Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom

There is growing interest in the use of metatranscriptomics to study virus community dynamics. We used RNA samples collected from harmful brown tides caused by the eukaryotic alga Aureococcus anophagefferens within New York (United States) estuaries and in the process observed how preprocessing of libraries by either selection for polyadenylation or reduction in ribosomal RNA (rRNA) influenced virus community analyses. As expected, more reads mapped to the A. anophagefferens genome in polyadenylation-selected libraries compared to the rRNA-reduced libraries, with reads mapped in each sample correlating to one another regardless of preprocessing of libraries. Yet, this trend was not seen for reads mapping to the Aureococcus anophagefferens Virus (AaV), where significantly more reads (approximately two orders of magnitude) were mapped to the AaV genome in the rRNA-reduced libraries. In the rRNA-reduced libraries, there was a strong and significant correlation between reads mappings to AaV and A. anophagefferens. Overall, polyadenylation-selected libraries produced fewer viral contigs, fewer reads mapped to viral contigs, and different proportions across viral realms and families, compared to their rRNA-reduced pairs. This study provides evidence that libraries generated by rRNA reduction and not selected for polyadenylation are more appropriate for quantitative characterization of viral communities in aquatic ecosystems by metatranscriptomics.

Download Full-text

Impacts of nutrients and grazing mortality on the abundance of Aureococcus anophagefferens during a New York brown tide bloom

Limnology and Oceanography ◽

10.4319/lo.2002.47.1.0129 ◽

2002 ◽

Vol 47 (1) ◽

pp. 129-141 ◽

Cited By ~ 99

Author(s):

Christopher J. Gobler ◽

Marc J. Renaghan ◽

Nathaniel J. Buck

Keyword(s):

New York ◽

Brown Tide ◽

Aureococcus Anophagefferens ◽

Grazing Mortality ◽

Brown Tide Bloom

Download Full-text

Three-Dimensional Movements and Habitat Selection of Young White Sharks (Carcharodon carcharias) Across a Temperate Continental Shelf Ecosystem

Frontiers in Marine Science ◽

10.3389/fmars.2021.643831 ◽

2021 ◽

Vol 8 ◽

Author(s):

Rachel L. Shaw ◽

Tobey H. Curtis ◽

Gregory Metzger ◽

Michael P. McCallister ◽

Alisa Newton ◽

...

Keyword(s):

New York ◽

Continental Shelf ◽

Three Dimensional ◽

Sea Surface ◽

Cold Pool ◽

Shark Species ◽

Carcharodon Carcharias ◽

Selection For ◽

Shelf Region

As highly mobile predators with extensive home ranges, some shark species often utilize a continuum of habitats across the continental shelf ranging from the surf zone to the open ocean. For many species, these cross-shelf distributions can change depending on ontogeny or seasonal conditions. Recent research has confirmed a white shark (Carcharodon carcharias) summer nursery off Long Island, New York; however, habitat characterization of this nursery has not yet been conducted nor has fine-scale analysis of vertical behavior. Between 2016 and 2019, 21 young-of-the-year and juvenile white sharks were fitted with satellite and acoustic tags to examine distribution and selection for a suite of oceanographic variables during their late summertime (i.e., August to October) residence in the New York Bight. Horizontal position estimates were used to extract a suite of environmental measurements via remote sensing platforms and were linked with vertical profiles to produce three-dimensional movements for a subset of individuals also fitted with pop-up satellite archival tags (n = 7). Sharks exhibited horizontal movements parallel to Long Island’s southern shoreline and coastal New Jersey, with distances from 0.1 to 131.5 km from shore. Log-likelihood chi-square analyses determined selection for waters with underlying bathymetry of 20–30 m, sea surface temperatures between 20.0 and 22.0°C, sea surface salinities between 31.0 and 32.0 ppt, and chlorophyll-a concentrations between 2.0 and 8.0 mg⋅m–3. Multiple individuals also traversed the mid- to outer shelf region after leaving the Montauk tagging area. Vertical depth profiles illustrated oscillations between the surface and 199 m of water, with an average swimming depth of 9.2 ± 8.9 m. Water column temperatures during these oscillations ranged between 7.9 and 26.2°C (mean = 19.5 ± 2.0°C) with several individuals traversing highly stratified regions presumably associated with a mid-shelf cold pool adjacent to the Hudson Shelf Valley. These results suggest young white sharks exhibit connectivity between the immediate shoreline and mid-continental shelf region, where they play important ecological roles as predators on a variety of species. Our study improves characterization of essential fish habitat for young white sharks and provides new insights into their reliance on this productive continental shelf ecosystem.

Download Full-text

Laboratory Culture-Based Characterization of the Resting Stage Cells of the Brown-Tide-Causing Pelagophyte, Aureococcus anophagefferens

Journal of Marine Science and Engineering ◽

10.3390/jmse8121027 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1027

Author(s):

Zhaopeng Ma ◽

Zhangxi Hu ◽

Yunyan Deng ◽

Lixia Shang ◽

Christophere J. Gobler ◽

...

Keyword(s):

Physiological State ◽

Laboratory Culture ◽

Vital Role ◽

Brown Tide ◽

Aureococcus Anophagefferens ◽

Vegetative Cells ◽

Cycle Plays ◽

Culture Maintenance

Life history (life cycle) plays a vital role in the ecology of some microalgae; however, the well-known brown-tide-causing pelagophyte Aureococcus anophagefferens has been barely investigated in this regard. Recently, based mainly on detections in marine sediments from China, we proved that this organism has a resting stage. We, therefore, conducted a follow-up study to characterize the resting stage cells (RSCs) of A. anophagefferens using the culture CCMP1984. The RSCs were spherical, larger than the vegetative cells, and smooth in cell surface and contained more aggregated plastid but more vacuolar space than vegetative cells. RSCs contained a conspicuous lipid-enriched red droplet. We found a 9.9-fold decrease in adenosine triphosphate (ATP) content from vegetative cells to RSCs, indicative of a "resting" or dormant physiological state. The RSCs stored for 3 months (at 4 °C in darkness) readily reverted back to vegetative growth within 20 days after being transferred to the conditions for routine culture maintenance. Our results indicate that the RSCs of A. anophagefferens are a dormant state that differs from vegetative cells morphologically and physiologically, and that RSCs likely enable the species to survive unfavorable conditions, seed annual blooms, and facilitate its cosmopolitan distribution that we recently documented.

Download Full-text

A Novel Immunofluorescence Flow Cytometry Technique Detects the Expansion of Brown Tides Caused by Aureoumbra lagunensis to the Caribbean Sea

Applied and Environmental Microbiology ◽

10.1128/aem.00888-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 4947-4957 ◽

Cited By ~ 13

Author(s):

F. Koch ◽

Y. Kang ◽

T. A. Villareal ◽

D. M. Anderson ◽

C. J. Gobler

Keyword(s):

Flow Cytometry ◽

Brown Tide ◽

Economic Damage ◽

Content Type ◽

Relative Standard ◽

Wide Range ◽

Brown Tides ◽

Indian River ◽

Brown Tide Bloom ◽

Aureoumbra Lagunensis

ABSTRACTDuring the past 3 decades, brown tides caused by the pelagophytesAureococcus anophagefferensandAureoumbra lagunensishave caused ecological and economic damage to coastal ecosystems across the globe. While blooms ofA. lagunensishad previously been confined to Texas, in 2012, an expansive brown tide occurred on Florida's East Coast, causing widespread disruption within the Indian River and Mosquito Lagoons and generating renewed interest in this organism. A major impediment to detailed investigations ofA. lagunensisin an ecosystem setting has been the absence of a rapid and reliable method for cell quantification. The combination of their small size (3 to 5 μm) and nondescript extracellular features makes identification and enumeration of these cells with conventional methods a challenge. Here we report the development of an immunological-based flow cytometry method that uses a fluorescently labeled antibody developed againstA. lagunensis. This method is species specific, sensitive (detection limit of 1.5 × 103cells ml−1), precise (1% relative standard deviation of replicated samples), and accurate (108% ± 8% recovery of spiked samples) over a wide range of cell concentrations. Furthermore, this method effectively quantifiesA. lagunensisin both glutaraldehyde- and formalin-preserved samples, yields a high throughput of samples (∼35 samples h−1), and is cost-effective, making it an ideal tool for managers and scientists. This method successfully documented the recurrence of a brown tide bloom in Florida in 2013. Bloom densities were highest in June (>2.0 × 106cells ml−1) and spanned >60 km from the Ponce de Leon inlet in the northern Mosquito Lagoon south to Titusville in the Indian River Lagoon. Low levels ofA. lagunensiscells were found >250 km south of this region. This method also quickly and accurately identifiedA. lagunensisas the causative agent of a 2013 brown tide bloom in Guantanamo Bay, Cuba, and thus should prove useful for both quantifying the dynamics of ongoing blooms ofA. lagunensisas well as documenting new outbreaks of this harmful alga.

Download Full-text

A Brown Tide Bloom Index based on the potential harmful effects of the brown tide alga, Aureococcus anophagefferens

Aquatic Ecosystem Health & Management ◽

10.1080/14634980290002011 ◽

2002 ◽

Vol 5 (4) ◽

pp. 435-441 ◽

Cited By ~ 23

Author(s):

Mary Downes Gastrich ◽

Catherine E. Wazniak

Keyword(s):

Brown Tide ◽

Aureococcus Anophagefferens ◽

Brown Tide Bloom ◽

Harmful Effects

Download Full-text

CHARACTERIZATION OF GEOLOGICAL OUTCROPS IN THE UPSTATE NEW YORK REGION USING GIGA-PIXEL PANORAMIC IMAGERY

10.1130/abs/2016ne-272192 ◽

2016 ◽

Author(s):

Paige Haney ◽

◽

Rachel Lee

Keyword(s):

New York ◽

Upstate New York

Download Full-text

Characterization of M dwarfs using optical mid-resolution spectra for exploration of small exoplanets

Publications of the Astronomical Society of Japan ◽

10.1093/pasj/psaa112 ◽

2020 ◽

Author(s):

Yohei Koizumi ◽

Masayuki Kuzuhara ◽

Masashi Omiya ◽

Teruyuki Hirano ◽

John Wisniewski ◽

...

Keyword(s):

Sample Selection ◽

Optical Spectra ◽

Average Error ◽

Spectral Energy ◽

M Dwarfs ◽

Energy Distributions ◽

Fitting Procedures ◽

Optical Region ◽

Selection For

Abstract We present the optical spectra of 338 nearby M dwarfs, and compute their spectral types, effective temperatures (Teff), and radii. Our spectra were obtained using several optical spectrometers with spectral resolutions that range from 1200 to 10000. As many as 97% of the observed M-type dwarfs have a spectral type of M3–M6, with a typical error of 0.4 subtype, among which the spectral types M4–M5 are the most common. We infer the Teff of our sample by fitting our spectra with theoretical spectra from the PHOENIX model. Our inferred Teff is calibrated with the optical spectra of M dwarfs whose Teff have been well determined with the calibrations that are supported by previous interferometric observations. Our fitting procedures utilize the VO absorption band (7320–7570 Å) and the optical region (5000–8000 Å), yielding typical errors of 128 K (VO band) and 85 K (optical region). We also determine the radii of our sample from their spectral energy distributions. We find most of our sample stars have radii of <0.6 R⊙, with the average error being 3%. Our catalog enables efficient sample selection for exoplanet surveys around nearby M-type dwarfs.

Download Full-text