Search for: All records

We sampled the respiratory mucus from voluntary blowhole exhalations (“blow”) of three healthy beluga whales (Delphinapterus leucas) under professional human care. Blow samples were collected from three resident belugas, one adult male (M1) and two adult females (F1, F2), with voluntary behaviors via non-invasive methods over three days in July 2021 (four days for M1). Samples were weighed and examined microscopically for the enumeration of eukaryotic and prokaryotic microbes, and then were used to evaluate carbon substrate use and taxonomic diversity of prokaryotic communities in the host respiratory sytem. Microscopical observations and 18S rRNA gene sequencing indicated the presence of eukaryotic microbiota, the ciliate generaPlanilaminaandKyaroikeusin all three individuals. Exposure of samples to different metabolic carbon substrates indicated significant differences in the number of carbon sources usable by the prokaryotic communities of different whales (range: 11-25 sources), as well as a signficantly decreased diversity of carbon sources used by the community in the habitat water (5 sources). Sequencing of the hypervariable V4 region of the 16S rRNA gene revealed 19 amplicon sequence variants (ASVs) that were present in all whale samples. The oldest femaleD. leucas(F2) had the lowest overall diversity, and was significantly different from M1 and F1 in taxon composition, including an anomalously low ratio of Baccillota: Bacteroidota (0.01) compared to the other whales. In comparisons of microbial community composition, M1 had a significantly higher diversity than F1 and F2. These results suggest that attention should be given to regular microbiome sampling, and indicate a need for the pairing of microbiome and clinical data for animals in aquaria. Overall, these data contribute to the growing database on the core respiratory microbiota in cohabiting cetaceans under professional human care, indicate the utility of non-invasive sampling, and help characterize a baseline for healthyD. leucas. 

Abstract Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity. 

Ciliates are abundant microplankton that are widely distributed in the ocean. In this paper, the distribution patterns of ciliate diversity in the South China Sea (SCS) were analyzed by compiling community data from previous publications. Based on morphological identification, a total of 592 ciliate species have been recorded in the SCS. The ciliate communities in intertidal, neritic and oceanic water areas were compared in terms of taxonomy, motility and feeding habit composition, respectively. Significant community variation was revealed among the three areas, but the difference between the intertidal area and the other two areas was more significant than that between neritic and oceanic areas. The distributions of ciliates within each of the three areas were also analyzed. In the intertidal water, the community was not significantly different among sites but did differ among habitat types. In neritic and oceanic areas, the spatial variation of communities among different sites was clearly observed. Comparison of communities by taxonomic and ecological traits (motility and feeding habit) indicated that these traits similarly revealed the geographical pattern of ciliates on a large scale in the SCS, but to distinguish the community variation on a local scale, taxonomic traits has higher resolution than ecological traits. In addition, we assessed the relative influences of environmental and spatial factors on assembly of ciliate communities in the SCS and found that environmental selection is the major process structuring the taxonomic composition in intertidal water, while spatial processes played significant roles in influencing the taxonomic composition in neritic and oceanic water. Among ecological traits, environmental selection had the most important impact on distributions. 

Abstract The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates,Schmidingerella arcuataandSchmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single‐cell ‘omics analyses (single‐cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger inS. meunieri, a 0%–0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist betweenS. arcuataandS. meunieriin common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species‐specific primers, which are used in this study as unique “architectural barcodes” to demonstrate the co‐occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification. 

During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding. 

Abstract Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.