PMID- 23892743
OWN - NLM
STAT- MEDLINE
DCOM- 20140307
LR  - 20221207
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Print)
IS  - 0099-2240 (Linking)
VI  - 79
IP  - 19
DP  - 2013 Oct
TI  - New methods for analysis of spatial distribution and coaggregation of microbial 
      populations in complex biofilms.
PG  - 5978-87
LID - 10.1128/AEM.01727-13 [doi]
AB  - In biofilms, microbial activities form gradients of substrates and electron 
      acceptors, creating a complex landscape of microhabitats, often resulting in 
      structured localization of the microbial populations present. To understand the 
      dynamic interplay between and within these populations, quantitative measurements 
      and statistical analysis of their localization patterns within the biofilms are 
      necessary, and adequate automated tools for such analyses are needed. We have 
      designed and applied new methods for fluorescence in situ hybridization (FISH) 
      and digital image analysis of directionally dependent (anisotropic) multispecies 
      biofilms. A sequential-FISH approach allowed multiple populations to be detected 
      in a biofilm sample. This was combined with an automated tool for 
      vertical-distribution analysis by generating in silico biofilm slices and the 
      recently developed Inflate algorithm for coaggregation analysis of microbial 
      populations in anisotropic biofilms. As a proof of principle, we show distinct 
      stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha 
      subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three 
      different types of wastewater biofilms, suggesting niche differentiation between 
      the N. oligotropha subclusters, which could explain their coexistence in the same 
      biofilms. Coaggregation analysis showed that N. oligotropha subcluster II 
      aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot 
      plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), 
      but not in a full-scale NTF, indicating important ecophysiological differences 
      between these phylogenetically closely related subclusters. By using 
      high-resolution quantitative methods applicable to any multispecies biofilm in 
      general, the ecological interactions of these complex ecosystems can be 
      understood in more detail.
FAU - Almstrand, Robert
AU  - Almstrand R
AD  - Department of Chemistry and Molecular Biology, Microbiology, University of 
      Gothenburg, Goteborg, Sweden.
FAU - Daims, Holger
AU  - Daims H
FAU - Persson, Frank
AU  - Persson F
FAU - Sorensson, Fred
AU  - Sorensson F
FAU - Hermansson, Malte
AU  - Hermansson M
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20130726
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
RN  - 0 (Waste Water)
SB  - IM
MH  - Algorithms
MH  - Automation, Laboratory/*methods
MH  - *Bacterial Adhesion
MH  - *Bacterial Physiological Phenomena
MH  - Biofilms/*growth & development
MH  - Image Processing, Computer-Assisted/*methods
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Microbiological Techniques/*methods
MH  - Wastewater/microbiology
PMC - PMC3811375
EDAT- 2013/07/31 06:00
MHDA- 2014/03/08 06:00
PMCR- 2013/10/01
CRDT- 2013/07/30 06:00
PHST- 2013/07/30 06:00 [entrez]
PHST- 2013/07/31 06:00 [pubmed]
PHST- 2014/03/08 06:00 [medline]
PHST- 2013/10/01 00:00 [pmc-release]
AID - AEM.01727-13 [pii]
AID - 01727-13 [pii]
AID - 10.1128/AEM.01727-13 [doi]
PST - ppublish
SO  - Appl Environ Microbiol. 2013 Oct;79(19):5978-87. doi: 10.1128/AEM.01727-13. Epub 
      2013 Jul 26.