Towards Automated Biometric Identification of Sea Turtles (Chelonia mydas)

Passive biometric identification enables wildlife monitoring with minimal disturbance. Using a motion-activated camera placed at an elevated position and facing downwards, images of sea turtle carapaces were collected, each belonging to one of sixteen Chelonia mydas juveniles. Then, co-variant and robust image descriptors from these images were learned, enabling indexing and retrieval. In this paper, several classification results of sea turtle carapaces using the learned image descriptors are presented. It was found that a template-based descriptor, i.e. Histogram of Oriented Gradients (HOG) performed much better during classification than keypoint-based descriptors. For our dataset, a high-dimensional descriptor is a must because of the minimal gradient and color information in the carapace images. Using HOG, we obtained an average classification accuracy of 65%.

Investigating quorum-quenching marine bacilli as potential biocontrol agents for protection of shrimps against Early Mortality Syndrome (EMS)

Early Mortality Syndrome (EMS) has been a major problem for shrimp aquaculture in Southeast Asia due to its epizootic prevalence within the region since the first reported case in 2009. This study explores the application of halophilic marine bacilli isolated from coral mucus and their quorum-quenching abilities as potential biocontrol agents in aquaculture systems to combat the causative agent of EMS, Vibrio parahaemolyticus. N-acylhomoserine lactone (AHL)-degrading (AiiA) activity was first screened by PCR then confirmed by bio-reporter assay, and a combination of 16S rDNA sequence analysis and quantitative phenotype assays including biofilm-formation and temperature-growth responses were used to demonstrate diversity amongst these quorum-quenching isolates. Three phenotypically distinct strains showing notable potential were chosen to undergo co-cultivation as a method for strain improvement via long term exposure to the pathogenic V. parahaemolyticus. The novel approach taken led to significant improvements in antagonism and quorum quenching activities as compared to the ancestral wild-type strains and offers a potential solution as well as pathway to improve existing beneficial microbes for one of the most pressing issues in shrimp aquacultures worldwide

Initial screening of mangrove endophytic fungi for antimicrobial compounds and heavy metal biosorption potential

Endophytic fungi provide protection to their host plant and the fungi often produce antimicrobial compounds to aid the host fighting off pathogens. These bioactive compounds were secondary metabolites which were often produced as waste- or by-products. In the present study, endophytic fungi isolated from mangrove plants and soils were characterized and their antimicrobial production and bioremediation potential of heavy metals copper (Cu) and zinc (Zn) were assessed. Twelve (12) isolated and identified endophytic fungi belonged to seven species; Penicillium, Curvularia, Diaporthe, Aspergillus, Guignardia, Neusartorya and Eupenicillium. Antimicrobial activities of these 12 fungal endophytes were tested against Gram negative bacteria; Bacillus subtilis, Staphylococcus aureus, Gram positive bacteria; Escherichia coli and fungi; Candida albicans and Aspergillus niger among others. Two isolates (related to Guignardia sp. and Neusartoya sp.) showed strong antimicrobial (and antifungal) activity whereas the rest showed no activity. Compounds were isolated from both isolates and screened using HPLC. Both isolates displayed chemically very interesting chromatograms as they possessed a high diversity of basic chemical structures and peaks over a wide range of polarities, with structures similar to Trimeric catechin and Helenalin among others. For bioremediation assessment, the results showed maximum biosorption capacity for two isolates related to Curvularia sp. and Neusartorya sp., with the former removing 25 mg Cu/g biomass and the latter removing 24 mg Zn/g biomass. Our results indicated the potential of mangrove endophytic fungi in producing bioactive compounds and also highlighted their potential for the treatment of heavy metal-contaminated wastewater

Features in the vertical structure of the meridional flow field over the continental rise east of Abaco, the Bahamas

Since Spring 2004, the RAPID-MOC mooring array (Monitoring the Atlantic Meridional Overturning Circulation at 26.5N) and the MOCHA array (Meridional Overturning Circulation and Heat-flux Array), have been a system continuously monitoring the Atlantic Meridional Circulation (MOC) in the subtropical North Atlantic. Using two year long current meter records (2004-2006), along with historical data (1986 – 1997), as decribed by Lee et.al. (1990) and Lee et.al. (1996) of the western boundary moorings, we analyze the vertical structure of the complex flow field in the Antilles Current (AC)/ Deep Western Boundary Current (DWBC) regim

Spatial and temporal dynamics of suspended sediment concentrations in coastal waters of the South China Sea, off Sarawak, Borneo: ocean colour remote sensing observations and analysis

High-quality ocean colour observations are increasingly accessible to support various monitoring and research activities for water quality measurements. In this paper, we present a newly developed regional total suspended solids (TSSs) empirical model using MODIS Aqua's Rrs(530) and Rrs(666) reflectance bands to investigate the spatial and temporal variation in TSS dynamics along the southwest coast of Sarawak, Borneo, with the application of the Open Data Cube (ODC) platform. The performance of this TSS retrieval model was evaluated using error metrics (bias = 1.0, MAE = 1.47, and RMSE = 0.22, in milligrams per litre) with a log10 transformation prior to calculation as well as using a k-fold cross-validation technique. The temporally averaged map of the TSS distribution, using daily MODIS Aqua satellite datasets from 2003 until 2019, revealed that large TSS plumes were detected – particularly in the Lupar and Rajang coastal areas – on a yearly basis. The average TSS concentration in these coastal waters was in the range of 15–20 mg L−1. Moreover, the spatial map of the TSS coefficient of variation (CV) indicated strong TSS variability (approximately 90 %) in the Samunsam–Sematan coastal areas, which could potentially impact nearby coral reef habitats in this region. Study of the temporal TSS variation provides further evidence that monsoonal patterns drive the TSS release in these tropical water systems, with distinct and widespread TSS plume variations observed between the northeast and southwest monsoon periods. A map of relative TSS distribution anomalies revealed strong spatial TSS variations in the Samunsam–Sematan coastal areas, while 2010 recorded a major increase (approximately 100 %) and widespread TSS distribution with respect to the long-term mean. Furthermore, study of the contribution of river discharge to the TSS distribution showed a weak correlation across time at both the Lupar and Rajang river mouth points. The variability in the TSS distribution across coastal river points was studied by investigating the variation in the TSS pixels at three transect points, stretching from the river mouth into territorial and open-water zones, for eight main rivers. The results showed a progressively decreasing pattern of nearly 50 % in relation to the distance from shore, with exceptions in the northeast regions of the study area. Essentially, our findings demonstrate that the TSS levels on the southwest coast of Sarawak are within local water quality standards, promoting various marine and socio-economic activities. This study presents the first observation of TSS distributions in Sarawak coastal systems with the application of remote sensing technologies and aims at enhancing coastal sediment management strategies for the sustainable use of coastal waters and their resources.</p

Investigating quorum-quenching marine bacilli as potential biocontrol agents for protection of shrimps against Early Mortality Syndrome (EMS)

Early Mortality Syndrome (EMS) has been a major problem for shrimp aquaculture in Southeast Asia due to its epizootic prevalence within the region since the first reported case in 2009. This study explores the application of halophilic marine bacilli isolated from coral mucus and their quorum-quenching abilities as potential biocontrol agents in aquaculture systems to combat the causative agent of EMS, Vibrio parahaemolyticus. N-acylhomoserine lactone (AHL)-degrading (AiiA) activity was first screened by PCR then confirmed by bio-reporter assay, and a combination of 16S rDNA sequence analysis and quantitative phenotype assays including biofilm-formation and temperature-growth responses were used to demonstrate diversity amongst these quorum-quenching isolates. Three phenotypically distinct strains showing notable potential were chosen to undergo co-cultivation as a method for strain improvement via long term exposure to the pathogenic V. parahaemolyticus. The novel approach taken led to significant improvements in antagonism and quorum quenching activities as compared to the ancestral wild-type strains and offers a potential solution as well as pathway to improve existing beneficial microbes for one of the most pressing issues in shrimp aquacultures worldwide

Nitrous oxide and methane in two tropical estuaries in a peat-dominated region of northwestern Borneo

Estuaries are sources of nitrous oxide (N2O) and methane (CH4) to the atmosphere. However, our present knowledge of N2O and CH4 emissions from estuaries in the tropics is very limited because data are scarce. In this study, we present first measurements of dissolved N2O and CH4 from two estuaries in a peat-dominated region of northwestern Borneo. Two campaigns (during the dry season in June 2013 and during the wet season in March 2014) were conducted in the estuaries of the Lupar and Saribas rivers. Median N2O concentrations ranged between 7.2 and 12.3 nmol L−1 and were higher in the marine end-member (13.0 ± 7.0 nmol L−1). CH4 concentrations were low in the coastal ocean (3.6 ± 0.2 nmol L−1) and higher in the estuaries (medians between 10.6 and 64.0 nmol L−1). The respiration of abundant organic matter and presumably anthropogenic input caused slight eutrophication, which did not lead to hypoxia or enhanced N2O concentrations, however. Generally, N2O concentrations were not related to dissolved inorganic nitrogen concentrations. Thus, the use of an emission factor for the calculation of N2O emissions from the inorganic nitrogen load leads to an overestimation of the flux from the Lupar and Saribas estuaries. N2O was negatively correlated with salinity during the dry season, which suggests a riverine source. In contrast, N2O concentrations during the wet season were not correlated with salinity but locally enhanced within the estuaries, implying that there were additional estuarine sources during the wet (i.e., monsoon) season. Estuarine CH4 distributions were not driven by freshwater input but rather by tidal variations. Both N2O and CH4 concentrations were more variable during the wet season. We infer that the wet season dominates the variability of the N2O and CH4 concentrations and subsequent emissions from tropical estuaries. Thus, we speculate that any changes in the Southeast Asian monsoon system will lead to changes in the N2O and CH4 emissions from these systems. We also suggest that the ongoing cultivation of peat soil in Borneo is likely to increase N2O emissions from these estuaries, while the effect on CH4 remains uncertain

Initial screening of mangrove endophytic fungi for antimicrobial compounds and heavy metal biosorption potential

Endophytic fungi provide protection to their host plant and the fungi often produce antimicrobial compounds to aid the host fighting off pathogens. These bioactive compounds were secondary metabolites which were often produced as waste- or by-products. In the present study, endophytic fungi isolated from mangrove plants and soils were characterized and their antimicrobial production and bioremediation potential of heavy metals copper (Cu) and zinc (Zn) were assessed. Twelve (12) isolated and identified endophytic fungi belonged to seven species; Penicillium, Curvularia, Diaporthe, Aspergillus, Guignardia, Neusartorya and Eupenicillium. Antimicrobial activities of these 12 fungal endophytes were tested against Gram negative bacteria; Bacillus subtilis, Staphylococcus aureus, Gram positive bacteria; Escherichia coli and fungi; Candida albicans and Aspergillus Niger among others. Two isolates (related to Guignardia sp. and Neusartoya sp.) showed strong antimicrobial (and antifungal) activity whereas the rest showed no activity. Compounds were isolated from both isolates and screened using HPLC. Both isolates displayed chemically very interesting chromatograms as they possessed a high diversity of basic chemical structures and peaks over a wide range of polarities, with structures similar to Trimeric catechin and Helenalin among others. For bioremediation assessment, the results showed maximum biosorption capacity for two isolates related to Curvularia sp. and Neusartorya sp., with the former removing 25 mg Cu/g biomass and the latter removing 24 mg Zn/g biomass. Our results indicated the potential of mangrove endophytic fungi in producing bioactive compounds and also highlighted their potential for the treatment of heavy metal-contaminated wastewate

Isolation, Identification and Screening of Antimicrobial Properties of the Marine-Derived Endophytic Fungi from Marine Brown Seaweed

Marine seaweeds are known to produce valuable medicinal compounds such as antioxidants and anticoagulants, and have been reported to display antimicrobial activity against gram positive and gram negative bacteria. Several studies have identified so-called endophytic fungi living inside their hosts as the source of active compounds. In this study marine brown seaweed, Padina sp., was studied with regards to their endophytic fungi to assess if they are the source of the reported antimicrobial activity. Twenty fungal isolates were isolated from Padina sp. collected off Talang-Talang Island, Sarawak, Malaysia. All isolates were screened for their antimicrobial properties and 11 out of 20 isolates displayed positive results. DNA was successfully extracted for five isolates and sequence analysis grouped all of them with other endophytic fungi. “Fungus 2” seems to be related to a so far uncultured endophytic fungus. “Fungus 19” showed the most promising antimicrobial properties and was chosen for further agar well assay and cytotoxicity testing. Its ethyl-acetate extract showed positive results in the agar well assay and also a cytotoxic effect on Artemia nauplii. The extract was screened using HPLC and showed a compound similar to a known anti-cancer compound, dihydromyricetin, which is also an anti-intoxicant, anti-inflammatory and anti-oxidative agent which may be responsible for the observed antimicrobial activity

Temperature and Salinity Profiling Analysis off Sarawak Waters, Malaysia

Prime Scientific Sailing Expedition (EPSP 2009), was carried out in the South China Sea (SCS) along Sarawak waters for nine days from 20 to 29 June 2009. The main objective was to enhance physical oceanography data to support the management of marine ecosystem and other marine resources off Sarawak waters. The main purpose of this present study is to construct vertical temperature and salinity structures off Sarawak waters and to define the water properties based on differ water depths. The temperature and salinity data were obtained using Conductivity-Temperature-Depth (CTD) from sea surface down to 523 m water depth. The measurement was done along the transect line that consists of 60 sampling stations involved with furthest distance offshore at ~471 km. Vertical profiles of temperature, salinity and temperature-salinity (T-S) diagrams of each station were plotted and analyzed based on location and water depth. Offshore sampling stations at water depth greater than 50 m are known as deep waters while near shore sampling station at water depth less than 50m is known as shallow waters. The constructed vertical profiles showed that as water depth increases, salinity increases whereas temperature decreases. Comparison of minimum and maximum temperature range of shallow and deep waters is 15°C and 1°C respectively. However, there is only 0.71°C difference of salinity between minimum salinity of shallow waters and deep waters. The seawater variable of Sarawak waters are impacted by the distance from mainland and its geographical location as well as the rivers influx into the SCS. Constant climate change due to seasonal monsoon and high rainfall as it is located in the tropical region contribute to the spatial temperature and salinity in this area. High rivers runoff into the SCS can reduce the salinity of the water at coastal area. Salinity increases as sampling location further offshore. High rainfall may decreases water temperature and salinity at water surface