C-DEBI Newsletter – October 1, 2019

Publications & Press

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mSystems
Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes – NEW!
Taylor M. Royalty*, Andrew D. Steen*
*C-DEBI Contributon 491

We applied theoretical and simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short-read sequences. First, a coupon collector equation was proposed as an analytical model for predicting sequencing effort as a function of microbial community structure. Characterization was performed by varying community structure properties such as richness, evenness, and genome size. Simulations demonstrated that while community richness and evenness influenced the sequencing effort required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion depended only on the relative abundance of the genome and its genome size. A second analysis evaluated the quantity, completion, and contamination of metagenome-assembled genomes (MAGs) as a function of sequencing effort on four preexisting sequence read data sets from different environments. These data sets were subsampled to various degrees of completeness to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A software tool, Genome Relative Abundance to Sequencing Effort (GRASE), was created to assist investigators to further explore this relationship. Reevaluation of the relationship between sequencing effort and binning success in the context of genome relative abundance, as opposed to base pairs, provides a constraint on sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort.

Microbiology Resource Announcements
Genome Sequence of Mariprofundus sp. Strain EBB-1, a Novel Marine Autotroph Isolated from an Iron-Sulfur Mineral – NEW!
Areli Lopez, Daniel Albino, Senay Beraki, Sondra Broomell, Ricardo Canela, Theadora Dingmon, Sabrina Estrada, Marwin Fernandez, Pratixaben Savalia, Kenneth H. Nealson, David Emerson, Roman A. Barco, Benjamin J. Tully, Jan P. Amend
C-DEBI Contribution 494*

Mariprofundus sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class Zetaproteobacteria with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences.

*This publication resulted from the work of C-DEBI's Community College Cultivation Cohort (C4) Research Experience for Undergraduates (REU).

Scientific Reports
Characteristics and Evolution of sill-driven off-axis hydrothermalism in Guaymas Basin – the Ringvent site – NEW!
Andreas P. Teske*, Luke J. McKay, Ana Christina Ravelo*, Ivano Aiello*, Carlos Mortera, Fernando Núñez-Useche, Carles Canet, Jeffrey P. Chanton, Benjamin Brunner, Christian Hensen, Gustavo A. Ramírez, Ryan J. Sibert, Tiffany Turner, Dylan White, Christopher R. Chambers, Andrew Buckley, Samantha B. Joye, S. Adam Soule, Daniel Lizarralde
*C-DEBI Contribution 495

The Guaymas Basin spreading center, at 2000 m depth in the Gulf of California, is overlain by a thick sedimentary cover. Across the basin, localized temperature anomalies, with active methane venting and seep fauna exist in response to magma emplacement into sediments. These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools. Although several cool sites resembling cold seeps have been characterized, the hydrothermally active stage of an off-axis site was lacking good examples. Here, we present a multidisciplinary characterization of Ringvent, an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center. Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation, but remains evident in thermal anomalies, hydrothermal biota coexisting with seep fauna, and porewater biogeochemical signatures indicative of hydrothermal circulation. Due to their broad potential distribution, small size and limited life span, such sites are hard to find and characterize, but they provide critical missing links to understand the complex evolution of hydrothermal systems.

 

Meetings & Activities

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Networked Speaker Series Seminar, THIS THURSDAY, October 3, 2019, 12:30pm PDT
With Dr. Jessica Labonté, Texas A&M Galveston on “You are what you eat: a geochemical and microbial study of a 3000-year old stratigraphic sediment succession.” Abstract: Microbes make up the majority of the biomass in sediment, where they play a role in cycling organic carbon and regulate the fluctuation of organic matter. In anoxic sediment, the relationships between geochemical gradients, genomic potential, and virus-host interactions remain understudied and poorly understood. I will present the results of our study of stratified sediments from anoxic sinkhole (Blackwood Sinkhole, Bahamas), where we analyzed the pore water chemistry analysis (nutrients, carbon, nitrogen), microbial community composition (16S rRNA gene and metagenomics), and virus-host interactions. Through the characterization of the relationships of microbes between each other and with their environment, we aim to identify the role organic and inorganic matter availability plays in shaping viral and prokaryotic communities, as well as how microbial communities shape their environment.

Missed the last seminar with Taylor Royalty on “Quantitatively partitioning microbial genomic traits among taxonomic ranks: implications for subsurface microbial communities?” Watch it on YouTube.

IODP-USSSP: Workshop on Demystifying the IODP Proposal Process for Early Career Scientists, February 17-20, 2020
The deadline to submit an application is October 18, 2019.

Goldschmidt 2020: Call for Session Proposals, Honolulu, HI, June 21-26 – NEW!
Goldschmidt is the foremost annual, international conference on geochemistry and related subjects, organized by the Geochemical Society and the European Association of Geochemistry. Session Proposal Deadline: October 18, 2019.

IODP: Submit an IODP Workshop Proposal – NEW!
The U.S. Science Support Program, associated with the International Ocean Discovery Program, is currently accepting proposals for planning workshops. Proposed workshops should promote the development of new ideas and strategies related to the study of the Earth’s processes and history using scientific ocean drilling. The workshop program encourages wide scientific community involvement to bring a broader and multidisciplinary approach to standing hypotheses and to explore new directions for IODP research and communication. Workshops may focus on a specific IODP scientific theme or topic, or they may focus on a geographic region, integrating multiple topics. Regionally-focused workshops offer opportunities to synthesize scientific results from past expeditions, or to develop drilling proposals for future expeditions. Prospective workshop proponents should consider long-term projected ship tracks in identifying potential geographic areas for focus. Workshops aimed at developing drilling proposals for implementation in the period beyond the current IODP science plan (2023) are welcomed. Funding may be requested for U.S.-based meetings or to support U.S. participants at larger international workshops. Broad-based scientific community involvement, co-sponsorship by related programs, and the active participation of early career researchers are strongly encouraged. The submission deadline is December 1, 2019.

Ongoing Activities:

• C-DEBI: Rolling call for Community Workshop support
• C-DEBI: Protocols.io Group Page
• C-DEBI: Subseafloor Cultures Database
• C-DEBI: Join us on LinkedIn

 

 

Best, 

 

Matt

 

— 

Matthew Janicak

Data Manager

Center for Dark Energy Biosphere Investigations (C-DEBI)

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

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