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Introduction: This multi‐centre retrospective cohort study aimed to determine whether the cause of an undiagnosed pleural effusion differed depending on if a patient presented as an outpatient or inpatient. Methods: A total of 1080 adult patients (556 inpatients and 524 outpatients) presenting primarily with an undiagnosed pleural effusion from 1 January 2021 to 31 December 2022 from four UK hospitals were included. Results: We found malignant effusions were more common in outpatients compared to inpatients (48.3% vs. 36.0% p < 0.0001). Infection was common in inpatients but uncommon in outpatients (36.2% vs. 5.0% p < 0.0001). Other causes in all patients included heart and/or renal failure (13.1%) and non‐specific pleuritis (5.6%). No diagnosis was possible in 11.8% of patients referred. Conclusion: Investigative pathways should vary depending on whether patients present as an inpatient or outpatient. [ABSTRACT FROM AUTHOR]

Marine plastic pollution is rapidly colonized by a biofilm of microorganisms associated with the control of biogeochemical cycles, plastic biodegradation, and potentially pathogenic activities. An extensive number of studies have described the taxonomic composition of this biofilm, referred to as the 'plastisphere', and previous reviews have reported on the influence of location, plastic type, and plastic-biodegradation ability on plastisphere formation. However, few studies have investigated the metabolic activity of this complex biofilm and how microbial pathogenicity and bioremediation could be regulated in this ecosystem. In this review, we highlight the understudied molecular and abiotic factors influencing plastisphere formation and microbial functioning beyond taxonomic description. In this context, we critically discuss the impacts of (i) organism-organism interaction, (ii) microbial cell wall composition, and (iii) commonly encountered plastic-bound co-pollutants (heavy metals, persistent organic pollutants, UV filters). For the first time, we review the anticipated impact of lipophilic organic UV-filters – found in plastic additives and sunscreens – on the plastisphere due to their reported affinity for plastics, persistence, and co-location at high concentrations in touristic coastal environments. Herein, we integrate the findings of 34 global studies exploring plastisphere composition, 35 studies quantifying co-pollutant concentrations, and draw upon 52 studies of cell -cell and -substrate interaction to deduce the inferred, yet still unknown, metabolic interactions within this niche. Finally, we provide novel future directions for the advancement of functional plastisphere research applying advanced molecular tools to new, and appropriate research questions. Data was compiled from 97 plastispheres across 34 different studies and an additional 87 studies relating to the impacts of plastisphere components on microbial species. The biotic and abiotic factors influencing microbial adhesion to different plastic polymers, including cell wall composition, and plastisphere location are considered. The impacts of heavy metals and organic co-pollutants – and for the first time, organic UV-filters – on plastisphere formation and function are reviewed and discussed. A change in direction from novel research questions to the use of state-of-the-art methodologies are recommended for the advancement of functional plastisphere research. [ABSTRACT FROM AUTHOR]

Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood– Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, ‘Candidatus Formimonas warabiya’ strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenomeassembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization. [ABSTRACT FROM AUTHOR]

Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, “DCMF”, was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/. [ABSTRACT FROM AUTHOR]

The folding and assembly of Rubisco large and small subunits into L8S8 holoenzyme in chloroplasts involves many auxiliary factors, including the chaperone BSD2. Here we identify apparent intermediary Rubisco‐BSD2 assembly complexes in the model C3 plant tobacco. We show BSD2 and Rubisco content decrease in tandem with leaf age with approximately half of the BSD2 in young leaves (~70 nmol BSD2 protomer.m2) stably integrated in putative intermediary Rubisco complexes that account for <0.2% of the L8S8 pool. RNAi‐silencing BSD2 production in transplastomic tobacco producing bacterial L2 Rubisco had no effect on leaf photosynthesis, cell ultrastructure, or plant growth. Genetic crossing the same RNAi‐bsd2 alleles into wild‐type tobacco however impaired L8S8 Rubisco production and plant growth, indicating the only critical function of BSD2 is in Rubisco biogenesis. Agrobacterium mediated transient expression of tobacco, Arabidopsis, or maize BSD2 reinstated Rubisco biogenesis in BSD2‐silenced tobacco. Overexpressing BSD2 in tobacco chloroplasts however did not alter Rubisco content, activation status, leaf photosynthesis rate, or plant growth in the field or in the glasshouse at 20°C or 35°C. Our findings indicate BSD2 functions exclusively in Rubisco biogenesis, can efficiently facilitate heterologous plant Rubisco assembly, and is produced in amounts nonlimiting to tobacco growth. The required sequence complementarity by plant Rubisco for components of its complex biogenesis interactome poses a significant obstacle to improving catalysis. Here we detail evidence that the Rubisco chaperone BSD2 forms stable intermediary complexes with Rubisco in tobacco and that BSD2 availability does not limit Rubisco biogenesis, photosynthesis, or plant growth in this model C3 plant. We show that the only critical role of BSD2 in tobacco is in Rubisco biogenesis and that BSD2 is not species‐specific and can effectively assemble Rubisco from differing plant species. This work provides a significant advance in engineering photosynthesis and in understanding the folding machinery of chloroplasts and Rubisco. [ABSTRACT FROM AUTHOR]

Dehalobacter sp. strain UNSWDHB can dechlorinate up to 4 mM trichloromethane at a rate of 0.1 mM per day to dichloromethane and 1,1,2-trichloroethane (1 mM, 0.1 mM per day) with the unprecedented product profile of 1,2-dichloroethane and vinyl chloride. 1,1,1-trichloroethane and 1,1-dichloroethane were slowly utilized by strain UNSWDHB and were not completely removed, with minimum threshold concentrations of 0.12 mM and 0.07 mM respectively under growth conditions. Enzyme kinetic experiments confirmed strong substrate affinity for trichloromethane and 1,1,2-trichloroethane ( Km = 30 and 62 µM respectively) and poor substrate affinity for 1,1,1-trichloroethane and 1,1-dichloroethane ( Km = 238 and 837 µM respectively). Comparison of enzyme kinetic and growth data with other trichloromethane respiring organisms ( Dehalobacter sp. strain CF and Desulfitobacterium sp. strain PR) suggests an adaptation of strain UNSWDHB to trichloromethane. The trichloromethane RDase (TmrA) expressed by strain UNSWDHB was identified by BN-PAGE and functionally characterized. Amino acid comparison of homologous RDases from all three organisms revealed only six significant amino acid substitutions/deletions, which are likely to be crucial for substrate specificity. Furthermore, strain UNSWDHB was shown to grow without exogenous supply of cobalamin confirming genomic-based predictions of a fully functional cobalamin synthetic pathway. [ABSTRACT FROM AUTHOR]