EX4484-6 MAG from anoxic enrichment with 5 mL of slurry enrichment containing protein, antibiotics and sulfate, transferred after 372 days into Widdel medium, containing protein, antibiotics and sulfate. Timepoint day 157, incubated at 20 degrees C.

BioSample Accession(s)

SAMEA117970313, ERS23962115

ENA-CHECKLIST

ERC000047

assembly software

SPAdes 3.15.5, megahit 1.2.9

binning software

concoct, metabat2

organism

Thermoplasmatota archaeon

broad-scale environmental context

marine sediment [ENVO:03000033] | coast [ENVO:01000687]

assembly quality

Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs

collection date

2021-12-02

sample derived from

SAMEA116057598

geographic location (longitude)

7.968191

taxonomic identity marker

multi-marker approach

binning parameters

differential coverage, tetranucleotide frequency

completeness score

97.86

contamination score

2.81

environmental medium

microbial community [PCO:1000004] | mesocosm [ENVO:01000620]

geographic location (latitude)

54.087627

scientific_name

Thermoplasmatota archaeon

local environmental context

anaerobic sediment [ENVO:00002045] | mud [ENVO:01000001]

metagenomic source

sediment metagenome

project name

Characterization of uncultivated Thermoplasmatota in anaerobic marine sediments of the Helgoland mud area

completeness software

checkm2

geographic location (country and/or sea)

North Sea

isolation_source

Sediment slurry from Helgoland mud area

Slurry incubation experiment with protein, antibiotics and sulfate, timepoint day 157, incubated at 20 degrees C, sediment from station 2-2, coreHE483, Helgoland mud area, North Sea, Germany - Archaeal 16S rRNA gene community (DNA)

BioSample Accession(s)

SAMEA116057598, ERS21055639

sample volume or weight for DNA extraction

2

sample_description

Slurry incubation experiment with protein, antibiotics and sulfate, timepoint day 157, incubated at 20 degrees C, sediment from station 2-2, coreHE483, Helgoland mud area, North Sea, Germany - Archaeal 16S rRNA gene community (DNA)

source material identifiers

slurry prepared in ratio 1:4 of sediment Helgoland mud area core 583/2-2 and sulfate-free artificial sea water; 5mL slurry transferred into anaerobic Widdel medium after 372 days

broad-scale environmental context

marine sediment [ENVO:03000033] | coast [ENVO:01000687]

collection date

2017-04-19T00:00

geographic location (longitude)

7.968191

sediment environmental package

sediment

collection date experiment

2021-02-12T00:00

sample collection device

syringe, needle

sample material processing

slurry sample was frozen at -20 degrees C until DNA extraction

oxygenation status of sample

anaerobic

relationship to oxygen

anaerobe

experimental factor

time series design [EFO:0001779] | different substrate additions

sample_title.1

Helgoland mud area slurry incubation - protein.antibiotics.sulfate - day 157

geographic location (country and/or sea)

North Sea

elevation

-28.8

ENA-CHECKLIST

ERC000021

amount or size of sample collected

0.002

submitted to insdc

true

organism

marine sediment metagenome

environmental package

sediment

replicate experiment

A

environmental medium

anaerobic sediment [ENVO:00002045] | mud [ENVO:01000001]

geographic location (latitude)

54.087627

scientific_name

marine sediment metagenome

sample collection method

slurry sampling in anoxic manner

target subfragment

V4

geographic location (region and locality)

Helgoland mud area, North Sea, Germany

investigation type

mimarks-survey

read_direction

fwd-rev

total depth of water column

28.8

pcr primers

FWD:CAGCMGCCGCGGTAA;REV:GGACTACVSGGGTATCTAAT

pcr conditions

initial denaturation:95_3; denaturation:98_0.2;annealing:60_0.15;elongation:72_0.15;final elongation:72_1

local environmental context

microbial community [PCO:1000004] | mesocosm [ENVO:01000620]

depth

45-70

project name

Characterization of uncultivated Thermoplasmatota in anaerobic marine sediments of the Helgoland mud area

sequencing method

Illumina NovaSeq 6000

nominal_length_noprim

253

substrated added experiment

protein, antibiotics, sulfate

sequencelane_id

HL32NDRXY_L1

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Metadata as EBI XML

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        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX13067160&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX13067160&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX13067163" alias="190304:f8340e7a-c5b3-43ec-a2f7-ef13ba251630" broker_name="German Federation for Biological Data (GFBio)" center_name="German Federation for Biological Data">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX13067163</PRIMARY_ID>
    <SUBMITTER_ID namespace="German Federation for Biological Data">190304:f8340e7a-c5b3-43ec-a2f7-ef13ba251630</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina NovaSeq 6000 paired end sequencing</TITLE>
  <STUDY_REF accession="ERP164333">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP164333</PRIMARY_ID>
      <SECONDARY_ID>PRJEB80318</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS21055639">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS21055639</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA116057598</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS21055639</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA30806864</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX13067163&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX13067163&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX13067164" alias="190302:f8340e7a-c5b3-43ec-a2f7-ef13ba251630" broker_name="German Federation for Biological Data (GFBio)" center_name="German Federation for Biological Data">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX13067164</PRIMARY_ID>
    <SUBMITTER_ID namespace="German Federation for Biological Data">190302:f8340e7a-c5b3-43ec-a2f7-ef13ba251630</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina NovaSeq 6000 paired end sequencing</TITLE>
  <STUDY_REF accession="ERP164333">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP164333</PRIMARY_ID>
      <SECONDARY_ID>PRJEB80318</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS21055639">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS21055639</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA116057598</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS21055639</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA30806864</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX13067164&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX13067164&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>