Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments
Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-ox...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2016-04-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/1913.pdf |
| _version_ | 1797421738324131840 |
|---|---|
| author | Elizabeth Trembath-Reichert David H. Case Victoria J. Orphan |
| author_facet | Elizabeth Trembath-Reichert David H. Case Victoria J. Orphan |
| author_sort | Elizabeth Trembath-Reichert |
| collection | DOAJ |
| description | Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems. |
| first_indexed | 2024-03-09T07:21:46Z |
| format | Article |
| id | doaj.art-42ef61562aa24a09b18562b7b13f1ca7 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:21:46Z |
| publishDate | 2016-04-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-42ef61562aa24a09b18562b7b13f1ca72023-12-03T07:15:08ZengPeerJ Inc.PeerJ2167-83592016-04-014e191310.7717/peerj.1913Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichmentsElizabeth Trembath-Reichert0David H. Case1Victoria J. Orphan2Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United StatesDepartment of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United StatesDepartment of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United StatesMethane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.https://peerj.com/articles/1913.pdfMagneto-FISHCo-occurrence networkEarth microbiome projectiTag sequencingAnaerobic oxidation of methaneMicrobial association |
| spellingShingle | Elizabeth Trembath-Reichert David H. Case Victoria J. Orphan Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments PeerJ Magneto-FISH Co-occurrence network Earth microbiome project iTag sequencing Anaerobic oxidation of methane Microbial association |
| title | Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments |
| title_full | Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments |
| title_fullStr | Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments |
| title_full_unstemmed | Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments |
| title_short | Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments |
| title_sort | characterization of microbial associations with methanotrophic archaea and sulfate reducing bacteria through statistical comparison of nested magneto fish enrichments |
| topic | Magneto-FISH Co-occurrence network Earth microbiome project iTag sequencing Anaerobic oxidation of methane Microbial association |
| url | https://peerj.com/articles/1913.pdf |
| work_keys_str_mv | AT elizabethtrembathreichert characterizationofmicrobialassociationswithmethanotrophicarchaeaandsulfatereducingbacteriathroughstatisticalcomparisonofnestedmagnetofishenrichments AT davidhcase characterizationofmicrobialassociationswithmethanotrophicarchaeaandsulfatereducingbacteriathroughstatisticalcomparisonofnestedmagnetofishenrichments AT victoriajorphan characterizationofmicrobialassociationswithmethanotrophicarchaeaandsulfatereducingbacteriathroughstatisticalcomparisonofnestedmagnetofishenrichments |