Evolution and phylogeography of Halimeda section Halimeda (Bryopsidales, Chlorophyta)

Nuclear ribosomal and plastid DNA sequences of specimens belonging to section Halimeda of the pantropical green seaweed genus Halimeda show that the group under scrutiny contains many more genetically delineable species than those recognized by classical taxonomy. Discordances between phylograms inferred from nuclear and plastid DNA sequences suggest that reticulate evolution has been involved in speciation within the clade. Nonetheless, our data do not allow ruling out certain alternative explanations for the discordances. Several pseudo-cryptic species are restricted to the margins of the generic distribution range. In a clade of H. cuneata sibling species from widely separated subtropical localities in the Indian Ocean, the South African sibling branches off first, leaving the Arabian and West Australian species as closest relatives. We hypothesize that geographic isolation of the siblings may have taken place following Pleistocene or Pliocene periods of climatic cooling during which subtropical species occupied larger distribution ranges. A more basal separation of Atlantic, Indo-Pacific, and Mediterranean species indicates vicariance. The alternative events that could have caused this vicariance are discussed.     

The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales,Chlorophyta): compact genomes and genes of bacterial origin

Background

Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified).

Results

Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.

Conclusions

The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1418-3) contains supplementary material, which is available to authorized users.     

Productivity and nutrient relationships in psammophytic versus epilithic forms of Bryopsidales (Chlorophyta): comparisons based on a short-term physiological assay

Members of the green algal order Bryopsidales (= Caulerpales) are important calcifying agents of tropical reefs and comprise two fundamentally different life-form groups: (1) epilithic species with limited attachment structures and (2) psammophytic forms that have extensive subterranean rhizoidal systems. Because the shallow-water habitats of the former have relatively low nitrogen (N) to phosphorus (P_i) ratios compared to the pore waters of the sedimentary carbonate-rich substrata in which the latter are anchored, we hypothesized that epilithic forms should tend to be relatively more limited by N, while psammophytic species should tend to show P_i limitation. In partial support of the hypothesis, light-saturated net photosynthesis (P_max) in the epilithic forms, Halimeda opuntia, H. lacrimosa and H. copiosa, tended to be enhanced by N, while P_i was inhibitory or had no effect. In contrast, the psammophytic forms, Udotea sp., U. conglutinata, H. monde, H. tuna and H. simulans, tended to be stimulated more by P_i, whereas N had little effect. The utility of a bioassay to assess macroalgal nutrient limitation, based on a physiological response (net P_max) to short-term nutrient pulses, is demonstrated.     

Field biology of Halimeda tuna (Bryopsidales, Chlorophyta) across a depth gradient: comparative growth, survivorship, recruitment, and reproduction

Growth, survivorship, recruitment, and reproduction of Halimeda tuna, a dominant green alga in many reef systems of the Florida Keys, were monitored at a shallow back reef (4–7m) and deep reef slope (15–22 m) on Conch Reef. Despite lower light intensities and similar grazing pressures, amphipod infestations, and epiphyte loads at both sites, the deeper site exhibited significantly higher growth rates in summer months over a 4-year period than found for the shallow population, possibly because of higher nutrient levels at depth and photoinhibition of shallow plants. Sexual reproductive events occurred simultaneously across the entire reef, with up to 5% of the population at both sites developing gametangia. New upright axes formed from zygotes, asexual fragmentation, or vegetative runners. Plants appear to have persistent basal stumps that survive harsh environmental conditions, even if upright, photosynthetic axes are removed. Sexual reproduction and smothering by epiphyte overgrowth are hypothesized to be two causes of death for individuals.     

Typification of species of Codium (Bryopsidales, Chlorophyta) described by Okamura

Type specimens of six species of Codium described by Okamura are illustrated, including the holotype of Codium barbatum and lectotypes of Codium coactum, Codium intricatum, Codium pugniforme, Codium saccatum, and Codium subtubulosum. All species are currently recognized except C. pugniforme, which is indistinguishable from the previously described Codium spongiosum Harvey, Codium subtubulosum was abandoned by Okamura in favor of the previously described Codium divaricatum Holmes, but because of the prior existence of C. divaricatum (C. Agardh) Biasoletto, C. subtubulosum is the correct name for this species.     

Cultivation ofMonostroma nitidum (Chlorophyta) in a river estuary,southern Japan

The green seaweedMonostroma nitidum Wittrock is cultivated in brackish waters of southern Japan and an ecological survey of its cultivation was carried out in the estuary of R. Shimanto over three years. Artificial seed culture began by collecting many gametes in April. The zygotes adhered to a plastic settlement board (20–30 cm long and 10 cm wide). The cultivated zygotes in the indoor tank increased gradually in size from 8 to 40m till early September. Maturation of the zygote was promoted by providing dark conditions for 2–3 weeks. The production of a concentrated zoospore solution was achieved by adding freshwater 2–3°C above that of the zygote culture tank and a photon flux density of 100mol m^–2 s^–1).The culture nets were set our horizontally at a level exposed for 4 h and were harvested 3–4 times till March. The total production was approximately 6–10 kg dry weight per net during culture periods. The total production of nets harvested 3–4 times per year was greater than that of nets harvested only once.     

The effect of monensin on gametogenesis and zoosporogenesis in the aquatic fungus,Allomyces macrogynus

Summary Cytoplasmic cleavage in the gametangia and zoosporangia ofA. macrogynus was studied using monensin, an ionophore known to disrupt several endomembrane functions in plant and animal cells. Monensin interfered with normal gamete and zoospore formation in a dose dependent manner such that at a 20 M concentration very abnormal cells were released from the reproductive structures. It was evident that monensin's effect was most pronounced during the first 25 minutes of gametogenesis and parallels in time the onset and continuation of the cytoplasmic cleavage events. Observations using fluorescence and differential interference contrast microscopy indicated that the ionophore inhibited normal cytoplasmic cleavage resulting in the production of multinucleate cells, many of which had either no flagella or multiple flagella. Transmission electron microscopy showed that the monensin-treated gametangia had many large vacuoles which contained amorphous electron-opaque material. X-ray microprobe analysis demonstrated that the elemental composition of the large vacuoles was identical to that of the dense globular inclusions seen in untreated gametangia, and morphological analysis confirmed the relationship between these endomembrane structures. Thus this swollen endomembrane component probably is not involved in the cleavage process. Single endomembrane cisternae which were very common in untreated gametangia were seldom seen in monensin-treated preparations. Instead, many smaller electron-transparent vacuoles were observed. These swollen cisternae may both represent monensin-modified Golgi apparatus equivalents and/or play a critical role during the process of gametogenesis and zoosporogenesis inA. macrogynus.     

Genotype versus phenotype variability in Chlorella and Micractinium (Chlorophyta, Trebouxiophyceae)

The most recent revision of the genus Chlorella, based on biochemical and SSU rDNA analyses, suggested a reduction to a set of four "true" spherical Chlorella species, while a growing number of morphologically different species such as Micractinium (formerly Micractiniaceae) were found to cluster within the clade of "true"Chlorella. In this study, the generic concept in Chlorellaceae to Chlorella and Micractinium was evaluated by means of combined SSU and ITS-2 rDNA sequence analyses and biotests to induce development of bristles on the cell wall. Molecular phylogenetic analyses of Chlorella and Micractinium strains confirmed their separation into two different genera. In addition, non-homoplasious synapomorphies (NHS) and compensatory base changes (CBC) in the secondary structures of SSU and ITS-2 rDNA sequences were found for both genera using this approach. The Micractinium clade can be differentiated into three different genotypes. Using culture medium of the rotifer Brachionus calyciflorus, phenotypic plasticity in Chlorella and Micractinium was studied. Non-bristled Micractinium cells developed bristles during incubation with Brachionus culture medium, whereas Chlorella did not produce bristles. Grazing experiments with Brachionus showed the rotifer preferred to feed on non-bristled cells. The dominance of colonies versus solitary cells in the Micractinium culture was not correlated with the "Brachionus factor". These results suggest that morphological characteristics like formation of bristles represent phenotypic adaptations to the conditions in the ecosystem.     

Gamete discharge by Bryopsis plumosa (Codiales, Chlorophyta) induced by blue and UV-A light

Gamete discharge by the coenocytic green alga Bryopsis plumosa (Hudson) C. Agardh is induced by light. The mature male gametangia consist of a mass of quiescent male gametes and a large central vacuole. Within a few minutes after the onset of irradiation, breakdown of the tonoplast of the central vacuole and initiation of gamete motility occur simultaneously. This is followed by a forced discharge of moving gametes through a hole ruptured at the subapical region of the gametangium. The action spectrum for the light-induced gamete discharge was determined from a series of fluence-response curves. This action spectrum, having two major maxima at 370 and 450 nm, indicates the involvement of a blue light/UV-A-absorbing photoreceptor previously described as ‘cryptochrome’.     

Electron microscopy of primary zoosporogenesis inPlasmodiophora brassicae

Primary zoosporogenesis in resting sporangia ofPlasmodiophora brassicae that had been incubated for 14 d in culture solution containing turnip seedlings was examined by transmission electron microscopy. A single zoospore differentiated within each sporangium, the differentiation being initiated by the emergence, of two flagella in the tight space formed by invagination of the plasma membrane within the sporangium. The differentiazing zoospore was similar in intracellular aspects to sporangia within clubroot galls. Then a deep groove formed on the zoospore cell body by further invagination of the plasma membrane. Two flagella appeared to coil around the zoospore cell body in parallel along this groove. Thereafter, the cell body lost the groove and became rounded following the protoplasmic condensation (contraction of cell body) during late development, and assumed an irregular shape at the stage of maturation. Intracellular features in, developing and mature zoospores were complicated, being characterized by electron-dense nuclei and mitochondria, microbodies, cored vesicles and various unidentified cytoplasmic vesicles and granules. A nucleolus-like region was observed only in the nucleus of the mature zoospore. A partially opened germ, pore was also seem in the sporangium containing the mature zoospore.     

Ontogenesis of monad pollen inPterostylis plumosa (Orchidaceae,Neottioideae)

Pterostylis plumosa (Neottioideae) is an orchid with monosulcate monad pollen. Tetrads may be isobilateral, decussate, tetrahedral, rhomboid or T-shaped, but all pollen grains have a similar shape. Those belonging to the same tetrads are contiguous from microspore release to opening of the anther, with the furrow oriented inwards. Sporophytic proteins are present outside the furrow. The tapetum is of the parietal type without orbicles. The increase in pollen grain size between meiosis and maturity is only three-fold. The generative cell is spherical when the pollen is mature. These features are discussed in relation to the primitive nature of the species.     

PCR-identification of Dunaliella salina (Volvocales, Chlorophyta) and its growth characteristics

The saline pond microalga, Dunaliella salina (Dunal) Teod. maintained in De Walne's (basal) medium under laboratory conditions was confirmed by amplifying the chromosomal DNA of the microalga by PCR with specific primers MA1 and MA2. Seaweed extracts obtained from Sargassum wightii and Ulva lactuca were amended separately at 1.0%, 1.5%, 2.0% and 2.5% levels to the basal medium in order to assess their potential on the growth and concentration of pigments, viz. Chl a, Chl b and beta-carotene of the alga. beta-Carotene was isolated and visible absorption spectrum was taken at 443 and 475 nm confirmed the presence of 9-cis-beta-carotene and all-trans-beta-carotene isomers. Maximum yield, highest division rate (mu) and highest pigment concentrations were observed in the cells grown in 1.5% S. wightii and 2.0% U. lactuca amended medium and these cells were subjected to DAPI staining. The results of epifluorescence microscopy and image analysis revealed a significant enhancement of the cell and nuclear area of the microalgae.     

<Emphasis Type=Italic>Siderocelis irregularis</Emphasis> (Chlorophyta,Trebouxiophyceae) in Lake Tanganyika (Africa)

Siderocelis irregularis Hindák, representing a genus Siderocelis (Naumann) Fott that is known from European temperate waters, was identified as a common phytoplankter in Lake Tanganyika. It was found aposymbiotic as well as ingested (possibly endosymbiotic) in lake heterotrophs, mainly Strombidium sp. and Vorticella spp. The morphology and ultrastructure of the species, studied with LM, SEM and TEM, are described with emphasis on the structure of the cell wall and the pyrenoid. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

Formation of multinucleate zoospores inPhytophthora infestans (Mont.) De Bary (Oomycetes,Pythiaceae)

Summary Zoospore formation in sporangia ofPhytophthora infestans, the causal agent of potatoes downy mildew disease, was influenced by reduction of oxygen tension, by application of a respiratory poison (KCN), and by an inhibitor of cytokinesis (cytochalasine B). As demonstrated by different methods of light microscopy, in all three cases the percentage of morphologically abnormal, multinucleate, multiflagellate cells increased. High concentrations of KCN caused a complete inhibition of zoospore formation. These effects are interpreted as disorders of the process of cytokinesis during zoosporogenesis.     

Bicarbonate enhances synchronous division of the giant nuclei of sporophytes in<Emphasis Type="Italic"> Bryopsis plumosa</Emphasis>

A mature sporophyte of Bryopsis plumosa (Hudson) C. Agardh forms a huge number of zoospores in its cell continuum. Zoospore formation starts with the division of a single giant nucleus and subsequent repeated mitosis. We found that an elevation of photosynthetic activity triggered the division of a mature giant nucleus. Transfer to short-day conditions was not necessary. Giant nuclei did not divide in darkness or in the presence of 1 μM DCMU. Giant nuclei of as many as 90% of sporophtyes started to divide following the addition of 5 mM NaHCO₃ to the growth medium under continuous white light (6–12 W m⁻²). Frequency of nuclear division increased with increased light intensity. By combining those parameters that promoted the division of giant nuclei, we developed the "two-step culture method" which is composed of preliminary and main cultures. This new method guarantees that giant nuclei of more than 90% of all sporophytes synchronously divide between 72 and 96 h after the transfer to the main culture (continuous white light of 12 W m⁻² in PES medium supplemented with 5 mM NaHCO₃).     

A simple method for mass isolation of protoplasts from species of Monostroma, Enteromorpha and Ulva (Chlorophyta, Ulvales)

A simple enzyme mixture containing 2% Cellulase Onozuka R–10 and1% Macerozyme R–10 prepared in deionised water supplemented with 3% NaCland 1 mM CaCl₂ was developed for isolating rapidlyprotoplasts from different species of Monostroma,Enteromorpha and Ulva. The yield fordifferent species of Monostroma ranged from 9.6 ×10⁶ to 10.2 × 10⁶ cells g^–1f. wt thallus, and forEnteromorpha from 3.48 × 10⁶ to 11.7× 10⁶ cells g^–1 f. wt and forUlva from 4.58 × 10⁶ to 26.8 ×10⁶ cells g^–1 f. wt. The overallregeneration rate of the protoplasts isolated was usually > 90% and showednormal morphogenesis. The method yields rapid mass production of viableprotoplasts with high regeneration rates.     

The novel light-harvesting pigment-protein complex ofMantoniella squamata (Chlorophyta): Phylogenetic implications

Summary A light-harvesting pigment-protein complex has been isolated fromMantoniella squamata (Micromonadophyceae, Chlorophyta) by nondenaturing polyacrylamide-gel electrophoresis. The complex runs as two bands of molecular weights 54,000 and 55,000. There are two constituent polypeptides of molecular weights 20,500 and 22,000. Antibodies were raised to the 20,500-dalton polypeptides from this complex and to the 24,500-dalton polypeptide from the analogous complex ofPedinomonas minor (Micromonadophyceae). The antibodies to theM. squamata polypeptide are specific for both polypeptides of theM. squamata light-harvesting complex, as well as for a 27,000-dalton polypeptide of undetermined function. The antibodies to theP. minor polypeptide are specific for polypeptide components of the light-harvesting complex of that alga. The antibodies specific for theM. squamata light-harvesting complex polypeptides do not cross react with any polypeptides ofP. minor thylakoid membranes, as demonstrated by crossed immunoelectrophoresis. Similarly, no polypeptides ofM. squamata thylakoids cross react with the antibodies specific forP. minor light-harvesting complex polypeptides. These results indicate that the light-harvesting complex ofM. squamata is structurally very different from that ofP. minor. In a survey of several land plants and green algae, including representatives of all classes of green algae, a light-harvesting complex homologous to that ofM. squamata was found only inMicromonas pusilla. All other organisms tested possessed a lightharvesting complex homologous to that ofP. minor. The evolutionary and taxonomic implications of the novelM. squamata light-harvesting complex are discussed.     

Species and ecads of Caulerpa (Ulvophyceae,Chlorophyta) in Malesia (South-East Asia): Taxonomy,biogeography and biodiversity

In the present paper 29 species ofCaulerpa from Indonesia, the Philippines and Papua New Guinea are listed, with reference to their distribution and occurrence of ecological phenotypes (ecads). Other names ofCaulerpa taxa recorded for Malesia in literature are dealt with in the paragraph on excluded and changed names. The variability and nomenclature of mainly the species recorded from Indonesia are discussed, especially regarding the implications of the recognition of ecads in several species. The ecads in the sectionSedoideae are discussed as an example of use of the designation ecad for a number of growth forms. Biogeography of the genusCaulerpa is discussed with focus on areas of high biodiversity, both inside and outside Malesia, followed by a discussion on biodiversity assessment. It is suggested that the genusCaulerpa is a good indicator for the quantitative assessment of biodiversity. The need for a modern world-monograph of this genus is stressed. Such a monograph can be a stimulus for ecosystem studies ofCaulerpa stands.     

Laboratory culture and taxonomy of two species ofPedobesia (Bryopsidales,Chlorophyceae) in Japan

The morphology ofPedobesia lamourouxii andDerbesia ryukyuensis, both collected in Shimoda and the adjacent areas in central Japan, was studied from field specimens and laboratory cultures. Specimens which had the same morphology as EuropeanP. lamourouxii produced stephanokont zoospores which developed into either prostrate filaments or expanded discoidal thalli similar to those described by Feldmann and Codomier (1974) and Feldmannet al. (1975). Erect filament identical with the thallus found in nature developed directly from prostrate filaments. The specimens which had morphology similar to that ofDerbesia ryukyuensis described by Yamada and Tanaka (1938) also produced stephanokont zoospores which developed similarly to those ofP. lamourouxii. This species is, therefore, a member ofPedobesia, and it is made a new combinationP. ryukyuensis (Yamada et Tanaka) Kobara et Chihara, comb. nov.     

Comparative ultrastructure of pyrenoids inTrebouxia (Microthamniales,Chlorophyta)

Pyrenoid ultrastructure has been investigated from cultures of all 26 species ofTrebouxia with the aim of establishing pyrenoids as a taxonomic character. Different arrangements and forms of thylakoid lamellae within the pyrenoid matrix allow eight pyrenoid types to be distinguished. Each type is characteristic of a group of species. Thegigantea- andimpressa-type are similar, differing only in the form of the tubules: short, branched tubules mark thegigantea-type; ± long and straight invaginations theimpressa-type. Thearboricola-type is characterized by meandering pyrenoid membranes developing from lamellae parallel with each other in young autospores. Pyrenoids of thegelatinosa-type are traversed by thin parallel-arranged tubules. Few thylakoids with a curved profile are typical of theirregularis-type. Thecorticola-type is different from all others in having a distinct starch sheath closely connected with the pyrenoid matrix and no pyrenoglobuli being associated with the pyrenoid membranes. No true pyrenoids have been found inT. magna andT. erici. Within the chloroplast, they have indistinct areas with pyrenoglobuli, but without differentiated thylakoids. Pyrenoid morphology is stable in culture on different media as well as in phycobionts within lichen thalli. Comparing the pyrenoid of a lichenizedTrebouxia with that from cultured species, the identification of the phycobiont within the lichen thallus is possible, without the need of culturing the algae. This has been shown in species ofParmelia andHypogymnia. New aspects for the taxonomy and systematics ofTrebouxia are discussed.Dedicated to Prof. DrLothar Geitler on the occasion of the 90th anniversary of his birthday.