PMID- 33060828
OWN - NLM
STAT- MEDLINE
DCOM- 20210421
LR  - 20230919
IS  - 1751-7370 (Electronic)
IS  - 1751-7362 (Print)
IS  - 1751-7362 (Linking)
VI  - 15
IP  - 2
DP  - 2021 Feb
TI  - Experimentally-validated correlation analysis reveals new anaerobic methane 
      oxidation partnerships with consortium-level heterogeneity in diazotrophy.
PG  - 377-396
LID - 10.1038/s41396-020-00757-1 [doi]
AB  - Archaeal anaerobic methanotrophs ("ANME") and sulfate-reducing 
      Deltaproteobacteria ("SRB") form symbiotic multicellular consortia capable of 
      anaerobic methane oxidation (AOM), and in so doing modulate methane flux from 
      marine sediments. The specificity with which ANME associate with particular SRB 
      partners in situ, however, is poorly understood. To characterize partnership 
      specificity in ANME-SRB consortia, we applied the correlation inference technique 
      SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment 
      samples, uncovering a strong positive correlation between ANME-2b and members of 
      a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this 
      association by examining 16S rRNA diversity in individual ANME-SRB consortia 
      sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence 
      in situ hybridization (FISH) microscopy using newly-designed probes targeting the 
      SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the 
      presence of a complete nifHDK operon required for diazotrophy, unusual in 
      published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g 
      within ANME-2b-SEEP-SRB1g consortia was then demonstrated by microscopy using 
      hybridization chain reaction (HCR-) FISH targeting nifH transcripts and 
      diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS 
      analysis of ANME-2b-SEEP-SRB1g consortia incubated with a headspace containing 
      CH(4) and (15)N(2) revealed differences in cellular (15)N-enrichment between the 
      two partners that varied between individual consortia, with SEEP-SRB1g cells 
      enriched in (15)N relative to ANME-2b in one consortium and the opposite pattern 
      observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of 
      nitrogen fixation, but with consortium-specific variation in whether the archaea 
      or bacterial partner is the dominant diazotroph.
FAU - Metcalfe, Kyle S
AU  - Metcalfe KS
AUID- ORCID: 0000-0002-2963-765X
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA. 
      ksmetcalfe@gmail.com.
FAU - Murali, Ranjani
AU  - Murali R
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
FAU - Mullin, Sean W
AU  - Mullin SW
AUID- ORCID: 0000-0002-6225-3279
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
FAU - Connon, Stephanie A
AU  - Connon SA
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
FAU - Orphan, Victoria J
AU  - Orphan VJ
AUID- ORCID: 0000-0002-5374-6178
AD  - Division of Geological and Planetary Sciences, California Institute of 
      Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA. 
      vorphan@gps.caltech.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20201015
PL  - England
TA  - ISME J
JT  - The ISME journal
JID - 101301086
RN  - 0 (RNA, Ribosomal, 16S)
RN  - OP0UW79H66 (Methane)
SB  - IM
MH  - Anaerobiosis
MH  - Archaea/genetics
MH  - Costa Rica
MH  - Geologic Sediments
MH  - In Situ Hybridization, Fluorescence
MH  - *Methane
MH  - *Nitrogen Fixation
MH  - Oxidation-Reduction
MH  - Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
PMC - PMC8027057
COIS- The authors declare that they have no conflict of interest.
EDAT- 2020/10/17 06:00
MHDA- 2021/04/22 06:00
PMCR- 2020/10/15
CRDT- 2020/10/16 05:47
PHST- 2020/04/10 00:00 [received]
PHST- 2020/08/21 00:00 [accepted]
PHST- 2020/07/28 00:00 [revised]
PHST- 2020/10/17 06:00 [pubmed]
PHST- 2021/04/22 06:00 [medline]
PHST- 2020/10/16 05:47 [entrez]
PHST- 2020/10/15 00:00 [pmc-release]
AID - 10.1038/s41396-020-00757-1 [pii]
AID - 757 [pii]
AID - 10.1038/s41396-020-00757-1 [doi]
PST - ppublish
SO  - ISME J. 2021 Feb;15(2):377-396. doi: 10.1038/s41396-020-00757-1. Epub 2020 Oct 
      15.