PMID- 27693754
OWN - NLM
STAT- MEDLINE
DCOM- 20170921
LR  - 20231111
IS  - 1872-8359 (Electronic)
IS  - 0167-7012 (Print)
IS  - 0167-7012 (Linking)
VI  - 131
DP  - 2016 Dec
TI  - Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by 
      combining fluorescence in situ hybridization (FISH) with multiple-energy 
      micro-focused X-ray fluorescence (ME muXRF).
PG  - 23-33
LID - S0167-7012(16)30268-8 [pii]
LID - 10.1016/j.mimet.2016.09.018 [doi]
AB  - Metal(loid)-contamination of the environment due to anthropogenic activities is a 
      global problem. Understanding the fate of contaminants requires elucidation of 
      biotic and abiotic factors that influence metal(loid) speciation from molecular 
      to field scales. Improved methods are needed to assess micro-scale processes, 
      such as those occurring at biogeochemical interfaces between plant tissues, 
      microbial cells, and metal(loid)s. Here we present an advanced method that 
      combines fluorescence in situ hybridization (FISH) with synchrotron-based 
      multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME muXRF) to 
      examine colocalization of bacteria and metal(loid)s on root surfaces of plants 
      used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a 
      small root section using SytoBC nucleic acid stain and FISH probes targeting the 
      domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, 
      or Actinobacteria). The same root region was then analyzed for elemental 
      distribution and metal(loid) speciation of As and Fe using ME muXRF. The FISH and 
      ME muXRF images were aligned using ImageJ software to correlate microbiological 
      and geochemical results. Results from quantitative analysis of colocalization 
      show a significantly higher fraction of As colocalized with Fe-oxide plaques on 
      the root surfaces (fraction of overlap 0.49+/-0.19) than to bacteria (0.072+/-0.052) 
      (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, 
      known for their metal tolerance, had a higher correlation with both As and Fe 
      than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how 
      coupling these micro-techniques can expand our understanding of micro-scale 
      interactions between roots, metal(loid)s and microbes, information that should 
      lead to improved mechanistic models of metal(loid) speciation and fate.
CI  - Copyright A(c) 2016 Elsevier B.V. All rights reserved.
FAU - Honeker, Linnea K
AU  - Honeker LK
AD  - Department of Soil, Water, and Environmental Science, P.O. Box 210038, University 
      of Arizona, Tucson, AZ 85721, United States. Electronic address: 
      linneah@email.arizona.edu.
FAU - Root, Robert A
AU  - Root RA
AD  - Department of Soil, Water, and Environmental Science, P.O. Box 210038, University 
      of Arizona, Tucson, AZ 85721, United States. Electronic address: 
      rroot@email.arizona.edu.
FAU - Chorover, Jon
AU  - Chorover J
AD  - Department of Soil, Water, and Environmental Science, P.O. Box 210038, University 
      of Arizona, Tucson, AZ 85721, United States. Electronic address: 
      chorover@email.arizona.edu.
FAU - Maier, Raina M
AU  - Maier RM
AD  - Department of Soil, Water, and Environmental Science, P.O. Box 210038, University 
      of Arizona, Tucson, AZ 85721, United States. Electronic address: 
      rmaier@ag.arizona.edu.
LA  - eng
GR  - P30 ES006694/ES/NIEHS NIH HHS/United States
GR  - P42 ES004940/ES/NIEHS NIH HHS/United States
GR  - T32 ES007091/ES/NIEHS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20160929
PL  - Netherlands
TA  - J Microbiol Methods
JT  - Journal of microbiological methods
JID - 8306883
RN  - 0 (DNA, Bacterial)
RN  - 0 (Metals)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (Soil Pollutants)
SB  - IM
MH  - Actinobacteria/genetics/isolation & purification
MH  - Bacteria/classification/genetics/*growth & development/isolation & purification
MH  - DNA, Bacterial
MH  - Electron Probe Microanalysis/methods
MH  - Environmental Monitoring/methods
MH  - Gammaproteobacteria/genetics/isolation & purification
MH  - Genes, Bacterial
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Metals/*analysis
MH  - Phylogeny
MH  - Plant Roots/*chemistry/*microbiology/*radiation effects
MH  - Plants/chemistry/microbiology
MH  - RNA, Ribosomal, 16S/genetics
MH  - Soil Microbiology
MH  - Soil Pollutants/analysis
MH  - Synchrotrons/instrumentation
MH  - X-Rays
PMC - PMC5127750
MID - NIHMS821817
OTO - NOTNLM
OT  - FISH
OT  - Phytostabilization
OT  - Root iron plaques
OT  - Root-colonizing bacteria
OT  - XRF
OT  - iTag sequencing
EDAT- 2016/10/26 06:00
MHDA- 2017/09/22 06:00
PMCR- 2017/12/01
CRDT- 2016/11/07 06:00
PHST- 2016/07/21 00:00 [received]
PHST- 2016/09/26 00:00 [revised]
PHST- 2016/09/26 00:00 [accepted]
PHST- 2016/10/26 06:00 [pubmed]
PHST- 2017/09/22 06:00 [medline]
PHST- 2016/11/07 06:00 [entrez]
PHST- 2017/12/01 00:00 [pmc-release]
AID - S0167-7012(16)30268-8 [pii]
AID - 10.1016/j.mimet.2016.09.018 [doi]
PST - ppublish
SO  - J Microbiol Methods. 2016 Dec;131:23-33. doi: 10.1016/j.mimet.2016.09.018. Epub 
      2016 Sep 29.