Distribution of adult and juvenile Acantharia (Protozoa Sarcodina) in the Atlantic Ocean

The distribution of Acantharia (both adult and juvenile forms)has been studied in 34 different areas (33 in the Atlantic Oceanand one in the Mediterranean Sea). A low percentage of adultAcantharia was observed in the areas of high latitude, whilean abundance was observed in the zones between the tropics andEquator. Juvenile forms always appear in very low percentagesand no particular reproduction areas are identifiable. Withregard to their vertical distribution one can observe a gradualincrease from the surface down to 300 m; after this depth, Acanthariadecrease while in deeper waters they are scarcely represented.The distribution of juvenile forms is very irregular, but thehighest average value can be found in very deep waters (between500 and 900 m). Moreover a different daily distribution wasobserved in the percentage of Acantharia in most of the superficiallayers: percentages were higher in the daytime hours than inthe nocturnal ones, considering seasonal changes, Spring wasfound to be the period of greatest abundance both of adult andjuvenile forms, while the lowest percentage was observed duringSummer.     

“Pitfalls in relative abundance estimation using eDNA metabarcoding”

Metabarcoding provides unparalleled information of overall ecosystem ecology and diversity, from occurrence to relative abundances, from micro‐ to macro‐organisms, including cryptic species and larval stages that would otherwise be impossible to identify. PCR is still the most cost‐effective and routinely used method to extract information from environmental samples coupled with high‐throughput sequencing (HTS). Nichols et al. ( 2018 ) metabarcoded nine soil environmental samples from Alaska and six mixtures of synthetic oligonucleotides, using a short fragment of the chloroplast trnL gene. The authors tested the effect of PCR replicates, different polymerase mixes and amplicon GC content on diversity estimates. Results show that occurrence data was not biased for any of the parameters tested and only insufficient PCR replicates could impair the detection of rare taxa. For abundance data, polymerases were found to differentially bias estimates of the relative amplicon abundances and this depended on GC content.     

Diversity,Ecology and Biogeochemistry of Cyst-Forming Acantharia (Radiolaria) in the Oceans

Marine planktonic organisms that undertake active vertical migrations over their life cycle are important contributors to downward particle flux in the oceans. Acantharia, globally distributed heterotrophic protists that are unique in building skeletons of celestite (strontium sulfate), can produce reproductive cysts covered by a heavy mineral shell that sink rapidly from surface to deep waters. We combined phylogenetic and biogeochemical analyses to explore the ecological and biogeochemical significance of this reproductive strategy. Phylogenetic analysis of the 18S and 28S rRNA genes of different cyst morphotypes collected in different oceans indicated that cyst-forming Acantharia belong to three early diverging and essentially non symbiotic clades from the orders Chaunacanthida and Holacanthida. Environmental high-throughput V9 tag sequences and clone libraries of the 18S rRNA showed that the three clades are widely distributed in the Indian, Atlantic and Pacific Oceans at different latitudes, but appear prominent in regions of higher primary productivity. Moreover, sequences of cyst-forming Acantharia were distributed evenly in both the photic and mesopelagic zone, a vertical distribution that we attribute to their life cycle where flagellated swarmers are released in deep waters from sinking cysts. Bathypelagic sediment traps in the subantarctic and oligotrophic subtropical Atlantic Ocean showed that downward flux of Acantharia was only large at high-latitudes and during a phytoplankton bloom. Their contribution to the total monthly particulate organic matter flux can represent up to 3%. High organic carbon export in cold waters would be a putative nutritional source for juveniles ascending in the water column. This study improves our understanding of the life cycle and biogeochemical contribution of Acantharia, and brings new insights into a remarkable reproductive strategy in marine protists.     

Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris

Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and microbes in the “Plastisphere”—the thin layer of life on the surface of PMD—has been technology‐limited. Research into microbe–microbe and microbe–substrate interactions requires knowledge of community phylogenetic composition but also tools to visualize spatial distributions of intact microbial biofilm communities. We developed a CLASI‐FISH (combinatorial labelling and spectral imaging – fluorescence in situ hybridization) method using confocal microscopy to study Plastisphere communities. We created a probe set consisting of three existing phylogenetic probes (targeting all Bacteria, Alpha‐, and Gammaproteobacteria) and four newly designed probes (targeting Bacteroidetes, Vibrionaceae, Rhodobacteraceae and Alteromonadaceae) labelled with a total of seven fluorophores and validated this probe set using pure cultures. Our nested probe set strategy increases confidence in taxonomic identification because targets are confirmed with two or more probes, reducing false positives. We simultaneously identified and visualized these taxa and their spatial distribution within the microbial biofilms on polyethylene samples in colonization time series experiments in coastal environments from three different biogeographical regions. Comparing the relative abundance of 16S rRNA gene amplicon sequencing data with cell‐count abundance data retrieved from the microscope images of the same samples showed a good agreement in bacterial composition. Microbial communities were heterogeneous, with direct spatial relationships between bacteria, cyanobacteria and eukaryotes such as diatoms but also micro‐metazoa. Our research provides a valuable resource to investigate biofilm development, succession and associations between specific microscopic taxa at micrometre scales.     

Molecular phylogeny and morphological evolution of the Acantharia (Radiolaria)

Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive molecular phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This molecular phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia.     

Temperature effects on “overwintering” phenology of a polyphagous,tropical fruit fly (Tephritidae) at the subtropical/temperate interface

Around the world, several pest tephritids are extending their ranges from warm tropical or Mediterranean climates into cooler temperate regions. The ability to tolerate climatic diversity is uncommon among insects, and understanding the population phenology drivers of such species across different parts of their range will be critical for their management. Here, we determined the role of temperature versus fruit availability on the population phenology of Queensland fruit fly, Bactrocera tryoni. Using a field site located at the subtropical/temperate interface, with host fruits continuously available, we monitored the development times and abundance of B. tryoni, a species which has invaded temperate Australia from the tropics. From fruit samples held at ambient and controlled conditions, the abundance of emerging flies was highly variable among collection dates, but the variance did not reflect the observed changes in temperature. For most samples, the survival rate of flies in a field site was lower than predicted by a day‐degree population model fitted with mean daily field temperatures. The development time of the immature stage in the field was prolonged, presumably due to cooler ambient conditions, but the fitted day‐degree population model consistently over‐predicted estimated development times. Our results indicate that at the subtropical/temperate interface, the decline in B. tryoni populations during winter is only partly driven by temperature and host availability. We classify B. tryoni as a climate generalist, which likely employs physiological as well as behavioural mechanisms to achieve broad climatic tolerance ranges.     

Isotope chirality in long‐armed multifunctional organosilicon (“Cephalopod”) molecules

Long‐armed multifunctional organosilicon molecules display self‐replicating and self‐perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry.     

Occurrence of iron-reducing compounds in biodelignified “palo podrido” wood samples

Palo podrido (literally, rotted log) and iron chelating compounds associated with it were characterized. Field-collected samples taken from palo podrido were sorted visually into three groups representing early, and two stages of advanced delignification (termed as EDS, ADS1 and ADS2, respectively). Lignin contents in these samples were 22.3%, 5.1% and 4.6%, respectively. Ethyl acetate extracts from ADS1 and ADS2 samples contained several aromatic carboxylic acids. Dihydroxyterephtalic acid was detected as the major compound in ADS1 extract and was found at low concentrations in ADS2 extract. Only the ADS1 extract exhibited a significant iron reduction activity, reducing 3.1% of an initial 500 μMFe³⁺ solution after the first minute of reaction. After 10 min reaction, 9.5% of the initial Fe³⁺ was reduced. Reduction activity expressed on the basis of extracted dry mass of ADS1 was 12.5 μmol of Fe³⁺ reduced/min/kg of dry wood.     

Considering sampling bias in close‐kin mark–recapture abundance estimates of Atlantic salmon

Genetic methods for the estimation of population size can be powerful alternatives to conventional methods. Close‐kin mark–recapture (CKMR) is based on the principles of conventional mark–recapture, but instead of being physically marked, individuals are marked through their close kin. The aim of this study was to evaluate the potential of CKMR for the estimation of spawner abundance in Atlantic salmon and how age, sex, spatial, and temporal sampling bias may affect CKMR estimates. Spawner abundance in a wild population was estimated from genetic samples of adults returning in 2018 and of their potential offspring collected in 2019. Adult samples were obtained in two ways. First, adults were sampled and released alive in the breeding habitat during spawning surveys. Second, genetic samples were collected from out‐migrating smolts PIT‐tagged in 2017 and registered when returning as adults in 2018. CKMR estimates based on adult samples collected during spawning surveys were somewhat higher than conventional counts. Uncertainty was small (CV < 0.15), due to the detection of a high number of parent–offspring pairs. Sampling of adults was age‐ and size‐biased and correction for those biases resulted in moderate changes in the CKMR estimate. Juvenile dispersal was limited, but spatially balanced sampling of adults rendered CKMR estimates robust to spatially biased sampling of juveniles. CKMR estimates based on returning PIT‐tagged adults were approximately twice as high as estimates based on samples collected during spawning surveys. We suggest that estimates based on PIT‐tagged fish reflect the total abundance of adults entering the river, while estimates based on samples collected during spawning surveys reflect the abundance of adults present in the breeding habitat at the time of spawning. Our study showed that CKMR can be used to estimate spawner abundance in Atlantic salmon, with a moderate sampling effort, but a carefully designed sampling regime is required.     

Multiple microalgal partners in symbiosis with the acantharian Acanthochiasma sp. (Radiolaria)

Acantharia (Radiolaria) are widespread and abundant heterotrophic marine protists, some of which can host endosymbiotic eukaryotic microalgae. Although this photosymbiotic association was first described at the end of the 19th century, the diversity of the symbiotic microalgae remains poorly characterized. Here, we examined the identity of the microalgae associated with the acantharian species Acanthochiasma sp. by sequencing partial 18S and internal transcribed spacer (ITS) ribosomal DNA genes from cultured symbionts and directly from isolated holobiont specimens. Single Acanthochiasma cells contained multiple symbiotic partners, including distantly related dinoflagellates (Heterocapsa sp., Pelagodinium sp., Azadinium sp. and Scrippsiella sp.) as well as a haptophyte (Chrysochromulina sp.). This original association of multiple symbiotic microalgae within a single host cell raises questions about the specificity and functioning of the relationship. These microalgae exhibit the common ecological feature of being abundant and widely distributed in coastal and oceanic waters, some occasionally forming extensive blooms. Some of the microalgal genera found in association with Acanthochiasma (i.e. Pelagodinium and Chrysochromulina) are known to occur in symbiosis with other heterotrophic protists such as Foraminifera and other Radiolaria, whereas Heterocapsa, Scrippsiella and Azadinium have never previously been reported to be involved in putative symbiotic relationships. The unusual association unveiled in this study contributes to our understanding of the ecological and evolutionary significance of photosymbiosis in Acantharia and also provides new insights into the nature of such partnerships in the planktonic realm.     

Transfemoral catheterization of the cavernous sinus outflow with comparison of “central” and “peripheral” gonadotropin patterns in bonnet monkeys

Concentrations of follicle stimulating hormone (FSH) and luteinizing hormone (LH) in central (C) samples obtained by transfemorally catheterizing the inferior petrosal sinus of female bonnet monkeys were compared with those in peripheral (P) samples obtained simultaneously from the saphenous veins of two intact and two oophorectomized bonnet monkeys, before, during, and after luteinizing hormone releasing hormone (LHRH) stimulation. Significant differences between central and peripheral gonadotropin concentrations were detected intermittently in the resting state, and tended to be magnified by LHRH administration. In one animal in which LHRH was fortuitously administered during the course of a spontaneous LH surge, a C/P ratio for LH of 12.71, the maximum observed, was obtained. Spectral analysis exhibited periodicity for LH and, to a lesser extent, for FSH in the oophorectomized, but not in the intact, animals.     

Proximate Composition and Nutrient Elements in the “Unusual” Algal “Jellies” of Lake Oguta in Southern Nigeria

The proximate composition, nutrient and trace elements of the planktonic algal “jellies” of Lake Oguta in Southern Nigeria, are provided as guides to their utilization and control, using flood (rainy) and dry season samples. These “jellies” are an unusual, macroscopic planktonic algal community in the lake, made up mostly of blue-green algae (Microcystis, Anabaena, Chroococcus) with some green algae (e. g. Spirogyra) and pennate diatoms (e.g. Navicula) rather epiphytic on the mucous jellies of the blue-green algae. Water content was high (98.2% mean, range 97.5-99.5%). Ash, protein and fat had values of 41.7 (39.0-46.2%), 16.9 (15.6-19.4%), and 2.0 (1.7-2.1%) respectively. Crude fibre and carbohydrates were high (25.8% and 12.4%). The levels of phosphorus and nitrogen were rather high, so were the major cations whose order of dominance (Ca > K > Mg > Na) differed from that of the lake water. Macronutrients increased in their concentrations during the rainy flood season while the reverse was the case with the micronutrients. Diagenesis of the endogenic minerals rather than anthropogenic factors are thought to be the reason for the seasonal changes in the ionic concentrations. Possible uses of the algal jellies are discussed as well as their control options.     

Two‐dimensional gel electrophoresis of gastric tissue in an alkaline pH range

2DE in combination with MS has facilitated the discovery of several proteins with altered abundance in gastric cancer. While acidic and wide pH ranges have been widely investigated, analysis in the alkaline pH range has not been specifically performed in gastric cancer to date. In the present study, we initially optimized the 2DE in alkaline pH range (pH 7–11) for gastric tissue samples. Using a modified lysis buffer, we analyzed pooled nontumor and tumor samples for proteins with altered abundance in gastric adenocarcinoma. We successfully identified 38 silver‐stained spots as 24 different proteins. Four of these were chosen for investigation with immunoblotting on individual paired samples to determine whether the changes seen in 2DE represent the overall abundance of the protein or possibly only a single form. While mitochondrial trifunctional protein (MTP) subunits were decreased in 2DE gels, immunoblotting identified their overall abundance as being differently dysregulated: in the gastric tumor samples, the MTP‐α subunit was decreased, and the MTP‐β subunit was increased. On the other hand, heterogenous nuclear ribonucleoprotein M and galectin‐4 were increased in the gastric tumor samples in both 2DE and immunoblotting.     

Radiolaria divided into Polycystina and Spasmaria in combined 18S and 28S rDNA phylogeny

Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.     

A critique of the “ultra‐high risk” and “transition” paradigm

The transdiagnostic expression of psychotic experiences in common mental disorder (anxiety/depression/substance use disorder) is associated with a poorer prognosis, and a small minority of people may indeed develop a clinical picture that meets criteria for schizophrenia. However, it appears neither useful nor valid to observe early states of multidimensional psychopathology in young people through the “schizo”‐prism, and apply misleadingly simple, unnecessary and inefficient binary concepts of “risk” and “transition”. A review of the “ultra‐high risk” (UHR) or “clinical high risk” (CHR) literature indicates that UHR/CHR samples are highly heterogeneous and represent individuals diagnosed with common mental disorder (anxiety/depression/substance use disorder) and a degree of psychotic experiences. Epidemiological research has shown that psychotic experiences are a (possibly non‐causal) marker of the severity of multidimensional psychopathology, driving poor outcome, yet notions of “risk” and “transition” in UHR/CHR research are restrictively defined on the basis of positive psychotic phenomena alone, ignoring how baseline differences in multidimensional psychopathology may differentially impact course and outcome. The concepts of “risk” and “transition” in UHR/CHR research are measured on the same dimensional scale, yet are used to produce artificial diagnostic shifts. In fact, “transition” in UHR/CHR research occurs mainly as a function of variable sample enrichment strategies rather than the UHR/CHR “criteria” themselves. Furthermore, transition rates in UHR/CHR research are inflated as they do not exclude false positives associated with the natural fluctuation of dimensional expression of psychosis. Biological associations with “transition” thus likely represent false positive findings, as was the initial claim of strong effects of omega‐3 polyunsatured fatty acids in UHR samples. A large body of UHR/CHR intervention research has focused on the questionable outcome of “transition”, which shows lack of correlation with functional outcome. It may be more productive to consider the full range of person‐specific psychopathology in all young individuals who seek help for mental health problems, instead of “policing” youngsters for the transdiagnostic dimension of psychosis. Instead of the relatively inefficient medical high‐risk approach, a public health perspective, focusing on improved access to a low‐stigma, high‐hope, small scale and youth‐specific environment with acceptable language and interventions may represent a more useful and efficient strategy.     

SELECTIVE RECOVERY OF MICROALGAE FROM DIVERSE HABITATS USING “PHYTO‐SPECIFIC” 16S rDNA PRIMERS1

Environmental PCR is a common tool for surveying aquatic microalgae; however, universal primers generally employed are not specific to phytoplankton and typically recover nonphotosynthetic bacteria at high frequencies. Using a 16S rDNA “phyto‐specific” primer, we were able to selectively amplify sequences of photosynthetic species from several mixed aquatic samples, even when large numbers of nonphotosynthetic microorganisms were present. We identified 21 microalgal sequences from three different habitats: salt marshes in Virginia, river basins in North Carolina, and sea ice in Alaska. In contrast, universal 16S primers recovered a majority of nonphotosynthetic organisms from some of the same samples. Our results indicate that phytoplankton‐specific primers are efficient in selectively amplifying a broad diversity of microalgae in mixed environmental samples and, therefore, can reduce the noise from extraneous species that often dominates molecular surveys of aquatic samples.     

Rapid analysis of disease state in liquid human serum combining infrared spectroscopy and “digital drying”

In recent years, the diagnosis of brain tumors has been investigated with attenuated total reflection‐Fourier transform infrared (ATR‐FTIR) spectroscopy on dried human serum samples to eliminate spectral interferences of the water component, with promising results. This research evaluates ATR‐FTIR on both liquid and air‐dried samples to investigate “digital drying” as an alternative approach for the analysis of spectra obtained from liquid samples. Digital drying approaches, consisting of water subtraction and least‐squares method, have demonstrated a greater random forest (RF) classification performance than the air‐dried spectra approach when discriminating cancer vs control samples, reaching sensitivity values higher than 93.0% and specificity values higher than 83.0%. Moreover, quantum cascade laser infrared (QCL‐IR) based spectroscopic imaging is utilized on liquid samples to assess the implications of a deep‐penetration light source on disease classification. The RF classification of QCL‐IR data has provided sensitivity and specificity amounting to 85.1% and 75.3% respectively.     

DeepQuanTR: MALDI‐MS‐based label‐free quantification of proteins in complex biological samples

The quantification of changes in protein abundance in complex biological specimens is essential for proteomic studies in basic and applied research. Here we report on the development and validation of the DeepQuanTR software for identification and quantification of differentially expressed proteins using LC‐MALDI‐MS. Following enzymatic digestion, HPLC peptide separation and normalization of MALDI‐MS signal intensities to the ones of internal standards, the software extracts peptide features, adjusts differences in HPLC retention times and performs a relative quantification of features. The annotation of multiple peptides to the corresponding parent protein allows the definition of a Protein Quant Value, which is related to protein abundance and which allows inter‐sample comparisons. The performance of DeepQuanTR was evaluated by analyzing 24 samples deriving from human serum spiked with different amounts of four proteins and eight complex samples of vascular proteins, derived from surgically resected human kidneys with cancer following ex vivo perfusion with a reactive ester biotin derivative. The identification and experimental validation of proteins, which were differentially regulated in cancerous lesions as compared with normal kidney, was used to demonstrate the power of DeepQuanTR. This software, which can easily be used with established proteomic methodologies, facilitates the relative quantification of proteins derived from a wide variety of different samples.     

Primary productivity by symbiont-bearing planktonic sarcodines (Acantharia, Radiolaria, Foraminifera) in surface waters near Bermuda

Rates of primary productivity by the symbiotic algae of a varietyof planktonic sarcodines (Acantharia, Radiolaria, Foraminifera)were measured at two times of the year in 1991 from surfacewaters of the Sargasso Sea near Bermuda Rates of symbiont production(expressed on a ‘per host’ basis) were not significantlydifferent for the two seasons, but measurements for individualsarcodine species varied by more than four orders of magnitudeand were roughly correlated with sarcodine size (and therebywith the biomass of the protozoan host). Overall, Acanthariahad the lowest production rates per host, while solitary andcolonial Radiolaria displayed the highest rates. Symbiont-bearingplanktonic sarcodines were always microenvironments of highlyconcentrated primary production in this oligotrophic oceanicenvironment. Rates of primary production within the volumesdefined by the extension of the cytoplasmic networks of thesarcodines generally exceeded rates of primary production inequivalent volumes of the seawater surrounding these associationsby more than four orders of magnitude and showed no clear differencesamong the sarcodine groups Total symbiont production, however,contributed a small fraction (generally <1%) of the totalprimary production in surface waters because of relatively lowsarcodine abundances (compared to other primary producers) andbecause of high total primary production in surface waters.Combining the production rates measured in this study with seasonalabundances of Acantharia and Foraminifera, however, indicatesthat these assemblages may have contributed an average of     

Evidence for longitudinal migration by a “sedentary” Brazilian flycatcher,the Ash‐throated Casiornis

The digitalization of museum collections and concurrent increase in citizen‐science initiatives is ushering in an era of unprecedented availability of primary biodiversity data. These changes permit a reappraisal of phenological patterns of tropical species. I examined spatio‐temporal variation in the distribution patterns of an ostensibly sedentary endemic Brazilian flycatcher, the Ash‐throated Casiornis (Casiornis fuscus), using both specimen data from museums and sighting records and rich media data from citizen‐science initiatives. I found compelling evidence for partial intratropical longitudinal migration to Amazonia and the Cerrado biomes from the species’ core range in the semi‐desert Caatinga biome and adjacent ecotones. These records from outside of the Caatinga were distributed during the height of the dry season from April to October, although the Caatinga is not entirely vacated at this time. This pattern of partial migration leads to a doubling of the distributional range of Ash‐throated Casiornises and strongly suggests that the species is a breeding near‐endemic of the Caatinga biome. This pattern was potentially previously not apparent because of significant biases in specimen collection between biomes, giving a false sense of abundance in the Brazilian Amazon.