In benthic marine ecosystems, small organisms that dwell within the habitat matrix comprise the majority of species richness but are inherently difficult to sample. This limits our ability to document the biodiversity of these ecosystems. Autonomous Reef Monitoring Structures (ARMS), artificial reefs that mimic the three-dimensional complexity of benthic habitats, can alleviate this challenge. However, ARMS have been applied infrequently in many temperate locations, including the United Kingdom (UK). To showcase the applicability of ARMS to the UK, this paper applies standardized Smithsonian ARMS protocols for image analysis as well as DNA barcoding and metabarcoding of the cytochrome c oxidase subunit I (COI) gene to 3 ARMS units deployed in the Sussex Inshore Fisheries and Conservation Authority (IFCA) Nearshore Trawling Exclusion zone, a conservation area created in 2021 to facilitate the recovery of seabed habitats. We document 176 genera across 22 eukaryotic phyla as well as 1,920 > 2 mm motile specimens with a biomass of 312 g. We identify 15 notable species, including the 4th UK record of Cephalothrix simula, a non-native poisonous nemertean with the potential to enter the food supply. We also assess the complementarity of image analysis and DNA metabarcoding in describing sessile communities, finding that the two methods produce meaningfully different estimates of relative abundance for some phyla, particularly Cnidaria (77x difference) and Bryozoa (72x difference). As our oceans come increasingly under threat from global change, it is imperative that we can accurately describe their biodiversity. We advocate for ARMS as a critical tool for measuring UK marine benthic biodiversity and discuss the use of ARMS in closing gaps in reference databases as well as in assessing ecosystem function and environmental disturbance in benthic habitats.

Societal Impact Statement Coconut palm expansion in West Africa will shape rural livelihoods and ecosystems. Our findings show that intensive practices reduce beneficial soil fungi and increase pathogens, threatening long-term productivity. Lower-intensity management that retains ground vegetation can sustain or boost yields while improving soil health. With typical planting densities and prices, these practices could generate an additional USD 800-1,200 per hectare annually, strengthening farmer income. Promoting biodiversity-friendly management and intercropping can enhance resilience, support food security and reduce pressure on natural habitats, offering a practical pathway to align agricultural development with environmental sustainability. L'expansion du cocotier en Afrique de l'Ouest affectera les moyens de subsistance dans les milieux ruraux ainsi que les & eacute;cosyst & egrave;mes. Nos r & eacute;sultats montrent que les pratiques agricoles intensives menacent la productivit & eacute; & agrave; long terme, car elles r & eacute;duisent l'abondance des champignons b & eacute;n & eacute;fiques du sol et augmentent, en revanche, celle des agents pathog & egrave;nes. & Agrave; l'inverse, une gestion moins intensive, qui conserve la v & eacute;g & eacute;tation au sol, peut maintenir ou augmenter les rendements tout en am & eacute;liorant la sant & eacute; des sols. Avec les densit & eacute;s de plantation courantes, ces pratiques pourraient g & eacute;n & eacute;rer un revenu suppl & eacute;mentaire de USD 800 & agrave; 1,200 par hectare et par an, augmentant ainsi les revenus des agriculteurs. La promotion de modes de gestion favorables & agrave; la biodiversit & eacute;, ainsi que de l'interculture, peut accro & icirc;tre la r & eacute;silience, soutenir la s & eacute;curit & eacute; alimentaire et r & eacute;duire la pression sur les habitats naturels, offrant une voie concr & egrave;te pour concilier d & eacute;veloppement agricole et durabilit & eacute; environnementale.

Abstract Microbial communities frequently coalesce through dispersal, disturbance, or deliberate transplantation, yet the dynamical consequences of such coalescence remain poorly understood. Here, we show that coalescence can function as a structural design mechanism to enhance microbial community robustness. Using a mechanistic consumer–resource model in which the balance between competition and metabolic cooperation is explicitly tunable, we quantify how interaction structure shapes both feasibility, namely the environmental domain supporting coexistence, and dynamical stability. Cooperation-dominated communities exhibit greater but more variable feasibility and intrinsic stability than competition-dominated communities. Strikingly, coalescing communities with maximally distinct interaction structures consistently maximizes both feasibility and stability by reducing alignment among interaction vectors and strengthening effective self-regulation in the resulting assemblage. Heterogeneous coalescence balances reduced facilitation, moderated interspecific effects, and stronger self-regulation. These results identify structural complementarity as a general principle for assembling robust microbial ecosystems and provide a theoretical foundation for microbiome engineering strategies that enhance persistence and functional stability.

Abstract The threat of climate change has renewed interest in the responses of communities and ecosystems to warming, with changes in size spectra expected to signify fundamental shifts in the structure and dynamics of these multispecies systems. While substantial empirical evidence has accumulated in recent years on such changes, we still lack general insights due to a limited coverage of warming scenarios that span spatial and temporal scales of relevance to natural systems. We addressed this gap by conducting an extensive freshwater mesocosm experiment across 36 large field mesocosms exposed to intergenerational warming treatments of up to +8 °C above ambient levels. We found a nonlinear decrease in the overall mean body size of zooplankton with warming, with a 57% reduction at +8 °C. This pattern was broadly consistent over two tested seasons and major taxonomic groups. We also detected some breakpoints in the community-level size-temperature relationship, indicating that the system’s response shifts noticeably above a certain level of warming. These results underscore the need to capture intergenerational responses to large gradients in warming at appropriate scales in time and space in order to better understand the effects of warming on natural communities and ecosystems.

ABSTRACT Marine sponges as natural samplers of environmental DNA (eDNA) are receiving growing attention as an untapped source of biodiversity data. However, little is known about the state of DNA (e.g., cellular or extracellular) that is captured by these samples and how this compares to conventional aquatic eDNA samples. Here, we present an artificial spiking experiment where DNA in cellular and extracellular states was added into tanks containing two sponge species. Aquatic eDNA samples and sponge natural sampler DNA (nsDNA) samples were collected over 7 days and DNA from the two states was quantified in each sample using quantitative real‐time PCR (qPCR). We found that there was a significant interaction between DNA state and sample type (eDNA and nsDNA), with lower detection and concentration of extracellular DNA, compared to cellular DNA, found in nsDNA samples. We also found that detection rate and concentration of DNA were significantly lower in nsDNA than in eDNA overall. During methodological testing, PCR inhibition was observed in both sponge species; this was prohibitive in one of the species. Further work to investigate the degree of PCR inhibition during nsDNA metabarcoding is important to understand its impact on the communities resolved using nsDNA methods. Synthesis and applications. We show that nsDNA may originate from a subset of the DNA present in environmental media, potentially providing a more stable picture of local communities. Natural samplers provide a promising option for hard‐to‐reach environments and for retrieving biodiversity data from archived samples; however, further work and optimization are required to understand what is and is not well represented by this sample type compared to widely applied aquatic eDNA approaches.

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.

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. 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 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. 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.

Abstract The democratisation of next‐generation sequencing has vastly increased the availability of sequencing data from metabarcoding. However, to effectively prepare these metabarcoding data for subsequent analysis, researchers must consistently apply several different bioinformatic tools—including those which denoise reads, cluster sequences and assign taxonomic identities. This often creates a bioinformatics bottleneck in workflows for non‐specialists due to obstacles around: (a) integrating different tools, (b) the inability to easily modify and rerun bioinformatic pipelines involving non‐scripted (‘point‐and‐click’) elements and (c) the multiple outputs that may be required of a single dataset (e.g. amplicon sequence variants [ASVs] and operational taxonomic units [OTUs]), which often results in users running pipelines multiple times. Here, we introduce SimpleMetaPipeline, an open‐source bioinformatics pipeline implemented in R, which addresses these obstacles. SimpleMetaPipeline integrates the most robust and commonly used existing bioinformatic tools in a single reproducible pipeline, with a streamlined choice of parameters, to generate a sequence data table containing alternative clustering and assignment options. SimpleMetaPipeline accepts demultiplexed paired‐end and single reads from multiple sequencing runs. We describe the pipeline and demonstrate how alternative annotations enable the easy implementation of multi‐algorithm agreement tests to strengthen inferences. SimpleMetaPipeline represents a valuable addition to the existing library of pipelines, providing easy and reproducible bioinformatics, including a range of commonly desired clustering and assignment options, such as OTUs and ASVs.

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 (two novel) complete genomes 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 is unknown and warrants closer surveillance.

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/m3 in the hospital emergency waiting area and the more frequent 164 000 copies/m3 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.

Our understanding of how microbes respond to pollutants is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience the effects of multiple pollutants simultaneously, and their responses to these mixtures of chemicals may not be readily predictable based on their responses to each pollutant in isolation. Here we extended the scope and complexity of previous multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors. This approach allowed us to identify fitness effects arising from potential high-order interactions among stressor responses. We found that the bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Responses to increasingly complex chemical mixtures were more likely to show a significant deviation from a null model based on the responses to each chemical alone. However, these net responses were mainly driven by lower-order interactions among a small number of chemicals, suggesting a limited role for complex high-order interactions. These results simplify the predictability of microbial populations and communities responding to multiple stressors, paving the way for the development of efficient next-generation eco-toxicological assays.

Coral reef sessile organisms inhabiting cryptic spaces and cavities of the reef matrix perform vital and varied functional roles but are often understudied in comparison to those on exposed surfaces. Here, we assess the composition of cryptobenthic taxa from three remote tropical reef sites (Central Indian Ocean) alongside a suite of in situ environmental parameters to determine if, or how, significant patterns of diversity are shaped by local abiotic factors. To achieve this, we carried out a point-count analysis of autonomous reef monitoring structure (ARMS) plate images and employed in situ instrumentation to recover long-term (12 months) profiles of flow velocity, wave heights, temperature, dissolved oxygen, and salinity, and short-term (3 weeks) profiles of light and pH. We recovered distinct environmental profiles between sampling sites and observed that ocean-facing reefs experienced frequent but short-lived cooling internal wave events and that these were key in shaping in situ temperature variability. By comparing temperature and wave height profiles recovered using in situ loggers with ex situ models, we discovered that global satellite products either failed to recover site-specific profiles or both over- and underestimated actual in situ conditions. We found that site choice and recruitment plate face (top or bottom) significantly impacted the percentage cover of bryozoans, gastropods, soft and calcified tube worms, as well as crustose coralline algae (CCA) and fleshy red, brown, and green encrusting macroalgae on ARMS. We observed significant correlations between the abundance of bryozoans, CCA, and colonial tunicates with lower mean temperature and higher mean dissolved oxygen profiles observed across sites. Red and brown encrusting macroalgae abundance correlated significantly with medium-to-high flow velocities and wave height profiles, as well as higher pH and dissolved oxygen. This study provides the first insight into cryptobenthic communities in the Chagos Archipelago marine-protected area and adds to our limited understanding of tropical reef sessile communities and their associations with environmental parameters in this region. With climate change accelerating the decline of reef ecosystems, integrating analyses of cryptobenthic organisms and in situ physicochemical factors are needed to understand how reef communities, if any, may withstand the impacts of climate change.

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.

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.

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.

Indoor, airborne, transmission of SARS-CoV-2 is a key infection route. We monitored fourteen different indoor spaces in order to assess the risk of SARS-CoV-2 transmission. PM2.5 and CO2 concentrations were simultaneously monitored in order to understand aerosol exposure and ventilation conditions. Average PM2.5 concentrations were highest in the underground station (261 ± 62.8 μgm−3), followed by outpatient and emergency rooms in hospitals located near major arterial roads (38.6 ± 20.4 μgm−3), the respiratory wards, medical day units and intensive care units recorded concentrations in the range of 5.9 to 1.1 μgm−3. Mean CO2 levels across all sites did not exceed 1000 ppm, the respiratory ward (788 ± 61 ppm) and the pub (bar) (744 ± 136 ppm) due to high occupancy. The estimated air change rates implied that there is sufficient ventilation in these spaces to manage increased levels of occupancy. The infection probability in the medical day unit of hospital 3, was 1.6-times and 2.2-times higher than the emergency and outpatient waiting rooms in hospitals 4 and 5, respectively. The temperature and relative humidity recorded at most sites was below 27 °C, and 40% and, in sites with high footfall and limited air exchange, such as the hospital medical day unit, indicate a high risk of airborne SARS-CoV-2 transmission.

Abstract 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 c 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.

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.

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 ( Branta canadensis ). 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. Firmicutes , Proteobacteria , and Bacteroidetes 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.

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.