Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.

Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

[This corrects the article DOI: 10.1371/journal.ppat.1011461.].

Clean your own house first: integrating sustainability into microbiology labs.

Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.

Fifty-year study of microplastics ingested by brachyuran and fish larvae in the central English North Sea.

Microplastics (MPs) are ubiquitous pollutants in marine environments. Among the many detrimental consequences of microplastic pollution, its consumption by marine biota is of particular relevance for human health, due to exposure through the food web. Long-term time-series biotic samples are overlooked sources of information for microplastics research. These collections are extremely valuable for the detection and monitoring of changes in marine environments. However, there are very few long-term studies (>10 years) of the uptake of microplastics by biota. Here, we used Dove Time Series planktonic samples (from 1971 to 2020) to assess the presence and prevalence of microplastics in the English North Sea coast over time. Fish and brachyuran larvae were selected due to their commercial importance and consequent implications for human health. A custom enzymatic digestion method was used to extract microplastics for FTIR-ATR polymer identification. An increasing cumulative trend in MP ingestion was identified. Cellophane and polyethylene terephthalate were the polymer types found most frequently in both taxa. Although a total higher microplastics uptake was observed in fish, consumption was not significantly different between taxa over time. Equally, results were not clearly related to microplastics shape or polymer type. This work did not find significant long-term evidence on the increasing uptake of microplastic particles by zooplankton over time. However, the results of this report identified additives, plasticisers, and other more complex and hazardous compounds that should not be released to the environment (e.g., bis-(2-hydroxyethyl) dimerate, propylene glycol ricinoleate) inside marine biota. The study detailed herein provides a case study for the use of long-term time-series in providing accurate assessments of microplastic pollution in marine biota.

Enzymatic digestion method development for long-term stored chitinaceous planktonic samples.

Different extraction methods have been proposed to study the ingestion of microplastics by marine organisms, including enzymatic digestion. While mussels have been the focus of research, crustaceans' enzymatic digestion has received little attention. An overlooked source of information for microplastic research is analysis of long-term time-series biotic samples. These collections are invaluable for the detection and monitoring of changes in ecosystems, especially those caused by anthropogenic factors. Here, crustacean larvae collected in two periods, 1985 and 2020, in the central North Sea were used to develop and optimise an effective and gentle enzymatic digestion method suitable for microplastic research. Sequential breakdown of these chitinaceous samples via a mechanical and surfactant (Sodium Dodecyl Sulphate 1% v/v) pre-treatment, followed by proteinase K (100 mU/mL) and chitinase (50 mU/mL) digestion, efficiently removed >96% of biomass of 1985 and 2020 samples. The optimised method was effective without interfering with the identification of naturally weathered microplastics via FTIR Spectroscopy.

New species of Eurythenes from hadal depths of the Mariana Trench, Pacific Ocean (Crustacea: Amphipoda).

Eurythenes S. I. Smith in Scudder, 1882 are one of the largest scavenging deep-sea amphipods (max. 154 mm) and are found in every ocean across an extensive bathymetric range from the shallow polar waters to hadal depths. Recent systematic studies of the genus have illuminated a cryptic species complex and highlighted the benefits of using a combination of morphological and molecular identification approaches. In this study, we present the ninth species, Eurythenes plasticus sp. nov., which was recovered using baited traps between the depths 6010 and 6949 m in the Mariana Trench (Northwest Pacific Ocean) in 2014. This new Eurythenes species was found to have distinct morphological characteristics and be a well-supported clade based on sequence variation at two mitochondrial regions (16S rDNA and COI). While this species is new to science and lives in the remote hadal zone, it is not exempt from the impacts of anthropogenic pollution. Indeed, one individual was found to have a microplastic fibre, 83.74% similar to polyethylene terephthalate (PET), in its hindgut. As this species has a bathymetric range spanning from abyssal to hadal depths in the Central Pacific Ocean basin, it offers further insights into the biogeography of Eurythenes.

Enrichment and Characterisation of a Mixed-Source Ethanologenic Community Degrading the Organic Fraction of Municipal Solid Waste Under Minimal Environmental Control.

The utilisation of the organic fraction of municipal solid waste as feedstock for bioethanol production could reduce the need for disposal of the ever-increasing amounts of municipal solid waste, especially in developing countries, and fits with the integrated goals of climate change mitigation and transport energy security. Mixed culture fermentation represents a suitable approach to handle the complexity and variability of such waste, avoiding expensive and vulnerable closed-control operational conditions. It is widely accepted that the control of pH in these systems can direct the fermentation process toward a desired fermentation product, however, little empirical evidence has been provided in respect of lignocellulosic waste substrates and different environmental inocula sources. We evaluated ethanol production from the organic fraction of municipal solid waste using five different inocula sources where lignocellulose degradation putatively occurs, namely, compost, woodland soil, rumen, cow faeces and anaerobic granular sludge, when incubated in batch microcosms at either initially neutral or acidic pH and under initially aerobic or anaerobic conditions. Although ethanol was produced by all the inocula tested, their performance was different in response to the imposed experimental conditions. Rumen and anaerobic granular sludge produced significantly the highest ethanol concentrations (∼30 mM) under initially neutral and acidic pH, respectively. A mixed-source community formed by mixing rumen and sludge (R + S) was then tested over a range of initial pH. In contrast to the differences observed for the individual inocula, the maximal ethanol production of the mixed community was not significantly different at initial pH of 5.5 and 7. Consistent with this broader functionality, the microbial community analyses confirmed the R + S community enriched comprised bacterial taxa representative of both original inocula. It was demonstrated that the interaction of initial pH and inocula source dictated ethanologenic activity from the organic fraction of municipal solid waste. Furthermore, the ethanologenic mixed-source community enriched, was comprised of taxa belonging to the two original inocula sources (rumen and sludge) and had a broader functionality. This information is relevant when diverse inocula sources are combined for mix culture fermentation studies as it experimentally demonstrates the benefits of diversity and function assembled from different inocula.