Current Search: UWF Theses and Dissertations (x) » Jeffrey, Wade H. (x)
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- Title
- LATITUDINAL PATTERNS OF CILIATE RDNA DIVERSITY IN THE SURFACE PLANKTON OF THE PACIFIC OCEAN.
- Author
- Covell, Marthe Adrienne, Caffrey, Jane M., Moss, Joseph A., Jeffrey, Wade H., Ryals, Phillip E., University of West Florida
- Abstract/Description
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Unicellular organisms known as ciliates (Phylum: Ciliophora) are a widespread and ecologically important group of eukaryotic microorganisms. Despite their critical roles in the microbial and planktonic food webs, their global distribution patterns remain poorly understood. It is unclear whether ciliates follow the same latitudinal gradient patterns that have been identified for macroscopic organisms, which generally show an increase in biodiversity and species richness approaching the equator...
Show moreUnicellular organisms known as ciliates (Phylum: Ciliophora) are a widespread and ecologically important group of eukaryotic microorganisms. Despite their critical roles in the microbial and planktonic food webs, their global distribution patterns remain poorly understood. It is unclear whether ciliates follow the same latitudinal gradient patterns that have been identified for macroscopic organisms, which generally show an increase in biodiversity and species richness approaching the equator. Some microbial ecologists believe that ciliates do not have the same types of dispersal limitations as larger organisms and therefore will have ubiquitous distribution, while others argue that there is evidence of endemic species in specialized oceanic environments In this study, ciliate rDNA diversity was examined along a 15,400 km transect of the Pacific Ocean in order to identify distributional patterns. A combination of molecular techniques including terminal restriction fragment length polymorphism (T-RFLP) analysis, molecular cloning, and DNA sequencing were used to document patterns of biodiversity. Statistical analyses show that there is no significant relationship between latitude and ciliate distribution. This study provides a broad understanding of the distribution patterns of marine ciliates, as well as adds to our understanding of the global biogeography of microscopic organisms.
Show less - Date Issued
- 2016
- Identifier
- WFE0000553, uwf:61241
- Format
- Document (PDF)
- Title
- MICROBIAL BIOGEOGRAPHY IN THE WATER COLUMN AND SEDIMENTS OF THE NORTHEASTERN GULF OF MEXICO.
- Author
- Henriksson, Nine Lisa, Snyder, Richard A., Moss, Joseph A., Pomory, Christopher M., Jeffrey, Wade H., University of West Florida
- Abstract/Description
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Through their metabolic activities marine microbes are essential for marine biogeochemical cycles. Charting their spatial distribution and biogeographical patterns is important in order to increase knowledge of what drives these microbial communities. We evaluated the bacterial communities at 22 locations in the northeast Gulf of Mexico during the summer months of 2013. Surface, water column, and surface sediment samples totaled 91 communities. Metadata and physical parameters measurements...
Show moreThrough their metabolic activities marine microbes are essential for marine biogeochemical cycles. Charting their spatial distribution and biogeographical patterns is important in order to increase knowledge of what drives these microbial communities. We evaluated the bacterial communities at 22 locations in the northeast Gulf of Mexico during the summer months of 2013. Surface, water column, and surface sediment samples totaled 91 communities. Metadata and physical parameters measurements were collected at each location. Seawater (~20L) was collected on Sterivex filters and stored at -80U+00B0 C until gDNA extraction and subsequent Illumina sequencing (MiSeq), targeting the 16S rRNA gene. OTU picking routines generated over 280,000 OTU's and identified >14 million sequences across the dataset. Alpha diversity estimates revealed significant distinction between water column samples (Surface and Intermediate samples) and benthic samples (Sediment, Core and WOC) in terms of richness and Chao1 diversity, with the latter group prevailing. The eight most prevalent OTU's comprised 15% of the dataset population and were predominantly located in water column samples; Synechococcus (5.29%), Alteromonas (1.6%) and Prochlorococcus (1.51%) were the only groups previously classified. In contrast, most of these highly abundant groups existed in very small numbers in the benthic samples. Significant correlation was found between environmental parameters and the water column biological community. According to primer6 BEST analysis, temperature, longitude, dissolved oxygen, fluorescence, and nitrate/nitrite exert notable influence on the northeast GoM bacterial community structure.
Show less - Date Issued
- 2017
- Identifier
- WFE0000572, uwf:61178
- Format
- Document (PDF)
- Title
- PERSISTENCE OF MOLECULAR INDICATORS FOR FECAL POLLUTION IN ENVIRONMENTAL WATERS, DEMONSTRATED IN MESOCOSMS USING A METHOD THAT DISTINGUISHES LIVE FROM DEAD MICROORGANISMS.
- Author
- Kennedy, Elizabeth Marie, Lepo, Joe E., Harwood, Valerie J., Jeffrey, Wade H., Snyder, Richard A., University of West Florida
- Abstract/Description
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Polymerase chain reaction (PCR) methods to detect indicators of fecal contamination are more rapid and specific than current government-recommended culture-based methods. However, PCR does not distinguish among live cells, dead cells or extracellular DNA. Propidium monoazide (PMA) is a DNA-binding dye that only permeates membrane-compromised (dead) cells. Once inside a dead cell, it binds DNA, preventing subsequent PCR amplification, allowing for PCR detection of only live cells. I used PMA...
Show morePolymerase chain reaction (PCR) methods to detect indicators of fecal contamination are more rapid and specific than current government-recommended culture-based methods. However, PCR does not distinguish among live cells, dead cells or extracellular DNA. Propidium monoazide (PMA) is a DNA-binding dye that only permeates membrane-compromised (dead) cells. Once inside a dead cell, it binds DNA, preventing subsequent PCR amplification, allowing for PCR detection of only live cells. I used PMA coupled with quantitative PCR (qPCR) to compare persistence of live human-associated Bacteroidetes (HB) and Methanobrevibacter smithii to dead HB and M. smithii and their extracellular DNA. The HB qPCR signal was detected for 5 to 6 days (d) in mesocosms and was unaffected by PMA treatment. Thus, HB DNA, detected by PCR, was due to live bacteria and would indicate recent human fecal contamination if present in natural water. In contrast, the M. smithii qPCR signal persisted the entire study without PMA treatment but only 5 to 6 d with PMA treatment. Thus, although live M. smithii decreased in the mesocosms, its DNA persisted. Thus, M. smithii DNA, as detected by PCR, could be due to live cells, dead cells or extracellular DNA, leading to false indication of fecal contamination.
Show less - Date Issued
- 2011
- Identifier
- WFE0000274, uwf:60885
- Format
- Document (PDF)
- Title
- QUANTIFYING HABITAT AND APPLE SNAIL (POMACEA PALUDOSA) DENSITY EFFECTS ON PREY AVAILABILITY TO SNAIL KITES (ROSTRHAMUS SOCIABILIS PLUMBEUS).
- Author
- Coppola, Philip Michael, Darby, Philip C., Jeffrey, Wade H., Meyer, Kenneth D., University of West Florida
- Abstract/Description
-
Everglades restoration efforts rely on quantitative data when modelling the effects of management on endangered wildlife populations. The focus of this study was to quantify the influence of environmental factors on Florida apple snail (Pomacea paludosa) availability to snail kites (Rostrhamus sociabilis plumbeus) within the Everglades. A mesocosm study with observations of live apple snails was performed within Everglades wetlands to determine the influence of water depth, water temperature,...
Show moreEverglades restoration efforts rely on quantitative data when modelling the effects of management on endangered wildlife populations. The focus of this study was to quantify the influence of environmental factors on Florida apple snail (Pomacea paludosa) availability to snail kites (Rostrhamus sociabilis plumbeus) within the Everglades. A mesocosm study with observations of live apple snails was performed within Everglades wetlands to determine the influence of water depth, water temperature, dissolved oxygen, and emergent vegetation structure on the proportion of apple snails available to foraging snail kites. In addition, a study analyzing snail kite prey species (native P. paludosa versus exotic P. maculata) and size preference was performed. The proportion of apple snails available to kites was most influenced by water depth and temperature, where warm, shallow water contained the highest proportion of snails available. Emergent vegetation did not affect snail surfacing behavior; however, it did influence the relative detectability of snails. Snail kites preferentially consumed intermediate-sized snails and showed no species preference. This study supports the recommendation that demographic modeling of Everglades-dependent wildlife should incorporate the most ecologically-pertinent parameters. Estimates of snail availability can be used to link two thus far-independent simulation models for snail kite and apple snail populations.
Show less - Date Issued
- 2016
- Identifier
- WFE0000552, uwf:61223
- Format
- Document (PDF)
- Title
- RESPONSES IN BACTERIOPLANKTON PRODUCTION AND COMMUNITY STRUCTURE AFTER EXPOSURE TO OIL AND DISPERSANT IN THE NORTHEASTERN GULF OF MEXICO.
- Author
- Houghton, Katelyn Ashley, Jeffrey, Wade H., Lepo, Joe E., Snyder, Richard A., University of West Florida
- Abstract/Description
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The Deepwater Horizon Oil Spill in 2010 significantly impacted the planktonic ecosystem of the northern Gulf of Mexico. A key element of this ecosystem is the bacterioplankton. They are the base to the food web and were the primary agents of oil degradation. It has been hypothesized that exposure to oil and or dispersants may change microbial community structure by selecting for those strains capable of utilizing oil carbon while selecting against others by toxic effects of oil and or...
Show moreThe Deepwater Horizon Oil Spill in 2010 significantly impacted the planktonic ecosystem of the northern Gulf of Mexico. A key element of this ecosystem is the bacterioplankton. They are the base to the food web and were the primary agents of oil degradation. It has been hypothesized that exposure to oil and or dispersants may change microbial community structure by selecting for those strains capable of utilizing oil carbon while selecting against others by toxic effects of oil and or dispersants. To view spatial and temporal variability in bacterioplankton community response, surface and near bottom water samples were collected at two sites, offshore Choctawhatchee Bay, Florida, in winter (December 2012) and summer (June 2013). Bioassays were performed on 1 L water samples amended with oil, oil and Corexit, and Corexit alone, and compared to an un-amended control. Samples were incubated at in situ temperatures for two days in the dark and 16S rRNA genes were amplified and sequenced. Community structure shifts and production changes were associated mostly with the oil treatment, while Corexit alone had the smallest effect. Trends for community response were more significantly influenced by collection site parameters, namely season and depth, than by treatments.
Show less - Date Issued
- 2015
- Identifier
- WFE0000481, uwf:61118
- Format
- Document (PDF)
- Title
- SPATIAL AND TEMPORAL VARIATIONS IN THE COMMUNITY STRUCTURE OF MARINE ARCHAEA IN THE NORTHEASTERN GULF OF MEXICO.
- Author
- Tominack, Sarah Anne, Snyder, Richard A., Moss, Joseph A., Riesenfeld, Christian S., Richardson, Terry D., Jeffrey, Wade H., University of West Florida
- Abstract/Description
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Archaea, once thought to solely inhabit extreme environments, are now known to be widespread and have major roles in biogeochemical cycling. Archaea are known to utilize refractory compounds as an energy source and compete with bacteria in the open ocean for labile, often limiting, nutrients. In the Gulf of Mexico the BP Deepwater Horizon oil well failure (2010) highlighted the need to better understand basic physical, chemical, and biological dynamics of the North Eastern Gulf of Mexico (NE...
Show moreArchaea, once thought to solely inhabit extreme environments, are now known to be widespread and have major roles in biogeochemical cycling. Archaea are known to utilize refractory compounds as an energy source and compete with bacteria in the open ocean for labile, often limiting, nutrients. In the Gulf of Mexico the BP Deepwater Horizon oil well failure (2010) highlighted the need to better understand basic physical, chemical, and biological dynamics of the North Eastern Gulf of Mexico (NE GoM). Through 16S rRNA clone library analysis, this study characterized the spatial and temporal dynamics of archaeal communities on the Northwest Florida Shelf in the NE GoM. In addition, patterns in physicochemical parameters were examined and relationships between Archaea and the environment in the NE GoM explored. Four main archaeal assemblages were observed: a seasonally independent near coastal assemblage, a seasonally dependent epipelagic assemblage, a seasonally independent mesopelagic assemblage, and a unique seasonally independent sediment assemblage. The main environmental factors associated with archaeal community structure in the water column were nutrients and salinity, but no environmental factors measured accounted for variability in sediment archaeal communities.
Show less - Date Issued
- 2015
- Identifier
- WFE0000492, uwf:61130
- Format
- Document (PDF)
- Title
- TAXONOMIC AND METABOLIC CHARACTERIZATION OF BACTERIA ISOLATED FROM GULF OF MEXICO SEDIMENTS AFFECTED BY THE DEEPWATER HORIZON OIL SPILL.
- Author
- Davis, Bryan David, Lepo, Joe Eugene, Snyder, Richard A., Jeffrey, Wade H., Riesenfeld, Christian, University of West Florida
- Abstract/Description
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Recent studies of microbial response to the BP Deepwater Horizon oil spill have relied on non-culture based molecular biological tools for community structure analyses. To complement these studies, we enriched and isolated bacteria that utilize petroleum hydrocarbons as their sole C-source from sediments within the zone of impact. Deep-sea and near-shore sediments collected along a transect crossing the well-head of the Gulf of Mexico (GoM) BP oil spill were stored at 4C. Homogenized...
Show moreRecent studies of microbial response to the BP Deepwater Horizon oil spill have relied on non-culture based molecular biological tools for community structure analyses. To complement these studies, we enriched and isolated bacteria that utilize petroleum hydrocarbons as their sole C-source from sediments within the zone of impact. Deep-sea and near-shore sediments collected along a transect crossing the well-head of the Gulf of Mexico (GoM) BP oil spill were stored at 4C. Homogenized sediments were inoculated into Bushnell-Haas broth containing n-hexadecane, a PAH mix, and artificially weathered crude oil. Enrichments were shaken at 25C until turbid, then streaked to trypticase-soy agar. Unique colonies inoculated to sole C-source (phenanthrene or n-hexadecane) media ensured ability to grow on those substrates. In total, 138 strains have been isolated and maintained. The 16S rRNA genes of isolates were PCR amplified and sequenced, elucidating 14 genera from bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria (all of which were within Class Gammaproteobacteria). Selected strains have been characterized using standard microbiological staining and testing. Many of our isolates represent bacterial taxa known to contain hydrocarbon degraders; individual isolates have been confirmed in our laboratory as presumptive hydrocarbon degraders.
Show less - Date Issued
- 2014
- Identifier
- WFE0000461, uwf:61131
- Format
- Document (PDF)
- Title
- TEMPORAL ANALYSIS OF BACTERIAL COMMUNITY STRUCTURE IN THE NORTH EASTERN GULF OF MEXICO.
- Author
- Knight, Katelyn T., Jeffrey, Wade H., Caffrey, Jane M., Snyder, Richard A., University of West Florida
- Abstract/Description
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Bacteria are found in all oceans around the globe and dominate marine processes because of their abundance and contribution to biogeochemical cycles. Resource availability and environmental parameters are both key factors in determining bacterioplankton growth and community structure. Understanding temporal changes in the microbial community structure in the Gulf of Mexico has the potential to shed new light on the dynamics of energy transfer and organic processing. A two-year seasonal study...
Show moreBacteria are found in all oceans around the globe and dominate marine processes because of their abundance and contribution to biogeochemical cycles. Resource availability and environmental parameters are both key factors in determining bacterioplankton growth and community structure. Understanding temporal changes in the microbial community structure in the Gulf of Mexico has the potential to shed new light on the dynamics of energy transfer and organic processing. A two-year seasonal study was conducted at a station 40 km south of Choctawhatchee Bay on the Florida Shelf in the Northeast Gulf of Mexico. A total of 31 water column samples were collected from surface and bottom waters (~90 m) and mid-water deep chlorophyll maxima, when present, at 12 different time points. In addition to microbial diversity, chemical, physical, and biological environmental parameters such as bacterial production, nutrients, temperature, salinity, chlorophyll a, and bacterial counts were also taken. 16S rRNA clone libraries generated 2,160 high quality clones that were used for community analysis. 535 OTUs were obtained at 97% similarity. Samples were analyzed in three different categorical groupings: all OTUs, all OTUs grouped together at order level, and OTUs without dominant taxa. Environmental patterns were seen to correlate directly with seasonal changes; however, community structure was independent of seasonal trends. Depth, nutrients, and salinity were seen to have a slight influence on the community structure. This shows that no single parameter is driving the community structure, but rather the community structure is the result of complex interactions between many factors.
Show less - Date Issued
- 2018
- Identifier
- WFE0000619, uwf:61281
- Format
- Document (PDF)
- Title
- THE EFFECT OF FISH SIZE, HABITAT TYPE, AND THE DEEPWATER HORIZON OIL SPILL ON RED SNAPPER, LUTJANUS CAMPECHANUS, DIET AND TROPHIC ECOLOGY IN THE NORTHERN GULF OF MEXICO.
- Author
- Tarnecki, Joseph Henry, Patterson, William F., III, Snyder, Dick A., Jeffrey, Wade H., University of West Florida
- Abstract/Description
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Red snapper, Lutjanus campechanus, were sampled with hook and line at natural (n = 33) and artificial (n = 27) reef sites in the northern Gulf of Mexico from 2009-2011. Stomachs (n = 708) were extracted and their contents preserved for gut content analysis, and muscle tissue samples (n = 200) were dissected and frozen for stable isotope ratio-mass spectrometry (delta13C, delta15N, and delta34S) analysis. Forty-eight percent of sampled fish had identifiable prey which were grouped into seven...
Show moreRed snapper, Lutjanus campechanus, were sampled with hook and line at natural (n = 33) and artificial (n = 27) reef sites in the northern Gulf of Mexico from 2009-2011. Stomachs (n = 708) were extracted and their contents preserved for gut content analysis, and muscle tissue samples (n = 200) were dissected and frozen for stable isotope ratio-mass spectrometry (delta13C, delta15N, and delta34S) analysis. Forty-eight percent of sampled fish had identifiable prey which were grouped into seven categories: fish, decapods, cephalopods, stomatopods, gastropods, zooplankton, and other invertebrates. A permutational multivariate analysis of variance (PERMANOVA) was computed to test the effect of fish size, habitat type, and the Deepwater Horizon Oil Spill (DHOS) on red snapper diet. Fish size (PERMANOVA, p = 0.021), and the DHOS (PERMANOVA, p = 0.001) were both significant effects in the model, but interactions between habitat type and the DHOS (PERMANOVA, p = 0.049) was also significant. Significant differences in diet among red snapper size categories were due to low trophic position prey items, such as pelagic zooplankton, being more abundant in the diet of larger (>500mm) red snapper, while red snapper in smaller size classes contained greater amounts of higher trophic level prey such decapods and fish. Although no significant difference existed in red snapper diet between habitat types, they consumed slightly higher amounts of decapods at artificial reefs (21.9% of total diet) than natural (14.8%). The significant DHOS effect was driven by an increase in fish and a decrease in zooplankton in red snapper diet following the spill; however, this effect cannot be interpreted independently given the significant interaction between habitat type and the DHOS effect. Zooplankton prey consumption declined and fish consumption increased for red snapper sampled at both artificial and natural reefs after the DHOS, but fish consumption increased to a greater extent at artificial reef sites following the spill. A significant increase in delta15N after the DHOS (ANOVA, p <0.001) also indicates red snapper sampled fed on higher trophic position prey following the spill, and lower delta34S values indicate an increase in benthic versus pelagic prey consumption following the DHOS (ANOVA, p <0.001). The ontogenetic shift in diet observed via gut content analysis was also apparent in the significant effect of fish size on delta15N (ANOVA, p = 0.015). Overall, results clearly indicate the DHOS affected red snapper diet and trophic position and likely affected the abundance of prey resources as well. Study results also confirm the utility of stable isotope analysis to infer aspects of reef fish trophic ecology.
Show less - Date Issued
- 2014
- Identifier
- WFE0000453, uwf:61087
- Format
- Document (PDF)
- Title
- THE EFFECTS OF HUMAN AND CLIMATIC IMPACTS ON SEDIMIENT NITROGEN DYNAMICS IN ESCAMBIA BAY, FLORIDA.
- Author
- Smith, Kristin Anne, Caffrey, Jane M., Jeffrey, Wade H., Snyder, Richard A., University of West Florida
- Abstract/Description
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Potential nitrification rates and benthic flux measurements (NO2-+NO3-, NH4+, DIP, DSi, and SOC) were measured during the fall of 2005 at 12 different sites in Escambia Bay, Florida. Escambia Bay is a highly productive estuary whose major environmental problems include urban and agricultural runoff and point source discharges. A significant industrial spill occurred in 1969 when Monsanto Industrial Plant contaminated the bay with polychlorinated biphenyls (PCBs), which are still present in...
Show morePotential nitrification rates and benthic flux measurements (NO2-+NO3-, NH4+, DIP, DSi, and SOC) were measured during the fall of 2005 at 12 different sites in Escambia Bay, Florida. Escambia Bay is a highly productive estuary whose major environmental problems include urban and agricultural runoff and point source discharges. A significant industrial spill occurred in 1969 when Monsanto Industrial Plant contaminated the bay with polychlorinated biphenyls (PCBs), which are still present in the sediment over 40 years later. While PCB effects on marine life are well documented, much less is known of its effects on sediment nitrogen dynamics. Due to the sensitivity of nitrifying bacteria, PCBs were hypothesized to inhibit potential nitrification rates, but this study found no trend between PCB content and potential nitrification rates. In addition to anthropogenic effects, climatic impacts, such as two hurricanes, have affected the bay in recent years. Benthic fluxes from 2005 were compared to prestorm flux data and no significant long term storm effects were found. Potential nitrification rates from 2005 were compared to prestorm 2004 potential nitrification rates and significant differences were seen at the shallow site, but not at the deeper site.
Show less - Date Issued
- 2006
- Identifier
- WFE0000008, uwf:60749
- Format
- Document (PDF)
- Title
- ULTRAVIOLET RADIATION AND TEMPERATURE EFFECTS ON BACTERIOPLANKTON COMMUNITY STRUCTURE IN LAKE GILES, PENNSYLVANIA.
- Author
- Hunter, Erin Mitchell, Jeffrey, Wade H., Caffrey, Jane M., Riesenfeld, Christian, Leech, Dina M., University of West Florida
- Abstract/Description
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Ultraviolet radiation (UVR) and temperature effects on bacterioplankton community structure were analyzed after a ten-day microcosm study following spring ice melt-out in Lake Giles, PA. Bacterial community DNA patterns and subsequent phylogenetic assignments were produced using terminal restriction length polymorphisms (T-RFLP) and matched to ribosomal database project (RDP-II) gene sequence entries. The primary environmental stressor shifting community composition was UVR, while warm or...
Show moreUltraviolet radiation (UVR) and temperature effects on bacterioplankton community structure were analyzed after a ten-day microcosm study following spring ice melt-out in Lake Giles, PA. Bacterial community DNA patterns and subsequent phylogenetic assignments were produced using terminal restriction length polymorphisms (T-RFLP) and matched to ribosomal database project (RDP-II) gene sequence entries. The primary environmental stressor shifting community composition was UVR, while warm or cold water incubations, at 5-degree increments, either increased or decreased the shift. All UVR exposed samples had decreased diversity and richness compared to UVR blocked samples. Warm water incubations under UVR stress maintained more diversity than cold-water incubations. Species dominance patterns were altered between phyla and within classes of bacteria in each sample. Specifically, Alphaproteobacteria, a dominant bacterial class with diverse members, had different species composition in UVR exposed and blocked samples. Possible UVR tolerance was assigned to different phyla or classes of bacteria. Alpha- and Betaproteobacteria, Firmicutes, and Chlorobi were assigned as UVR resistant. With less certainty Gammaproteobacteria and Cyanobacteria were also assigned UVR resistant. Phylum Tenericutes was assigned as UVR sensitive. The results present a first approximation of UVR resistance and sensitivity to bacterioplankton from Lake Giles using TRFLP and predicted gene sequences.
Show less - Date Issued
- 2014
- Identifier
- WFE0000445, uwf:61098
- Format
- Document (PDF)