Blue Carbon Science, Management and Policy Across a Tropical Urban Landscape

The ability of vegetated coastal ecosystems to sequester high rates of “blue” carbon over millennial time scales has attracted the interest of national and international policy makers as a tool for climate change mitigation. Whereas focus on blue carbon conservation has been mostly on threatened rural seascapes, there is scope to consider blue carbon dynamics along highly fragmented and developed urban coastlines. The tropical city state of Singapore is used as a case study of urban blue carbon knowledge generation, how blue carbon changes over time with urban development, and how such knowledge can be integrated into urban planning alongside municipal and national climate change obligations. A systematic review of blue carbon studies in Singapore was used to support a qualitative review of Singapore’s blue carbon ecosystems, carbon budget, changes through time and urban planning and policy. Habitat loss across all blue carbon ecosystems is coarsely estimated to have resulted in the release of ∼12.6 million tonnes of carbon dioxide since the beginning of the 20th century. However, Singapore’s remaining blue carbon ecosystems still store an estimated 568,971 – 577,227 tonnes of carbon (equivalent to 2.1 million tonnes of carbon dioxide) nationally, with a small proportion of initial loss offset by habitat restoration. Carbon is now a key topic on the urban development and planning agenda, as well as nationally through Singapore’s contributions to the Paris Agreement. The experiences of Singapore show that coastal ecosystems and their blue carbon stocks can be successfully managed along an urban coastline, and can help inform blue carbon science and management along other rapidly urbanizing coastlines throughout the tropics

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Interactive effects of ocean acidification and declining water quality on tropical seagrass physiology

Primary productivity is the conversion of inorganic carbon into structural and nonstructural carbon (growth and storage) and is thereby the basis of the ecosystem services provided by seagrass meadows. These services include provision of habitat, carbon sequestration, stabilisation and trapping of sediments as well as food for invertebrates, fish, and mega-herbivores. Increased carbon dioxide (CO₂) dissolved in seawater (ocean acidification, OA), can enable seagrass productivity to increase even though they also use HCO₃⁻ as an alternate form of dissolved inorganic carbon (DIC). However, productivity responses to increasing pCO₂ might be affected by other environmental factors that influence metabolic processes, such as water temperature and local water quality. The lack of empirical evidence for interactive effects of OA and localized impacts (e.g. light, nutrients) hampers our ability to factor these into predictive models and into coastal management decision-making processes. Therefore, in this thesis I aimed to investigate the physiological responses of tropical Great Barrier Reef (GBR) seagrass species to increasing pCO₂ (simulating OA), temperature, and key water quality parameters. In an initial experiment (Chapter 2), productivity and growth responses of common tropical seagrass species, Cymodocea serrulata, Halodule uninervis and Thalassia hemprichii, to CO₂ enrichment were quantified. The seagrasses were exposed for two weeks to pCO₂ levels (442 – 1204 μatm) approximating the range of end-of-century emission scenarios. Net productivity and carbon budgets (PG:R) significantly increased with a rise in pCO₂ in all three species. The degree of productivity rise with pCO₂ was similar across species. While increased productivity in H. uninervis and T. hemprichii resulted in faster growth from CO₂ enrichment, this was not the case for C. serrulata. Varying carbon allocation strategies among species might have contributed to observed differences in growth responses and so internal carbon allocation was further explored in a later experiment (Chapter 5). When light availability is reduced from declining water quality (e.g. land run-off), preference for utilisation of the DIC species (CO₂ vs HCO₃⁻), and therefore response to increasing pCO₂, might be affected. To test this, C. serrulata and H. uninervis were exposed to two DIC concentrations (447 and 1077 μatm pCO₂), and three light treatments (35, 100 and 380 μmol m-2 s-1) for two weeks (Chapter 3). DIC uptake mechanisms were separately examined by measuring net photosynthetic rates while subjecting C. serrulata and H. uninervis to changes in light and addition of bicarbonate (HCO₃⁻) use inhibitor (carbonic anhydrase inhibitor, acetazolamide) and TRIS buffer (pH 8.0). DIC enrichment stimulated maximum photosynthetic rates (Pmax) more in C. serrulata grown under lower light levels (36 – 60% increase) than for those in high light (4% increase) (DIC × light: P = 0.049). This was due to C. serrulata's greater dependence on CO₂ in low light. However, this increase due to DIC did not compensate for low light, as net productivity of DIC-enriched plants at low light was 85 – 208 % lower than non-DIC enriched plants growing under high light. In contrast, photosynthetic responses in H. uninervis increased with higher light and were independent of the concentrations of the DIC substrates available. H. uninervis has more flexible HCO₃⁻ uptake pathways. Light availability strongly affected productivity and also influenced productivity responses to DIC enrichment, via both carbon fixation and acquisition processes. Nitrogen availability can limit productivity responses to OA, since nitrogenderived metabolites are required for carbon assimilation. In Chapter 4, the hypothesis that CO₂ and nitrate enrichment can have additive effects on seagrass productivity and biomass was tested. Nitrogen uptake and assimilation, photosynthesis, growth, and carbon allocation responses of H. uninervis and T. hemprichii to OA scenarios (428, 734 and 1213 μatm pCO₂) under two nutrient levels (0.3 and 1.9 μM NO3 -, approximating average GBR flood plume levels) were measured. Net productivity (53 – 78 %) and growth (18 – 52 %) in H. uninervis increased with CO₂ enrichment (P < 0.05), but were not affected by nitrate enrichment. T. hemprichii did not show significant changes with pCO₂ or nitrate by the end of the experiment (24 days) in net productivity and growth. There was no evidence that nitrogen demand increased with pCO₂ enrichment in either species. Overall, nutrient increases to levels approximating flood plumes levels in the GBR only had small effects on seagrass metabolism, and high tissue nutrient concentrations (2.53 – 2.75 %N) suggest that only small responses occurred because they were not nutrient limited. Changes in ambient growth temperature can modulate seagrass response to OA by affecting assimilation and utilization of CO₂. Yet the combined effects of temperature and CO₂ enrichment on seagrass carbon metabolism are not known. In Chapter 5, C. serrulata and H. uninervis were exposed to three temperatures (20°C, 25°C and 30°C, spanning seasonal variation) and three target pCO₂ levels (present day 353 – 485 μatm; high 915 – 1102 μatm; extreme 1658 – 2297 μatm) for seven weeks. Net productivity, biomass allocation and enzyme activity as a proxy for carbon translocation (sucrosephosphate synthase SPS and sucrose synthase SS) were measured. Net productivity in C. serrulata and H. uninervis increased by 109 % and 197 % (P < 0.001) over the 10ºC rise (20 – 30ºC), respectively. In addition, temperature rise stimulated the increase of aboveground biomass in C. serrulata (26 – 35 %; P = 0.012) and H. uninervis (42 – 88 %; P = 0.006). Differences in the allocation of fixed carbon in response to temperature were evident. At warmer temperatures (where net productivity was highest), C. serrulata exported more carbohydrates to its rhizomes, while H. uninervis increased shoot density. In comparison, responses to CO₂ enrichment were limited to C. serrulata increasing above- to- below-ground ratio (P = 0.003) and H. uninervis increasing net productivity the least at 30ºC (pCO₂ × temperature: P = 0.047). This study highlights that temperature exerts a much stronger control over carbon metabolism than CO₂ enrichment in tropical seagrasses. In summary, the effects of OA on seagrass physiology varied with light availability and water temperature. Ocean acidification cannot fully compensate for productivity losses caused by reduced light. Nitrate fertilization did not enhance seagrass productivity responses to CO₂ enrichment, but it might have indirect impacts encouraging the growth of algae, which can thrive in nutrient and CO₂ enriched conditions. An overall analysis (Chapter 6) of results from all chapters suggests that nutrient status (leaf N content) might be a strong determinant of CO₂ responses, as C. serrulata and H. uninervis increased productivity at high pCO₂ when their tissue nutrient concentrations were elevated, but not at low tissue nutrient concentrations. Species-specific responses to OA and environmental parameters were consistently demonstrated, warning against the generalisation of responses across seagrass species. Overall, seagrass productivity can increase under OA, which is likely to make them future "winners" (sensu. Fabricius et al 2011) among tropical marine habitats; however localised conditions will affect their response and many of these remain untested

Interactive effects of ocean acidification and declining water quality on tropical seagrass physiology

Primary productivity is the conversion of inorganic carbon into structural and nonstructural carbon (growth and storage) and is thereby the basis of the ecosystem services provided by seagrass meadows. These services include provision of habitat, carbon sequestration, stabilisation and trapping of sediments as well as food for invertebrates, fish, and mega-herbivores. Increased carbon dioxide (CO₂) dissolved in seawater (ocean acidification, OA), can enable seagrass productivity to increase even though they also use HCO₃⁻ as an alternate form of dissolved inorganic carbon (DIC). However, productivity responses to increasing pCO₂ might be affected by other environmental factors that influence metabolic processes, such as water temperature and local water quality. The lack of empirical evidence for interactive effects of OA and localized impacts (e.g. light, nutrients) hampers our ability to factor these into predictive models and into coastal management decision-making processes. Therefore, in this thesis I aimed to investigate the physiological responses of tropical Great Barrier Reef (GBR) seagrass species to increasing pCO₂ (simulating OA), temperature, and key water quality parameters. In an initial experiment (Chapter 2), productivity and growth responses of common tropical seagrass species, Cymodocea serrulata, Halodule uninervis and Thalassia hemprichii, to CO₂ enrichment were quantified. The seagrasses were exposed for two weeks to pCO₂ levels (442 – 1204 μatm) approximating the range of end-of-century emission scenarios. Net productivity and carbon budgets (PG:R) significantly increased with a rise in pCO₂ in all three species. The degree of productivity rise with pCO₂ was similar across species. While increased productivity in H. uninervis and T. hemprichii resulted in faster growth from CO₂ enrichment, this was not the case for C. serrulata. Varying carbon allocation strategies among species might have contributed to observed differences in growth responses and so internal carbon allocation was further explored in a later experiment (Chapter 5). When light availability is reduced from declining water quality (e.g. land run-off), preference for utilisation of the DIC species (CO₂ vs HCO₃⁻), and therefore response to increasing pCO₂, might be affected. To test this, C. serrulata and H. uninervis were exposed to two DIC concentrations (447 and 1077 μatm pCO₂), and three light treatments (35, 100 and 380 μmol m-2 s-1) for two weeks (Chapter 3). DIC uptake mechanisms were separately examined by measuring net photosynthetic rates while subjecting C. serrulata and H. uninervis to changes in light and addition of bicarbonate (HCO₃⁻) use inhibitor (carbonic anhydrase inhibitor, acetazolamide) and TRIS buffer (pH 8.0). DIC enrichment stimulated maximum photosynthetic rates (Pmax) more in C. serrulata grown under lower light levels (36 – 60% increase) than for those in high light (4% increase) (DIC × light: P = 0.049). This was due to C. serrulata's greater dependence on CO₂ in low light. However, this increase due to DIC did not compensate for low light, as net productivity of DIC-enriched plants at low light was 85 – 208 % lower than non-DIC enriched plants growing under high light. In contrast, photosynthetic responses in H. uninervis increased with higher light and were independent of the concentrations of the DIC substrates available. H. uninervis has more flexible HCO₃⁻ uptake pathways. Light availability strongly affected productivity and also influenced productivity responses to DIC enrichment, via both carbon fixation and acquisition processes. Nitrogen availability can limit productivity responses to OA, since nitrogenderived metabolites are required for carbon assimilation. In Chapter 4, the hypothesis that CO₂ and nitrate enrichment can have additive effects on seagrass productivity and biomass was tested. Nitrogen uptake and assimilation, photosynthesis, growth, and carbon allocation responses of H. uninervis and T. hemprichii to OA scenarios (428, 734 and 1213 μatm pCO₂) under two nutrient levels (0.3 and 1.9 μM NO3 -, approximating average GBR flood plume levels) were measured. Net productivity (53 – 78 %) and growth (18 – 52 %) in H. uninervis increased with CO₂ enrichment (P < 0.05), but were not affected by nitrate enrichment. T. hemprichii did not show significant changes with pCO₂ or nitrate by the end of the experiment (24 days) in net productivity and growth. There was no evidence that nitrogen demand increased with pCO₂ enrichment in either species. Overall, nutrient increases to levels approximating flood plumes levels in the GBR only had small effects on seagrass metabolism, and high tissue nutrient concentrations (2.53 – 2.75 %N) suggest that only small responses occurred because they were not nutrient limited. Changes in ambient growth temperature can modulate seagrass response to OA by affecting assimilation and utilization of CO₂. Yet the combined effects of temperature and CO₂ enrichment on seagrass carbon metabolism are not known. In Chapter 5, C. serrulata and H. uninervis were exposed to three temperatures (20°C, 25°C and 30°C, spanning seasonal variation) and three target pCO₂ levels (present day 353 – 485 μatm; high 915 – 1102 μatm; extreme 1658 – 2297 μatm) for seven weeks. Net productivity, biomass allocation and enzyme activity as a proxy for carbon translocation (sucrosephosphate synthase SPS and sucrose synthase SS) were measured. Net productivity in C. serrulata and H. uninervis increased by 109 % and 197 % (P < 0.001) over the 10ºC rise (20 – 30ºC), respectively. In addition, temperature rise stimulated the increase of aboveground biomass in C. serrulata (26 – 35 %; P = 0.012) and H. uninervis (42 – 88 %; P = 0.006). Differences in the allocation of fixed carbon in response to temperature were evident. At warmer temperatures (where net productivity was highest), C. serrulata exported more carbohydrates to its rhizomes, while H. uninervis increased shoot density. In comparison, responses to CO₂ enrichment were limited to C. serrulata increasing above- to- below-ground ratio (P = 0.003) and H. uninervis increasing net productivity the least at 30ºC (pCO₂ × temperature: P = 0.047). This study highlights that temperature exerts a much stronger control over carbon metabolism than CO₂ enrichment in tropical seagrasses. In summary, the effects of OA on seagrass physiology varied with light availability and water temperature. Ocean acidification cannot fully compensate for productivity losses caused by reduced light. Nitrate fertilization did not enhance seagrass productivity responses to CO₂ enrichment, but it might have indirect impacts encouraging the growth of algae, which can thrive in nutrient and CO₂ enriched conditions. An overall analysis (Chapter 6) of results from all chapters suggests that nutrient status (leaf N content) might be a strong determinant of CO₂ responses, as C. serrulata and H. uninervis increased productivity at high pCO₂ when their tissue nutrient concentrations were elevated, but not at low tissue nutrient concentrations. Species-specific responses to OA and environmental parameters were consistently demonstrated, warning against the generalisation of responses across seagrass species. Overall, seagrass productivity can increase under OA, which is likely to make them future "winners" (sensu. Fabricius et al 2011) among tropical marine habitats; however localised conditions will affect their response and many of these remain untested

Light-induced morphological plasticity in the scleractinian coral Goniastrea pectinata and its functional significance

10.1007/s00338-010-0631-4Coral Reefs293797-808CORF

Observations on staminate flowers of Cymodocea serrulata in ex situ aquarium

10.26107/NIS-2020-0007Nature In Singapore1357-60Singapor

Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses

10.7717/peerj.12899PeerJ10e12899-e1289

Female flowers of tropical seagrass Syringodium isoetifolium (Alismatales: Cymodoceaceae) in an ex-situ aquarium

Nature in Singapore131-5Singapor

Image_3_Dugongs (Dugong dugon) along hyper-urbanized coastlines.tif

Coastal development and the increased anthropogenic use of sea spaces have rapidly degraded coastal habitats throughout Southeast Asia. We study how these activities impact dugong (Dugong dugon) population(s) along hyper-urbanized coastlines of the Johor and Singapore Straits through literature reviews and field surveys. Our review recovered sixty-nine live observations and carcass observations of dugongs between 1820 and 2021. The eastern Johor Strait is identified as a dugong hotspot. We observed peaks in observations coincident with the Northeast and Southwest monsoons. Distribution patterns of dugong observations were likely driven by a combination of natural and anthropogenic factors such as seasonality in seagrass abundance, tidal cycles, wind patterns and vessel traffic. Our field surveys ascertained active foraging sites along the anthropogenically disturbed Johor Strait and western Singapore Strait. Evident from our study is the importance of reef-associated seagrass meadows as refugia for foraging dugongs along areas of high anthropogenic use. This study provides an ecological baseline for dugong research along the Johor and Singapore Straits—within the data-poor western Malay Archipelago—, and aids in the design of sustainable management strategies and conservation programs for dugongs along areas where urbanization is commonplace.</p