236 Chapter 8 Table 1. Microbial ecology analysis toolkit employed in current PhD thesis. + refers to “least” and ++++ “most”. Reverse Transcriptase (RT)- quantitative Polymerase Chain Reaction (qPCR), Fluorescent In Situ Hybridization (FISH), Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatograpy-Mass Spectrometry coupled to Quadruple Time of Flight detector (LC-MS-qTOF). *Asterisk indicate methods were outsourced. Chapter(s) Physiological potential Biases Technical Difficulty Cost Environmental Relevance/ Biotechnological Potential META-OMICS *16S rRNA gene amplicon 2-3,6-7 + ++++ + + *Metagenomics 2 to 7 ++ ++ ++ ++ *Metatranscriptomics 4 to 6 +++ +++ +++ +++ Metaproteomics 6 +++ +++ ++++ ++++ Metabolomics (LC-MS-qTOF) 6 ++++ +++ ++++ +++ ACTIVITY – FUNCTION (RT)-qPCR 4, 6 ++ ++ + + qPCR 6 + + + + Activity Assays (GC-MS) 2, 5 to 7 ++ ++ ++ ++ FISH and staining – Confocal Microscopy 6 ++ ++ +++ ++ DETERMINATION / QUANTIFICATOIN Storage compounds (PHAs) 5 to 6 ++ ++ + + +++ Sialic acids 6 ++ ++ +++ ++ +++ CULTURING Complex cultures – Bioreactor 3 ++ + +++ ++++ ++++ Highly enriched cultures - Bioreactor 4 to 6 ++++ +++ +++ ++++ +++ Complex cultures – Batch 2 and 7 + +++ ++ ++ ++ Highly enriched cultures - Batch 2 and 7 +++ ++++ + ++ ++
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