Damian M Menning, Ph.D. (Former Employee)
Science and Products
Shrew (Sorex sp.) Gut Contents Identified by DNA Metabarcoding, North America, 1968-2016 Shrew (Sorex sp.) Gut Contents Identified by DNA Metabarcoding, North America, 1968-2016
This data package contains four tables related to helminths and bacteria identified in the guts of North American shrews (Genus: Sorex). Tables include: two tables of specimen information about each shrew, such as species, museum collection identification, and NCBI accession IDs; one table of NBCI GenBank accession numbers of previously identified DNA sequences used in this study to...
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.
Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017 Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017
Fragment data from 11 nuclear microsatellite loci and sequence data from the mitochondrial cytochrome b gene were gathered from Arctic cod (Boreogadus saida) in the Beaufort and Chukchi seas. Mitogenomic analyses of Arctic cod and three other co-distributed gadoids (Polar cod [Arctogadus glacialis], Saffron cod [Eleginus gracilis], Walleye Pollock [Gadus chalcogrammus]) were also...
Filter Total Items: 16
Abundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon Abundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon
Rhodoliths are important foundation species of the benthic photic zone but are poorly known and rarely studied in Alaska. A bed of Lithothamnion soriferum rhodoliths was discovered in 2008 in Kinzarof Lagoon, Alaska, a shallow-water embayment dominated by eelgrass (Zostera marina). Rhodolith presence and biomass were estimated to assess trends and environmental factors that may influence
Authors
David H. Ward, Courtney Amundson, Patrick Fitzmorris, Damian M. Menning, Joel Markis, Kristine M. Sowl, Sandra C. Lindstrom
Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific
Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in...
Authors
Damian M. Menning, Hunter A Gravley, Melissa N. Cady, Daniel J Pepin, Sandy Wyllie-Echeverria, David H. Ward, Sandra L. Talbot
Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae) Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)
Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital...
Authors
Stephen E. Greiman, Joseph A. Cook, Timothy Odem, Katelyn Cranmer, Schuyler W Liphardt, Damian M. Menning, Sarah A. Sonsthagen, Sandra L. Talbot
Environmental DNA: An emerging tool for understanding aquatic biodiversity Environmental DNA: An emerging tool for understanding aquatic biodiversity
Field surveys for aquatic organisms provide critical information that is important for robust resource management. However, such surveys are expensive and labor intensive, particularly in large, remote landscapes like those that characterize much of Alaska. Traditionally, characterizing aquatic biodiversity necessitated the physical capture and identification of individual organisms...
Authors
Trey Simmons, Damian M. Menning, Sandra L. Talbot
Are migratory waterfowl vectors of seagrass pathogens? Are migratory waterfowl vectors of seagrass pathogens?
Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of plant pathogens. Extensive meadows of eelgrass (Zostera marina) in southwest Alaska support hundreds of thousands of waterfowl during fall migration and may be susceptible to plant pathogens. We recovered DNA of organisms pathogenic to eelgrass from...
Authors
Damian M. Menning, David H. Ward, Sandy Wyllie-Echeverria, Kevin Sage, Megan C. Gravley, Hunter Gravley, Sandra L. Talbot
Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA
Accurate and timely data regarding freshwater fish communities is important for informed decision-making by local, state, tribal, and federal land and resource managers; however, conducting traditional gear-based fish surveys can be an expensive and time-consuming process, particularly in remote areas, like those that characterize much of Alaska. To help address this challenge, we...
Authors
Damian M. Menning, Trey Simmons, Sandra L. Talbot
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.
Science and Products
Shrew (Sorex sp.) Gut Contents Identified by DNA Metabarcoding, North America, 1968-2016 Shrew (Sorex sp.) Gut Contents Identified by DNA Metabarcoding, North America, 1968-2016
This data package contains four tables related to helminths and bacteria identified in the guts of North American shrews (Genus: Sorex). Tables include: two tables of specimen information about each shrew, such as species, museum collection identification, and NCBI accession IDs; one table of NBCI GenBank accession numbers of previously identified DNA sequences used in this study to...
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.
Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017 Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017
Fragment data from 11 nuclear microsatellite loci and sequence data from the mitochondrial cytochrome b gene were gathered from Arctic cod (Boreogadus saida) in the Beaufort and Chukchi seas. Mitogenomic analyses of Arctic cod and three other co-distributed gadoids (Polar cod [Arctogadus glacialis], Saffron cod [Eleginus gracilis], Walleye Pollock [Gadus chalcogrammus]) were also...
Filter Total Items: 16
Abundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon Abundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon
Rhodoliths are important foundation species of the benthic photic zone but are poorly known and rarely studied in Alaska. A bed of Lithothamnion soriferum rhodoliths was discovered in 2008 in Kinzarof Lagoon, Alaska, a shallow-water embayment dominated by eelgrass (Zostera marina). Rhodolith presence and biomass were estimated to assess trends and environmental factors that may influence
Authors
David H. Ward, Courtney Amundson, Patrick Fitzmorris, Damian M. Menning, Joel Markis, Kristine M. Sowl, Sandra C. Lindstrom
Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific
Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in...
Authors
Damian M. Menning, Hunter A Gravley, Melissa N. Cady, Daniel J Pepin, Sandy Wyllie-Echeverria, David H. Ward, Sandra L. Talbot
Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae) Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)
Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital...
Authors
Stephen E. Greiman, Joseph A. Cook, Timothy Odem, Katelyn Cranmer, Schuyler W Liphardt, Damian M. Menning, Sarah A. Sonsthagen, Sandra L. Talbot
Environmental DNA: An emerging tool for understanding aquatic biodiversity Environmental DNA: An emerging tool for understanding aquatic biodiversity
Field surveys for aquatic organisms provide critical information that is important for robust resource management. However, such surveys are expensive and labor intensive, particularly in large, remote landscapes like those that characterize much of Alaska. Traditionally, characterizing aquatic biodiversity necessitated the physical capture and identification of individual organisms...
Authors
Trey Simmons, Damian M. Menning, Sandra L. Talbot
Are migratory waterfowl vectors of seagrass pathogens? Are migratory waterfowl vectors of seagrass pathogens?
Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of plant pathogens. Extensive meadows of eelgrass (Zostera marina) in southwest Alaska support hundreds of thousands of waterfowl during fall migration and may be susceptible to plant pathogens. We recovered DNA of organisms pathogenic to eelgrass from...
Authors
Damian M. Menning, David H. Ward, Sandy Wyllie-Echeverria, Kevin Sage, Megan C. Gravley, Hunter Gravley, Sandra L. Talbot
Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA
Accurate and timely data regarding freshwater fish communities is important for informed decision-making by local, state, tribal, and federal land and resource managers; however, conducting traditional gear-based fish surveys can be an expensive and time-consuming process, particularly in remote areas, like those that characterize much of Alaska. To help address this challenge, we...
Authors
Damian M. Menning, Trey Simmons, Sandra L. Talbot
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.