Evidence map›Paper›PMID 39696556›Full record

ArticleEnvironmental microbiome2024

Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.

Yuki Amano, Rohan Sachdeva, Daniel Gittins, Karthik Anantharaman, Shufei Lei, Luis E Valentin-Alvarado, Spencer Diamond, Hikari Beppu, Teruki Iwatsuki, Akihito Mochizuki and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Environmental microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. Article
  2. 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

18 authors.

Yuki AmanoNuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Ibaraki, 4-33 Muramatsu Tokai, Japan. amano.yuki@jaea.go.jp.
Rohan SachdevaInnovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
Daniel GittinsInnovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
Karthik AnantharamanDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Shufei LeiDepartment of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, 94720, USA.
Luis E Valentin-AlvaradoInnovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
Spencer DiamondInnovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
Hikari BeppuNuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Ibaraki, 4-33 Muramatsu Tokai, Japan.
Teruki IwatsukiHoronobe Underground Research Center, Japan Atomic Energy Agency, 432-2, Hokushin, Horonobe, Hokkaido, Japan.
Akihito MochizukiHoronobe Underground Research Center, Japan Atomic Energy Agency, 432-2, Hokushin, Horonobe, Hokkaido, Japan.
Kazuya MiyakawaHoronobe Underground Research Center, Japan Atomic Energy Agency, 432-2, Hokushin, Horonobe, Hokkaido, Japan.
Eiichi IshiiHoronobe Underground Research Center, Japan Atomic Energy Agency, 432-2, Hokushin, Horonobe, Hokkaido, Japan.
Hiroaki MurakamiHoronobe Underground Research Center, Japan Atomic Energy Agency, 432-2, Hokushin, Horonobe, Hokkaido, Japan.
Alexander L JaffeDepartment of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
Cindy CastelleInnovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
Adi LavyDepartment of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, 94720, USA.
Yohey SuzukiDepartment of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, Japan.
Jillian F BanfieldInnovative Genomics Institute, University of California, Berkeley, CA, 94720, USA. jbanfield@berkeley.edu.

Funding

National Science Foundation OCE2049478NSF "Four Networks for Geologic Hydrogen Storage" 2230766the Japan Society for the Promotion of Science 19K05342The Ministry of Economy, Trade and Industry of Japan JPJ007597the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy DE-AC02-05CH11231
6 · The paper itself

Abstract

backgroundUnderground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO

resultsWe reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO

conclusionsOur analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.

Indexed as

GraniteGroundwaterMetagenomics microbiomeSedimentary rocksStabilityUnderground research laboratory

Identifiers

PMID39696556
PMCPMC11657941

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.