The virtual microbiome: A computational framework to evaluate microbiome analyses.

Microbiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtual microbiomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information and optimizing the use of this information.

Biomagnification and temporal trends (1990-2021) of perfluoroalkyl substances in striped dolphins (Stenella coeruleoalba) from the NW Mediterranean sea.

Poly- and Perfluoroalkyl Substances (PFAS) are a well-known class of pollutants which can bioaccumulate and biomagnify with a vast majority being highly persistent. This study aims to determine the biomagnification rates of PFAS in sexually mature striped dolphins and to assess temporal trends on PFAS concentrations over the past three decades (1990-2021) in the North-Western Mediterranean Sea. Thirteen and 17 of the 19 targeted PFAS were detected in the samples of the dolphins' digestive content and liver, respectively, at concentrations ranging between 43 and 1609 ng/g wet weight, and 254 and 7010 ng/g wet weight, respectively. The most abundant compounds in both types of samples were linear perfluorooctanesulfonic acid (n-PFOS) and perfluorooctanesulfonamide (FOSA), which were present in all samples, followed by perfluoroundecanoic acid (PFUnDA), perfluorotridecanoic acid (PFTrDA) and perfluorononanoic acid (PFNA). Long-chain PFAS (i.e., PFCAs C ≥ 7 and PFSAs C ≥ 6) biomagnified to a greater extent than short-chain PFAS, suggesting a potential effect on the health of striped dolphins. Environmental Quality Standards concentrations set in 2014 by the European Union were exceeded in half of the samples of digestive content, suggesting that polluted prey may pose potential health risks for striped dolphins. Concentrations of most long-chain PFAS increased from 1990 to 2004-2009, then stabilized during 2014-2021, possibly following country regulations and industrial initiatives. The current study highlights the persistent presence of banned PFAS and may contribute to future ecological risk assessments and the design of management strategies to mitigate PFAS pollution in marine ecosystems.

Plastic degradation by insect hexamerins: Near-atomic resolution structures of the polyethylene-degrading proteins from the wax worm saliva.

Plastic waste management is a pressing ecological, social, and economic challenge. The saliva of the lepidopteran Galleria mellonella larvae is capable of oxidizing and depolymerizing polyethylene in hours at room temperature. Here, we analyze by cryo-electron microscopy (cryo-EM) G. mellonella's saliva directly from the native source. The three-dimensional reconstructions reveal that the buccal secretion is mainly composed of four hexamerins belonging to the hemocyanin/phenoloxidase family, renamed Demetra, Cibeles, Ceres, and a previously unidentified factor termed Cora. Functional assays show that this factor, as its counterparts Demetra and Ceres, is also able to oxidize and degrade polyethylene. The cryo-EM data and the x-ray analysis from purified fractions show that they self-assemble primarily into three macromolecular complexes with striking structural differences that likely modulate their activity. Overall, these results establish the ground to further explore the hexamerins' functionalities, their role in vivo, and their eventual biotechnological application.

Plant uptake of perfluoroalkyl substances in freshwater environments (Dongzhulong and Xiaoqing Rivers, China).

This study provides new knowledge on the mobility, behavior, and partitioning of 17 perfluoroalkyl substances (PFASs) in the water-sediment-plant system along the Dongzhulong and Xiaoqing Rivers. The fate of PFASs in these rivers is also discussed. The study area is affected by the industrial production of perfluorooctanoic acid (PFOA). The ∑PFASs in water and sediments close to the industrial discharge were 84,000 ± 2000 ng/L and 2300 ± 200 ng/g dw, respectively, with the concentrations decreasing along the river due to dilution. PFOA was the dominant compound (74-97% of the ∑PFASs), although other PFASs were identified close to urban areas. Principal component analysis and solid-liquid distribution coefficients revealed that long-chain PFASs accumulated in the sediment whereas short-chain PFASs remained in the water all along the river. PFASs were taken up by plants and remobilized to different plant compartments according to shoot concentration factors (SCFs), root concentration factors (RCF), and transfer factors (TFs). Among the four plant species studied, floating plants absorbed high levels of PFASs, while rooted species translocated short-chain PFASs from the roots to the shoots. Therefore, floating species, due to their high uptake capacity and large proliferation rate, could eventually be used for phytoremediation.

Distribution and ten-year temporal trends (2009-2018) of perfluoroalkyl substances in gull eggs from Spanish breeding colonies.

Gull eggs are excellent bioindicators of environmental pollution as reflect the contamination levels of coastal areas, especially of persistent and bioacumulative compounds such as perfluoroalkyl substances (PFAS). This study aims to evaluate the geographical distribution and 10-year temporal trends (2009-2018) of 17 PFAS in eggs of two gull species (Larus michahellis and Larus audouinii) from 5 main Spanish colonies. ∑PFAS ranged from 13.7 ± 5.9 to 164 ± 17 ng g-1 wet weight and higher concentrations were observed in L. audouinii than in L. michahellis. Perfluorooctane sulfonate (PFOS) was the predominant compound in all samples, followed by perfluoroundecanoic acid (PFUnA) and perfluorotridecanoic acid (PFTriDA). Perfluorododecanoic acid (PFDoA), perfluorodecanoic acid (PFDA) and perfluorooctanoic acid (PFNA) were also found in all studied areas but at lower concentrations, while perfluorooctanoic acid (PFOA) was only detected in the Medes Islands. Principal Component Analysis revealed the co-occurrence of the 6 detected PFAS, and differentiated samples from Ebro Delta and Medes Islands, both located in the North-Eastern Mediterranean Sea, with high contribution of all PFAS, from Chafarinas and Atlantic Islands with lower concentration levels and variability. Also, different patterns were observed among colonies, suggesting the fish-based diet plays an important role in PFAS bioaccumulation. In all colonies, except for the Medes Islands, ∑PFAS decreased through the 10-year study period, with PFOS, PFUnA, and PFTriDA showing a significant concentration reduction in a colony-specific manner. This study demonstrates the usefulness and importance of continuous systematic long-term monitoring to determine the geographical distribution and temporal variations of PFAS in marine protected areas using gull eggs as bioindicators of environmental pollution.