ensure the reliability of our identification procedure, we conducted a meticulous comparison of the DNA alignment, constructed a phylogenetic tree, and determined the percentage of identical nucleotides. The findings of our study reveal the significant value of the ITS genomic region as a tool for distinguishing and identifying morphologically similar chlorophyta. Moreover, our results demonstrate that both the ITS1 and ITS2 regions are capable of effectively discriminating isolates from one another; however, ITS2 is preferred due to its greater intraspecific variation. These results underscore the indispensability of employing ITS barcoding in microalgae identification, highlighting the limitations of relying solely on morphological characterization.

Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta)

Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.

Microcystis pangenome reveals cryptic diversity within and across morphospecies

Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.

Diversity of algae and their biotechnological potential

This chapter will discuss the diversity of algae and show that the diversity is much greater than just obligately oxygenic photosynthetic algae and that it includes many mixotrophic and heterotrophic organisms that are more similar to the major groups of microorganisms. The photosynthetic groups are seen as part of the plant kingdom, whereas the non-photosynthetic groups are not related to plants at all. The organisation of algal groups has become complex and confusing - The chapter will address the problems within this area of eukaryotic taxonomy. The metabolic diversity of algae and the ability to genetically engineer algae are key components in developing the biotechnology of algae. As more researchers become interested in exploiting algae for a number of industrial products, it is important to understand the relationships between different groups of algae and the relationships of algae with the rest of the living world.

The use of integrative taxonomy in Octocorallia (Cnidaria: Anthozoa): a literature survey

Octocorals are problematic in their systematics, and the extent of their biodiversity is poorly understood. Integrative taxonomy (the use of two or more lines of evidence for the delimitation and description of taxa) is seen as a promising way to produce more robust species hypotheses and achieve taxonomic progress in this group. However, many octocoral descriptions continue to rely on morphological evidence alone, and the prevalence of integrative methods is unclear. Here, a literature survey was conducted to gain an overview of historical description rates and to examine trends in the publication of integrative descriptions between the years 2000 and 2020. We find that recent description rates are among the highest in the history of octocoral taxonomy, and although increasing, integrative taxon descriptions remain in the minority overall. We also find that integrative taxonomy has been applied unevenly across octocoral groups and geographical regions. Description rates show no signs of slowing, and no ceiling of total species richness has yet come into view. Coupled with a continued overreliance on morphological variation, particularly at the species level, this suggests that we might be adding to the workload of taxa requiring future revision faster than such instances can be resolved.

Community assessment of crustose calcifying red algae as coral recruitment substrates

Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and to their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) are a species rich group of seaweeds that have been identified as important recruitment substrates for scleractinian corals. Most studies on the settlement preference of coral larvae on CCRA use morphological species identifications that can lead to unreliable species identification and do not allow for examining species-specific interactions between coral larvae and CCRA. Accurate identifications of CCRA species is important for coral reef restoration and management to assess CCRA community composition and to detect CCRA species that are favored as coral recruitment substrates. In this study, DNA sequence analysis, was used to identify CCRA species to (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles and (2) assess if the coral Acropora surculosa preferred any of these CCRA species as recruitment substrates. The CCRA community assemblages on the coral recruitment tiles was species-rich, comprising 27 distinct CCRA species of the orders Corallinales and Peyssonneliales which constitute new species records for Guam. Lithophylloideae sp. 1 (Corallinales) was the CCRA species that was significantly favored by coral larvae as a recruitment substrate. Lithophylloideae sp. 1 showed to hold a valuable ecological role for coral larval recruitment preference. Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and contained most A. surculosa recruits. DNA barcoding revealed a high taxonomic diversity of CCRA species on a microhabitat scale and provided detailed insight into the species-specific ecological interactions between CCRA and corals. With a steady decline in coral cover, detailed information on species interactions that drive reef recovery is valuable for the planning of marine management actions and restoration efforts.

The study of algal diversity from fresh water bodies of Chimmony Wildlife Sanctuary, Kerala, India

The algal diversity of the freshwater ecosystem is very significant because they are the primary energy producers in the food web. The study for the algal diversity was conducted at Chimmony Wildlife Sanctuary, Thrissur, Kerala, India, from selected sampling sites (Pookoyil thodu, Kidakkapara thodu, Viraku thodu, Nellipara thodu, Anaporu thodu, Kodakallu thodu, Odan thodu, Mullapara thodu, Payampara thodu, Chimmony dam). The identified algal species belong to four different classes: Chlorophyceae, Euglenineae, Rhodophyceae, and Cyanophyceae. Sixty-one algal species were identified, represented by 37 genera, 22 families, and 14 orders. Among the four, Chlorophyceae was the dominant class.

Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. "desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata, supported by a high-quality genome assembly

Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. "desiccata" UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. "desiccata" UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.

Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms

Interactions between bacteria and phytoplankton in aqueous ecosystems are both complex and dynamic, with associations that range from mutualism to parasitism. This review focuses on algicidal interactions, in which bacteria are capable of controlling algal growth through physical association or the production of algicidal compounds. While there is some evidence for bacterial control of algal growth in the field, our understanding of these interactions is largely based on laboratory culture experiments. Here, the range of these algicidal interactions is discussed, including specificity of bacterial control, mechanisms for activity, and insights into the chemical and biochemical analysis of these interactions. The development of algicidal bacteria or compounds derived from bacteria for control of harmful algal blooms is reviewed with a focus on environmentally friendly or sustainable methods of application. Potential avenues for future research and further development and application of bacterial algicides for the control of algal blooms are presented.

Isolation and identification of microalgal strains with potential as carotenoids producers from a municipal solid waste landfill

Derived from their great capacity of adaptation, microalgae have several industrial applications, including pigment production for nutraceutical sector. However, the scarcity of studies on the diversity and life histories from several environments, highlight the need for more research on new species and habitats. Based on this, the present study assessed the microalgal diversity in water bodies of a municipal solid waste (MSW) landfill in Asturias (Spain). A total of 14 strains were successfully isolated and scaled up in liquid monocultures. They were identified through a combination of morphologic features with molecular assignation by DNA barcoding via the 18S and ITS1-5.8S-ITS2 genes. The results of the genetic procedures (BLAST assignments and the 18S and ITS1-5.8S-ITS2 genealogies) showed that 10 of the 14 assayed isolates were identified at the species level. The available genetic data were not sufficient for species classifications of the remaining isolates. It is possible that some might be new species not previously studied or described. Indeed, a new species, Coelastrella cogersae, was proposed in this study. Moreover, 3 of the 14 isolates (including the newly proposed species) exhibited caretogenic activity under specific conditions during the culture. These results are a great step forward in both the screening of lesser-known environments and the discovery of new sources of bioactive compounds. The study could be of great value to the nutraceutical industries and markets.

Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy

Contemporary delimitation of species and populations in the microbial domain relies on an integrative approach combining molecular and morphological techniques. In case of the dinophyte Peridinium volzii, a considerable number of infraspecific taxonomic entities have been reported, but it is unclear at present whether the corresponding traits are stable within reproductively isolated units or refer to intraspecific variability. We established 26 monoclonal strains from Central Europe with a morphology that is consistent for P. volzii and characterised them by sequences gained from the rRNA operon. Ten of such strains, representative for the entire diversity observed, were investigated in detail morphologically using light and electron microscopy. In the molecular tree, P. volzii was monophyletic, sister group of Peridinium willei, and three ITS ribotypes could be distinguished. Some traits corresponding to previously described varieties and forms were found in individual cells across the strains under investigation, but not as stable characters correlating to certain ribotypes. We also observed new morphological variability (e.g., unusual shape of plate 4″). Cell size and displacement of the cingulum were significantly different between certain ribotypes but in turn, such diagnostic traits are impossible to assign to already described taxa due to their ambiguity. Based on the small first apical plate as diagnostic trait and putative apomorphy, P. volzii is a characteristic species but the present data given, we are reserved to accept more than a single reproductive unit. Thus, more research is necessary, including a focus on species delimitation to putative close relatives such as Peridinium maeandricum.

Diversity and taxonomic revision of tribes Rhipileae and Rhipiliopsideae (Halimedaceae, Chlorophyta) based on molecular and morphological data

Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographic distribution. Our study provided an in-depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species-rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL, and 18S rDNA), and morpho-anatomic observations. Our results revealed an unexpected diversity of 38 morphologically validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in the tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.

The Structural Difference of Isobaric N-Glycans of Two Microalgae Samples Reveals Taxonomic Distance

Microalgae of the Chlorella clade are extensively investigated as an environmentally friendly source of renewable biofuels and high-value nutrients. In addition, essentially unprocessed Chlorella serves as wholesome food additive. A recent study on 80 commercial Chlorella preparations revealed an unexpected variety of protein-linked N-glycan patterns with unprecedented structural features, such as the occurrence of arabinose. Two groups of products exhibited a characteristic major N-glycan isobaric to the Man2GlcNAc2XylFuc N-glycan known from pineapple stem bromelain, but tandem mass spectrometry (MS/MS) analysis pointed at two types of N-glycan different from the bromelain structure, as well as from each other. Here we report the exact structures of these two novel N-glycan structures, elucidated by nuclear magnetic resonance spectroscopy and MS/MS, as well as on their phylogenetic context. Despite their humble size, these two N-glycans exhibited a very different design with structural features unrelated to those recently described for other Chlorella-clade strains. The major glycans of this study presented several novel structural features such as substitution by arabinose or xylose of the internal N-acetylglucosamine, as well as methylated sugars. ITS1-5.8S-ITS2 rDNA barcode analyses revealed that the xylose-containing structure derived from a product primarily comprising Scenedesmus species, and the arabinose-containing glycan type related to Chlorella species (SAG211-34 and FACHB-31) and to Auxenochlorella. This is another example where characteristic N-glycan structures distinguish phylogenetically different groups of microalgae.

Trends in the detection of aquatic non-indigenous species across global marine, estuarine and freshwater ecosystems: A 50-year perspective

Aim:

The introduction of aquatic non-indigenous species (ANS) has become a major driver for global changes in species biogeography. We examined spatial patterns and temporal trends of ANS detections since 1965 to inform conservation policy and management.

Location:

Global.

Methods:

We assembled an extensive dataset of first records of detection of ANS (1965–2015) across 49 aquatic ecosystems, including the (a) year of first collection, (b) population status and (c) potential pathway(s) of introduction. Data were analysed at global and regional levels to assess patterns of detection rate, richness and transport pathways.

Results:

An annual mean of 43 (±16 SD) primary detections of ANS occurred–one new detection every 8.4 days for 50 years. The global rate of detections was relatively stable during 1965–1995, but increased rapidly after this time, peaking at roughly 66 primary detections per year during 2005–2010 and then declining marginally. Detection rates were variable within and across regions through time. Arthropods, molluscs and fishes were the most frequently reported ANS. Most ANS were likely introduced as stowaways in ships’ ballast water or biofouling, although direct evidence is typically absent.

Main conclusions:

This synthesis highlights the magnitude of recent ANS detections, yet almost certainly represents an underestimate as many ANS go unreported due to limited search effort and diminishing taxonomic expertise. Temporal rates of detection are also confounded by reporting lags, likely contributing to the lower detection rate observed in recent years. There is a critical need to implement standardized, repeated methods across regions and taxa to improve the quality of global-scale comparisons and sustain core measures over longer time-scales. It will be fundamental to fill in knowledge gaps given that invasion data representing broad regions of the world's oceans are not yet readily available and to maintain knowledge pipelines for adaptive management.

Chlorocladiella gen. nov. (Pithophoraceae, Cladophorales, Chlorophyta), Including Four New Species From Various Freshwater Habitats in China

Samples of Pithophoraceae, collected in diverse freshwater and damp terrestrial habitats from tropical and subtropical China, were characterized morphologically and ultrastructurally, and their phylogenetic position was determined based on nuclear ribosomal DNA sequences. Our phylogenetic analysis resolved a novel lineage of Pithophoraceae, sister to Aegagropilopsis. Based on our phylogenetic results, morphological observations and comparative rDNA ITS2 secondary structure analysis, we propose Chlorocladiella gen. nov., characterized by a well-developed system of prostrate filaments, and describe four new species, C. cochlea sp. nov., C. erecta sp. nov., C. medogensis sp. nov., and C. pisformis sp. nov. Two species were found growing on damp soil, which is an unusual habitat for cladophoralean green algae, indicating that the diversity of Cladophorales in terrestrial habitats may be greater than currently recognized.

Taxonomic determination of the cryptogenic red alga, Chondria tumulosa sp. nov., (Rhodomelaceae, Rhodophyta) from Papahānaumokuākea Marine National Monument, Hawai'i, USA: A new species displaying invasive characteristics

Survey cruises by the National Oceanic and Atmospheric Administration (NOAA) in 2016 and 2019 yielded specimens of an undetermined red alga that rapidly attained alarming levels of benthic coverage at Pearl and Hermes Atoll, Papahānaumokuākea Marine National Monument, Hawai'i. By 2019 the seaweed had covered large expanses on the northeast side of the atoll with mat-like, extensive growth of entangled thalli. Specimens were analyzed using light microscopy and molecular analysis, and were compared to morphological descriptions in the literature for closely related taxa. Light microscopy demonstrated that the specimens likely belonged to the rhodomelacean genus Chondria, yet comparisons to taxonomic literature revealed no morphological match. DNA sequence analyses of the mitochondrial COI barcode marker, the plastidial rbcL gene, and the nuclear SSU gene confirmed its genus-level placement and demonstrated that this alga was unique compared to all other available sequences. Based on these data, this cryptogenic seaweed is here proposed as a new species: Chondria tumulosa A.R.Sherwood & J.M.Huisman sp. nov. Chondria tumulosa is distinct from all other species of Chondria based on its large, robust thalli, a mat-forming tendency, large axial diameter in mature branches (which decreases in diameter with subsequent orders of branching), terete axes, and bluntly rounded apices. Although C. tumulosa does not meet the criteria for the definition of an invasive species given that it has not been confirmed as introduced to Pearl and Hermes Atoll, this seaweed is not closely related to any known Hawaiian native species and is of particular concern given its sudden appearance and rapid increase in abundance in the Papahānaumokuākea Marine National Monument; an uninhabited, remote, and pristine island chain to the northwest of the Main Hawaiian Islands.

Dictyosphaerium-like morphotype in terrestrial algae: what is Xerochlorella (Trebouxiophyceae, Chlorophyta)?1

Several strains of terrestrial algae isolated from biological soil crusts in Germany and Ukraine were identified by morphological methods as the widely distributed species Dictyosphaerium minutum (=Dictyosphaerium chlorelloides). Investigation of the phylogeny showed their position unexpectedly outside of Chlorellaceae (Trebouxiophyceae) and distantly from Chlorella chlorelloides, to which this taxon was attributed after revision of the genus Chlorella based on an integrative approach. SSU rRNA phylogeny determined the position of our strains inside a clade recently described as a new genus of the cryptic alga Xerochlorella olmiae isolated from desert biological soil crusts in the United States. Investigation of the morphology of the authentic strain of X. olmiae showed Dictyosphaerium-like morphology, as well as some other characters, common for our strains and morphospecies D. minutum. The latter alga was described as terrestrial and subsequently united with the earlier described aquatic representative D. chlorelloides because of their similar morphology. The revision of Chlorella mentioned above provided only one aquatic strain (D. chlorelloides), which determined its position in the genus. But terrestrial strains of the morphospecies were not investigated phylogenetically. Our study showed that the terrestrial D. minutum is not related to the morphologically similar D. chlorelloides (=Chlorella chlorelloides, Chlorellaceae), and instead represented a separate lineage in the Trebouxiophyceae, recently described as genus Xerochlorella. Therefore, revision of Xerochlorella is proposed, including nomenclatural combinations, epitypifications, and emendations of two species: X. minuta and X. dichotoma. New characters of the genus based on investigation of morphology and ultrastructure were determined.

Macroalgal germplasm banking for conservation, food security, and industry

Ex situ seed banking was first conceptualized and implemented in the early 20th century to maintain and protect crop lines. Today, ex situ seed banking is important for the preservation of heirloom strains, biodiversity conservation and ecosystem restoration, and diverse research applications. However, these efforts primarily target microalgae and terrestrial plants. Although some collections include macroalgae (i.e., seaweeds), they are relatively few and have yet to be connected via any international, coordinated initiative. In this piece, we provide a brief introduction to macroalgal germplasm banking and its application to conservation, industry, and mariculture. We argue that concerted effort should be made globally in germline preservation of marine algal species via germplasm banking with an overview of the technical advances for feasibility and ensured success.

Seaweed germplasm banking is an important resource for biodiversity conservation, human food security, and industry innovation. This Perspective article maintains that an international, coordinative initiative is needed to fully develop and capitalize on this resource.

The N-glycans of Chlorella sorokiniana and a related strain contain arabinose but have strikingly different structures

The many emerging applications of microalgae such as Chlorella also instigate interest in their ability to conduct protein modifications such as N-glycosylation. Chlorella vulgaris has recently been shown to equip its proteins with highly O-methylated oligomannosidic N-glycans. Two other frequently occurring species names are Chlorella sorokiniana and Chlorella pyrenoidosa-even though the latter is taxonomically ill defined. We analyzed by mass spectrometry and nuclear magnetic resonance spectroscopy the N-glycans of type culture collection strains of C. sorokiniana and of a commercial product labeled C. pyrenoidosa. Both samples contained arabinose, which has hitherto not been found in N-glycans. Apart from this only commonality, the structures differed fundamentally from each other and from that of N-glycans of land plants. Despite these differences, the two algae lines exhibited considerable homology in their ITS1-5.8S-ITS2 rDNA sequences. These drastic differences of N-glycan structures between species belonging to the very same genus provoke questions as to the biological function on a unicellular organism.

N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated

Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man₅GlcNAc₂) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It's possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

BACKGROUND

Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution.

RESULTS

To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795 ), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements.

CONCLUSION

This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Background

Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution.

Results

To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: 10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements.

Conclusion

This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4763-1) contains supplementary material, which is available to authorized users.

Seasonal recruitment and survival strategies of Palisada cervicornis comb. nov. (Ceramiales, Rhodophyta) in coral reefs

As marine tropical ecosystems deteriorate and lose biodiversity, their communities are shifting to being dominated by a few species, altering ecosystem's functioning and services. Macroalgae are becoming dominant on coral reefs, and are frequently observed outcompeting corals. Turf algal assemblages are the base of energy flow in these systems and one of the most abundant types of macroalgae on coral reefs, but little is known about their biology and diversity. Through molecular and morphological analyses, we identified the turf-forming species Laurencia cervicornis, and by studying seasonal recruitment and the impact of herbivorous fishes on its abundance, we describe its survival strategy. The molecular analyses used a total of 45 rbcL gene sequences including eight current genera within the Laurencia complex and two new sequences of L. cervicornis and strongly support the new combination of Palisada cervicornis comb. nov. In addition, a detailed morphological characterization including the description of reproductive structures is provided. Palisada cervicornis was seen recruiting in all seasons but was typically in low abundance. Specimens grown on tiles in fish exclosure cages were devoured in less than 4 h when offered to fishes. Even though many species of the Laurencia complex have chemicals that deter herbivory, species within the genus Palisada lack feeding deterrents and thus are highly palatable. We suggest that P. cervicornis is a palatable species that seems to survive in the community by obtaining a size-refuge from herbivory within turf communities.

Molecular phylogeny and taxonomic revision of the genus Wittrockiella (Pithophoraceae, Cladophorales), including the descriptions of W. australis sp. nov. and W. zosterae sp. nov

Wittrockiella is a small genus of filamentous green algae that occurs in habitats with reduced or fluctuating salinities. Many aspects of the basic biology of these algae are still unknown and the phylogenetic relationships within the genus have not been fully explored. We provide a phylogeny based on three ribosomal markers (ITS, LSU, and SSU rDNA) of the genus, including broad intraspecific sampling for W. lyallii and W. salina, recommendations for the use of existing names are made, and highlight aspects of their physiology and life cycle. Molecular data indicate that there are five species of Wittrockiella. Two new species, W. australis and W. zosterae, are described, both are endophytes. Although W. lyallii and W. salina can be identified morphologically, there are no diagnostic morphological characters to distinguish between W. amphibia, W. australis, and W. zosterae. A range of low molecular weight carbohydrates were analyzed but proved to not be taxonomically informative. The distribution range of W. salina is extended to the Northern Hemisphere as this species has been found in brackish lakes in Japan. Furthermore, it is shown that there are no grounds to recognize W. salina var. kraftii, which was described as an endemic variety from a freshwater habitat on Lord Howe Island, Australia. Culture experiments indicate that W. australis has a preference for growth in lower salinities over full seawater. For W. amphibia and W. zosterae, sexual reproduction is documented, and the split of these species is possibly attributable to polyploidization.

Historical biogeography of the highly diverse brown seaweed Lobophora (Dictyotales, Phaeophyceae)

The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98-121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (-75 to -60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.

Mismatch of morphological and molecular identifications in native and invasive subspecies of Codium fragile (Bryopsidophyceae, Chlorophyta)

Several subspecies are defined within Codium fragile, including the invasive C. fragile ssp. fragile, first reported in New Zealand in 1973. An endemic subspecies, C. fragile ssp. novae-zelandiae, is also found throughout New Zealand. The two subspecies exhibit morphological and molecular variation, although these have never been evaluated together. We compared variation between subspecies at locations in Auckland, identifying subspecies using rps3-rpl16 DNA sequence data, and assessing gross morphological differences, anatomical utricle characters and morphometrics. The taxonomic utility of the morphometric data sets was assessed by linear discriminant analysis. Utricle characters and measurements varied within individual thalli and between different preservation methods. The phenotypes of both subspecies were highly variable and influenced by environment. Accurate subspecies delimitation using morphological data was not possible; the discriminant analyses performed no better than chance for all combinations of the morphological data. Specimens from New Zealand, Canada, Australia and Ireland were sequenced using both the rps3-rpl16 and tufA plastid markers. The tufA elongation factor was shown to be a good candidate for differentiating subspecies of C. fragile. This marker is twice the length of the rps3-rpl16 spacer, shows greater variation between ssp. fragile and novae-zelandiae, and is less prone to sequencing error. A simple restriction enzyme digest of the tufA amplicon can distinguish ssp. fragile and ssp. novae-zelandiae. Our study expands the known range of the ssp. fragile in New Zealand, including the first record of this subspecies from the west coast of Auckland, and points to a need to re-evaluate morphological and molecular criteria for subspecies currently defined within C. fragile.

Genetic and morphological variation in an ecosystem engineer, Lithophyllum byssoides (Corallinales, Rhodophyta)

Lithophyllum byssoides is a common coralline alga in the intertidal zone of Mediterranean coasts, where it produces biogenic concretions housing a high algal and invertebrate biodiversity. This species is an ecosystem engineer and is considered a target for conservation efforts, but designing effective conservation strategies currently is impossible due to lack of information about its population structure. The morphological and molecular variation of L. byssoides was investigated using morphoanatomy and DNA sequences (psbA and cox2,3) obtained from populations at 15 localities on the Italian and Croatian coasts. Lithophyllum byssoides exhibited a high number of haplotypes (31 psbA haplotypes and 24 cox2,3 haplotypes) in the central Mediterranean. The psbA and cox2,3 phylogenies were congruent and showed seven lineages. For most of these clades, the distribution was limited to one or a few localities, but one of them (clade 7) was widespread across the central Mediterranean, spanning the main biogeographic boundaries recognized in this area. The central Mediterranean populations formed a lineage separate from Atlantic samples; psbA pair-wise divergences suggested that recognition of Atlantic and Mediterranean L. byssoides as different species may be appropriate. The central Mediterranean haplotype patterns of L. byssoides were interpreted as resulting from past climatic events in the hydrogeological history of the Mediterranean Sea. The high haplotype diversity and the restricted spatial distribution of the seven lineages suggest that individual populations should be managed as independent units.

Molecular phylogeny of the Cladophoraceae (Cladophorales, Ulvophyceae), with the resurrection of Acrocladus Nägeli and Willeella Børgesen, and the description of Lurbica gen. nov. and Pseudorhizoclonium gen. nov

The taxonomy of the Cladophoraceae, a large family of filamentous green algae, has been problematic for a long time due to morphological simplicity, parallel evolution, phenotypic plasticity, and unknown distribution ranges. Partial large subunit (LSU) rDNA sequences were generated for 362 isolates, and the analyses of a concatenated dataset consisting of unique LSU and small subunit (SSU) rDNA sequences of 95 specimens greatly clarified the phylogeny of the Cladophoraceae. The phylogenetic reconstructions showed that the three currently accepted genera Chaetomorpha, Cladophora, and Rhizoclonium are polyphyletic. The backbone of the phylogeny is robust and the relationships of the main lineages were inferred with high support, only the phylogenetic position of both Chaetomorpha melagonium and Cladophora rupestris could not be inferred unambiguously. There have been at least three independent switches between branched and unbranched morphologies within the Cladophoraceae. Freshwater environments have been colonized twice independently, namely by the freshwater Cladophora species as well as by several lineages of the Rhizoclonium riparium clade. In an effort to establish monophyletic genera, the genera Acrocladus and Willeella are resurrected and two new genera are described: Pseudorhizoclonium and Lurbica.

Discovery pattern and species number of scale insects (Hemiptera: Coccoidea)

Few investigations have been made of the species description trend of scale insects. The present study reports the discovery pattern and taxonomic efforts for this group based on global species and a literature dataset. In addition, three asymptotic models (Logistic, Gompertz, and Extreme Value) based on a discovery curve were used to predict the species number of scale insects. Our results showed that the species description rate has been changing over time, with certain peaks and valleys in the past 250 years. The mean number of species described per year was 30, with the highest number of 195 described species in 1985. The increasing number of authors and the almost constant proportion of species described by 10% most prolific authors since the 1900s suggested that taxonomic effort has been increasing over time. The Gompertz model with lowest AIC value suggested that there are about 10,450 species of scale insects on Earth, nearly 30% of which remain to be described. Our study offers insights into the discovery pattern of scale insect diversity.

DNA Barcoding Green Microalgae Isolated from Neotropical Inland Waters

This study evaluated the feasibility of using the Ribulose Bisphosphate Carboxylase Large subunit gene (rbcL) and the Internal Transcribed Spacers 1 and 2 of the nuclear rDNA (nuITS1 and nuITS2) markers for identifying a very diverse, albeit poorly known group, of green microalgae from neotropical inland waters. Fifty-one freshwater green microalgae strains isolated from Brazil, the largest biodiversity reservoir in the neotropics, were submitted to DNA barcoding. Currently available universal primers for ITS1-5.8S-ITS2 region amplification were sufficient to successfully amplify and sequence 47 (92%) of the samples. On the other hand, new sets of primers had to be designed for rbcL, which allowed 96% of the samples to be sequenced. Thirty-five percent of the strains could be unambiguously identified to the species level based either on nuITS1 or nuITS2 sequences' using barcode gap calculations. nuITS2 Compensatory Base Change (CBC) and ITS1-5.8S-ITS2 region phylogenetic analysis, together with morphological inspection, confirmed the identification accuracy. In contrast, only 6% of the strains could be assigned to the correct species based solely on rbcL sequences. In conclusion, the data presented here indicates that either nuITS1 or nuITS2 are useful markers for DNA barcoding of freshwater green microalgae, with advantage for nuITS2 due to the larger availability of analytical tools and reference barcodes deposited at databases for this marker.

Conservation of biodiversity through taxonomy, data publication, and collaborative infrastructures

Taxonomy is the foundation of biodiversity science because it furthers discovery of new species. Globally, there have never been so many people involved in naming species new to science. The number of new marine species described per decade has never been greater. Nevertheless, it is estimated that tens of thousands of marine species, and hundreds of thousands of terrestrial species, are yet to be discovered; many of which may already be in specimen collections. However, naming species is only a first step in documenting knowledge about their biology, biogeography, and ecology. Considering the threats to biodiversity, new knowledge of existing species and discovery of undescribed species and their subsequent study are urgently required. To accelerate this research, we recommend, and cite examples of, more and better communication: use of collaborative online databases; easier access to knowledge and specimens; production of taxonomic revisions and species identification guides; engagement of nonspecialists; and international collaboration. "Data-sharing" should be abandoned in favor of mandated data publication by the conservation science community. Such a step requires support from peer reviewers, editors, journals, and conservation organizations. Online data publication infrastructures (e.g., Global Biodiversity Information Facility, Ocean Biogeographic Information System) illustrate gaps in biodiversity sampling and may provide common ground for long-term international collaboration between scientists and conservation organizations.

How does molecular-assisted identification affect our estimation of α, β and γ biodiversity? An example from understory red seaweeds (Rhodophyta) of Laminaria kelp forests in Brittany, France

Using two distinct identification methods, one based on morphological characters only and the other combining morphological and molecular characters (integrative identification method), we investigated the differences in the biodiversity patterns of red seaweed communities associated with kelp forests at various spatial scales: the regional diversity of Brittany, France (γ-diversity), the local diversity at different Breton sites (α-diversity) and the differentiation in species diversity and abundances among those sites (β-diversity). To characterise α and β diversities, we conducted an initial survey in winter 2011 at 20 sites belonging to four different sub-regions, with specimens collected from six quadrats of 0.10 m(2) at each site, three in the tidal zone dominated by Laminaria digitata and three in the zone dominated by Laminaria hyperborea. To further characterise the regional diversity, we carried out another survey combining several sampling methods (quadrats and visual census) in different seasons (winter, spring and summer) and different years (2011 and 2012). In all, we collected 1990 specimens that were assigned to 76 taxa with the identification method based on morphological characters and 139 taxa using the integrative method. For γ and α diversity, the use of molecular characters revealed several cases of cryptic diversity and both increased the number of identified taxa and improved their taxonomic resolution. However, the addition of molecular characters for specimen identification only slightly affected estimates of β-diversity.

O, Jesus PB, Bahia RG, Khader S, Alves-da-Silva SM, Guimarães SM, Pereira SM, Caires TA, Meurer T, Cassano V, Werner VR, Gama Jr. WAD, Silva WJD. Update of the Brazilian floristic list of Algae and Cyanobacteria

Abstract An updated synthesis of cyanobacteria and algae information is presented for Brazil aiming to refine the data gathered to date and evaluate the progress of the biodiversity knowledge about these organisms in the country since the publication of the Catálogo de Plantas e Fungos do Brasil. The results of 2015 showed an increase of 1,250 species (35.7%) when compared to 2010, reaching a total of 4,747 species. The most diverse classes in species number were the Bacillariophyceae, Conjugatophyceae, Florideophyceae, Cyanophyceae, Dinophyceae and Euglenophyceae. Bacillariophyceae and Cyanophyceae had the highest increase in species number in the five-year interval. The Southeast and South regions were the most diverse, however, the Northeast, with the states of Piauí and Sergipe, and the Central-west region, with Mato Grosso, Goiás and Distrito Federal, also stood out in the national algal biodiversity scenario. Despite the shortage of taxonomists and limited infrastructure, the results showed a significant improvement in the knowledge regarding the diversity of cyanobacteria and algae in the country during the study period, starting to even out regional geographical differences caused by subsampling.

Toward an inordinate fondness for stars, beetles and Lobophora? Species diversity of the genus Lobophora (Dictyotales, Phaeophyceae) in New Caledonia

Until the recent use of molecular markers, species diversity of Lobophora, an ecologically important brown algal genus with a worldwide distribution in temperate and tropical seas, has been critically underestimated. Using a DNA-based taxonomic approach, we re-examined diversity of the genus from New Caledonia in the Southwest Pacific Ocean. First, species were delineated using general mixed Yule coalescent-based and barcoding gap approaches applied to a mitochondrial cox3 data set. Results were subsequently confirmed using chloroplast psbA and rbcL data sets. Species delimitation analyses agreed well across markers and delimitation algorithms, with the barcoding gap approach being slightly more conservative. Analyses of the cox3 data set resulted in 31-39 molecular operational taxonomic units (MOTUs), four of which are previously described species (L. asiatica, L. crassa, L. nigrescens s.l., L. pachyventera). Of the remaining MOTUs for which we obtained a representative number of sequences and results are corroborated across analyses and genes, we described 10 species de novo: L. abaculusa, L. abscondita, L. densa, L. dimorpha, L. gibbera, L. hederacea, L. monticola, L. petila, L. rosacea, and L. undulata. Our study presents an excellent case of how a traditional morphology-based taxonomy fails to provide accurate estimates of algal diversity. Furthermore, the level of Lobophora diversity unveiled from a single locality in the Pacific Ocean raises important questions with respect to the global diversity of the genus, the distributions and range sizes of the individual species, as well as the mechanisms facilitating coexistence.

Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment

Algal taxonomy is a key discipline in phycology and is critical for algal genetics, physiology, ecology, applied phycology, and particularly bioassessment. Taxonomic identification is the most common analysis and hypothesis-testing endeavor in science. Errors of identification are often related to the inherent problem of small organisms with morphologies that are difficult to distinguish without research-grade microscopes and taxonomic expertise in phycology. Proposed molecular approaches for taxonomic identification from environmental samples promise rapid, potentially inexpensive, and more thorough culture-independent identification of all algal species present in a sample of interest. Molecular identification has been used in biodiversity and conservation, but it also has great potential for applications in bioassessment. Comparisons of morphological and molecular identification of benthic algal communities are improved by the identification of more taxa; however, automated identification technology does not allow for the simultaneous analysis of thousands of samples. Currently, morphological identification is used to verify molecular taxonomic identities, but with the increased number of taxa verified in algal gene libraries, molecular identification will become a universal tool in biological studies. Thus, in this report, successful application of molecular techniques related to algal bioassessment is discussed.

The rise and fall of Picobiliphytes: how assumed autotrophs turned out to be heterotrophs

Algae are significant members of Earth's biodiversity. Having been studied for a long time, the discovery of new algal phyla is extremely unusual. Recently, the enigmatic "Picobiliphyta," a group of uncultured eukaryotes unveiled using molecular tools, were claimed to represent an unrecognized early branching algal lineage with a nucleomorph (remnant nucleus of a secondary algal endosymbiont) in their plastids. However, subsequent studies rejected the presence of a nucleomorph, and single-cell genomic studies failed to detect any plastid-related genes, ruling out the possibility of plastid occurrence. The isolation of the first "picobiliphyte," Picomonas judraskeda, a tiny organism that feeds on very small (<150 nm) organic particles, came as final proof of their non-photosynthetic lifestyle. Consequently, the group has been renamed Picozoa. The passage from "picobiliphytes" to "picozoa" illustrates the crucial role that classical protistology should play to provide sound biological context for the wealth of data produced by modern molecular techniques.