Evidence map›Paper›PMID 38273328›Full record

ArticleMicrobiome2024

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism.

Luis E Valentin-Alvarado, Sirine C Fakra, Alexander J Probst, Jonathan R Giska, Alexander L Jaffe, Luke M Oltrogge, Jacob West-Roberts, Joel Rowland, Michael Manga, David F Savage and 3 more

Open access · goldAbstract readVideo-Audio Media
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
6.4field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed, 15 citations in OpenAlex.

  1. Article
  2. Article
  3. Beyond genomics in Patescibacteria: A trove of unexplored biology packed into ultrasmall bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  4. Towards AI-designed genomes using a variational autoencoder.Proceedings. Biological sciences · 2024
    Article
  5. Article
  6. Article
  7. "Applied and environmental microbiology · 2023
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 7 institutions in 3 countries.

Luis E Valentin-AlvaradoGraduate Group in Microbiology, University of California, Berkeley, CA, USA.
Sirine C FakraAdvanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Alexander J ProbstEarth and Planetary Science, University of California, Berkeley, CA, USA.
Jonathan R GiskaEarth and Planetary Science, University of California, Berkeley, CA, USA.
Alexander L JaffeGraduate Group in Microbiology, University of California, Berkeley, CA, USA.
Luke M OltroggeDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Jacob West-RobertsEnvironmental Science, Policy and Management, University of California, Berkeley, CA, USA.
Joel RowlandEarth and Planetary Science, University of California, Berkeley, CA, USA.
Michael MangaEarth and Planetary Science, University of California, Berkeley, CA, USA.
David F SavageInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Chris GreeningDepartment of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
Brett J BakerDepartment of Integrative Biology, University of Texas, Austin, USA.
Jillian F BanfieldInnovative Genomics Institute, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
University of California, Berkeley · USUniversity of Duisburg-Essen · DEAustralian Regenerative Medicine Institute · AUHoward Hughes Medical Institute · USLawrence Berkeley National Laboratory · USPlanetary Science Institute · USThe University of Texas at Austin · US

Funding

Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human DiseaseRM1HG009490 · NHGRI · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI Brittany S. Adamson, Martin Joseph Ankrah Aryee · 2017 to 2026
$22.7M
NHGRI NIH HHS RM1 HG009490NIH grants 1R01GM12763NSF grants 0909701, 1344424, 1724986, AND 2116573US DOE Office of Science User Facility DE-AC02-05CH11231
6 · The paper itself

Abstract

backgroundBiofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

resultsSulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L

conclusionsOur combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.

Indexed as

EcosystemGroundwaterBacteriaBiofilmsHydrogenOxidation-ReductionPhylogenySulfidesSulfurHydrogenSulfidesSulfurCandidate phyla radiationGroundwater microbiomeSynchrotron-based spectromicroscopy

Identifiers

PMID38273328
PMCPMC10811913
OpenAlexW4391238607

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.