Damian M Menning, Ph.D. (Former Employee)
Science and Products
Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City
This dataset describes the number and detection of Giardia cysts and Cryptosporidium oocysts in water samples collected from creeks and lakes in Anchorage, Alaska during 2021.
Detection of the Aquatic Invasive Species (AIS) Elodea canadensis and E. nuttallii Using Environmental DNA (eDNA), Alaska Detection of the Aquatic Invasive Species (AIS) Elodea canadensis and E. nuttallii Using Environmental DNA (eDNA), Alaska
This data set is comprised of one table with sampling information and National Center for Biotechnology Information (NCBI) BioProject accession numbers for sequence information of this amplicon-based study targeting Elodea canadensis and E. nuttallii in freshwater systems of Alaska from environmental samples. Highly conserved primers which can differentiate these species of interest were...
Southern Beaufort Sea Polar Bear Diet and Gut Microbiota Data, 2015-2019 Southern Beaufort Sea Polar Bear Diet and Gut Microbiota Data, 2015-2019
This dataset is one table with data collected and derived from polar bears sampled in Alaska's southern Beaufort Sea during 2015-2019. Data include demographic and morphometric information from each sampled polar bear, gut microbiome diversity indices derived from fecal DNA metabarcoding, and the proportion of prey species detected in individual bear diets derived from quantitative fatty...
Gavia Species Identification and Diet Composition from Feces, Central North Slope, Alaska, 2012-2014 Gavia Species Identification and Diet Composition from Feces, Central North Slope, Alaska, 2012-2014
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Loon (Gavia sp.) and fish species expected in lake systems of the North Slope of Alaska from fecal samples. Highly conserved primers which could differentiate species of interest were developed for five portions of gavia...
Detection of Multiple Fish Species Using Environmental DNA (eDNA), Alaska 2018 Detection of Multiple Fish Species Using Environmental DNA (eDNA), Alaska 2018
This release provides results of an environmental DNA (eDNA) study of fish identified in seven Alaskan lakes, three streams, and a positive control. Samples included replicates for multiple sampling dates and locations. The reference list and conserved primer sets to identify species present were developed using publicly available data (https://www.ncbi.nlm.nih.gov/genbank/). Highly...
Detection of Seagrass Pathogens using Environmental DNA (eDNA), North Pacific, 2016-Present Detection of Seagrass Pathogens using Environmental DNA (eDNA), North Pacific, 2016-Present
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove)...
Filter Total Items: 16
Detection of Giardia and Cryptosporidium in surface water of a subarctic city Detection of Giardia and Cryptosporidium in surface water of a subarctic city
Giardia and Cryptosporidium spp. are globally distributed protozoan parasites that can cause gastrointestinal disease in humans and animals. These zoonotic parasites and their ecological relationships have been understudied in Alaska and elsewhere, despite being identified as priority zoonotic pathogens. We aimed to detect and characterize Giardia and Cryptosporidium spp. in waterbodies...
Authors
Christina Ahlstrom, Michael P. Carey, Damian M. Menning, Jonathan A. O’Donnell, Andrew M. Ramey
Environmental DNA as a tool for better understanding the distribution, abundance, and health of Atlantic and Pacific salmon Environmental DNA as a tool for better understanding the distribution, abundance, and health of Atlantic and Pacific salmon
The development and application of approaches to detect and quantify environmental DNA (eDNA) have potential to improve our understanding of the distribution, abundance, and health of Atlantic Salmon Salmo salar and Pacific salmon Oncorhynchus spp. Here, we review 61 articles focusing on eDNA applications pertaining to salmon occupying natural habitat and aquaculture facilities in the...
Authors
Andrew M. Ramey, Cherie Marie Mckeeman, Eleni Leto Petrou, Damian M. Menning, Ora L. Russ, Andres Lopez
Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina) Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and...
Authors
Lei Yu, Marina Khachaturyan, Michael Matschiner, Adam Healey, Diane Bauer, Brenda Cameron, Mathieu Cusson, J. Emmett Duffy, F. Joel Fodrie, Diana Gill, Jane Grimwood, Masakazu Hori, Kevin Hovel, A. Randall Hughes, Marlene Jahnke, J. Jenkins, K. Keymanesh, C. Kruschel, S. Mamidi, Damian M. Menning, P. Moksnes, M. Nakaoka, C. Pennacchio, K. Reiss, F. Rossi, J. Ruesink, S. Schultz, S. Talbott, R. Unsworth, David H. Ward, T. Dagan, J. Schmutz, J. A. Eisen, J. Stachowicz, Y. Van de Peer, J. L. Olsen, T. B. H. Reusch
eDNA Metabarcoding Analyses of Diet in Yellow-Billed Loons of Northern Alaska eDNA Metabarcoding Analyses of Diet in Yellow-Billed Loons of Northern Alaska
Environmental DNA is a burgeoning tool used to address wide-ranging scientific questions, including determining diets of difficult-to-sample predators. Loons are large piscivorous diving birds that capture and consume prey underwater, making it nearly impossible to visually determine their diet via observation alone. Identifying species' diets is important for understanding basic life...
Authors
Damian M. Menning, Brian D. Uher-Koch, Melanie J. Flamme, Trey Simmons, Joel Schmutz, Sandra Talbot
Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations
This study developed and evaluated DNA metabarcoding to identify the presence of pinniped and cetacean prey DNA in fecal samples of East Greenland (EG) and Southern Beaufort Sea (SB) polar bears Ursus maritimus sampled in the spring of 2015-2019. Prey DNA was detected in half (49/92) of all samples, and when detected, ringed seal Pusa hispida was the predominant prey species, identified...
Authors
Megan Franz, L Whyte, Todd C. Atwood, Damian M. Menning, Sarah A. Sonsthagen, Sandra Talbot, Kristin L. Laidre, Emmanuel Gonzalez, Melissa McKinney
Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep
Objectives Dall’s sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference...
Authors
Kelly E. Williams, Damian M. Menning, Eric J. Wald, Sandra L. Talbot, Kumi L. Rattenbury, Laura R. Prugh
Non-USGS Publications**
Quasem, I., A. N. Achille, B. A. Caddick, T. A. Carter, C. Daniels, J. A. Delaney, V. Delic, K. A. Denton, M. C. Duran, M. K. Fatica, C. M. Ference, J. P. Galkiewicz, A. M. Garcia, J. D. Hendrick, S. A. Horton, M. S. Kun, P. W. Koch, T. M. Lee, C. R. McCabe, S. McHale, L. D. McDaniel, D. M. Menning, K. J. Menning, H. Mirzaei-Souderjani, S. Mostajabian, D. A. Nicholson, C. K. Nugent, N. P. Osman, D. I. Pappas, A. M. Rocha, K. Rosario, H. Rubelmann, J. A. Schwartz, K. W. Seeley, C. M. Staley, E. M. Wallace, T. M. Wong, B. L. Zielinski, T. E. Hanson, and K. M. Scott. 2017. Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs. FEMS Microbiology Letters 364(14):fnx148. doi:10.1093/femsle/fnx148
Menning, D. M., W. A. Carraher-Stross, E. D. Graham, D. N. Thomas, A. R. Phillips, R. J. Scharping, and J. R. Garey. 2017. Aquifer Discharge Drives Microbial Community Change in Karst Estuaries. Estuaries and Coasts 41(2):430-443. doi:10.1007/s12237-017-0281-7
Menning, D. M., J. G. Wynn, and J. R. Garey. 2015. Karst estuaries are governed by interactions between inland hydrological conditions and sea level. Journal of Hydrology 527:718-733. doi:10.1016/j.jhydrol.2015.05.021
Menning, D. M., L. M. Boop, E. D. Graham, and J. R. Garey. 2014. Molecular analyses of microbial abundance and diversity in the water column of anchialine caves in Mallorca, Spain. International Journal of Speleology 43:217-226. doi:10.5038/1827-806X.43.2.9
Garey, J. R. and D. M. Menning. 2012. The dynamics of community structure within a submarine coastal spring with an anchialine source. Natura Croatica 21(1):43-46.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Python Scripts for Bioinformatics Python Scripts for Bioinformatics
Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process.
Science and Products
Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City Data for Detection of Giardia and Cryptosporidium Parasites in Surface Water of a Subarctic City
This dataset describes the number and detection of Giardia cysts and Cryptosporidium oocysts in water samples collected from creeks and lakes in Anchorage, Alaska during 2021.
Detection of the Aquatic Invasive Species (AIS) Elodea canadensis and E. nuttallii Using Environmental DNA (eDNA), Alaska Detection of the Aquatic Invasive Species (AIS) Elodea canadensis and E. nuttallii Using Environmental DNA (eDNA), Alaska
This data set is comprised of one table with sampling information and National Center for Biotechnology Information (NCBI) BioProject accession numbers for sequence information of this amplicon-based study targeting Elodea canadensis and E. nuttallii in freshwater systems of Alaska from environmental samples. Highly conserved primers which can differentiate these species of interest were...
Southern Beaufort Sea Polar Bear Diet and Gut Microbiota Data, 2015-2019 Southern Beaufort Sea Polar Bear Diet and Gut Microbiota Data, 2015-2019
This dataset is one table with data collected and derived from polar bears sampled in Alaska's southern Beaufort Sea during 2015-2019. Data include demographic and morphometric information from each sampled polar bear, gut microbiome diversity indices derived from fecal DNA metabarcoding, and the proportion of prey species detected in individual bear diets derived from quantitative fatty...
Gavia Species Identification and Diet Composition from Feces, Central North Slope, Alaska, 2012-2014 Gavia Species Identification and Diet Composition from Feces, Central North Slope, Alaska, 2012-2014
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Loon (Gavia sp.) and fish species expected in lake systems of the North Slope of Alaska from fecal samples. Highly conserved primers which could differentiate species of interest were developed for five portions of gavia...
Detection of Multiple Fish Species Using Environmental DNA (eDNA), Alaska 2018 Detection of Multiple Fish Species Using Environmental DNA (eDNA), Alaska 2018
This release provides results of an environmental DNA (eDNA) study of fish identified in seven Alaskan lakes, three streams, and a positive control. Samples included replicates for multiple sampling dates and locations. The reference list and conserved primer sets to identify species present were developed using publicly available data (https://www.ncbi.nlm.nih.gov/genbank/). Highly...
Detection of Seagrass Pathogens using Environmental DNA (eDNA), North Pacific, 2016-Present Detection of Seagrass Pathogens using Environmental DNA (eDNA), North Pacific, 2016-Present
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove)...
Filter Total Items: 16
Detection of Giardia and Cryptosporidium in surface water of a subarctic city Detection of Giardia and Cryptosporidium in surface water of a subarctic city
Giardia and Cryptosporidium spp. are globally distributed protozoan parasites that can cause gastrointestinal disease in humans and animals. These zoonotic parasites and their ecological relationships have been understudied in Alaska and elsewhere, despite being identified as priority zoonotic pathogens. We aimed to detect and characterize Giardia and Cryptosporidium spp. in waterbodies...
Authors
Christina Ahlstrom, Michael P. Carey, Damian M. Menning, Jonathan A. O’Donnell, Andrew M. Ramey
Environmental DNA as a tool for better understanding the distribution, abundance, and health of Atlantic and Pacific salmon Environmental DNA as a tool for better understanding the distribution, abundance, and health of Atlantic and Pacific salmon
The development and application of approaches to detect and quantify environmental DNA (eDNA) have potential to improve our understanding of the distribution, abundance, and health of Atlantic Salmon Salmo salar and Pacific salmon Oncorhynchus spp. Here, we review 61 articles focusing on eDNA applications pertaining to salmon occupying natural habitat and aquaculture facilities in the...
Authors
Andrew M. Ramey, Cherie Marie Mckeeman, Eleni Leto Petrou, Damian M. Menning, Ora L. Russ, Andres Lopez
Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina) Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and...
Authors
Lei Yu, Marina Khachaturyan, Michael Matschiner, Adam Healey, Diane Bauer, Brenda Cameron, Mathieu Cusson, J. Emmett Duffy, F. Joel Fodrie, Diana Gill, Jane Grimwood, Masakazu Hori, Kevin Hovel, A. Randall Hughes, Marlene Jahnke, J. Jenkins, K. Keymanesh, C. Kruschel, S. Mamidi, Damian M. Menning, P. Moksnes, M. Nakaoka, C. Pennacchio, K. Reiss, F. Rossi, J. Ruesink, S. Schultz, S. Talbott, R. Unsworth, David H. Ward, T. Dagan, J. Schmutz, J. A. Eisen, J. Stachowicz, Y. Van de Peer, J. L. Olsen, T. B. H. Reusch
eDNA Metabarcoding Analyses of Diet in Yellow-Billed Loons of Northern Alaska eDNA Metabarcoding Analyses of Diet in Yellow-Billed Loons of Northern Alaska
Environmental DNA is a burgeoning tool used to address wide-ranging scientific questions, including determining diets of difficult-to-sample predators. Loons are large piscivorous diving birds that capture and consume prey underwater, making it nearly impossible to visually determine their diet via observation alone. Identifying species' diets is important for understanding basic life...
Authors
Damian M. Menning, Brian D. Uher-Koch, Melanie J. Flamme, Trey Simmons, Joel Schmutz, Sandra Talbot
Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations
This study developed and evaluated DNA metabarcoding to identify the presence of pinniped and cetacean prey DNA in fecal samples of East Greenland (EG) and Southern Beaufort Sea (SB) polar bears Ursus maritimus sampled in the spring of 2015-2019. Prey DNA was detected in half (49/92) of all samples, and when detected, ringed seal Pusa hispida was the predominant prey species, identified...
Authors
Megan Franz, L Whyte, Todd C. Atwood, Damian M. Menning, Sarah A. Sonsthagen, Sandra Talbot, Kristin L. Laidre, Emmanuel Gonzalez, Melissa McKinney
Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep
Objectives Dall’s sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference...
Authors
Kelly E. Williams, Damian M. Menning, Eric J. Wald, Sandra L. Talbot, Kumi L. Rattenbury, Laura R. Prugh
Non-USGS Publications**
Quasem, I., A. N. Achille, B. A. Caddick, T. A. Carter, C. Daniels, J. A. Delaney, V. Delic, K. A. Denton, M. C. Duran, M. K. Fatica, C. M. Ference, J. P. Galkiewicz, A. M. Garcia, J. D. Hendrick, S. A. Horton, M. S. Kun, P. W. Koch, T. M. Lee, C. R. McCabe, S. McHale, L. D. McDaniel, D. M. Menning, K. J. Menning, H. Mirzaei-Souderjani, S. Mostajabian, D. A. Nicholson, C. K. Nugent, N. P. Osman, D. I. Pappas, A. M. Rocha, K. Rosario, H. Rubelmann, J. A. Schwartz, K. W. Seeley, C. M. Staley, E. M. Wallace, T. M. Wong, B. L. Zielinski, T. E. Hanson, and K. M. Scott. 2017. Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs. FEMS Microbiology Letters 364(14):fnx148. doi:10.1093/femsle/fnx148
Menning, D. M., W. A. Carraher-Stross, E. D. Graham, D. N. Thomas, A. R. Phillips, R. J. Scharping, and J. R. Garey. 2017. Aquifer Discharge Drives Microbial Community Change in Karst Estuaries. Estuaries and Coasts 41(2):430-443. doi:10.1007/s12237-017-0281-7
Menning, D. M., J. G. Wynn, and J. R. Garey. 2015. Karst estuaries are governed by interactions between inland hydrological conditions and sea level. Journal of Hydrology 527:718-733. doi:10.1016/j.jhydrol.2015.05.021
Menning, D. M., L. M. Boop, E. D. Graham, and J. R. Garey. 2014. Molecular analyses of microbial abundance and diversity in the water column of anchialine caves in Mallorca, Spain. International Journal of Speleology 43:217-226. doi:10.5038/1827-806X.43.2.9
Garey, J. R. and D. M. Menning. 2012. The dynamics of community structure within a submarine coastal spring with an anchialine source. Natura Croatica 21(1):43-46.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Python Scripts for Bioinformatics Python Scripts for Bioinformatics
Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process.