Microbial Ecology

, Volume 70, Issue 3, pp 766–784 | Cite as

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA

  • Olivia U. MasonEmail author
  • David H. CaseEmail author
  • Thomas H. Naehr
  • Raymond W. Lee
  • Randal B. Thomas
  • Jake V. Bailey
  • Victoria J. OrphanEmail author
Environmental Microbiology


Anaerobic oxidation of methane (AOM) impacts carbon cycling by acting as a methane sink and by sequestering inorganic carbon via AOM-induced carbonate precipitation. These precipitates commonly take the form of carbonate nodules that form within methane seep sediments. The timing and sequence of nodule formation within methane seep sediments are not well understood. Further, the microbial diversity associated with sediment-hosted nodules has not been well characterized and the degree to which nodules reflect the microbial assemblage in surrounding sediments is unknown. Here, we conducted a comparative study of microbial assemblages in methane-derived authigenic carbonate nodules and their host sediments using molecular, mineralogical, and geochemical methods. Analysis of 16S rRNA gene diversity from paired carbonate nodules and sediments revealed that both sample types contained methanotrophic archaea (ANME-1 and ANME-2) and syntrophic sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae), as well as other microbial community members. The combination of geochemical and molecular data from Eel River Basin and Hydrate Ridge suggested that some nodules formed in situ and captured the local sediment-hosted microbial community, while other nodules may have been translocated or may represent a record of conditions prior to the contemporary environment. Taken together, this comparative analysis offers clues to the formation regimes and mechanisms of sediment-hosted carbonate nodules.


Anaerobic methanotrophs Carbonate concretions Cold seeps ANME Sulfate-reducing bacteria 



VO conceived of the study and collected the samples at sea. OM processed the samples and optimized DNA extraction, as well as TRFLP and clone library analyses. DC performed iTAG processing and analyses, beta diversity analyses, and was the coordinating author of the manuscript. TN provided XRD data, RL performed the isotopic composition analyses, JB provided thin section images, and RT performed the pore water geochemical measurements. DC, OM, and VO principally contributed to writing the manuscript. Three anonymous reviews provided constructive suggestions to improve the manuscript. Elizabeth Trembath-Reichert, Stephanie Connon, and Jeff Marlow helped with customization of the Silva115_NR99 database. Alexis Pasulka provided helpful discussion regarding ordination and statistical probing of microbial communities. Josh Steele also provided discussion on ecological statistics and aided with bench-top lab work. Benjamin Harrison helped with TRFLP data interpretation. Jeff Marlow provided useful feedback on the manuscript. The crew of the R/V Atlantis cruise AT-15-11, as well as the pilots of DSV Alvin dives AD4249 and 4256, aided in sample recovery at sea. Funding for this work was provided by a National Science Foundation grant (BIO-OCE 0825791) to VO and an early career grant by the United States Department of Energy, Office of Biological and Environmental Research (DE-SC0003940) to VO. This research was also supported by a grant from the NASA Astrobiology Institute (Award #NNA13AA92A) to VO. This is NAI-Life Underground Publication 009. DC was funded by a National Science Foundation Graduate Research Fellowship.

Supplementary material

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Earth, Ocean and Atmospheric ScienceFlorida State UniversityTallahasseeUSA
  2. 2.Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaUSA
  3. 3.Department of Physical and Environmental SciencesTexas A&M University-Corpus ChristiCorpus ChristiUSA
  4. 4.School of Biological SciencesWashington State UniversityPullmanUSA
  5. 5.US Geological SurveyMenlo ParkUSA
  6. 6.Department of Earth SciencesUniversity of MinnesotaMinneapolisUSA

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