The effect of natural and anthropogenic nutrient and sediment loads on coral oxidative stress on runoff-exposed reefs

Recently, corals on the Great Barrier (GBR) have suffered mass bleaching. The link between ocean warming and coral bleaching is understood to be due to temperature-dependence of complex physiological processes in the coral host and algal symbiont. Here we use a coupled catchment-hydrodynamic-biogeochemical model, with detailed zooxanthellae photophysiology including photoadaptation, photoacclimation and reactive oxygen build-up, to investigate whether natural and anthropogenic catchment loads impact on coral bleaching on the GBR. For the wet season of 2017, simulations show the cross-shelf water quality gradient, driven by both natural and anthropogenic loads, generated a contrasting zooxanthellae physiological state on inshore versus mid-shelf reefs. The relatively small catchment flows and loads delivered during 2017, however, generated small river plumes with limited impact on water quality. Simulations show the removal of the anthropogenic fraction of the catchment loads delivered in 2017 would have had a negligible impact on bleaching rates

LAPORAN INDIVIDU KEGIATAN PENGALAMAN LAPANGAN (PPL) PERIODE 18 JULI s.d 15 SEPTEMBER 2016 SMA NEGERI 2 BANGUNTAPAN

Praktik Pengalaman Lapangan (PPL) merupakan suatu wadah untuk menerapkan/mengaplikasikan ilmu yang selama ini telah dipelajari dalam bidang keahlian maupun ilmu keguruan yang berkaitan dengan peserta didik dalam proses belajar mengajar. Praktik pengalaman lapangan atau praktik mengajar ini mulai dilaksanakan pada tanggal 18 Juli s.d. 15 September 2016 berlokasi di SMA N 2 Banguntapan. Dalam praktik mengajar mahasiswa terlebih dahulu melaksanakan persiapan pembelajaran, yaitu membuat perencanaan pembelajaran dimulai dengan membuat rencana pelaksanaan pembelajaran sampai dengan evaluasi yang dilaksanakan. Kemudian melakukan koordinasi dan konsultasi kepada guru pembimbing di sekolah tersebut. Dalam bimbingan PPL, mahasiswa (penulis) mendapatkan kesempatan untuk melaksanakan pembelajaran di kelas X IPS 1 dan X IPS 2. Kurikulum yang digunakan adalah Kurikulum 2013 (K13). Begitu pula dengan penulisan Rencana Pelaksanaan Pembelajarannya (RPP), penggunaan metode pembelajaran yang diterapkan adalah dengan metode Problem Based Learning dan Cooperative Learning. Sedangkan media yang digunakan adalah White Board, LCD, spidol, lembar kerja dan mengadakan tugas individu untuk mengetahui sejauh mana kemampuan siswa dalam memahami materi yang telah disampaikan. Pada tahap pelaksanaan, mahasiswa mengajar sebanyak 6 kali dengan alokasi masingmasing 3 jam pelajaran setiap pertemuan. Program kegiatan PPL dapat terlaksana dengan baik dan lancar berkat adanya bimbingan dan arahan dari guru pembimbing dan dosen pembimbing selama praktik mengajar serta peran aktif peserta didik selama berlangsungnya KBM. Selain itu terlaksananya program PPL ini tidak terlepas dari dukungan dan bantuan dari pihak sekolah yang telah memberikan keluasan kesempatan kepada para mahasiswa PPL untuk mengembangkan potensi yang dimilikinya

Impact of catchment-derived nutrients and sediments on marine water quality on the Great Barrier Reef: an application of the eReefs marine modelling system

Water quality of the Great Barrier Reef (GBR) is determined by a range of natural and anthropogenic drivers that are resolved in the eReefs coupled hydrodynamic - biogeochemical marine model forced by a process-based catchment model, GBR Dynamic SedNet. Model simulations presented here quantify the impact of anthropogenic catchment loads of sediments and nutrients on a range of marine water quality variables. Simulations of 2011–2018 show that reduction of anthropogenic catchment loads results in improved water quality, especially within river plumes. Within the 16 resolved river plumes, anthropogenic loads increased chlorophyll concentration by 0.10 (0.02–0.25) mg Chl m−3. Reductions of anthropogenic loads following proposed Reef 2050 Water Quality Improvement Plan targets reduced chlorophyll concentration in the plumes by 0.04 (0.01–0.10) mg Chl m−3. Our simulations demonstrate the impact of anthropogenic loads on GBR water quality and quantify the benefits of improved catchment management

Transformation in a changing climate: a research agenda

The concept of transformation in relation to climate and other global change is increasingly receiving attention. The concept provides important opportunities to help examine how rapid and fundamental change to address contemporary global challenges can be facilitated. This paper contributes to discussions about transformation by providing a social science, arts and humanities perspective to open up discussion and set out a research agenda about what it means to transform and the dimensions, limitations and possibilities for transformation. Key focal areas include: (1) change theories, (2) knowing whether transformation has occurred or is occurring; (3) knowledge production and use; (4), governance; (5) how dimensions of social justice inform transformation; (6) the limits of human nature; (7) the role of the utopian impulse; (8) working with the present to create new futures; and (9) human consciousness. In addition to presenting a set of research questions around these themes the paper highlights that much deeper engagement with complex social processes is required; that there are vast opportunities for social science, humanities and the arts to engage more directly with the climate challenge; that there is a need for a massive upscaling of efforts to understand and shape desired forms of change; and that, in addition to helping answer important questions about how to facilitate change, a key role of the social sciences, humanities and the arts in addressing climate change is to critique current societal patterns and to open up new thinking. Through such critique and by being more explicit about what is meant by transformation, greater opportunities will be provided for opening up a dialogue about change, possible futures and about what it means to re-shape the way in which people live

High adult mortality in disease-challenged frog populations increases vulnerability to drought

Pathogen emergence can drive major changes in host population demography, with implications for population dynamics and sensitivity to environmental fluctuations. The amphibian disease chytridiomycosis, caused by infection with the fungal pathogen Batrachochytrium dendrobatidis (Bd), is implicated in the severe decline of over 200 amphibian species. In species that have declined but not become extinct, Bd persists and can cause substantial ongoing mortality. High rates of mortality associated with Bd may drive major changes in host demography, but this process is poorly understood. Here, we compared population age structure of Bd-infected populations, Bd-free populations, and museum specimens collected prior to Bd emergence for the endangered Australian frog, Litoria verreauxii alpina (alpine tree frog). We then used population simulations to investigate how pathogen-associated demographic shifts affect the ability of populations to persist in stochastic environments. We found that Bd-infected populations have a severely truncated age structure associated with very high rates of annual adult mortality. Near-complete annual adult turnover in Bd-infected populations means that individuals breed once, compared with Bd-free populations where adults may breed across multiple years. Our simulations showed that truncated age structure erodes the capacity of populations to withstand periodic recruitment failure; a common challenge for species reproducing in uncertain environments. We document previously undescribed demographic shifts associated with a globally emerging pathogen and demonstrate how these shifts alter host ecology. Truncation of age structure associated with Bd effectively reduces host niche width, and can help explain the contraction of L. v. alpina to perennial waterbodies where the risk of drought-induced recruitment failure is low. Reduced capacity to tolerate other sources of mortality may explain variation in decline severity among other chytridiomycosis-challenged species and highlights the potential to mitigate disease impacts through minimising other sources of mortality

Recent Asian origin of chytrid fungi causing global amphibian declines

Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide

Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi

T.W.J.G., M.C.F., D.S.S., A.L., E.C., F.C.C., J.B., A.A.C., C.M., F.S., B.R.S., S.O., were supported through the Biodiversa project RACE: Risk Assessment of Chytridiomycosis to European Amphibian Biodiversity (NERC standard grant NE/K014455/1 and NE/E006701/1; ANR-08-BDVA-002-03). M.C.F., J.S., C.W., P.G. were supported by the Leverhulme Trust (RPG-2014-273), M.C.F., A.C., C.W. were supported by the Morris Animal Foundation. J.V. was supported by the Bolyai János Research Grant of the Hunagrian Academy of Sciences (BO/00597/14). F.G. and D.G. were supported by the Conservation Leadership Programme Future Conservationist Award. C.S.A. was supported by Fondecyt (No. 1181758). M.C.F. and A.C. were supported by. Mohamed bin Zayed Species Conservation Fund Project (152510704). GMR held a doctoral scholarship (SFRH/BD/69194/2010) from Fundação para a Ciência e a Tecnologia. L.F.T., C.L., L.P.R. K.R.Z., T.Y.J., T.S.J. were supported by São Paulo Research Foundation (FAPESP #2016/25358-3), the National Counsel of Technological and Scientific Development (CNPq #300896/2016–6) and a Catalyzing New International Collaborations grant from the United States NSF (OISE-1159513). C.S.A. was supported by Fondecyt (No. 1181758). T.M.D. was supported by the Royal Geographical Society and the Royal Zoological Society of Scotland. B.W. was supported by the National Research Foundation of Korea (2015R1D1A1A01057282).Peer reviewedPublisher PD

Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi

© The Author(s) 2018.Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.T.W.J.G., M.C.F., D.S.S., A.L., E.C., F.C.C., J.B., A.A.C., C.M., F.S., B.R.S., S.O., were supported through the Biodiversa project RACE: Risk Assessment of Chytridiomycosis to European Amphibian Biodiversity (NERC standard grant NE/K014455/1 and NE/E006701/1; ANR-08-BDVA-002-03). M.C.F., J.S., C.W., P.G. were supported by the Leverhulme Trust (RPG-2014-273), M.C.F., A.C., C.W. were supported by the Morris Animal Foundation. J.V. was supported by the Bolyai János Research Grant of the Hunagrian Academy of Sciences (BO/00597/14). F.G. and D.G. were supported by the Conservation Leadership Programme Future Conservationist Award. C.S.A. was supported by Fondecyt (No. 1181758). M.C.F. and A.C. were supported by. Mohamed bin Zayed Species Conservation Fund Project (152510704). GMR held a doctoral scholarship (SFRH/ BD/69194/2010) from Fundação para a Ciência e a Tecnologia. L.F.T., C.L., L.P.R. K.R.Z., T.Y.J., T.S.J. were supported by São Paulo Research Foundation (FAPESP #2016/25358-3), the National Counsel of Technological and Scientifc Development (CNPq #300896/2016–6) and a Catalyzing New International Collaborations grant from the United States NSF (OISE-1159513). C.S.A. was supported by Fondecyt (No. 1181758). T.M.D. was supported by the Royal Geographical Society and the Royal Zoological Society of Scotland. B.W. was supported by the National Research Foundation of Korea (2015R1D1A1A01057282).Peer Reviewe

Occurrence and significance of long-chain (ω-1)-hydroxy fatty acids in methane-utilizing bacteria

The cell residue derived (H-labile lipid) hydroxy fatty acid composition of 16 strains of methane-utilizing (methanotrophic) bacteria have been analysed as part of a larger program which is investigating the taxonomy and potential uses of these bacteria. The hydroxy fatty acid compositions were determined by GC and GC-MS. Of the 16 strains, 5 strains including Methylosinus sporium UQM3306, Methylocystis parvus UQM3309 and Methylocystis minimus UQM3497 were found to contain long-chain (C, C and C) (ω-1)-hydroxy fatty acids. The total concentration of (ω-1)-hydroxy fatty acids varied between 65 and 500 ng/g. Although only a limited number of species have been analysed to date, a number of differences were apparent when comparing the (ω-1)-hydroxy acid profiles. The type II methanotrophic bacteria generally contained higher relative concentrations of the (ω-1)-hydroxy acids than found in the type I methanotrophs. These differences may prove to be useful in taxonomic, environmental and organic geochemical investigations

A mechanistic model of coral bleaching due to temperature-mediated light-driven reactive oxygen build-up in zooxanthellae.

Mass coral bleaching has emerged in the 21st century as the greatest threat to the health of the world's reefs. A sophisticated process understanding of bleaching at the polyp scale has now been achieved through laboratory and field studies, but this knowledge is yet to be applied in mechanistic models of shelf-scale reef systems. In this study we develop a mechanistic model of the coral-symbiont relationship that considers temperature-mediated build-up of reactive oxygen species due to excess light, leading to zooxanthellae expulsion. The model explicitly represents the coral host biomass, as well as zooxanthellae biomass, intracellular pigment concentration, nutrient status, and the dynamics of reaction centres and the xanthophyll cycle. Photophysiological processes represented include photoadaptation, xanthophyll cycle dynamics, and reaction centre state transitions. The mechanistic model of the coral-symbiont relationship is incorporated into a $\sim$1 km resolution coupled hydrodynamic - biogeochemical model that encompasses the entire $\sim$2000 km length of the Great Barrier Reef. A simulation of the 2016 bleaching event shows the model is able to capture the broadscale features of the observed bleaching, but fails to capture bleaching on offshore reefs due to the model's grid being unable to resolve the bathymetry of shallow platforms surrounded by deep water. To further analyse the model behaviour, a $\sim$200 m resolution nested simulation of Davies Reef (18$^{\circ}$49'S, 147$^{\circ}$38'E) is undertaken. We use this nested model to demonstrate the depth gradient in zooxanthellae response to thermal stress. Finally, we discuss the uncertainties in the bleaching model, which lie primarily in quantifying the link between reactive oxygen build-up and the expulsion process. Through the mechanistic representation of environmental forcing, this model of coral bleaching applied in realistic environmental conditions has the potential to generate more detailed predictions than the presently-available satellite-based coral bleaching metrics, and can be used to evaluate proposed management strategies