PMID- 27303371
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20160615
LR  - 20201001
IS  - 1664-302X (Print)
IS  - 1664-302X (Electronic)
IS  - 1664-302X (Linking)
VI  - 7
DP  - 2016
TI  - Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for 
      Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the 
      Environment.
PG  - 774
LID - 10.3389/fmicb.2016.00774 [doi]
LID - 774
AB  - 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 
      (13)C-acetate, (15)N-ammonium, and (33)S-sulfate. Using a cluster analysis 
      technique based on fuzzy c-means to group cells according to their isotope 
      ((13)C/(12)C, (15)N/(14)N, and (33)S/(32)S) 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.
FAU - Dawson, Katherine S
AU  - Dawson KS
AD  - Division of Geological and Planetary Sciences, California Institute of Technology 
      Pasadena, CA, USA.
FAU - Scheller, Silvan
AU  - Scheller S
AD  - Division of Geological and Planetary Sciences, California Institute of Technology 
      Pasadena, CA, USA.
FAU - Dillon, Jesse G
AU  - Dillon JG
AD  - Department of Biological Sciences, California State University Long Beach Long 
      Beach, CA, USA.
FAU - Orphan, Victoria J
AU  - Orphan VJ
AD  - Division of Geological and Planetary Sciences, California Institute of Technology 
      Pasadena, CA, USA.
LA  - eng
PT  - Journal Article
DEP - 20160526
PL  - Switzerland
TA  - Front Microbiol
JT  - Frontiers in microbiology
JID - 101548977
PMC - PMC4881376
OTO - NOTNLM
OT  - NanoSIMS
OT  - cluster analysis
OT  - ecophysiology
OT  - stable isotope probing
OT  - sulfur-cycling
EDAT- 2016/06/16 06:00
MHDA- 2016/06/16 06:01
PMCR- 2016/05/26
CRDT- 2016/06/16 06:00
PHST- 2016/01/11 00:00 [received]
PHST- 2016/05/09 00:00 [accepted]
PHST- 2016/06/16 06:00 [entrez]
PHST- 2016/06/16 06:00 [pubmed]
PHST- 2016/06/16 06:01 [medline]
PHST- 2016/05/26 00:00 [pmc-release]
AID - 10.3389/fmicb.2016.00774 [doi]
PST - epublish
SO  - Front Microbiol. 2016 May 26;7:774. doi: 10.3389/fmicb.2016.00774. eCollection 
      2016.