PHYLOGENETIC PLACEMENT,GENOME SIZE,AND GC CONTENT OF THE LIQUID‐HYDROCARBON‐PRODUCING GREEN MICROALGA BOTRYOCOCCUS BRAUNII STRAIN BERKELEY (SHOWA) (CHLOROPHYTA)1

We report the genome size and the GC content, and perform a phylogenetic analysis on Botryococcus braunii Kütz., a green, colony‐forming, hydrocarbon‐rich alga that is an attractive source for biopetroleum. While the chemistry of the hydrocarbons produced by the B race of B. braunii has been studied for many years, there is a deficiency of information concerning the molecular biology of this alga. In addition, there has been some discrepancy as to the phylogenetic placement of the Berkeley (or Showa) strain of the B race. To clarify its classification, we isolated the Berkeley strain nuclear SSU (18S) rRNA gene and β‐actin cDNA and used these sequences for phylogenetic analysis to determine that the Berkeley strain belongs to the Trebouxiophyceae class. This finding is in agreement with other B races of B. braunii, indicating the Berkeley strain is a true B race of B. braunii. To better understand molecular aspects of B. braunii, we obtained the Berkeley strain genome size as a first step in genome sequencing. Using flow cytometry, we determined the B. braunii Berkeley genome size to be 166.2 ± 2.2 Mb. We also estimated the GC content of the Berkeley strain as 54.4 ± 1.2% for expressed gene sequences.     

PHYLOGENETIC POSITION OF BOTRYOCOCCUS BRAUNII (CHLOROPHYCEAE) BASED ON SMALL SUBUNIT RIBOSOMAL RNA SEQUENCE DATA1

A small subunit ribosomal RNA (16S-like rRNA) in the hydrocarbon-rich microalga Botryococcus braunii Kützing (Chlorophyceae) was amplified using RNA polymerase chain reaction, and its sequence was determined. The sequence data of B. braunii were analyzed with those of several other algae in order to determine phylogenetic relationships among these algae. Phylogenetic analysis indicated B. braunii to be a member of the Chlorophyta and possibly related to Characium vacuolatum and Dunaliella parva.     

GROWTH AND BRANCHED HYDROCARBON PRODUCTION IN A STRAIN OF BOTRYOCOCCUS BRAUNII (CHLOROPHYTA)1

A strain Botryococcus braunii Kütz. that produces high levels of branched hydrocarbons (botryococcenes) was grown under different environmental conditions to investigate the relationship between growth and hydrocarbon production. Carbon dioxide concentration had the most significant influence on growth; 0.3% CO₂-enriched cultures demonstrated a minimum mass doubling time of ca. 40 h, compared to ca. 6 days for ambient air cultures grown on the same buffered growth medium. The botryococcene fraction, which consisted of 10 identified compounds (C_nH_2n-10; n = 30–34), usually constituted ca. 25–40% of the culture dry weight under various growth regimes, including nitrogen- and/or phosphate-deficiencies. CO₂ enrichment initially favored the production of the lower botryococcenes (C₃₀–C₃₂), whereas relatively slow-growing ambient air cultures accumulated C₃₃ and C₃₄ compounds. Colony color changed in response to different light intensities. High light increased the carotenoid/chlorophyll ratio, which resulted in orange colonies. Cultures exposed to low light intensity appeared green. This change in coloration was reversible over a period of a few days, and at no time were the linear hydrocarbons characteristic of the other form of the alga detected. Ostensible colony color is not, therefore, a reliable indicator of qualitative hydrocarbon content. Sequential solvent extraction experiments indicated that up to ca. 7% of the botryococcene fraction was intracellular and that the remainder was located within the colonial matrix. The internal (cellular) pool principally consisted of C₃₀–C₃₂ botryococcenes, whereas the external (colonial matrix) pool contained >99% of the C₃₃ and C₃₄ compounds, in addition to large amounts of the lower botryococcenes. These results, taken in conjunction with other data, are compatible with the hypothesis that the C₃₀ botryococcene is the precursor, presumably via methylation, of the higher botryococcenes.     

ULTRASTRUCTURE OF ACTIVE AND RESTING COLONIES OF BOTRYOCOCCUS BRAUNII (CHLOROPHYCEAE)1

The ultrastructure of resting state colonies of Botryococcus braunii Kützing from two localities is compared to active state colonies maintained in the laboratory. Qualitative hydrocarbon analyses confirmed the physiological status of each sample according to the precedent in the literature; resting state colonies contained botryococcenes, while active state colonies contained a predominance of straight-chain olefins. The ultrastructure of resting and active state colonies is fundamentally similar. The chloroplast of resting state cells contains fewer thylakoids and larger relative numbers of plastoglobuli than the chloroplast of active state cells maintained under favorable growth conditions. Previously undescribed phenomena include the cytochemical demonstration of polyphosphate bodies microbody-like organelles and ER-ribosomal-mitochondrial complexes. Attempts to elicit the transition of active to resting state colonies utilizing different light intensities and/or nitrogen deficient media were unsuccessful. Instead, these experiments induced the formation of yellow or whitish-brown senescent colonies which always contained a predominance of olefins. Senescent cells contain reduced, peripherally displaced organelles. Most of the cytoplasm is occupied by vacuoles and lipid (probably hydrocarbon) inclusions. Morphologically identifiable polyphosphate bodies are usually small or absent. Observations pertinent to the mechanism of hydrocarbon secretion were in basic agreement with previously published information. The outer cell wall, or trilamellar structure (TLS), was recently as the primary site of hydrocarbon accumulation and production. The role of the TLS in hydrocarbon biosynthesis, however, should be cautiously regarded without additional evidence.     

ALLELOCHEMICALS OF BOTRYOCOCCUS BRAUNII (CHLOROPHYCEAE)1

The alga Botryococcus braunii Kützing (Chlorophyceae) present in Liyu Lake (Huanlien County, Taiwan) has toxic effects on a variety of aquatic organisms. Blooms of this alga, which typically occur in autumn, are associated with fish deaths in this lake. Experiments using 15 phytoplankton and 5 zooplankton isolated from Liyu Lake indicate that these plankton exhibit various susceptibilities to B. braunii. A close correlation between the degree of susceptibility tested in the laboratory and the absence of certain phytoplankton during B. braunii blooms in the lake was observed, suggesting allelopathic effects. Isolation, identification, and verification with authentic compounds indicated that allelochemicals were a mixture of free fatty acids, including α‐linolenic, oleic, linolic, and palmitic acids. Compared with other phytoplankton isolates, B. braunii produced significantly higher amounts of free fatty acids, particularly of oleic and α‐linolenic acids. The role of these fatty acids in favoring dominance of B. braunii in the natural environment was elucidated.     

VARIABILITY OF CELL WALL STRUCTURE AND HYDROCARBON TYPE IN DIFFERENT STRAINS OF BOTRYOCOCCUS BRAUNII1

Different samples of Botryococcus braunii Kütz., freshly collected from nature or laboratory-grown from culture collection strains, were studied by electron microscopy and their hydrocarbon content analyzed. Although the general internal structure of the cells was rather constant, the organization of the outer walls forming the hydrocarbon-rich matrix of the colonies differed greatly from one sample to another. In the majority of cultivated strains, the colonies were rather small, the different successive external walls remained distinct and all strains contained dienic or trienic hydrocarbons. In contrast, most of the collected samples possessed large colonies with a rather compact matrix formed by the hydrocarbon-rich part of the successive closely appressed external wall layers. These samples contained polyunsaturated hydrocarbons, i.e. botryococcenes. Well defined cell caps which sheared off the cells were observed only in those strains with a compact matrix. The Austin strain and some collected samples, however, were intermediate with rather small colonies, dense matrix, definite cell caps and dienic hydrocarbons. Thus, the hydrocarbon composition did not correlate directly with the variations in wall structure; however, the occurence of dienic and botryococcene-like hydrocarbons together in one strain was never observed, although analyzed at various stages of growth. Thus, the existence of distinct strains of Botryococcus braunii, some synthesizing dienes, others botryococcenes, appears highly probable.     

STRUCTURE AND CHEMISTRY OF A NEW CHEMICAL RACE OF BOTRYOCOCCUS BRAUNII (CHLOROPHYCEAE) THAT PRODUCES LYCOPADIENE,A TETRATERPENOID HYDROCARBON1

New strains of the hydrocarbon rich alga Botryococcus braunii Kützing were isolated from water samples collected in three tropical freshwater lakes. These strains synthesize lycopadiene, a tetraterpenoid metabolite, as their sole hydrocarbon. The morphological and ultrastructural characteristics of these algae are similar to those reported for previously described strains which produce either alkadienes or botryococcenes. The pyriform shaped cells are embedded in a colonial matrix formed by layers of closely appressed external walls: this dense matrix is impregnated by the hydrocarbon and some other lipids. We believe the new strains synthesizing lycopadiene form a third chemical race in B. braunii, besides the alkadiene and botryococcene races, rather than a different species. Like the other two types of hydrocarbons, lycopadiene was produced primarily during the exponential and linear growth phases. The major fatty acid in the three races was oleic acid. This fatty acid was predominant in the alkadiene race; palmitic and octacosenoic acid also were present in appreciable amounts in the three races. Cholest-5-en-3β-ol, 24-methylcholest-5-en-3β-ol and 24-ethylcho-lest-5-en-3β-ol occurred in the three races; three unidentified sterols also were detected in the lycopadiene race. Moreover, the presence of very long chain alkenyl-phenols in the lipids of algae of the alkadiene race was not observed in the botryococcene and lycopadiene races. Of the polysaccharides released in the medium, galactose appeared as a primary component: it predominated in the botryococcene race. The other major constituents were fucose for the alkadiene race and glucose and fucose for the lycopadiene race. Although morphologically similar, some important chemical differences exist among algae classified as B. braunii.     

INORGANIC CARBON AND ACETATE ASSIMILATION IN BOTRYOCOCCUS BRAUNII(CHLOROPHYTA)1

Assimilation of ¹⁴CO₂ or ¹⁴C-acetate by the hydrocarbon producing alga Botryococcus braunii Kützing was investigated to determine the allocation of incorporated ¹⁴C among early metabolites of photosynthesis and secondary metabolites. When the cells were exposed to NaH¹⁴CO₃ for 10 sec, over 90% of incorporated ¹⁴C was detected in phosphoglycerate, suggesting that this alga assimilates inorganic carbon by the C-3 pathway. The distribution pattern of ¹⁴C in the number of metabolites revealed that organic acids, neutral sugars and amino acids were first labelled with ¹⁴C, and, after lag periods of a few minutes, lipids including hydrocarbon were increasingly labelled. Addition of 5 mM acetate to the culture medium did not affect the growth of this alga but enhanced cellular respiration. The incorporation of ¹⁴CO₂ into the lipid fraction was stimulated, but net photosynthesis was inhibited by the addition of acetate. ¹⁴C-acetate was incorporated into lipids at a very low rate in comparison with the rate of ¹⁴CO₂ incorporation.     

一株葡萄藻的分离、鉴定及产烃性能评价

研究从我国海南博鳌海边的淡水池塘水样分离获得一株绿藻ENN41。显微形态观察表明,ENN41的形态特征属于葡萄藻。进一步克隆ENN41的核糖体小亚基18S rRNA片段,利用分子生物学软件进行比对分析,结果表明ENN41的18S rRNA基因序列与布朗葡萄藻（Botryococcus braunii）同源性最高,说明ENN41为一株布朗葡萄藻（B.braunii）。ENN41在柱式反应器中培养16d,单位体积产率为0.483 g/（Ld）,粗烃占干重的含量为56.6%;主要脂肪酸为油酸（C18:1）、十八碳四烯酸（C18:4）和棕榈酸（C16:0）,三者之和占总脂肪酸的72.6%;利用尼罗红染色,清晰可见大量的油脂分布在细胞内和胞外基质中。ENN41在板式反应器中培养16d,单位体积产率为0.234 g/（Ld）,粗烃占干重的含量为20.0%。上述研究表明,ENN41是具有较高的生长速度和粗烃积累能力的布朗葡萄藻（B.braunii）藻株,具有产业化应用潜力。     

BACTERIAL INFLUENCE UPON GROWTH AND HYDROCARBON PRODUCTION OF THE GREEN ALGA BOTRYOCOCCUS BRAUNII1

Batch cultures of the hydrocarbon-rich alga Botryococcus braunii, Kütz. (axenic strains, non-axenic strains, associations with selected microorganisms) were examined with regard to total biomass and hydrocarbons at the onset of the stationary phase. Pronounced variations, related to the origin of the strains and to growth conditions, were observed with axenic cultures. It also appeared that the presence of microorganisms is not essential for high hydrocarbon production. Nevertheless, numerous bacteria were shown to exert considerable influence, antagonistic or beneficial, on B. braunii growth yield and hydrocarbon production. Such effects were strongly dependent on the species involved and on culture conditions. The presence of various microorganisms can influence not only the quantity of hydrocarbons produced, but also their level in the algal biomass and their relative abundance. However, their chemical structure is not affected. Intricate relationships were observed in B. braunii-bacteria systems and numerous factors (including, in some cultures, large positive effects due to bacterially produced CO₂) were implicated. Accordingly, specific associations should provide appropriate conditions for renewable hydrocarbon production via B. braunii large scale cultures.     

MORPHOLOGICAL AND ULTRASTRUCTURAL FEATURES OF A STRAIN OF BOTRYOCOCCUS TERRIBILIS (TREBOUXIOPHYCEAE) FROM BRAZIL1

The genus Botryococcus comprises a group of cosmopolitan species of freshwater colonial green algae, some of which synthesize and accumulate an unusually high level (15–76%) of liquid hydrocarbons. This characteristic suggests the possibility of exploiting species from this group as renewable sources for jet fuel. An oil‐rich strain of Botryococcus (Trebouxiophyceae) was isolated from a freshwater pond in the state of Bahia, Brazil, and is presently maintained under standard conditions at the Culture Collection of the Institute of Biology, Federal University of Bahia. The taxonomic classification of the species was based on light microscopy (LM); and TEM and SEM were used to better characterize its features, which have never before been described at this level. The LM characterization included the size of the colonies (35.7–157 μm) and cells (8–10 × 5–9 μm) and their connection in sub‐colonies by mucilaginous strands, as well as the presence of mucilaginous processes on the periphery of some of the colonies, with most of the cells included inside the colony. Reproduction occurred through divisions into two to four autospores. These features characterized the species as Botryococcus terribilis Komárek and Marvan. The TEM study showed, in addition to the presence of starch grains, pyrenoids that are penetrated by thick thylakoids. The pyrenoid bodies appear as electron‐dense protein inclusions located in the chloroplast and surrounded by a starch sheath. These structures, which contain most if not all of the Ribulose‐1,5‐bisphosphate carboxylase oxygenase in several algal species that have been studied closely, are newly discovered for this species.     

DIVERSITY AND PHYLOGENETIC PLACEMENT OF BRACTEACOCCUS TEREG (CHLOROPHYCEAE,CHLOROPHYTA) BASED ON 18S RIBOSOMAL RNA GENE SEQUENCE DATA1

Sequence data from the nuclear small-subunit ribosomal RNA gene was obtained for nine strains of Bracteacoccus Tereg, representing at least five morphological species and four distinct geographic locations. These, along with sequence data from two additional chlorophycean taxa, Spongiochloris spongiosa Starr and Ascochloris multinucleata Bold et MacEntee, and 48 published sequences from green algal taxa, were used to determine the phylogenetic placement of Bracteacoccus with respect to other chlorophycean green algae. Results support the monophyly of Bracteacoccus strains, contrasting with patterns observed so far for many other coccoid green algae. The range of variation among Bracteacoccus strains is similar to that of other congeners. Basal body orientation in Bracteacoccus has been interpreted as clockwise; however, the 18S data point to a relationship between Bracteacoccus and taxa with the directly opposed configuration of the flagellar apparatus. No close relationship was found to the multinucleated green coccoids with clockwise orientation of basal bodies, such as Spongiochloris, or to those with parallel basal bodies, such as Spermatozopsis. However, 18S data confirm that the motile and vegetative cells of Bracteacoccus are structurally distinct from the representatives of sphaeroplealean families currently studied. It is premature to reclassify Bracteacoccus until 18S comparisons can be made with additional sphaeroplealean taxa and with algae with similar flagellar structure such as Dictyochloris and Heterochlamydomonas.     

PHYLOGENETIC POSITION OF THE OOCYSTACEAE (CHLOROPHYTA)

The complete 18S rRNA gene sequences of three Oocystis A. Braun species (Oocystaceae) and three other chlorococcal algae, Tetrachlorella alternans (G. M. Smith) Korš. (Scenedesmaceae), Makinoella tosaensis Okada (Scenedesmaceae), and Amphikrikos cf. nanus (Fott & Heynig) Hind. (Chlorellaceae) were determined and subjected to four different phylogenetic analysis algorithms. Independent of the reconstruction method, these taxa clustered together as a monophyletic group (Oocystaceae) within the Trebouxiophyceae. This result was supported by high bootstrap values. A comparison of morphological data with the phylogenetic reconstructions indicated that the evolution of Oocystaceae was accompanied by a reduction in the number of plastids. This study fully supports the taxonomic assignment of the Oocystaceae as a distinct family. The diacritic criterion that the cell walls are composed of several cellulose layers with perpendicular fibril orientations is in accordance with the molecular data.     

HYPERSALINE SOIL SUPPORTS A DIVERSE COMMUNITY OF DUNALIELLA (CHLOROPHYCEAE)1

Numerous isolates of the green halophile Dunaliella were studied as part of a survey of microbial diversity at the Great Salt Plains (GSP) in Oklahoma, USA. The GSP is a large (～65 km²) salt flat with extreme temporal and spatial fluctuations in salinity and temperature. Although the flagellate halophile Dunaliella is common worldwide, nearly all cultured isolates are from saline habitats that are primarily aquatic rather than primarily terrestrial. The diverse GSP Dunaliella strains exhibit three morphotypes: a predominantly motile form, a motile form with a prominent palmelloid phase (nonmotile, mucilage rich), and a palmelloid form with a weakly motile phase. All had broad salinity optima well below typical in situ salinities at the GSP, and two of the palmelloid isolates grew as well in freshwater as in highly saline media. Molecular phylogenetic and evolutionary analyses revealed that Dunaliella from the GSP (and two similar habitats in the Great Basin, USA) are allied with D. viridis Teodor. but possess phylogenetic diversity in excess of existing global isolates from aquatic habitats. In addition, isolates from primarily terrestrial habitats exhibit statistically higher rates of nucleotide substitution than the phylogenetically homogeneous set of primarily aquatic Dunaliella taxa. We hypothesize that dynamically extreme saline soil habitats may select for different and more diverse Dunaliella lineages than more stable saline aquatic habitats. We also propose Dunaliella as a tractable microbial model for in situ testing of evolutionary and phylogeographic hypotheses.     

JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE,INCERTAE SEDIS) PREVIOUSLY RECORDED BY ENVIRONMENTAL SEQUENCING1

The diversity of eukaryotic microorganisms is far from fully described, as indicated by the vast number of unassigned genotypes retrieved by environmental sequencing or metagenomics. We isolated several strains of unicellular green algae from algal biofilms growing on tree bark in a Southeast Asian tropical rainforest and determined them to be relatives of an unidentified lineage of environmental 18S rDNA sequences, thus uncovering its cellular identity. Light, confocal, and electron microscope observations and sequencing the 18S rRNA gene revealed that the strains represent two different species within an apparently new genus, described here as Jenufa gen. nov. Both species formed minute coccoid cells with an irregular globular outline, a smooth cell wall, and a single parietal chloroplast without a pyrenoid. The two species, described herein as J. perforata and J. minuta, differed in chloroplast morphology and cell wall structure. Phylogenetic analyses of 18S rRNA gene sequences showed a firm relationship between the two species and placed the Jenufa lineage in an unresolved position within the CS clade (Chlamydomonadales + Sphaeropleales) of the class Chlorophyceae, although possible affinities to the genus Golenkinia were suggested both by maximum‐likelihood (ML) and Bayesian methods. Furthermore, two almost identical environmental 18S rDNA sequences from an endolithic microbial community occurring in dolomite rock in the central Alps turned out to be specifically related to, yet apparently distinct from, the sequence of J. minuta, indicating the existence of an undescribed Jenufa species occurring in the temperate zone.     

PHYLOGENY OF CARTERIA (CHLOROPHYCEAE) INFERRED FROM MOLECULAR AND ORGANISMAL DATA1

Comparative ultrastructural data have shown that at least 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. lunzensis, C. crucifera, and C. olivieri, 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 interpretations 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 (morphological, ultra-structural, life history, and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monophyly 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.     

EVOLUTIONARY CONSEQUENCES OF THE LOSS OF PHOTOSYNTHESIS IN CHLAMYDOMONADACEAE: PHYLOGENETIC ANALYSIS OF Rrn18 (18S rDNA) IN 13 POLYTOMA STRAINS (CHLOROPHYTA)1

Complete sequences of the Rrn 18 genes were obtained from 13 strains of the nonphotosynthetic algal genus Polytoma. Phylogenetic analyses showed that these strains formed two clades. One clade shows only modest sequence diversity but is represented by strains collected at widely dispersed sites in Europe and America. The other clade consists of a single isolate from the Canary Islands. Both clades lie well within the extended clade that includes all species of Chlamydomonas for which sequence data are available. The two Polytoma clades are separated from each other by several green species, suggesting that the extant nonphotosynthetic Chlamydomonadaceae arose from photosynthetic ancestors at least twice. These results suggest that nonphotosynthetic mutants are capable of establishing lineages that can spread widely but have a higher probability of extinction than their photosynthetic congeners.     

PHYLOGENETIC POSITION OF KOLIELLA (CHLOROPHYTA) AS INFERRED FROM NUCLEAR AND CHLOROPLAST SMALL SUBUNIT rDNA

The phylogenetic position of Koliella , a chlorophyte characterized by Klebsormidium type cell division, was inferred from analyses of partial 18S rDNA and partial 16S rDNA. Parsimony and distance analyses of separate and combined data sets indicated that the members of Koliella belonged to Trebouxiophyceae, and high decay indices and bootstrap values supported this affinity. However, the genus appeared to be polyphyletic. Koliella spiculiformis , the nomenclatural type of the genus, was allied with Nannochloris eucaryota and the "true" chlorellas ( Chlorella vulgaris , C. lobophora , C. sorokiniana , and C. kessleri ). The close relatives of Koliella longiseta (≡ Raphidonema longiseta ) and Koliella sempervirens appeared to be Stichococcus bacillaris and some species traditionally classified in Chlorella that were characterized by the production of secondary carotenoids under nitrogen-deficient conditions. This clade was also supported by the presence of a relatively phylogenetically stable group I intron (1506) in the 18S rRNA gene. Because of the presence of Klebsormidium type cell division, some authors regarded the members of Koliella as closely related to charophytes. Molecular analyses, however, did not confirm this affinity and suggested that a Klebsormidium type cell division is homoplastic in green plants.