Kinetic study and optimization of total solids for anaerobic digestion of kitchen waste: Bangladesh perspective.

Kitchen waste from hotels and homes is one of the major problems for urban and rural environment and could be one of the best sources of renewable energy by producing biogas through anaerobic digestion. A research work was undertaken to assess the methane potential of kitchen waste at different total solids (TS) content. Kitchen wastes such as spoiled rice, brinjal, potato, papaya, tomato, fish and poultry parts etc., which are easily decomposed, were selected for this study. Batch experiments were set up under ambient temperature. Kitchen waste was added to the batch digester at different TS content (5, 7, 10, 12 and 15%) and sealed for 146 days until the gas production stopped. Substrate characteristics were analyzed before and after the anaerobic digestion. The highest methane yield was 78.12 L/kg VS at 15% TS content followed by 12, 10, 7 and 5%. Different kinetic parameters were determined using a logistic model and the model showed a good fit with the experimental results. After modelling using Minitab®, the optimum TS content for kitchen waste was found to be 14.90%.

Pectinolytic Bacterial Consortia Reduce Jute Retting Period and Improve Fibre Quality.

Jute fibre is the second most important fibre next to cotton. It is obtained from the bark of plant through microbial retting process. Here we report optimized microbial retting protocol that can lower retting period and produce high fibre quality. A total of 451 bacterial colonies have been isolated from five jute retting water samples in Bangladesh. Higher pectinolytic bacterial isolates were predominant in the later stage of jute retting. Out of these, 168 isolates have been screened by both semi-quantitative and quantitative pectinase, xylanase and cellulase enzyme assay. Among them, 144 isolates have been selected on the basis of extra cellular enzyme activity of these three enzymes. 16 s ribosomal gene sequencing analysis identified 2 phyla- Firmicutis (80.55%) and Proteobacteria (19.45%). To check the synergistic and antagonistic effect 10 selected isolates were tested in 167 different combinations. Three best combinations were identified that lowered retting period from 18-21 days to 10 days producing high quality fibre in both laboratory and field trial. This improved retting technology can be adopted in industrial scale for the production of quality jute fibre in a controlled condition in reduced water quantity without polluting the environment.

Microbial load in bio-slurry from different biogas plants in Bangladesh.

OBJECTIVE: The study was aimed to isolate, identify, and characterize common indicator bacteria, including Escherichia coli, Salmonella spp., and Staphylococcus spp. in manure and bio-slurry samples of different livestock farms and biogas plants of Bangladesh. MATERIALS AND METHODS: A total of 114 samples of manure and bio-slurry were collected from different livestock farms and biogas plants in Bangladesh. The total viable count (TVC), E. coli, Salmonella spp., and Staphylococcus spp. counts were determined by the spread plate technique method. Isolation and identification were performed by colony characteristics, staining, biochemical tests, and, finally, by using PCR. Antibiotic susceptibility test of the isolated bacteria was tested against commonly used antibiotics by using the disk diffusion method. RESULTS: The mean TVC, E. coli, Salmonella spp., and Staphylococcus spp. counts were ranged from 8.19-10.75, 5.2-6.96, 5.81-6.87, 5.68-7.68 in manure samples and 7.26-8.65, 3.82-5.2, 4-5.54, 3.14-5.9 log cfu/gm in bio-slurry, respectively. In anaerobic digester after 30 days digestion, the presence of E. coli, Salmonella spp., and Staphylococcus spp. varied from 0-5.11, 0-4.84, and 0-5.59 log cfu/gm at 25°C, 27°C, 29°C, and 45°C temperature. Above-mentioned bacteria were absent in bio-slurry collected from anaerobic digester after 60 days digestion at environmental temperature. Bacterial counts were reduced significantly in both household slurry pits and experimental anaerobic digester. Antibiotic susceptibility results revealed that multidrug-resistant indicator bacteria were present in the bio-slurry samples. CONCLUSION: Our findings conclude that the microbial load after treatment of animal manure via anaerobic digestion (Biogas plant) was grossly reduced and the reduction of bacterial pathogen depends on the duration and temperature of digestion.

Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute.

BACKGROUND: With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method for targeted gene expression analysis due to its sensitivity and reproducibility. However, calculating relative expression requires reference genes, which must be stable across various biological conditions. For this purposes, 11 prospective genes namely, 28S RNA, ACT7, CYP, EF1A, EF2, ETIF3E, GAPDH, PP2Ac, PTB, UBC2 and UBI1 were evaluated for their potential use as reference genes in jute. RESULTS: The expression stabilities of eleven prospective genes were analyzed in various jute plant tissues, such as the root, stick, bark, leaf, flower, seed and fiber, as well as under abiotic (waterlogged, drought and salinity) and biotic stress (infestation with Macrophomina phaseolina) conditions with different time points. All 11 genes were variably expressed in different tissues and stress conditions. To find suitable reference genes in different sample sets, a comprehensive approach based on four statistical algorithms such as GeNorm, BestKeeper, NormFinder the ΔCt was used. The PP2Ac and EF2 genes were the most stably expressed across the different tissues. ACT7 and UBC2 were suitable reference genes under drought stress, and CYP and PP2Ac were the most appropriate after inoculation with Macrophomina phaseolina. Under salinity stress, PP2Ac and UBC2 were the best genes, and ACT7 and PP2Ac were the most suitable under waterlogged conditions. CONCLUSION: Expression stability of reference genes from jute varied in different tissues and selected experimental conditions. Our results provide a valuable resource for the accurate normalization of gene expression experiments in fiber research for important bast fiber crops.

Comparative genomics of two jute species and insight into fibre biogenesis.

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production1. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina.

BACKGROUND: Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. It can grow rapidly in infected plants and subsequently produces a large amount of sclerotia that plugs the vessels, resulting in wilting of the plant. RESULTS: We sequenced and assembled ~49 Mb into 15 super-scaffolds covering 92.83% of the M. phaseolina genome. We predict 14,249 open reading frames (ORFs) of which 9,934 are validated by the transcriptome. This phytopathogen has an abundance of secreted oxidases, peroxidases, and hydrolytic enzymes for degrading cell wall polysaccharides and lignocelluloses to penetrate into the host tissue. To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. A strikingly distinct set of carbohydrate esterases (CE) are present in M. phaseolina, with the CE9 and CE10 families remarkably higher than any other fungi. The phenotypic microarray data indicates that M. phaseolina can adapt to a wide range of osmotic and pH environments. As a broad host range pathogen, M. phaseolina possesses a large number of pathogen-host interaction genes including those for adhesion, signal transduction, cell wall breakdown, purine biosynthesis, and potent mycotoxin patulin. CONCLUSIONS: The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. Further understanding of the M. phaseolina genome-based plant-pathogen interactions will be instrumental in designing rational strategies for disease control, essential to ensuring global agricultural crop production and security.