US Long-Term Ecological Research Network

Microbial Observatory at North Temperate Lakes LTER Microbial Community Composition in Lakes - Taxonomic characteristics of the clones at North Temperate Lakes LTER 2000 - 2007

Abstract
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by taxonomic characteristics of the clone allows the user to retrieve clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation). The data can be filtered by clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class). The output includes links to individual clone records, which contain more detailed information about how the clone was generated (researcher, library ID, project ID, primer sets used, etc.).
Dataset ID
83
Date Range
-
Maintenance
completed
Metadata Provider
Methods
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by taxonomic characteristics of the clone allows the user to retrieve clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation). The data can be filtered by clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class). The output includes links to individual clone records, which contain more detailed information about how the clone was generated (researcher, library ID, project ID, primer sets used, etc.).
NTL Keyword
Short Name
MOCLON2
Version Number
3

Microbial Observatory at North Temperate Lakes LTER Microbial Community Composition in lakes - Ecological characteristics of the sample at North Temperate Lakes LTER 2002 - 2007

Abstract
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by ecological characteristics of the sample allows the user to retrieve sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The data can be filtered by lake name, sample date, lake information (region, type, size, depth), and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The output includes links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample
Dataset ID
81
Date Range
-
Maintenance
completed
Metadata Provider
Methods
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by ecological characteristics of the sample allows the user to retrieve sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The data can be filtered by lake name, sample date, lake information (region, type, size, depth), and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The output includes links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample
NTL Keyword
Short Name
MOENV
Version Number
21

Microbial Observatory at North Temperate Lakes LTER Microbial Bacterial Respiration in Lakes at North Temperate Lakes LTER 2000 - 2002

Abstract
Lake Mendota, Madison, Wisconsin. Bacterial respiration of bacteria passing a 70 micron mesh. Based on bacterial growth efficiency determined empirically on bacteria production and oxygen depletion on microbes passing a 1 micron mesh. All samples from integrated sample of epilimnion to thermocline or 12 meters, which ever was more shallow. Method based on Roland, F. and J. J. Cole. 1999. Regulation of bacterial growth efficiency in a large turbid estuary. Aquatic Microbial Ecology 20:31-38 Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season Number of sites: 1
Dataset ID
51
Date Range
-
LTER Keywords
Maintenance
completed
Metadata Provider
Methods
Bacterial respiration of bacteria passing a 70 micron mesh. Based on bacterial growth efficiency determined empirically on bacteria production and oxygen depletion on microbes passing a 1 micron mesh. All samples from integrated sample of epilimnion to thermocline or 12 meters, which ever was more shallow. Method based on Roland, F. and J. J. Cole. 1999. Regulation of bacterial growth efficiency in a large turbid estuary. Aquatic Microbial Ecology 20:31-38 Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season Number of sites: 1
Short Name
MOBR1
Version Number
4

Microbial Observatory at North Temperate Lakes LTER Microbial Bacterial Production in Lakes at North Temperate Lakes LTER 2000 - 2002

Abstract
Net production of bacteria passing a 70 micron mesh, or bacteria passing a 1 micron mesh, calculated incorporation of 3H labeled leucine into cell proteins. Method based on microcentrifuge method of Smith, David C., and Farooq Azam. 1992. A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine, Marine Microbial Food Webs 6(2):107-114. Nanomolar treatments refer to leucine concentration for calculation of isotopic dilution and necessary leucine concentration to saturate uptake into bacterial cells. For a good example on how to calculate isotopic dilution see Pace. Michael L., and Jonathan J. Cole. Primary and bacterial production in lakes: are they coupled over depth? Plankton Research 16(6):661-672. Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season Number of sites: 4
Dataset ID
50
Date Range
-
LTER Keywords
Maintenance
completed
Metadata Provider
Methods
Net production of bacteria passing a 70 micron mesh, or bacteria passing a 1 micron mesh, calculated incorporation of 3H labeled leucine into cell proteins. Method based on microcentrifuge method of Smith, David C., and Farooq Azam. 1992. A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine, Marine Microbial Food Webs 6(2):107-114. Nanomolar treatments refer to leucine concentration for calculation of isotopic dilution and necessary leucine concentration to saturate uptake into bacterial cells. For a good example on how to calculate isotopic dilution see Pace. Michael L., and Jonathan J. Cole. Primary and bacterial production in lakes: are they coupled over depth? Plankton Research 16(6):661-672. Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season Number of sites: 4
Short Name
MOBP1
Version Number
4

Microbial Observatory at North Temperate Lakes LTER Summary of Microbial Activity 2000 - 2002

Abstract
Summary of Microbial Observatory data from the bacterial production, planktonic respiration and alakline phosphatase activity databases, plus bacterial cell counts from epifluorescence microscopy using DAPI cell stain. Information on integrated sample depth and incubation temperature is also included Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season Number of sites: 4
Core Areas
Dataset ID
46
Date Range
-
LTER Keywords
Maintenance
completed
Metadata Provider
Methods
this is a summary dataset based on knb-lter-ntl.45, knb-later-ntl.50, and knb-lter-ntl.51 where the methods are described in detail. in addition bacterial cell counts were optained from epifluorescence microscopy using DAPI cell stain.
Short Name
MOACT2
Version Number
4
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