Philippa Kaur

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Summary of SCTLD microbiome studiesInitially, datasets were acquired from 17 SCTLD studies, but one study [24] did not pass quality filtering and was removed from the analysis, resulting in 16 SCTLD studies used in this meta-analysis. In addition, one Acropora spp. rapid tissue loss (RTL) disease study was included for comparison of bacteria which may be associated more generally with coral tissue loss diseases (Supplementary Table 1). The combined dataset included 2425 samples, representing various coral species and environments described below. A total of 63 miscellaneous samples such as lab controls were included in this total (Supplementary Table 1). Samples from the studies were sequenced using five primer pairs: CS1-515F/CS2-806R [31] with additional 5’ linker sequences [32] (n = 79), 515FY [33]/806RB [34] (n = 1219), S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21 [35] (n = 31), 515F/806R [31] (n = 49), and 515F [31]/Arch806R [36] (n = 984; Fig. 1A). Although five primer pairs were used across studies, only the forward reads were evaluated in this analysis (see “Methods”). A description of the differences between 515F primers can be found in detail [34].Fig. 1: The number of aquaria and field samples for each coral species.A small subunit (SSU) rRNA gene primer sets, B sample type, and C disease state. NAs in (A, B) represent sediment and seawater samples. Coral species codes represent the following: Acropora cervicornis (ACER), Acropora palmata (APAL), Colpophyllia natans (CNAT), Diploria labyrinthiformis (DLAB), Dichocoenia stokesii (DSTO), Montastraea cavernosa (MCAV), Meandrina meandrites (MMEA), Orbicella annularis (OANN), Orbicella faveolata (OFAV), Orbicella franksi (OFRA), Porites astreoides (PAST), Pseudodiploria clivosa (PCLI), Pseudodiploria strigosa (PSTR), Stephanocoenia intersepta (SINT), and Siderastrea siderea (SSID).Full size imageSamples were collected throughout Florida and the U.S. Virgin Islands (USVI). Field samples totaled 1274, representing 40 sites, and a further 1088 samples were from aquaria (i.e., laboratory-based experiments; Fig. 1). Thirteen SCTLD-susceptible coral species were included, with Montastraea cavernosa (MCAV; n = 543) and Orbicella faveolata (OFAV; n = 357) most represented and Pseudodiploria clivosa (PCLI; n = 6) and Orbicella franksi (OFRA; n = 7) least represented (Fig. 1). Coral samples (n = 2031) were from three compartments: mucus only (n = 393), mucus and surface tissue (tissue slurry; n = 1585), and skeleton samples with embedded coral tissue (tissue slurry skeleton; n = 53). Seawater (n = 198) and sediment (n = 133) samples from both the field and aquaria experiments also were included to evaluate potential sources of transmission of disease-associated bacteria (Fig. 1B). For seawater from aquaria experiments, 18 L samples were collected [27], while in the field between 60 mL and 1 L samples were collected [11, 25]. In sediment aquaria experiments, 2 mL samples were collected [12], and in the field, approximately 5 mL samples were collected (of the 5 mL, DNA was extracted from 0.25 g sediment [11]). Coral samples represented three SCTLD health states: apparently healthy colonies (AH), which was the most represented (n = 1021), followed by lesions on diseased colonies (DL; n = 661), and unaffected areas on diseased colonies (DU; n = 349; Fig. 1C). AH represents grossly normal tissue, DU grossly normal tissue on diseased colonies, and DL grossly abnormal tissue.Differences in the microbial composition were found in AH corals among zones (vulnerable, endemic, and epidemic)Differences in alpha-diversity were tested among three SCTLD zones: vulnerable (i.e., locations where the disease had not been observed/reported), endemic (i.e., locations where a disease outbreak had moved through the reef and no or few colonies had active lesions), and epidemic (i.e., locations where the outbreak was active and prevalent). For alpha-diversity, for AH field-sourced samples, after filtering, 41,504 amplicon sequence variants (ASVs) remained, which were reduced to 15,021 following rarefaction. Among the filtered AH samples, Shannon (alpha) diversity from the vulnerable zone was slightly higher (estimated marginal means (emmean) = 3.95) compared to the epidemic zone (emmean = 3.70), but this was not significant (Supplementary Fig. 1). For beta-diversity, both within and between-group differences were tested using a filtered counts table. Within-group beta-diversity (variation in microbial composition or dispersion) was not different between zones, but was significant for all comparisons between zones (PERMANOVA, P-adjusted (Padj) More

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When studying windfarm developments at the European region scale, the high densities of windfarm developments on blanket bog in Galicia and Greater Manchester (north England) are influenced by the total extent of the recognised blanket bog which is lower in Spain (31.2 km2 total extent) and in Greater Manchester (40.8 km2 total extent) in comparison to other regions (Fig. 1), although no relationship between the total extent of recognised blanket bog and the windfarm developments (wind turbines, tracks and total affected area) was found. Although the rest of the European regions across Spain showed lower densities of windfarm infrastructures (Fig. 2), the total extent of recognised blanket bogs across those regions was under 1 km2 (Fig. 1) meaning that the majority of recognised Spanish blanket bogs could be under threat due to their small size and the potential impact of windfarm infrastructures, if installed. In addition to this, previously unrecognised Spanish blanket bogs that have now been reported17 that could also be under pressure as the lack of formal recognition and protection leaves this habitat exposed to a range of anthropogenic activities, including windfarm developments. In fact, some examples of blanket bogs with extensive damage have been identified and reported in Galicia25, and more recently in Cantabrian blanket bogs17.Spanish unmapped areas of blanket bog at the edge-of-range of this habitat in the south of Europe are, therefore, particularly at risk from windfarm developments, and may disappear before their extent and importance can be defined40. Currently, new renewable energy regulations have been developed as a result of the climate emergency, and several windfarm developments have been proposed in ecologically sensitive areas, where blanket bogs have been reported (e.g. Sierra del Escudo, Spain) increasing the pressure on this habitat. Spanish blanket bogs also have specific characteristics, such as their small size as a consequence of the topographical limitations (e.g. slope) for their development26, meaning that they usually only cover the hill summits, where wind energy potential is at its greatest. Since blanket bogs are small and the windfarm development may cover all of the hill summit for their installation, many blanket bogs will be irrevocably damaged40.Most of the Galician blanket bogs were protected in 1999, under the Natura 2000 network and were declared as Special Area of Conservation (SAC) in 2014. However, between 1999 and 2012, Galician blanket bogs underwent severe and significant alterations in the peatland surface as a consequence of the large number of windfarm developments41 that were established during the period (Table A—Supplementary information), even when the site was incorporated into the Natura 2000 network (Table B—Supplementary information). Despite available scientific evidence that showed the potential environmental risks for these vulnerable ecosystems, windfarms were installed in what this work found to be the most extensive windfarm infrastructures across recognised European blanket bogs (Fig. 2).The incomplete current understanding of the extent of Spanish blanket bogs highlights the need to improve the completeness and representativeness of their current records across the Spanish Atlantic biogeographical region to include, within Natura 2000, a sufficient cover of their occupied area, in proportion to the representation of this natural habitat type in the Member state, for which it could therefore be concluded that the network is complete. Due to the increasing evidence highlighting how important the transitional areas are within the blanket bog complex42, other peatland types and wet heaths should be also considered when recognising and protecting blanket bogs. Mapping unrecorded blanket bogs must be a priority to fully understand the geographical and climatic range of this habitat, and obligatory protection under the Habitats Directive (92/43/EEC) is key to protecting the southern edge-of-range of this habitat.In addition to the lack of protection and updated inventories, the priority status included in the Habitats Directive, key to promoting their protection and restoration, is only for active blanket bogs, excluding other degraded blanket bogs with the potential to be active (carbon sinks), if they are restored. An approach similar to that of Scotland, where degraded blanket bogs are included33,39, could promote blanket bog restoration across Europe and improve the protection of this natural carbon storage.Many countries have also misinterpreted the active status of the blanket bog meaning that it is difficult to define whether the recognised blanket bog habitat is classed as a priority or not. Some countries, such as the Republic of Ireland, have classified as 7130 only active blanket bogs36, meaning that degraded blanket bogs lack appropriate classification and incorrectly applying the Habitat Directive designation as not all blanket bogs are included. The priority status is given when the habitat is particularly vulnerable or unique to the EU and necessitates additional measures for their protection and surveillance; however, whilst some blanket bogs may not act currently as carbon sinks, they still contain large amounts of carbon, and when restored they can recover their carbon sink function1, and then act to mitigate climate change.The issue of windfarm developments across the Republic of Ireland has been previously reported using a peat map43. However, despite researchers highlighting the importance of excluding vulnerable peatland ecosystems in future developments44, new areas of windfarms have been built affecting further recognised blanket bogs. At least 79 wind turbines have been installed in the Republic of Ireland since 2008 on recognised blanket bogs (Table A—Supplementary information) representing the 9.8% of the total onshore turbines installed in the country (Table 3), highlighting the importance of this conflict. The contribution of wind energy production to electricity supply was predicted to be up to 30% by 202044. In 2020, wind energy consumed in the Republic of Ireland represented 36%45. This represented an average annual increase of wind energy consumption of 16.9%45 between 2005 and 2020, which may explain part of the increase of 42% in wind turbines since 2008 (Table A—Supplementary information).Table 3 Total % of turbines on blanket bog (recognised/national inventories) in relation with the total turbines installed by country.Full size tableAcross Europe, several governments have developed climate action plans that over the next decade promote renewable energies to reduce carbon emissions. The government of the Republic of Ireland is aiming to generate up to 80% of electricity from renewable energy by 2030, providing support for onshore windfarm developments with an increase of up to 32% of the renewable energy production by 2030, but with a favourable preference for offshore wind energy production (up to 52% of the renewable energy production)46. This may help to reduce the conflict between blanket bogs and windfarm developments. Currently, windfarm annual energy production on blanket bogs accounts for 263.4 MW, 6.1% of the total production of wind energy in the Republic of Ireland47.The promotion of onshore wind energy production46 and the lack of protection of the full extent of blanket bogs are also threats that need to be considered in the Republic of Ireland. In 2008, a peat map was published showing the distribution of blanket bogs and raised bogs across the Republic of Ireland43. However, the inventory of current recognised blanket bogs under the Habitats Directive does not cover the full extent reported in this research43. While the total extent of recognised blanket bogs under the Habitats Directive 92/43/ECC reported a total of 3621 km2 of blanket bogs36, the real extent of blanket bogs across the country could be up to 2.5 times more (9202 km2)43, highlighting the lack of protection and the potential further increase of the windfarms and peatlands conflict in the Republic of Ireland as it happens in Spain and Scotland.The lack of recognition of blanket bog habitat in combination with the promotion of wind energy production across the island of Ireland could affect further areas of blanket bog, increasing the degradation of blanket bogs. An urgent review of inventories needs to be promoted in both countries, the Republic of Ireland and Northern Ireland, to fully assess the impact of the extensive areas of windfarms across the whole island.In Scotland, the pressure of windfarm developments on blanket bogs is also evident, where the Scottish Planning Policy considers classes 1 and 2 as areas of significant protection; although, windfarm developments may be possible under some circumstances48 as is permitted under the Habitats Directive across the EU29. However, to assess the impacts of windfarms on peatlands in a consistent way and evaluate the environmental impact of potential new developments on carbon-rich soils, a carbon calculator has been developed by the Scottish Government49. The carbon calculator allows users to estimate the carbon savings of windfarms installed on peatlands, although they highlight the importance of long-term management in relation to the final net carbon calculation49. Nonetheless, installing windfarms on non-degraded peatlands has been reported as unlikely to reduce carbon emissions even when the management has been considered carefully and it should be avoided 30. Therefore, peatlands under classes 1 and 2 considered by the Scottish government as a priority should be excluded from any windfarm developments (currently representing over 16% of onshore turbines, Table 3); especially considering the current policy of increasing onshore windfarms in Scotland50. Long-term research is needed to fully assess the impacts before new windfarm developments are installed.The difference between the recognised blanket bogs included in the EU Habitats Directive and the Scottish national inventory highlights the importance of updating and defining the complete extent of blanket bogs to facilitate their protection and restoration.In this novel research, the extent of windfarm developments across all recognised European blanket bogs under the Habitats Directive have been assessed. Large extents of blanket bogs have already been damaged, concentrated in the edge-of-range of this habitat and directly affecting hundreds of hectares of blanket bog across the rest of Europe. The full potential long-term damage to the habitat functionality is still unclear, but scientific evidence supports the negative impacts of windfarm developments on this critical habitat. European blanket bogs need further scientific evidence to demonstrate the real benefit of incentivising the reduction of carbon emissions by installing onshore windfarm infrastructures on peatlands which are causing the degradation of the most important long-term natural carbon sink and storage ecosystems. A strategic restoration plan and appropriate relevant legislation would be beneficial to promote the safeguarding of blanket bogs in the UK after Brexit. An urgent revision and compliance of the legislation regarding the protection of blanket bogs needs to be implemented, especially under the current trend of promotion and increasing legislation on renewable energy to reduce carbon emissions. An improvement of the national inventories across the EU and UK protected area networks is critical to implement the recognition, protection, and restoration of this habitat, in order to guarantee its favourable conservation status and its function as a long-term carbon sink to mitigate climate change. More

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Decline in organism size is seen as a major biological response to climate change, and can be particularly pronounced in aquatic ectotherms such as fish, with subsequent implications for fishery yield and food security. However, as well as being modulated by climate factors, the fish population size structure can also be impacted by biotic (competition, predation) and other human factors (harvesting). For migrating species such as salmon, while smaller size may represent reduced size at maturity, it may also indicate faster maturation. More

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