Microbial Community Biomarker in Barnegat Bay Microbial Community Biomarker in Barnegat Bay Evangelina Pena 1 , Lora McGuinness 1 , Gary Taghon 1 , Lee Kerkhof 1 Introduction Efforts to remediate anthropogenic impacts in estuarine environments would benefit from a community bio-indicator with a rapid response time to demonstrate effectiveness. In this project, sediment samples were collected from specific sites in Barnegat Bay, N.J., and microbial communities were assayed as potential bio-indicators. Single-celled organisms were analyzed since they have a short lifespan and can respond rapidly to changes within their environment. To better understand these microbial populations, an assessment of ribosomal RNA genes and the functional gene (nosZ-nitrous oxide reductase) was performed to identify Bacteria, Eukaryotes, Archaea, and denitrifying populations. Preliminary results indicated that the microbiota correlated with environmental factors such as salinity, dissolved oxygen and latitude. These results suggest that single-celled organisms can be effective biomarkers for water quality within Barnegat Bay or in other coastal systems, which are critical habitats for marine and human populations. Methods Initially, 100 sediment samples were collected for a more comprehensive study on the ecological health of Barnegat Bay in 2012. For this assessment we selected 16 subsamples based on dissolved oxygen level and distribution throughout the bay. Sediments were obtained by vanVeen grab, the 2 top centimeters were homogenized transported back to the laboratory under ice and stored in -20º C until processing. Frozen sediments were extracted by phenol-chloroform method (McGuinness et. al, 2006). Target genes were amplified by PCR using domain-specific ribosomal primers (Corredor, 2005) and universal primers for nosZ (Scala and Kerkhof, 2000). T-RFLP fingerprinting was completed utilizing Mnl I, Hae III and HhaI enzymes (McGuinness et. al, 2006). Rutgers University 1 , New Brunswick, New Jersey 08901 Contact Information: Evangelina Pena [email protected] Institute of Marine and Coastal Sciences Rutgers University New Brunswick, New Jersey 08901 Results Sample Replicability To test the homogeneity of our samples in the same site, we conducted two fully separate experiments and compared their fingerprints. 16S PCR Gel Amplification λ B30 B31 B33 B44 B68 B73 16s DNA Extraction Gel Amplification λ B17 B30 B31 16S DNA Extraction Gel Amplification 16S rRNA Genes Site 1 Site 2 Site 3 Site 4 Site 5 Site 6 Site 7 Site 8 Site 8 Site 1 Site 2 Site 4 Site 5 Site 6 Site 7 Figure 1 Figure 2 Conclusions Distinct clusters were observed between the Northern and Southern part of the bay for nearly all target genes. Samples with close proximity but different chemical parameters had a high percentage similarity. Bacteria – Northern and Southern parts of the bay have a similarity ranging from 65-90%. Bacterial communities were the most diverse throughout the transect and displayed in low oxygen clusters. Eukaryotes – Were less diverse with fewer similarities between northern and southern communities (11%). The clustering with dissolved oxygen was also less apparent. Archaea – Only 7 out of 16 samples were above our PCR detection levels and also had low oxygen clusters (data not shown). Denitrifiers – There is about 45% similarity between the two large groups that were found in the dendrogram. Discussion: Samples were only 50% saturated (not anaerobic), which supports the notion of how diverse and rapidly changing these populations can be. The next step in this project is to figure out specific species that are in the samples to be able to identify more patterns and take a closer look to Archaea Bacteria Eukaryotes 16S rRNA Genes 18S rRNA Genes nosZ Genes Denitrifiers Acknowledgements This work was made possible through funding by the Research in Ocean Sciences (RIOS) Program/Gary Taghon – P.I., New Jersey Department of Environmental Protection for a comprehensive action plan to address the ecological health of Barnegat Bay, and partial support by Rutgers University and National Science Foundation. A special thank you to Rose Petrecca and Charlotte Fuller for Barnegat Bay data sample collection and Caroline Fahey and Natalia Gonzalez for the personal support and lab assistance. References: McGuinness, L. M, Salganik, M., Vega, L., Pickering, K. D. and Lee J. Kerkhof. 2006. Replicability of Bacterial Communities in Denitrifying Bioreactors as Measured by PCR/T-RFLP Analysis. Env. Science and Tech. 40: 509-515. Corredor, J. Wawrik, B., Paul, J. Tran, H., Kerkhof, L, Lopez, J., Dieppa, A. and O. Cardenas. 2004. Geochemical Rate-RNA integration
Microbial Community Biomarker in Barnegat Bay Evangelina Pena 1, Lora McGuinness 1, Gary Taghon 1, Lee Kerkhof 1 Introduction Efforts to remediate anthropogenic.
Jan 11, 2016
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Microbial Community Biomarker in Barnegat BayMicrobial Community Biomarker in Barnegat BayEvangelina Pena1, Lora McGuinness1, Gary Taghon1, Lee Kerkhof1
IntroductionEfforts to remediate anthropogenic impacts in estuarine environments would benefit from a community bio-indicator with a rapid response time to demonstrate effectiveness. In this project, sediment samples were collected from specific sites in Barnegat Bay, N.J., and microbial communities were assayed as potential bio-indicators. Single-celled organisms were analyzed since they have a short lifespan and can respond rapidly to changes within their environment. To better understand these microbial populations, an assessment of ribosomal RNA genes and the functional gene (nosZ-nitrous oxide reductase) was performed to identify Bacteria, Eukaryotes, Archaea, and denitrifying populations. Preliminary results indicated that the microbiota correlated with environmental factors such as salinity, dissolved oxygen and latitude. These results suggest that single-celled organisms can be effective biomarkers for water quality within Barnegat Bay or in other coastal systems, which are critical habitats for marine and human populations.
MethodsInitially, 100 sediment samples were collected for a more comprehensive study on the ecological health of Barnegat Bay in 2012. For this assessment we selected 16 subsamples based on dissolved oxygen level and distribution throughout the bay. Sediments were obtained by vanVeen grab, the 2 top centimeters were homogenized transported back to the laboratory under ice and stored in -20º C until processing. Frozen sediments were extracted by phenol-chloroform method (McGuinness et. al, 2006). Target genes were amplified by PCR using domain-specific ribosomal primers (Corredor, 2005) and universal primers for nosZ (Scala and Kerkhof, 2000). T-RFLP fingerprinting was completed utilizing Mnl I, Hae III and HhaI enzymes (McGuinness et. al, 2006).
Rutgers University1, New Brunswick, New Jersey 08901
Contact Information:Evangelina Pena
[email protected] of Marine and Coastal Sciences
Rutgers University New Brunswick, New Jersey 08901
Results
Sample Replicability
To test the homogeneity of our samples in the same site, we conducted two fully separate experiments and compared their fingerprints.
16S PCR Gel Amplification
λ B30 B31 B33 B44 B68 B73
16s DNA Extraction Gel Amplification
λ B17 B30 B31
16S DNA Extraction Gel Amplification
16S rRNA Genes
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6Site 7
Site 8Site 8
Site 1
Site 2
Site 4
Site 5
Site 6Site 7
Figure 1 Figure 2
ConclusionsDistinct clusters were observed between the Northern and Southern part of the bay for nearly all target genes. Samples with close proximity but different chemical parameters had a high percentage similarity. Bacteria – Northern and Southern parts of the bay have a similarity ranging from 65-90%. Bacterial communities were the most diverse throughout the transect and displayed in low oxygen clusters. Eukaryotes – Were less diverse with fewer similarities between northern and southern communities (11%). The clustering with dissolved oxygen was also less apparent. Archaea – Only 7 out of 16 samples were above our PCR detection levels and also had low oxygen clusters (data not shown).Denitrifiers – There is about 45% similarity between the two large groups that were found in the dendrogram.
Discussion:Samples were only 50% saturated (not anaerobic), which supports the notion of how diverse and rapidly changing these populations can be.The next step in this project is to figure out specific species that are in the samples to be able to identify more patterns and take a closer look to identify a bio-indicator.
Archaea
Bacteria
Eukaryotes
16S rRNA Genes
18S rRNA Genes
nosZ Genes Denitrifiers
Acknowledgements This work was made possible through funding by the Research in Ocean Sciences (RIOS) Program/Gary Taghon – P.I., New Jersey Department of Environmental Protection for a comprehensive action plan to address the ecological health of Barnegat Bay, and partial support by Rutgers University and National Science Foundation. A special thank you to Rose Petrecca and Charlotte Fuller for Barnegat Bay data sample collection and Caroline Fahey and Natalia Gonzalez for the personal support and lab assistance.
References: McGuinness, L. M, Salganik, M., Vega, L., Pickering, K. D. and Lee J. Kerkhof. 2006. Replicability of Bacterial Communities in Denitrifying Bioreactors as Measured by PCR/T-RFLP Analysis. Env. Science and Tech. 40: 509-515.Corredor, J. Wawrik, B., Paul, J. Tran, H., Kerkhof, L, Lopez, J., Dieppa, A. and O. Cardenas. 2004. Geochemical Rate-RNA integration study: Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Gene Transcription and Photosynthetic Capacity of Planktonic Photoautotrophs. Appl. Environ. Microbiol. 70: 5459–5468Scala, D. and L. Kerkhof. 2000. Horizontal Heterogeniety in Denitrifying Bacterial Assemblages in Marine Sediments Using TRFLP Analysis. Appl. Environ. Microbiol. 66: 1980-1986
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