Lignocelllulolytic microbial communities
Metagenomic analysis of lignocellulolytic microbial communities
The metagenomic samples were prepared from:  (i) Native microflora in an industrial sugarcane bagasse collection site at Phu Kheio Bio-Energy factory, Chaiyapoom, Thailand. Six samples (BG_env1-BG_env6) were collected from different regions in the bagasse pile with different microenvironmental conditions.  (2) Native microflora in cow rumen fluid. Three samples (CR_env1-CR_env3) were collected from three groups of cows fed with different diet.  (3) Native microflora in activated sludge from a pulp mill in Ratchaburi, Thailand (AS_env1)  (4) Structurally stable lignocellulose degrading microbial consottia constructed from the above samples using successive subcultivation method in PCS medium containing alkali-pretreated rice straw as a carbon source. Three stable consortia were obtained (BG_stable MC/ CR_stable MC/ AS_stable MC) from pool samples of BG_env, CR_env, and AS_env1.
 Lignocellulosic biomass is the most abundant organic carbon reservoir on earth, providing a renewable carbon source for the chemosphere and the prospective biorefinery industry. Decomposition of lignocelluloses in nature involves complex cooperative actions of various microbes producing different lignocelluloytic enzymes attacking the cellulosic and non-cellulosic components of plant biomass. To understand microbial communities and metabolic genes in lignocellulosic degradation, culture-independent direct 454 pyrosequencing metagenomes has been applied to study the diversity and metabolic capabilities in various lignocellulosic environments.  The project consists of four experiments: 1. Tagged 16S rRNA gene pyrosequencing: the microbial community in lignocellulosic ecological niche has been unveiled by the high-throughput tagged 16S rRNA gene pyrosequencing. The samples were collected from industrial bagasse collection site at a sugar mill; (ii) cow rumen fluid; and (iii) activated sludge from a pulp mill, and the structurally stable lignocellulolytic microbial consortia constructed from microflora in these sites using successive subcultivation method. 2. Shotgun pyrosequencing of bagasse metagenome: lignocellulolytic enzyme systems and metabolic gene potential of microorganisms in interior region of bagasse collection site were explored using shotgun metagenome pyrosequencing. 3. Shotgun pyrosequencing of microcoms in consortium: lignocellulolytic enzyme systems and metabolic gene potential of microorganisms in stable consortium were explored using shotgun metagenome pyrosequencing. 4. Fosmid bagasse library: the fosmid library was constructed from metagenome of uncultured microflora in bagasse pile by 454 pyrosequencing, which allows us to recover the genes of interest for further cloning and expression study.  This study gives insights into biodiversity and metabolic potential of lignocellulose degrading microbial communities in environments, providing a basis for understanding microbial process in nature and for biotechnological application. 