1
nature research | reporting summary
April 2020
Corresponding author(s):
Fabai Wu & Victoria Orphan
Last updated by author(s):
November 7, 2021
Reporting Summary
Nature Research wishes to improve the reproducibility of the work that we publish. This form provides structure for consistency
and transparency
in reporting. For further information on Nature Research policies, see our
Editorial Policies
and the
Editorial Policy Checklist
.
Statistics
For all statistical analyses, confirm that the following items are present in the figure legend, table legend, main text, or Me
thods section.
n/a
Confirmed
The exact sample size (
Ŷ
) for each experimental group/condition, given as a discrete number and unit of measurement
A statement on whether measurements were taken from distinct samples or whether the same sample was measured repeatedly
The statistical test(s) used AND whether they are one- or two-sided
KŶůLJĐŽŵŵŽŶƚĞƐƚƐƐŚŽƵůĚďĞĚĞƐĐƌŝďĞĚƐŽůĞůLJďLJŶĂŵĞ͖ĚĞƐĐƌŝďĞ
ŵŽƌĞĐŽŵƉůĞdžƚĞĐŚŶŝƋƵĞƐŝŶƚŚĞDĞƚŚŽĚƐƐĞĐƚŝŽŶ͘
A description of all covariates tested
A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons
A full description of the statistical parameters including central tendency (e.g. means) or other basic estimates (e.g. regress
ion coefficient)
AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals)
For null hypothesis testing, the test statistic (e.g.
&
,
ƚ
,
ƌ
) with confidence intervals, effect sizes, degrees of freedom and
W
value noted
'ŝǀĞWǀĂůƵĞƐĂƐĞdžĂĐƚǀĂůƵĞƐǁŚĞŶĞǀĞƌƐƵŝƚĂďůĞ͘
For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings
For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes
Estimates of effect sizes (e.g. Cohen's
Ě
, Pearson's
ƌ
), indicating how they were calculated
KƵƌǁĞďĐŽůůĞĐƚŝŽŶŽŶ
ƐƚĂƚŝƐƚŝĐƐĨŽƌďŝŽůŽŐŝƐƚƐ
ĐŽŶƚĂŝŶƐĂƌƚŝĐůĞƐŽŶŵĂŶLJŽĨƚŚĞƉŽŝŶƚƐĂďŽǀĞ͘
Software and code
Policy information about
availability of computer code
Data collection
Zen black version ELYRA was used for the acquisition of fluorescent images on Zeiss microscope.
Data analysis
DADA2 v1.9.1 ;R package(v3.6.0); canu v2.1; BamM v2.5.0; pilon v1.22; bedtools v2.29.2; LRScaf v1.1.10; SPAdes v3.14.1; metabat
2 v2.15;
MIRA v4 package; ANIcalculator v1.0; SINA v1.2.11; EggNOG mapper v2; cctyper 1.1.4; PSI-BLAST (https://blast.ncbi.nlm.nih.gov);
CDD search
(https://blast.ncbi.nlm.nih.gov); PHANNs (https://edwards.sdsu.edu/phanns); CheckM v1.1.3; hmmer v3.3.2; IQtree v2.1.2; UFBoo
t v2;
MUSCLE v3.8.1551, anvi’o v6.2; ASM-Clust v1; blast v2.2.26; MAFFT v7.475; trimAl v1.4.1; minimap2 v2.17; catfasta2phyml (https:
//
github.com/nylander/catfasta2phyml); custom script for amino acid recoding (https://github.com/dspeth/bioinfo_scripts/tree/mast
er/
phylogeny); custom matlab scripts under https://github.com/wufabai/genomics.
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published lit
erature, software must be made available to editors and
reviewers. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research
guidelines for submitting code & software
for further information.
Data
Policy information about
availability of data
All manuscripts must include a
data availability statement
. This statement should provide the following information, where applicable:
- Accession codes, unique identifiers, or web links for publicly available datasets
- A list of figures that have associated raw data
- A description of any restrictions on data availability
The assembled genomes and raw metagenomic sequencing reads can be found on NCBI database under BioProject PRJNA721962, which wa
s made publicly
available on November 8, 2021.
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nature research | reporting summary
April 2020
Field-specific reporting
Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before m
aking your selection.
Life sciences
Behavioural & social sciences
Ecological, evolutionary & environmental sciences
For a reference copy of the document with all sections, see
nature.com/documents/nr-reporting-summary-flat.pdf
Ecological, evolutionary & environmental sciences study design
All studies must disclose on these points even when the disclosure is negative.
Study description
Anaerobic laboratory cultivation using artificial sea water
Research sample
Sediment and Rocks collected from hydrothermal vents. The samples were chosen due to their geographical proximity to the vents
with diffusive venting, which provide nutrients that fuel the local ecosystem.
Sampling strategy
Samples were collected in an anaerobic chamber using pipettes. Sample sizes were empirical determined, typically 1ml in volume,
to
allow extraction of sufficient amount of DNA while causing the least amount of disturbance to the existing microbiome.
Data collection
16S rRNA Amplicon sequencing data using Illumina MiSeq were collected by Laragen. Full-Length 16S rRNA Sequencing data using
PacBio Sequel II were collected by Brigham Young University Sequencing Center. Metagenomic sequencing data via Illumina
HiSeq2000 were collected by Novogen. Metagenomic sequencing data via Oxford Nanopore MinION were collected by author Igor A.
Antoshechkin.
Timing and spatial scale
The sampling of the initial rock and sediment samples were respectively carried out at the Auka vent field, Pescadero basin, Me
xico
on November 2, 2017 and on November 14, 2018. The sampling of rock incubations were sampled inside of the anaerobic chamber
at Caltech between November 8, 2018 and December 15, 2019 with an increasing interval from 3 weeks to 8 months. The exact
dates are specified in Supplementary Table 2. The sediment incubations were sampled on date June 23, July 29, and September 23,
2019.
Data exclusions
All sequencing data were used for analyses without exclusion.
Reproducibility
The paper focuses on bioinformatics analyses, and all analyses can be reproduced using publicly available software packages
provided in the Methods section. The DNA samples were analyzed twice during the rock incubation at 2-4 months around the time
when the AAG phylotypes started to emerge. No specific incubation conditions had experimental replicates.
Randomization
The experiments were designed to discover novel organisms from any possible condition. The work does not focus on the effect of
environmental parameters.
Blinding
We do not carry out randomized testing on experimental subjects, as the experiments were designed to discover novel organisms
from any possible condition. There is no visual link between the samples and the microbes of interest, and there is a minimum o
f 2
months between the time of sampling and the time of sequencing data output, blinding neither increase nor decrease bias.
Did the study involve field work?
Yes
No
Field work, collection and transport
Field conditions
Field sites are 3.6 km below sea level, collected at natural conditions on the dates and location provided in the Methods secti
on. The
local temperature were measure at around 40 °C, although with uncertainty due to the strong temperature gradient at the samplin
g
site.
Location
[23°57’N; 108°51’W] [23°57’N; 108°52’W] [23°53’N; 108°48’W]
Access & import/export
Sample collection accompanied by and under the construction local scientists under permission granted by local government. Samp
le
collection permits for the expedition was granted by la Dirección General de Ordenamiento Pesquero y Acuícola, Comisión Naciona
l
de Acuacultura y Pesca (CONAPESCA: Permiso de Pesca de Fomento No. PPFE/DGOPA-200/18) and la Dirección General de Geografía
y Medio Ambiente, Instituto Nacional de Estadística y Geografía (INEGI: Autorización EG0122018), with the associated Diplomatic
Note number 18-2083 (CTC/07345/18) from la Secretaría de Relaciones Exteriores - Agencia Mexicana de Cooperación Internacional
para el Desarrollo / Dirección General de Cooperación Técnica y Científica. The permit EG0072017 for the 2017 cruise was grante
d on
April 18, 2017. The permit EG0122018 for the 2018 cruise was granted on July 25, 2018.
Disturbance
Samples were collected outside the major chimney area to result in minimal influence on the macrofauna and the structural integ
rity
of the chimneys.
Reporting for specific materials, systems and methods
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nature research | reporting summary
April 2020
We require information from authors about some types of materials, experimental systems and methods used in many studies. Here,
indicate whether each material,
system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the approp
riate section before selecting a response.
Materials & experimental systems
n/a
Involved in the study
Antibodies
Eukaryotic cell lines
Palaeontology and archaeology
Animals and other organisms
Human research participants
Clinical data
Dual use research of concern
Methods
n/a
Involved in the study
ChIP-seq
Flow cytometry
MRI-based neuroimaging