Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity

Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages

Oscillating diurnal rhythms of gene transcription, metabolic activity, and behavior are found in all three domains of life. However, diel cycles in naturally occurring heterotrophic bacteria and archaea have rarely been observed. Here, we report time-resolved whole-genome transcriptome profiles of multiple, naturally occurring oceanic bacterial populations sampled in situ over 3 days. As anticipated, the cyanobacterial transcriptome exhibited pronounced diel periodicity. Unexpectedly, several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts. Furthermore, diel oscillations in different heterotrophic bacterial groups suggested population-specific timing of peak transcript expression in a variety of metabolic gene suites. These staggered multispecies waves of diel gene transcription may influence both the tempo and the mode of matter and energy transformation in the sea.Gordon and Betty Moore Foundation (GBMF 492.01)Gordon and Betty Moore Foundation (GBMF 3777)National Science Foundation (U.S.) (Grant EF0424599)David & Lucile Packard Foundatio

Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007

We assess the application of the second-generation Environmental Sample Processor (ESP) for the detection of harmful algal bloom (HAB) species in field and laboratory settings using two molecular probe techniques: a sandwich hybridization assay (SHA) and fluorescent in situ hybridization (FISH). During spring 2006, the first time this new instrument was deployed, the ESP successfully automated application of DNA probe arrays for various HAB species and other planktonic taxa, but non-specific background binding on the SHA probe array support made results interpretation problematic. Following 2006, the DNA array support membrane that we were using was replaced with a different membrane, and the SHA chemistry was adjusted. The sensitivity and dynamic range of these modifications were assessed using 96-well plate and ESP array SHA formats for several HAB species found commonly in Monterey Bay over a range of concentrations; responses were significantly correlated (p < 0.01). Modified arrays were deployed in 2007. Compared to 2006, probe arrays showed improved signal:noise, and remote detection of various HAB species was demonstrated. We confirmed that the ESP and affiliated assays can detect HAB populations at levels below those posing human health concerns, and results can be related to prevailing environmental conditions in near real-time

Microbial community transcriptional networks are conserved in three domains at ocean basin scales

Planktonic microbial communities in the ocean are typically dominated by several cosmopolitan clades of Bacteria, Archaea, and Eukarya characterized by their ribosomal RNA gene phylogenies and genomic features. Although the environments these communities inhabit range from coastal to open ocean waters, how the biological dynamics vary between such disparate habitats is not well known. To gain insight into the differential activities of microbial populations inhabiting different oceanic provinces we compared the daily metatranscriptome profiles of related microbial populations inhabiting surface waters of both a coastal California upwelling region (CC) as well as the oligotrophic North Pacific Subtropical Gyre (NPSG). Transcriptional networks revealed that the dominant photoautotrophic microbes in each environment (Ostreococcus in CC, Prochlorococcus in NPSG) were central determinants of overall community transcriptome dynamics. Furthermore, heterotrophic bacterial clades common to both ecosystems (SAR11, SAR116, SAR86, SAR406, and Roseobacter) displayed conserved, genome-wide inter- and intrataxon transcriptional patterns and diel cycles. Populations of SAR11 and SAR86 clades in particular exhibited tightly coordinated transcriptional patterns in both coastal and pelagic ecosystems, suggesting that specific biological interactions between these groups are widespread in nature. Our results identify common diurnally oscillating behaviors among diverse planktonic microbial species regardless of habitat, suggesting that highly conserved temporally phased biotic interactions are ubiquitous among planktonic microbial communities worldwide.Gordon and Betty Moore Foundation (3777)National Science Foundation (U.S.) (Grant EF0424599)Simons Foundation (Simons Collaboration on Ocean Processes and Ecology

Analysis of toxic and non-toxic Alexandrium (Dinophyceae) species using ribosomal RNA gene sequences

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution November 1992Sequences of small subunit (Ss) and large subunit (Ls) ribosomal RNA genes (rDNA) from the marine dinoflagellates Alexandrium tamarense, A. catenella, A. fundyense, A. affine, A. minutum, A. lusitanicum and A. andersoni were compared to assess the organisms' relationships. Cultures represent isolates from North America, Western Europe, Thailand, Japan, Australia and the ballast water of several cargo vessels, and include both toxic and non-toxic strains. An emphasis was placed on the A. tamarense/catenella/fundyense "species complex," a group of morphotypically-similar organisms found in many regions of the world. Two distinct SsrRNA genes, termed the "A gene" and the "B gene," were found in a toxic A. fundyense isolated from eastern North America. The B gene is considered to be a pseudogene. A restriction fragment length polymorphism (RFLP) assay developed to detect the A and B genes revealed five distinct groups of Alexandrium isolates. Three subdivide the A. tamarense/catenella/fundyense complex, but do not correlate with morphospecies designations. The two remaining groups are associated with cultures that clearly differ morphologically from the A. tamarense/ catenella/fundyense group: the fourth group consists of A. affine isolates, and the fifth group is represented by A. minutum, A.lusitanicum and A. andersoni. The B gene was only found in A. tamarense/catenella/ fundyense, but not in all members of this species complex. The B gene is not uniformly distributed among global populations of Alexandrium. All A. tamarense/catenella/fundyense isolates from North America harbor this gene, but it has also been found in some A. tamarense from scattered locations in Japan, as well as in A. tamarense from the ballast water of one cargo vessel which was on a defined run from Japan to Australia. The B gene may be endemic to North American populations of A. tamarense/catenella/fundyense. It is possible that in the recent past North American A. tamarense were introduced to Japanese waters, and cysts of these organisms have been transported from Japan to Australia. A subset of isolates examined using the the RFLP assay were also compared by cloning and sequencing a fragment of their LsrDNA. Eight major classes of LsrDNA sequences, termed "ribotypes," were identified. Five ribotypes subdivide members of the A. tamarense/catenella!fundyense complex; all isolates containing the B gene cluster as one ribotype. The three remaining ribotypes are typified by: 1) A. affine; 2) A. minutum and A. lusitanicum; and, 3) A. andersoni. LsrDNAs from A. minutum and A. lusitanicum are indistinguishable. A. minutum!lusitanicum/andersoni may represent another Alexandrium species complex, analogous to the A. tamarense/catenella/fundyense group. An organisms' ability to produce toxin appears to be correlated with its LsrDNA phylogenetic lineage. Ribotypes ascribed by the LsrDNA sequences are in complete agreement with, and offer a finer-scale resolution of, groups defined by SsrDNA restriction patterns. The SsrDNA RFLP groups and LsrDNA ribotypes are useful species- and population-specific markers. Alexandrium tamarense/catenella/fundyense exist as geneticallydistinct "strains" (populations), not three genetically-distinct species: representatives collected from the same geographic region appear the most similar, regardless of morphotype, whereas those from geographicallyseparated populations are more divergent even when the same morphospecies are compared. Contrary to this general pattern, A. tamarense/catenella from Japan were found to be exceptionally heterogeneous. Ballast water samples show that viable cysts (resting spores) of toxigenic A. tamarense/catenella are being discharged into Australian ports from multiple, genetically-distinct source populations. The rDNA sequences were also used to test theories accounting for the evolution and global dispersal of A. tamarense/catenella/fundyense. Results suggest a monophyletic radiation of these organisms from a common ancestor that included, or gave rise to, multiple morphotypes. Populations appear to have diverged as a result of vicariance (geographic isolation). The co-occurrence of genetically-distinct strains of these organisms is an indication of dispersal. An example of this is seen in Japan where an introduction of North American A. tamarense appears likely. Determining the timing of dispersal events is problematic if based strictly on rDNA sequence similarities, since these molecules undergo change on a scale of millions of years.This work was supported in part by a grant from the National Science Foundation to D. M. Anderson (contract number OCE89- 11226), the Woods Hole Oceanographic Institution Ocean Ventures Fund and the Woods Hole Oceanographic Institution Education Office

Representations of ‘risky’ drinking during pregnancy on Mumsnet: A discourse analysis

IntroductionOnline forums provide an environment for peer discussions to anonymously share experiences about sensitive topics. In this article we explore discussions about alcohol use during pregnancy, including representations of ‘appropriate’ behaviour and risks, in relation to alcohol use.MethodsWe sampled Mumsnet posts from 2016 to 2021 and analysed these using a two-staged approach: describing the content of original posts and employing discourse analysis on the entire thread which focused on unpacking the significance, activity and identity within the discourse.ResultsSeventy-three threads with 1554 replies analysed. Users engaged with different sources of evidence and mentioned guidelines and scientific sources, though most commonly provided, requested and appreciated anecdotal information. Risk was discussed in several ways but all users engaged with ‘othering’ drinking they perceived as risky. Only a few prescribed risks to any and all levels of drinking. There was a lack of knowledge around drinking while trying to conceive and early pregnancy. Expectations and norms of behaviour during pregnancy engaged in a ‘good motherhood’ discourse. Users positioned their drinking according to perceived norms through language choices; when not pregnant (or unknowingly pregnant) being ‘plastered’ was justified but when pregnant drinking only ‘sips’ or ‘tiny’ quantities of alcohol was considered appropriate.Discussion and ConclusionsForum users demonstrated a desire to adhere to ‘responsible motherhood’, which did not equate to abstinence if consumption was perceived as acceptable and justified. Future research should explore information needs and effective approaches to health communication for pregnant women or those planning pregnancy

Targeted sampling by autonomous underwater vehicles

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, Y., Ryan, J. P., Kieft, B., Hobson, B. W., McEwen, R. S., Godin, M. A., Harvey, J. B., Barone, B., Bellingham, J. G., Birch, J. M., Scholin, C. A., & Chavez, F. P. Targeted sampling by autonomous underwater vehicles. Frontiers in Marine Science, 6 (2019): 415, doi:10.3389/fmars.2019.00415.In the vast ocean, many ecologically important phenomena are temporally episodic, localized in space, and move according to local currents. To effectively study these complex and evolving phenomena, methods that enable autonomous platforms to detect and respond to targeted phenomena are required. Such capabilities allow for directed sensing and water sample acquisition in the most relevant and informative locations, as compared against static grid surveys. To meet this need, we have designed algorithms for autonomous underwater vehicles that detect oceanic features in real time and direct vehicle and sampling behaviors as dictated by research objectives. These methods have successfully been applied in a series of field programs to study a range of phenomena such as harmful algal blooms, coastal upwelling fronts, and microbial processes in open-ocean eddies. In this review we highlight these applications and discuss future directions.This work was supported by the David and Lucile Packard Foundation. The 2015 experiment in Monterey Bay was partially supported by NOAA Ecology and Oceanography of Harmful Algal Blooms (ECOHAB) Grant NA11NOS4780030. The 2018 SCOPE Hawaiian Eddy Experiment was partially supported by the National Science Foundation (OCE-0962032 and OCE-1337601), Simons Foundation Grant #329108, the Gordon and Betty Moore Foundation (Grant #3777, #3794, and #2728), and the Schmidt Ocean Institute for R/V Falkor Cruise FK180310. Publication of this paper was funded by the Schmidt Ocean Institute

Diversity and toxicity of Pseudo-nitzschia species in Monterey Bay : perspectives from targeted and adaptive sampling

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Harmful Algae 78 (2018): 129-141, doi:10.1016/j.hal.2018.08.006.Monterey Bay, California experiences near-annual blooms of Pseudo-nitzschia that can affect marine animal health and the economy, including impacts to tourism and commercial/recreational fisheries. One species in particular, P. australis, has been implicated in the most toxic of events, however other species within the genus can contribute to widespread variability in community structure and associated toxicity across years. Current monitoring methods are limited in their spatial coverage as well as their ability to capture the full suite of species present, thereby hindering understanding of HAB events and limiting predictive accuracy. An integrated deployment of multiple in situ platforms, some with autonomous adaptive sampling capabilities, occurred during two divergent bloom years in the bay, and uncovered detailed aspects of population and toxicity dynamics. A bloom in 2013 was characterized by spatial differences in Pseudo39 nitzschia populations, with the low-toxin producer P. fraudulenta dominating the inshore community and toxic P. australis dominating the offshore community. An exceptionally toxic bloom in 2015 developed as a diverse Pseudo-nitzschia community abruptly transitioned into a bloom of highly toxic P. australis within the time frame of a week. Increases in cell density and proliferation coincided with strong upwelling of nutrients. High toxicity was driven by silicate limitation of the dense bloom. This temporal shift in species composition mirrored the shift observed further north in the California Current System off Oregon and Washington. The broad scope of sampling and unique platform capabilities employed during these studies revealed important patterns in bloom formation and persistence for Pseudo-nitzschia. Results underscore the benefit of expanded biological observing capabilities and targeted sampling methods to capture more comprehensive spatial and temporal scales for studying and predicting future events.This work was supported by the National Oceanic and Atmospheric Administration (NA11NOS4780055, NA11NOS4780056, NA11NOS4780030) and a fellowship to H. Bowers from the Packard Foundation

Temporal patterns and individual characteristics of compulsory treatment orders for mental disorders in Scotland from 2007 to 2020

BackgroundCompulsory mental health treatment has increased globally. In Scotland, compulsory treatment for &gt;28 days is permitted under hospital- and community-based compulsory treatment orders. Community-based compulsory treatment has not been shown to lead to improved outcomes, and scrutiny of their use is needed.AimsTo describe the trend, duration and demographic characteristics of compulsory treatment orders in Scotland over a 14-year period.MethodWe conducted a retrospective analysis of order use in Scotland from 1 January 2007 to 31 December 2020, focusing on the (a) number and demographic characteristics of those treated, (b) duration, (c) extensions beyond the 6-month review point and (d) characteristics of new versus continued orders.ResultsThe number of individuals on a community-based order increased by 118% (571 v. 1243) from 2007 to 2020, compared with a 16% increase (1316 v. 1532) for hospital-based orders. Of orders starting in 2007, 57.3% were extended, compared with 43.7% in 2020. The median duration was 6 months for first-time orders and 9 months for subsequent orders, which were longest for males (median 11 months); those of African, Caribbean or Black (median 11 months), Asian (median 11 months) and mixed ethnicity (median 10 months); and individuals from the most deprived communities (median 10 months).ConclusionsThere has been a marked rise of community-based compulsory treatment orders in Scotland. If existing trends continue, there will be more people receiving care under community-based orders than hospital-based orders, fundamentally changing the nature of involuntary treatment. Further work needs to explore associations between demographic and diagnostic characteristics on order duration

Heterosigma akashiwo in central California waters

Heterosigma akashiwo (Hada) gives rise to red tides along the Atlantic and Pacific coasts and is known to produce brevetoxins. This investigation establishes baseline information showing the presence of H. akashiwo along the central California coast based on water samples collected from the Santa Cruz pier in Monterey Bay (on the open coast) and the Berkeley pier in San Francisco Bay. Light and electron microscopy as well as two species-specific DNA probe methods based on cell homogenates preparations were employed to detect H. akashiwo during the 2001-2002 field study. The DNA probe methods consisted of a sandwich hybridization assay (SHA), which targets ribosomal RNA (rRNA), and an end-point polymerase chain reaction (PCR) assay, which targets internal transcribed spacer (ITS) sequences of rRNA genes. The SHA was used to provide semi-quantitative data showing the intermittent presence of the species during a 13-month period in Monterey Bay. Samples that showed a variety of responses in the SHA (negative as well as the highest) were then subjected to the PCR assay in an attempt to confirm species identification using an independent DNA probe method that employs cell homogenates; samples included those from Monterey Bay and one from a red tide event in San Francisco Bay. SHA and PCR assays agreed on the presence or absence of H. akashiwo. Gene products from two field samples positive for H. akashiwo by PCR were cloned and sequenced and found to be identical to those of that species in GenBank. When the same samples were viewed by light microscopy, however, H. akashiwo cells were only seen in the sample with the highest abundance of that species, as evidenced by SHA. It was extremely difficult to recognize naturally occurring H. akashiwo using light microscopy in field samples that had been preserved with Lugol's iodine, including samples that gave positive results by cell homogenate methods. Results of this study indicate that H. akashiwo is present along the open California coast and could easily be missed in routine phytoplankton surveys. Despite its presence, H. akashiwo does not appear to routinely bloom with sufficient densities to cause harmful outbreaks of the frequency and severity documented in some other coastal environments. Molecular identification techniques may be the preferred approach over light microscopy when there is a need to rapidly screen many samples for fragile, harmful species and those that are otherwise problematic to identify based on their gross morphology alone. © 2005 Elsevier B.V. All rights reserved