Search

Non-symbiotic diazotrophic microbes are important contributors to global N budgets in cereal crops. Knowledge of the biogeography of the organisms in this functional guild increases our understanding of biological N fixation in diverse locations and climates. Here, we describe the diazotrophic community in the previously unstudied, extensive ricefields of southeast Missouri, using restriction fragment length polymorphism (RFLP) analysis and sequencing of nifH gene clones. While nine RFLP patterns were observed in random nifH clones, these groups were not all supported by gene sequencing, suggesting that the RFLP of nifH genes alone is not suitable for describing diazotrophic guilds. Dozens of nifH clones from Missouri ricefield soils were sequenced and analyzed phylogenetically. The nifH genes detected were predominantly from Geobacteraceae, most closely related to Geobacter and Geomonas species. There were substantial clusters of nifH clones most closely related to Desulfovibrionales and other Proteobacteria. Many of the clones did not closely cluster with nifH sequences from known isolates or clades. No cyanobacterial or archaeal sequences were detected in the Missouri ricefield soils. The microbial guild fixing N appeared to be rich in anaerobes and lithotrophs. Organisms in Geobacter and Geomonas seem to be cosmopolitan, but endemism was evident, since nifH clones were recovered that formed clusters not previously reported from ricefields in other locations. [ABSTRACT FROM AUTHOR]

An enormous body of research is focused on finding ways to commercialize carotenoids produced by the unicellular green alga, Haematococcus, often without the benefit of a sound phylogenetic assessment. Evidence of cryptic diversity in the genus means that comparing results of pigment studies may be confounded by the absence of a phylogenetic framework. Moreover, previous work has identified unnamed strains that are likely candidates for species status. We reconstructed the phylogeny of an expanded sampling of Haematococcus isolates utilizing data from nuclear ribosomal markers (18S rRNA gene, 26S rRNA gene, internal transcribed spacer [ITS]-1, 5.8S rRNA gene, and ITS-2) and the rbcL gene. In addition, we gathered morphological, ultrastructural and pigment data from key isolates of Haematococcus. Our expanded data and taxon sampling support the concept of a new species, H. privus, found exclusively in North America. Despite overlap in numerous morphological traits, results indicate that ratios of protoplast length to width and akinete diameter may be useful for discriminating Haematococcus lineages. High growth rate and robust astaxanthin yield indicate that H. rubicundus (SAG 34-1c) is worthy of additional scrutiny as a pigment source. With the description of H. privus, the evidence supports the existence of at least five, species-level lineages in the genus. Our phylogenetic assessment provides the tools to frame future pigment investigations of Haematococcus in an updated evolutionary context. In addition, our investigation highlighted open questions regarding polyploidy and sexuality in Haematococcus which demonstrate that much remains to be discovered about this green flagellate. [ABSTRACT FROM AUTHOR]

Abstract Aided by a host of bioinformatics tools, primary and secondary structural analyses of the internal transcribed spacer 2 (ITS2) from the eukaryotic ribosomal RNA repeat have a long and enviable record of service to diversity studies of fungi, plants and protists. Automation of annotation, secondary structure estimation and sequence alignment have become routine for the vast majority of ITS2 sequences. Challenges to the bioinformatics pipeline for ITS2 analysis generally arise in cases where the sequence length lies well outside the norm. These sequences generally defy protocols for annotation and secondary structure prediction. The long ITS2 sequences (ca. 600 nucleotides) from the green alga, Jenufa , offered an opportunity to explore this problem. Custom BLAST parameters revealed the presence of 4-helix structures (200–250 nucleotides) embedded in the 5′ portion of several long ITS2 sequences of Jenufa. Of special note is the ITS2 sequence of J. lobulosa where a 4-helix structure was obtained for both the embedded ITS2 and for the complete sequence. Phylogenetic analysis of these typically-sized sequences resolved Golenkinia longispicula as the sister to Jenufa. Our observations indicate that other long ITS2 sequences should be examined for evidence of expansion or duplication. In addition, if the embedded ITS2 sequences are functional, then ribogenesis is almost certainly more diverse than is already apparent from studies of humans and yeast. Highlights • Custom BLAST parameters revealed the presence of 4-helix structures embedded in the long ITS2 sequences of Jenufa • For J. lobulosa a 4-helix structure was obtained for both the embedded ITS2 and for the complete sequence • ITS2 sequence-structure phylogenetics affirmed an alliance between Jenufa and Golenkinia (Chlorophyta, Chlorophyceae) [ABSTRACT FROM AUTHOR]

Although considered rare, airborne pollen can be deposited far from its place of origin under a confluence of favorable conditions. Temporally anomalous records of Cupressacean pollen collected from January air samples in London, Ontario, Canada have been cited as a new case of long-distance transport. Data on pollination season implicated Juniperus ashei (mountain cedar), with populations in central Texas and south central Oklahoma, as the nearest source of the Cupressacean pollen in the Canadian air samples. This finding is of special significance given the allergenicity of mountain cedar pollen. While microscopy is used extensively to identify particles in the air spora, pollen from all members of the Cupressaceae, including Juniperus, are morphologically indistinguishable. Consequently, we implemented a molecular approach to characterize Juniperus pollen using PCR in order to test the long-distance transport hypothesis. Our PCR results using species-specific primers confirmed that the anomalous Cupressacean pollen collected in Canada was from J. ashei. Forward trajectory analysis from source areas in Texas and the Arbuckle Mountains in Oklahoma and backward trajectory analysis from the destination area near London, Ontario were completed using models implemented in HYSPLIT4 (Hybrid Single-Particle Lagrangian Integrated Trajectory). Results from these trajectory analyses strongly supported the conclusion that the J. ashei pollen detected in Canada had its origins in Texas or Oklahoma. The results from the molecular findings are significant as they provide a new method to confirm the long-distance transport of pollen that bears allergenic importance. [ABSTRACT FROM AUTHOR]

Background and Aims The green algal class Chlorophyceae comprises five orders (Chlamydomonadales, Sphaeropleales, Chaetophorales, Chaetopeltidales and Oedogoniales). Attempts to resolve the relationships among these groups have met with limited success. Studies of single genes (18S rRNA, 26S rRNA, rbcL or atpB) have largely failed to unambiguously resolve the relative positions of Oedogoniales, Chaetophorales and Chaetopeltidales (the OCC taxa). In contrast, recent genomics analyses of plastid data from OCC exemplars provided a robust phylogenetic analysis that supports a monophyletic OCC alliance. Methods An ITS2 data set was assembled to independently test the OCC hypothesis and to evaluate the performance of these data in assessing green algal phylogeny at the ordinal or class level. Sequence-structure analysis designed for use with ITS2 data was employed for phylogenetic reconstruction. Key Results Results of this study yielded trees that were, in general, topologically congruent with the results from the genomic analyses, including support for the monophyly of the OCC alliance. Conclusions Not all nodes from the ITS2 analyses exhibited robust support, but our investigation demonstrates that sequence-structure analyses of ITS2 provide a taxon-rich means of testing phylogenetic hypotheses at high taxonomic levels. Thus, the ITS2 data, in the context of sequence-structure analysis, provide an economical supplement or alternative to the single-marker approaches used in green algal phylogeny. [ABSTRACT FROM AUTHOR]

Background: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings: Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages. [ABSTRACT FROM AUTHOR]

Abstract: Studies of alpha-2-macroglobulin (α2M), a universal protease inhibitor, have indicated that it plays a unique and critical role in the innate immune system of vertebrate and invertebrate animals. The distinctive mechanism of pathogen inhibition – through physical entrapment of the pathogen-derived protease – makes α2M an ideal candidate for molecular evolutionary analysis. Furthermore, recent studies revealed that the Osteichthyes are characterized by levels of α2M diversification that exceed those recorded in other animal groups. Our study of Danio rerio (zebrafish) indicated that (1) two distinct lineages of α2M and α2M-like isoforms exist and (2) at least some codons in the functional domains of α2M have been subjected to positive Darwinian selection. The findings of several hot-spots for nonsynonymous substitutions in the two functional domains such as bait region and receptor binding domain, suggest that host-immune selection have played a dominant role in these two genomic regions of α2M. The presence of two, non-monophyletic α2M lineages in zebrafish provides compelling evidence of an ancient gene duplication event. The accelerated rate of nucleotide substitution in the functional domains of α2M is consistent with similar observations of other immune system components. [Copyright &y& Elsevier]

The hydrodictyacean green algal lineage has been the focus of much research due to the fossil record of at least some members, their ornamented cell walls, and their distinctive reproductive strategies. The phylogeny of the family was, until recently, exclusively morphology based. This investigation examines hydrodictyacean isolates from several culture collections, focusing on sequences from ribosomal data: 18S rDNA, 26S rDNA (partial), and internal transcribed spacer (ITS)-2 data. Results from phylogenetic analyses of independent and combined data matrices support the Hydrodictyaceae as a monophyletic lineage that includes isolates of Chlorotetraedron, Hydrodictyon, Pediastrum, Sorastrum, and Tetraedron. Phylogenetic analyses of rDNA data indicate that the three-dimensional coenobium of Hydrodictyon is evolutionarily distinct from the three-dimensional coenobium of Sorastrum. The more robust aspects of the ITS-2 data corroborate the 18S+26S rDNA topology and provide a structural autapomorphy for the Hydrodictyaceae and Neochloridaceae, that is, an abridgment of helix IV in the secondary structure. The rDNA data do not support monophyly of Pediastrum but rather suggest the existence of four additional hydrodictyacean genera: Monactinus, Parapediastrum, Pseudopediastrum, and Stauridium. [ABSTRACT FROM AUTHOR]

The phylogenetic affinities of Lobocharacium coloradoense were investigated by analysis of combined 18S and 26S rDNA data. Results from both parsimony and likelihood methods supported a close alliance among Lobocharacium , Characiosiphon , and Characiochloris. These three taxa formed a clade near the base of the “Dunaliella ” group within the chlamydomonad lineage. Protosiphon , which exhibits a siphonous habit similar to Characiosiphon and Lobocharacium , was not resolved as a close ally of the latter two taxa. The Lobocharacium alliance was characterized by the presence of an attachment pad associated with the nonmotile vegetative stage and pyrenoids that possess cytoplasmic invaginations. The pyrenoid feature is an ultrastructural trait that has now been observed in five different chlorophycean lineages. The Lobocharacium–Characiosiphon–Characiochloris clade is not predicted by any classifications of green algae. Additional taxon and data sampling need to be completed to resolve inconsistencies between the molecular phylogenetic evidence and at least some of the current family-level taxa. [ABSTRACT FROM AUTHOR]

Ultrastructural analyses of the flagellar apparatus suggested that Sphaeroplea, Atractomorpha, the Hydrodictyaceae, and the Neochloridaceae, all of which produce biflagellate motile cells with directly opposed (DO) basal bodies, are allied in an order Sphaeropleales. Recent studies of 18S rDNA sequence data supported an alliance of the DO group, but no data from Sphaeroplea and its allies were included. This investigation presented a test of the phylogenetic hypothesis suggested by the flagellar apparatus evidence using sequence data from the nuclear-encoded small-subunit rDNA (18S) and large subunit rDNA (26S) genes, combined with additional taxon sampling. Results from phylogenetic analyses weakly supported monophyly of biflagellate DO taxa and indicated that pyrenoids with cytoplasmic invaginations are present in numerous distinct lineages. Analysis of both molecular data sets supported a class Chlorophyceae comprised of at least six major groups that generally correspond to currently recognized orders or families: Chaetophorales, Chae- topeltidales, Chlamydomonadales, Sphaeropleales, Sphaeropleaceae, and Oedogoniales. In addition, Cylindrocapsa, Elakatothrix, Treubaria, and Trochiscia formed a seventh chlorophycean clade that is new to science. This investigation demonstrated that the 26S rDNA gene provides more phylogenetic signal, per unit sequence, than the 18S rDNA gene and that combined analysis yields topologies with more robust support than independent analysis of either data set. [ABSTRACT FROM AUTHOR]

Comparative specificity of sporangial wall autolysins (i.e. vegetative lyric enzymes [VIE]) derived from sporulating cultures has been used to group Chlamydomonas taxa into 15 different VLE types. The VLE-14 group including isolates of C. geitleri, C. noctigama, C. monoica, C. pinicola, C. terricola, and C. hindakii, is one of the largest of these VLE groups. Genetic studies have shown that a number of the VLE-14 taxa are interfertile, albeit with little on reduced viability of progeny. A reevaluation of the VLE-14 group suggested that all members should be regarded a distinct isolates of C. noctigama. The present investigation tests the phylogenetic implications of the VLE evidence and examines the validity of the taxonomic reevaluation in a phylogenetic context by analysis of 18S rRNA gene sequence data. Results from analysis of the sequence data are consistent with an interpretation of the VLE evidence as indicative of monophyletic taxa. Phylogenetic analysis of the sequence data are also consistent with the taxonomic reevaluation and reidentification of the group. However, at least some of the VLE-14 isolates studied in this investigation fit criteria for distinct biologic or phylogenetic species. It is concluded that the VLE-14 taxa represent a very closely allied group that includes some isolates that are in the early stages of speciation by reproductive isolation. [ABSTRACT FROM AUTHOR]

The unicellular,biflagellate genus Chloromonas differs from its ally, Chlamydomonas, primarily by the absence of pyrenoids in the vegetative stage of the former. As with most green flagellate genera, little is known about phylogenetic affinities within and among Chloromonas species. Phylogenetic analyses of nuclear-encoded small-subunit ribosomal RNA gene sequences demonstrate that a sampling of five Chloromonas taxa, obtained from major culture collections, do not form a monophyletic group However, only three of these isolates, Chloromonas clathrata, Chloromonas serbinowi, and Chloromonas rosae, are diagnosable morphologically as Chloromonas species by the absence of a pyrenoid in the vegetative stage. The three diagnosable Chloromonas taxa form an alliance with two pyrenoid-bearing chlamydomonads, Chlamydomonas augustae and Chlamydomonas serbinowi, which represents the basal lineage within the clade, each of the diagnosable Chloromonas taxa and their pyrenoid bearing Chlamydomonas allies were isolated originally from mountain soils, snow, or cold peat. These observations suggest that habitat, independent of pyrenoid status, may be most closely linked to the natural history of this clade of chlamydomonad flagellates. [ABSTRACT FROM AUTHOR]

The distribution of loroxanthin in chlorophycean flagellates is consistent with their phylogeny as inferred from molecular and organismal characters. Although polarity of this character cannot yet be determined, if the absence of loroxanthin is plasiomorphic for chlorophycean flagellates, the presence of loroxanthin defines a clade that includes the Euchlamydomonas morphological groups, two other species of Chlamydomonas, C. asymmetrica and C. oblonga, and Gonium pectorale. A subsequent reversal to loroxanthin absence is apomorphic for the more complex volvocacean taxa. These results suggest that loroxanthin distribution will be useful for resolving phylogenetic questions in green algae. [ABSTRACT FROM AUTHOR]

Comparative ultrastructural data have shown that atleast two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small and large subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1)testing hypotheses that distinct groups of species exist within the genus and 2)assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C.lunzenis, C. crucifera, and C.oliveri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox and Eudorina). Two other Carteria taxa, C.radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretation of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphologica, ultrastructural, life history and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monopophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus. [ABSTRACT FROM AUTHOR]

The genus Chlamydomonas Ehrenberg may contain as many as 450 described species. Morphological, physiological and molecular data show that variation among some Chlamydomonas species can be great, leading to speculation that multiple, generic-level lineages exist within this genus. The most recent systematic studies of Chlamydomonas have led to proposals of nine distinct morphological and 15 distinct sporangial autolysin groups. Partial sequences from the nuclear small subunit rRNAs from 14 Chlamydomonas species representing 12 autolysin and four morphological groups, and from three flagellates thought to be related to Chlamydomonas were determined in a phylogenetic study of relationships among these algae. Sequence comparisons among some Chlamydomonas species revealed differences comparable to the sequence divergence between soybeans and cycads. Cladistic analysis of the sequence data suggests that multiple lineages exist among species of Chlamydomonas. Some of these lineages represent alliances of both Chlamydomonas and non-Chlamydomonas taxa; thus, the current taxonomy does not reflect natural, or monophyletic, groups. Collectively, these lineages may represent distinct families or even orders. [ABSTRACT FROM AUTHOR]

A systematic investigation of the genus Sphaeroplea was conducted using cladistic analyses of both structural and isozyme characters for the same set of taxa. The structural data were not able to fully resolve some of the taxa while the isozyme data did produce a tree in which all nodes were supported by data. The structural characters were relatively consistent with one another, whereas the isozyme characters were much less internally consistent. Results from independent, cladistic analyses of both data sets support the concept that among those Sphaeroplea species investigated, S. fragilis Buchheim et Hoffman had an early divergence. The two data sets differed primarily in that the structural data support monophyly of the genus Sphaeroplea and the isozyme data do not. The greater relative consistency of the structural data suggest better support for trees inferred from its analysis Furthermore, searches for character congruence between the two data sets revealed isozyme data which support monophyly of the genus Sphearoplea, but had been overwhelmed by conflicting isozyme characters. [ABSTRACT FROM AUTHOR]

Cirri are curled appendages borne on the surface of mature zygotes in some members of the green algal family Sphaeropleaceae. Structures equivalent to cirri have not been reported previously in any green algae. We found cirri in four taxa: Sphaeroplea fragilis Buchheim et Hoffman, Atractomorpha porcata Hoffman, and two new undescribed species of Atractomorpha from Africa. Zygotes of seven other sphaeropleacean taxa were examined, but they did not produce cirri. Cirri may be either simple or compound. Simple cirri are less than 0.5 μm in diameter and show no evidence of longitudinal striations or subunits. Compound cirri are more massive (commonly 2.0-3.5 μm, and up to 4 μm diameter in S. fragilis) and possess longitudinal striations suggesting that each is formed of longitudinally arranged subunits ca. 0.5 μm in diameter. Simple and compound cirri are formed by zygotes of all four tax that produce cirri. Both types may occur on the same zygote. Nonetheless, the patterns of variation in length, shape, and distribution of the two types of cirri are sufficiently distinct to characterize each taxon. Energy dispersive X-ray microanalysis (EDX) shows that cirri lack appreciable mineralization and are thus primarily organic in nature. The potential value of cirri as a taxonomic character in the Sphaeropleaceae is discussed. [ABSTRACT FROM AUTHOR]

Male gametes have been studied in Sphaeroplea robusta (Chlorophyeae) using both light and electron microscopy Mature gametes are typically biflagellate and possess a single, large mitochondrion that dominates the anterior third of the cell directly posterior to the basal bodies. One or more microbodies are closely associated with the mitochondrion. Contractile vacuoles occur anterior to the elongated nucleus which, in fully mature gametes possesses condensed chromatin. The reduced, starch-filled chloroplast lacks an associated eyespot and occupies a posterior position. A thin, anteriorly directed process or extension of the chloroplast parallels a portion of one of the multistranded flagellar roots. The paired basal bodies are directly opposed with no demonstrable offset, and are connetted by an arched distal fiber with a highly elaborated central striated region that forms the apical cone a feature characteristic of male gametes in most species of Sphaeroplea. Possession of a striated distal fiber, a crucinte flagellar root system (i.e. two-stranded microtubular roots alternating with multistranded roots), and directly opposed basal bodies are consistent with the alga's chlorophycean effciencies. [ABSTRACT FROM AUTHOR]

The use of 18S rDNA sequences for inferring phylogenies, in particular for higher taxonomic level analysis, has a long tradition in phycology. Similar to ITS2, the 18S rDNA displays a conserved secondary structure that could be used simultaneously with the primary sequence to increase the amount of information used when inferring phylogenetic relationships. Sequence-structure phylogenetics is already established for ITS2 research. Secondary structures no longer simply guide alignments and trees but are used simultaneously by encoding the sequence-structure information into a 12-letter alphabet. We used the knowledge gathered from the extensive body of ITS2 research regarding sequence-structure phylogenetics and applied it to 18S rRNA data; we present THESES db, the Algae 18S rDNA Sequence-Structure Database (), which contains sequences and their individual secondary structures for three major groups of algae (Chlorophyta, Bacillariophyta and Rhodophyta). This database was designed to serve as the starting point for future 18S rDNA sequence-structure based phylogenetic analyses that will eventually extend beyond phycology. One hundred phylogenetic trees generated from 18S sequence-only datasets and from parallel 18S sequence-structure datasets were compared for each taxon analyzed in this study (diatoms, green algae and red algae). Half of the comparisons produced trees with different topologies that frequently related to the status of sister genera. Using the lineage information for each species as listed in GenBank, we determined that the sequence-structure approach resolved a genus as monophyletic, while the sequence-only approach failed to do so in comparisons that comprised 3% of the cases examined. The reverse was true for a total of 8.3% of the comparisons that we generated. Future work, both in our labs and among the broader phycological community, will provide additional data to test the accuracy and robustness of a sequence-structure approach at different taxonomic ranks. [ABSTRACT FROM AUTHOR]

The Great Salt Plains (GSP) in north-central Oklahoma, USA is an expansive salt flat (∼65 km2) that is part of the federally protected Salt Plains National Wildlife Refuge. The GSP serves as an ideal environment to study the microbial diversity of a terrestrial, hypersaline system that experiences wide fluctuations in freshwater influx and diel temperature. Our study assessed cyanobacterial diversity at the GSP by focusing on the taxonomic and physiological diversity of GSP isolates, and the 16S rRNA phylogenetic diversity of isolates and environmental clones from three sites (north, central, and south). Taxonomic diversity of isolates was limited to a few genera (mostly Phormidium and Geitlerinema), but physiological diversity based on halotolerance ranges was strikingly more diverse, even between strains of the same phylotype. The phylogenetic tree revealed diversity that spanned a number of cyanobacterial lineages, although diversity at each site was dominated by only a few phylotypes. Unlike other hypersaline systems, a number of environmental clones from the GSP were members of the heterocystous lineage. Although a number of cyanobacterial isolates were close matches with prevalent environmental clones, it is not certain if these clones reflect the same halotolerance ranges of their matching isolates. This caveat is based on the notable disparities we found between strains of the same phylotype and their inherent halotolerance. Our findings support the hypothesis that variable or poikilotrophic environments promote diversification, and in particular, select for variation in ecotype more than phylotype. [ABSTRACT FROM AUTHOR]

Dunaliella, a commercially important chlorophyte, is globally distributed in saline habitats. Morphological species have not been definitively reconciled with phylogenetic analyses. Considerable genetic diversity continues to be discovered in new isolates, especially from soil and benthic habitats. Twenty‐nine new isolates from Great Salt Lake, Utah, many from benthic or supralittoral habitats, were phylogenetically analyzed using ITS1+5.8S+ITS2 in comparison to a broad sampling of available sequences. A few new isolates align in one branch of a bifurcated monophyletic Dunaliella salina clade and several cluster within monophyletic D. viridis. Several others align with relatively few unnamed strains from other locations, comprising a diverse clade that may represent two or more new species. The overall Dunaliella clade is relatively robust, but the nearest outgroups are ambiguously placed with extremely long branches. About half of the isolates, all from benthic or supralittoral habitats, have been persistently sarcinoid in liquid media since isolation. This trait is spread across the Dunaliella phylogeny. The morphology of two sarcinoid strains was documented with light microscopy, revealing an extensive glycocalyx. Clumping behavior of unicellular and sarcinoid strains was unaffected by presence or absence of Mg2+ or Ca2+, addition of lectin‐inhibiting monosaccharides, or water‐soluble factors from morphologically opposite strains. Results from this investigation have significantly expanded our current understanding of Dunaliella diversity, but it seems likely that much remains to be discovered with additional sampling. [ABSTRACT FROM AUTHOR]

Primary and secondary structural data from the internal transcribed spacer two (ITS2) have been used extensively for diversity studies of many different eukaryotic organisms, including the green algae. Ease of amplification is due, at least in part, to the fact that ITS2 is part of the tandemly-repeated rRNA array. The potential confounding influence of intragenomic variability has yet to be addressed except in a few organisms. Moreover, few of the assessments of intragenomic variation have taken advantage of the deep sequencing capacity of sequence-by-synthesis protocols. We present results from our adaptation of the 16S Metagenomics Sequencing Library Preparation/Illumina protocol for deep sequencing of the ITS2 genes in selected isolates of the green algal genus, Haematococcus. Deep sequencing yielded from just under 20,000 to more than 500,000 merged reads, outpacing results from recent pyrosequencing efforts. Furthermore, a conservative evaluation of these data revealed a range of three to six ITS2 sequence haplotypes (defined as unique sets of nucleotide polymorphisms) across the taxon sampling. The frequency of the dominant haplotype ranged from 0.35 to 0.98. In all but two cases, the haplotype with the greatest frequency corresponded to a sequence obtained by the Sanger method using PCR templates. Our data also show that results from the sequencing-by-synthesis approach are reproducible. In addition to advancing our understanding of ribosomal RNA variation, the results of this investigation will allow us to begin testing hypotheses regarding the maintenance of homogeneity across multi-copy genes. [ABSTRACT FROM AUTHOR]

Ettlia is a green algal genus comprised of several economically important species that have contributed to a taxonomic nightmare for phycologists - the recognition that coccoid green algae are polyphyletic on a grand scale. This taxonomic confusion is slowly being resolved with the aid of molecular evidence and, in some cases, new structural data. The most recent investigation using 18S ribosomal (r)DNA data corroborated an extraordinarily close alliance between Haematococcus pluvialis, a predominantly flagellate unicell, and the coccoid alga, Ettlia carotinosa. This putative evolutionary relationship between the green algal species H. pluvialis and E. carotinosa has, once again, placed coccoid algae at the center of systematic debate. The only apparent similarity between these two species is the ability to produce astaxanthin. Because the 18S rDNA results were not particularly robust, additional data from the internal transcribed spacer 2 rRNA and 26S rRNA genes were collected. Results from analyses of these data corroborated a close alliance between E. carotinosa and H. pluvialis. In addition, the 18S rDNA data set was expanded using new, published data from other species of Ettlia. Phylogenetic analyses of this updated matrix confirmed the existence of at least four distinct Ettlia lineages. These observations indicated that (1) additional taxonomic revision of the genus Ettlia is needed, (2) E. carotinosa need not be merged into the genus Haematococcus, (3) the case of H. pluvialis and E. carotinosa is an example of ciyptic similarity, and (4) the extraordinarily close alliance between E. carotinosa and H. pluvialis offers an ideal system to study patterns of gene expression and morphogenesis in unicellular eukaryotes. [ABSTRACT FROM AUTHOR]

We analyzed the ITS2 primary and secondary structure (including Compensatory Base Changes ( CBCs)) of 17 new Dunaliella strains (11 D. viridis, two D. tertiolecta, and four Dunaliella sp.), and compared these with other Dunaliella sequences available from the ITS2 database to circumscribe their taxonomic position. The ITS2 primary and secondary structure analysis positioned the majority of D. viridis strains in four main clades, showing that D. viridis is polyphyletic. The detection of at least one CBC among these clades strongly suggests that they could correspond to different biological species. Unexpectedly, while D. viridis var. euchlora ( CCAP19/21) was positioned within the subgenus Dunaliella, D. viridis var. palmelloides ( CCAP11/34) was positioned clearly outside this subgenus, suggesting that this taxon may not be properly placed in Dunaliella. Furthermore, the detection of at least three compensatory base changes ( CBCs) between D. viridis var. palmelloides ( CCAP11/34) and the other strains analyzed, confirm that this strain is a different species. For these reasons we propose re-naming D. viridis var. palmelloides ( CCAP11/34) to incertae sedis, and D. viridis var. euchlora ( CCAP19/21) to Dunaliella sp. Therefore, the ITS2 primary and secondary structure data suggest a taxonomic re-structuring of D. viridis. [ABSTRACT FROM AUTHOR]

We provide molecular phylogenetic evidence that the obscure genera Palmophyllum Kütz. and Verdigellas D. L. Ballant. et J. N. Norris form a distinct and early diverging lineage of green algae. These palmelloid seaweeds generally persist in deep waters, where grazing pressure and competition for space are reduced. Their distinctness warrants recognition as a new order, the Palmophyllales. Although phylogenetic analyses of both the 18S rRNA gene and two chloroplast genes ( atpB and rbcL) are in agreement with a deep-branching Palmophyllales, the genes are in conflict about its exact phylogenetic placement. Analysis of the nuclear ribosomal DNA allies the Palmophyllales with the prasinophyte genera Prasinococcus and Prasinoderma (Prasinococcales), while the plastid gene phylogeny placed Palmophyllum and Verdigellas as sister clade to all other Chlorophyta. [ABSTRACT FROM AUTHOR]