Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

Katherine S. Dawson, Silvan Scheller, Jesse G. Dillon, Victoria J. Orphan

Research output: Contribution to journalArticle

5 Citations (Scopus)

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 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) 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.

Original languageEnglish (US)
Article number774
JournalFrontiers in Microbiology
Volume7
Issue numberMAY
DOIs
StatePublished - Jan 1 2016

Fingerprint

Secondary Ion Mass Spectrometry
Sulfur
Isotopes
Cluster Analysis
Biofilms
Fluorescence In Situ Hybridization
Deltaproteobacteria
Population
Phenotype
Gammaproteobacteria
Ammonium Sulfate
Dermatoglyphics
Metabolic Networks and Pathways
Microscopy
Respiration
Acetates

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Microbiology (medical)

Keywords

  • Cluster analysis
  • Ecophysiology
  • NanoSIMS
  • Stable isotope probing
  • Sulfur-cycling

Cite this

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Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment. / Dawson, Katherine S.; Scheller, Silvan; Dillon, Jesse G.; Orphan, Victoria J.

In: Frontiers in Microbiology, Vol. 7, No. MAY, 774, 01.01.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

AU - Dawson, Katherine S.

AU - Scheller, Silvan

AU - Dillon, Jesse G.

AU - Orphan, Victoria J.

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KW - NanoSIMS

KW - Stable isotope probing

KW - Sulfur-cycling

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