Abundance and diversity of Planctomycetes in a Tyrrhenian coastal system of central Italy

Abstract

The phylum Planctomycetes is involved in important processes, such as the mineralization of algal biomass and the removal of nitrogen. Using a combination of 16S rRNA sequence analysis and in situ hybridization, we analyzed the diversity and dynamics of Planctomycetes in a shallow meso-eutrophic lake, Lago di Paola, Italy. Planctomycetes detected by the probe PLA46 accounted for 1 to 5% of prokaryotic picoplankton. Abundances were higher in the coastal lake than in the adjacent marine waters. In the surface waters of the lake, the numbers of Planctomycetes fluctuated greatly, reaching a maximum of 1.5 × 10 6 cells ml −1 in July. The hypoxic bottom waters had less variable cell abundances. The Planctomycetes counts were positively correlated with chlorophyll a concentrations, confirming the role of this phylum in the degradation of algal biomass. We obtained 70 almost full-length 16S rRNA gene sequences of Planctomycetes from 2 libraries. Four distinct clades could be identified. The Pirellula-related group F and the uncultured Planctomycetes group B both had the highest identity with sequences retrieved from marine habitats, whereas the Pirellula-related group E was affiliated with sequences known from freshwater and brackish water environments. The Planctomyces-related group A seems to have a wide habitat range. Catalyzed reported deposition fluorescence in situ hybridization with newly developed probes revealed abundances of the 4 clades in surface and bottom waters ranging from 1 × 10 3 to 5 × 10 4 cells ml −1. Together, the 4 clade-specific probes identified only about a quarter of the Planctomycetes detected by probe PLA46. This indicates that the diversity of Planctomycetes has not yet been fully explored. KEY WORDS: Coastal lake ecology · Planctomycetes · Bacterial diversity · FISH · CARD-FISH · 16S rRNA gene sequencing Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 65: [129][130][131][132][133][134][135][136][137][138][139][140][141] 2011 Most cultured strains have been isolated from marine, freshwater and terrestrial habitats (Bauld & Staley 1976, Franzmann & Skerman 1984, Giovannoni et al. 1987, Schlesner 1994, Wang et al. 2002. Despite the recent success in isolating new members of the Planctomycetes from aquatic (Fukunaga et al. 2009, Winkelmann & Harder 2009) and terrestrial habitats (Kulichevskaya et al. 2007(Kulichevskaya et al. , 2008(Kulichevskaya et al. , 2009, the phylum continues to be one of the least represented in microbial culture collections. Planctomycetes are most commonly heterotrophs (Fuerst 1995), with the notable exception being the autotrophic anammox bacteria, which catalyze anaerobic ammonia oxidation with nitrite (Strous et al. 1999).Studies based on molecular methods, such as 16S ribosomal RNA (rRNA) gene sequencing and fluorescence in situ hybridization (FISH), have revealed a broad distribution of Planctomycetes in aquatic environments. They have been detected in the marine water column (DeLong et al. 1993, Vergin...

Temporal and Vertical Variation in Microbial Community Composition in Response to Physicochemical Characteristics in a Water Column of Highly Eutrophied Jinhae Bay, South Korea

“…Some of the OTUs predominantly seen at low DO concentrations in this study have been reported in other studies on aquatic marine environments. Planctomyces and unclassified Pirellulaceae belong to Planctomycetes, whose abundance correlates with change in oxygen conditions [Pizzetti et al, 2011]. Furthermore, Planctomyces have been reported to use ammonium to reduce nitrite during anaerobic ammonium oxidation [Schmidt et al, 2002].…”

Bringing Planctomycetes into pure culture

“…These organisms are widespread and have been described in many marine environments, including brackish and marine water from the Kiel Fjord on the Baltic Sea (Schlesner et al, 2004), meso-eutrophic lakes (Pizzetti et al, 2011b), other European seas (Winkelmann and Harder, 2009; Pizzetti et al, 2011a), marine snow (DeLong et al, 1993; Vergin et al, 1998), diatom blooms in Oregon coastal waters (Morris et al, 2006), tissues of the Mediterranean sponge Aplysina aerophoba (Pimentel-Elardo et al, 2003; Gade et al, 2004), and the giant tiger prawn, Penaeus monodon (Fuerst et al, 1991) as well as the biofilm of Laminaria hyperborea (Bengtsson and Ovreas, 2010). However, the only taxonomically described organism is Pirellula sp.…”

Physiologic and metabolic characterization of a new marine isolate (BM39) of Pantoea sp. producing high levels of exopolysaccharide

“…Sea salinity in BM39 sampling area is around 38 ‰ all the year [42,43] and was measured at 37.8 ‰ during sampling.…”