skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on May 2, 2020

Title: An archaeal symbiont-host association from the deep terrestrial subsurface

Abstract

DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, but little is known about their interactions with other microorganisms that reside there. In this work, we offer evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These findings give insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.

Authors:
 [1];  [1];  [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [1]
  1. Univ. of Duisburg-Essen (Germany)
  2. Utrecht Univ., Den Burg (Netherlands)
  3. Utrecht Univ., Den Burg (Netherlands); Uppsala Univ. (Sweden)
  4. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Swedish Research Council (SRC)
OSTI Identifier:
1572835
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 13; Journal Issue: 8; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Schwank, Katrin, Bornemann, Till L. V., Dombrowski, Nina, Spang, Anja, Banfield, Jillian F., and Probst, Alexander J. An archaeal symbiont-host association from the deep terrestrial subsurface. United States: N. p., 2019. Web. doi:10.1038/s41396-019-0421-0.
Schwank, Katrin, Bornemann, Till L. V., Dombrowski, Nina, Spang, Anja, Banfield, Jillian F., & Probst, Alexander J. An archaeal symbiont-host association from the deep terrestrial subsurface. United States. doi:10.1038/s41396-019-0421-0.
Schwank, Katrin, Bornemann, Till L. V., Dombrowski, Nina, Spang, Anja, Banfield, Jillian F., and Probst, Alexander J. Thu . "An archaeal symbiont-host association from the deep terrestrial subsurface". United States. doi:10.1038/s41396-019-0421-0.
@article{osti_1572835,
title = {An archaeal symbiont-host association from the deep terrestrial subsurface},
author = {Schwank, Katrin and Bornemann, Till L. V. and Dombrowski, Nina and Spang, Anja and Banfield, Jillian F. and Probst, Alexander J.},
abstractNote = {DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, but little is known about their interactions with other microorganisms that reside there. In this work, we offer evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These findings give insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.},
doi = {10.1038/s41396-019-0421-0},
journal = {The ISME Journal},
number = 8,
volume = 13,
place = {United States},
year = {2019},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on May 2, 2020
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ
journal, July 2017

  • Golyshina, Olga V.; Toshchakov, Stepan V.; Makarova, Kira S.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/s41467-017-00104-7

MaGe: a microbial genome annotation system supported by synteny results
journal, January 2006


MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells
journal, October 2015

  • Schimak, Mario P.; Kleiner, Manuel; Wetzel, Silke
  • Applied and Environmental Microbiology, Vol. 82, Issue 1
  • DOI: 10.1128/AEM.02776-15

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis
journal, September 2018


Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
journal, January 2018

  • Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.
  • Nature Microbiology, Vol. 3, Issue 3
  • DOI: 10.1038/s41564-017-0098-y

The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
journal, October 2003

  • Waters, E.; Hohn, M. J.; Ahel, I.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
  • DOI: 10.1073/pnas.1735403100

Natural Communities of Novel Archaea and Bacteria Growing in Cold Sulfurous Springs with a String-of-Pearls-Like Morphology
journal, May 2001


Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon
journal, October 2008

  • Comolli, Luis R.; Baker, Brett J.; Downing, Kenneth H.
  • The ISME Journal, Vol. 3, Issue 2
  • DOI: 10.1038/ismej.2008.99

Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms
journal, June 2017


A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
journal, May 2002

  • Huber, Harald; Hohn, Michael J.; Rachel, Reinhard
  • Nature, Vol. 417, Issue 6884
  • DOI: 10.1038/417063a

Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’
journal, July 2016

  • Villanueva, Laura; Schouten, Stefan; Damsté, Jaap S. Sinninghe
  • Environmental Microbiology, Vol. 19, Issue 1
  • DOI: 10.1111/1462-2920.13361

Proteomic Characterization of Cellular and Molecular Processes that Enable the Nanoarchaeum equitans-Ignicoccus hospitalis Relationship
journal, August 2011


A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans
journal, June 2017


Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface
journal, November 2014

  • Probst, Alexander J.; Weinmaier, Thomas; Raymann, Kasie
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms6497

Enigmatic, ultrasmall, uncultivated Archaea
journal, April 2010

  • Baker, B. J.; Comolli, L. R.; Dick, G. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 19
  • DOI: 10.1073/pnas.0914470107

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015

  • Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
  • Current Biology, Vol. 25, Issue 6
  • DOI: 10.1016/j.cub.2015.01.014

    Works referencing / citing this record:

    Unexpected host dependency of Antarctic Nanohaloarchaeota
    journal, June 2019

    • Hamm, Joshua N.; Erdmann, Susanne; Eloe-Fadrosh, Emiley A.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 29
    • DOI: 10.1073/pnas.1905179116