Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.3K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.3K
The Soil Ecosystem02:23

The Soil Ecosystem

21.6K
Plants obtain inorganic minerals and water from the soil, which acts as a natural medium for land plants. The composition and quality of soil depend not only on the chemical constituents but also on the presence of living organisms. In general, soils contain three major components:
21.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Evolutionary history drives organ-specific variability in plant non-structural carbohydrates.

Nature ecology & evolution·2026
Same author

Continental Contrasts in Climate Extremes That Control Tree Fecundity.

Global change biology·2026
Same author

Harvest legacies and climate change interact to shape forest structure and biomass through time.

Journal of environmental management·2025
Same author

Inorganic nitrogen and organic matter jointly regulate ectomycorrhizal fungi-mediated iron acquisition.

The New phytologist·2025
Same author

Drivers of forest productivity in two regions of the United States: Relative impacts of management and environmental variables.

Journal of environmental management·2025
Same author

Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States.

Global change biology·2024

Related Experiment Video

Updated: Sep 8, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
07:33

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

30.8K

The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.

Zoey R Werbin1, Briana Hackos2, Jorge Lopez-Nava3

  • 1Department of Biology, Boston University, Boston, MA, 02215, USA.

F1000Research
|June 17, 2022
PubMed
Summary

This study introduces a bioinformatics pipeline to analyze the National Ecological Observatory Network's (NEON) soil metagenomic data. This accessible workflow helps researchers explore soil microbial communities and their ecological functions.

Keywords:
metagenomicsmicrobial ecologysoil microbiometutorialworkflow

More Related Videos

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
09:55

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

27.2K
The MPLEx Protocol for Multi-omic Analyses of Soil Samples
10:12

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Published on: May 30, 2018

11.1K

Related Experiment Videos

Last Updated: Sep 8, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
07:33

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

30.8K
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
09:55

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

27.2K
The MPLEx Protocol for Multi-omic Analyses of Soil Samples
10:12

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Published on: May 30, 2018

11.1K

Area of Science:

  • Environmental Science
  • Microbiology
  • Bioinformatics

Background:

  • The National Ecological Observatory Network (NEON) has released a large dataset of soil metagenomes from 47 US sites.
  • NEON data is open-access and includes programming tutorials, but lacks specific guidance for soil shotgun metagenomic data analysis.
  • Understanding soil microbial communities is crucial for ecological research.

Purpose of the Study:

  • To provide an introductory tutorial for accessing and analyzing NEON's soil shotgun metagenomic dataset.
  • To present a bioinformatics pipeline tailored for the complexity of soil microbiomes.
  • To enhance the accessibility of NEON soil metagenomic data for ecological studies.

Main Methods:

  • Development of a bioinformatics pipeline for processing raw soil metagenome sequencing reads.
  • Implementation of steps including read cleaning, taxonomic classification, and genome assembly.
  • Gene annotation using custom protein databases and data export for downstream analysis.

Main Results:

  • A comprehensive workflow for analyzing soil shotgun metagenomic data is described.
  • The pipeline addresses the high complexity and diversity inherent in soil microbial communities.
  • Methods for taxonomic classification, genome assembly, and gene annotation are detailed.

Conclusions:

  • The presented workflow increases the accessibility of NEON's soil metagenomic data.
  • This resource empowers researchers to investigate soil microbial communities and their ecological roles.
  • The tutorial facilitates the use of large-scale soil metagenomic datasets in ecological research.