Impact of iron addition on phosphorus dynamics in sediments of a shallow peat lake 10 years after treatment

Internal phosphorus (P) loading is a key water quality challenge for shallow lakes. Addition of iron (Fe) salts has been used to enhance P retention in lake sediments. However, its effects on sediment geochemistry are poorly studied, albeit pivotal for remediation success. Here, we assess the factors controlling the retention of P and long-term effects following application of FeCl3 (0.5–1 mol Fe/m2, 2010) in the eutrophic, shallow peat lake Terra Nova (the Netherlands). Treatment reduced P levels in the lake for two years, but afterwards summer release of P intensified, resulting in higher surface water P concentrations than before treatment. Porewater and sediment analyses indicate that the majority of the added Fe is still undergoing redox cycling within the top 10 cm of sediment accounting for the binding of up to 70 % of sedimentary P. Sequential extractions further suggest that organic matter (OM) plays a key role in the resulting P and Fe dynamics: While reduction of P binding Fe(III) phases results in P release to porewaters, the produced Fe2+ remains bound to the solid phase presumably stabilized by OM. This causes P release from the sediments in excess to Fe during temporary low oxygen conditions in summer months, as confirmed by whole core flux incubation experiments. Quantitative coprecipitation of P with Fe upon reoxygenation of the water body is then impossible, leading to a gradual increase in surface water P. This first long-term study on a shallow peat lake underpins the role of OM for Fe cycling and the need to carefully consider the sediment properties and diagenetic pathways in the planning of Fe-amendments

Innate immunity against HIV: a priority target for HIV prevention research

This review summarizes recent advances and current gaps in understanding of innate immunity to human immunodeficiency virus (HIV) infection, and identifies key scientific priorities to enable application of this knowledge to the development of novel prevention strategies (vaccines and microbicides). It builds on productive discussion and new data arising out of a workshop on innate immunity against HIV held at the European Commission in Brussels, together with recent observations from the literature

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Quantifying fracture geometry with X-ray tomography: Technique of Iterative Local Thresholding (TILT) for 3D image segmentation

This paper presents a new method—the Technique of Iterative Local Thresholding (TILT)—for processing 3D X-ray computed tomography (xCT) images for visualization and quantification of rock fractures. The TILT method includes the following advancements. First, custom masks are generated by a fracture-dilation procedure, which significantly amplifies the fracture signal on the intensity histogram used for local thresholding. Second, TILT is particularly well suited for fracture characterization in granular rocks because the multi-scale Hessian fracture (MHF) filter has been incorporated to distinguish fractures from pores in the rock matrix. Third, TILT wraps the thresholding and fracture isolation steps in an optimized iterative routine for binary segmentation, minimizing human intervention and enabling automated processing of large 3D datasets. As an illustrative example, we applied TILT to 3D xCT images of reacted and unreacted fractured limestone cores. Other segmentation methods were also applied to provide insights regarding variability in image processing. The results show that TILT significantly enhanced separability of grayscale intensities, outperformed the other methods in automation, and was successful in isolating fractures from the porous rock matrix. Because the other methods are more likely to misclassify fracture edges as void and/or have limited capacity in distinguishing fractures from pores, those methods estimated larger fracture volumes (up to 80 %), surface areas (up to 60 %), and roughness (up to a factor of 2). These differences in fracture geometry would lead to significant disparities in hydraulic permeability predictions, as determined by 2D flow simulations

Global Warming and Continued External Loading Alters Nitrogen and Phosphorus Balance in the Franconian Lake District

<p>Data belonging to Limnology and Oceanography upload:</p> <p>Global Warming and Continued External Loading Alters Nitrogen and Phosphorus Balance in a Temperate Reservoir System.</p> <p>Global warming will intensify in the coming century. Consequently cycling of phosphorus and nitrogen in reservoirs will be affected which could lead to aggravated phytoplankton blooms. For now few case studies have simultaneously investigated effects of warming on cycling of both nitrogen and phosphorus. In this context, the study focused on the Franconian Lake District’s four reservoirs, covering the period from 2000 to 2019. Changes in water temperatures (which increased by 0.3 to 1°C annually), the extension of thermal stratification (9 to 19 days per decade) and hypolimnetic anoxia (14 to 36 days per decade) were determined. These shifts led to decreases in nitrogen concentrations but increases in phosphorus concentrations. Increased denitrification rates reduced nitrogen levels early in the year and ammonification in the anoxic hypolimnia showed only marginal increases, not compensating for denitrification losses. Conversely, phosphorus concentrations increased particularly in the increasingly anoxic summer months. This was ascribed to release of ortho-phosphate from mineralization and redox-sensitive phosphorus fractions in the sediment. Opposing trends led to a sharp decrease in the total nitrogen to total phosphorus (TN:TP) ratios. The study also revealed an increase in bio-available ortho-phosphate and ammonium. Combined the altered nutrient composition could lead to proliferation of bloom-forming, nitrogen-fixing diazotrophic cyanobacteria. This study suggests that most temperate reservoirs and lakes, suffering from ongoing external and internal nutrient loads, will probably experience further reductions in TN:TP-ratio in a warmer world. To mitigate indirect effects of warming, new strategies are required to decrease phosphorus inflows and manage legacy phosphorus release from sediments.</p&gt

Evolutionary stabilization of cooperative toxin production through a bacterium-plasmid-phage interplay

Colicins are toxins produced and released by Enterobacteriaceae to kill competitors in the gut. While group A colicins employ a division of labor strategy to liberate the toxin into the environment via colicin-specific lysis, group B colicin systems lack cognate lysis genes. In Salmonella enterica serovar Typhimurium (S. Tm), the group B colicin Ib (ColIb) is released by temperate phage-mediated bacteriolysis. Phage-mediated ColIb release promotes S. Tm fitness against competing Escherichia coli. It remained unclear how prophage-mediated lysis is realized in a clonal population of ColIb producers and if prophages contribute to evolutionary stability of toxin release in S. Tm. Here, we show that prophage-mediated lysis occurs in an S. Tm subpopulation only, thereby introducing phenotypic heterogeneity to the system. We established a mathematical model to study the dynamic interplay of S. Tm, ColIb, and a temperate phage in the presence of a competing species. Using this model, we studied long-term evolution of phage lysis rates in a fluctuating infection scenario. This revealed that phage lysis evolves as bet-hedging strategy that maxi-mizes phage spread, regardless of whether colicin is present or not. We conclude that the ColIb system, lacking its own lysis gene, is making use of the evolutionary stable phage strategy to be released. Prophage lysis genes are highly prevalent in nontyphoidal Salmonella genomes. This suggests that the release of ColIb by temperate phages is widespread. In conclusion, our findings shed new light on the evolution and ecology of group B colicin systems. IMPORTANCE Bacteria are excellent model organisms to study mechanisms of social evolution. The production of public goods, e.g., toxin release by cell lysis in clonal bacterial populations, is a frequently studied example of cooperative behavior. Here, we analyze evolutionary stabilization of toxin release by the enteric pathogen Sal-monella. The release of colicin Ib (ColIb), which is used by Salmonella to gain an edge against competing microbiota following infection, is coupled to bacterial lysis mediated by temperate phages. Here, we show that phage-dependent lysis and subsequent release of colicin and phage particles occurs only in part of the ColIb-expressing Salmonella population. This phenotypic heterogeneity in lysis, which rep-resents an essential step in the temperate phage life cycle, has evolved as a bet-hedging strategy under fluctuating environments such as the gastrointestinal tract. Our findings suggest that prophages can thereby evolutionarily stabilize costly toxin release in bacterial populations