MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL.

Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

SUMMARYTo understand the effects of global climate change on reef-building corals, a thorough investigation of their physiological mechanisms of acclimatization is warranted. However, static temperature manipulations may underestimate the thermal complexity of the reefs in which many corals live. For instance, corals of Houbihu, Taiwan, experience changes in temperature of up to 10°C over the course of a day during spring-tide upwelling events. To better understand the phenotypic plasticity of these corals, a laboratory-based experiment was conducted whereby specimens of Seriatopora hystrix from an upwelling reef (Houbihu) and conspecifics from a non-upwelling reef (Houwan) were exposed to both a stable seawater temperature (26°C) regime and a regime characterized by a 6°C fluctuation (23-29°C) over a 12h period for 7days. A suite of physiological and molecular parameters was measured in samples of both treatments, as well as in experimental controls, to determine site of origin (SO) and temperature treatment (TT) responses. Only chlorophyll a (chl a) concentration and growth demonstrated the hypothesized trend of higher levels when exposed to a TT that mimicked SO conditions. In contrast, chl a, maximum dark-adapted quantum yield of photosystem II (F v /F m ), and Symbiodinium ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL), photosystem I (psI, subunit III) and phosphoglycolate phosphatase (pgpase) mRNA expression demonstrated significant TT effects. Specifically, levels of these response variables were higher in samples exposed to a variable temperature regime, suggesting that S. hystrix may acclimate to fluctuating temperatures by increasing its capacity for photosynthesis.Supplementary material available online at http://jeb.biologists.org/cgi/content/full/215/23/4183/DC1 Key words: acclimation, coral reef, endosymbiosis, gene expression, photosynthesis, Symbiodinium. susceptible to impact by unexpected environmental variability, and results must always be interpreted conservatively.With this in mind, by conducting a laboratory-based reciprocal transplant (LBRT) study, we took advantage of the thermally unique and dynamic environments of southern Taiwan in order to gain insight into how a common reef-building scleractinian, Seriatopora hystrix Dana 1846, acclimates to changes in seawater temperature. Coral colonies were collected from both Houbihu, a reef within Nanwan Bay that experiences episodic summer upwelling (Putnam et al., 2010), and Houwan, a reef on the western side of the Hengchun Peninsula that does not experience this phenomenon, and specimens from each site were incubated at either stable (26°C) or variable (23-29°C over a 12h period) temperature for 7days. This laboratory-based approach was also utilized in place of a reciprocal transplant in situ because of the multitude of other abiotic parameters (e.g. nutrient and dissolved oxygen levels) that are affected by upwelling events in Taiwan (Chen et al., 2004); while the physiological response to upwelling is indeed a worthy avenue ...

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Due to the potential for increasing ocean temperatures to detrimentally impact reef-building corals, there is an urgent need to better understand not only the coral thermal stress response, but also natural variation in their sub-cellular composition. To address this issue, while simultaneously developing a molecular platform for studying one of the most common Taiwanese reef corals, Seriatopora hystrix, 1,092 cDNA clones were sequenced and characterized. Subsequently, RNA, DNA and protein were extracted sequentially from colonies exposed to elevated (30°C) temperature for 48 hours. From the RNA phase, a heat shock protein-70 (hsp70)-like gene, deemed hsp/c, was identified in the coral host, and expression of this gene was measured with real-time quantitative PCR (qPCR) in both the host anthozoan and endosymbiotic dinoflagellates (genus Symbiodinium). While mRNA levels were not affected by temperature in either member, hsp/c expression was temporally variable in both and co-varied within biopsies. From the DNA phase, host and Symbiodinium hsp/c genome copy proportions (GCPs) were calculated to track changes in the biological composition of the holobiont during the experiment. While there was no temperature effect on either host or Symbiodinium GCP, both demonstrated significant temporal variation. Finally, total soluble protein was responsive to neither temperature nor exposure time, though the protein/DNA ratio varied significantly over time. Collectively, it appears that time, and not temperature, is a more important driver of the variation in these parameters, highlighting the need to consider natural variation in both gene expression and the molecular make-up of coral holobionts when conducting manipulative studies. This represents the first study to survey multiple macromolecules from both compartments of an endosymbiotic organism with methodologies that reflect their dual-compartmental nature, ideally generating a framework for assessing molecular-level changes within corals and other endosymbioses exposed to changes in their environment.

The coral mucus may harbor commensal bacteria that inhibit growth of pathogens. Therefore, there is a need to understand the dynamics of bacterial communities between the coral mucus and tissues. Nubbins of Acropora muricata were subjected to increasing water temperatures of 26°C-33°C, to simultaneously explore the bacterial diversity in coral mucus and tissues by 16S rRNA gene amplicon sequencing. Photochemical efficiency of symbiotic dinoflagellates within the corals declined above 31°C. Both the mucus and tissues of healthy A. muricata were dominated by γ-Proteobacteria, but under thermal stress there was a shift towards bacteria from the Verrucomicrobiaceae and α-Proteobacteria. Members of Cyanobacteria, Flavobacteria and Sphingobacteria also become more prominent at higher temperatures. The relative abundance of Vibrio spp. in the coral mucus increased at 29°C, but at 31°C, there was a drop in the relative abundance of Vibrio spp. in the mucus, with a reciprocal increase in the tissues. On the other hand, during bleaching, the relative abundance of Endozoicomonas spp. decreased in the tissues with a reciprocal increase in the mucus. This is the first systematic experiment that shows the potential for a bacterial community shift between the coral surface mucus and tissues in a thermally stressed coral.

We compared responses of adults and larvae of the brooding corals Pocillopora damicornis and Seriatopora hystrix to 12-h exposures to constant temperature treatments (211C, 281C, or 301C) and a treatment in which temperature fluctuated from 281 to 211C, simulating daily temperature variation generated by tidally driven upwelling in their natural habitat (Nanwan Bay, southern Taiwan). In all treatments, the maximum dark-adapted quantum yield of photosystem II (F V /F M ) of the larvae was B49% lower than that of adult corals; F V /F M in the larvae also differed among temperature treatments, with the highest values in the fluctuating treatment. These results show that the larvae of at least P. damicornis are more sensitive to temperature than adults, and suggest that larvae are physiologically well suited to fluctuating temperature regimes. To assess whether the timing of larval release affected their performance, larvae of P. damicornis were compared among release days within a single reproductive event. Groups of larvae released on nine consecutive days differed significantly in size, Symbiodinium content, and F V /F M . This demonstration of functional differences among coral larvae that are released on different dates within a single reproductive event creates the potential for advantages to accrue from the coincidence of larval phenotypes with temporally varying conditions. Adult colonies may experience selective advantages by producing broods of functionally variable larvae, in order to match extreme phenotypes to unusual environmental conditions.