Comparison of different primer sets for use in Automated Ribosomal Intergenic Spacer Analysis of complex bacterial communities.
ABSTRACT ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the façade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxi…
The genesis of actively growing siliceous stromatolites: Evidence from Lake Specchio di Venere, Pantelleria Island, Italy
This study documents the attributes of siliceous stromatolites growing in the Lake Specchio di Venere, on the volcanic island of Pantelleria, Italy, in a setting characterized by very shallow cold waters and pools and by scattered hydrothermal activity, which exhales mainly CO2, at emission point temperatures of 34 to 58 °C. The saturation indexes indicate that the lake waters are saturated with respect to tridymite, cristobalite, chalcedony and quartz, and slightly undersaturated with respect to amorphous silica. Common roughly laminated and poorly lithified stromatolites show scanning electron microscope (SEM) evidence for silicified microbial mat structures, including biofilms, filamento…
Geosphere-biosphere interactions in bio-activity volcanic lakes: Evidences from Hule and Rìo Cuarto (Costa Rica)
Hule and R ́ıo Cuarto are maar lakes located 11 and 18 km N of Poa ́s volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemica…
Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin
Urania basin in the deep Mediterranean Sea houses a lake that is >100 m deep, devoid of oxygen, 6 times more saline than seawater, and has very high levels of methane and particularly sulfide (up to 16 mM), making it among the most sulfidic water bodies on Earth. Along the depth profile there are 2 chemoclines, a steep one with the overlying oxic seawater, and another between anoxic brines of different density, where gradients of salinity, electron donors and acceptors occur. To identify and differentiate the microbes and processes contributing to the turnover of organic matter and sulfide along the water column, these chemoclines were sampled at a high resolution. Bacterial cell numbers…