Woong Kim

Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars

BackgroundRoses (Rosa sp.), which belong to the family Rosaceae, are the most economically important ornamental plants—making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs are limited in molecular resources which can greatly enhance and speed breeding efforts. A better understanding of important genes that contribute to important floral development and desired phenotypes will lead to improved rose cultivars. For this study, we analyzed rose miRNAs and the rose flower transcriptome in order to generate a database to expound upon current knowledge regarding regulation of important floral characteristics. A rose genetic database will enable comprehensive analysis of gene expression and regulation via miRNA among different Rosa cultivars.ResultsWe produced more than 0.5 million reads from expressed sequences, totalling more than 110 million bp. From these, we generated 35,657, 31,434, 34,725, and 39,722 flower unigenes from Rosa hybrid: ‘Vital’, ‘Maroussia’, and ‘Sympathy’ and Rosa rugosa Thunb. , respectively. The unigenes were assigned functional annotations, domains, metabolic pathways, Gene Ontology (GO) terms, Plant Ontology (PO) terms, and MIPS Functional Catalogue (FunCat) terms. Rose flower transcripts were compared with genes from whole genome sequences of Rosaceae members (apple, strawberry, and peach) and grape. We also produced approximately 40 million small RNA reads from flower tissue for Rosa, representing 267 unique miRNA tags. Among identified miRNAs, 25 of them were novel and 242 of them were conserved miRNAs. Statistical analyses of miRNA profiles revealed both shared and species-specific miRNAs, which presumably effect flower development and phenotypes.ConclusionsIn this study, we constructed a Rose miRNA and transcriptome database, and we analyzed the miRNAs and transcriptome generated from the flower tissues of four Rosa cultivars. The database provides a comprehensive genetic resource which can be used to better understand rose flower development and to identify candidate genes for important phenotypes.

Absolute dominance of hydrogenotrophic methanogens in full-scale anaerobic sewage sludge digesters.

Anaerobic digestion (AD) is gaining increasing attention due to the ability to covert organic pollutants into energy-rich biogas and, accordingly, growing interest is paid to the microbial ecology of AD systems. Despite extensive efforts, AD microbial ecology is still limitedly understood, especially due to the lack of quantitative information on the structures and dynamics of AD microbial communities. Such knowledge gap is particularly pronounced in sewage sludge AD processes although treating sewage sludge is among the major practical applications of AD. Therefore, we examined the microbial communities in three full-scale sewage sludge digesters using qualitative and quantitative molecular techniques in combination: denaturing gradient gel electrophoresis (DGGE) and real-time polymerase chain reaction (PCR). Eight out of eleven bacterial sequences retrieved from the DGGE analysis were not affiliated to any known species while all eleven archaeal sequences were assigned to known methanogen species. Quantitative real-time PCR analysis revealed that, based on the 16S rRNA gene abundance, the hydrogenotrophic order Methanomicrobiales is the most dominant methanogen group (> 94% of the total methanogen population) in all digesters. This corresponds well to the prevailing occurrence of the DGGE bands related to Methanolinea and Methanospirillum, both belonging to the order Methanomicrobiales, in all sludge samples. It is therefore suggested that hydrogenotrophic methanogens, especially Methanomicrobiales strains, are likely the major players responsible for biogas production in the digesters studied. Our observation is contrary to the conventional understanding that aceticlastic methanogens generally dominate methanogen communities in stable AD environments, suggesting the need for further studies on the dominance relationship in various AD systems.

Comparison of methanogenic community structure and anaerobic process performance treating swine wastewater between pilot and optimized lab scale bioreactors

To investigate methanogenic community structure and process performance of anaerobic digestion treating swine wastewater at different scale, a pilot plant with 20 m(3) of effective working volume and lab scale methanogenic digester with 6L working volume were operated for 71 days and 6 turnover periods, respectively. During the steady state of anaerobic digestion, COD and VS removal efficiency in pilot plant were 65.3±3.2, 51.6±4.3%, respectively, which was similar to those in lab scale. However, calculated VFAs removal efficiency and methane yield were lower in pilot plant than in lab scale digester. Also, organics removal efficiencies, which consist of total carbohydrates, proteins, and lipids, were different between pilot and lab scale. These results were thought to be due to the ratio of carbohydrates to proteins in the raw swine wastewater. As a result of qualitative microbial analysis, Methanoculleus receptaculii, and Methanoculleus bourgensis, were commonly concerned with methane production.

Temporal variation in methanogen communities of four different full-scale anaerobic digesters treating food waste-recycling wastewater.

Methanogen communities were investigated using 454 pyrosequencing in four different full-scale anaerobic digesters treating food waste-recycling wastewater. Seasonal samples were collected for 2 years, and 24 samples were available for microbial analysis from a plug flow thermophilic (PT) digester, a continuously-stirred tank thermophilic (CT) digester, an upflow anerobic sludge blanket mesophilic (UM) digester, and a continuously-stirred tank mesophilic (CM) digester. Methanoculleus, Methanobacterium, Methanothermobacter, and Methanosaeta were revealed to be key methanogens in full-scale anaerobic digestion process treating food waste-recycling wastewater. In the PT digester, Methanoculleus was dominant (96.8%). In the CT digester, Methanoculleus was dominant (95.4%) during the first year of operation, but the dominant genus was shifted to Methanothermobacter (98.5%) due to pH increase. In the UM digester, Methanosaeta was dominant (87.2%). In the CM digester, Methanoculleus was constantly dominant (74.8%) except during CM5 when Methanosaeta was dominant (62.6%) due to the low residual acetate concentration (0.1 g/L).

Algal-bacterial process for the simultaneous detoxification of thiocyanate-containing wastewater and maximized lipid production under photoautotrophic/photoheterotrophic conditions

In this work, a cooperative algal-bacterial system that efficiently degrades thiocyanate (SCN(-)), a toxic contaminant, and exhibits high lipid productivity, was developed. A consortium of mixed bacteria (activated sludge) and microalgae was sequentially cultivated under photoautotrophic and photoheterotrophic modes. The hydrolysis of SCN(-) to ammonium (NH4(+))-nitrogen and subsequent nitrification steps were performed by the initial activated sludge under lithoautotrophic conditions. The NH4(+) and oxidized forms of nitrogen, nitrite (NO2(-)) and nitrate (NO3(-)), were then assimilated and removed by the microalgal cells when light was supplied. After the degradation of SCN(-), the cultivation mode was changed to photoheterotrophic conditions in a sequential manner. Algal-bacterial cultures containing Chlorella protothecoides and Ettlia sp. yielded significantly increased lipid productivity under photoheterotrophic conditions compared to photoautotrophic conditions (28.7- and 17.3-fold higher, respectively). Statistical methodologies were also used to investigate the effects of volatile fatty acids and yeast extract on biomass and lipid production.

Microalgae-mediated simultaneous treatment of toxic thiocyanate and production of biodiesel

In this work, a method for simultaneously degrading the toxic pollutant, thiocyanate, and producing microalgal lipids using mixed microbial communities was developed. Aerobic activated sludge was used as the seed culture and thiocyanate was used as the sole nitrogen source. Two cultivation methods were sequentially employed: a lithoautotrophic mode and a photoautotrophic mode. Thiocyanate hydrolysis and a nitrification was found to occur under the first (lithoautotrophic) condition, while the oxidized forms of nitrogen were assimilated by the photoautotrophic consortium and lipids were produced under the second condition. The final culture exhibited good settling efficiency (∼ 70% settling over 10 min), which can benefit downstream processing. The highest CO2 fixation rate and lipid productivity were observed with 2.5% and 5% CO2, respectively. The proposed integrated algal-bacterial system appears to be a feasible and even beneficial option for thiocyanate treatment and production of microbial lipids.

A comprehensive study on algal–bacterial communities shift during thiocyanate degradation in a microalga-mediated process

Changes in algal and bacterial communities during thiocyanate (SCN(-)) decomposition in a microalga-mediated process were studied. Pyrosequencing indicated that Thiobacillus bacteria and Micractinium algae predominated during SCN(-) hydrolysis, even after its complete degradation. Principal components analysis and evenness profiles (based on the Pareto-Lorenz curve) suggested that the changes in the bacterial communities were driven by nitrogen and sulfur oxidation, pH changes, and photoautotrophic conditions. The populations of predominant microalgae remained relatively stable during SCN(-) hydrolysis, but the proportion of bacteria - especially nitrifying bacteria - fluctuated. Thus, the initial microalgal population may be crucial in determining which microorganisms dominate when the preferred nitrogen source becomes limited. The results also demonstrated that microalgae and SCN(-)-hydrolyzing bacteria can coexist, that microalgae can be effectively used with these bacteria to completely treat SCN(-), and that the structure of the algal-bacterial community is more stable than the community of nitrifying bacteria alone during SCN(-) degradation.

Effect of temperature and hydraulic retention time on volatile fatty acid production based on bacterial community structure in anaerobic acidogenesis using swine wastewater

To investigate the effect of hydraulic retention time (HRT) and temperature (T) on bacterial community structure and volatile fatty acids (VFAs) production of an acidogenic process, and VFA production and changes in the bacterial community in three identical automated anaerobic continuously-stirred tank reactors were analyzed using response surface analysis (RSA) and nonmetric multidimensional scaling (NMDS). For RSA, 11 trials were conducted to find the combination of T and HRT under which VFA production was greatest; VFA production was affected more by HRT than by T. To identify the bacterial community structure in each trial, DNA from each experimental point of the RSA was analyzed using denaturating gradient gel electrophoresis (DGGE), and eight bacteria species were detected. NMDS was conducted on band intensities obtained using DGGE, and bacterial community structure was affected more by T than by HRT. Taken together, these results suggest that VFA production during acidogenesis was more dependent on the physicochemical properties of acidogens, such as their specific growth rate or contact time with of substrates, than on changes in the microbial community.

Quantitative analysis of microbial community structure in two-phase anaerobic digesters treating food wastewater

An acidogenic reactor with a 0.5-L working volume and a methanogenic digester with a 5-L of working volume were operated for 150 days on a continuous mode to investigate the structure of a microbial community during food wastewater treatment. During the steady state of anaerobic digestion, volatile solids (VS) removal efficiency in the pilot plant was approximately 65%. The bacterial population was higher than any other methanogens detected during the entire anaerobic process and treatment of raw food wastewater. Methanomicrobiales (MMB), Methanosarcinales (MSL), and Methanobacteriales (MBT) were detected during digestion. The methanogenic population present in the acidogenic reactor was directly affected by the archaeal community in raw food wastewater. However, the shift of microbial community in the methanogenic digester was relatively gradual. The performance of methanogenic digester might be more related to the change of microbial metabolism affected by the physicochemical properties of the input substrate.

Effect of shear stress on the growth of continuous culture of Synechocystis PCC 6803 in a flat-panel photobioreactor

The effect of hydrodynamic forces generated by air bubbles on cell growth of continuous culture of Synechocystis PCC 6803 was studied in a flat-panel photobioreactor. Keeping all relevant parameters constant enables the optimization of individual parameters, for which a continuous cultivation approach has significant advantages. Continuous culture of Synechocystis PCC 6803 was cultivated under different gas velocities from 0.022 m s−1 up to 0.128 m s−1. Based on direct determination of effective growth rate at constant cell densities, cell damage due to shear stress induced by the increasing gas velocity at the sparger was directly observed. A significant decrease of effective growth rate was observed at gas velocity of 0.085 m s−1 generated at the gas flow rate of 200 ml min−1, indicating cell damage by shear stress. Optimization of gas volume and the development of an effective aeration system corresponding to a given reactor setup is important to realize a reliable cell growth.