Identifying Priority Conservation Areas of Largehead Hairtail (Trichiurus japonicus) Nursery Grounds in the East China Sea

Identifying the spatio-temporal distribution hotspots of fishes and allocating priority conservation areas could facilitate the spatial planning and efficient management. As a flagship commercial fishery species, Largehead hairtail (Trichiurus japonicus) has been over-exploited since the early 2000s. Therefore, the spatio-temporal management of largehead hairtail nursery grounds could effective help its recovery. This study aims to predict juvenile largehead hairtail distribution patterns and identify priority conservation areas for nursery grounds. A two-stage hierarchical Bayesian spatio-temporal model was applied on independent scientific survey data (Catch per unit effort, CPUE) and geographic/physical variables (Depth, Distance to the coast, Sea bottom temperature, Dissolved oxygen concentration and Net primary production) to analyze the probability of occurrence and abundance distribution of juvenile largehead hairtail. We assessed the importance of each variable for explaining the occurrence and abundance. Using persistence index, we measured the robustness of hotspots and identified persistent hotspots for priority conservation areas. Selected models showed good predictive capacity on occurrence probability (AUC = 0.81) and abundance distribution (r = 0.89) of juvenile largehead hairtail. Dissolved oxygen, net primary production, and sea bottom temperature significantly affected the probability of occurrence, while distance to the coast also affected the abundance distribution. Three stable nursery grounds were identified in Zhejiang inshore waters, the largest one was located on the east margin of the East China Sea hairtail national aquatic germplasm resources conservation zones (TCZ), suggesting that the core area of nursery grounds occurs outside the protected areas. Therefore, recognition of these sites and their associated geographic/oceanic attributes provides clear targets for optimizing largehead hairtail conservation efforts in the East China Sea. We suggested that the eastern and southern areas of TCZ should be included in conservation planning for an effective management within a network of marine protected areas.

Power laws from the bird species abundance distribution

A recent study found that bird species with fewer individuals are abundant, but large species are rare. We show that this new data strongly suggests a power-law distribution rather than the most accepted log-normal. Moreover, we discuss extinction risk across the bird phylogeny and future conservation efforts by profiting from the hierarchical structure revealed by the new data.

To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli , sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, as almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

Microplastic Pollution in The Topsoil of Hot And Dried Areas, Human Exposure and Source Assessment, Aghili Plain, Iran

Although the distribution of microplastic (MPs) has been studied in different environmental compartments during the last decade, there is still a knowledge gap in their distribution and abundances in soil. This study aimed to investigate the abundance, distribution, and type of MPs in the soil of Aghili plain as a hot and dry area in southwest of Iran. In this study, composite soil samples (n=102) were collected from the residential and agricultural areas in Aghili plain, Iran. A combination of visual observations, Scanning Electron Microscopy (SEM) – Energy-dispersive X-ray spectroscopy (EDS), and Raman micro -spectroscopy was conducted to quantify and characterize MPs in soil samples. The intakes of MPs in adults and children were estimated through two exposure EPA scenarios. The total MPs loading in the studies soil was 11.93 ± 0.9 items in Kg-1 of surface soil in Aghili plain. The MPs had various morphology (fiber, pellet, fragment, and spherule shapes), colors (white-transparent, yellow-orange, red-pink, blue-green and black-grey colors), and sizes (<100 µm up to 1000 ≤ µm). Black-grey fibers in size less than 100 μm were dominant MPs in soil samples using a binocular microscope. Trace amounts of C, N, O, Na, P, Si revealed by EDS suggested the organic and inorganic contaminations on the surface of identified MPs. Intake of MPs per day/year through ingestion of polluted soil was calculated. Mean normal and acute exposure was estimated at 0.435 and 0.871 MPs per year through ingestion by children and adults, respectively.

Speed fluctuations of bacterial replisomes

Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, the dynamics of replisomes along the genome is poorly characterised, especially in vivo. In this paper, we link the replisome dynamics with the DNA abundance distribution measured in an exponentially growing bacterial population. Our approach permits to accurately infer the replisome dynamics along the genome from deep sequencing measurements. As an application, we experimentally measured the DNA abundance distribution in Escherichia coli populations growing at different temperatures. We find that the average replisome speed increases nearly five-fold between 17°C and 37°C. Further, we observe wave-like variations of the replisome speed along the genome. These variations are correlated with previously observed variations of the mutation rate along the genome. We interpret this correlation as a speed--error trade-off and discuss its possible dynamical origin. Our approach has the potential to elucidate replication dynamics in E. coli mutants and in other bacterial species.