Journal article
Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment
Frontiers in microbiology, v 7(MAY), 774
26 May 2016
PMID: 27303371
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with C-13-acetate, N-15-ammonium, and S-33-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (C-13/C-12, N-15/N-14, and S-33/S-32) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned 2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.
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Details
- Title
- Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment
- Creators
- Katherine S. Dawson - California Institute of TechnologySilvan Scheller - California Institute of TechnologyJesse G. Dillon - California State University, Long BeachVictoria J. Orphan - California Institute of Technology
- Publication Details
- Frontiers in microbiology, v 7(MAY), 774
- Publisher
- Frontiers Media Sa
- Number of pages
- 15
- Grant note
- NNA13AA92A / NASA Astrobiology Institute EAR-1123391 / National Science Foundation; National Science Foundation (NSF) 1124398 / Directorate For Geosciences; Division Of Earth Sciences; National Science Foundation (NSF); NSF - Directorate for Geosciences (GEO) GBIVIF 3306 / Gordon and Betty Moore Foundation; Gordon & Betty Moore Foundation
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Environmental Biogeochemistry
- Web of Science ID
- WOS:000376485300001
- Scopus ID
- 2-s2.0-84973473439
- Other Identifier
- 991022207051404721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Microbiology