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...

Construction of phylogenetic trees using concatenated ribosomal protein genes to determine evolutionary relationships. Uses IQ-TREE with maximum likelihood approach and bootstrap support.

Fresh plant tissue is collected during peak hydration, weighed fresh, dried at controlled temperature, then reweighed to calculate water content as the difference between wet and dry weights.

Taxonomic classification of microbial communities using ribosomal protein S3 (rpS3) marker genes identified through Hidden Markov Models and phylogenetic analysis.

Sediment samples collected in 15-cm increments using 5 cm diameter soil core sampler with slide hammer, then 8.3 cm diameter bucket auger after reaching coarse alluvium.

Normalization of transcriptomic data using Transcripts Per Million (TPM) method.