Protocols

Surface sterilization of plant tissues followed by DNA extraction and high-throughput sequencing of the ITS region to characterize fungal endophyte communities. Community composition and diversity met...

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

Standard litterbag method deployed across elevation gradient to study litter decomposition rates and microbial succession. Involves placing known masses of litter in mesh bags and retrieving over time...

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.

Extraction of iron and manganese from sediments using 0.5 N HCl with hydroxylamine hydrochloride in anaerobic conditions, followed by ICP-AES analysis. This method targets metals associated with reduc...

Fourier Transform Infrared spectroscopy analysis of ground needle samples to quantify functional group concentrations including aromatics, ethers, amides, and carbonyls. Uses attenuated-total-reflecti...

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.

Transmission electron microscopy with energy dispersive X-ray spectroscopy performed under anoxic conditions using vacuum transfer holders to map elemental distributions in redox-sensitive particles.

Extraction of plant metabolites using methanol/acetonitrile/water solvent followed by liquid chromatography-mass spectrometry analysis. Characterizes plant metabolomic profiles for correlation with fu...

Computational pipeline using VirSorter2 and CheckV for viral sequence identification, followed by clustering into viral operational taxonomic units and taxonomic/host prediction.

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