Microclimc: A mechanistic model of above, below and within-canopy microclimate

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordClimate strongly influences ecological patterns and processes at scales ranging from local to global. Studies of ecological responses to climate usually rely on data derived from weather stations, where temperature and humidity may differ substantially from that in the microenvironments in which organisms reside. To help remedy this, we present a model that leverages first principles physics to predict microclimate above, within, and below the canopy in any terrestrial location on earth, made freely available as an R software package. The model can be run in one of two modes. In the first, heat and vapour exchange within and below canopy are modelled as transient processes, thus accounting for fine temporal-resolution changes. In the second, steady-state conditions are assumed, enabling conditions at hourly intervals or longer to be estimated with greater computational efficiency. We validated both modes of the model with empirical below-canopy thermal measurements from several locations globally, resulting in hourly predictions with mean absolute error of 2.77 °C and 2.79 °C for the transient and steady-state modes respectively. Alongside the microclimate model, several functions are provided to assist data assimilation, as well as different parameterizations to capture a variety of habitats, allowing flexible application even when little is known about the study location. The model's modular design in a programming language familiar to ecological researchers provides easy access to the modelling of site-specific climate forcing, in an attempt to more closely unify the fields of micrometeorology and ecology.Met Office Hadley Centre Climate Programme (HCCP)European Regional Development Fund (ERDF)National Science Foundatio

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km² resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-km² pixels (summarized from 8500 unique temperature sensors) across all the world’s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Novel temperatures are already widespread beneath the world’s tropical forest canopies

Acknowledgements: D.H.K. acknowledges support from the National Science Foundation Graduate Research Fellowship Program (DGE-1842473). M.B. and J.S. acknowledge core funding from ETH Zurich. M.S. was funded by a grant from the Ministry of Education, Youth and Sports of the Czech Republic (grant no. LTT19018). J.O acknowledges support from Vlaamse Interuniversitaire Raad (under Inter University Cooperation with Mountains of the Moon University (IUC-MMU), grant no. UG2019IUC027A103). I.M.D.M was supported by the Natural Environment Research Council (grant no. NE/W006618/1). J.F., R.O.N. and J.B were supported by the Natural Environment Research Council (grant no. NE/X015262/1). We thank the three anonymous reviewers for their valuable comments and suggestions, which improved the final paper.AbstractTropical forest biodiversity is potentially at high risk from climate change, but most species reside within or below the canopy, where they are buffered from extreme temperatures. Here, by modelling the hourly below-canopy climate conditions of 300,000 tropical forest locations globally between 1990 and 2019, we show that recent small increases in below-canopy temperature (&lt;1 °C) have led to highly novel temperature regimes across most of the tropics. This is the case even within contiguous forest, suggesting that tropical forests are sensitive to climate change. However, across the globe, some forest areas have experienced relatively non-novel temperature regimes and thus serve as important climate refugia that require urgent protection and restoration. This pantropical analysis of changes in below-canopy climatic conditions challenges the prevailing notion that tropical forest canopies reduce the severity of climate change impacts.</jats:p

Winters are changing: snow effects on Arctic and alpine tundra ecosystems

Snow is an important driver of ecosystem processes in cold biomes. Snow accumulation determines ground temperature, light conditions, and moisture availability during winter. It also affects the growing season's start and end, and plant access to moisture and nutrients. Here, we review the current knowledge of the snow cover's role for vegetation, plant- animal interactions, permafrost conditions, microbial processes, and biogeochemical cycling. We also compare studies of natural snow gradients with snow experimental manipulation studies to assess time scale difference of these approaches. The number of tundra snow studies has increased considerably in recent years, yet we still lack a comprehensive overview of how altered snow conditions will affect these ecosystems. Specifically, we found a mismatch in the timing of snowmelt when comparing studies of natural snow gradients with snow manipulations. We found that snowmelt timing achieved by snow addition and snow removal manipulations (average 7.9 days advance and 5.5 days delay, respectively) were substantially lower than the temporal variation over natural spatial gradients within a given year (mean range 56 days) or among years (mean range 32 days). Differences between snow study approaches need to be accounted for when projecting snow dynamics and their impact on ecosystems in future climates

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov.

Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachia influence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We report here the genome, phylogenetics, and biogeography of a ubiquitous and novel Rickettsiales species that primarily associates with marine organisms. We previously showed that this bacterium was found in scleractinian corals, responds to nutrient exposure, and is associated with reduced host growth and increased mortality. This bacterium, like other Rickettsiales, has a reduced genome indicative of a parasitic lifestyle. Phylogenetic analysis places this Rickettsiales within a new genus we define as "Candidatus Aquarickettsia." Using data from the Earth Microbiome Project and SRA databases, we also demonstrate that members of "Ca. Aquarickettsia" are found globally in dozens of invertebrate lineages. The coral-associated "Candidatus A. rohweri" is the first finished genome in this new clade. "Ca. A. rohweri" lacks genes to synthesize most sugars and amino acids but possesses several genes linked to pathogenicity including Tlc, an antiporter that exchanges host ATP for ADP, and a complete Type IV secretion system. Despite its inability to metabolize nitrogen, "Ca. A. rohweri" possesses the NtrY-NtrX two-component system involved in sensing and responding to extracellular nitrogen. Given these data, along with visualization of the parasite in host tissues, we hypothesize that "Ca. A. rohweri" reduces coral health by consuming host nutrients and energy, thus weakening and eventually killing host cells. Last, we hypothesize that nutrient enrichment, which is increasingly common on coral reefs, encourages unrestricted growth of "Ca. A. rohweri" in its host by providing abundant N-rich metabolites to be scavenged