Publications
16 results found
Williams J, Pettorelli N, Hartmann A, et al., 2023, Decline of a distinct coral reef holobiont community under ocean acidification, Microbiome, ISSN: 2049-2618
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 CO2 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 colonized 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 provide evidence that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to envi
Ransome E, Hobbs F, Jones S, et al., 2023, Evaluating the transmission risk of SARS-CoV-2 from sewage pollution, Science of the Total Environment, Vol: 858, Pages: 1-8, ISSN: 0048-9697
The presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated waters is poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. This study investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over eight months for SARS-CoV-2 RNA and infectious virus. Bivalves were also sampled as an indicator species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. No evidence of SARS-CoV-2 RNA or infectious virus was found in UK samples, in contrast to RNA positive samples from Serbia. Furthermore, this study shows that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for <3 days, while SARS-CoV-2 RNA is detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that detection of viral RNA alone is not an indication of pathogen spillover.
Jones S, Bell T, Coleman CM, et al., 2022, Testing bats in rehabilitation for SARS-CoV-2 before release into the wild, Conservation Science and Practice, Vol: 4, ISSN: 2578-4854
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.
Chung KF, Abubakar-Waziri H, Kalaiarasan G, et al., 2022, SARS-CoV2 and Air Pollution Interactions: Airborne Transmission and COVID-19, Molecular Frontiers Journal, Vol: 06, Pages: 1-6, ISSN: 2529-7325
<jats:p> A link between outdoor pollution of particulate matter (PM) and the mortality from COVID-19 disease has been reported. The potential interaction of SARS-CoV2 emitted from an infected subject in the form of droplets or as an aerosol with PM[Formula: see text] (PM of 2.5 [Formula: see text]m or less in aerodynamic diameter) may modulate SARS-CoV2 replication and infectivity. This may represent an important airborne route of transmission, which could lead to pneumonia and a poor outcome from COVID-19. Further studies are needed to assess the potential infectivity and severity of such transmission. </jats:p>
Casey JM, Ransome E, Collins AG, et al., 2021, DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity, Environmental DNA, Vol: 3, Pages: 1229-1246, ISSN: 2637-4943
<jats:title>Abstract</jats:title><jats:p>DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome <jats:italic>c</jats:italic> oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image‐based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.</jats:p>
Smith TP, Mombrikotb S, Ransome E, et al., 2021, Latent functional diversity may accelerate microbial community responses to environmental fluctuations, Publisher: Cold Spring Harbor Laboratory
Whether and how whole ecological communities can respond to climate change remains an open question. With their fast generation times and abundant functional diversity, microbes in particular harbor great potential to exhibit community-level adaptation through a combination of strain-level adaptation, phenotypic plasticity, and species sorting. However, the relative importance of these mechanisms remains unclear. Here, through a novel laboratory experiment, we show that bacterial communities can exhibit a remarkable degree of community-level adaptability through a combination of phenotypic plasticity and species sorting alone. Specifically, by culturing soil communities from a single location at six temperatures between 4°C and 50°C, we find that multiple strains well adapted to different temperatures can be isolated from the community, without immigration or strain-level adaptation. This is made possible by the ability of strains with different physiological and life history traits to “switch on” under suitable conditions, with phylogenetically distinct K-specialist taxa favoured under cooler conditions, and r-specialist taxa in warmer conditions. Our findings provide new insights into microbial community adaptation, and suggest that microbial community function is likely to respond rapidly to climatic fluctuations, through changes in species composition during repeated community assembly dynamics.
Reynard N, Ellison E, Wilson A, et al., 2020, The contribution of coastal blue carbon ecosystems to climate change mitigation and adaptation, The contribution of coastal blue carbon ecosystems to climate change mitigation and adaptation, www.imperial.ac.uk/Grantham, Publisher: The Grantham Institute, BP34
This briefing paper explores the potential for marine coastal ecosystems that store carbon, blue carbon ecosystems (BCEs), to help both limit climate change and adapt to the impacts of a changing climate. It also considers the range of benefits BCEs bring to coastal communities, and makes recommendations for policy approaches.
Makiola A, Compson ZG, Baird DJ, et al., 2020, Key questions for next-generation biomonitoring, Frontiers in Environmental Science, Vol: 7, Pages: 1-14, ISSN: 2296-665X
Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels—from genes to entire ecosystems. Here, we frame 10 key questions that we envisage will drive the field of NGB over the next decade. While not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field. These questions have been grouped into current- and outlook-related categories, corresponding to the organization of this paper.
Rivett D, Jones M, Ramoneda J, et al., 2018, Elevated success of multispecies bacterial invasions impacts community composition during ecological succession, Ecology Letters, Vol: 21, Pages: 516-524, ISSN: 1461-023X
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.
Drovetski SV, OMahoney M, Ransome EJ, et al., 2018, Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese, Scientific Reports, Vol: 8
<jats:title>Abstract</jats:title><jats:p>Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (<jats:italic>Branta canadensis</jats:italic>). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. <jats:italic>Firmicutes</jats:italic>, <jats:italic>Proteobacteria</jats:italic>, and <jats:italic>Bacteroidetes</jats:italic> accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.</jats:p>
Hartmann AC, Petras D, Quinn RA, et al., 2017, Meta-mass shift chemical profiling of metabolomes from coral reefs, Proceedings of the National Academy of Sciences of the United States of America, Vol: 114, Pages: 11685-11690, ISSN: 0027-8424
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., H2, CH2, COCH2). 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.
Ransome E, Geller JB, Timmers M, et al., 2017, The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia, PLOS ONE, Vol: 12, Pages: e0175066-e0175066
Ransome E, Rowley SJ, Thomas S, et al., 2014, Disturbance to conserved bacterial communities in the cold-water gorgonian coral<i>Eunicella verrucosa</i>, FEMS Microbiology Ecology, Pages: n/a-n/a, ISSN: 0168-6496
Ransome E, Munn CB, Halliday N, et al., 2014, Diverse profiles of<i>N</i>-acyl-homoserine lactone molecules found in cnidarians, FEMS Microbiology Ecology, Vol: 87, Pages: 315-329, ISSN: 0168-6496
Martin S, Rodolfo-Metalpa R, Ransome E, et al., 2008, Effects of naturally acidified seawater on seagrass calcareous epibionts, Biology Letters, Vol: 4, Pages: 689-692, ISSN: 1744-9561
<jats:p> Surface ocean pH is likely to decrease by up to 0.4 units by 2100 due to the uptake of anthropogenic CO <jats:sub>2</jats:sub> 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 CO <jats:sub>2</jats:sub> partial pressure in aquaria and at a volcanic vent area where seagrass habitat has been exposed to high CO <jats:sub>2</jats:sub> 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 CO <jats:sub>2</jats:sub> . 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. </jats:p>
Hall-Spencer JM, Rodolfo-Metalpa R, Martin S, et al., 2008, Volcanic carbon dioxide vents show ecosystem effects of ocean acidification, Nature, Vol: 454, Pages: 96-99, ISSN: 0028-0836
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