Yuuhiko Tanabe

Recombination, cryptic clades and neutral molecular divergence of the microcystin synthetase (mcy) genes of toxic cyanobacterium Microcystis aeruginosa.

BackgroundThe water-bloom-forming cyanobacterium Microcystis aeruginosa is a known producer of various kinds of toxic and bioactive chemicals. Of these, hepatotoxic cyclic heptapeptides microcystins have been studied most intensively due to increasing concerns for human health risks and environmental damage. More than 70 variants of microcystins are known, and a single microcystin synthetase (mcy) gene cluster consisting of 10 genes (mcyA to mcyJ) has been identified to be responsible for the production of all known variants of microcystins. Our previous multilocus sequence typing (MLST) analysis of the seven housekeeping genes indicated that microcystin-producing strains of M. aeruginosa are classified into two phylogenetic groups.ResultsTo investigate whether the mcy genes are genetically structured similarly as in MLST analysis of the housekeeping genes and to identify the evolutionary forces responsible for the genetic divergence of these genes, we used 118 mcy-positive isolates to perform phylogenetic and population genetic analyses of mcy genes based on three mcy loci within the mcy gene cluster (mcyD, mcyG, and mcyJ), none of which is involved in the production of different microcystin variants. Both individual phylogenetic analysis and multilocus genealogical analysis of the mcy genes divided our isolates into two clades, consistent with the MLST phylogeny based on seven housekeeping loci. No shared characteristics within each clade are known, and microcystin analyses did not identify any compositional trend specific to each clade. Statistical analyses for recombination indicated that recombination among the mcy genes is much more frequent within clades than between, suggesting that recombination has been an important force maintaining the cryptic divergence of mcy genes. On the other hand, a series of statistical tests provided no strong evidence for selection to explain the deep divergence of the mcy genes. Furthermore, analysis of molecular variance (AMOVA) indicated a low level of geographic structuring in the genetic diversity of mcy.ConclusionOur phylogenetic analyses suggest that the mcy genes of M. aeruginosa are subdivided into two cryptic clades, consistent with the phylogeny determined by MLST. Population genetic analyses suggest that these two clades have primarily been maintained as a result of homology-dependent recombination and neutral genetic drift.

Local Expansion of a Panmictic Lineage of Water Bloom-Forming Cyanobacterium Microcystis aeruginosa

In previous studies, we have demonstrated that the population structure of the bloom-forming cyanobacterium Microcystis aeruginosa is clonal. Expanded multilocus sequence typing analysis of M. aeruginosa using 412 isolates identified five intraspecific lineages suggested to be panmictic while maintaining overall clonal structure probably due to a reduced recombination rate between lineages. Interestingly, since 2005 most strains belonging to one of these panmictic clusters (group G) have been found in a particular locality (Lake Kasumigaura Basin) in Japan. In this locality, multiple, similar but distinct genotypes of this lineage predominated in the bloom, a pattern that is unprecedented for M. aeruginosa. The population structure underlying blooms associated with this lineage is comparable to epidemics of pathogens. Our results may reveal an expansion of the possible adaptive lineage in a localized aquatic environment, providing us with a unique opportunity to investigate its ecological and biogeographical consequences.

Energy innovation potential of oleaginous microalgae

Algae have contributed greatly to the creation of the Earth’s environment and the development of human civilization. Currently, microalgae are considered to be among the most promising sources for biofuel. Most microalgae accumulate triacylglycerols; however, fatty acid methyl esters produced from triacylglycerols by transesterification have critical end-use issues. Hydrocarbons produced by Botryococcus and Aurantiochytrium are the most suitable algal oils for replacing existing transportation fuels and are highly compatible with existing petroleum infrastructure. Over the years, many technologies have been investigated for achieving sustainable biofuel production using oleaginous microalgae; however, existing techniques of algal fuel production are suitable mainly for small-scale procedures or for the recovery or removal of high-value products. This situation strongly influences life cycle assessment studies for algal fuel production, and published life cycle assessments show different and discrepant results – reliable data on inputs and outputs from industrial-scale experiments are needed for solving these problems. The estimated cost of algal fuel production is still high compared with that of fossil crude oils. The integration of water treatment and algal biomass production, in a coupled hybrid production system comprising of phototrophic and heterotrophic algae, has tremendous potential for improving the economy of future algal fuels.

Fine-scale spatial and temporal genetic differentiation of water bloom-forming cyanobacterium Microcystis aeruginosa: revealed by multilocus sequence typing.

Accumulating evidence suggests that physical isolation can potentially make a significant contribution to microbial population structure and incipient speciation. However, the effect of geographic factors on population structure has not been explicitly studied for ubiquitous cyanobacteria such as a water bloom-forming Microcystis aeruginosa. To investigate whether a fine-scale geographic structure is developed within M. aeruginosa, 96 isolates from five Japanese lakes separated by < 55 km were analysed using multilocus sequence typing. The results of multilocus sequence typing analyses indicated that M. aeruginosa was not phylogeographically structured, although a high level of genetic differentiation was observed among locations (FST  = 0.372). Most surprisingly, the highest levels of genetic differentiation were observed between populations at the same location at different times of the same year, and between those separated by only 3 km on the same day. The isolation-by-distance pattern was not supported, but not completely ruled out. Taken together, our results suggest that geographic factors, if present, have far less impact on the fine-scale spatial genetic diversity of M. aeruginosa than local genetic drift or, possibly, selection.

Complete Genome Sequence of Microcystis aeruginosa NIES-2549, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan

ABSTRACT Microcystis aeruginosa NIES-2549 is a freshwater bloom-forming cyanobacterium isolated from Lake Kasumigaura, Japan. We report the complete 4.29-Mbp genome sequence of NIES-2549 and its annotation and discuss the genetic diversity of M. aeruginosa strains. This is the third genome sequence of M. aeruginosa isolated from Lake Kasumigaura.

The fast-growing strain of hydrocarbon-rich green alga Botryococcus braunii, BOT-22, is a vitamin B12 autotroph

Botryococcus braunii is one of the most promising microalgal feedstocks for biofuel production because it accumulates a large amount of hydrocarbons within the colony. Several researchers have used vitamin-free media for short-term culture experiments of B. braunii. However, vitamin requirements of B. braunii have never been explicitly described. Therefore, the consequences of long-term vitamin deficiency remain unclear. To investigate the vitamin B12 (cobalamin) requirement of B. braunii, the growth characteristics and oil productivity were compared using an axenic strain B. braunii BOT-22, one of the fast-growing strains, with and without vitamin B12 supplementation. The growth rate, maximum biomass concentration, and lipid content did not differ between cultures with and without vitamin B12 supplements. In addition, an in silico survey of the transcriptomic dataset of B. braunii BOT-22 identified a putative gene fragment coding for the vitamin B12-independent methionine synthetase (metE), which is a hallmark of the vitamin B12 autotrophy in algae. In conclusion, these data suggest that B. braunii BOT-22 is a vitamin B12 autotroph.

Draft Genome Sequence of Microcystis aeruginosa NIES-98, a Non-Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan

ABSTRACT Microcystis aeruginosa is a well-known bloom-forming cyanobacterium. We newly sequenced the whole genome of M. aeruginosa NIES-98, which is a non-microcystin-producing strain isolated from Lake Kasumigaura, Japan. The genome contains approximately 5.0 Mbp, with an average G+C content of 42.41% and 5,140 predicted protein-coding genes.

Adaptation of the Freshwater Bloom-Forming Cyanobacterium Microcystis aeruginosa to Brackish Water Is Driven by Recent Horizontal Transfer of Sucrose Genes

Microcystis aeruginosa is a bloom-forming cyanobacterium found in eutrophic water bodies worldwide. M. aeruginosa blooms usually occur in freshwater; however, they have also been reported to occur in brackish water. Because M. aeruginosa often produces the cyanotoxin microcystin, they are a major concern to public health and environment. Despite this, the ecology, genomic basis, and evolutionary process underlying the M. aeruginosa bloom invasion from fresh to brackish water have been poorly investigated. Hence, in the present study, we have sequenced and characterized genomes of two newly discovered salt-tolerant M. aeruginosa strains obtained from Japanese brackish water lakes (Lakes Shinji and Tofutsu). Both genomes contain a set of genes for the synthesis of osmolyte sucrose (sppA, spsA, and susA), hitherto identified in only one strain (PCC 7806) of M. aeruginosa. Chemical and gene expression analyses confirmed sucrose accumulation induced by salt. A comprehensive genetic survey of >200 strains indicated that sucrose genes are extremely rare in M. aeruginosa. Most surprisingly, comparative genome analyses of the three strains indicated extremely low genetic diversity in the sucrose genes compared with other core genome genes, suggesting very recent acquisitions via horizontal transfer. Invasion of M. aeruginosa blooms into brackish water may be a recent event triggered by anthropogenic eutrophication of brackish water.