Abiotic and biotic factors controlling sexual reproduction in populations of Pseudo-nitzschia pungens (Bacillariophyceae)

Pseudo-nitzschia pungens is a widely distributed marine pennate diatom. Hybrid zones, regions in which two different genotypes may interbreed, are important areas for speciation and ecology, and have been reported across the globe for this species. However, sexual reproduction between differing clades in the natural environment is yet to be observed and is difficult to predict. Here we carried out experiments using two mono-clonal cultures of P. pungens from different genotypes to measure the frequency and timing of sexual reproduction across varying biotic (growth phases and cell activity potential) and abiotic conditions (nutrients, light, turbulence). We found the mating rates and number of zygotes gradually decreased from exponential to late stationary growth phases. The maximum zygote abundance observed was 1,390 cells mL− 1 and the maximum mating rate was 7.1%, both which occurred during the exponential growth phase. Conversely, only 9 cells mL− 1 and a maximum mating rate of 0.1% was observed during the late stationary phase. We also found the higher the relative potential cell activity (rPCA) in parent cells, as determined by the concentration of chlorophyll a per cell and the ratio of colony formation during parent cultivations, revealed higher mating rates. Furthermore, sexual events were reduced under nutrient enrichment conditions, and mating pairs and zygotes were not formed under aphotic (dark) or shaking culture conditions (150 rpm). In order to understand the sexual reproduction of Pseudonitzschia in the natural environment, our results highlight that it is most likely the combination of both biotic (growth phase, Chl. a content) and abiotic factors (nutrients, light, turbulence) that will determine the successful union of intraspecific populations of P. pungens in any given region

A database of marine phytoplankton abundance, biomass and species composition in Australian waters

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

First report of the potentially toxic marine diatom Pseudo-nitzschia simulans (Bacillariophyceae) from the East Australian Current

Certain species of the marine diatom genus Pseudo‐nitzschia are responsible for the production of the domoic acid (DA), a neurotoxin that can bioaccumulate in the food chain and cause amnesic shellfish poisoning (ASP) in animals and humans. This study extends our knowledge by reporting on the first observation of the potentially toxic species Pseudo‐nitzschia simulans from this region. One clonal strain of P. simulans was isolated from the East Australian Current and characterized using light and transmission electron microscopy, and phylogenetic analyses based on regions of the internal transcribed spacer (ITS) and the D1–D3 region of the large subunit (LSU) of the nuclear‐encoded ribosomal deoxyribonucleic acid (rDNA), as well as examined for DA production as measured by liquid chromatography–mass spectrometry. Although this strain was non‐toxic under the defined growth conditions, the results unambiguously confirmed that this isolate is the potentially toxic species P. simulans – the first report of this species from the Southern Hemisphere

Map of the East Australian Current (EAC) as shown travelling south along the south-eastern Australian coastline and indicated by the warm sea-surface temperature.

<p>Station CTD44 (- 32.465°N, 153.705°S) is shown by black star. Sea surface data was compiled using the average highest available quality sea surface temperatures data from 12 to 17 September 2016 (NOAA-19 MOS—SRS Satellite—SST L3S - 06 day composite—day and night time composite) and eastward geostrophic current velocity data of 17 September 2016 (IMOS–Ocean Current—Gridded sea level anomaly—Near real time) (IMOS, 2016a and b).</p

Location, date, time and physico-chemical characteristics of the seawater sampled at the surface (3-5m depth) and at the deepest sampling point (20–20.5m) on board the <i>RV Investigator</i>.

<p>Location, date, time and physico-chemical characteristics of the seawater sampled at the surface (3-5m depth) and at the deepest sampling point (20–20.5m) on board the <i>RV Investigator</i>.</p

List of <i>Pseudo-nitzschia</i> strains, clone designation, collection location and date/time sampled, as well as accession numbers for the LSU rDNA and ITS/5.8 rDNA sequences established in the present study.

<p>List of <i>Pseudo-nitzschia</i> strains, clone designation, collection location and date/time sampled, as well as accession numbers for the LSU rDNA and ITS/5.8 rDNA sequences established in the present study.</p

<i>Pseudo-nitzschia hallegraeffii</i> sp. nov.

<p>A-F) transmission electron microscopy; A) whole valves (scale bar 10 μm, strain CTD44_3); B. mid-valves showing large central interspace (scale bar 1 μm, strain CTD44_3); C) mid-valve showing interstriae, fibulae and two rows of poroids (scale bar 1 μm, strain CTD44_3); D) valve end (scale bar 0.5 μm, strain CTD44_2); E) cingulum girdle bands: V = valvocopula, II = second copula, III = third copula (scale bar 1 μm, strain CTD44_3); F) valvocopula showing poroid structure of two poroids wide and one or two poroids high (scale bar 1 μm, strain CTD44_3).</p

Primers used for the amplification of the LSU and ITS/5.8 regions of rDNA from clonal cultures of <i>Pseudo-nitzschia</i> established in this study.

<p>Primers used for the amplification of the LSU and ITS/5.8 regions of rDNA from clonal cultures of <i>Pseudo-nitzschia</i> established in this study.</p

Results of mating experiments between all pair-wise combinations of <i>Pseudo-nitzschia</i> strains available.

<p>Results of mating experiments between all pair-wise combinations of <i>Pseudo-nitzschia</i> strains available.</p