Microbal size spectra from diverse marine ecosystems

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1996.Includes bibliographical references.by Karina Y.H. Gin.Sc.D

Draft Genome Sequences of Two Benthic Cyanobacteria, Oscillatoriales USR 001 and Nostoc sp. MBR 210, Isolated from Tropical Freshwater Lakes

Genomes of two filamentous benthic cyanobacteria were obtained from cocultures obtained from two freshwater lakes. The cultures were obtained by first growing cyanobacterial trichome on solid medium, followed by subculturing in freshwater media. Subsequent shotgun sequencing, de novo assembly, and genomic binning yielded almost complete genomes of Oscillatoriales USR 001 and Nostoc sp. MBR 210.Singapore. National Research FoundationSingapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modelin

Co-gasification of woody biomass and chicken manure: Syngas production, biochar reutilization, and cost-benefit analysis

The management and disposal of livestock manure has become one of the top environmental issues at a global scale in line with the tremendous growth of poultry industry over the past decades. In this work, a potential alternative method for the disposal of chicken manure from Singapore local hen layer farms was studied. Gasification was proposed as the green technology to convert chicken manure into clean energy. Through gasification experiments in a 10 kW fixed bed downdraft gasifier, it was found that chicken manure was indeed a compatible feedstock for gasification in the presence of wood waste. The co-gasification of 30 wt% chicken manure and 70 wt% wood waste produced syngas of comparable quality to that of gasification of pure wood waste, with a syngas lower heating value (LHV) of 5.23 MJ/Nm3 and 4.68 MJ/Nm3, respectively. Furthermore, the capability of the gasification derived biochar in the removal of an emerging contaminant (artificial sweetener such as Acesulfame, Saccharin and Cyclamate) via adsorption was also conducted in the second part of this study. The results showed that the biochar was effective in the removal of the contaminant and the mechanism of adsorption of artificial sweetener by biochar was postulated to be likely via electrostatic interaction as well as specific interaction. Finally, we conducted a cost-benefit analysis for the deployment of a gasification system in a hen layer farm using a Monte Carlo simulation model

Draft Genome Sequence of a Tropical Freshwater Cyanobacterium, Limnothrix sp. Strain P13C2

A nonaxenic unialgal culture of Limnothrix sp. strain P13C2 was obtained through multiple subculturing of an inoculum obtained from a tropical freshwater lake. Here, we report the genome of P13C2 of 4.6 Mbp, extracted from the metagenome of this coculture.Singapore-MIT Alliance for Research and Technology (SMART)Singapore. National Research Foundation (NRF, 1102-IRIS-14-02

Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production

A non-axenic unialgal culture containing a Subsection V (Stigonematales) cyanobacterium, Hapalosiphon strain MRB 220, was obtained from a benthic freshwater algal mat through multiple transfers following growth in sterile media. Physiological characterization demonstrated the culture was capable of nitrogen-fixation and production of the off flavor compound 2-methylisoborneol (2-MIB). Total DNA isolated from this culture was sequenced using Illumina HiSeq and de novo assembled into contigs. The genome of MRB 220 was separated from co-occurring heterotrophic bacteria using sequence homology and compositional approaches, and its purity was confirmed based on best BLAST hit classification and principle component analysis of the tetranucleotide frequencies of fragmented contigs. The genome of ~7.4 Mbp contains 6,345 protein coding genes with 4,320 of these having functional prediction including predicted pathways for biosynthesis of the secondary metabolite welwitindolinone. Analyses of 16S rRNA gene and whole genome sequence average nucleotide identity indicated close relatedness of MRB 220 to the genera Hapalosiphon and Fischerella within the order Stigonematales. Microscopic examination showed that MRB 220 formed heterocystous branched filaments, thereby supporting identification of strain MRB 220 as a morphospecies of Hapalosiphon. Availability of the draft genome of Hapalosiphon strain MRB 220 enables future work to elucidate the pathway and dynamics for biosynthesis of 2-MIB and other secondary metabolites and understand the ecology and physiology of Stigonematales cyanobacteria in tropical freshwaters.Singapore. National Research Foundation (under its Environmental & Water Technologies Strategic Research Programme and administered by the Environment & Water Industry Programme Office (EWI) of the PUB (Grant number: 1102-IRIS-14-02))Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology’s (SMART) Center for Environmental Sensing and Modeling (CENSAM) research program

Rapid detection and enumeration of bacteria and viruses in water supplies

Analysis of microbial contamination of water sources demand speed of analysis, specificity and sensitivity as fundamental prerequisites for the detection of microbial indicators and waterborne pathogens. To date, the standard detection method for microbes is the cell culture assay. However, there are significant limitations associated with this method, i.e., they are time-consuming, have low sensitivity and are labor-intensive. In addition, many microbes are still non-culturable and cannot be detected by conventional culture-based methods. These difficulties point towards an urgent need to develop faster and more accurate methodologies for detecting target pathogens or their indicators, which do not depend on culturability. This report summarizes the usefulness of a number of molecular and immunological protocols which exploit state-of-the-art molecular techniques such as Real-Time Quantitative PCR, In Situ PCR, and Fluorescent in Situ Hybridization in combination with flow cytometry for the detection of indicator microbes and pathogens

Monitoring Antimicrobial Resistance Dissemination in Aquatic Systems

This special issue on Antimicrobial Resistance in Environmental Waters features 11 articles on monitoring and surveillance of antimicrobial resistance (AMR) in natural aquatic systems (reservoirs, rivers), and effluent discharge from water treatment plants to assess the effectiveness of AMR removal and resulting loads in treated waters. The occurrence and distribution of antimicrobials, antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was determined by utilizing a variety of techniques including liquid chromatography—mass spectrometry in tandem (LC-MS/MS), traditional culturing, antibiotic susceptibility testing (AST), molecular and OMIC approaches. Some of the key elements of AMR studies presented in this special issue highlight the underlying drivers of AMR contamination in the environment and evaluation of the hazard imposed on aquatic organisms in receiving environments through ecological risk assessments. As described in this issue, screening antimicrobial peptide (AMP) libraries for biofilm disruption and antimicrobial candidates are promising avenues for the development of new treatment options to eradicate resistance. This editorial puts into perspective the current AMR problem in the environment and potential new methods which could be applied to surveillance and monitoring efforts

Population dynamics of cyanomyovirus in a tropical Eutrophic reservoir

Samples from three stations in Kranji Reservoir, Singapore (n = 21) were collected and analyzed for cyanomyovirus abundance and diversity. A total of 73 different g20 (viral capsid assembly protein genes) amino acid sequences were obtained from this study. A phylogenetic analysis revealed that the 73 segments were distributed in six major clusters (α to ζ), with four unique subclusters, which were identified as KRM-I, KRM-II, KRM-III, and KRM-IV. The cyanophage community in Kranji Reservoir exhibited a large degree of diversity; the clones obtained in this study showed similarities to those from many different environments, including oceans, lakes, bays, and paddy floodwater, as well as clones from paddy field soils. However, the sequences in this study were generally found to be more closely related to the g20 sequences of freshwaters and brackish waters than those from marine environments. The rarefaction curves and Chao 1 indices from this study showed that the diversity of the cyanomyovirus community was greater during the Inter-monsoon periods than the Southwest and Northeast Monsoons. A few seasonal changes in the taxa were observed: (i) Cluster ζ was absent during the Southwest Monsoon, and (ii) most of the samples fell into Group 3 in the PCA score plot during the Northeast Monsoon, and the fraction of Cluster ɛ increased significantly.Published versio