Andrew R. Juhl

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the worlds oceans.

MECHANISMS OF FLUID SHEAR-INDUCED INHIBITION OF POPULATION GROWTH IN A RED-TIDE DINOFLAGELLATE1

Net population growth of some dinoflagellates is inhibited by fluid shear at shear stresses comparable with those generated during oceanic turbulence. Decreased net growth may occur through lowered cell division, increased mortality, or both. The dominant mechanism under various flow conditions was determined for the red‐tide dinoflagellate Lingulodinium polyedrum (Stein) Dodge. Cell division and mortality were determined by direct observation of isolated cells in 0.5‐mL cultures that were shaken to generate unquantified fluid shear. Larger volume cultures were exposed to quantified laminar shear in Couette‐flow chambers (0.004–0.019 N·m−2 shear stress) and to unquantified flow in shaken flasks. In these larger cultures, cell division frequency was calculated from flow cytometric measurements of DNA·cell−1. The mechanism by which shear inhibits net growth of L. polyedrum depends on shear stress level and growth conditions. Observations on the isolated cells showed that shaking inhibited growth by lowering cell division without increased mortality. Similar results were found for early exponential‐phase cultures exposed to the lowest experimental shear stress in Couette‐flow chambers. However, mortality occurred when a late exponential‐phase culture was exposed to the same low shear stress and was inferred to occur in cultures exposed to higher shear stresses. Elevated mortality in those treatments was confirmed using behavioral, morphological, and physiological assays. The results predict that cell division in L. polyedrum populations will be inhibited by levels of oceanic turbulence common for near‐surface waters. Shear‐induced mortality is not expected unless shear‐stress levels are unusually high or when cellular condition resembles late exponential/stationary phase cultures.

Antibiotic-resistant bacteria in the Hudson River Estuary linked to wet weather sewage contamination

Heterotrophic bacteria resistant to tetracycline and ampicillin were assessed in waterways of the New York City metropolitan area using culture-dependent approaches and 16S rRNA gene sequence analysis of resultant isolates. Resistant microbes were detected at all 10 sampling sites in monthly research cruises on the lower Hudson River Estuary (HRE), with highest concentrations detected at nearshore sites. Higher frequency sampling was conducted in Flushing Bay, to enumerate resistant microbes under both dry and wet weather conditions. Concentrations of ampicillin- and tetracycline-resistant bacteria, in paired samples, were positively correlated with one another and increased following precipitation. Counts of the fecal indicator, Enterococcus, were positively correlated with levels of resistant bacteria, suggesting a shared sewage-associated source. Analysis of 16S rRNA from isolates identified a phylogenetically diverse group of resistant bacteria, including genera containing opportunistic pathogens. The occurrence of Enterobacteriaceae, a family of enteric bacteria, was found to be significantly higher in resistant isolates compared to total heterotrophic bacteria and increased following precipitation. This study is the first to document the widespread distribution of antibiotic-resistant bacteria in the HRE and to demonstrate clearly a link between the abundance of antibiotic-resistant bacteria and levels of sewage-associated bacteria in an estuary.

Environmental controls on coastal coarse aerosols: implications for microbial content and deposition in the near-shore environment.

Coarse aerosols (particle diameter (D(p)) > 2 μm) produced in coastal surf zones carry chemical and microbial content to shore, forming a connection between oceanic, atmospheric, and terrestrial systems that is potentially relevant to coastal ecology and human health. In this context, the effects of tidal height, wind speed, and fog on coastal coarse aerosols and microbial content were quantified on the southern coast of Maine, USA. Aerosols at this site displayed clear marine influence and had high concentrations of ecologically relevant nutrients. Coarse aerosol concentrations significantly increased with tidal height (i.e., decreasing distance from waterline), onshore wind speed, and fog presence. As onshore wind speeds rose above 3 m s(-1), the mean half-deposition distance of coarse aerosols increased to an observed maximum of 47.6 ± 10.9 m from the waters edge at wind speeds from 5.5-8 m s(-1). Tidal height and fog presence did not significantly influence total microbial aerosol concentrations but did have a significant effect on culturable microbial aerosol fallout. At low wind speeds, culturable microbial aerosols falling out near-shore decreased by half at a distance of only 1.7 ± 0.4 m from the waters edge, indicating that these microbes may be associated with large coarse aerosols with rapid settling rates.

Effect of environmental variables on eukaryotic microbial community structure of land-fast Arctic sea ice

Sea ice microbial community structure affects carbon and nutrient cycling in polar seas, but its susceptibility to changing environmental conditions is not well understood. We studied the eukaryotic microbial community in sea ice cores recovered near Point Barrow, AK in May 2006 by documenting the composition of the community in relation to vertical depth within the cores, as well as light availability (mainly as variable snow cover) and nutrient concentrations. We applied a combination of epifluorescence microscopy, denaturing gradient gel electrophoresis and clone libraries of a section of the 18S rRNA gene in order to compare the community structure of the major eukaryotic microbial phylotypes in the ice. We find that the community composition of the sea ice is more affected by the depth horizon in the ice than by light availability, although there are significant differences in the abundance of some groups between light regimes. Epifluorescence microscopy shows a shift from predominantly heterotrophic life styles in the upper ice to autotrophy prevailing in the bottom ice. This is supported by the statistical analysis of the similarity between the samples based on the denaturing gradient gel electrophoresis banding patterns, which shows a clear difference between upper and lower ice sections with respect to phylotypes and their proportional abundance. Clone libraries constructed using diatom-specific primers confirm the high diversity of diatoms in the sea ice, and support the microscopic counts. Evidence of protistan grazing upon diatoms was also found in lower sections of the core, with implications for carbon and nutrient recycling in the ice.

Local Environmental Pollution Strongly Influences Culturable Bacterial Aerosols at an Urban Aquatic Superfund Site

In polluted environments, when microbial aerosols originate locally, species composition of the aerosols should reflect the polluted source. To test the connection between local environmental pollution and microbial aerosols near an urban waterfront, we characterized bacterial aerosols at Newtown Creek (NTC), a public waterway and Superfund site in a densely populated area of New York, NY, USA. Culturable bacterial aerosol fallout rate and surface water bacterial concentrations were at least an order of magnitude greater at NTC than at a neighboring, less polluted waterfront and a nonurban coastal site in Maine. The NTC culturable bacterial aerosol community was significantly different in taxonomic structure from previous urban and coastal aerosol studies, particularly in relative abundances of Actinobacteria and Proteobacteria. Twenty-four percent of the operational taxonomic units in the NTC overall (air + water) bacterial isolate library were most similar to bacterial 16S rRNA gene sequences previously described in terrestrial or aquatic environments contaminated with sewage, hydrocarbons, heavy metals, and other industrial waste. This study is the first to examine the community composition and local deposition of bacterial aerosols from an aquatic Superfund site. The findings have important implications for the use of aeration remediation in polluted aquatic environments and suggest a novel pathway of microbial exposure in densely populated urban communities containing contaminated soil and water.

Hydrodynamic stimulation of dinoflagellate bioluminescence: a computational and experimental study

SUMMARY Dinoflagellate bioluminescence provides a near-instantaneous reporter of cell response to flow. Although both fluid shear stress and acceleration are thought to be stimulatory, previous studies have used flow fields dominated by shear. In the present study, computational and experimental approaches were used to assess the relative contributions to bioluminescence stimulation of shear stress and acceleration in a laminar converging nozzle. This flow field is characterized by separate regions of pronounced acceleration away from the walls, and shear along the wall. Bioluminescence of the dinoflagellates Lingulodinium polyedrum and Ceratocorys horrida, chosen because of their previously characterized different flow sensitivities, was imaged with a low-light video system. Numerical simulations were used to calculate the position of stimulated cells and the levels of acceleration and shear stress at these positions. Cells were stimulated at the nozzle throat within the wall boundary layer where, for that downstream position, shear stress was relatively high and acceleration relatively low. Cells of C. horrida were always stimulated significantly higher in the flow field than cells of L. polyedrum and at lower flow rates, consistent with their greater flow sensitivity. For both species, shear stress levels at the position of stimulated cells were similar to but slightly greater than previously determined response thresholds using independent flow fields. L. polyedrum did not respond in conditions where acceleration was as high as 20 g. These results indicate that shear stress, rather than acceleration, was the stimulatory component of flow. Thus, even in conditions of high acceleration, dinoflagellate bioluminescence is an effective marker of shear stress.

Toxicity of Alexandrium lusitanicum to gastropod larvae is not caused by paralytic-shellfish-poisoning toxins

Laboratory grazing experiments compared ingestion of two subclones of the dinoflagellate Alexandrium lusitanicum by gastropod veliger larvae (Nassarius sp.). While the two prey subclones originated from the same monoclonal isolate of A. lusitanicum, one possessed the ability to produce paralytic-shellfish-poisoning toxins (PSTs), while the other did not. Ingestion rates on the two Alexandrium subclones were not significantly different over a range of prey concentrations (approximately 100 - 660 cells ml-1), indicating that PSTs did not serve as a grazing deterrent for these larvae. However, ingestion rates on both subclones were low at the higher prey concentrations tested. Mortality of the predators also increased linearly with concentration of either subclone. These observations indicated that both A. lusitanicum subclones produced an unknown substance that inhibited and killed the grazers. Veliger mortality was not induced by culture filtrates or lysates, suggesting either that the substance was either highly labile or that contact with intact cells was required. Because toxic algae can produce multiple bioactive substances, experimental demonstrations of alleopathic effects of toxic species should not be assigned to known toxins without supporting evidence. In addition, the results show that the effectiveness of algal grazing deterrents can increase with cell concentration, which may have implications for bloom dynamics.

Challenges to Managing Microbial Fecal Pollution in Coastal Environments: Extra-Enteric Ecology and Microbial Exchange Among Water, Sediment, and Air

Human population growth, especially in coastal urban cities, increases the potential for fecal pollution of adjacent waterways, requiring continued advances in pollution monitoring and management. Infections remain the largest health risk from contact with fecal- and sewage-polluted waters, and a small number of fecal indicator bacteria (FIB) are used as primary pollution assessment tools. While FIB continue to be useful tools, some of the assumptions about the behavior of FIB in the environment, and the associated pathways for pathogen exposure, have come into question. Research into the extra-enteric ecology of these indicators has identified management-relevant complexities including particle association, prolonged environmental persistence, and multidirectional microbial exchange among water, sediment, and air. These complexities provide opportunities for improving current monitoring and modeling strategies and to better understand exposure pathways for sewage-related infections.

Spatial patterns of pharmaceuticals and wastewater tracers in the Hudson River Estuary

The widespread use of pharmaceuticals by human populations results in their sustained discharge to surface waters via wastewater treatment plants (WWTPs). In this study, 16 highly prescribed pharmaceuticals were quantified along a 250 km transect of the Hudson River Estuary and New York Harbor to describe their sources and spatial patterns. Sampling was conducted over two dry weather periods in May and July 2016, at 72 sites which included mid-channel and nearshore sites, as well as locations influenced by tributaries and WWTP outfalls. The detection frequency of the study pharmaceuticals was almost identical between the May and July sampling periods at 55% and 52%, respectively. Six pharmaceuticals were measurable at 92% or more of the sites during both sampling periods, illustrating their ubiquitous presence throughout the study area. Individual pharmaceutical concentrations were highly variable spatially, ranging from non-detect to 3810 ng/L during the study. Major factors controlling concentrations were proximity and magnitude of WWTP discharges, inputs from tributaries and tidal mixing. Two compounds, sucralose and caffeine, were evaluated as tracers to identify wastewater sources and assess pharmaceutical behavior. Sucralose was useful in identifying wastewater inputs to the river and concentrations showed excellent correlations with numerous pharmaceuticals in the study. Caffeine-sucralose ratios showed potential in identifying discharges of untreated wastewater occurring during a combined sewage overflow event. Many of the study pharmaceuticals were present throughout the Hudson River Estuary as a consequence of sustained wastewater discharge. Whereas some concentrations were above published effects levels, a more complete risk assessment is needed to understand the potential for ecological impacts due to pharmaceuticals in the Hudson River Estuary.