Publications

Photo 1: Typical examples of coral- (A) and algae-dominated (B) reef communities in the central Red Sea. The distance between the two sites is only 500 m. Changes from coral to algal dominance are observed globally, often as a result of local and/or global anthropogenic disturbances leading to the loss of live coral cover and the subsequent establishment of fast-growing algae. The consequences of these community changes for key ecosystem functions, such as primary productivity, calcification, organic matter, and nutrient recycling mediated by the underlying benthic communities are poorly understood. The alterations of these processes remain particularly uncertain with regard to the combined effects of environmental change. Photo credit: Florian Roth. Photo 2: Experiments were carried out at Abu Shosha reef located in the central Red Sea on the west coast of Saudi Arabia. The reef is characterized by a heterogeneous mosaic of patches of coral- and algae-dominated communities. Thus, this site allowed for the quantification of the functionality of both communities under identical environmental conditions. The detailed composition of benthic communities used for this experiment was assessed multiple times during the study period by benthic surveys and modern photogrammetry tools to account for the reef's structural complexity. Photo credit: Florian Roth. Photo 3: We used in situ incubations of natural coral- and algae-dominated reef communities to measure fluxes of oxygen, dissolved inorganic carbon, total alkalinity, dissolved organic carbon, and dissolved inorganic nitrogen. This non-invasive approach provides reproducible measurements of biogeochemical processes of structurally complex benthic communities. Thereby, it also accounts for the components of the carbon and nitrogen pool that are remineralized by microbial communities or cryptic fauna within the reef matrix. Photo credit: Holger Anlauf. Photo 4: A total of 2520 syringes with water drawn from the incubations chambers were collected to monitor changes in water chemistry and biological variables during the experiments; (A) a researcher collecting water samples from an algae-dominated reef community; (B) custom-made syringe-holders were used to stop the syringes from floating away; and (C) on the boat, water samples were filtered and/or processed directly for the highest quality in water chemistry measurements in the laboratory later on. Photo credit: (A) Holger Anlauf; (B) Florian Roth; (C) Luis Silva. These photographs illustrate the article “High summer temperatures amplify functional differences between coral- and algae-dominated reef communities” by Florian Roth, Nils Rädecker, Susana Carvalho, Carlos M. Duarte, Vincent Saderne, Andrea Anton, Luis Silva, Maria Ll. Calleja, Xosé Anxelu G. Morán, Christian R. Voolstra, Benjamin Kürten, Burton H. Jones, and Christian Wild published in Ecology. https://doi.org/10.1002/ecy.3226.

Data prediction and imputation are important parts of marine animal movement trajectory analysis as they can help researchers understand animal movement patterns and address missing data issues. Compared with traditional methods, deep learning methods can usually provide enhanced pattern extraction capabilities, but their applications in marine data analysis are still limited. In this research, we propose a composite deep learning model to improve the accuracy of marine animal trajectory prediction and imputation. The model extracts patterns from the trajectories with an encoder network and reconstructs the trajectories using these patterns with a decoder network. We use attention mechanisms to highlight certain extracted patterns as well for the decoder. We also feed these patterns into a second decoder for prediction and imputation. Therefore, our approach is a coupling of unsupervised learning with the encoder and the first decoder and supervised learning with the encoder and the second decoder. Experimental results demonstrate that our approach can reduce errors by at least 10% on average comparing with other methods.

Life has been evolving in the oceans much longer than it has on land, resulting in highly diverse ocean organisms—particularly microbes like bacteria and archaea. Ocean microbes perform crucial functions that influence the health of the ocean and ultimately impact Earth’s climate. To understand the diversity and functions of marine organisms, scientists have used a powerful technique called metagenomics to study the DNA of all the organisms present in an ocean-water sample at once. In our research, we combined results from multiple ocean metagenomic studies, taken from various locations and depth zones across the world’s oceans, to produce a global ocean genome composed of 317.5 million groups of similar genes—approximately half of which could be categorized by type of organism and function. This unprecedented amount of data has much to teach us about varied ocean habitats and can help scientists answer many questions about ocean organisms and their functions.

The shoot demography and rhizome growth of Syringodium filiforme Kutz. and Halodule wrightii Aschers. were studied, based on plant dating techniques, to account for their role as pioneer in the succession sequence of Canbbean seagrasses. Results demonstrated that these species are able to develop dense meadows, supporting biomasses in excess of 500 g DW m They produced more than 2000 g DW m-2 yr-' due to their high leaf (5.0 to 8 5 yr.') and rhizome (2 0 to 3.3 yr') turnover. Rhizome growth and branch~ng rates were very high, allowing these seagrasses to rapidly occupy the space they colonise. The rapid rhizome turnover involved, however, a high shoot mortality rate and low 11fe expectancy (average shoot life expectancy 100 to 180 d). This implies that, while these pioneer species are able to rapidly occupy the space they colonise, their established shoots cannot occupy that space for a s long a s the more longlived species Thalassia testudinum. We suggest, therefore. that the role of seagrass species a s pioneer or climax species is independent of their capacity to support dense, productive populations, and is closely related to shoot longevity and rhizome turnover.

Responses of cnidarian-Symbiodiniaceae associations to warming are determined, in part, by high-frequency temperature variability. Yet, the role of such variability in determining specific maximum temperature thresholds of cnidarian holobionts (the ecological units comprised of cnidarian hosts and associated microorganisms, including Symbiodiniaceae) remains untested. Here we contrasted the thermal resilience (that is the ability to resist stress) of a model symbiotic cnidarian from the Red Sea (jellyfish of the genus Cassiopea) under stable and diel oscillating temperature conditions that provide night-time reprieves from daily maximum temperatures. Holobionts were subjected to two thermal trajectories; one that increased but plateaued at 2 °C below identified bleaching thresholds and another that increased incrementally until holobionts bleached. We used behavior, growth, photochemical efficiency, Symbiodiniaceae (symbiont) cell density, and total chlorophyll cell content to characterize thermal resilience and examined Symbiodiniaceae community composition responses at 1 and 13 days of exposure, and post-bleaching. Lower night-time temperatures, resulting in lower daily mean temperatures, allowed holobionts to withstand daily maximum temperatures close to their bleaching thresholds for two extra days than those under stable maximum temperature conditions. Lower night-time temperatures increased the bleaching threshold of the holobionts, whereby holobionts exposed to night-time thermal reprieves tolerated a more extreme daily mean temperature of 40.6 ºC and reached a daily thermal maxima 4 ºC higher than those under stable temperature conditions. However, post-bleaching observations indicate that night-time temperature reprieves did not prevent symbiont cell or pigment loss. Symbiodiniaceae communities were unaffected by lower night-time temperatures and no directional changes indicative of symbiont shuffling/ selection of thermally tolerant lineages were observed. We show that stable experimental treatments may fail to accurately identify maximum thermal thresholds of non-calcifying cnidarians and limit their relevance to in situ environments that are often characterized by high levels of temperature fluctuations.

The data shown in this table were compiled from the literature by conducting a Boolean search in Google Scholar using the word combinations “seagrass accretion rate” “mangrove accretion rate” and “salt marshes accretion rate”.From each study, the geographic area where the data were obtained, the sediment accretion and/or soil elevation rates, the method used and the source are reported in the table. For the method used, a broad explanation of the RSET (Rod Surface Elevation Table) and the MH (marker horizon) techniques is presented in Cahoon et al. (2006). This compilation is a contribution to the CSIRO Costal Carbon Cluster project. The methodology used is widely explained at: Cahoon, Donald R., Philippe F. Hensel, Tom Spencer, Denise J. Reed, Karen L. McKee, and Neil Saintilan. Coastal wetland vulnerability to relative sea-level rise: wetland elevation trends and process controls. In Wetlands and natural resource management, pp. 271-292. Springer Berlin Heidelberg, 2006.