Application of bead array technology to community dynamics of marine phytoplankton

Abstract

Studies of the dynamics of marine microplanktonic systems have been hampered by a lack of high-throughput technologies for the simultaneous identification and quantification of the many taxa comprising such communities. To address this problem, we describe a DNA-hybridizationbased method of analysis employing bead array technology. Species-and/or genus-specific probes for 8 phytoplankton taxa were designed and applied to the microplankton community sampled from coastal waters off La Jolla, California, over an exploratory time series 10 d in length. Bulk DNA extractions from 1 l of seawater were used without PCR amplification. Taxa analyzed comprised 4 dinoflagellates, 3 diatoms, and 1 coccolithophorid. The results demonstrated that specifically targeted oligonucleotide probes can be used in this fashion with a high degree of binding-specificity, dependent on hybridization temperature, and that standard curves relative to target-cell concentration can be constructed. The use of 2 different probes for each taxon can provide added confidence that probes are taxon-specific. Further, single-species assays and multiplexed assays were generally in good agreement, as were assays of replicate seawater samples. Once sets of probes are developed for particular groups of taxa, the bead array system appears to provide a technological platform with great promise for high-throughput analyses of microplanktonic communities.

Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays

“…Bandyopadhyay et al 2007) and environmental (Baums et al 2007) samples. Applications of this technology have also been used to determine bacteria and phytoplankton abundances from the marine environment (Ellison & Burton 2005, Scorzetti et al 2009, Mayali et al 2010.…”

“…Bandyopadhyay et al 2007) and environmental (Baums et al 2007) samples. Applications of this technology have also been used to determine bacteria and phytoplankton abundances from the marine environment (Ellison & Burton 2005, Scorzetti et al 2009, Mayali et al 2010.For the present study, we developed probes for bead-array assays based on rpoC1 gene sequences. We did this to assess changes in the diversity and abundance of marine Synechococcus from a 1 yr timeseries of coastal samples and along a coastal to openocean transect from the Southern California Bight in the northeastern Pacific Ocean.…”

Application of environmental sample processor (ESP) methodology for quantifying Pseudo‐nitzschia australis using ribosomal RNA‐targeted probes in sandwich and fluorescent in situ hybridization formats

“…A variety of molecular probe assays applied in cell-free and whole-cell formats aid in the detection and quantification of Pseudo-nitzschia species (e.g., Scholin et al 2003), as well as a wide range of naturally occurring microorganisms. Such approaches include fluorescent in situ hybridization (FISH) (e.g., Lim et al 1993;Groben et al 2004), fluorescently labeled antibodies and lectins (e.g., Vrieling et al 1994;Sako et al 1996;Rhodes 1998;, sandwich hybridization (e.g., Scholin et al 1996;Tyrrell et al 2002), probe arrays (e.g., Loy et al 2002;Metfies and Medlin 2004;Ellison and Burton 2005), and a variety of nucleic acid amplification methods that target specific signature sequences (e.g., Bowers et al 2000;Penna and Magnani 2000;Bolch 2001;Litaker and Tester 2002;Casper et al 2004).…”

Luminex detection of fecal indicators in river samples, marine recreational water, and beach sand

“…The Luminex system has primarily been used for clinical applications (Dunbar et al, 2003;Dunbar, 2006), although some environmental applications have been reported (Ellison and Burton, 2005;Spiro et al, 2000;Spiro and Lowe, 2002). Any molecule or chemical group that can be recognized by reactive or complementary functional groups can be immobilized to the surface of the microspheres.…”