Current Search:  high-throughput sequencing (x)

View All Items

  • CSV Spreadsheet
(1 - 3 of 3)
Impact of nitrogen on microbial diversity and function
Title
Impact of nitrogen on microbial diversity and function.
Creator
Garcia, Juan Carlos
Abstract / Description
River bacterioplankton communities, influenced by watershed usage, are responsible for water purification. Bacterioplankton may be critical in the degradation of dissolved organic nitrogen: the major nitrogen pool in the Caloosahatchee River, Florida. We investigated how freshwater discharge influences estuarine bacterioplankton and how the freshwater-originated DON is utilized by estuarine bacterioplankton. Microcosm experiments were conducted during low and high discharge using two upstream...
Show moreRiver bacterioplankton communities, influenced by watershed usage, are responsible for water purification. Bacterioplankton may be critical in the degradation of dissolved organic nitrogen: the major nitrogen pool in the Caloosahatchee River, Florida. We investigated how freshwater discharge influences estuarine bacterioplankton and how the freshwater-originated DON is utilized by estuarine bacterioplankton. Microcosm experiments were conducted during low and high discharge using two upstream freshwater samples: one site primarily influenced by Lake Okeechobee and the other site moderately influenced by an agricultural watershed. These freshwater samples were filtered to eliminate indigenous microbial populations, then mixed with estuarine bacterioplankton. High-throughput sequencing revealed that bacterioplankton differed between low and high discharge and were influenced by salinity. Alphaproteobacteria and Bacteroidetes dominated in low discharge while Bacteroidetes and Cyanobacteria dominated during high discharge. In the microcosm experiment, DON concentration decreased with increasing cell densities, suggesting that the DON was utilized as a carbon and nitrogen source. Band signals in denaturing gradient gel electrophoresis corresponding to Alphaproteobacteria and Actinobacteria decreased while Gammaproteobacteria increased during the 1 month incubation. This data suggests that estuarine bacterioplankton communities are influenced by variations in discharge patterns and use freshwater-originated DON as demonstrated by a shift in community structure. Bacteria in the genus Nitrosospira play the vital role of converting ammonia to nitrite via the enzymes ammonia monooxygenase and hydroxylamine oxidoreductase. Nitrosospira lacus strain APG3, isolated from Green Lake, Seattle, WA is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium that can grow at temperatures as low as 4°C. Nitrosospira lacus is able to grow over a wide pH range (5-9) and like other Nitrosospira, is susceptible to high ammonium concentrations. APG3 showed the ability to grow at low pH and use urea which may allow it to survive more efficiently in soil environments. 16S rRNA analysis revealed that the closest relative of APG3 is Nitrosospira multiformis (cluster 3). When using ANI values to compare APG3 to Nitrosospira multiformis, the ANI value demonstrates that they are related but different species that share less than half of their genome. Nitrosospira lacus is the first isolated cluster 0 representative. The distribution of Nitrosospira lacus like sequences reveals a habitat limitation to tropical and subtropical areas with a preference for waterlogged areas. The draft genome sequence comprises 3,107,181 bases at 272-fold coverage. The assembled draft genome consists of 84 contigs with an average size of 41,181 bp and a G+C content of 53.6%. The genome contains 3,147 protein-coding DNA sequences, 44 tRNA genes, and a single 16S-23S-5S rRNA operon. The genome revealed that Nitrosospira lacus represents a new species of cluster 0 Nitrosospira, which contains a slew of genes that allow it to incorporate nutrients from the environment. The genome of N. lacus when compared to other ammonia-oxidizing bacteria most closely resembles that of N. multiformis.The presence of hydrogenase and urease, suggests that Nitrosospira lacus may be able to meet its energy needs via alternative pathways. N. lacus also contains genes to cope with various degrees of stress, including detoxification, cold and heat shock proteins and oxidative and osmotic stress, copper, cobalt, zinc, and cadmium resistance. This unique genetic makeup may allow Nitrosospira lacus adaptability to a wide range of freshwater habitats.
Show less
Date Issued
2015
Identifier
Garcia_fgcu_1743_10123
Format
Document (PDF)
A high-resolution molecular method for identification of smalltooth sawfish prey
Title
A high-resolution molecular method for identification of smalltooth sawfish prey.
Creator
Hancock, Taylor Lee
Abstract / Description
The foundation of food web analysis is a solid understanding of predator-prey associations. Traditional dietary studies of fishes have been by stomach content analysis. However, these methods are not applicable to Critically Endangered species such as the smalltooth sawfish (Pristis pectinata). Previous research using the combination of stable isotope signatures from fin clips and 18S rRNA gene sequencing of fecal samples identified the smalltooth sawfish as piscivorous at high taxonomic...
Show moreThe foundation of food web analysis is a solid understanding of predator-prey associations. Traditional dietary studies of fishes have been by stomach content analysis. However, these methods are not applicable to Critically Endangered species such as the smalltooth sawfish (Pristis pectinata). Previous research using the combination of stable isotope signatures from fin clips and 18S rRNA gene sequencing of fecal samples identified the smalltooth sawfish as piscivorous at high taxonomic levels. Here, we present a high taxonomic resolution molecular technique for identification of prey using opportunistically acquired fecal samples. To assess potential biases, primer sets of two mitochondrial genes, 12S and 16S rRNA, were used alongside 18S rRNA, which targets a wider spectrum of taxa. In total, 19 fish species, from 7 orders and 11 families, native to the Gulf of Mexico were successfully identified, including one ray, the southern stingray (Dasyatis americana). Silver perch (Bairdiella chrysoura), bay anchovy (Anchoa mitchilli), tidewater mojarra (Eucinostomus harengulus), spotted seatrout (Cynoscion nebulosus), ladyfish (Elops saurus), and spot (Leiostomus xanthurus) were most prevalent in our analysis. The sawfish prey identified comprised diverse taxa, indicating that this species is a generalist piscivore. These findings and the molecular approach used will aid recovery planning for the smalltooth sawfish and has the potential to reveal previously unknown predator-prey associations from a wide range of taxa, being specifically desirable for use with rare and hard to sample species.
Show less
Date Issued
2019-06-05
Identifier
fgcu_ETD_0296
Format
Document (PDF)
Sympatric elasmobranchs and fecal samples provide insight into the trophic ecology of the smalltooth sawfish
Title
Sympatric elasmobranchs and fecal samples provide insight into the trophic ecology of the smalltooth sawfish.
Creator
Poulakis, Gregg R, Urakawa, Hidetoshi, Stevens, Philip W., DeAngelo, Jacquelyn A., Timmers, Amy A., Grubbs, R.Dean, Fisk, Aaron T., Olin, Jill A.
Abstract / Description
Growing concerns about the conservation of elasmobranchs have prompted a surge in research, because scientific studies that can support management actions are needed. Sawfishes are among the most threatened fishes worldwide and epitomize the challenge of conserving widely distributed, large-bodied marine fishes. We used a comparative approach to provide data on the trophic ecology of the smalltooth sawfish Pristis pectinata in the western Atlantic coastal waters of southwest Florida, USA....
Show moreGrowing concerns about the conservation of elasmobranchs have prompted a surge in research, because scientific studies that can support management actions are needed. Sawfishes are among the most threatened fishes worldwide and epitomize the challenge of conserving widely distributed, large-bodied marine fishes. We used a comparative approach to provide data on the trophic ecology of the smalltooth sawfish Pristis pectinata in the western Atlantic coastal waters of southwest Florida, USA. Specifically, we applied (1) stable isotope techniques to fin tissues of smalltooth sawfish and 2 sympatric elasmobranch species that have well-documented diets (i.e. bull shark Carcharhinus leucas and cownose ray Rhinoptera bonasus), and muscle tissue from a variety of known and potential prey species; and (2) an 18S rRNA gene sequencing technique to identify prey taxa in sawfish fecal samples. These analyses provided evidence that the smalltooth sawfish feeds primarily on teleost and elasmobranch fishes at all life stages even though sawfish move from estuarine to coastal habitats during their ontogeny. Although both sawfish and bull sharks occupy estuarine waters as juveniles and are piscivorous, the results also indicate that these species partition habitat. The cownose ray has been thought of as migratory throughout its range, but these data indicate that non-migratory, estuarine populations exist at lower latitudes. Collectively, these results will aid in the development of management decisions regarding these species and in improving long-term recovery planning for the smalltooth sawfish.
Show less
Date Issued
2017-06-15
Identifier
10.3354/esr00824, fgcu_ir_000033, http://www.int-res.com/abstracts/esr/v32/p491-506/
Format
Citation