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Background: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome., Results: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO 2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation., Conclusions: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract., (© 2024. The Author(s).)

Our understanding of how microbes respond to micropollutants, such as pesticides, is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience multiple pollutants simultaneously. Here we perform a matrix of multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors (antibiotics, herbicides, fungicides and pesticides). We found that bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Increasingly complex chemical mixtures were both more likely to negatively impact bacterial growth in monoculture and more likely to reveal net interactive effects. A mixed co-culture of strains proved more resilient to increasingly complex mixtures and revealed fewer interactions in the growth response. These results show predictability in microbial population responses to chemical stressors and could increase the utility of next-generation eco-toxicological assays., (© 2024. The Author(s).)

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine complete genomes, including two novel coronavirus species, across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk warrants closer surveillance., (© 2023. The Author(s).)

Background: Spread of SARS-CoV2 by aerosol is considered an important mode of transmission over distances >2 m, particularly indoors., Objectives: We determined whether SARS-CoV2 could be detected in the air of enclosed/semi-enclosed public spaces., Methods and Analysis: Between March 2021 and December 2021 during the easing of COVID-19 pandemic restrictions after a period of lockdown, we used total suspended and size-segregated particulate matter (PM) samplers for the detection of SARS-CoV2 in hospitals wards and waiting areas, on public transport, in a university campus and in a primary school in West London., Results: We collected 207 samples, of which 20 (9.7%) were positive for SARS-CoV2 using quantitative PCR. Positive samples were collected from hospital patient waiting areas, from hospital wards treating patients with COVID-19 using stationary samplers and from train carriages in London underground using personal samplers. Mean virus concentrations varied between 429 500 copies/m 3 in the hospital emergency waiting area and the more frequent 164 000 copies/m 3 found in other areas. There were more frequent positive samples from PM samplers in the PM2.5 fractions compared with PM10 and PM1. Culture on Vero cells of all collected samples gave negative results., Conclusion: During a period of partial opening during the COVID-19 pandemic in London, we detected SARS-CoV2 RNA in the air of hospital waiting areas and wards and of London Underground train carriage. More research is needed to determine the transmission potential of SARS-CoV2 detected in the air., Competing Interests: Competing interests: All authors have completed the ICMJE uniform disclosure form at www.icmje.org/disclosure-of-interest/ and declare: support from UKRI EPSRC COVID-19 rapid response grant number EP/V052462/1 for the submitted; no financial relationships with any organisations that might have an interest in the submitted work in the previous 3 years; no other relationships or activities that could appear to have influenced the submitted work., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)

How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically and functionally distinct communities emerge at each of these temperatures, with K -strategist taxa favored under cooler conditions and r -strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation) is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to 'switch on' at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity., Competing Interests: TS, SM, ER, DK, SP, TB No competing interests declared, (© 2022, Smith et al.)

Several studies have suggested SARS-CoV-2 originated from a viral ancestor in bats, but whether transmission occurred directly or via an intermediary host to humans remains unknown. Concerns of spillover of SARS-CoV-2 into wild bat populations are hindering bat rehabilitation and conservation efforts in the United Kingdom and elsewhere. Current protocols state that animals cared for by individuals who have tested positive for SARS-CoV-2 cannot be released into the wild and must be isolated to reduce the risk of transmission to wild populations. Here, we propose a reverse transcription-quantitative polymerase chain reaction (RT-qPCR)-based protocol for detection of SARS-CoV-2 in bats, using fecal sampling. Bats from the United Kingdom were tested following suspected exposure to SARS-CoV-2 and tested negative for the virus. With current UK and international legislation, the identification of SARS-CoV-2 infection in wild animals is becoming increasingly important, and protocols such as the one developed here will help improve understanding and mitigation of SARS-CoV-2 in the future., (© 2022 The Authors. Conservation Science and Practice published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Background: Intrahepatic cholangiocarcinoma (IHC) is a malignancy with an increasing incidence. Surgery is the only treatment modality associated with long term survival. The objective of this study is to utilize a nationwide representative database to quantify the trends in incidence, and surgery for IHC in the United States from 2004-2014, as well as identify any disparities in the receipt of surgery., Methods: All patients admitted with a diagnosis of IHC between 2005 and 2014 were identified from the Nationwide Inpatient Sample (NIS) database. Trends in the number of IHC admissions and surgery procedures as well as outcomes were examined, and a multivariate analysis was used to determine the effects of demographic and clinical co-variables on resection rates., Results: An estimated total of 104,045 IHC related admissions occurred between 2005 and 2014. The hospitalization rate for IHC increased by nearly 2-fold in 2014 [38.9 per 100,000 (95% CI, 35.7-42.2)] from 18.1 per 100,000 (95% CI, 15.8-20.3) in 2005. Liver resections increased 248% (P<0.01) with an increasing majority being performed at teaching hospitals and 56% being minor resections. There was an increase in estimated hospital charges from $87,124 to $148,613 (P<0.001) and decrease in LOS from 12 days to 10 days (P<0.01). Inpatient mortality for IHC decreased significantly from 11% to 8.4% (P=0.004), from year 2005 to 2014 respectively. Age >80 years (OR =0.45; 95% CI, 0.33-0.60), Black race (OR =0.50; 95% CI, 0.39-063), Hispanic race (OR =0.59; 95% CI, 0.45-0.79), Medicaid insurance (OR =0.58; 95% CI, 0.42-0.79) and Elixhauser comorbidity score >3 (OR =0.58; 95% CI, 0.47-0.73) were associated with decreased rates of resection., Conclusions: Overall hospitalization and volume of surgery for IHC has increased dramatically over the past decade. There has been an increase in cost, decrease in LOS and inpatient mortality during the period. Socioeconomic and racial disparities were observed in the receipt of surgery for IHC. Additional work is needed to understand the complex interplay between socioeconomic status and race in in the treatment of IHC., Competing Interests: Conflicts of Interest: Presented at the SSAT’s 59th Annual Meeting at Digestive Disease Week, June 2-5, 2018, in Washington, DC.

Successful microbial invasions are determined by a species' ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre-invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community., (© 2018 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.)

Untargeted metabolomics of environmental samples routinely detects thousands of small molecules, the vast majority of which cannot be identified. Meta-mass shift chemical (MeMSChem) profiling was developed to identify mass differences between related molecules using molecular networks. This approach illuminates metabolome-wide relationships between molecules and the putative chemical groups that differentiate them (e.g., H 2 , CH 2 , COCH 2 ). MeMSChem profiling was used to analyze a publicly available metabolomic dataset of coral, algal, and fungal mat holobionts (i.e., the host and its associated microbes and viruses) sampled from some of Earth's most remote and pristine coral reefs. Each type of holobiont had distinct mass shift profiles, even when the analysis was restricted to molecules found in all samples. This result suggests that holobionts modify the same molecules in different ways and offers insights into the generation of molecular diversity. Three genera of stony corals had distinct patterns of molecular relatedness despite their high degree of taxonomic relatedness. MeMSChem profiles also partially differentiated between individuals, suggesting that every coral reef holobiont is a potential source of novel chemical diversity., Competing Interests: The authors declare no conflict of interest., (Copyright © 2017 the Author(s). Published by PNAS.)

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on coral reefs in Mo'orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol (NOAA method) combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at ≥ 97% similarity increased more than 7-fold (5.1% to 38.6%) using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors (9.7%) due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a ≥ 85% sequence identity cut-off provided more accurate results (0.7% errors) and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world.

The bacterial communities associated with healthy and diseased colonies of the cold-water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. Significant differences in community structure between healthy and diseased samples were discovered, as were differences in the level of disturbance to these communities at each site; this correlated with depth and sediment load. The majority of cloned sequences from healthy coral tissue affiliated with the Gammaproteobacteria. The stability of the bacterial community and dominance of specific genera found across visibly healthy colonies suggest the presence of a specific microbial community. Affiliations included a high proportion of Endozoicomonas sequences, which were most similar to sequences found in tropical corals. This genus has been found in a number of invertebrates and is suggested to have a role in coral health and in the metabolisation of dimethylsulfoniopropionate (DMSP) produced by zooxanthellae. However, screening of colonies for the presence of zooxanthellae produced a negative result. Diseased colonies showed a decrease in affiliated clones and an increase in clones related to potentially harmful/transient microorganisms but no increase in a particular pathogen. This study demonstrates that a better understanding of these bacterial communities, the factors that affect them and their role in coral health and disease will be of critical importance in predicting future threats to temperate gorgonian communities., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

Many marine habitats, such as the surface and tissues of marine invertebrates, including corals, harbour diverse populations of microorganisms, which are thought to play a role in the health of their hosts and influence mutualistic and competitive interactions. Investigating the presence and stability of quorum sensing (QS) in these ecosystems may shed light on the roles and control of these bacterial communities. Samples of 13 cnidarian species were screened for the presence and diversity of N-acyl-homoserine lactones (AHLs; a prevalent type of QS molecule) using thin-layer chromatography and an Agrobacterium tumefaciens NTL4 biosensor. Ten of 13 were found to harbour species-specific, conserved AHL profiles. AHLs were confirmed in Anemonia viridis using liquid chromatography tandem mass spectrometry. To assess temporal role and stability, AHLs were investigated in A. viridis from intertidal pools over 16 h. Patterns of AHLs showed conserved profiles except for two mid-chain length AHLs, which increased significantly over the day, peaking at 20:00, but had no correlation with pool chemistry. Denaturing gel electrophoresis of RT-PCR-amplified bacterial 16S rRNA showed the presence of an active bacterial community that changed in composition alongside AHL profiles and contained a number of bands that affiliate with known AHL-producing bacteria. Investigations into the quorum sensing-controlled, species-specific roles of these bacterial communities and how these regulatory circuits are influenced by the coral host and members of the bacterial community are imperative to expand our knowledge of these interactions with respect to the maintenance of coral health., (© 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

Surface ocean pH is likely to decrease by up to 0.4 units by 2100 due to the uptake of anthropogenic CO2 from the atmosphere. Short-term experiments have revealed that this degree of seawater acidification can alter calcification rates in certain planktonic and benthic organisms, although the effects recorded may be shock responses and the long-term ecological effects are unknown. Here, we show the response of calcareous seagrass epibionts to elevated CO2 partial pressure in aquaria and at a volcanic vent area where seagrass habitat has been exposed to high CO2 levels for decades. Coralline algae were the dominant contributors to calcium carbonate mass on seagrass blades at normal pH but were absent from the system at mean pH 7.7 and were dissolved in aquaria enriched with CO2. In the field, bryozoans were the only calcifiers present on seagrass blades at mean pH 7.7 where the total mass of epiphytic calcium carbonate was 90 per cent lower than that at pH 8.2. These findings suggest that ocean acidification may have dramatic effects on the diversity of seagrass habitats and lead to a shift in the biogeochemical cycling of both carbon and carbonate in coastal ecosystems dominated by seagrass beds.

Bifidobacteriaceae were isolated from saliva and infected dentine by using a mupirocin-based selective medium. Of the saliva samples, 94% harbored bifids. The mean concentration (+/- the standard error) was 4.46 (+/-0.12) log(10)(CFU per ml + 1), and the predominant isolates were Bifidobacterium dentium, B. longum, Scardovia inopinata, Parascardovia denticolens, and Alloscardovia omnicolens.

The atmospheric partial pressure of carbon dioxide (p(CO(2))) will almost certainly be double that of pre-industrial levels by 2100 and will be considerably higher than at any time during the past few million years. The oceans are a principal sink for anthropogenic CO(2) where it is estimated to have caused a 30% increase in the concentration of H(+) in ocean surface waters since the early 1900s and may lead to a drop in seawater pH of up to 0.5 units by 2100 (refs 2, 3). Our understanding of how increased ocean acidity may affect marine ecosystems is at present very limited as almost all studies have been in vitro, short-term, rapid perturbation experiments on isolated elements of the ecosystem. Here we show the effects of acidification on benthic ecosystems at shallow coastal sites where volcanic CO(2) vents lower the pH of the water column. Along gradients of normal pH (8.1-8.2) to lowered pH (mean 7.8-7.9, minimum 7.4-7.5), typical rocky shore communities with abundant calcareous organisms shifted to communities lacking scleractinian corals with significant reductions in sea urchin and coralline algal abundance. To our knowledge, this is the first ecosystem-scale validation of predictions that these important groups of organisms are susceptible to elevated amounts of p(CO(2)). Sea-grass production was highest in an area at mean pH 7.6 (1,827 (mu)atm p(CO(2))) where coralline algal biomass was significantly reduced and gastropod shells were dissolving due to periods of carbonate sub-saturation. The species populating the vent sites comprise a suite of organisms that are resilient to naturally high concentrations of p(CO(2)) and indicate that ocean acidification may benefit highly invasive non-native algal species. Our results provide the first in situ insights into how shallow water marine communities might change when susceptible organisms are removed owing to ocean acidification.