Protocols

Systematic collection of sediment samples from floodplain sites at regular depth intervals followed by DNA extraction and metagenomic sequencing to characterize microbial communities.

Standard Illumina library preparation using Nextera XT kit followed by paired-end sequencing on HiSeq 2500 platform to generate comprehensive metagenomic datasets from phylloplane microbial communitie...

Standard metagenomics pipeline involving assembly with MEGAHIT, binning with multiple tools, dereplication, and taxonomic classification using GTDB-tk.

Manual identification and curation of large genome fragments using GC content, coverage patterns, and taxonomic profiles to assemble complete extrachromosomal genomes.

Comprehensive Hidden Markov Model analysis of metagenomic sequences to identify and quantify metabolic functions across biogeochemical pathways. Uses both standardized TIGR-FAM and custom HMM database...