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Lake Tana is Ethiopia’s largest lake and is infested with invasive water hyacinth (E. crassipes), which endangers the lake’s biodiversity and habitat. Using appropriate remote sensing detection methods and determining the seasonal distribution of the weed is important for decision-making, water resource management, and environmental protection. As the demand for the reliable estimation of E. crassipes mapping from satellite data grows, comparing the performance of different machine learning algorithms could help in identifying the most effective method for E. crassipes detection in the lake. Therefore, this study aimed to examine the ability of random forest (RF), support vector machine (SVM), and classification and regression tree (CART) machine learning algorithms to detect E. crassipes and estimating seasonal spatial coverage of the weed on the Google Earth Engine (GEE) platform using Landsat 8 and Sentinel 2 images. Cloud-masked monthly median composite Landsat 8 and Sentinel 2 data from October 2021 and 2022, January 2022 and 2023, March 2022, and June 2022 were used to represent autumn, winter, spring, and summer, respectively. Four spectral indices were derived and used in combination with spectral bands to improve the E. crassipes detection accuracy. All methods achieved greater than 95% and 90% overall accuracy when using Sentinel 2 and Landsat 8 images, respectively. Using both data sets, all methods achieved a greater than 93% F1 score for E. crassipes detection. Though the difference in performance between the methods was small, the RF was the most accurate, while the SVM and CART methods had the same accuracy. The maximum E. crassipes coverage area was observed in autumn (22.4 km2), while the minimum (2.2 km2) was observed in summer. Based on Sentinel 2 data, the E. crassipes area coverage decreased significantly by 62.5% from winter to spring and increased significantly by 81.7% from summer to autumn. The findings suggested that the RF classifier was the most accurate E. crassipes detection algorithm, and autumn was an appropriate season for E. crassipes detection in Lake Tana.

Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.

The most widely used method for measuring bacterial production is tritium-labeled leucine (3H-Leu). Although this method provides methodological simplicity and high sensitivity, the employment of radioactive isotopes is often restricted by regulations, particularly in field settings. In this study, we developed a non-radioactive method for measuring bacterial productivity based on the protein synthesis rate, using deuterium-labeled leucine ((CD3)2CDCD2CD(NH2)COOH; D10-Leu); the proposed method was then compared and verified with the3H-Leu method. The procedures of the proposed method are (1) incorporation of D10-Leu by bacteria, (2) acid hydrolysis (HCl) to amino acids and (3) quantification of D10-Leu (m/z142.10) by liquid chromatography mass spectrometry (LC-MS/MS). In the LC-MS/MS analysis, we detected a larger amount of D9-Leu (m/z141.10) and D8-Leu (m/z140.10) than that of D10-Leu, suggesting that incorporated D10-Leu was rapidly metabolized such as in deamination and aminotransferase reactions. The incorporation rates of D10-Leu, D10-Leu + D9-Leu (D10+D9-Leu) and D10-Leu + D9-Leu + D8-Leu (D10+D9+D8-Leu) were significantly positively correlated to that of3H-Leu, confirming the validity of the proposed method. Since D7-Leu (m/z139.10) could not be detected, the amount of exogenous leucine incorporated into protein can be accurately estimated through D10+D9+D8-Leu measurement. The new compound-based quantification method using stable isotope-labeled leucine can be a powerful tool to estimate pure protein synthesis rate for measuring bacterial production.

Microalgae are widely utilized in commercial industries. The addition of a modified artificial medium (soil extract) could enhance their growth. Soil extract collected from the Raja Musa peat swamp and mineral soil from the Ayer Hitam Forest Reserve (AHFR), Selangor, Malaysia, were treated using various extraction methods. Carteria radiosa PHG2-A01, Neochloris conjuncta, and Nephrochlamys subsolitaria were grown in microplates at 25 °C, light intensity 33.75 µmol photons m−2s−1 for 9 days. N. conjuncta dominated the growth in 121 °C twice extraction method AFHR samples, with 47.17% increment. The highest concentrations of ammonia and nitrate were detected in the medium with soil extract treated with 121 °C twice extraction method, yielding the concentrations of 2 mg NL−1 and 35 mg NL−1 for ammonia and nitrate of RM soil and 2 mg NL−1 and 2.85 mg NL−1 for the AH soil. These extracts are proved successful as a microalgal growth stimulant, increasing revenue and the need for enriched medium. The high rate of nutrient recovery has the potential to serve as a growth promoter for microalgae.

The assessment of water-extractable organic matter using an autoclave can provide useful information on physical, chemical, and biological changes within the soil. The present study used virgin forest soils from Chini Forest Reserve, Langkawi Island, and Kenyir Forest Reserve (Malaysia), extracted using different extraction methods. The dissolved organic carbon (DOC), total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and ammonium-nitrate content were higher in the autoclave treatments, up to 3.0, 1.3, 1.2, and 1.4 times more than by natural extraction (extracted for 24 h at room temperature). Overall, the highest extractable DOC, TDN, TDP, ammonium and nitrate could be seen under autoclaved conditions 121 °C 2×, up to 146.74 mg C/L, 8.97 mg N/L, 0.23 mg P/L, 5.43 mg N mg/L and 3.47 N mg/L, respectively. The soil extracts became slightly acidic with a higher temperature and longer duration. Similar trends were observed in the humic and nonhumic substances, where different types of soil extract treatments influenced the concentrations of the fractions. Different soil extraction methods can provide further details, thus widening the application of soil extracts, especially in microbes.

Soil extracts are useful nutrients to enhance the growth of microalgae. Therefore, the present study attempts for the use of virgin soils from Peninsular Malaysia as growth enhancer. Soils collected from Raja Musa Forest Reserve (RMFR) and Ayer Hitam Forest Reserve (AHFR) were treated using different extraction methods. The total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and dissolved organic carbon (DOC) concentrations in the autoclave methods were relatively higher than natural extraction with up to 132.0 mg N/L, 10.7 mg P/L, and 2629 mg C/L, respectively for RMFR. The results of TDN, TDP, and DOC suggested that the best extraction methods are autoclaved at 121 &deg, C twice with increasing 87%, 84%, and 95%, respectively. Chlorella vulgaris TRG 4C dominated the growth at 121 &deg, C twice extraction method in the RMRF and AHRF samples, with increasing 54.3% and 14%, respectively. The specific growth rate (&micro, ) of both microalgae were relatively higher, 0.23 d&minus, 1 in the Ayer Hitam Soil. This extract served well as a microalgal growth promoter, reducing the cost and the needs for synthetic medium. Mass production of microalgae as aquatic feed will be attempted eventually. The high recovery rate of nutrients has a huge potential to serve as a growth promoter for microalgae.

Natural growth-promoting nutrients extracted from aquaculture sludge waste can be used to maximise microalgal growth. This study identified the influence of aquaculture sludge extract (SE) on four microalgae species. Conway or Bold's Basal Media (BBM) was supplemented with SE collected from a Sabak Bernam shrimp pond (SB) and Kota Puteri fish pond (KP), and tested using a novel microplate-incubation technique. Five different autoclave extraction treatment parameters were assessed for both collected SE, i.e., 1-h at 105 °C, 2-h at 105 °C, 1-h at 121 °C, 2-h at 121 °C, and 24-h at room temperature (natural extraction). Microalgae culture in the microplates containing control (media) and enriched (media + SE) samples were incubated for nine days, at 25 °C with the light intensity of 33.75 μmol photons m−2 s−1 at 12-h light/dark cycle. The total dissolved nitrogen (TDN) and total dissolved phosphorus (TDP) in KP SE were 44.0–82.0 mg L−1 and 0.96–8.60 mg L−1. TDN (8.0%–515.0%) and TDP (105%–186 %) were relatively higher in KP SE compared to SB SE. The growth of microalgae species Nannochloropsis ocenica showed significant differences (p < 0.05) between the five extraction treatments from SB and the control. However, Chlorella vulgaris, Neochloris conjuncta, and Nephroclamys subsolitaria showed no significant differences (p > 0.05) in SB SE. N. ocenica, C. vulgaris, and N. conjuncta showed significant differences (p < 0.05) between five extraction treatments from KP and the control while N. subsolitaria showed no significant difference (p > 0.05). The specific growth rate (SGR) in the exponential phase of all microalgae species were relatively higher in SB SE compared to KP SE. While the organic matter content of KP SE was relatively higher, there were no significant differences in microalgae growth compared to SB SE. Nonetheless, modified SE did influence microalgae growth compared to the control. This study shows that modified SE could be used as enrichment media for microalgae cultivation., Aquaculture sludge extracts, Autoclave extraction parameters, Chlorella vulgaris, Nannochloropsis ocenica, Neochloris conjuncta, Nephroclamys subsolitaria, Agricultural Science; Environmental Science; Earth Sciences

The tropical climate is seemingly stable with little variation in environmental factors throughout the year. However, a growing number of studies have reported monsoon-driven changes in zooplankton communities in tropical waters. This study examined the monsoonal and spatial variation in the zooplankton community in Sepanggar Bay, Malaysia. Samples were collected from 9 stations throughout the bay in June and October 2017, March and June 2018, coinciding with the southwest monsoon (SWM), northeast monsoon (NEM) and the intermonsoon periods (INTER). Significant seasonal difference was observed for the measured hydrographic parameters (chlorophyll-a, salinity, temperature) with highest values recorded during INTER for chlorophyll-a, NEM for salinity, and SWM 2 for temperature. Throughout the study, 110 zooplankton taxa were identified, and copepods dominated total zooplankton abundance by 70%. Zooplankton abundance increased from 17925 ± 8616 inds. m − 3 during SWM 1 to peak at 47628 ± 55488 inds. m − 3 during INTER and reached a minimum of (16136 ± 22334 inds. m − 3 during NEM. Zooplankton abundances were relatively higher at nearshore stations compared with offshore stations, but was not statistically significant. Four distinct assemblages were obtained from Hierarchical Cluster analysis (HCA), suggesting the influence of monsoon in shaping the zooplankton community. The dominant zooplankton shifted from copepods during SWM1, INTER, and NEM, to tintinnids during SWM 2. Canonical Correspondence Analysis (CCA) revealed temperature and salinity to be strongly associated with zooplankton community, indicating seasonal variations in these environmental factors driven by monsoon which influenced the zooplankton community structure in the bay. Distinct shifts in the zooplankton composition and abundance relative to the monsoon seasons provide new insights into the seasonal sensitivity of zooplankton in tropical coastal ecosystems.

Daily field surveys were conducted at a coastal-shelf station in Sagami Bay, Japan after the passage of typhoon Malou in 2010 to evaluate the after-effect of a typhoon passage on the physical-chemical environment, phytoplankton bloom formation and microbial processes within and below the euphotic layer. The passage of Malou induced an abrupt decrease in salinity and increased loading of nutrients to the euphotic layer. Dinoflagellates dominated the phytoplankton community at the surface, whereas diatoms dominated below the surface just after the passage of Malou. Four days later, the dominant dinoflagellate taxa at the surface changed from Protoperidinium spp. to Prorocentrum spp. and Ceratium spp., indicating a dinoflagellate community succession from heterotrophic to autotrophic functional groups. Five days after passage, the dominant phytoplankton taxa shifted from dinoflagellates to diatom groups of Chaetoceros spp. and Cerataulina spp. throughout the water column. Below the euphotic layer, there were increases in diatom frustules, mainly composed of Chaetoceros spp. and Cerataulina spp., bacterial abundance and NH4+ concentrations. Diatom carbon biomass contributed to approximately half of particulate organic carbon (POC) below the euphotic layer, suggesting a significant contribution of diatoms to POC sinking flux after the passage of a typhoon. Bacterial abundance was positively correlated to both phaeopigment concentrations (p

GCOM-C/SGLI is a multi-wavelength optical radiometer launched on December 23, 2017. The data provision has started from December 20, 2018. In this research, we briefly introduce standard Level 2 products and their validation results based on in situ data. Mean absolute percentage differences are 16.3 - 69.6% for NLW between 380 - 670 nm, 39 and 64.5% for AOT at 670 nm and 865 nm, 27.9% for CHL and 44.2% for aCDOM. Although the number of in situ validation data are still scare for a few ocean color products, the accuracy of GCOM-C/SGLI data will be improved by our future efforts of calibration/validation activities.

This study aimed to clarify the vertical differences in bacterial growth and grazing pressure on bacteria by heterotrophic nanoflagellates (HNF) and to identify the controlling factors of bacterial growth in temperate coastal waters of Sagami Bay, Japan. In addition to environmental factors, the annual monthly variations in bacterial growth rate (BGR) and the relative abundance of bacteria to HNF (BA/HNFA) were investigated in the euphotic and disphotic layers between May 2012 and May 2013. Significant vertical differences in BGR and BA/HNFA were evident between the two layers during the thermal stratification times of May to October 2012 and April to May 2013. BGR indicated significantly stronger limitation of bacterial growth in the euphotic layer compared to the disphotic layer. In contrast, significantly lower BA/HNFA was observed in the euphotic layer, suggesting significantly higher grazing pressure on bacteria by HNF. However, significant differences in BGR and BA/HNFA were not observed between the two layers from November 2012 to Match 2013, when the water column was well-mixed vertically due to the cooling and wind-induced mixing of surface water. This study indicates that bacteria in the euphotic layer grow less actively and are more vulnerable to predatory grazing by HNF relative to the disphotic layer during the stratification period. Further, multiple regression analyses indicate that bacterial growth was most controlled by the concentrations of chlorophyll a and dissolved organic carbon in the euphotic and disphotic layers, respectively.

Monsoon-driven changes of environmental factors have been reported to be significantly variable and affects the phytoplankton community in tropical waters. This study examined the monsoonal changes of environmental parameters and the coastal phytoplankton community, including potential harmful algal bloom species, in the waters of Kota Kinabalu, Sabah, Malaysia. Bi-weekly observations were conducted from August 2017 to January 2019, covering the Southwest Monsoon (SWM), Northeast Monsoon (NEM), and inter-monsoon periods (IMPs). Sea surface temperature, salinity, and daily average photosynthetic active radiation (PAR) were significantly different between the SWM and the NEM. Total phytoplankton densities were significantly higher in the SWM with median cell densities of 1.12 × 104 cells L−1 compared to the NEM with 3.98 × 103 cells L−1. Nutrient measurements indicated that the waters were mesotrophic, with low phosphate (P) levels ( μ M-P on average). N:P ratios were often above the Redfield ratio (16N:1P), while high Si:N (>1) and Si:P ratios (>16Si:1P) indicated that silicate was not limiting, a condition favourable for diatom growth. Phytoplankton dynamics shifted from a dinoflagellate-dominant community (Protoperidinium spp. and Prorocentrum spp.) to a diatom-dominant community (Leptocylindrus spp. and Dactyliosolen spp.) during the NEM, which was preceded by a peak in silicate and nitrate. Later, Chaetoceros spp. became dominant during the second SWM. The presence of intermittent increases in Margalefidinium polykrikoides and Pyrodinium bahamense var. compressum cell densities may trigger future blooms in these waters. Canonical Correspondence Analysis suggests that the dinoflagellate-dominant community was driven by changes in PAR and Si:N while changes in N:P and salinity shaped the diatom-dominant community. The shifts of the phytoplankton community composition in relation to the different monsoonal periods suggests that the monsoons function as environmental drivers which structure the phytoplankton community of this coastal ecosystem.

After the passage of typhoon Malou in 2010, daily field samplings were conducted at both inshore (Sta. A) and offshore (Sta. M) stations in Sagami Bay, Japan, to evaluate responses of bacteria and phytoplankton to variations of physical-chemical environments induced by typhoon passage. Malou passage caused an abrupt decline of salinity and a large increase in the amount of nutrients at both stations. The relationships between salinity and nutrient concentrations suggested that major nutrient sources were terrestrial runoff at Sta. M and sediment resuspension in addition to terrestrial runoff at Sta. A. Bacterial production (BP) at Sta. A showed 114 ± 21 mg C m −3 d −1 one day after Malou passage, while primary production (PP) was 76 ± 8 mg C m −3 d −1 , suggesting the dominance of BP (BP/PP ratio = 1.5). PP exceeded BP two days after Malou passage, and then reached a maximum of 554 ± 32 mg C m −3 d −1 five days later (BP/PP ratio = 0.10). PP was always dominant at Sta. M throughout the study period (BP/PP ratio = 0.13 ± 0.05). The ratio of BP to bacterial abundance (BP/BA ratio) at Sta. M showed a positive correlation with PP, suggesting that bacterial productivity depended on autochthonous substrates derived from phytoplankton. The BP/BA ratio at Sta. A showed no relationship with PP, suggesting that bacterial productivity was enhanced not only by PP, but also loading of allochthonous substrates. BP/BA ratios at both stations increased exponentially with the increase of PO 4 and NH 4 concentrations; these concentrations are likely coming from sediment pore waters. The results suggest that sediment resuspension induced by typhoon passage enhanced bacterial productivity abruptly just after the passage at an inshore station. The bacterial response could be regulated by difference in relative contribution of nutrient sources after the passage of typhoon.

The 18-year time-series shows in situ ultraviolet radiation (UVR) and photosynthetically active radiation (PAR) diffuse attenuation coefficient K d (λ) have recurrent seasonal variability of high/low attenuation during summer/winter months, respectively, dependent on variability in water column stratification and concentrations of bio-optical properties. The mid-latitude coastal survey station displayed significant seasonality of the mixed layer depth (MLD) between 12 and 82 m which modified the distribution of chlorophyll a (4.6–24.9 mg m −2 ) and absorption of colored dissolved organic matter [ a CDOM (320 nm) 0.043–1.34 m − 1 ]. The median K d (320 nm) displayed significant seasonality at 0.19–0.74 m − 1 (C.V. = 44.1%) and seasonal variability within the euphotic layer [ Z 10% (320 nm) = 7–20%]. High attenuation of UVR with relatively moderate attenuation of PAR was consistently observed during the summer months when increased concentrations of terrestrially derived CDOM coupled with a shallow MLD were present. The winter season showed the opposite of low UVR and PAR attenuation due to a relatively deeper MLD coupled with low concentrations of bio-optical properties. Although the long term K d (λ) did not vary significantly during the time-series, analysis of the interannual variability suggests there are positive and negative phases following the Pacific Decadal Oscillation (PDO) vis-a-vis variability in bio-optical properties ( p

Accurate determination of the diurnal variability and daily insolation of surface (0(+) ) and subsurface (0(-) ) irradiance are essential to estimate several physical, chemical and biological processes occurring at the surface layer of marine environments. Natural downwelling PAR and spectral UVR were examined on eight occasions at 0(+) and 0(-) to refine empirical models, particularly in the UVR spectrum. The diurnal variability in UVR and PAR were wavelength dependent and were modeled by a sinusoidal equation. The best fit for PAR at 0(+) and 0(-) was the sinusoid power of n = 2 and n = 2.5, respectively. In the UVR spectrum, sinusoids increased as wavelengths decreased ranging from n = 2-5. Higher n values in the UV-B spectrum suggest sharper increase/decrease near sunrise and sunset hours, ultimately reducing the final value of daily insolation at specified wavelengths. Calculated daily insolation of UV-B/(UV-A + PAR) ratio suggests that photoinhibition from exposure to UV-B occurs within a shorter biologically effective day length than PAR, and is high during summer and low during winter. These results suggest that biogeochemical calculations based on diurnal models of irradiance measurements would benefit from accurate solar noon references and wavelength specificity, particularly in the UVR spectrum.

Developing rapid in situ optical detection techniques for discriminating the potential for harmful algal blooms is an ongoing goal for scientists around the world. The utility of a profiling 9-wavelength Multi-Exciter fluorometer in concert with other bio-optical measurements was examined using isolate cultures in the laboratory and a field survey in the East Johor Strait, Singapore. Background bio-optical measurements of field isolate cultures confirmed the difficulty in discerning between diatoms and dinoflagellates, although raphidophytes and the dinoflagellate Karlodinium sp. did show unique bio-optical signatures. Significant relationships were found between the Multi-Exciter 470 nm signal and traditional chlorophyll a pigment measurements both in the laboratory and field ( p a specific-absorbance and -fluorescence relationships showed the potential for identifying phytoplankton groups based on the slope of the relationship between them. The 6-station field survey in the East Johor Strait displayed relatively shallow depths (5.06 ± 0.81 m), warm temperatures (29.88 ± 0.26 °C), low salinity (25.81 ± 1.48) and high phytoplankton biomass (17.6 ± 11.7 μg Chl- a L − 1 ). Absorbance and Multi-Exciter fluorometric measurements from the field did not reveal similar optical signatures from studied laboratory isolates, although the 435 nm:570 nm and 470 nm:525 nm fluorometric ratios displayed distinct profile responses. However, these wavelength-to-wavelength ratio signatures were not identified, and further investigation is required. The results suggest that in situ fluorometry coupled with phytoplankton absorption properties could assist in defining bloom parameters and enhance our ability in determining and detecting pre-bloom conditions.

Cyanobacteria are important organisms in the marine ecosystem as they play vital roles in nutrient cycling and oxygen production. In this study, tropical marine cyanobacterial communities from various sites in Southeast Asia and their associated ecological parameters were examined. 16S rRNA sequences of 1502 bp were obtained for barcode amplicon sequencing using the Nanopore MinION™ sequencing platform. Planktonic and benthic cyanobacteria were observed with total of 40 genera and 46 species of cyanobacteria identified from sites in Sabah and Singapore. Species richness analyses showed that the cyanobacterial community from the West Johor Strait was approximately two times greater than that of the East Johor Strait and the Singapore Strait. This is due to the variability in ecological parameters measured between sites such as rainfall, salinity and temperature. This is the first study that has employed this technology for phytoplankton samples with species resolution, providing insight to the diversity of cyanobacteria present in tropical marine ecosystems. Furthermore, the portability of this sequencer enables the real-time monitoring of coastal environments for the specific detection and identification of harmful algal bloom species.

In order to test the hypothesis that the microbial enrichment in the sea-surface microlayer (SML) over coral reefs is significant, we investigated the abundance and production of the microbial community in the SML and sub-surface water (SSW) at a fringing coral reef of Malaysia. Samples were taken at 2 coral sites with different live coral coverage as well as one offshore site. We detected substantially high enrichment factors (EFs) in abundance (where EF = SML/SSW: the ratio of microbial abundance in the SML relative to SSW) for all biological groups at all sites: up to 6.0 for heterotrophic bacteria, 4.2 for cyanobacteria, 18.8 for autotrophic nanoflagellates and 22.6 for heterotrophic nanoflagellates. We also found that the enrichment factors of microorganisms in coral reefs were remarkably higher than in other marine ecosystems, and a higher concentration of microorganisms was observed in the higher coral coverage site, probably due to higher organic matter released by corals. The higher microbial abundance in the SML over coral reefs may enhance gaseous exchange and carbon flow in the food web through the air–sea interface.

The East coast of Peninsular Malaysia is strongly influenced by the North-East (NE) monsoon, and may significantly influence the optical environment of coral-reef ecosystems. However, our knowledge of temporal variability, including episodic events, of environmental factors in Asian tropical regions is still limited. The objectives of this study were to (1) observe temporal variability in ultraviolet radiation (UVR) and photosynthetically active radiation (PAR) attenuation and (2) determine the bio-optical factors regulating the optical environment in shallow coral-reef waters. Downwelling UVR and PAR irradiance and in situ bio-optical factors were measured monthly near Bidong Island on the East coast of Peninsular Malaysia from June 2010 to June 2011. The NE monsoon was recognized between November 2010 and January 2011. The highest diffuse attenuation coefficient at 305 nm was 2.05 ± 0.03 m−1 in a coral-reef area on December 2010. The most significant bio-optical factor at 305, 380, 440 nm during the NE monsoon season was CDOM (89 ± 8% at 305 nm, 84 ± 9% at 380 nm and 49 ± 17% at 440 nm). All UVR attenuation coefficients showed significant correlations with the CDOM absorption coefficients (aCDOM). CDOM with relatively low S275-295 during the NE monsoon season (0.0177 ± 0.0020 nm−1) suggests terrestrial sources, which is also supported by the correlation between salinity and aCDOM(305). A significant correlation between S275-295 and the carbon specific absorbance coefficient (a*(305)) suggest the potential to measure DOC optically in these waters. The high CDOM during the NE monsoon season may have an important role to reduce harmful UVR exposure reaching benthic communities.

Biologically diverse coral-reef ecosystems are both directly and indirectly susceptible to changes in the spectral ultraviolet radiation (UVR) distribution. The purpose of this study was to (1) measure the variability of UVR and photosynthetically active radiation (PAR) penetration in the water above coral reefs around the Malaysian peninsula, (2) measure the variability and distribution of UVR-specific biogeochemical factors, and (3) determine the impact of biogeochemical variability as it affects the UVR:PAR ratio. Downwelling UVR and PAR irradiance and bio-optically derived biogeochemical factors were measured at 14 coral survey stations around the Malaysian peninsula from August 10–29, 2007. The West Coast was characterized by relatively shallow mean 10% UV-B (320 nm) penetration (1.68 ± 1.12 m), high chlorophyll (3.00 ± 4.72 μg l−1), high chromophoric dissolved organic matter (CDOM; 6.61 ± 3.31 ppb), high particulate organic carbon (POC; 190.65 ± 97.99 mg m−3), and low dissolved organic carbon (DOC; 1.34 ± 0.65 mg m−3). By contrast, the East Coast was characterized by relatively deep mean 10% UV-B penetration (5.03 ± 2.19 m), low chlorophyll (0.34 ± 0.22 μg l−1), low CDOM (1.45 ± 0.44 ppb), low POC (103.21 ± 37.93 mg m−3), and relatively high DOC (1.91 ± 1.03 mg m−3). The UVR:PAR ratio was relatively higher on the East Coast relative to the West Coast, suggesting variable concentrations of UVR-specific absorbing components. At all sites, UVR attenuation coefficients showed significant correlations with CDOM, but were spatially dependent with regard to chlorophyll a, POC, and DOC. The results suggest that bio-optically significant CDOM and DOC factors are uncoupled in coral-reef communities of Malaysia. Furthermore, the results support prior studies that show chromophorically active concentrations of DOM and POC are significantly altering the amount of UVR penetration above coral reefs and may be notable factors in regulating intricate biogeochemical cycles around benthic coral communities in Malaysia.

Buoy-mooring platforms are advantageous for time-series validation and vicarious calibration of ocean color satellites because of their high temporal resolution and ability to perform under adverse weather conditions. Bio-optical data collected on the Bermuda Testbed Mooring (BTM) were used for comparison with satellite ocean color data in an effort to further standardize sampling and data processing methods for high quality satellite-mooring comparisons. Average percentage differences between satellite-measured and mooring-derived water leaving radiances were about 20% at the blue wavelengths, decreasing to as low as 11% in the blue-green to green wavebands. Based on a series of data processing methods and analyses, recommendations concerning rigor of quality control for collected data, optimal averaging of high-frequency data, sensor self-shading wind corrections, and instrumentation placement requirements are given for the design and application of optical moorings for ocean color satellite validation. Although buoy-mooring platforms are considered to be among the very best methods to validate ocean color satellite measurements, match-up discrepancies due to water column variability and atmospheric corrections remain important issues.

Macronutrients, photosynthetic pigments, and particle export were assessed in two eddies during the E-Flux I and III cruises to investigate linkages between biogeochemical properties and export flux in Hawaiian lee cyclonic eddies. Cyclone Noah (E-Flux I), speculated to be in the 'decay' stage, exhibited modest increases in macronutrients and photosynthetic pigments at the eddy center compared to ambient waters. Cyclone Opal (E-Flux III) also exhibited modest increases in macronutrient concentrations, but a 2-fold enhancement in total chlorophyll a (TChl a) concentration within the eddy center. As indicated by fucoxanthin concentrations, the phytoplankton community in the deep chlorophyll maximum (DCM) of Opal was comprised mainly of diatoms. During an 8-day time series in the center of Opal, TChl a concentration and fucoxanthin in the DCM decreased by � 50%, which was potentially triggered by silicic acid limitation. Despite the presence of a substantial diatom bloom, Opal did not deliver the expected export of particulate carbon and nitrogen, but rather a large biogenic silica export (� 4-fold increase relative to export in surrounding waters). Results suggest that controls on the life cycle of a Hawaiian lee cyclone are likely a combination of physical (eddy dynamics), chemical (nutrient limitation), and biological (growth and grazing imbalance) processes. Comparisons between Noah and Opal and previously studied cyclones in the region point to a relationship between the spin-up duration of a cyclone and the resulting biological response. Nonetheless, Hawaiian lee cyclones, which strongly influence the biogeochemistry of areas 100's of km in scale in the subtropical North Pacific Ocean, still remain an enigma.

Interdisciplinary observations of mesoscale eddies were made to the west of the island of Hawai’i. A central goal of the studies is to improve our understanding of the coupling of physical, biological, and biogeochemical processes that occur within these eddies. A specific objective was to test the hypothesis that the physical mechanisms of mesoscale eddies result in increases in nutrient availability to the euphotic layer, increases in primary production, changes in biological community compositions and size distributions, and increases in carbon flux to the deep sea. Data were obtained from ships, surface drifters, and satellite sensors during three separate field experiments. Variability was associated with two well-developed cyclonic, cold-core mesoscale eddies, Cyclone Noah and Cyclone Opal, which were observed during the E-Flux I (survey November 6–20, 2004) and E-Flux III (survey March 10–27, 2005) field campaigns, respectively. No mesoscale eddies were found during E-Flux II (survey January 10–19) when winds were erratic in magnitude and direction, supporting the hypothesis that persistent trade winds drive the production of cold-core mesoscale eddies in the lee of the Hawaiian Islands. Cold-core eddies were present in the E-Flux study area for about 2/3 of a year beginning May 1, 2004 and trade winds prevailed for about 3/4 of the same year. Both Cyclone Noah and Cyclone Opal were generated during strong, persistent northeasterly trade wind conditions and appeared downwind of the ’Alenuihaha Channel separating the islands of Maui and Hawai’i. The likely production mechanism for both mesoscale cold-core eddies involves localized wind-stress-curl-induced upwelling produced by trade wind forcing. Cyclone Noah was likely spun up by strong trade winds just to the southwest of the ’Alenuihaha Channel ( ∼ 20 . 10 ∘ N , 156 . 40 ∘ W ) between August 13 and 21, 2004 based on MODIS satellite sea-surface temperature (SST) imagery and QuikScat satellite wind data, and apparently began to dissipate by mid-December 2004. Cyclone Opal was likely spun up by strong trade winds between February 2 and 18, 2005 southwest of the ’Alenuihaha Channel ( ∼ 20 . 30 ∘ N , 156 . 30 ∘ W ), but was no longer evident in April 2005. Both Cyclone Noah and Cyclone Opal had strong physical, chemical, and biological expressions and displayed similar maximum tangential current speeds of ∼ 60 cm s - 1 . However, Cyclone Opal was more symmetric and larger in scale (roughly 180–200 km in diameter compared to ∼ 160 km in horizontal scale for Cyclone Noah). Both mesoscale eddies displayed significant doming in their centers and in some cases outcroppings of isothermal, isopycnal, nutrient, and chlorophyll a isopleths. After formation and a slow drift southward, Cyclone Noah remained in nearly the same location (roughly 19 . 60 ∘ N , 156 . 50 ∘ W ) during the 3-week in situ sampling period, whereas Cyclone Opal drifted southward by ∼ 165 km over a similar time span of sampling. Interestingly, the physical manifestations of both features were relatively unchanged during the ship-based surveys; however, the biology appears to have evolved within Cyclone Opal. The present report sets the context for several other E-Flux studies.

E-Flux III (March 10–28, 2005) was the third and last field experiment of the E-Flux project. The main goal of the project was to investigate the physical, biological and chemical characteristics of mesoscale eddies that form in the lee of Maui and the Island of Hawai’i, focusing on the physical–biogeochemical interactions. The primary focus of E-Flux III was the cyclonic cold-core eddy Opal, which first appeared in the NOAA GOES sea-surface temperature (SST) imagery during the second half of February 2005. During the experiment, Cyclone Opal moved over 160 km, generally southward. Thus, the sampling design had to be constantly adjusted in order to obtain quasi-synoptic observations of the eddy. Analyses of ship transect-depth profiles of CTD, optical and acoustic Doppler current profiler (ADCP) data revealed a well-developed feature characterized by a fairly symmetric circular shape with a radius of about 80 km. Depth profiles of temperature, salinity and density were characterized by an intense doming of isothermal, isohaline and isopycnal surfaces. Isopleths of nutrient concentrations were roughly parallel to isopycnals, indicating the upwelling of deep nutrient-rich water. The deep chlorophyll maximum layer (DCML) shoaled from a depth of about 130 m in the outer regions of the eddy to about 60 m in the center. Chlorophyll concentrations reached their maximum values in Opal's core region (about 40 km in diameter), where nutrients were upwelled into the euphotic layer. ADCP velocity data clearly showed the cyclonic circulation associated with Opal. Vertical sections of tangential velocities were characterized by values that increased linearly with radial distance from near zero close to the center to a maximum of about 60 cm s - 1 at roughly 25 km from the center, and then slowly decayed. The vertical extent of the cyclonic circulation was primarily limited to the upper mixed layer, as tangential velocities decayed quite rapidly within a depth range of 90–130 m. Potential vorticity analysis suggests that only a relatively small (about 50 km in diameter) and shallow (to a depth of approximately 70 m) portion of the eddy is isolated from the surrounding waters. Radial movements of water can occur between the center of the eddy and the outer regions along density surfaces within an isopycnal range of σ – t 23.6 ( σ t = 23.6 kg m - 3 ) and σ – t 24.4 ( σ t = 24.4 kg m - 3 ). Thus the biogeochemistry of the system might have been greatly influenced by these lateral exchanges of water at depth, especially during Opal's southward migration. While the eddy was translating, deep water in front of the eddy might have been upwelled into the core region, leading to an additional injection of nutrients into the euphotic zone. At the same time, part of the chlorophyll-rich waters in the core region might have remained behind the translating eddy and, thus contributed to the formation of an eddy wake characterized by relatively high chlorophyll concentrations.

Quasi-synoptic observations of the horizontal and vertical structure of a cold-core cyclonic mesoscale eddy feature (Cyclone Noah) were conducted in the lee of Hawai’i from November 4–22, 2004 as part of the E-Flux interdisciplinary collaborative research program. Cyclone Noah appears to have spun up to the southwest of the ‘Alenuihaha Channel (between Maui and Hawai’i) as a result of strong and persistent northeasterly trade winds through the channel. Shipboard hydrographic surveys 2.5 months later suggest that Noah weakened and was in a hypothesized spin-down phase of its life cycle. Although the initial surface expression of Noah was limited in scale to ∼40 km in diameter and, as evidenced by surface temperatures, 2–3 °C cooler than the surrounding waters, depth profiles revealed a fully developed semi-elliptical shallow feature (∼200 m), ∼144 km long and ∼90 km wide (based on sigma-t=23 kg m−3) with tangential speeds of 40–80 cm s−1, and substantial isopycnal doming. Potential vorticity distribution of Noah suggests that radial horizontal flow of the core water was inhibited from the surface to depths of ∼75 m, with high vorticity confined above the sigma-t=23.5 kg m−3 isopycnal surface. Upward displacements of isopycnal surfaces in the eddy's center (∼50 m) were congruent with enhanced pigment concentrations (0.50 mg m−3). Comparisons of the results obtained for E-Flux I (Noah) and E-Flux III (Opal) suggest that translation characteristics of cyclonic Hawaiian lee eddies may be important in establishing the biogeochemical and biological responses of the oligotrophic ocean to cyclonic eddies.

We investigated the chromophoric dissolved organic matter (CDOM) of river water in the Sakawa River and of surface water in the vicinity of the river’s mouth in Sagami Bay, Japan, during the period from July 2003 to July 2004. Absorption by CDOM was modeled as a logarithmic function. As a qualitative index of CDOM, the slope (S) of this function was estimated for a wavelength range from 280 to 500 nm. As a quantitative index of CDOM, the integration of absorption was determined between 280 and 500 nm (Σ 280 500 a CDOM). High seasonal variability of S values was observed at the marine station. The S values at the upstream stations were related to chlorophyll a concentrations but not to bacterial abundance, whereas the integrated values at upstream stations were correlated with precipitation. Seasonal variability in the integrated values was low at the downstream stations, where the effect of effluent from nonpoint sources and sewage treatment plants was strong. Anthropogenic CDOM at the downstream stations appeared to be degraded by microbial utilization and photodegradation, whereas terrestrially derived CDOM at the upstream stations was less degraded. These qualitative differences in CDOM and the marked effect of dilution by seawater near the Sakawa River mouth suggest that the dynamics of CDOM in riverine and coastal environments should be studied with careful consideration of both spatial and temporal variations, particularly in small estuaries.

Mesoscale eddies may play a critical role in ocean biogeochemistry by increasing nutrient supply, primary production, and efficiency of the biological pump, that is, the ratio of carbon export to primary production in otherwise nutrient-deficient waters. We examined a diatom bloom within a cold-core cyclonic eddy off Hawai`i. Eddy primary production, community biomass, and size composition were markedly enhanced but had little effect on the carbon export ratio. Instead, the system functioned as a selective silica pump. Strong trophic coupling and inefficient organic export may be general characteristics of community perturbation responses in the warm waters of the Pacific Ocean.

The eastern tropical Pacific includes 28 million km2 of ocean between 23.5°N and S and Central/South America and 140°W, and contains the eastern and equatorial branches of the north and South Pacific subtropical gyres plus two equatorial and two coastal countercurrents. Spatial patterns of primary production are in general determined by supply of macronutrients (nitrate, phosphate) from below the thermocline. Where the thermocline is shallow and intersects the lighted euphotic zone, biological production is enhanced. In the eastern tropical Pacific thermocline depth is controlled by three interrelated processes: a basin-scale east/west thermocline tilt, a basin-scale thermocline shoaling at the gyre margins, and local wind-driven upwelling. These processes regulate supply of nutrient-rich subsurface waters to the euphotic zone, and on their basis we have divided the eastern tropical Pacific into seven main regions. Primary production and its physical and chemical controls are described for each. Enhanced rates of macronutrient supply maintains levels of primary production in the eastern tropical Pacific above those of the oligotrophic subtropical gyres to the north and south. On the other hand lack of the micronutrient iron limits phytoplankton growth (and nitrogen fixation) over large portions of the open-ocean eastern tropical Pacific, depressing rates of primary production and resulting in the so-called high nitrate-low chlorophyll condition. Very high rates of primary production can occur in those coastal areas where both macronutrients and iron are supplied in abundance to surface waters. In these eutrophic coastal areas large phytoplankton cells dominate; conversely, in the open-ocean small cells are dominant. In a ‘shadow zone’ between the subtropical gyres with limited subsurface ventilation, enough production sinks and decays to produce anoxic and denitrified waters which spread beneath very large parts of the eastern tropical Pacific. Seasonal cycles are weak over much of the open-ocean eastern tropical Pacific, although several eutrophic coastal areas do exhibit substantial seasonality. The ENSO fluctuation, however, is an exceedingly important source of interannual variability in this region. El Nino in general results in a depressed thermocline and thus reduced rates of macronutrient supply and primary production. The multi-decadal PDO is likely also an important source of variability, with the ‘El Viejo’ phase of the PDO resulting in warmer and lower nutrient and productivity conditions similar to El Nino. On average the eastern tropical Pacific is moderately productive and, relative to Pacific and global means, its productivity and area are roughly equivalent. For example, it occupies about 18% of the Pacific Ocean by area and accounts for 22–23% of its productivity. Similarly, it occupies about 9% of the global ocean and accounts for 10% of its productivity. While representative, these average values obscure very substantial spatial and temporal variability that characterizes the dynamics of this tropical ocean.

In order to study the mechanism of the bloom formation of Noctiluca scintillans, the relationship between the variation in the abundance of N. scintillans and environmental factors was examined in the coastal waters of Sagami Bay, Japan. Hydrographic (temperature, salinity, water stability), biological (chlorophyll a concentration, zooplankton biomass) and meteorological (rainfall, wind velocity, wind direction) factors were investigated from 1997 to 2004. For all years, the abundance of N. scintillans started to increase from March and reached a maximum in spring between April and May. The abundance in 1997 and 2000 was relatively high compared to the other years while the abundance in 1998 and 2004 was relatively low. A stepwise multiple linear regression analysis showed that the wind direction and rainfall were significantly correlated with the variation in the abundance of N. scintillans. Our results suggest that bloom formation can be separated into a threestep process: (i) initial increase in the abundance of N. scintillans attributed to an increase in optimum hydrographic and biological factors, (ii) N. scintillans is then accumulated by convergence of seawater by the factors of low rainfall and wind and (iii) swarmer-effects suggested enhanced bloom formation. Accumulation is considered to be a key trigger in this process of the formation of large-scale blooms.

UVR and PAR wavelengths are attenuated to different extents within the water column, causing variations in spectral composition with depth. The present investigation (a) describes the variability of UVR and PAR penetration at a station in the temperate coastal waters of Sagami Bay and determines (b) the characteristics of relative UVR penetration to the euphotic zone. Examination of the seasonal irradiance profile measurements indicated eight measurements displaying two distinct attenuation coefficients (K d ) for specific UVR wavelengths and PAR. The two attenuation coefficients observed from specific wavelengths in the water column may be caused not only by chlorophyll pigments, but also by dissolved organic material in the upper layer. The 1% depth of surface UVR at 305, 320, 340, and 380 nm averaged 10.8 ± 5.7, 14.9 ± 9.5, 19.8 ± 12.1, and 30.4 ± 17.6 m, respectively. The depth of euphotic layer displayed less variability averaging 62 ± 15 m throughout the entire study. Relative UVR penetration within the euphotic zone averaged 17.8 ± 8.1, 22.9 ± 10, 30.5 ± 13.8, and 46 ± 46.9% for 305, 320, 340, and 380 nm, respectively. A large variation of the relative transmission of UVR within the euphotic zone was found although the spectral composition was relatively stable in the air throughout the study.

The subdiscipline field of ocean optics has advanced dramatically in the last 2 decade due to a culmination of advances. These advances include large strides in our quantitative understanding of theoretical ocean optics, technological innovations in instrumentation and progress in utilizing interdisciplinary observational platforms. Theoretical understandings of ocean optical processes have evolved from the ability to quantify phytoplankton biomass from fluorescence to the quantification of phytoplankton classes and the development of proxies for quantification of biogeochemical parameters. Technological innovations have evolved from one-cast broadband scalar photosynthetically active radiation (PAR) sensors to multifunctional hyperspectral sensors capable of long-term deployments on moored buoy platforms. The facilitation of interdisciplinary observational platforms such as ocean color remote sensing satellites, moored buoys, drifters, autonomous underwater vehicles (AUVs) and gliders has also advanced our understanding of spatial and temporal variability of various ocean optics properties. The objectives of this study are to evaluate the progression of our understanding of theoretical ocean optics due to recent advances in optical sensors and their applicability to advanced ocean observational platforms, such as moored buoy observatories. Specifically, we will present recent advances in measurement techniques for the inherent and apparent optical properties of seawater obtained from time-series measurements from moored buoy platforms from both complex coastal and relatively stable open ocean environments. The in situ time-series measurements of inherent and apparent optical properties, namely the optical absorption and backscattering coefficients, and upwelling and downwelling attenuation coefficients, as potential proxies for biogeochemical parameters will be discussed. We will also suggest potential quality control and data analysis protocols necessary for quality time-series optical measurements from moored buoy platforms. Special consideration will be given to the current and future direction of ocean optics towards deriving the concentration, composition and size of biological and geochemical properties while assessing innovations in technology pertaining to ocean optics.

Calanus sinicus is a large calanoid copepod and a dominant species in the coastal waters of Japan. During a research cruise in Sagami Bay on 18 June 1996, we found C. sinicus performing an “unusual” diel vertical migration (DVM), a behavior that has not been reported in previous studies on this species. This study examined the DVM of C. sinicus under different light environments and revealed the copepod’s characteristic response to light. Field and laboratory results show that the DVM of C. sinicus is flexible and also confirmed its sensitivity and its rapid response to changing light environments. It is suggested that C. sinicus reacts to changes in absolute light intensity. This feature may be common in oceanic copepod species. The copepod’s quick reaction to light variation provides decreased predation risks and increased feeding opportunities, which make them a dominant survivor in coastal water habitats.

The study identifies the relative contribution of various bio-optical factors to the total attenuation of ultraviolet radiation (UVR) wavelengths and photosynthetically active radiation (PAR) in temperate coastal waters of Japan by surveying the physical properties of the water column, UVR and PAR penetration, and the absorption characteristics of dissolved and particulate material. Spectral absorbance properties of pigment (aph), detritus (ad) and chromophoric dissolved organic material (aCDOM) displayed both seasonal and wavelength specific variability. On an annual basis, absorbance by aCDOM was the highest absorbing fraction (47–59%) for the UVR wavelengths measured (305, 320, 340 and 380 nm) but decreased (32%) at 450 nm. Contribution of pigments to total absorbance was highest (40–60%) during a spring bloom for both UVR and PAR. A large variability (C.V. > 42%) for annual average attenuation coefficients (Kd[λ]) at respective wavelengths observed suggests that the spectral composition of the water column changes throughout the year in this region. A significant relationship was observed between Kd(λ) and aCDOM at 305, 320, 340 and 380 nm only (P < 0.01) but not for 450 nm (PAR) indicating the role of CDOM in regulating variations in Kd(λ), particularly in the UVR range. The slope S, obtained from a natural-log plot of the absorption coefficient of CDOM against wavelength, ranged between 0.014 and 0.036 nm−1 annually (average = 0.020±0.007, C.V. = 35%) and suggests seasonal changes in the origin of CDOM between terrestrial (low S) and biogenous (high S) CDOM.