Recent studies have demonstrated the presence of abundant microbes in several subglacial environm... more Recent studies have demonstrated the presence of abundant microbes in several subglacial environments, including alpine and polar glaciers and the giant Antarctic subglacial lake, Lake Vostok. Some indirect isotopic and geochemical evidence indicate that microbial communities may be active in these cold, dark, extreme environments. We have been using molecular biology, microbiology, and geochemistry tools to correlate the identity of
Grímsvötn, an active volcano beneath the Vatnajökull glacier in Iceland, hosts a subglacial calde... more Grímsvötn, an active volcano beneath the Vatnajökull glacier in Iceland, hosts a subglacial caldera lake (Gudmundsson, Sigmundsson and Björnsson 1997 Nature 389, 954). Except for earlier geochemical measurements (Ágústsdóttir and Brantley 1994 J. Geophys. Res. 99, 9505), the lake and its possible biota have remained unexplored. In June 2002 we penetrated the 300-meter ice sheet over the lake using hot-water
This chapter examines experimental design considerations for a population-based approach for iden... more This chapter examines experimental design considerations for a population-based approach for identifying microorganisms involved in specific in situ functions. Although this chapter focuses on a particular population-based approach, many of the experimental design considerations discussed here apply to a wide range of rRNA gene-based population studies and sequence selective PCR assays. This chapter examines an experimental approach that uses the population-based strategy. The approach has the following three phases: (i) identifying populations of rRNA genes whose abundances correlate with the functional parameter, (ii) validating the rRNA gene correlates identified in phase I by using an independent quantitative assay, and (iii) isolating the microorganisms identified by the rRNA gene correlates and reintroducing them into the environment to assess their functions in situ. This approach was recently used to identify microorganisms that suppress the population development of the plant parasitic nematode Heterodera schachtii in southern California soil. Functional gradients are created by manipulating the microbial community with methods such as differential heat treatments, targeted antimicrobial agents, and nutritional amendments. Microbial community composition is examined by rRNA gene analysis. Nucleotide sequence analysis of rRNA gene clone libraries can be used to generate detailed depictions of microbial community composition. PCR assays can be validated by using them to amplify DNAs extracted from different environmental samples and then cloning and sequencing several randomly selected clones from each sample. The assays can be considered selective if they exclusively amplify the target sequence.
Recent studies have demonstrated the presence of abundant microbes in several subglacial environm... more Recent studies have demonstrated the presence of abundant microbes in several subglacial environments, including alpine and polar glaciers and the giant Antarctic subglacial lake, Lake Vostok. Some indirect isotopic and geochemical evidence indicate that microbial communities may be active in these cold, dark, extreme environments. We have been using molecular biology, microbiology, and geochemistry tools to correlate the identity of
Grímsvötn, an active volcano beneath the Vatnajökull glacier in Iceland, hosts a subglacial calde... more Grímsvötn, an active volcano beneath the Vatnajökull glacier in Iceland, hosts a subglacial caldera lake (Gudmundsson, Sigmundsson and Björnsson 1997 Nature 389, 954). Except for earlier geochemical measurements (Ágústsdóttir and Brantley 1994 J. Geophys. Res. 99, 9505), the lake and its possible biota have remained unexplored. In June 2002 we penetrated the 300-meter ice sheet over the lake using hot-water
This chapter examines experimental design considerations for a population-based approach for iden... more This chapter examines experimental design considerations for a population-based approach for identifying microorganisms involved in specific in situ functions. Although this chapter focuses on a particular population-based approach, many of the experimental design considerations discussed here apply to a wide range of rRNA gene-based population studies and sequence selective PCR assays. This chapter examines an experimental approach that uses the population-based strategy. The approach has the following three phases: (i) identifying populations of rRNA genes whose abundances correlate with the functional parameter, (ii) validating the rRNA gene correlates identified in phase I by using an independent quantitative assay, and (iii) isolating the microorganisms identified by the rRNA gene correlates and reintroducing them into the environment to assess their functions in situ. This approach was recently used to identify microorganisms that suppress the population development of the plant parasitic nematode Heterodera schachtii in southern California soil. Functional gradients are created by manipulating the microbial community with methods such as differential heat treatments, targeted antimicrobial agents, and nutritional amendments. Microbial community composition is examined by rRNA gene analysis. Nucleotide sequence analysis of rRNA gene clone libraries can be used to generate detailed depictions of microbial community composition. PCR assays can be validated by using them to amplify DNAs extracted from different environmental samples and then cloning and sequencing several randomly selected clones from each sample. The assays can be considered selective if they exclusively amplify the target sequence.
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