Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Program Information
• Funding

This dataset includes links to diversity-generating retroelement sequences files in .fasta format.  There are separate .fasta files for reverse transcriptase protein sequences and variable protein sequences.  These sequences were derived from previously generated sequence accessions at the National Center for Biotechnology Information (NCBI).  Original sampling took place near Rifle, Colorado​ between 2011 and 2012.

To access the .fasta files and the list of source sequences, click the "Get Data" button at the top of this page.

A bioinformatic analysis of metagenome-assembled genomes to identify retroelements was performed. This study used data from several previously described sampling efforts (Brown et al. 2015, Castelle et al. 2015, and Anantharaman et al. 2016). Original sampling was conducted within an unconfined aquifer at the Rifle Integrated Field Research Challenge (IFRC) site, which is adjacent to the Colorado River, near Rifle, Colorado, USA (39.5291, -107.7721).  Samples were collected between August 25th to December 12th of 2011, and August 2nd to December 12th of 2012. Sequencing of these samples took place at the Joint Genome Institute using the Illumina HiSeq 2000 platform to generate 2 × 150 paired-end reads.

For more information about sampling methodology see Paul et al. 2017. 

These sequences were processed using Python v2.7.12, and Geneious v8.1.4.

Marine methanotrophic ecosystems are responsible for consuming around 75 Tg of methane annually, preventing this potent greenhouse gas from entering the atmosphere. These microbial ecosystems thus play a vital role in the global climate system. The nature of these communities depends on the presence or absence of oxygen: methanotrophy is a bacterial lifestyle in aerobic shallow sediments, but in deeper anaerobic sediments it is the exclusive province of archaea, in syntrophy with sulfate-reducing bacteria. It is known which phyla are most commonly found in methanotrophic environments. However, because of these environments' physical inaccessibility and because nearly all microbes from these systems have resisted cultivation, understanding of these communities lags far behind their importance. The cultivation-resistance of microbial hosts from these systems has additionally prevented the use of classical methods to study the viral community. Thus, to date science is largely unable to fill in the broad outlines of marine methanotrophic biodiversity, to fully describe the microbial communities or determine what shapes them.

This project seeks to define the importance of viruses in structuring functional, genetic, and taxonomic diversity in methanotrophic marine ecosystems. The underlying assertion is that viruses structure the diversity of archaeal and bacterial communities in these ecosystems by causing both mortality and horizontal gene transfer. To establish viral contributions to biodiversity of aerobic and anaerobic marine methanotrophic ecosystems, this project combines biogeochemical, genomic, and metagenomic approaches, in both field and laboratory settings.

The project first seeks to assess viral activity in situ by extending established stable isotope probing techniques to quantify rates of viral production at sea floor methane seeps. The same techniques will be used to track the flow of carbon from methane to microbes to viruses and to isolate genetic material from just those organisms that actively cycle methane-derived carbon, enabling the production of microbial and viral metagenomes that are anchored in ecosystem function. Comparisons among these metagenomes will reveal any functional sequences in transit between organisms, providing the basis for an evaluation of the relationships between functional and genetic diversity. At the same time, single-cell whole-genome amplification will pinpoint individual cells for comparison with the microbial and viral assemblages, permitting assessment of the relationships between taxonomic and genetic diversity. Last, the comparison of genomic and metagenomic data both within and across distinctive marine methanotrophic ecosystems will enable analysis of the relationship between functional and taxonomic diversity.

(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program.  [MORE from NSF]

The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.