Jui-Yu Chou

Multiple Molecular Mechanisms Cause Reproductive Isolation between Three Yeast Species

Incompatibility between nuclear and mitochondrial genomes in yeast species may represent a general mechanism of reproductive isolation during yeast evolution.

Speciation through cytonuclear incompatibility: Insights from yeast and implications for higher eukaryotes

Several features of the yeast mitochondrial genome, including high mutation rate, dynamic genomic structure, small effective population size, and dispensability for cellular viability, make it a promising candidate for generating hybrid incompatibility and driving speciation. Cytonuclear incompatibility, a specific type of Dobzhansky‐Muller genetic incompatibility caused by improper interactions between mitochondrial and nuclear genomes, has previously been observed in a variety of organisms, yet its role in speciation remains obscure. Recent studies in Saccharomyces yeast species provide a new insight, with experimental evidence that cytonuclear incompatibility and DNA sequence divergence are both causes of the reproductive isolation of different yeast species. Interestingly, these two mechanisms seem to be perfectly complementary to each other in terms of their effects and evolutionary trajectories. Direct molecular analyses of the incompatible genes in yeasts have started to shed light on the evolutionary forces driving speciation.

Indole-3-acetic acid: A widespread physiological code in interactions of fungi with other organisms

Plants as well as microorganisms, including bacteria and fungi, produce indole-3-acetic acid (IAA). IAA is the most common plant hormone of the auxin class and it regulates various aspects of plant growth and development. Thus, research is underway globally to exploit the potential for developing IAA-producing fungi for promoting plant growth and protection for sustainable agriculture. Phylogenetic evidence suggests that IAA biosynthesis evolved independently in bacteria, microalgae, fungi, and plants. Present studies show that IAA regulates the physiological response and gene expression in these microorganisms. The convergent evolution of IAA production leads to the hypothesis that natural selection might have favored IAA as a widespread physiological code in these microorganisms and their interactions. We summarize recent studies of IAA biosynthetic pathways and discuss the role of IAA in fungal ecology.

Indole-3-acetic acid-producing yeasts in the phyllosphere of the carnivorous plant Drosera indica L

Yeasts are widely distributed in nature and exist in association with other microorganisms as normal inhabitants of soil, vegetation, and aqueous environments. In this study, 12 yeast strains were enriched and isolated from leaf samples of the carnivorous plant Drosera indica L., which is currently threatened because of restricted habitats and use in herbal industries. According to similarities in large subunit and small subunit ribosomal RNA gene sequences, we identified 2 yeast species in 2 genera of the phylum Ascomycota, and 5 yeast species in 5 genera of the phylum Basidiomycota. All of the isolated yeasts produced indole-3-acetic acid (IAA) when cultivated in YPD broth supplemented with 0.1% L-tryptophan. Growth conditions, such as the pH and temperature of the medium, influenced yeast IAA production. Our results also suggested the existence of a tryptophan-independent IAA biosynthetic pathway. We evaluated the effects of various concentrations of exogenous IAA on yeast growth and observed that IAA produced by wild yeasts modifies auxin-inducible gene expression in Arabidopsis. Our data suggest that yeasts can promote plant growth and support ongoing prospecting of yeast strains for inclusion into biofertilizer for sustainable agriculture.

Investigation of the molecular and morphological variability in Batrachospermum arcuatum (Batrachospermales, Rhodophyta) from geographically distant locations

Vis M.L., Feng J., Chiasson W.B., Xie S.-L., Stancheva R., Entwisle T.J., Chou J.-Y. and Wang W.-L. Investigation of the molecular and morphological variability in Batrachospermum arcuatum (Batrachospermales, Rhodophyta) from geographically distant locations. Phycologia 49: 545–553. DOI: 10.2216/10-04.1 Phylogeographic patterns in Batrachospermum arcuatum were investigated using the mitochondrial intergenic spacer between the cytochrome oxidase subunit 2 and 3 (cox2-3 spacer) from locations worldwide. Sixteen locations were sampled in six regions as follows: three locations in Bulgaria, two in China, three in the northwestern United States, one in New Zealand, six in Hawaii and one in Taiwan. Sequencing of 107 individuals resulted in 12 haplotypes. In the United States and Bulgaria, there was considerable sequence divergence among haplotypes. Likewise in the Hawaiian Islands, there was variation among haplotypes, and each island appeared to have a single haplotype represented. Three closely related haplotypes were present at the Taiwan location. The New Zealand sample was identical to one of the haplotypes from the northwestern United States. Individuals representing the 12 cox2-3 spacer haplotypes were sequenced for the rbcL gene. In the combined analysis, the Hawaii and Taiwan samples were a well-supported clade as were two Bulgaria samples. The US and New Zealand haplotypes formed a well-supported clade and likewise the China samples, but the relationship of the third Bulgaria haplotype to these others was unresolved. The specimens showed morphological variation among localities and regions, but no morphological features appeared to be diagnostic of the molecular results. Batrachospermum arcuatum appears to be a widespread taxon with considerable morphological plasticity that does not coincide with the substantial molecular variation. Alternatively, B. arcuatum may harbour cryptic species. There appears to be a temperate origin of the taxon and a derived group of haplotypes from tropical regions.

Plant growth-promoting traits of yeasts isolated from the phyllosphere and rhizosphere of Drosera spatulata Lab.

Microorganisms can promote plant growth through direct and indirect mechanisms. Compared with the use of bacteria and mycorrhizal fungi, the use of yeasts as plant growth-promoting (PGP) agents has not been extensively investigated. In this study, yeast isolates from the phyllosphere and rhizosphere of the medicinally important plant Drosera spatulata Lab. were assessed for their PGP traits. All isolates were tested for indole-3-acetic acid-, ammonia-, and polyamine-producing abilities, calcium phosphate and zinc oxide solubilizing ability, and catalase activity. Furthermore, the activities of siderophore, 1-aminocyclopropane-1-carboxylate deaminase, and fungal cell wall-degrading enzymes were assessed. The antagonistic action of yeasts against pathogenic Glomerella cingulata was evaluated. The cocultivation of Nicotiana benthamiana with yeast isolates enhanced plant growth, indicating a potential yeast-plant interaction. Our study results highlight the potential use of yeasts as plant biofertilizers under controlled and field conditions.

The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease.

Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases.

Variation in Indole-3-Acetic Acid Production by Wild Saccharomyces cerevisiae and S. paradoxus Strains from Diverse Ecological Sources and Its Effect on Growth

Phytohormone indole-3-acetic acid (IAA) is the most common naturally occurring and most thoroughly studied plant growth regulator. Microbial synthesis of IAA has long been known. Microbial IAA biosynthesis has been proposed as possibly occurring through multiple pathways, as has been proven in plants. However, the biosynthetic pathways of IAA and the ecological roles of IAA in yeast have not been widely studied. In this study, we investigated the variation in IAA production and its effect on the growth of Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus yeasts from diverse ecological sources. We found that almost all Saccharomyces yeasts produced IAA when cultured in medium supplemented with the primary precursor of IAA, L-tryptophan (L-Trp). However, when cultured in medium without L-Trp, IAA production was only detected in three strains. Furthermore, exogenous added IAA exerted stimulatory and inhibitory effects on yeast growth. Interestingly, a negative correlation was observed between the amount of IAA production in the yeast cultures and the IAA inhibition ratio of their growth.

Simple Patchy-Based Simulators Used to Explore Pondscape Systematic Dynamics

Thousands of farm ponds disappeared on the tableland in Taoyuan County, Taiwan since 1920s. The number of farm ponds that have disappeared is 1,895 (37%), 2,667 ponds remain (52%), and only 537 (11%) new ponds were created within a 757 km2 area in Taoyuan, Taiwan between 1926 and 1960. In this study, a geographic information system (GIS) and logistic stepwise regression model were used to detect pond-loss rates and to understand the driving forces behind pondscape changes. The logistic stepwise regression model was used to develop a series of relationships between pondscapes affected by intrinsic driving forces (patch size, perimeter, and patch shape) and external driving forces (distance from the edge of the ponds to the edges of roads, rivers, and canals). The authors concluded that the loss of ponds was caused by pond intrinsic factors, such as pond perimeter; a large perimeter increases the chances of pond loss, but also increases the possibility of creating new ponds. However, a large perimeter is closely associated with circular shapes (lower value of the mean pond-patch fractal dimension [MPFD]), which characterize the majority of newly created ponds. The method used in this study might be helpful to those seeking to protect this unique landscape by enabling the monitoring of patch-loss problems by using simple patchy-based simulators.

Indole-3-acetic-acid-induced phenotypic plasticity in Desmodesmus algae

Phenotypic plasticity is the ability of a single genotype of an organism to exhibit variable phenotypes in response to fluctuating environments. It plays a crucial role in their evolutionary success. In natural environments, the importance of interactions between microalgae and other microorganisms is generally well appreciated, but the effects of these interactions on algal phenotypic plasticity has not been investigated. In this study, it revealed that indole-3-acetic acid (IAA), the most common naturally occurring plant hormone, can exert stimulatory at low concentrations and inhibitory effects at high concentrations on the growth of the green alga Desmodesmus. The morphological characteristics of Desmodesmus changed drastically under exposure to IAA compared with the algae in the control environment. The proportion of Desmodesmus unicells in monocultures increased with the IAA concentration, and these unicells exhibited less possibility of sedimentation than large cells. Furthermore, we discovered that lipid droplets accumulated in algal cells grown at a high IAA concentration. Results also demonstrated that the presence of algal competitor further stimulated inducible morphological changes in Desmodesmus populations. The relative abundance of competitors influenced the proportion of induced morphological changes. The results indicate that phenotypic plasticity in microalgae can be a response to fluctuating environments, in which algae optimize the cost–benefit ratio.