A comparative assessment of molecular biological and direct microscopic techniques for assessing aquatic systems

Charles W Knapp, David L Findlay, Karen A Kidd, David W. Graham

Research output: Contribution to journalArticle

Abstract

Molecular techniques have clear value for community characterization; however, almost all previous datasets are based upon non-molecular measurements and it is hard to compare "old" data with "new" data because few correlations have been made. Therefore, the purpose of this evaluation was to simultaneously use molecular and non-molecular methods within the same sampling program to determine how data compare. Three methods were used for characterizing microbial populations in Lake 260 (L260) at Experimental Lakes Area (Ontario, Canada) during a whole-lake exposure study. Methods included whole-cell microscopic counts (for bacteria, cyanobacteria, algae and zooplankton), chlorophyll a, and small sub-unit (ssu)-rRNA hybridization using EUB-338, EUB-785, CYAN-785-a/b, EUCA-1379 and UNIV-1390 gene probes. Strong correlations were found between the EUB-785 probe signal and "bacteria minus cyanobacteria" direct counts, and the EUB-338 probe signal and "bacteria plus cyanobacteria" counts. Furthermore, the difference in probe signal between EUB-338 and EUB-785 (a presumptive signature for cyanobacteria and plastids) correlated with cyanobacterial direct counts and also with chlorophyll a. However, EUCA-1379 probe signal did not correlate with algae counts, and UNIV-1390 probe signal only correlated with total bacteria counts. Results suggest that, although ssu-rRNA methods are fast, reproducible, and specifically detect "viable" organisms, their use may be limited to non-eukaryotic populations unless new probes are developed that are more specific.
LanguageEnglish
Pages465-473
Number of pages8
JournalEnvironmental Monitoring and Assessment
Volume145
Issue number1-3
DOIs
Publication statusPublished - Oct 2008

Fingerprint

probe
cyanobacterium
Bacteria
Lakes
bacterium
Chlorophyll
Algae
chlorophyll a
lake
alga
plastid
zooplankton
Genes
Sampling
method
Cyanobacteria
gene
sampling

Keywords

  • 16S rRNA
  • algae
  • bacteria
  • chlorophyll
  • hybridization
  • microscopy
  • plastid
  • Whole-lake

Cite this

@article{6a21747e04334022b8ddaa3e19528b6d,
title = "A comparative assessment of molecular biological and direct microscopic techniques for assessing aquatic systems",
abstract = "Molecular techniques have clear value for community characterization; however, almost all previous datasets are based upon non-molecular measurements and it is hard to compare {"}old{"} data with {"}new{"} data because few correlations have been made. Therefore, the purpose of this evaluation was to simultaneously use molecular and non-molecular methods within the same sampling program to determine how data compare. Three methods were used for characterizing microbial populations in Lake 260 (L260) at Experimental Lakes Area (Ontario, Canada) during a whole-lake exposure study. Methods included whole-cell microscopic counts (for bacteria, cyanobacteria, algae and zooplankton), chlorophyll a, and small sub-unit (ssu)-rRNA hybridization using EUB-338, EUB-785, CYAN-785-a/b, EUCA-1379 and UNIV-1390 gene probes. Strong correlations were found between the EUB-785 probe signal and {"}bacteria minus cyanobacteria{"} direct counts, and the EUB-338 probe signal and {"}bacteria plus cyanobacteria{"} counts. Furthermore, the difference in probe signal between EUB-338 and EUB-785 (a presumptive signature for cyanobacteria and plastids) correlated with cyanobacterial direct counts and also with chlorophyll a. However, EUCA-1379 probe signal did not correlate with algae counts, and UNIV-1390 probe signal only correlated with total bacteria counts. Results suggest that, although ssu-rRNA methods are fast, reproducible, and specifically detect {"}viable{"} organisms, their use may be limited to non-eukaryotic populations unless new probes are developed that are more specific.",
keywords = "16S rRNA, algae, bacteria, chlorophyll, hybridization, microscopy, plastid, Whole-lake",
author = "Knapp, {Charles W} and Findlay, {David L} and Kidd, {Karen A} and Graham, {David W.}",
year = "2008",
month = "10",
doi = "10.1007/s10661-007-0055-y",
language = "English",
volume = "145",
pages = "465--473",
journal = "Environmental Monitoring and Assessment",
issn = "0167-6369",
number = "1-3",

}

A comparative assessment of molecular biological and direct microscopic techniques for assessing aquatic systems. / Knapp, Charles W; Findlay, David L; Kidd, Karen A; Graham, David W.

In: Environmental Monitoring and Assessment, Vol. 145, No. 1-3, 10.2008, p. 465-473.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A comparative assessment of molecular biological and direct microscopic techniques for assessing aquatic systems

AU - Knapp, Charles W

AU - Findlay, David L

AU - Kidd, Karen A

AU - Graham, David W.

PY - 2008/10

Y1 - 2008/10

N2 - Molecular techniques have clear value for community characterization; however, almost all previous datasets are based upon non-molecular measurements and it is hard to compare "old" data with "new" data because few correlations have been made. Therefore, the purpose of this evaluation was to simultaneously use molecular and non-molecular methods within the same sampling program to determine how data compare. Three methods were used for characterizing microbial populations in Lake 260 (L260) at Experimental Lakes Area (Ontario, Canada) during a whole-lake exposure study. Methods included whole-cell microscopic counts (for bacteria, cyanobacteria, algae and zooplankton), chlorophyll a, and small sub-unit (ssu)-rRNA hybridization using EUB-338, EUB-785, CYAN-785-a/b, EUCA-1379 and UNIV-1390 gene probes. Strong correlations were found between the EUB-785 probe signal and "bacteria minus cyanobacteria" direct counts, and the EUB-338 probe signal and "bacteria plus cyanobacteria" counts. Furthermore, the difference in probe signal between EUB-338 and EUB-785 (a presumptive signature for cyanobacteria and plastids) correlated with cyanobacterial direct counts and also with chlorophyll a. However, EUCA-1379 probe signal did not correlate with algae counts, and UNIV-1390 probe signal only correlated with total bacteria counts. Results suggest that, although ssu-rRNA methods are fast, reproducible, and specifically detect "viable" organisms, their use may be limited to non-eukaryotic populations unless new probes are developed that are more specific.

AB - Molecular techniques have clear value for community characterization; however, almost all previous datasets are based upon non-molecular measurements and it is hard to compare "old" data with "new" data because few correlations have been made. Therefore, the purpose of this evaluation was to simultaneously use molecular and non-molecular methods within the same sampling program to determine how data compare. Three methods were used for characterizing microbial populations in Lake 260 (L260) at Experimental Lakes Area (Ontario, Canada) during a whole-lake exposure study. Methods included whole-cell microscopic counts (for bacteria, cyanobacteria, algae and zooplankton), chlorophyll a, and small sub-unit (ssu)-rRNA hybridization using EUB-338, EUB-785, CYAN-785-a/b, EUCA-1379 and UNIV-1390 gene probes. Strong correlations were found between the EUB-785 probe signal and "bacteria minus cyanobacteria" direct counts, and the EUB-338 probe signal and "bacteria plus cyanobacteria" counts. Furthermore, the difference in probe signal between EUB-338 and EUB-785 (a presumptive signature for cyanobacteria and plastids) correlated with cyanobacterial direct counts and also with chlorophyll a. However, EUCA-1379 probe signal did not correlate with algae counts, and UNIV-1390 probe signal only correlated with total bacteria counts. Results suggest that, although ssu-rRNA methods are fast, reproducible, and specifically detect "viable" organisms, their use may be limited to non-eukaryotic populations unless new probes are developed that are more specific.

KW - 16S rRNA

KW - algae

KW - bacteria

KW - chlorophyll

KW - hybridization

KW - microscopy

KW - plastid

KW - Whole-lake

UR - http://dx.doi.org/10.1007/s10661-007-0055-y

U2 - 10.1007/s10661-007-0055-y

DO - 10.1007/s10661-007-0055-y

M3 - Article

VL - 145

SP - 465

EP - 473

JO - Environmental Monitoring and Assessment

T2 - Environmental Monitoring and Assessment

JF - Environmental Monitoring and Assessment

SN - 0167-6369

IS - 1-3

ER -