Molecular phylogeny,systematics, and revision of the type species of Lobomonas,L. francei (Volvocales,Chlorophyta) and closely related taxa

In the present study, three new strains of the rare volvocalean green alga Lobomonas were isolated from field‐collected samples, one from Sardinia (Italy) and two from Argentina, and comparatively studied. The Sardinian and one of the Argentinian strains were identified as Lobomonas francei, the type species of the genus, whereas the second Argentinian strain corresponded to L. panduriformis. Two additional nominal species of Lobomonas from culture collections (L. rostrata and L. sphaerica) were included in the analysis and shown to be morphologically and molecularly identical to the L. francei strains. The presence, number, and shapes of cell wall lobes, the diagnostic criterion of Lobomonas, were shown to be highly variable depending on the chemical composition of the culture medium used. The analyses by SEM gave evidence that the cell wall lobes in Lobomonas originate at the junctions of adjacent cell wall plates by extrusion of gelatinous material. The four L. francei strains had identical nrRNA gene sequences and differed by only one or two substitutions in the ITS1 + ITS2 sequences. In the phylogenetic analyses, L. francei and L. panduriformis were sister taxa; however, another nominal Lobomonas species (L. monstruosa) did not belong to this genus. Lobomonas, together with taxa designated as Vitreochlamys, Tetraspora, and Paulschulzia, formed a monophyletic group that in the combined analyses was sister to the “Chlamydomonas/Volvox‐clade.” Based on these results, Lobomonas was revised, the diagnosis of the type species emended, a lectotype and an epitype designated, and several taxa synonymized with the type species.     

Three gene phylogeny of the Thoreales (Rhodophyta) reveals high species diversity

The freshwater red algal order Thoreales has triphasic life history composed of a diminutive diploid “Chantransia” stage, a distinctive macroscopic gametophyte with multi‐axial growth and carposporophytes that develop on the gametophyte thallus. This order is comprised of two genera, Thorea and Nemalionopsis. Thorea has been widely reported with numerous species, whereas Nemalionopsis has been more rarely observed with only a few species described. DNA sequences from three loci (rbcL, cox1, and LSU) were used to examine the phylogenetic affinity of specimens collected from geographically distant locations including North America, South America, Europe, Pacific Islands, Southeast Asia, China, and India. Sixteen species of Thorea and two species of Nemalionopsis were recognized. Morphological observations confirmed the distinctness of the two genera and also provided some characters to distinguish species. However, many of the collections were in “Chantransia” stage rather than gametophyte stage, meaning that key diagnostic morphological characters were unavailable. Three new species are proposed primarily based on the DNA sequence data generated in this study, Thorea kokosinga‐pueschelii, T. mauitukitukii, and T. quisqueyana. In addition to these newly described species, one DNA sequence from GenBank was not closely associated with other Thorea clades and may represent further diversity in the genus. Two species in Nemalionopsis are recognized, N. shawii and N. parkeri nom. et stat. nov. Thorea harbors more diversity than had been recognized by morphological data alone. Distribution data indicated that Nemalionopsis is common in the Pacific region, whereas Thorea is more globally distributed. Most species of Thorea have a regional distribution, but Thorea hispida appears to be cosmopolitan.     

Biomass production and fatty acid accumulation in Chlorella sp. (strain DEC1B) isolated from a petrol refinery in Huelva (Spain)

A microalgal strain was established from Cepsa's refinery wastewater treatment plant in Huelva (southwest of Spain). Genetic analysis of the chloroplastic rbcL gene encoding for the large subunit of the ribulose bisphosphate carboxylase enzyme (Rubisco) showed the strain had high homology with other known rbcL sequences of the genus Chlorella. The strain grows well autotrophically in minimum mineral medium, with a growth rate of 0.28 ± 0.012 day^?1 and a biomass productivity of 138.9 ± 6.7 mg L^?1 day^?1. N‐starvation and/or over illumination with 650 µmol photons m^?2 s^?1 of PAR light on the cultures induced a significant increase in the intracellular content of lipids in this microalga. Total lipids were extracted from the strain biomass with 2:1 chloroform‐methanol, and they accounted for approximately 50% of the dry biomass. Polyunsaturated fatty acids (PUFAs) represented 60.4% of the total fatty acids found in the strain, thus making this biomass attractive as a high added‐value product source. The strain was able to grow efficiently in the refinery treated wastewater from which it was isolated, providing an attractive advantage for further development of more sustainable algal biomass production processes at reduced costs close to a petrol refinery area.     

Crusticorallina gen. nov., a nongeniculate genus in the subfamily Corallinoideae (Corallinales,Rhodophyta)

Molecular phylogenetic analyses of 18S rDNA (SSU) gene sequences confirm the placement of Crusticorallina gen. nov. in Corallinoideae, the first nongeniculate genus in an otherwise geniculate subfamily. Crusticorallina is distinguished from all other coralline genera by the following suite of morpho‐anatomical characters: (i) sunken, uniporate gametangial and bi/tetrasporangial conceptacles, (ii) cells linked by cell fusions, not secondary pit connections, (iii) an epithallus of 1 or 2 cell layers, (iv) a hypothallus that occupies 50% or more of the total thallus thickness, (v) elongate meristematic cells, and (vi) trichocytes absent. Four species are recognized based on rbcL, psbA and COI‐5P sequences, C. painei sp. nov., the generitype, C. adhaerens sp. nov., C. nootkana sp. nov. and C. muricata comb. nov., previously known as Pseudolithophyllum muricatum. Type material of Lithophyllum muricatum, basionym of C. muricata, in TRH comprises at least two taxa, and therefore we accept the previously designated lectotype specimen in UC that we sequenced to confirm its identity. Crusticorallina species are very difficult to distinguish using morpho‐anatomical and/or habitat characters, although at specific sites, some species may be distinguished by a combination of morpho‐anatomy, habitat and biogeography. The Northeast Pacific now boasts six coralline endemic genera, far more than any other region of the world.     

Subunit control of Rubisco biosynthesis – a relic of an endosymbiotic past?

Subunits of multiprotein complexes in the chloroplasts of eukaryotic cells are frequently the products of protein synthesis in the nucleus-cytoplasm and the organelle. The mechanisms that integrate gene expression in the two compartments are poorly understood. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a model of nuclear-chloroplast interactions because it is a relatively simple example of a multimeric complex, being composed of nuclear DNA-encoded (RbcS) small subunits (SS) and chloroplast DNA-encoded ( rbcL) large subunits (LS). One means by which RbcS and rbcL expression are coordinated is by the adjustment of subunit stoichiometries in response to the abundance of unassembled subunits. This type of integration occurs by two principal mechanisms. When SS accumulation is limiting (as in antisense mutants of tobacco), LS levels are primarily adjusted to those of the SS at the level of rbcL mRNA translation initiation. On the other hand, when LS accumulation is limiting (as in some rbcL nonsense and missense mutants), SS levels are adjusted to those of the LS at the level of protein degradation. These two mechanisms may be ubiquitous and serve as either fine-tune or course controls during normal growth and development. Autogenous control is a central theme of prokaryotic gene regulation, and intergenomic regulation of RbcS and rbcL expression by subunit concentrations may be a relic of an endosymbiotic past.     

Characteristics and utility of nuclear-encoded large-subunit ribosomal gene sequences in phylogenetic studies of red algae

Primer sequences are described for amplifying and sequencing a large fragment (approximately 2500 b.p.) of the nuclear-encoded large-subunit ribosomal RNA gene (LSU) from red algae. In comparison to RuBisCo large-subunit gene (rbcL) and nuclear-encoded small-subunit ribosomal RNA gene (SSU) sequence data, LSU sequence data was intermediate in the number of phylogenetically informative positions and sequence divergence. Parsimony analysis of LSU sequences for 16 Gelidiales species resolved some nodes unresolved in rbcL and SSU parsimony trees. An analysis of LSU sequences from 13 species of red algae classified in 11 orders suggests that this gene may be useful in studies of higher-level relationships of red algae.     

Systematic Position of the Rhoipteleaceae: Evidence from Nucleotide Sequences of rbc L Gene

Systematic position of the Rhoipteleaceae was investigated using nucleotide sequences of the chloroplast gene rbcL. Two sets of parsimony analyses were conducted, one using Bauera as the outgroup and the other using Cercidiphyllum-Liquidambar as outgroups. The results of these analyses are consistent. Rhoiptelea is allied with sampled Jug-landaceous genera in the rbcL phylogeny, suggesting its close relationship with the Juglandaceae.     

Molecular and morphological characterization of the Achnanthidium minutissimum complex (Bacillariophyta) in Petuniabukta (Spitsbergen,High Arctic) including the description of A. digitatum sp. nov.

Recent morphology-based investigations of freshwater Arctic diatoms suggest that many species remain to be discovered, reflecting a unique polar flora. During a survey of the freshwater diatom flora of northern Billefjorden, including the Petuniabukta fjord region (Spitsbergen), several morphodemes belonging to the Achnanthidium minutissimum species complex were recorded. Molecular phylogenies based on rbcL, 28S and 18S sequences, including single cells from Canada and strains from Marion Island (sub-Antarctica) and GenBank revealed the presence of 12 distinct A. minutissimum complex lineages, of which three contained strains from Spitsbergen. One Arctic lineage is described as a new species. Achnanthidium digitatum sp. nov. is morphologically characterized by narrow, linear to only slightly lanceolate valves and usually two areolae per stria. The two remaining Arctic lineages are in need of a more complete morphological and molecular comparison with other representatives of the A. minutissimum complex to clarify their taxonomic identity. It is argued that implementation of molecular data in the taxonomy of Achnanthidium will be essential to solve the taxonomic problems associated with this group, eventually resulting in a better understanding of the biogeography and niche differentiation of different species belonging to the A. minutissimum complex. Ideally, this should be based on more variable genes than the currently widely used 18S, which does not have a species level resolution in the A. minutissimum complex.     

Genetic differentiation and distribution of Pyropia acanthophora (Bangiales,Rhodophyta) in the Philippines

Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.