38 research outputs found
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Clades of huge phages from across Earth's ecosystems.
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems
Widespread anatoxin-a detection in benthic cyanobacterial mats throughout a river network.
Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.
The Ecology of Benthic Toxigenic Anabaena and Phormidium (Cyanobacteria) in the Eel River, California
Cyanobacteria are ubiquitous in aquatic ecosystems across the earth. In many environments they are present at low abundances, however under certain environmental conditions cyanobacteria bloom and become one of the dominant organisms in an waterbody, degrading aquatic food webs and water quality. Cyanobacteria evolved over 2 billion years ago, and cyanobacterial harmful algal blooms (cyanoHABs) have been documented for decades. Of particular concern is the production of cyanotoxins, secondary metabolites toxic to humans and other organisms, by certain strains of cyanobacteria. Most research of cyanoHABs has been of planktonic blooms in lakes or estuaries, and cyanotoxin production by benthic cyanobacteria in rivers has been more recent, but in many rivers benthic cyanobacteria are the primary source of cyanotoxins. With field surveys and monitoring, manipulative field experiments, and genome-resolved metagenomics, this dissertation investigated the ecology of benthic cyanobacteria in the Eel River, California.Like most coastal rivers in Northern California, the Eel River is in a Mediterranean climate. During the seasonal summer drought rivers become shallow, slow flowing, and warm, excellent habitat for benthic algal production. Non-toxic benthic algae are consumed by vertebrate and invertebrate grazers and are foundational to the aquatic summer food web. However, these benthic algal assemblages can tip towards toxicity when cyanobacteria begin to dominate the assemblage. Over a dozen dogs have died in the Eel River since the year 2000 due to ingesting cyanobacteria. Neighboring watersheds have also experienced dog deaths from cyanotoxin poisoning, and benthic cyanobacterial mats are an increasing public health concern in multiple Northern California rivers. Prior to this dissertation there were few data on the distribution and ecology of benthic toxigenic cyanobacteria in California rivers. During the summers of 2013-2015, I documented spatial and temporal patterns of cyanobacterial occurrence and cyanotoxin concentrations in the watershed, showing widespread distribution of anatoxin-a produced by benthic cyanobacteria. Solid phase adsorption toxin tracking (SPATT) samplers were deployed weekly to record dissolved microcystin and anatoxin-a levels at 10 sites throughout the watershed, and 187 cyanobacterial mat samples were collected from 31 sites to measure intracellular anatoxin-a and microcystins. Anatoxin-a levels were higher than microcystin for both SPATT and cyanobacterial mat samples. Species of benthic Anabaena and Phormidium were frequently found to produce cyanotoxins in the Eel watershed. Of the benthic mats sampled, 50% had detectable anatoxin-a (mean µg g-1 DW= 1.71, max= 70.93), while 24% had detectable microcystins (mean µg g-1 DW= 0.067, max= 2.29). SPATT cyanotoxin levels peaked in mid-summer in warm mainstem reaches of the watershed. This is one of the first documentations of widespread anatoxin-a occurrence and anatoxin-a production by benthic cyanobacterial mats in a North American watershed.Field experiments were used to study the buoyancy of benthic Anabaena spp. mats to understand implications for Anabaena dispersal. Experiments addressed oxygen bubble production and dissolution on the buoyancy of Anabaena dominated benthic mats in response to light exposure. Samples of Anabaena dominated mats were harvested from the South Fork Eel River and placed in settling columns to measure floating and sinking velocities, or deployed into in situ ambient and low light treatments to measure the effect of light on flotation. Floating and sinking occurred within minutes and were driven by oxygen bubbles produced during photosynthesis, rather than intracellular changes in carbohydrates or gas vesicles. Light experiment results showed that in a natural ambient light regime, mats remained floating for at least 4 days, while in low light mats begin to sink in <24 hours. The ability of Anabaena mats to maintain their buoyancy will markedly increase their downstream dispersal distances. Increased buoyancy also allows toxin-containing mats to collect along shorelines, increasing threats to human and animal public health.Within cyanobacterial mats are a consortia of microbes interacting together to process and exchange molecules to maintain their growth. Currently, little is known about the diversity of the biosynthetic capacities of cyanobacterial species and associated microbes in freshwater benthic mats in rivers. I sampled 22 Phormidium mats collected across the Eel River network and used genome-resolved metagenomics to 1) investigate cyanobacterial and co-occurring microbial assemblage diversity, 2) probe their metabolic potential, and 3) evaluate their capacities for toxin production. From the genomes of seven strains from one species group we describe the first anatoxin-a operon from the genus Phormidium. Importantly, community composition within the mat appears to be associated with the presence of cyanobacteria capable of producing anatoxin-a. Bacteroidetes, Proteobacteria, and novel Verrucomicrobia dominated the microbial assemblages. Interestingly, some mats also contained Candidate Phylum Kapabacteria and Candidate Phyla Radiation bacteria from Absconditabacteria (SR1), Parcubacteria (OD1) and Doudnabacteria (SM2F11). Although the majority of genomes were unique to a particular sample, metabolic diversity was low across samples. In addition to oxygenic photosynthesis and carbon respiration, metabolic capacities include aerobic anoxygenic photosynthesis, sulfur compound oxidation and breakdown of urea. These results show the importance of organic carbon and nitrogen to energy flow and nutrient cycling within mats and the interactions between potential anatoxin-a production and microbial assemblage composition.By combining watershed-scale observations, field experiments, and genomic analyses this dissertation provides novel information about the ecology of toxigenic benthic cyanobacteria in California rivers. Comprehensive knowledge of the ecology of benthic cyanobacteria is necessary to understand it’s impacts to public and ecosystem health and to better predict where and when blooms might occur in rivers
Microcoleus (Cyanobacteria) form watershed‐wide populations without strong gradients in population structure
Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal
International audienc
Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal
International audienceBenthic cyanobacteria in rivers produce cyanotoxins and affect aquatic food webs, but knowledge of their ecology lags behind planktonic cyanobacteria. The buoyancy of benthic Anabaena spp. mats was studied to understand implications for Anabaena dispersal in the Eel River, California. Field experiments were used to investigate the effects of oxygen bubble production and dissolution on the buoyancy of Anabaena dominated benthic mats in response to light exposure. Samples of Anabaena dominated mats were harvested from the South Fork Eel River and placed in settling columns to measure floating and sinking velocities, or deployed into in situ ambient and low light treatments to measure the effect of light on flotation. Floating and sinking occurred within minutes and were driven by oxygen bubbles produced during photosynthesis, rather than intracellular changes in carbohydrates or gas vesicles. Light experiment results showed that in a natural ambient light regime, mats remained floating for at least 4days, while in low light mats begin to sink in <24h. Floating Anabaena samples were collected from five sites in the watershed and found to contain the cyanotoxins anatoxin-a and microcystin, with higher concentrations of anatoxin-a (median 560, max 30,693ng/gDW) than microcystin (median 30, max 37ng/gDW). The ability of Anabaena mats to maintain their buoyancy will markedly increase their downstream dispersal distances. Increased buoyancy also allows toxin-containing mats to collect along shorelines, increasing threats to human and animal public health
Insight into functional and toxicological diversity of cyanobacterial mat communities in the Eel River
Toxic benthic cyanobacteria have started to attract attention after long neglect due to increased reports of their potential for secondary metabolites production. Particularly, this includes potent neurotoxins in the anatoxin class. Cyanobacteria commonly grow on the surfaces on riverbeds and these biofilms consist of assemblages of cyanobacteria and other microorganisms. So far, the vast majority of studies have focused solely on the cyanobacterial component, neglecting the diversity of the whole microbial assemblage and their interactions. We sampled cyanobacterial mats from the Eel River and resolved their community composition using genome-resolved metagenomics. The analyses revealed the regular presence of a range of heterotopic and viral components alongside dominant cyanobacterial taxa. Cyanobacterial genomes often encoded biosynthetic gene clusters of known toxins, as well as other metabolites belonging to different secondary metabolite classes. Several biosynthetic gene clusters were found across examined cyanobacterial genomes, and the presence of specific heterotrophic components. Our findings raise the importance of examining and characterizing the full microbial community that exists within cyanobacterial mats to understand when cyanobacteria possess toxic gene clusters and how that is correlated with the presence of surrounding microbial assemblage
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A Simple Approach to Modeling Light Attenuation in the Sacramento–San Joaquin Delta Using Commonly Available Data
The diffuse attenuation coefficient of photosynthetically active radiation (KdPAR) is commonly used to predict light attenuation in aquatic productivity models, but obtaining measurements of PAR to compute KdPAR is difficult. In situ calculations of KdPAR require multiple measurements of PAR through the water column, and these measurements are infeasible for real-time recording. Instead, predictive models using surface-water measurements may be used. Traditional KdPAR models are based on open-ocean habitats and rely on chlorophyll—as a proxy measurement for phytoplankton abundance—as the main predictive parameter. However, elevated suspended sediments and dissolved organic materials may also affect KdPAR values of inland water bodies and estuaries. In this study, we leverage KdPAR calculations derived from in situ light measurements collected along with surface-water-quality parameters across the Sacramento-San Joaquin River Delta in California, USA (the Delta). Sampling occurred between January of 2013 and May of 2014. We also explored regional and seasonal effects, but these did not clearly affect the model. Ultimately, the best-performing model included surface-level turbidity only (R2 = 0.91). The simplicity of the model facilitates use of KdPAR estimates for a variety of purposes throughout the Delta, including euphotic depth calculations, and as inputs to primary-productivity and habitat-suitability models. We demonstrate the model’s usability with two open-sources data sets (one spatially dense, and one temporally dense), and estimate KdPAR, euphotic depth, and primary productivity within the Delta. We provide calculations for each estimation, allowing users to easily adopt these models and apply them to their own data or with open-sourced data, which are abundant