Choon Weng Lee

Complete degradation of dimethyl phthalate by biochemical cooperation of the Bacillus thuringiensis strain isolated from cotton field soil

Dimethyl phthalate (DMP), a phthalate ester, is widely used in cosmetics, perfumes, and plasticizers. It has been classified as a suspected endocrine disruptor by many countries. The present study describes the biodegradation of DMP by a new aerobic bacterium, isolated from soil samples of a cotton field by an enrichment culture technique utilizing DMP as the sole source of carbon and energy. The isolate was identified as Bacillus thuringiensis based on the morphological and biochemical characteristics as well as gene sequence analysis. Bacillus thuringiensis grows best in a mineral salt medium of pH 7.0 at 30 °C incubation for 48 hours. The effects of temperature, inoculum size, substrate concentration and incubation time on DMP degradation were also studied. Bacillus thuringiensis is able to biodegrade 400 mg L−1 of DMP under aerobic conditions with 99% degradation potential. A combination of GC and GC-MS analysis revealed a complete DMP biodegradation pathway. The results indicate that Bacillus thuringiensis may prove a promising source for DMP bioremediation at a commercial scale.

Dynamics of bacterial respiration and related growth efficiency, dissolved nutrients and dissolved oxygen concentration in a subarctic coastal embayment

Temporal variations in dissolved oxygen, nutrient concentrations and oxygen utilization rates ( 75% of the organic matter flux through bacteria could be mineralized to CO2.

Temporal Variation of Bacterial Respiration and Growth Efficiency in Tropical Coastal Waters

ABSTRACT We investigated the temporal variation of bacterial production, respiration, and growth efficiency in the tropical coastal waters of Peninsular Malaysia. We selected five stations including two estuaries and three coastal water stations. The temperature was relatively stable (averaging around 29.5°C), whereas salinity was more variable in the estuaries. We also measured dissolved organic carbon and nitrogen (DOC and DON, respectively) concentrations. DOC generally ranged from 100 to 900 μM, whereas DON ranged from 0 to 32 μM. Bacterial respiration ranged from 0.5 to 3.2 μM O2 h−1, whereas bacterial production ranged from 0.05 to 0.51 μM C h−1. Bacterial growth efficiency was calculated as bacterial production/(bacterial production + respiration), and ranged from 0.02 to 0.40. Multiple correlation analyses revealed that bacterial production was dependent upon primary production (r2 = 0.169, df = 31, and P < 0.02) whereas bacterial respiration was dependent upon both substrate quality (i.e., DOC/DON ratio) (r2 = 0.137, df = 32, and P = 0.03) and temperature (r2 = 0.113, df = 36, and P = 0.04). Substrate quality was the most important factor (r2 = 0.119, df = 33, and P = 0.04) for the regulation of bacterial growth efficiency. Using bacterial growth efficiency values, the average bacterial carbon demand calculated was from 5.30 to 11.28 μM C h−1. When the bacterial carbon demand was compared with primary productivity, we found that net heterotrophy was established at only two stations. The ratio of bacterial carbon demand to net primary production correlated significantly with bacterial growth efficiency (r2 = 0.341, df = 35, and P < 0.001). From nonlinear regression analysis, we found that net heterotrophy was established when bacterial growth efficiency was <0.08. Our study showed the extent of net heterotrophy in these waters and illustrated the importance of heterotrophic microbial processes in coastal aquatic food webs.

Bacterial abundance and production, and their relation to primary production in tropical coastal waters of Peninsular Malaysia

In the present study, the relationship between bacteria and phytoplankton in tropical coastal waters was investigated. The bacterial abundance, bacterial production, chlorophyll a concentration and net primary production were measured at several locations in the coastal waters of Peninsular Malaysia. Chlorophyll a concentration ranged from 0.40 to 32.81 μg L–1, whereas bacterial abundance ranged from 0.1 to 97.5 × 106 cells mL–1. Net primary production ranged from 8.49 to 55.95 μg C L–1 h–1, whereas bacterial production ranged from 0.17 to 70.66 μg C L–1 h–1. In the present study, the carbon conversion factor used to convert bacterial production (cells mL–1 h–1) into carbon units ranged from 10 to 32.8 fg C cell–1, and was estimated from the bacterial size distribution measured at each location. Both phototrophic and heterotrophic biomass (bacteria–chlorophyll a) and activity (bacterial production–net primary production) were significantly correlated, although their correlation coefficients (r2) were relatively low (r2 = 0.188 and r2 = 0.218 respectively). Linear regression analyses provided the following equations to represent the relationship between: bacteria and chlorophyll a (Chl a), log Bacteria = 0.413 log Chl a + 6.057 (P = 0.003); and between bacterial production (BP) and net primary production (NPP), log BP = 0.896 log NPP – 0.394 (P = 0.004), which fitted with published results well. Comparison of annual carbon fluxes confirmed the prevalence of net heterotrophy in these coastal waters, and together with the low correlation coefficients, suggested the role of allochthonous organic matter in supporting heterotrophic activity.

Differential expression of a subset of ribosomal protein genes in cell lines derived from human nasopharyngeal epithelium.

Extraribosomal functions of human ribosomal proteins (RPs) include the regulation of cellular growth and differentiation, and are inferred from studies that linked congenital disorders and cancer to the deregulated expression of RP genes. We have previously shown the upregulation and downregulation of RP genes in tumors of colorectal and nasopharyngeal carcinomas (NPCs), respectively. Herein, we show that a subset of RP genes for the large ribosomal subunit is differentially expressed among cell lines derived from the human nasopharyngeal epithelium. Three such genes (RPL27, RPL37a and RPL41) were found to be significantly downregulated in all cell lines derived from NPC tissues compared with a nonmalignant nasopharyngeal epithelial cell line. The expression of RPL37a and RPL41 genes in human nasopharyngeal tissues has not been reported previously. Our findings support earlier suspicions on the existence of NPC-associated RP genes, and indicate their importance in human nasopharyngeal organogenesis.

Carbon Flux Through Bacteria in a Eutrophic Tropical Environment: Port Klang Waters

Port Klang waters is eutrophic and long term data showed that its water quality is deteriorating. We observed the occurrence of hypoxia due to very low GPP that was limited by NO3. Although primary production is the basis of aquatic food web, and supported both CR and BCD, episodes of uncoupling were observed. Uncoupling occurred especially when GPP was very low, and generally BCD and GPP were balanced. Our results showed that only 2% of C consumed by bacteria were passed onto protists. This suggested that the microbial loop was not an efficient pathway to recycle organic matter as a substantial amount of carbon was lost.

Investigating the decay rates of Escherichia coli relative to Vibrio parahemolyticus and Salmonella Typhi in tropical coastal waters.

Using the size fractionation method, we measured the decay rates of Escherichia coli, Salmonella Typhi and Vibrio parahaemolyticus in the coastal waters of Peninsular Malaysia. The size fractions were total or unfiltered, <250 μm, <20 μm, <2 μm, <0.7 μm, <0.2 μm and <0.02 μm. We also carried out abiotic (inorganic nutrients) and biotic (bacterial abundance, production and protistan bacterivory) measurements at Port Dickson, Klang and Kuantan. Klang had highest nutrient concentrations whereas both bacterial production and protistan bacterivory rates were highest at Kuantan. We observed signs of protist-bacteria coupling via the following correlations: Protistan bacterivory-Bacterial Production: r = 0.773, df = 11, p < 0.01; Protist-Bacteria: r = 0.586, df = 12, p < 0.05. However none of the bacterial decay rates were correlated with the biotic variables measured. E. coli and Salmonella decay rates were generally higher in the larger fraction (>0.7 μm) than in the smaller fraction (<0.7 μm) suggesting the more important role played by protists. E. coli and Salmonella also decreased in the <0.02 μm fraction and suggested that these non-halophilic bacteria did not survive well in seawater. In contrast, Vibrio grew well in seawater. There was usually an increase in Vibrio after one day incubation. Our results confirmed that decay or loss rates of E. coli did not match that of Vibrio, and also did not correlate with Salmonella decay rates. However E. coli showed persistence where its decay rates were generally lower than Salmonella.

The contribution of heterotrophic nanoflagellate grazing towards bacterial mortality in tropical waters: comparing estuaries and coastal ecosystems

Heterotrophic nanoflagellate (HNF) grazing depends on both temperature and trophic status of an ecosystem. As most microbes already function at their temperature optimum in tropical waters, we hypothesised that HNF grazing rates would be higher in more productive sites such as estuaries than in less productive areas such as coastal waters. We sampled two estuaries and three coastal sites along the Straits of Malacca and the South China Sea near the Malaysia Peninsula. Bacterial abundance ranged 0.9–6.3 × 106 cells mL–1, whereas HNF abundance ranged 1.8–10.1 ×103 cells mL–1. Bacterial production ranged 1.1–12.7 × 105 cells mL–1 h–1, whereas HNF grazing rates were an order of magnitude lower at 1.0–78.5 × 104 cells mL–1 h–1. Bacterial abundance, net bacterial production and HNF grazing rates were higher in estuaries than coastal waters but HNF abundance did not differ between the two areas. Across all stations, HNF grazing rates increased with bacterial production, and accounted for ~33% of bacterial production. Our results suggest that in the tropical waters studied, there was a bacterial production–grazing imbalance. Other loss factors such as viral lysis, sedimentation or the presence of benthic filter feeders could account for this imbalance.

Recombination between linear double-stranded DNA substrates in vivo

Recombineering technology in Escherichia coli enables targeting of linear donor DNA to circular recipient DNA using short shared homology sequences. In this work, we demonstrate that recombineering is also able to support recombination between a pair of linear DNA substrates (linear/linear recombineering) in vivo in E. coli. Linear DNA up to 100 kb is accurately modified and remains intact without undergoing rearrangements after recombination. This system will be valuable for direct in vivo manipulation of large linear DNA including the N15 and PY54 prophages and linear animal viruses, and for assembly of linear constructs as artificial chromosome vectors.

Investigating the spatial distribution of phototrophic picoplankton in a tropical estuary

We sampled extensively (29 stations) at the Klang estuarine system over a 3-day scientific expedition. We measured physical and chemical variables (temperature, salinity, dissolved oxygen, total suspended solids, dissolved inorganic nutrients) and related them to the spatial distribution of phototrophic picoplankton (Ppico). Multivariate analysis of variance of the physicochemical variables showed the heterogeneity of the Klang estuarine system where the stations at each transect were significantly different (Rao’s F18, 36 = 8.401, p < 0.001). Correlation analyses also showed that variables related to Ppico abundance and growth were mutually exclusive. Distribution of Ppico was best explained by the physical mixing between freshwater and seawater whereas Ppico growth was correlated with temperature.