In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study ...perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.
Shotgun sequencing bypasses the need for metabarcoding in viromics, although it is prone to high background noises and biases towards double-stranded DNA viruses.Protein-level assembly can be a better tool to use on virome data as they predict more protein sequences from complex unknown metagenomes.Using viral discovery methods can help to resolve the full diversity of viral fraction of microbiome data.Culture-independent methods such as viral-tagging can be used to measure the phage host range in the human body.
Increases in atmospheric temperature and nutrients from land are thought to be promoting the expansion of harmful cyanobacteria in lakes worldwide, yet to date there has been no quantitative ...synthesis of long‐term trends. To test whether cyanobacteria have increased in abundance over the past ~ 200 years and evaluate the relative influence of potential causal mechanisms, we synthesised 108 highly resolved sedimentary time series and 18 decadal‐scale monitoring records from north temperate‐subarctic lakes. We demonstrate that: (1) cyanobacteria have increased significantly since c. 1800 ce, (2) they have increased disproportionately relative to other phytoplankton, and (3) cyanobacteria increased more rapidly post c. 1945 ce. Variation among lakes in the rates of increase was explained best by nutrient concentration (phosphorus and nitrogen), and temperature was of secondary importance. Although cyanobacterial biomass has declined in some managed lakes with reduced nutrient influx, the larger spatio‐temporal scale of sedimentary records show continued increases in cyanobacteria throughout the north temperate‐subarctic regions.
We studied the community structure of crustacean zooplankton along the biogeographical zones of the St. Lawrence River (Québec, Canada), to evaluate how the riverscale hydrological network formed by ...water masses, and local-scale aquatic environment, influenced the distribution of crustacean groups (cladocerans, calanoids, cyclopoids and harpacticoids) during the spring (high discharge) and summer (low discharge) hydroperiods. Zooplankton and environmental data were sampled at 52 sites forming 16 transects along the fluvial section zone (FSZ), the fluvial estuary zone (FEZ) and the estuarine transition zone (ETZ) of the St. Lawrence River in May and August 2006. We compared zooplankton community composition among biogeographical zones and fluvial lakes and across the fluvial estuarine continuum. Analyses were carried out using asymmetric eigenvector maps (AEM), redundancy analysis (RDA), and variation partitioning. Spatial distribution patterns revealed a complex river model. Riverscale discontinuities between the fluvial and estuarine transition zones, and the hydrological network of water masses in the fluvial zones, explained better the spatial zooplankton distribution patterns along the fluvial estuarine continuum than the local environment. Spatial variation in the flow network and environmental conditions were the main drivers of zooplankton distributions in spring whereas the flow network of water masses was the most influential factor in summer.
There is growing concern that harmful cyanobacterial blooms are increasing in frequency and occurrence around the world. Although nutrient enrichment is commonly identified as a key predictor of ...cyanobacterial abundance and dominance in freshwaters, several studies have shown that variables related to climate change can also play an important role. Based on our analysis of the literature, we hypothesized that temperature or water‐column stability will be the primary drivers of cyanobacterial abundance in stratified lakes whereas nutrients will be the stronger predictors in frequently mixing water bodies. To test this hypothesis, as well as quantify the drivers of cyanobacteria over different scales and identify interactions between nutrients and climate‐related variables, we applied linear and nonlinear mixed‐effect modeling techniques to seasonal time‐series data from multiple lakes. We first compared time series of cyanobacterial dominance to a published lake survey and found that the models were similar. Using time‐series data of cyanobacterial biomass, we identified important interactions among nutrients and climate‐related variables; dimictic basin experienced a heightened susceptibility to cyanobacterial blooms under stratified eutrophic conditions, whereas polymictic basins were less sensitive to changes in temperature or stratification. Overall, our results show that due to predictable interactions among nutrients and temperature, polymictic and dimictic lakes are expected to respond differently to future climate warming and eutrophication.
Stunting, a severe and multigenerational growth impairment, globally affects 22% of children under the age of 5 years. Stunted children have altered gut bacterial communities with higher proportions ...of Proteobacteria, a phylum with several known human pathogens. Despite the links between an altered gut microbiota and stunting, the role of bacteriophages, highly abundant bacterial viruses, is unknown. Here, we describe the gut bacterial and bacteriophage communities of Bangladeshi stunted children younger than 38 months. We show that these children harbor distinct gut bacteriophages relative to their non-stunted counterparts. In vitro, these gut bacteriophages are infectious and can regulate bacterial abundance and composition in an age-specific manner, highlighting their possible role in the pathophysiology of child stunting. Specifically, Proteobacteria from non-stunted children increased in the presence of phages from younger stunted children, suggesting that phages could contribute to the bacterial community changes observed in child stunting.
Agriculturally driven changes in soil phosphorus (P) are known to have persistent effects on local ecosystem structure and function, but regional patterns of soil P recovery following cessation of ...agriculture are less well understood. We synthesized data from 94 published studies to assess evidence of these land‐use legacies throughout the world by comparing soil labile and total P content in abandoned agricultural areas to that of reference ecosystems or sites remaining in agriculture. Our meta‐analysis shows that soil P content was typically elevated after abandonment compared to reference levels, but reduced compared to soils that remained under agriculture. There were more pronounced differences in the legacies of past agriculture on soil P across regions than between the types of land use practiced prior to abandonment (cropland, pasture, or forage grassland). However, consistent patterns of soil P enrichment or depletion according to soil order and types of post‐agricultural vegetation suggest that these factors may mediate agricultural legacies on soil P. We also used mixed effects models to examine the role of multiple variables on soil P recovery following agriculture. Time since cessation of agriculture was highly influential on soil P legacies, with clear reductions in the degree of labile and total P enrichment relative to reference ecosystems over time. Soil characteristics (clay content and pH) were strongly related to changes in labile P compared to reference sites, but these were relatively unimportant for total P. The duration of past agricultural use and climate were weakly related to changes in total P only. Our finding of reductions in the degree of soil P alteration over time relative to reference conditions reveals the potential to mitigate these land‐use legacies in some soils. Better ability to predict dynamics of soil nutrient recovery after termination of agricultural use is essential to ecosystem management following land‐use change.
Aim: Scientists, governments and non-governmental organizations are increasingly moving towards the collection of large, open-access data. In aquatic sciences, this effort is expanding the scope of ...questions and analyses that can be performed to further our knowledge of the global drivers of water quality. Cyanotoxin concentration is one variable that has received considerable attention, and although strong local-scale models have been described in the literature, modelling cyanotoxin concentrations across broader spatial scales has been more difficult. Commonly used statistical frameworks have not fully captured the complex response of toxic algal blooms to global change, limiting our ability to predict and mitigate the impairment of freshwaters by toxic algae. Here, we advance our understanding of emergent drivers of cyanotoxins across a structured landscape by applying a hierarchical "hurdle" model. Location: Lakes and reservoirs in the conterminous United States n = 1127. Methods: We studied cyanobacteria and their toxins microcystins during the 2007 summer period. We applied a hierarchical zero-altered model to test the importance of multi-scale interactions among environmental features in driving microcystin concentrations above the limit of detection. We then used boosted regression trees BRTs to identify environmental thresholds associated with severe impairment by microcystins. Results: Accounting for numerous non-detections, spatial heterogeneity and cross-scale interactions substantially improved continental-scale predictions of bloom toxicity. Our model accounted for 55% of the variance in the probability of detecting microcystins across the United States, and 26% of the variability in microcystin concentrations once detected. BRTs further showed that although both local and regional drivers were associated with microcystin concentrations at low to intermediate provisional guidelines, only local drivers came into play when predicting higher limits. Main conclusions: Identifying the interaction between local and regional processes is key to understanding the heterogeneous responses of microcystins to environmental change. Our framework could increase the effectiveness of continental-scale analyses for many different water variables.
Rare earth elements (REEs) have been recently identified as emergent contaminants because of their numerous and increasing applications in technology. The impact of REEs on downstream ecosystems, ...notably aquatic organisms, is of particular concern, but has to date been largely overlooked. The purpose of this study was thus to evaluate the toxicity of lanthanide metals, lutetium (Lu) and dysprosium (Dy) in rainbow trout after 96 h of exposure. The lethal concentration (LC50) was determined and the expression of 14 genes involved in different pathways such as oxidative stress, xenobiotic detoxification, mitochondrial respiration, DNA repair, protein folding and turnover, inflammation, calcium binding and ammonia metabolism were quantified in surviving fish. In parallel, lipid peroxidation (LPO), DNA damage (DSB), metallothionein level (MT) and cyclooxygenase activity (COX) were examined. The acute 96 h-LC50 data revealed that Lu was more toxic than Dy (1.9 and 11.0 mg/L, respectively) and was able to affect all investigated pathways by changing the expression of the studied genes, to the exception of superoxide dismutase (SOD), catalase (CAT) and glutathione-S-transferase (GST). It also induced a decrease in DNA repair at concentrations 29 times below the LC50. This suggests that Lu could trigger a general stress to disrupt the cell homeostasis leading to genotoxicity without promoting oxidative stress. However, Dy induced modulation in the expression of genes involved in the protection against oxidative stress, detoxification, mitochondrial respiration, immunomodulation, protein turnover and an increase in the DNA strand breaks at concentrations 170 times lower than LC50. Changes in mRNA level transcripts could represent an early signal to prevent against toxicity of Dy, which exhibited inflammatory and genotoxic effects. This study thus provides useful knowledge enhancing our understanding of survival strategies developed by rainbow trout to cope with the presence of lanthanides in the environment.
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•Lutetium (Lu) was more toxic than dysprosium (Dy) in trout, after acute exposure.•Dy altered genes involved in detoxification, protein turnover, DNA repair and energy.•By opposition to Dy, Lu also affected ammonia metabolism and calcium binding pathways.•Both lanthanides are genotoxic but only Dy induced inflammatory effects.
To date, studies examining the impact of agriculture on freshwater systems have been spatially confined (that is, single drainage basin or regional level). Across regions, there are considerable ...differences in a number of factors, including geology, catchment morphometry, and hydrology that affect water quality. Given this heterogeneity, it is unknown whether agricultural activities have a pervasive impact on lake trophic state across large spatial scales. To address this issue, we tested whether the proportion of agricultural land in a catchment (% Agr) could explain a significant portion of the variation in lake water quality at a broad inter-regional scale. As shallow, productive systems have been shown to be particularly susceptible to eutrophication, we further investigated how lake mean depth modulates the relationship between % Agr and lake total phosphorus (TP) concentration. We applied both traditional meta-analytic techniques and more sophisticated linear mixed-effects models to a dataset of 358 temperate lakes that spanned an extensive spatial gradient (5°E to 73°W) to address these issues. With meta-analytical techniques we detected an across-study correlation between TP and % Agr of 0.53 (one-tailed P-value = 0.021). The across-study correlation coefficient between TP and mean depth was substantially lower (r = -0.38; P = 0.057). With linear mixed-effects modeling, we detected among-study variability, which arises from differences in pre-impact (background) lake trophic state and in the relationship between lake mean depth and lake TP. To our knowledge, this is the first quantitative synthesis that defines the influence of agriculture on lake water quality at such a broad spatial scale. Syntheses such as these are required to define the global relationship between agricultural land-use and water quality.
African tropical lakes provide vital ecosystem services including food and water to some of the fastest growing human populations, yet they are among the most understudied ecosystems in the world. ...The consequences of climate change and other stressors on the tropical lakes of Africa have been informed by long-term analyses, but these studies have largely focused on the massive Great Rift Valley lakes. Our objective was to evaluate how recent climate change has altered the functioning and services of smaller tropical lakes, which are far more abundant on the landscape. Based on a paired analysis of 20 years of high-resolution water column data and a paleolimnological record from a small crater lake in western Uganda, we present evidence that even a modest warming of the air (∼0.9°C increase over 20 years) and changes in the timing and intensity of rainfall can have significant consequences on the dynamics of this common tropical lake type. For example, we observed a significant nonlinear increase (R(2) adj = 0.23, e.d.f. = 7, p<0.0001) in thermal stability over the past 20 years. This resulted in the expansion of anoxic waters and consequent deterioration of fish habitat and appears to have abated primary production; processes that may impair ecosystem services for a vulnerable human population. This study on a system representative of small tropical crater lakes highlights the far-reaching effects of global climatic change on tropical waters. Increased research efforts into tropical aquatic ecosystem health and the development of sound management practices are necessary in order to strengthen adaptive capabilities in tropical regions.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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