Explore the vast range of titles available.

The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene transcriptional termination factors, we identified ZC3H4. Its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is predominantly metazoan –interesting when considering its impact on enhancer RNAs that are less prominent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as playing an important role in restricting non-coding transcription in multicellular organisms.

Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance–decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community.

Phytoplankton community structure is shaped by both bottom–up factors, such as nutrient availability, and top–down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.

Microbial diversity varies at multiple spatial scales, but little is known about how climate change may influence this variation. Here we assessed the free-living bacterioplankton composition of thaw ponds over a north-south gradient of permafrost degradation in the eastern Canadian subarctic. Three nested spatial scales were compared: 1) among ponds within individual valleys 2) between two valleys within each landscape type, and 3) between landscape types (southern sporadic versus northern discontinuous permafrost). As a reference point, we sampled rock-basin lakes whose formation was not related to permafrost thawing. β-diversity was low at the smallest scale despite marked differences in limnological properties among neighboring ponds. β-diversity was high among valleys, associated with greater environmental heterogeneity. The largest differences were between landscape types and appeared to reflect the concomitant effects of environmental filtering and dispersal limitation. Raup–Crick β-diversity indicated that community assembly was driven by both stochastic (random extinction, dispersal, ecological drift) and deterministic (environmental filtering) processes. Communities sampled in the most degraded valley appeared primarily assembled through stochastic processes, while environmental filtering played a greater role at the other valleys. These results imply that climate warming and ongoing permafrost degradation will influence microbial community assembly, which in turn is likely to affect the functioning of thaw pond ecosystems.

Perkinsea constitutes a lineage within the Alveolata eukaryotic superphylum, mainly composed of parasitic organisms. Some described species represent significant ecological and economic threats due to their invasive ability and pathogenicity, which can lead to mortality events. However, the genetic diversity of these described species is just the tip of the iceberg. Environmental surveys targeting this lineage are still scarce and mainly limited to the Northern Hemisphere. Here, we aim to conduct an in depth exploration of the Perkinsea group, uncovering the diversity across a variety of environments, including those beyond freshwater and marine ecosystems. We seek to identify and describe putative novel organisms based on their genetic signatures. In this study, we conducted an extensive analysis of a metabarcoding dataset, focusing on the V4 region of the 18S rRNA gene (the EukBank dataset), to investigate the diversity, distribution and environmental preferences of the Perkinsea. Our results reveal a remarkable diversity within the Perkinsea, with 1568 Amplicon Sequence Variants (ASVs) identified across thousands of environmental samples. Surprisingly, we showed a substantial diversity of Perkinsea within soil samples (269 ASVs), challenging the previous assumption that this group is confined to marine and freshwater environments. In addition, we revealed that a notable proportion of Perkinsea ASVs (428 ASVs) could correspond to putative new organisms, encompassing the well-established taxonomic group Perkinsidae. Finally, our study shed light on previously unveiled taxonomic groups, including the Xcellidae, and revealed their environmental distribution. These findings demonstrate that Perkinsea exhibits far greater diversity than previously detected and surprisingly extends beyond marine and freshwater environments. The meta-analysis conducted in this study has unveiled the existence of previously unknown clusters within the Perkinsea lineage, solely identified based on their genetic signatures. Considering the ecological and economic importance of described Perkinsea species, these results suggest that Perkinsea may play a significant, yet previously unrecognized, role across a wide range of environments, spanning from soil environments to the abyssal zone of the open ocean with important implications for ecosystem functioning.

Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1–V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.

The Arctic Ocean (AO) is changing at an unprecedented rate, with ongoing sea ice loss, warming and freshening impacting the extent and duration of primary productivity over summer months. Surface microbial eukaryotes are vulnerable to such changes, but basic knowledge of the spatial variability of surface communities is limited. Here, we sampled microbial eukaryotes in surface waters of the Beaufort Sea from four contrasting environments: the Canada Basin (open ocean), the Mackenzie Trough (river-influenced), the Nuvuk region (coastal) and the under-ice system of the Canada Basin. Microbial community structure and composition varied significantly among the systems, with the most phylogenetically diverse communities being found in the more coastal systems. Further analysis of environmental factors showed potential vulnerability to change in the most specialised community, which was found in the samples taken in water immediately beneath the sea ice, and where the community was distinguished by rare species. In the context of ongoing sea ice loss, specialised ice-associated microbial assemblages may transition towards more generalist assemblages, with implications for the eventual loss of biodiversity and associated ecosystem function in the Arctic Ocean.

About the Authors: Aurelie Chambouvet * E-mail: aurelie.chambouvet@univ-brest.fr Affiliation: CNRS, Univ Brest, IRD, Ifremer, LEMAR, Plouzané, France ORCID logo http://orcid.org/0000-0003-3932-0098 Vanessa Smilansky Affiliation: Biosciences, Living Systems Institute, University of Exeter, Exeter, United Kingdom Miloslav Jirků Affiliation: Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic Marcos Isidoro-Ayza Affiliation: Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America Sarah Itoïz Affiliation: CNRS, Univ Brest, IRD, Ifremer, LEMAR, Plouzané, France Evelyne Derelle Affiliation: CNRS, Univ Brest, IRD, Ifremer, LEMAR, Plouzané, France Adam Monier Affiliation: Biosciences, Living Systems Institute, University of Exeter, Exeter, United Kingdom David J. Gower Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom ORCID logo http://orcid.org/0000-0002-1725-8863 Mark Wilkinson Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom ORCID logo http://orcid.org/0000-0002-9459-8976 Michael J. Yabsley Affiliation: Warnell School of Forestry and Natural Resources and the Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America Julius Lukeš Affiliations Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic, Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic Thomas A. Richards Affiliations Biosciences, Living Systems Institute, University of Exeter, Exeter, United Kingdom, Department of Zoology, University of Oxford, Oxford, United Kingdom Citation: Chambouvet A, Smilansky V, Jirků M, Isidoro-Ayza M, Itoïz S, Derelle E, et al. The following causes of amphibian decline have been suggested: 1) invasive species causing ecosystem change, 2) overexploitation of natural environments, 3) changes in land use, 4) global environmental change, such as global warming, 5) increased use of pesticides and other polluting chemicals, and 6) the emergence and/or spread of infectious diseases [1–3]. B. Micrographs of tadpole liver and intestine samples infected by protists belonging to the Alveolata superphylum. a. Light microscopy of macrophages containing several oocysts of both Nematopsis temporariae (Gregarines) and Goussia noelleri (Coccidia) from tadpole liver samples of Rana dalmatina, fresh mounts, NIC [6] b. Histological section of infected liver tissue samples from a River frog (Rana heckscheri) tadpole mass mortality event in southwestern Georgia (USA) in 2006, stained with hematoxylin–eosin (Yabsley, unpublished). c. Light microscopy of putatively commensal ciliate Balantidium sp. from tadpole intestine samples of Bombina bombina, fresh mounts, NIC (Jirků, unpublished). While chytridiomycosis and Ranavirus infections have been extensively documented for adult amphibians, understanding of these and other diseases in the larval phase of an amphibian life cycle (i.e., tadpoles) is limited because dead or diseased tadpoles are often not collected for postmortem assessment.

Most eukaryotic microbial diversity is uncultivated, under-studied and lacks nuclear genome data. Mitochondrial genome sampling is more comprehensive, but many phylogenetically important groups remain unsampled. Here, using a single-cell sorting approach combining tubulin-specific labelling with photopigment exclusion, we sorted flagellated heterotrophic unicellular eukaryotes from Pacific Ocean samples. We recovered 206 single amplified genomes, predominantly from underrepresented branches on the tree of life. Seventy single amplified genomes contained unique mitochondrial contigs, including 21 complete or near-complete mitochondrial genomes from formerly under-sampled phylogenetic branches, including telonemids, katablepharids, cercozoans and marine stramenopiles, effectively doubling the number of available samples of heterotrophic flagellate mitochondrial genomes. Collectively, these data identify a dynamic history of mitochondrial genome evolution including intron gain and loss, extensive patterns of genetic code variation and complex patterns of gene loss. Surprisingly, we found that stramenopile mitochondrial content is highly plastic, resembling patterns of variation previously observed only in plants. Single-cell sequencing of flagellated heterotrophic unicellular eukaryotes provides insights into the dynamics of mitochondrial genome evolution.

Prasinophytes occur in all oceans but rarely dominate phytoplankton populations. In contrast, a single ecotype of the prasinophyte Micromonas is frequently the most abundant photosynthetic taxon reported in the Arctic from summer through autumn. However, seasonal dynamics of prasinophytes outside of this period are little known. To address this, we analyzed high-throughput V4 18S rRNA amplicon data collected from November to July in the Amundsen Gulf Region, Beaufort Sea, Arctic. Surprisingly during polar sunset in November and December, we found a high proportion of reads from both DNA and RNA belonging to another prasinophyte, Bathycoccus . We then analyzed a metagenome from a December sample and the resulting Bathycoccus metagenome assembled genome (MAG) covered ~90% of the Bathycoccus Ban7 reference genome. In contrast, only ~20% of a reference Micromonas genome was found in the metagenome. Our phylogenetic analysis of marker genes placed the Arctic Bathycoccus in the B1 coastal clade. In addition, substitution rates of 129 coding DNA sequences were ~1.6% divergent between the Arctic MAG and coastal Chilean upwelling MAGs and 17.3% between it and a South East Atlantic open ocean MAG in the B2 Clade. The metagenomic analysis also revealed a winter viral community highly skewed toward viruses targeting Micromonas , with a much lower diversity of viruses targeting Bathycoccus . Overall a combination of Micromonas being relatively less able to maintain activity under dark winter conditions and viral suppression of Micromonas may have contributed to the success of Bathycoccus in the Amundsen Gulf during winter.