Seasonal and Spatial Variability in Lake Michigan Sediment Small-Subunit rRNA Concentrations

Abstract

We have used molecular biological methods to study the distribution of microbial small-subunit rRNAs (SSU rRNAs), in relation to chemical profiles, in offshore Lake Michigan sediments. The sampling site is at a depth of 100 m, with temperatures of 2 to 4°C year-round. RNA extracted from sediment was probed with radiolabeled oligonucleotides targeting bacterial, archaeal, and eukaryotic SSU rRNAs, as well as with a universal probe. The coverage of these probes in relation to the present sequence database is discussed. Because ribosome production is growth rate regulated, rRNA concentrations are an indicator of the microbial populations active in situ. Over a 1-year period, changes in sedimentary SSU rRNA concentrations followed seasonal changes in surface water temperature and SSU rRNA concentration. Sedimentary depth profiles of oxygen, reduced manganese and iron, and sulfate changed relatively little from season to season, but the nitrate concentration was approximately fivefold higher in April and June 1997 than at the other times sampling was done. We propose that sediment microbial SSU rRNA concentrations at our sampling site are influenced by seasonal inputs from the water column, particularly the settling of the spring diatom bloom, and that the timing of this input may be modulated by grazers, such that ammonia becomes available to sediment microbes sooner than fresh organic carbon. Nitrate production from ammonia by autotrophic nitrifying bacteria, combined with low activity of heterotrophic denitrifying bacteria in the absence of readily degradable organic carbon, could account for the cooccurrence of high nitrate and low SSU rRNA concentrations.Molecular microbiological methods based on nucleic acid (RNA and DNA) extraction can yield information about the in situ distribution and activities of multiple microbial groups simultaneously from a relatively small volume of sample. They are especially useful for sediments, where numerous different species are present and chemical composition and microbial populations can change on a scale of millimeters to centimeters. Molecular methods are also free of the well-known biases associated with traditional culture-based approaches, such as the preferential recovery of species that are well adapted to laboratory conditions, although issues such as extraction efficiency have yet to be fully resolved.In this study, we have used oligonucleotide probes to characterize small-subunit rRNAs (SSU rRNAs) extracted from sediments at an offshore Lake Michigan site. SSU rRNA is an essential component of the ribosome, the RNA-protein complex responsible for protein synthesis in both prokaryotes and eukaryotes. rRNA-encoding genes (rDNAs) from thousands of species have now been sequenced and used to infer phylogenetic relationships based on nucleotide sequence divergence (67). Because the ribosome content generally increases with growth rate (reviewed in reference 33) and decreases with starvation (see, e.g., references 14, 23, and 46), rRNA quantitation by oligonucleotide prob...

Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)

“…A solution to this problem might be to target RNA molecules directly instead of their genes. As opposed to rRNA genes, significant quantities of rRNA are produced only in active microbes (46). The heterotrophic stramenopiles detected in our study were restricted to the chemocline (18 m) and lower redox transition zone (23 m) (Fig.…”

Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt

“…Euryarchaeota had previously been detected by phylogenetic analyses in sediments of temperate freshwater environments (e.g. MacGregor et al 1997, Abreu et al 2001 but not in the water column (Crump & Baross 2000). Recently, using universal archaeal primers developed for soil Archaea, Galand et al (2006) identified 2 novel euryarchaeotal groups, Rice Cluster-V (RC-V) and Lake Dagow Sediment (LDS), in the water of a large Arctic river, the Mackenzie River, during maximum open water conditions (October 2002).…”

“…16S rRNA sequences belonging to non-extremophilic aquatic Archaea were first discovered in the oxygenated water column of the Pacific and Atlantic Oceans (DeLong 1992, Fuhrman et al 1992; however, it is now clear that these organisms are ubiquitously present in marine systems (Massana et al 2000, Herndl et al 2005, Wuchter 2006, Wuchter et al 2006b), lakes (MacGregor et al 1997, Schleper et al 1997, Keough et al 2003) and rivers (Crump & Baross 2000, Abreu et al 2001, Bouvier & del Giorgio 2002, Galand et al 2006, 2008, Garneau et al 2006. Several studies have focused on the distribution of archaeal assemblages in the water column and sediments along salinity gradients in estuaries (Crump & Baross 2000, Abreu et al 2001, Bouvier & del Giorgio 2002.…”

Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea

“…The stratified water column in the Black Sea is believed to host more active and diverse microbial assemblages than anywhere else in the pelagic ocean (14). As such, the Black Sea is an excellent model system for studying oxic/anoxic interfaces, essentially stretching a chemocline normally encountered on the submillimeter scale over tens of meters.Although other oxic/anoxic regions exist and reports of molecular characterization of microbial communities from the Cariaco Trench (23) or sedimentary systems (12,22,40,42) have been published, few systematic profiles of the transition between oxic and anoxic bacterial communities beyond a domain-or group-specific approach have been reported. The purpose of this study was to characterize the Bacteria and Archaea populations in the Black Sea at a species-specific level and to correlate the vertical distribution of the various prokaryotic plankton with the profiles of terminal electron acceptors that occur throughout the oxic/anoxic chemocline.…”