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)...
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
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 Carey, Damian Menning, Jonathan O’Donnell, Andrew 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 Ramey, Cherie Mckeeman, Eleni Leto Petrou, Damian Menning, Ora 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. Fodrie, Diana Gill, Jane Grimwood, Masakazu Hori, Kevin Hovel, A. Hughes, Marlene Jahnke, J. Jenkins, K. Keymanesh, C. Kruschel, S. Mamidi, Damian Menning, P. Moksnes, M. Nakaoka, C. Pennacchio, K. Reiss, F. Rossi, J. Ruesink, S. Schultz, S. Talbott, R. Unsworth, David Ward, T. Dagan, J. Schmutz, J. Eisen, J. Stachowicz, Y. Van de Peer, J. Olsen, T. 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 Menning, Brian Uher-Koch, Melanie 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 Atwood, Damian Menning, Sarah Sonsthagen, Sandra Talbot, Kristin 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 Williams, Damian Menning, Eric Wald, Sandra Talbot, Kumi Rattenbury, Laura R. Prugh
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 Ward, Courtney Amundson, Patrick Fitzmorris, Damian Menning, Joel Markis, Kristine Sowl, Sandra 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 Menning, Hunter Gravley, Melissa Cady, Daniel Pepin, Sandy Wyllie-Echeverria, David Ward, Sandra 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 Greiman, Joseph Cook, Timothy Odem, Katelyn Cranmer, Schuyler Liphardt, Damian Menning, Sarah Sonsthagen, Sandra 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 Menning, Sandra 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 Menning, David Ward, Sandy Wyllie-Echeverria, Kevin Sage, Megan Gravley, Hunter Gravley, Sandra 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 Menning, Trey Simmons, Sandra 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.
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)...
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
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 Carey, Damian Menning, Jonathan O’Donnell, Andrew 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 Ramey, Cherie Mckeeman, Eleni Leto Petrou, Damian Menning, Ora 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. Fodrie, Diana Gill, Jane Grimwood, Masakazu Hori, Kevin Hovel, A. Hughes, Marlene Jahnke, J. Jenkins, K. Keymanesh, C. Kruschel, S. Mamidi, Damian Menning, P. Moksnes, M. Nakaoka, C. Pennacchio, K. Reiss, F. Rossi, J. Ruesink, S. Schultz, S. Talbott, R. Unsworth, David Ward, T. Dagan, J. Schmutz, J. Eisen, J. Stachowicz, Y. Van de Peer, J. Olsen, T. 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 Menning, Brian Uher-Koch, Melanie 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 Atwood, Damian Menning, Sarah Sonsthagen, Sandra Talbot, Kristin 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 Williams, Damian Menning, Eric Wald, Sandra Talbot, Kumi Rattenbury, Laura R. Prugh
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 Ward, Courtney Amundson, Patrick Fitzmorris, Damian Menning, Joel Markis, Kristine Sowl, Sandra 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 Menning, Hunter Gravley, Melissa Cady, Daniel Pepin, Sandy Wyllie-Echeverria, David Ward, Sandra 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 Greiman, Joseph Cook, Timothy Odem, Katelyn Cranmer, Schuyler Liphardt, Damian Menning, Sarah Sonsthagen, Sandra 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 Menning, Sandra 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 Menning, David Ward, Sandy Wyllie-Echeverria, Kevin Sage, Megan Gravley, Hunter Gravley, Sandra 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 Menning, Trey Simmons, Sandra 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.
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.