Removal of potentially toxic elements from water with the moss-tufa micro-filtration system.

Mosses are an integral component in the tufa sedimentary landscape. In this study, we investigated the use of the porous moss-tufa structure as a filtration system for removing potentially toxic elements (PTEs) from water samples. Three species of mosses that commonly grow on tufa were selected, and the PTEs filtered by the moss-tufa system were identified by inductively coupled plasma mass spectrometry. The bioconcentration factor (BCF) of mosses was calculated to compare the enrichment effects of different mosses on PTEs. Likewise, the level of PTEs flowing through the moss-tufa system was measured, and the water quality removal rate (C) was calculated accordingly. The results revealed that the moss-tufa system was mainly composed of Fissidens grandifrons Brid., Hydrogonium dixonianum P. C. Chen, and Cratoneuron filicinum (Hedw.) Spruce var. filicinum. Among these, Fissidens grandifrons Brid. reported the highest retention capacity for PTEs. Collectively, the moss-tufa filtration system displayed a strong retention capacity and removal rate of Mn, Pb, and Ni from the water sample. The removal of PTEs by the moss-tufa system was mainly based on the enrichment of mosses and the adsorption-retention ability of tufa. In conclusion, the moss-tufa micro-filtration system displayed the effective removal of PTEs from water samples and could be applied to control the levels of toxic elements in karst water bodies.

Phytochemical Analysis and Molecular Identification of Green Macroalgae Caulerpa spp. from Bali, Indonesia.

The studies of the Bulung Boni and Bulung Anggur (Caulerpa spp.) species and secondary metabolites are still very limited. Proper identification will support various aspects, such as cultivation, utilization, and economic interests. Moreover, understanding the secondary metabolites will assist in developing algae-based products. This study aimed to identify these indigenous Caulerpa algae and analyze their bioactive components. The tufA sequence was employed as a molecular marker in DNA barcoding, and its bioactive components were identified using the GC-MS method. The phylogenetic tree was generated in MEGA 11 using the maximum likelihood method, and the robustness of the tree was evaluated using bootstrapping with 1000 replicates. This study revealed that Bulung Boni is strongly connected to Caulerpa cylindracea. However, Bulung Anggur shows no close relationship to other Caulerpa species. GC-MS analysis of ethanolic extracts of Bulung Boni and Bulung Anggur showed the presence of 11 and 13 compounds, respectively. The majority of the compounds found in these algae have been shown to possess biological properties, such as antioxidant, antibacterial, anticancer, anti-inflammation, and antidiabetic. Further study is necessary to compare the data obtained using different molecular markers in DNA barcoding, and to elucidate other undisclosed compounds in these Caulerpa algae.

Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes.

Filamentous green algae Chaetophorales present numerous taxonomic problems as many other green algae. Phylogenetic analyses based on nuclear genes have limited solutions. Studies with appropriate chloroplast molecular markers may solve this problems; however, suitable molecular markers for the order Chaetophorales are still unknown. In this study, 50 chloroplast genomes of Chlorophyceae, including 15 of Chaetophorales, were subjected to single protein-coding gene phylogenetic analyses, and substitution rate and evolutionary rate assays, and PCR amplification verification was conducted to screen the suitable molecular markers. Phylogenetic analyses of three chloroplast representative genes (psaB, tufA, and rbcL) amplified from 124 strains of Chaetophorales showed that phylogenetic relationships were not improved by increasing the number of samples, implying that the genes themselves, rather than limited samples, were the reason for the unsupported Topology I. Seven genes (atpF, atpI, ccsA, cemA, chlB, psbB, and rpl2) with robust support were selected to be the most suitable molecular markers for phylogenetic analyses of Chaetophorales, and the concatenated seven genes could replace the time-consuming and labor-intensive phylogenetic analyses based on chloroplast genome to some extent. To further solve the taxonomic problems of Chaetophorales, suitable chloroplast markers combined with more taxon-rich approach could be helpful and efficient.

Diversity of the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta) from the east and gulf coast of the United States based on molecular data.

Ulva (Ulvophyceae, Chlorophyta) is common in intertidal environments and can also be found in freshwater ecosystems. The difficulty to morphologically identify Ulva species due to cryptic diversity and morphological plasticity has caused a taxonomic conundrum. Fortunately, molecular data have begun to unravel a better understanding of its diversity. Here, we present a molecular analysis with 247 samples of Ulva from the Gulf of Mexico and Atlantic USA based on chloroplast (rbcL and tufA) and nuclear (ITS1-5.8S-ITS2) molecular markers. Twenty-four Ulva taxa had previously been reported for this area based on morphology and earlier molecular studies mostly from Northeastern USA and Canada. In this study, sixteen Ulva clades were identified representing 13 named clades and putatively three undescribed species. Only nine of the 24 taxa previously reported for the Western Atlantic were confirmed. Four species were identified for the first time in the U.S. East and Gulf Coast (U. aragoënsis, U. californica, U. meridionalis, and U. tepida). This study provides a foundation for future research on Ulva in this area and reiterates the necessity of using molecular-assisted identifications for this group.

Modeling the Relationships between the Height and Spectrum of Submerged Tufa Barrage Using UAV-Derived Geometric Bathymetry and Digital Orthoimages.

Tufa barrages play an important role in fluviatile tufa ecosystems and sedimentary records. Quantifying the height of tufa barrage is significant for understanding the evolution and development of the Holocene tufa barrage systems. However, for submerged tufa barrages, there is no low-cost non-contact method to retrieve barrage height. Generally, it is difficult to recognize small tufa barrages by means of remotely sensed satellite data, but the combination of unmanned aerial vehicles (UAV) and Structure-from-Motion (SfM) photogrammetry makes it possible. In this study, we used a fixed-wing UAV and a consumer-grade camera to acquire images of the submerged tufa barrage in Lying Dragon Lake, Jiuzhaigou National Nature Reserve, China, and estimated the height of the tufa barrage through UAV-based photogrammetric bathymetry. On this foundation, the relationship between barrage height and its spectrum was established through band ratio analysis using UAV-derived geometric bathymetry and digital orthoimages, which provided an alternative strategy to characterize the height of submerged tufa barrages. However, the spectral characteristics of submerged tufa barrages will oscillate with changes in the environmental conditions. In future research, we will consider using a dedicated aquatic multispectral camera to improve the experimentation.

Operon Concatenation Is an Ancient Feature That Restricts the Potential to Rearrange Bacterial Chromosomes.

The last common ancestor of the Gammaproteobacteria carried an important 40-kb chromosome section encoding 51 proteins of the transcriptional and translational machinery. These genes were organized into eight contiguous operons (rrnB-tufB-secE-rpoBC-str-S10-spc-alpha). Over 2 Gy of evolution, in different lineages, some of the operons became separated by multigene insertions. Surprisingly, in many Enterobacteriaceae, much of the ancient organization is conserved, indicating a strong selective force on the operons to remain colinear. Here, we show for one operon pair, tufB-secE in Salmonella, that an interruption of contiguity significantly reduces growth rate. Our data show that the tufB-secE operons are concatenated by an interoperon terminator-promoter overlap that plays a significant role regulating gene expression. Interrupting operon contiguity interferes with this regulation, reducing cellular fitness. Six operons of the ancestral chromosome section remain contiguous in Salmonella (tufB-secE-rpoBC and S10-spc-alpha) and, strikingly, each of these operon pairs is also connected by an interoperon terminator-promoter overlap. Accordingly, we propose that operon concatenation is an ancient feature that restricts the potential to rearrange bacterial chromosomes and can select for the maintenance of a colinear operon organization over billions of years.

Morphology and molecular phylogeny of coccoid green algae Coelastrella sensu lato (Scenedesmaceae, Sphaeropeales), including the description of three new species and two new varieties.

The genus Coelastrella was established by Chodat (Bull. Soc. Bot. Geneve, 13 [1922] 66), and was characterized as being unicellular or in few-celled aggregations with many longitudinal ribs on the cell wall. Many species of this genus showed strong ability to accumulate carotenoids and oils, so they have recently attracted much attention from researchers due to its potential applicability in the energy and food industries. In this study, a total of 23 strains of Coelastrella were sampled from China, and three new species and two new varieties were described: C. thermophila sp. nov., C. yingshanensis sp. nov., C. tenuitheca sp. nov., C. thermophila var. globulina var. nov., C. rubescens var. oocystiformis var. nov. Besides 18S rDNA and ITS2 sequences, we have newly sequenced the tufA gene marker for this taxon. Phylogenetic analysis combined with morphological studies revealed four morphotypes within the Coelastrella sensu lato clade, which contained the morphotype of original Coelastrella, original Scotiellopsis, Asterarcys, and morphotype of C. vacuolata and C. tenuitheca sp. nov. The relationships between morphological differences and phylogenic diversity based on different markers were discussed. Our results support that 18S rDNA was too conserved to be used a species-specific or even a genus-specific marker in this clade. The topology of tufA gene-based phylogenetic tree had a better match with the morphological findings.

Conspecificity of the model organism Ulva mutabilis and Ulva compressa (Ulvophyceae, Chlorophyta).

As one of the most abundant and ubiquitous representatives of marine and brackish coastal macrophytobenthos communities, the genus Ulva is not only an important primary producer but also of ecological and morphogenetic interest to many scientists. Ulva mutabilis became an important model organism to study morphogenesis and mutualistic interactions of macroalgae and microorganisms. Here, we report that our collections of Ulva compressa Linnaeus (1753) from Germany are conspecific with the type strains of the model organism U. mutabilis Føyn (1958), which were originally collected at Olhão on the south coast of Portugal and have from that time on been maintained in culture as gametophytic and parthenogenetic lab strains. Different approaches were used to test conspecificity: (i) comparisons of vegetative and reproductive features of cultured material of U. mutabilis and German U. compressa demonstrated a shared morphological pattern; (ii) gametes of U. compressa and U. mutabilis successfully mated and developed into fertile sporophytic first-generation offspring; (iii) molecular phylogenetics and species delimitation analyses based on the Generalized Mixed Yule-Coalescent method showed that U. mutabilis isolates (sl-G[mt+]) and (wt-G[mt-]) and U. compressa belong to a unique Molecular Operational Taxonomic Unit. According to these findings, there is sufficient evidence that U. mutabilis and U. compressa should be regarded as conspecific.

Cyanobacterial Contribution to Travertine Deposition in the Hoyoux River System, Belgium.

Travertine deposition is a landscape-forming process, usually building a series of calcareous barriers differentiating the river flow into a series of cascades and ponds. The process of carbonate precipitation is a complex relationship between biogenic and abiotic causative agents, involving adapted microbial assemblages but also requiring high levels of carbonate saturation, spontaneous degassing of carbon dioxide and slightly alkaline pH. We have analysed calcareous crusts and water chemistry from four sampling sites along the Hoyoux River and its Triffoy tributary (Belgium) in winter, spring, summer and autumn 2014. Different surface textures of travertine deposits correlated with particular microenvironments and were influenced by the local water flow. In all microenvironments, we have identified the cyanobacterium Phormidium incrustatum (Nägeli) Gomont as the organism primarily responsible for carbonate precipitation and travertine fabric by combining morphological analysis with molecular sequencing (16S rRNA gene and ITS, the Internal Transcribed Spacer fragments), targeting both field populations and cultures to exclude opportunistic microorganisms responding favourably to culture conditions. Several closely related cyanobacterial strains were cultured; however, only one proved identical with the sequences obtained from the field population by direct PCR. This strain was the dominant primary producer in the calcareous deposits under study and in similar streams in Europe. The dominance of one organism that had a demonstrated association with carbonate precipitation presented a valuable opportunity to study its function in construction, preservation and fossilisation potential of ambient temperature travertine deposits. These relationships were examined using scanning electron microscopy and Raman microspectroscopy.

Molecular determination of kleptoplast origins from the sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) reveals cryptic bryopsidalean (Chlorophyta) diversity in the Hawaiian Islands.

The sacoglossan sea slug species complex Plakobranchus ocellatus is a common algivore throughout the tropical Pacific, including the Hawaiian Islands. Plakobranchus ocellatus is kleptoplastic-it sequesters and retains algal chloroplasts-a characteristic that can be exploited to molecularly characterize diminutive bryopsidalean algae that are typically difficult to locate, collect, and identify. Previous DNA barcode analyses of both P. ocellatus and its kleptoplasts have been conducted primarily in the western Pacific and have only minimally sampled the most eastern populations in the Hawaiian Islands. Using two chloroplast markers, rbcL and tufA, kleptoplast samples from an Oahu population of P. ocellatus were amplified and cloned to identify their algal sources. Plakobranchus ocellatus sequester chloroplasts from up to 11 bryopsidalean algal species, all but one being diminutive in thallus size. Notably, eight of the detected algal species were new records to the Hawaiian Islands. A sequestration preference study demonstrated that the O'ahu population of P. ocellatus preferentially sequesters chloroplasts from diminutive, epilithic taxa. Using coxI barcoding of P. ocellatus, we showed the O'ahu population to be part of a clade that includes sequences from the neighboring island Maui, Australia, and the Philippines. The use of P. ocellatus as a novel sampling tool allows the exploration of the green algal community diversity and composition at a fine scale.

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.

Membrane engineering via trans unsaturated fatty acids production improves Escherichia coli robustness and production of biorenewables.

Constructing microbial biocatalysts that produce biorenewables at economically viable yields and titers is often hampered by product toxicity. For production of short chain fatty acids, membrane damage is considered the primary mechanism of toxicity, particularly in regards to membrane integrity. Previous engineering efforts in Escherichia coli to increase membrane integrity, with the goal of increasing fatty acid tolerance and production, have had mixed results. Herein, a novel approach was used to reconstruct the E. coli membrane by enabling production of a novel membrane component. Specifically, trans unsaturated fatty acids (TUFA) were produced and incorporated into the membrane of E. coli MG1655 by expression of cis-trans isomerase (Cti) from Pseudomonas aeruginosa. While the engineered strain was found to have no increase in membrane integrity, a significant decrease in membrane fluidity was observed, meaning that membrane polarization and rigidity were increased by TUFA incorporation. As a result, tolerance to exogenously added octanoic acid and production of octanoic acid were both increased relative to the wild-type strain. This membrane engineering strategy to improve octanoic acid tolerance was found to require fine-tuning of TUFA abundance. Besides improving tolerance and production of carboxylic acids, TUFA production also enabled increased tolerance in E. coli to other bio-products, e.g. alcohols, organic acids, aromatic compounds, a variety of adverse industrial conditions, e.g. low pH, high temperature, and also elevated styrene production, another versatile bio-chemical product. TUFA permitted enhanced growth due to alleviation of bio-product toxicity, demonstrating the general effectiveness of this membrane engineering strategy towards improving strain robustness.

New Ulvaceae (Ulvophyceae, Chlorophyta) from mesophotic ecosystems across the Hawaiian Archipelago.

Ulvalean algae (Chlorophyta) are most commonly described from intertidal and shallow subtidal marine environments worldwide, but are less well known from mesophotic environments. Their morphological simplicity and phenotypic plasticity make accurate species determinations difficult, even at the generic level. Here, we describe the mesophotic Ulvales species composition from 13 locations across 2,300 km of the Hawaiian Archipelago. Twenty-eight representative Ulvales specimens from 64 to 125 m depths were collected using technical diving, submersibles, and remotely operated vehicles. Morphological and molecular characters suggest that mesophotic Ulvales in Hawaiian waters form unique communities comprising four species within the genera Ulva and Umbraulva, each with discrete geographic and/or depth-related distributional patterns. Three genetically distinct taxa are supported by both plastid (rbcL and tufA) and nuclear (ITS1) markers, and are presented here as new species: Umbraulva kaloakulau, Ulva ohiohilulu, and Ulva iliohaha. We also propose a new Umbraulva species (Umbraulva kuaweuweu), which is closely related to subtidal records from New Zealand and Australia, but not formally described. To our knowledge, these are the first marine species descriptions from Hawai'i resulting from the collaboration of traditional Hawaiian nomenclature specialists, cultural practitioners and scientists. The difficulty of finding reliable diagnostic morphological characters for these species reflects a common problem worldwide of achieving accurate identification of ulvalean taxa using solely morphological criteria. Mesophotic Ulvales appear to be distinct from shallow-water populations in Hawai'i, but their degree of similarity to mesophotic floras in other locations in the Pacific remains unknown.

Return to the Taung cave paradigm.

OBJECTIVES: The Taung hominin fossil was recovered in 1924 during quarry operations in the tufa formations of the Buxton Limeworks. Reconstructions of the depositional environment of the juvenile Australopithecus skull have concentrated on the types of caves that form within the tufa. Hopley et al. (Am J Phys Anthropol 151 (2013) 316-324) proposed a new model in which the pink carbonate deposits, in which many of the Taung fossils are found, formed as open terrestrial pedogenic deposits. The objective here is to challenge that notion. MATERIALS AND METHODS: Observations of the depositional environments at Taung are based upon the University of the Witwatersrand paleontological excavations at the Buxton Limeworks from 1988 to 1993, and subsequent laboratory analysis of the fossils and sediments. RESULTS: Hopley et al. (Am J Phys Anthropol 151 (2013) 316-324) conflate numerous distinct outcroppings of the pink carbonates as a single "unit." The excavations revealed numerous fossiliferous deposits that differ greatly in taphonomic origins and formation processes, and that cannot be considered a "unit" despite the commonality of pink carbonates. There are deposits that fit the model proposed by Hopley et al. (Am J Phys Anthropol 151 (2013) 316-324), but they are not the ones that yielded the most significant fossils. DISCUSSION: Most of the fossiliferous deposits, including those most likely to have yielded the Taung hominin, are best reconstructed as being of karst origins.

A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA.

BACKGROUND: In spite of their ecological importance as primary producers and microbioeroders of marine calcium carbonate (CaCO3) substrata, endolithic phototrophs spanning both prokaryotic (the cyanobacteria) and eukaryotic algae lack established molecular resources for their facilitated survey with high throughput sequencing. Here, the development of a metabarcoding framework for the elongation factor EF-Ttu (tufA) was tested on four Illumina-sequenced marine CaCO3 microfloras for the characterization of their endolithic phototrophs, especially the abundant bioeroding Ostreobium spp. (Ulvophyceae). The framework consists of novel tufA degenerate primers and a comprehensive database enabling Operational Taxonomic Unit (OTU) identification at multiple taxonomic ranks with percent identity thresholds determined herein. RESULTS: The newly established tufA database comprises 4057 non-redundant sequences (from 1339 eukaryotic and prokaryotic phototrophs, and 2718 prokaryotic heterotrophs) including 27 classes in 10 phyla of phototrophic diversity summarized from data mining on GenBank(®), our barcoding of >150 clones produced from coral reef microfloras, and >300 eukaryotic phototrophs (>230 Ulvophyceae including >100 'Ostreobium' spp., and >70 Florideophyceae, Phaeophyceae and miscellaneous taxa). Illumina metabarcoding with the newly designed primers resulted in 802 robust OTUs including 618 phototrophs and 184 heterotrophs (77 and 23% of OTUs, respectively). Phototrophic OTUs belonged to 14 classes of phototrophs found in seven phyla, and represented ~98% of all reads. The phylogenetic profiles of coral reef microfloras showed few OTUs in large abundance (proportion of reads) for the Chlorophyta (Ulvophyceae, i.e. Ostreobium and Phaeophila), the Rhodophyta (Florideophyceae) and Haptophyta (Coccolithophyceae), and a large diversity (richness) of OTUs in lower abundance for the Cyanophyta (Cyanophyceae) and the Ochrophyta (the diatoms, 'Bacillariophyta'). The bioerosive 'Ostreobium' spp. represented four families in a large clade of subordinal divergence, i.e. the Ostreobidineae, and a fifth, phylogenetically remote family in the suborder Halimedineae (provisionally assigned as the 'Pseudostreobiaceae'). Together they harbor 85-95 delimited cryptic species of endolithic microsiphons. CONCLUSIONS: The novel degenerate primers allowed for amplification of endolithic phototrophs across a wide phylogenetic breadth as well as their recovery in very large proportions of reads (overall 98%) and diversity (overall 77% of OTUs). The established companion tufA database and determined identity thresholds allow for OTU identification at multiple taxonomic ranks to facilitate the monitoring of phototrophic assemblages via metabarcoding, especially endolithic communities rich in bioeroding Ulvophyceae, such as those harboring 'Ostreobium' spp., Phaeophila spp. and associated algal diversity.

Functional characterization of RelBE toxin-antitoxin system in probiotic Bifidobacterium longum JDM301.

Toxin-antitoxin (TA) systems are widespread in bacteria and archaea. However, the roles of chromosomally encoded TA systems in bacterial physiology are still open to debate. In this study, a TA module-relBE in Bifidobacterium longum JDM301 (relBE(Bif)) was identified and its function in stress response was evaluated. Bioinformatics analysis of the whole genome sequences of JDM301 revealed a pair of linked genes encoding a RelBE-like TA system (RelBE(Bif)). Our results revealed a bicistronic operon formed by relBE(Bif) in JDM301. Over-expression of RelE(Bif) had a toxic effect on Escherichia coli, which could be neutralized by co-expression of its cognate antitoxin, RelB(Bif) Our data also demonstrated that RelE(Bif) is an mRNA interferase and that the activity of RelE(Bif) can be inhibited by RelB(Bif) These results suggest that RelE(Bif) is a toxic nuclease which arrests cell growth through mRNA degradation, and that the activity of RelE(Bif) can be abolished by co-expression of RelB(Bif) In addition, we also found that the expression of RelBE(Bif) is increased during osmotic stress, suggesting that RelBE(Bif) is activated under this adverse condition. Our results imply that the RelBE(Bif) TA module may represent a cell growth modulator which helps B. longum to deal with osmotic stress.

Seasonal succession of the travertine-forming desmid Oocardium stratum.

The calcifying Conjugatophyte Oocardium stratum occurs exclusively in spring-associated limestones (SAL) with active meteogene limestone deposition. The macroscopic colonies of Oocardium stratum form hemispherical, pinhead-like structures with a diameter of 0.5-2.0 mm. As its autecology is still poorly understood, we focused on the seasonal development of Oocardium stratum and linked environmental factors to its abundance. The study was conducted in a rivulet in Lunz/See (Austria) for 16 months on a weekly (growing season) to monthly (winter season) basis. Oocardium colonies were found throughout the whole year, with maximum abundance during the mid-summer months July and August. Repeated macro-mapping of three SAL sites measuring 750 cm(2) each showed a maximum Oocardium cover of around 30% in August; two smaller peaks developed in early summer and late autumn with ~10% cover. Diatom mats dominated by Cymbella excisiformis occurred in spring, autumn and winter, with more than 75% cover. The seasonal change between Oocardium and diatoms in limestone-precipitating springs causes a typical sequence pattern of limestone layers. Redundancy analysis revealed water temperature and bicarbonate content as the main structuring factors; these control the occurrence and growth of Oocardium, reflecting season as a background variable. Optimum growth conditions for Oocardium were an alkalinity around 4.7 meq · L(-1) and a water temperature around 13°C. Site openness, nitrate and dissolved carbon dioxide were inversely related to Oocardium biomass, the opposite for diatoms. Other environmental factors such as total ions or soluble reactive phosphorus had no significant influence on Oocardium stratum abundance.

Chodatodesmus australis sp. nov. (Scenedesmaceae, Chlorophyta) from Antarctica, with the emended description of the genus Chodatodesmus, and circumscription of Flechtneria rotunda gen. et sp. nov.

The family Scenedesmaceae is a taxonomically complicated group due to its simple morphology, high phenotypic plasticity, and the presence of cryptic taxa. Over the years several taxonomic revisions, based on molecular data, affected the family. Here, we describe a new scenedesmacean species from Antarctica, Chodatodesmus australis, based on phylogenetic analyses of data from nuclear (ITS2 spacer, 18S rDNA), and plastid (rbcL, tufA) markers. Morphological (LM and SEM) and ultrastructural (TEM) observations, carried out both on the holotype of C. australis and on the generitype of Chodatodesmus, allow us to emend the original generic description of this genus. Our molecular and phylogenetic data also reveal the existence of a new monotypic genus, Flechtneria, inside the family Scenedesmaceae and lead to the taxonomic reassignment of some microalgal strains available in International Culture Collections to new taxa. Of the considered genomic regions, the tufA gene was the easiest to amplify and sequence and it showed the highest phylogenetic signal, even if the number of sequences already available for this marker in the public databases was considerably lower than for the other chosen loci. The rbcL gene also provided good phylogenetic signal, but its amplification and sequencing were generally more problematic. The nuclear markers gave lower phylogenetic signals, but the 18S rDNA allowed distinction at the genus level and the ITS2 spacer had the advantage that secondary structures could be considered in the analyses. The use of more than one molecular locus is suggested to obtain reliable results in the characterization of scenedesmacean strains.

A re-assessment of the infra-generic classification of the genus Caulerpa (Caulerpaceae, Chlorophyta) inferred from a time-calibrated molecular phylogeny.

The siphonous green algal family Caulerpaceae includes the monotypic genus Caulerpella and the species-rich genus Caulerpa. A molecular phylogeny was inferred from chloroplast tufA and rbcL DNA sequences analyzed together with a five marker dataset of non-caulerpacean siphonous green algae. Six Caulerpaceae lineages were revealed, but relationships between them remained largely unresolved. A Caulerpella clade representing multiple cryptic species was nested within the genus Caulerpa. Therefore, that genus is subsumed and Caulerpa ambigua Okamura is reinstated. Caulerpa subgenus status is proposed for the six lineages substantiated by morphological characters, viz., three monotypic subgenera Cliftonii, Hedleyi, and Caulerpella, subgenus Araucarioideae exhibiting stolons covered with scale-like appendages, subgenus Charoideae characterized by a verticillate branching mode, and subgenus Caulerpa for a clade regarded as the Caulerpa core clade. The latter subgenus is subdivided in two sections, i.e., Sedoideae for species with pyrenoids and a species-rich section Caulerpa. A single section with the same name is proposed for each of the other five subgenera. In addition, species status is proposed for Caulerpa filicoides var. andamanensis (W.R. Taylor). All Caulerpa species without sequence data were examined (or data were taken from species descriptions) and classified in the new classification scheme. A temporal framework of Caulerpa diversification is provided by calibrating the phylogeny in geological time. The chronogram suggests that Caulerpa diversified into subgenera and sections after the Triassic-Jurassic mass extinction and that infra-section species radiation happened after the Cretaceous-Tertiary mass extinction.

The New Genus Caulinema Revealed New Insights into the Generic Relationship of the Order Ulotrichales (Ulvophyceae, Chlorophyta).

Traditionally, the order Ulotrichales comprised green algae of an unbranched, uniseriate, filamentous morphology. However, since the establishment of ultrastructural features, the circumscription of this order has dramatically changed. Some genera and species have been excluded from this order and others with different morphologies (sarcinoid, branched filaments or even parenchymatous taxa) have been included. Phylogenetic analyses have confirmed the monophyly of this order, but its differentiation from the Ulvales and Acrosiphoniales remains difficult because of the lack of synapomorphies at every level (morphology, molecular signatures). To demonstrate the difficulties of placement into genera and orders, we investigated two sarcinoid taxa with the absence of zoospore formation. SSU and ITS rDNA tree topology and the ITS-2/CBC approach revealed that both strains SAG 2661 and CCAP 312/1 belong to Ulosarcina terrestrica and the newly erected genus Caulinema, respectively. The species conception using this approach was evaluated by sequencing the plastid-coding gene tufA, a commonly used barcode marker for green algae. All three molecular markers resulted in similar topologies at the generic and species levels, which is consistent with the ITS-2/CBC approach and tufA for barcoding. The reevaluation of the ultrastructural features revealed that the presence of organic scales on the surfaces of motile cells is characteristic for the order Ulotrichales and can be used for separation from the closely related orders. As a consequence of our study, we propose the new genus Caulinema for strain CCAP 312/1.