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- Admixture; Ammodramus ; diagnostic markers; hybridization; next-generation sequencing (1)
- Ammodramus caudacutus ; Ammodramus nelsoni ; ecological niche models; genotype-habitat associations; hybridization; mosaic hybrid zone; Nelson's sparrow; Saltmarsh sparrow (1)
- Ammodramus nelsoni (1)
- Bacterial community (1)
- Biochemical responses (1)
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- Composite method; concentration; constituent; flux; nutrient; R; software; solute load models; uncertainty; watershed (1)
- Defense responses (1)
- Disease ecology (1)
- Emergent pathogen (1)
- Entropy (1)
- Forest soils (1)
- Hemolysin (1)
- Hibridación (1)
- MLSA (1)
- Microbiome (1)
- Nitrogen deposition (1)
- Nitrogen; river; land use; spatial distribution; coastal watershed; model (1)
- OTUs (1)
- Oligotypes (1)
- Palabras clave: Ammodramus caudacutus (1)
- Pathogen evolution (1)
- Plumaje (1)
- Population structure (1)
- Pyrosequencing (1)
- QIIME software (1)
- Variación morfológica (1)
- Vibriosis (1)
Articles 1 - 14 of 14
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Permanent Draft Genome Sequence Of Frankia Sp. Strain Avci1, A Nitrogen-Fixing Actinobacterium Isolated From The Root Nodules Of Alnus Viridis Subsp. Crispa Grown In Canada, Erik Swanson, Rediet Oshone, Stephen D. Simpson, Krystalynne Morris, Feseha Abebe-Akele, William Kelley Thomas, Louis S. Tisa
Permanent Draft Genome Sequence Of Frankia Sp. Strain Avci1, A Nitrogen-Fixing Actinobacterium Isolated From The Root Nodules Of Alnus Viridis Subsp. Crispa Grown In Canada, Erik Swanson, Rediet Oshone, Stephen D. Simpson, Krystalynne Morris, Feseha Abebe-Akele, William Kelley Thomas, Louis S. Tisa
New Hampshire Agricultural Experiment Station Publications
Frankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa, is a member of Frankia lineage Ia, which is able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report a 7.7-Mbp draft genome sequence with a G+C content of 72.41% and 6,470 candidate protein-encoding genes.
Genotype-Environment Associations Support A Mosaic Hybrid Zone Between Two Tidal Marsh Birds, Jennifer Walsh, Rebecca J. Rowe, Brian J. Olsen, W. Gregory Shriver, Adrienne I. Kovach
Genotype-Environment Associations Support A Mosaic Hybrid Zone Between Two Tidal Marsh Birds, Jennifer Walsh, Rebecca J. Rowe, Brian J. Olsen, W. Gregory Shriver, Adrienne I. Kovach
New Hampshire Agricultural Experiment Station Publications
Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh-level characteristics in shaping a hybrid zone between two recently diverged avian taxa – Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co-occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid …
Permanent Draft Genome Sequence Of Frankia Sp. Strain Acn1ag, A Nitrogen-Fixing Actinobacterium Isolated From The Root Nodules Of Alnus Glutinosa, Erik Swanson, Rediet Oshone, Stephen D. Simpson, Krystalynne Morris, Feseha Abebe-Akele, William Kelley Thomas, Louis S. Tisa
Permanent Draft Genome Sequence Of Frankia Sp. Strain Acn1ag, A Nitrogen-Fixing Actinobacterium Isolated From The Root Nodules Of Alnus Glutinosa, Erik Swanson, Rediet Oshone, Stephen D. Simpson, Krystalynne Morris, Feseha Abebe-Akele, William Kelley Thomas, Louis S. Tisa
New Hampshire Agricultural Experiment Station Publications
Frankia strain ACN1ag is a member of Frankia lineage Ia, which are able to re-infect plants of the Betulaceae and Myricaceae families. Here, we report a 7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate protein-encoding genes.
Reducing Bias And Quantifying Uncertainty In Watershed Flux Estimates: The R Package Loadflex, Alison P. Appling, Miguel C. Leon, William H. Mcdowell
Reducing Bias And Quantifying Uncertainty In Watershed Flux Estimates: The R Package Loadflex, Alison P. Appling, Miguel C. Leon, William H. Mcdowell
New Hampshire Agricultural Experiment Station Publications
Many ecological insights into the function of rivers and watersheds emerge from quantifying the flux of solutes or suspended materials in rivers. Numerous methods for flux estimation have been described, and each has its strengths and weaknesses. Currently, the largest practical challenges in flux estimation are to select among these methods and to implement or apply whichever method is chosen. To ease this process of method selection and application, we have written an R software package called loadflex that implements several of the most popular methods for flux estimation, including regressions, interpolations, and the special case of interpolation known as …
An Index To Characterize The Spatial Distribution Of Land Use Within Watersheds And Implications For River Network Nutrient Removal And Export, Madeleine M. Mineau, Wilfred M. Wollheim, Robert J. Stewart
An Index To Characterize The Spatial Distribution Of Land Use Within Watersheds And Implications For River Network Nutrient Removal And Export, Madeleine M. Mineau, Wilfred M. Wollheim, Robert J. Stewart
New Hampshire Agricultural Experiment Station Publications
The spatial distribution of land use and associated nutrient inputs may influence the efficacy of in-stream nutrient removal; however, the effect of source location on N removal and watershed N export has not been quantified. We present the skewness index, a metric to quantify the spatial distribution of land use within watersheds. Using this index and a river network nitrogen removal model, we quantified the effect of varying the location of developed land use within two watersheds on nutrient removal and export. The quantity and location of developed land use as well as runoff affected nitrogen removal and export. Because …
Draft Genome Sequence Of Frankia Sp. Strain Dc12, An Atypical, Noninfective, Ineffective Isolate From Datisca Cannabina, Louis S. Tisa, Nicholas Beauchemin, Michael N. Cantor, Teal R. Furnholm, Faten Ghodhbane-Gtari, Lynne Goodwin, Alex Copeland, Maher Gtari, Marcel Huntemann, Natalia Ivanova, Nikos Kyrpides, Victor Markowitz, Kostas Mavrommatis, Natalia Mikhailova, Imen Nouioui, Rediet Oshone, Galina Ovchinnikova, Ioanna Pagani, Krishnaveni Palaniappan, Amrita Pati
Draft Genome Sequence Of Frankia Sp. Strain Dc12, An Atypical, Noninfective, Ineffective Isolate From Datisca Cannabina, Louis S. Tisa, Nicholas Beauchemin, Michael N. Cantor, Teal R. Furnholm, Faten Ghodhbane-Gtari, Lynne Goodwin, Alex Copeland, Maher Gtari, Marcel Huntemann, Natalia Ivanova, Nikos Kyrpides, Victor Markowitz, Kostas Mavrommatis, Natalia Mikhailova, Imen Nouioui, Rediet Oshone, Galina Ovchinnikova, Ioanna Pagani, Krishnaveni Palaniappan, Amrita Pati
New Hampshire Agricultural Experiment Station Publications
Frankia sp. strain DC12, isolated from root nodules of Datisca cannabina, is a member of the fourth lineage of Frankia, which is unable to reinfect actinorhizal plants. Here, we report its 6.88-Mbp high-quality draft genome sequence, with a G+C content of 71.92% and 5,858 candidate protein-coding genes.
Long-Term Trends Of Changes In Pine And Oak Foliar Nitrogen Metabolism In Response To Chronic Nitrogen Amendments At Harvard Forest, Ma, Rakesh Minocha, Swathi A. Turlapati, Stephanie Long, William H. Mcdowell, Subhash C. Minocha
Long-Term Trends Of Changes In Pine And Oak Foliar Nitrogen Metabolism In Response To Chronic Nitrogen Amendments At Harvard Forest, Ma, Rakesh Minocha, Swathi A. Turlapati, Stephanie Long, William H. Mcdowell, Subhash C. Minocha
New Hampshire Agricultural Experiment Station Publications
We evaluated the long-term (1995–2008) trends in foliar and sapwood metabolism, soil solution chemistry and tree mortality rates in response to chronic nitrogen (N) additions to pine and hardwood stands at the Harvard Forest Long Term Ecological Research (LTER) site. Common stress-related metabolites like polyamines (PAs), free amino acids (AAs) and inorganic elements were analyzed for control, low N (LN, 50 kg NH4NO3 ha−1 year−1) and high N (HN, 150 kg NH4NO3 ha−1 year−1) treatments. In the pine stands, partitioning of excess N into foliar PAs and AAs increased with both N treatments until 2002. By 2005, several of these …
Elucidation Of The Photorhabdus Temperata Genome And Generation Of A Transposon Mutant Library To Identify Motility Mutants Altered In Pathogenesis, Sheldon G. Hurst Iv, Holli Rowedder, Brandye Michaels, Hannah Bullock, Ryan Jackobeck, Feseha Abebe-Akele, Umjia Durakovic, Jon Gately, Erik Janicki, Louis S. Tisa
Elucidation Of The Photorhabdus Temperata Genome And Generation Of A Transposon Mutant Library To Identify Motility Mutants Altered In Pathogenesis, Sheldon G. Hurst Iv, Holli Rowedder, Brandye Michaels, Hannah Bullock, Ryan Jackobeck, Feseha Abebe-Akele, Umjia Durakovic, Jon Gately, Erik Janicki, Louis S. Tisa
New Hampshire Agricultural Experiment Station Publications
The entomopathogenic nematode Heterorhabditis bacteriophora forms a specific mutualistic association with its bacterial partner Photorhabdus temperata. The microbial symbiont is required for nematode growth and development, and symbiont recognition is strain specific. The aim of this study was to sequence the genome of P. temperata and identify genes that plays a role in the pathogenesis of the Photorhabdus-Heterorhabditis symbiosis. A draft genome sequence of P. temperata strain NC19 was generated. The 5.2-Mb genome was organized into 17 scaffolds and contained 4,808 coding sequences (CDS). A genetic approach was also pursued to identify mutants with altered motility. A bank of 10,000 …
Relationship Of Phenotypic Variation And Genetic Admixture In The Saltmarsh–Nelson's Sparrow Hybrid Zone, Jennifer Walsh, W. Gregory Shriver, Brian J. Olsen, Kathleen M. O'Brien, Adrienne I. Kovach
Relationship Of Phenotypic Variation And Genetic Admixture In The Saltmarsh–Nelson's Sparrow Hybrid Zone, Jennifer Walsh, W. Gregory Shriver, Brian J. Olsen, Kathleen M. O'Brien, Adrienne I. Kovach
New Hampshire Agricultural Experiment Station Publications
Hybridization is influential in shaping species' dynamics and has many evolutionary and conservation implications. Identification of hybrid individuals typically relies on morphological data, but the assumption that hybrids express intermediate traits is not always valid, because of complex patterns of introgression and selection. We characterized phenotypic and genotypic variation across a hybrid zone between 2 tidal-marsh birds, the Saltmarsh Sparrow (Ammodramus caudacutus) and Nelson's Sparrow (A. nelsoni) (n = 290), and we sought to identify morphological traits that could be used to classify admixed individuals. Sparrows were sampled from a total of 34 marshes, including 23 sympatric and 11 putatively …
Development Of Diagnostic Microsatellite Markers From Whole‐Genome Sequences Of Ammodramus Sparrows For Assessing Admixture In A Hybrid Zone, Adrienne I. Kovach, Jennifer Walsh, Jordan Ramsdell, William Kelley Thomas
Development Of Diagnostic Microsatellite Markers From Whole‐Genome Sequences Of Ammodramus Sparrows For Assessing Admixture In A Hybrid Zone, Adrienne I. Kovach, Jennifer Walsh, Jordan Ramsdell, William Kelley Thomas
New Hampshire Agricultural Experiment Station Publications
Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared …
Genetic Characterization Of Clinical And Environmental Vibrio Parahaemolyticus From The Northeast Usa Reveals Emerging Resident And Non-Indigenous Pathogen Lineages, Feng Xu, Saba Ilyas, Jeffrey A. Hall, Stephen H. Jones, Vaughn S. Cooper, Cheryl A. Whistler
Genetic Characterization Of Clinical And Environmental Vibrio Parahaemolyticus From The Northeast Usa Reveals Emerging Resident And Non-Indigenous Pathogen Lineages, Feng Xu, Saba Ilyas, Jeffrey A. Hall, Stephen H. Jones, Vaughn S. Cooper, Cheryl A. Whistler
New Hampshire Agricultural Experiment Station Publications
Gastric infections caused by the environmentally transmitted pathogen, Vibrio parahaemolyticus, have increased over the last two decades, including in many parts of the United States (US). However, until recently, infections linked to shellfish from the cool northeastern US waters were rare. Cases have risen in the Northeast, consistent with changes in local V. parahaemolyticus populations toward greater abundance or a shift in constituent pathogens. We examined 94 clinical isolates from a period of increasing disease in the region and compared them to 200 environmental counterparts to identify resident and non-indigenous lineages and to gain insight into the emergence of pathogenic …
Use Of Whole Genome Phylogeny And Comparisons In The Development Of A Multiplex-Pcr Assay To Identify Sequence Type 36 Vibrio Parahaemolyticus, Cheryl A. Whistler, Jeffrey A. Hall, Feng Xu, Saba Ilyas, Puskar Siwakoti, Vaughn S. Cooper, Stephen H. Jones
Use Of Whole Genome Phylogeny And Comparisons In The Development Of A Multiplex-Pcr Assay To Identify Sequence Type 36 Vibrio Parahaemolyticus, Cheryl A. Whistler, Jeffrey A. Hall, Feng Xu, Saba Ilyas, Puskar Siwakoti, Vaughn S. Cooper, Stephen H. Jones
New Hampshire Agricultural Experiment Station Publications
Vibrio parahaemolyticus sequence type (ST) 36 strains that are native to the Pacific Ocean have recently caused multi-state outbreaks of gastroenteritis linked to shellfish harvested from the Atlantic Ocean. Whole genome comparisons of 295 genomes of V. parahaemolyticus, including several traced to northeastern US sources, were used to identify diagnostic loci: one putatively encoding an endonuclease (prp), and two others potentially conferring O-antigenic properties (cps and flp). The combination of all three loci was present only in one clade of closely-related strains, of ST36, ST59 and one additional unknown sequence type. However, each locus was also identified outside this clade, …
Oligotyping Reveals Stronger Relationship Of Organic Soil Bacterial Community Structure With N-Amendments And Soil Chemistry In Comparison To That Of Mineral Soil At Harvard Forest, Ma, Usa, Swathi A. Turlapati, Rakesh Minocha, Stephanie Long, Jordan Ramsdell, Subhash C. Minocha
Oligotyping Reveals Stronger Relationship Of Organic Soil Bacterial Community Structure With N-Amendments And Soil Chemistry In Comparison To That Of Mineral Soil At Harvard Forest, Ma, Usa, Swathi A. Turlapati, Rakesh Minocha, Stephanie Long, Jordan Ramsdell, Subhash C. Minocha
New Hampshire Agricultural Experiment Station Publications
The impact of chronic nitrogen amendments on bacterial communities was evaluated at Harvard Forest, Petersham, MA, USA. Thirty soil samples (3 treatments × 2 soil horizons × 5 subplots) were collected in 2009 from untreated (control), low nitrogen-amended (LN; 50 kg NH4NO3 ha-1 yr-1) and high nitrogen-amended (HN; 150 kg NH4NO3 ha-1 yr-1) plots. PCR-amplified partial 16S rRNA gene sequences made from soil DNA were subjected to pyrosequencing (Turlapati et al., 2013) and analyses using oligotyping. The parameters M (the minimum count of the most abundant unique sequence in an oligotype) and s (the minimum number of samples in which …
Cultivating The Uncultured: Growing The Recalcitrant Cluster-2 Frankia Strains, Maher Gtari, Faten Ghodhbane-Gtari, Imen Nouioui, Amir Ktari, Karima Hezbri, Wajdi Mimouni, Imed Sbissi, Amani Ayari, Takashi Yamanaka, Philippe Normand, Louis S. Tisa, Abdellatif Boudabous
Cultivating The Uncultured: Growing The Recalcitrant Cluster-2 Frankia Strains, Maher Gtari, Faten Ghodhbane-Gtari, Imen Nouioui, Amir Ktari, Karima Hezbri, Wajdi Mimouni, Imed Sbissi, Amani Ayari, Takashi Yamanaka, Philippe Normand, Louis S. Tisa, Abdellatif Boudabous
New Hampshire Agricultural Experiment Station Publications
The repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles …