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nature research | reporting summary
October 2018
Corresponding author(s):
Jared R. Leadbetter
Last updated by author(s):
Apr 13, 2020
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
Authors & Referees
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 (
n
) 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
Only common tests should be described solely by name; describe more complex techniques in the Methods section.
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.
F
,
t
,
r
) with confidence intervals, effect sizes, degrees of freedom and
P
value noted
Give P values as exact values whenever suitable.
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
d
, Pearson's
r
), indicating how they were calculated
Our web collection on
statistics for biologists
contains articles on many of the points above.
Software and code
Policy information about
availability of computer code
Data collection
Zeiss Stemmi 2000-C stereomicroscope, Zeiss Axioplan 2 Imaging Microscope, Panasonic Lumix GH3 and G85 microfourthirds-lens-mou
nt
cameras, Olympus BX51 epifluorescence microscope, Nicolet Magna 860 Fourier transform infrared (FTIR) spectrophotometer, Zeiss
1550VP field emission SEM, Agilent 8800 inductively coupled plasma mass spectrometer, Bio-Rad C1000 Thermal Cycler with CFX96 R
eal-
Time System, Illumina HiSeq2500, Agilent Technologies Bioanalyzer, CAMECA NanoSIMS 50L
Data analysis
Databases: NCBI (ncbi.nlm.nih.gov), JGI IMG (https://img.jgi.doe.gov/cgi-bin/mer/main.cgi), SILVA Ref NR 99 Database Release 11
9,
Genome Taxonomy Database (GTDB) v0.2.2
Data Analysis: QIIME v1.8.0, UCLUST v7.11.0.667, ARB software v6.0.2, SINA v1.2.11, daime v2.1, RTA v1.18.64, bcl2fastq v1.8.4,
Trimmomatic v0.36, Spades v3.11.1, mmgenome v0.7.1, bowtie2 v2.3.4.1, CheckM v1.0.6, GTDB v0.2.2, MrBayes v3.2.6, RAxML v8.1.
7,
sortmerna v2.0, kallisto v0.44.0, sleuth v0.30.0, BBMap v37.93, PRED-TMBB (http://bioinformatics.biol.uoa.gr/PRED-TMBB/),
Look@NanoSIMS v2019-05-14
Data Visualization: iTOL (https://itol.embl.de/), Adobe Photoshop CC 2019, Adobe Illustrator CC 2019, Adobe Lightroom CC 2019
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/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
All sequencing data has been deposited at National Center for Biotechnology Information (NCBI) under BioProject PRJNA562312. Th
e cloned 16S rRNA gene
sequences of “Ca. Manganitrophus noduliformans” (Species A) and Ramlibacter lithotrophicus (Species B) from the co-culture have
been deposited at GenBank
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nature research | reporting summary
October 2018
under accession numbers MN381734 and MN381735, respectively. The iTAG sequences from 3 different enrichments has been deposited
at SRA under accession
numbers SRR10031198-SRR10031200. Genome sequences of the co-culture, from which the genome of Ca. M. noduliformans was reconstr
ucted, have been
deposited under BioSample SAMN12638105 with raw sequences deposited at SRA under accession number SRR10032644; the reconstructe
d genome of Ca. M.
noduliformans has been deposited at DDBJ/ENA/GenBank under accession number VTOW00000000. Genome sequences of R. lithotrophicus
strain RBP-1 have
been deposited under BioSample SAMN12638106 with raw sequences deposited at SRA under accession number SRR10031379; the reconst
ructed genome of R.
lithotrophicus strain RBP-1 has been deposited at DDBJ/ENA/GenBank under accession number VTOX00000000. Additionally, reconstru
cted genomes have been
deposited in Joint Genome Institute (JGI) Genomes Online Database Study ID Gs0134339, with Integrated Microbial Genome ID 27841
32095 for Ca. M.
noduliformans and ID 2778260901 for R. lithotrophicus strain RBP-1. Transcriptome sequence data for the 7 biological replicates
have been deposited at SRA under
accession numbers SRR10060009, SRR10060010, SRR10060011, SRR10060012, SRR10060013, SRR10060017, SRR10060018. Unique biological
materials are
available upon reasonable request.
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
Life sciences study design
All studies must disclose on these points even when the disclosure is negative.
Sample size
No statistical methods were used to predetermine sample size. "Sample" as intended here seems to more relevant for the concept
of deciding
sample size in terms of numbers of animals or human subjects to include in a study. Here, as a microbiologist, we are almost al
ways dealing
with populations of tens of millions or more, its really quite a different issue. Aside from that, "sample" means very differen
t things in
different contexts, and it is not clear at all how statistics would replace sound experimental design in many of them. We have
looked at the
Nature document that details a past questionnaire, and see several well articulated responses from colleagues that touch on thi
s.
Data exclusions
No data were excluded in the results. No data exclusion criteria were pre established. Again, it seems this tailored for large
r studies on
animals and human subjects, and not clear how "pre-establishing" would come into play here.
Replication
Technical and biological replication was performed as indicated in individual experiments reported. All attempts at replication
were successful.
Randomization
Randomization was not relevant to this study, it was not a randomized controlled trial. As a standard in microbiology, samples
were obtained
from a larger population of an enrichment culture to inoculate experimental groups.
Blinding
None. This was not a clinical trial or a randomized controlled trial.
Reporting for specific materials, systems and methods
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
Animals and other organisms
Human research participants
Clinical data
Methods
n/a
Involved in the study
ChIP-seq
Flow cytometry
MRI-based neuroimaging