Modeling Contaminant Microbes in Rivers During Both Baseflow and Stormflow.
Ontology highlight
ABSTRACT:
SUBMITTER: Drummond JD
PROVIDER: S-EPMC9286818 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The concept of fitness is often reduced to a single component, such as the replication rate in a given habitat. For species with multi-step life cycles, this can be an unjustified oversimplification, as every step of the life cycle can contribute to the overall reproductive success in a specific way. In particular, this applies to microbes that spend part of their life cycles associated to a host. In this case, there is a selection pressure not only on the replication rates, but also on the phenotypic traits associated to migrating from the external environment to the host and vice-versa (i.e., the migration rates). Here, we investigate a simple model of a microbial lineage living, replicating, migrating and competing in and between two compartments: a host and an environment. We perform a sensitivity analysis on the overall growth rate to determine the selection gradient experienced by the microbial lineage. We focus on the direction of selection at each point of the phenotypic space, defining an optimal way for the microbial lineage to increase its fitness. We show that microbes can adapt to the two-compartment life cycle through either changes in replication or migration rates, depending on the initial values of the traits, the initial distribution across the two compartments, the intensity of competition, and the time scales involved in the life cycle versus the time scale of adaptation (which determines the adequate probing time to measure fitness). Overall, our model provides a conceptual framework to study the selection on microbes experiencing a host-associated life cycle.
| S-EPMC8630024 | biostudies-literature
Project description:The mobilization and land-to-ocean transfer of dissolved organic carbon (DOC) in Arctic watersheds is intricately linked with the region's climate and water cycle, and furthermore at risk of changes from climate warming and associated impacts. This study quantifies model-simulated estimates of runoff, surface and active layer leachate DOC concentrations and loadings to western Arctic rivers, specifically for basins that drain into coastal waters between and including the Yukon and Mackenzie Rivers. Model validation leverages data from other field measurements, synthesis studies, and modeling efforts. The simulations effectively quantify DOC leaching in surface and subsurface runoff and broadly capture the seasonal cycle in DOC concentration and mass loadings reported from other studies that use river-based measurements. A marked east-west gradient in simulated spring and summer DOC concentrations of 24 drainage basins on the North Slope of Alaska is captured by the modeling, consistent with independent data derived from river sampling. Simulated loadings for the Mackenzie and Yukon show reasonable agreement with estimates of DOC export for annual totals and four of the six seasonal comparisons. Nearly equivalent loading occurs to rivers which drain north to the Beaufort Sea and west to the Bering and Chukchi Seas. The modeling framework provides a basis for understanding carbon export to coastal waters and for assessing impacts of hydrological cycle intensification and permafrost thaw with ongoing warming in the Arctic.
| S-EPMC9286382 | biostudies-literature
Project description:Human-induced (i.e., secondary) salinization affects aquatic biodiversity and ecosystem functioning worldwide. While agriculture or resource extraction are the main drivers of secondary salinization in arid and semi-arid regions of the world, the application of deicing road salt in winter can be an important source of salts entering freshwaters in cold regions. Alpine rivers are probably affected by salinization, especially in highly populated mountain regions, although this remains to be explored. In this study, we analyzed multi-year conductance time series from four rivers in the European Alps and demonstrated that the application of deicing road salt is linked to peaking rivers' salinity levels during late winter/early spring. Especially in small catchments with more urban surfaces close to the rivers, conductance increased during constant low-flow periods in late winter and was less correlated with discharge than in summer. Thus, our results suggest that small rivers highly connected to urban infrastructures are prone to considerable salinity peaks during late winter/early spring. Given the low natural level of salinities in Alpine rivers, the aquatic biodiversity might be significantly affected by the recorded changes in conductance, with potential consequences on ecosystem functioning. Thereby, we urge the research community to assess the impact of secondary salinization in Alpine rivers and call for an implementation of management practices to prevent the degradation of these pristine and valuable ecosystems.
| S-EPMC7840655 | biostudies-literature
Project description:Chinese surface waters are severely polluted by nutrients. This study addresses three challenges in nutrient modeling for rivers in China: (1) difficulties in transferring modeling results across biophysical and administrative scales, (2) poor representation of the locations of point sources, and (3) limited incorporation of the direct discharge of manure to rivers. The objective of this study is, therefore, to quantify inputs of nitrogen (N) and phosphorus (P) to Chinese rivers from different sources at multiple scales. We developed a novel multi-scale modeling approach including a detailed, state-of-the-art representation of point sources of nutrients in rivers. The model results show that the river pollution and source attributions differ among spatial scales. Point sources accounted for 75% of the total dissolved phosphorus (TDP) inputs to rivers in China in 2012, and diffuse sources accounted for 72% of the total dissolved nitrogen (TDN) inputs. One-third of the sub-basins accounted for more than half of the pollution. Downscaling to the smallest scale (polygons) reveals that 14% and 9% of the area contribute to more than half of the calculated TDN and TDP pollution, respectively. Sources of pollution vary considerably among and within counties. Clearly, multi-scale modeling may help to develop effective policies for water pollution.
| S-EPMC6706797 | biostudies-literature
Project description:Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (?15N and ?18O of nitrate and ?11B) and fecal indicators to trace nitrate sources and pathways to the stream. We tested this approach on two rivers in an agricultural region of SW France. Boron isotopic ratios evidenced inflow from anthropogenic waters, microbiological markers revealed organic contaminations from both human and animal wastes. Nitrate ?15N and ?18O traced inputs from the surface leaching during high flow events and from the subsurface drainage in base flow regime. They also showed that denitrification occurred within the soils before reaching the rivers. Furthermore, this study highlighted the determinant role of the soil compartment in nitrate formation and recycling with important spatial heterogeneity and temporal variability.
| S-EPMC5288703 | biostudies-other
Project description:We present a framework to model microbial transformations in chemostats and retentostats under transient or quasi-steady state conditions. The model accounts for transformation-induced isotope fractionation and mass-transfer across the cell membrane. It also verifies that the isotope fractionation ? can be evaluated as the difference of substrate-specific isotope ratios between inflow and outflow. We explicitly considered that the dropwise feeding of substrate into the reactor at very low dilution rates leads to transient behavior of concentrations and transformation rates and use this information to validate conditions under which a quasi-steady state treatment is justified. We demonstrate the practicality of the code by modeling a chemostat experiment of atrazine degradation at low dilution/growth rates by the strain Arthrobacter aurescens TC1. Our results shed light on the interplay of processes that control biodegradation and isotope fractionation of contaminants at low (?g/L) concentration levels. With the help of the model, an estimate of the mass-transfer coefficient of atrazine through the cell membrane was achieved (0.0025 s-1).
| S-EPMC6986770 | biostudies-literature
Project description:Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project.org/package=BacArena) to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of the human gut. For our P. aeruginosa model, we found that cross-feeding of fermentation products cause a spatial differentiation of emerging metabolic phenotypes in the biofilm over time. In the human gut model community, we found that spatial gradients of mucus glycans are important for niche formations which shape the overall community structure. Additionally, we could provide novel hypothesis concerning the metabolic interactions between the microbes. These results demonstrate the importance of spatial and temporal multi-scale modeling approaches such as BacArena.
| S-EPMC5460873 | biostudies-literature
Project description:Microbes during aerobic fermentation Raw sequence reads
| PRJNA713407 | ENA
Project description:How people value rivers, wetlands and floodplains influences their attitudes, beliefs and behaviours towards these ecosystems, and can shape policy and management interventions. Better understanding why people value rivers, wetlands and floodplains and their key ecosystem components, such as vegetation, helps to determine what factors underpin the social legitimacy required for effective management of these systems. This study sought to ascertain perspectives on the value of non-woody vegetation in river-floodplain systems via an online survey. The survey found that participants valued non-woody vegetation for their provision of a range of ecosystem functions and services, with strong emphasis on ecological aspects such as regulation functions, habitat provision and biodiversity. However, the inclusion of a question framed to focus on stories or narratives resulted in a different emphasis. Responses indicated that non-woody vegetation, and rivers, wetlands and floodplains were valued for the way they made people feel through lived experiences such as recreational activities, personal interactions with nature, educational and research experiences. This highlights the important role of storytelling in navigating complex natural resource management challenges and ascertaining a deeper understanding of values that moves beyond provision of function to feeling. Improved understanding of the diverse ways people value and interact with river-floodplain systems will help develop narratives and forms of engagement that foster shared understanding, empathy and collaboration. Appreciation of plural values such as the provision of functions and services along with the role of emotional connections and lived experience will likely increase lasting engagement of the general public with management to protect and restore river-floodplain systems.
| S-EPMC10786729 | biostudies-literature
Project description:In eukaryotic cells, DNA is packaged into chromatin where nucleosomes are the basic packaging unit. Important cellular processes including gene expression, DNA replication, and DNA repair require nucleosomal DNA to be unwrapped so that functional proteins can access their target sites, which otherwise are sterically occluded. A key question in this process is what the unwrapped conformations individual nucleosomes adopt within chromatin are. Here, we develop a concurrent nucleosome unwrapping model to address this question. We hypothesize that for a given end-to-end distance of the nucleosomal DNA, the nucleosomal DNA stochastically unwraps from the histone core from both ends independently and that this combination of unwrapping from both sides results in a significant increase in the average distance between the DNA extending from both sides of the nucleosomes. We test our model on recently published experiments using a DNA origami nanocaliper that quantifies nucleosome unwrapping and achieve good agreement between experiment and model prediction. We then investigate the DNA origami caliper distribution when attached to a hexasome (a nucleosome lacking an H2A/H2B dimer). A significant shift in the caliper angle distribution caused by the asymmetric structural features of the hexasome seen experimentally is consistent with the model. Our modeling approach may be more broadly useful to the interpretation of other studies of nucleosome dynamics, chromatin dynamics, and regulatory processes involving nucleosome unwrapping, as well as more generally to optimization of future DNA origami designs to probe mechanical properties of biomolecules.
| S-EPMC6895690 | biostudies-literature