Draft genome of novel cyanobacteria Sphaerothrix Gracilis isolated from coastal microplastics reveal insights to chemical ecology, bloom and plastic-utilization potential.

Cyanobacteria are oxygenic photosynthetic organisms which are found across many ecosystems, including freshwater and marine habitats. They are also found on natural and artificial surfaces. In this study, we cultured and characterise a novel cyanobacterium from the surfaces of foam microplastics of tropical coastal waters. We study the chemical ecology of this cyanobacterium, Sphaerothrix gracilis gen. et sp. nov., together with its potential to form harmful cyanobacterial blooms and bioremediation applications to combat plastic pollution. The genome of S. gracilis spanned 6.7 Mbp, with identification of antibiotic resistance, nitrogen-fixation, plastic-degrading and genes involved in harmful metabolite production. The transport of potentially harmful S. gracilis in coastal environments could have severe implications on human health and food security, especially in times of a cyanobacterial bloom.

Effect of monsoon on microplastic bioavailability and ingestion by zooplankton in tropical coastal waters of Sabah.

Plankton seasonality in tropical coastal waters is becoming more apparent as a result of monsoon-driven changes in environmental conditions, but research on the monsoonal variation of microplastics (MP) is still limited. We examined the monsoonal variation of MP in the water column and their ingestion by zooplankton in Sepanggar Bay, Sabah, Malaysia. MP concentrations were significantly higher during the Southwest monsoon whereas MP ingestions showed no monsoonal difference across major zooplankton taxa. Canonical Correspondence Analysis (CCA) and Generalized Additive Models (GAM) indicate that MP concentrations were driven by changes in rainfall and salinity while MP bioavailability to zooplankton was consistent regardless of monsoon. MP ingestion increased progressively up the planktonic food chain, and bioavailability of fibers and small-sized MP of high-density polymers to zooplankton was proportionately higher. Distinct changes in the MP concentration relative to the monsoons provide new insights into the seasonal variation of MP in tropical coastal ecosystems.

Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition.

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.

Marine microplastics in the ASEAN region: A review of the current state of knowledge.

Microplastic pollution is a prevalent and serious problem in marine environments. These particles have a detrimental impact on marine ecosystems. They are harmful to marine organisms and are known to be a habitat for toxic microorganisms. Marine microplastics have been identified in beach sand, the seafloor and also in marine biota. Although research investigating the presence of microplastics in various marine environments have increased across the years, studies in Southeast Asia are still relatively limited. In this paper, 36 studies on marine microplastic pollution in Southeast Asia were reviewed and discussed, focusing on microplastics in beach and benthic sediments, seawater and marine organisms. These studies have shown that the presence of fishing harbours, aquaculture farms, and tourism result in an increased abundance of microplastics. The illegal and improper disposal of waste from village settlements and factories also contribute to the high abundance of microplastics observed. Hence, it is crucial to identify the hotspots of microplastic pollution, for assessment and mitigation purposes. Future studies should aim to standardize protocols and quantification, to allow for better quantification and assessment of the levels of microplastic contamination for monitoring purposes.

Assessment of Aqueous Extraction Methods on Extractable Organic Matter and Hydrophobic/Hydrophilic Fractions of Virgin Forest Soils.

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.

Development of photosynthetic carbon fixation model using multi-excitation wavelength fast repetition rate fluorometry in Lake Biwa.

Direct measurements of gross primary productivity (GPP) in the water column are essential, but can be spatially and temporally restrictive. Fast repetition rate fluorometry (FRRf) is a bio-optical technique based on chlorophyll a (Chl-a) fluorescence that can estimate the electron transport rate (ETRPSII) at photosystem II (PSII) of phytoplankton in real time. However, the derivation of phytoplankton GPP in carbon units from ETRPSII remains challenging because the electron requirement for carbon fixation (Фe,C), which is mechanistically 4 mol e- mol C-1 or above, can vary depending on multiple factors. In addition, FRRf studies are limited in freshwater lakes where phosphorus limitation and cyanobacterial blooms are common. The goal of the present study is to construct a robust Фe,C model for freshwater ecosystems using simultaneous measurements of ETRPSII by FRRf with multi-excitation wavelengths coupled with a traditional carbon fixation rate by the 13C method. The study was conducted in oligotrophic and mesotrophic parts of Lake Biwa from July 2018 to May 2019. The combination of excitation light at 444, 512 and 633 nm correctly estimated ETRPSII of cyanobacteria. The apparent range of Фe,C in the phytoplankton community was 1.1-31.0 mol e- mol C-1 during the study period. A generalised linear model showed that the best fit including 12 physicochemical and biological factors explained 67% of the variance in Фe,C. Among all factors, water temperature was the most significant, while photosynthetically active radiation intensity was not. This study quantifies the in situ FRRf method in a freshwater ecosystem, discusses core issues in the methodology to calculate Фe,C, and assesses the applicability of the method for lake GPP prediction.

Kinetics Growth and Recovery of Valuable Nutrients from Selangor Peat Swamp and Pristine Forest Soils Using Different Extraction Methods as Potential Microalgae Growth Enhancers.

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 °C twice with increasing 87%, 84%, and 95%, respectively. Chlorella vulgaris TRG 4C dominated the growth at 121 °C twice extraction method in the RMRF and AHRF samples, with increasing 54.3% and 14%, respectively. The specific growth rate (µ) of both microalgae were relatively higher, 0.23 d-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.

Enhancement of targeted microalgae species growth using aquaculture sludge extracts.

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.

Estimating the Diurnal Cycle and Daily Insolation of Ultraviolet and Photosynthetically Active Radiation at the Sea Surface.

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.

Mesoscale eddies drive increased silica export in the subtropical Pacific Ocean.

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 Hawaii. 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.