Quantification of total RNA by ethidium bromide fluorescence may not accurately reflect the RNA mass

BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature

This report describes BioDry (patent pending), a method for reliably preserving the biomolecules associated with aquatic microbial biomass samples, without the need of hazardous materials (e.g. liquid nitrogen, preservatives, etc.), freezing, or bulky storage/sampling equipment. Gel electrophoresis analysis of nucleic acid extracts from samples treated in the lab with the BioDry method indicated that molecular integrity was protected in samples stored at room temperature for up to 30 days. Analysis of 16S/18S rRNA genes for presence/absence and relative abundance of microorganisms using both 454-pyrosequencing and TRFLP profiling revealed statistically indistinguishable communities from control samples that were frozen in liquid nitrogen immediately after collection. Seawater and river water biomass samples collected with a portable BioDry “field unit", constructed from off-the-shelf materials and a battery-operated pumping system, also displayed high levels of community rRNA preservation, despite a slight decrease in nucleic acid recovery over the course of storage for 30 days. Functional mRNA and protein pools from the field samples were also effectively conserved with BioDry, as assessed by respective RT-PCR amplification and western blot of ribulose-1-5-bisphosphate carboxylase/oxygenase. Collectively, these results demonstrate that BioDry can adequately preserve a suite of biomolecules from aquatic biomass at ambient temperatures for up to a month, giving it great potential for high resolution sampling in remote locations or on autonomous platforms where space and power are limited.

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site

Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to uranium addition. In this study, uranium amendments were made to groundwater samples from a site of ongoing biostimulation with acetate. The active microbes in the planktonic phase were deduced by monitoring ribosomes production via RT-PCR. The results indicated several microorganisms were synthesizing ribosomes in proportion with uranium amendment up to 2 μM. Concentrations of U (VI) >2 μM were generally found to inhibit ribosome synthesis. Two active bacteria responding to uranium addition in the field were close relatives of Desulfobacter postgateii and Geobacter bemidjiensis. Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites.

Rapid screening of a large insert BAC library for specific 16S rRNA genes using TRFLP

It is widely believed that the vast majority of microbes in the environment have-yet-to-be cultured using standard techniques. Bulk DNA from microbial communities is therefore often cloned into large insert vectors (e.g. bacterial artificial chromosomes [BAC] or cosmids) in order to study the genetic properties of these as yet (un)-cultured bacteria. In a typical BAC experiment, tens of thousands of clones are generated with only a small fraction of colonies containing the target(s) of interest. Efficient screening methodologies are therefore needed to allow targeted clone isolation. In this paper, we describe a rapid, inexpensive protocol that allows for the identification of specific 16S ribosomal RNA genes in a metagenomic library arrayed into 384-well microtiter plates. The rapid screening protocol employs Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis to identify wells containing specific T-RF peaks. A nested approach using multiplexed samples of 384, 48, 8, and single colony analysis is described and applied in order to survey a BAC library generated from a marine microbial community off the coast of New Jersey. Screening revealed a total of 50 different 16 rRNA genes within the BAC library. Overall, the multiplexing format provided a simple, cost effective methodology for detecting clones bearing a target gene of interest in a large clone library. However, the limitations of screening BAC libraries using PCR methodologies and recommendations for improved screening efficiency using this approach are also discussed.

Detection and characterization of a dehalogenating microorganism by terminal restriction fragment length polymorphism fingerprinting of 16S rRNA in a sulfidogenic, 2-bromophenol-utilizing enrichment

Terminal restriction fragment length polymorphism analysis of reverse-transcribed 16S rRNA during periods of community flux was used as a tool to delineate the roles of the members of a 2-bromophenol-degrading, sulfate-reducing consortium. Starved, washed cultures were amended with 2-bromophenol plus sulfate, 2-bromophenol plus hydrogen, phenol plus sulfate, or phenol with no electron acceptor and were monitored for substrate use. In the presence of sulfate, 2-bromophenol and phenol were completely degraded. In the absence of sulfate, 2-bromophenol was dehalogenated and phenol accumulated. Direct terminal restriction fragment length polymorphism fingerprinting of the 16S rRNA in the various subcultures indicated that phylotype 2BP-48 (a Desulfovibrio-like sequence) was responsible for the dehalogenation of 2-bromophenol. A stable coculture was established which contained predominantly 2BP-48 and a second Desulfovibrio-like bacterium (designated BP212 based on terminal restriction fragment length polymorphism fingerprinting) that was capable of dehalogenating 2-bromophenol to phenol. Strain 2BP-48 in the coculture could couple reductive dehalogenation to growth with 2-bromophenol, 2,6-dibromophenol, or 2-iodophenol and lactate or formate as the electron donor. In addition to halophenols, strain 2BP-48 appears to use sulfate, sulfite, and thiosulfate as electron acceptors and is capable of simultaneous sulfidogenesis and reductive dehalogenation in the presence of sulfate.

Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth

Nine strains of marine Proteobacteria were assayed for nucleic acid content during non-steady-state growth to assess whether a species-specific growth rate based on rRNA content is feasible for environmental samples. The large and small ribosomal subunits and genomic DNA were quantified using image analysis. It was found that the maximal intracellular concentration of 16S rRNA during batch growth for the bacteria averaged 155 fg+/-60 (S.D.) per cell for eight of the nine marine bacteria in the exponential phase (with the exception of one strain, Pac 218). The dilution/decay of 16S rRNA/cell was rapid with a return to pre-shift up values within 6-12 h for all strains except Vibrio fisherii. An overall relationship between the RNA:DNA ratio and the specific growth rate for non-steady-state growth for all bacterial strains was not observed as previously described for other Proteobacteria during steady-state growth. However, a predictable relationship between rRNA content and growth rate for many isolates during batch growth was observed. Furthermore, the rapid kinetics of intracellular rRNA levels indicates it will be feasible to assess whether specific bacteria are in steady state or non-steady state in the marine environment. If the condition of steady state is met for a specific Proteobacterial group in an environmental sample, it will be possible to estimate species-specific growth rates by measuring rRNA content.

Ligand regulation of juvenile hormone binding protein mRNA in mutant Manduca sexta

Insect hemolymph juvenile hormone binding protein (hJHBP) regulates peripheral titers of its ligands, the juvenile hormones. In larvae of the black (bl) strain of the tobacco hornworm, Manduca sexta, treatment with small doses of juvenile hormone I (JH I) can also regulate titers of hJHBP. To further investigate this regulation, responsiveness of hJHBP mRNA expression to JH I was characterized in vivo. RNA analyzes revealed that transcript levels in fat body, the site of hJHBP synthesis, increased fivefold within several hours of treatment with physiological doses of hormone and remained elevated for approximately 16 h. Sensitivity to JH treatment was found to vary temporally. To ensure transcript identity, a wild-type cDNA clone and a bl RT-PCR fragment were sequenced and found to be 99% homologous. Together, these results suggest that JH participates in regulating expression of its transport protein in bl larvae by modifying the in vivo abundance of hJHBP's mRNA transcript.