URLhttps://www.bco-dmo.org/dataset/683021
Download URLhttps://www.bco-dmo.org/dataset/683021/data/download
Media Typetext/tab-separated-values
CreatedFebruary 24, 2017
ModifiedOctober 8, 2018
StatePreliminary and in progress
Brief DescriptionChloroflexi accessions

Acquisition Description

Methodology from Fullerton and Moyer (2016). See paper for references cited below.

Sample collection. Subsurface sediments were collected on IODP expedition 331 (Deep Hot Biosphere) from 1 September through 4 October 2010 (Fig. 1). Onboard contamination testing of sites C0015 (126°53=E, 27°47=N; hole B; section 1H-5; 5.6mbsf) and C0017 (126°55=E, 27°47=N; hole C; section 1H-7; 26.6 m bsf) found no indication of interior-core contamination using fluorescent microspheres (both holes C0015B and C0017C) and perfluorocarbon tracer (hole C0017C only). The sample from hole C0017C was also verified by PCR-generated phylotype comparisons based on 97% similarity to phylotypes obtained from drilling mud at a contamination level of 1% or less (26). Subsamples were aseptically collected from the interiors of whole-round cores and stored in cryovials with 27% (vol/vol) glycerol at -80°C.

Single-cell source. Core depths were chosen from sites C0015 and C0017, which were characterized as weakly oxidized pumiceous gravels with no detected sulfide mineralization and less than 0.1 wt% total organic carbon, total nitrogen, and total sulfur (25). The selected samples for single-cell genomes were from subsurface depths of 5.6 m bsf from hole C0015B and from 26.6 m bsf from hole C0017C. Temperatures were estimated at ~10.5°C for C0015B and ~8.1°C for C0017C at these depths. Details of geochemistry and lithography have been previously described (12, 24, 25).

Single-cell sorting, amplification, sequencing, and annotation. Samples from sites C0015 and C0017 (Fig. 1) were diluted with 1 ml of filter-sterilized artificial seawater (27), making a slurry, and then passed through a 90-um nylon mesh filter twice and centrifuged at ~500 ug for 2 min to produce a particle-free cell suspension. The suspension was then processed using fluorescence-activated single-cell sorting at the Single Cell Genome Center (SCGC) at Bigelow Laboratory for Ocean Sciences. Single-cell sorting and multiple displacement amplification (MDA) have been previously described (28). The amplified SSU rRNA gene sequences (27F/907R) were classified using the Ribosomal Database Project (RDP) online classifier (28, 29). Based on their SSU rRNA gene identities, nine Chloroflexi SAGs (of the total 29 unique MDA reactions identified after cell sorting) were chosen for whole-genome sequencing. These SAGs were sequenced and assembled, and contamination was checked by the SCGC, using previously well-described parameters (28, 29). Assembly was done using SPAdes v.3.0.0 (30). All contigs were compared to ensure no cross contamination among SAGs and the NCBI nt database, which was followed by tetramer principal-component analysis as previously described (31-33). These analyses revealed no contamination. The full name for each of the SAGs was shortened, e.g., Anaerolineales bacterium SCGC AC-711-B22 was shortened to An-B22. Phylogeny was abbreviated as follows: Anaerolineales to An, Dehalococcoidales to De, and Thermoflexales to Th. The assembled genomes were annotated using RAST (34). Gene annotations were compared to NCBI GenBank via BLASTn, and the results can be found in Tables S2 to S4 in the supplemental material.

The Anaerolineales SAGs were compared to the genome of Anaerolinea thermophila UNI-1 (GenBank accession number NC_014960) and the single Thermoflexales SAG to that of Thermoflexus hugenholtzii JAD2 (NCBI BioProject PRJNA195829), as they were determined to be their closest respective relatives. The type strain A. thermophila UNI-1 was isolated from an anaerobic granular sludge reactor treating fried soybean curd manufacturing wastewater in Japan (35), while the type strain T. hugenholtzii JAD2 was isolated from the sediment of Great Boiling Spring in Nevada (36). Both are considered thermophilic, Gram-negative, nonspore-forming, heterotrophic bacteria that grow in multicellular filaments (36, 37).

Phylogenetic analysis. SSU rRNA gene sequences and phylogenetic relatives were aligned using the Silva SINA aligner (38). For the rdhA analysis, amino acids were aligned using ClustalW within Geneious (39, 40). The resulting alignments were manually screened and then used to create a phylogenetic consensus tree using MrBayes within Geneious (41). Parameters included using the HKY85 substitution model, the chain length set at 1,100,000, and a subsampling frequency of 200. Priors were set with an unconstrained branch length. The average nucleotide identity (ANI) was calculated for the SAGs and selected genomes, with the BLAST parameters as previously described (42).

Genome completeness estimates. Genome completeness estimates were determined with BLASTP using predicted amino acid sequences against a set of single-copy core genes (43). To be considered valid, all proteins must have at least 30% identity over at least 30% of the length of the core gene (44). The core gene group is made up of 66 previously established genes belonging to a nonredundant list as examined by gene ontology (GO) annotations (44, 45).

Accession numbers. The SSU rRNA gene sequences obtained from MDA have been submitted to the NCBI GenBank database (accession numbers KT119838 to KT119846). All the SAGs have been made public in the Integrated Microbial Genomes (IMG) database (IMG submission identifiers [IDs] 68650, 69642 to 69645, 69647 to 69649, and 69684).

Processing Description

BCO-DMO Processing Notes:
Created a servable data file from metadata and data provided by the PI and created links to accession pages at NCBI and IMG, when available.

Instruments

Instance Description

Genetic analyses performed at Single Cell Genome Center (SCGC) at Bigelow Laboratory for Ocean Sciences

General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Instance Description

Genetic analyses performed at Single Cell Genome Center (SCGC) at Bigelow Laboratory for Ocean Sciences

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

cruise_id [cruise_id]
Details
cruise_id
cruise identifier
cruise designation; name
cruise_description [Cruise Name]
Details
cruise_description
description of site
The cruise_name is a local name chosen by project investigators for a research expedition on a vessel, as opposed to the formal/official cruise ID asserted by the vessel operator.
site [site]
Details
site
site identification
Sampling site identification.
date_collected [date]
Details
date_collected
date sample was collected; formatted as yyyy-mm-dd

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

site_description [site_descrip]
Details
site_description
description of site

Description or characteristics of a sampling site

station [sta]
Details
station
station identifier

station number; generally sequential; a unique number designating a general geographic location at which one or more sampling activities may occur.

This term has been deprecated and replaced by station.

lat [latitude]
Details
lat
latitude at which sample was collected

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Details
lon
longitude at which sample was collected

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

Details
hole
drill hole identifier

Description or characteristics of a sampling site

section [sample]
Details
section
drill core sample section

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

depth_bsf [depth_bsf]
Details
depth_bsf
depth below seafloor

depth below seafloor.  Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).

Details
gene
gene that was sequenced
text description of sample collected
service [sampling_method]
Details
service
method: Single Amplified Genome
Method used to collect sample, for example Bongo net or Methot trawl.
taxon_name [taxon]
Details
taxon_name
description of taxon

taxonomic group or entity. This may be a family, class, genus, species, etc.; usually this parameter will contain a mixture of taxonomic entities.

NCBI_BioSample [accession number]
Details
NCBI_BioSample
NCBI BioSample identifier
Database identifier assigned by repository and linked to GenBank or other repository.
BioSample_link [external_link]
Details
BioSample_link
link to NCBI BioSample page

Link to an external data entry.

NCBI_accession_number [accession number]
Details
NCBI_accession_number
NCBI accession number
Database identifier assigned by repository and linked to GenBank or other repository.
accession_link [external_link]
Details
accession_link
link to NCBI accession number page

Link to an external data entry.

IMG_taxon_id [accession number]
Details
IMG_taxon_id
IMG taxon id
Database identifier assigned by repository and linked to GenBank or other repository.
IMG_link [external_link]
Details
IMG_link
link to IMG taxon id page

Link to an external data entry.

Dataset Maintainers

NameAffiliationContact
Craig L. MoyerWestern Washington University (WWU)
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleIron-oxidizing Bacteria from the Okinawa Trough Deep Subsurface Biosphere
AcronymSubsurface FeOBs
URLhttps://www.bco-dmo.org/project/557453
CreatedMay 1, 2015
ModifiedJanuary 12, 2017
Project Description

Description from NSF award abstract:
Communities of Fe-oxidizing Bacteria (FeOB) are common at sites of hydrothermal venting and are known to form complex communities in microbial mats, hydrothermal sediments, oceanic crustal basalts and borehole fluids (among others) that are iron-rich and low in oxygen. Studies from sites around the Pacific Ocean have found the Zetaproteobacteria to be ubiquitous members of these FeOB communities. Previously, borehole fluids from the Southern Mariana Backarc have been shown to support several novel and distinct lineages of endemic Zetaproteobacteria. Sampling from the deep subsurface at the Iheya North hydrothermal field (IODP Expedition 331) explores this deep subsurface FeOB biodiversity and has resulted in multiple enrichments using both microaerophilic and anaerobic culturing conditions. Zetaproteobacteria have been detected at levels up to 13% of the total bacterial community from these subsurface core samples. This project expands post-cruise analyses to focus on assessing these FeOB subsurface communities using a combined single cell genomics, community-level metagenomics and a FeOB directed cultivation approach. This approach will allow insights into the exclusive physiology and metabolism of these Zetaproteobacteria thereby demonstrating key features as to how they survive, compete and grow within these complex subsurface microbial communities. A comparative analysis (from an evolutionary standpoint) to determine the unique differences between subsurface Zetaproteobacteria and those living above the seafloor surface is an integral part of this effort.

A better understanding of Zetaproteobacteria is of central interest to scientists interested in areas of earth science and oceanography because they illustrate how microbes can influence geochemical cycling and mineral deposition. Furthermore, morphological structures similar to those produced by Zetaproteobacteria can still be identified 100's of millions (and possibly billions) of years back in the rock record, making them of paleontological (and potentially of exobiological) interest. As knowledge of extant populations grows, it is possible they will also help to inform us of environmental change in past Earth history. From a practical standpoint, these organisms might be thought of as 'micro-machines', spinning out threads of iron oxyhydroxide that coalesce in unknown ways. These oxides are known to be highly reactive with a range of other metals, organic compounds, and nutrients, thus impacting many other biogeochemical cycles. In particular, this study allows the opportunity to compare and contrast a known monophyletic class of Proteobacteria, to study the differences between subsurface and supersurface lineages of Zetaproteobacteria, thereby yielding fundamental clues into microbial biogeography. A wealth of educational outreach opportunities will be made possible by this work, including graduate education, research experiences for undergraduates, and teacher training.

Related Publications:

Fullerton, H. and C. L. Moyer. 2016. Comparative single-cell genomics of Chloroflexi from the Okinawa Trough deep subsurface biosphere. Appl. Environ. Microbiol. 82:3000-3008. doi: 10.1128/AEM.00624-16

Takai, K., Mottl, M. J., Nielsen, S. H. H., and the IODP Expedition 331 Scientists: IODP Expedition 331: Strong and Expansive Subseafloor Hydrothermal Activities in the Okinawa Trough, Sci. Dril., 13, 19-27, doi:10.5194/sd-13-19-2012, 2012.

Yanagawa K, Nunoura T, McAllister SM, Hirai M, Breuker A, Brandt L, House CH, Moyer CL, Birrien J-L, Aoike K, Sunamura M, Urabe T, Mottl MJ and Takai K (2013) The first microbiological contamination assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya North hydrothermal field in the Mid-Okinawa Trough (IODP Expedition 331). Front. Microbiol. 4:327. doi:10.3389/fmicb.2013.00327.

Project Maintainers
NameAffiliationRoleContact
Craig L. MoyerWestern Washington University (WWU)Principal Investigator
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