Suspended particulate matter (SPM) has been known as an important variable in the organic matter flow of coastal ecosystem. Half of burial carbon in seagrass meadows is contributed by allochthonous sources that compose the SPM such as phytoplankton, seagrass detritus, marine snow aggregates and terrestrially derived particles. Each composition of the SPM contributes different roles and is important to be identified, for instance, the exact contribution of seagrass detritus will be useful for determination of carbon export through the detritus form in seagrass meadows. Here, the SPM of seagrass meadows is studied in Bintan Island and the Selayar Archipelago. The aim of this research is to determine the source origin of the SPM using a stable isotope signature. In order to fulfill this aim, the objectives are defined as: (1) to specify the stable isotope signature (δ¹³C and δ¹⁵N) of the SPM, and (2) to determine the proportional distribution of the SPM’s prospectus sources. The result shows that the possibility of the source origin of the SPM includes a seagrass fraction (Enhalus acoroides and Thalassia hemprichii), terrestrial C4 plant, macroalgae, and terrestrial C3 plant. The SPM lies between the marine- and terrigenous-end members. However, it seems that the SPM is more to be terrigenous-end and allochthonous. According to a Bayesian mixing model, the terrestrial C4 has the highest contribution of the SPM at all sites except Barugaia and Pasi Island in Selayar (i.e., the highest contribution of the SPM is from the detritus of E. acoroides). The second contribution has been contributed by either seagrass detritus (E. acoroides or Th. hemprichii) or terrestrial C3 plant. The finding of this study indicates that there is a strong influence of the terrigenous sources in the SPM of the seagrass meadows.

In this study, the horizontal and vertical distribution of primary production (PP) and its monthly variations were described based on field data collected from the Daya Bay in January–December of 2016. The relationships between PP and environmental factors were analyzed using a general additive model (GAM). Significant seasonal differences were observed in the horizontal distribution of PP, while vertical distribution showed a relatively consistent unimodal pattern. The monthly average PP (calculated by carbon) ranged from 48.03 to 390.56 mg/(m²·h), with an annual average of 182.77 mg/(m²·h). The highest PP was observed in May and the lowest in November. Additionally, the overall trend in PP was spring>summer>winter>autumn, and spring PP was approximately three times that of autumn PP. GAM analysis revealed that temperature, bottom salinity, phytoplankton, and photosynthetically active radiation (PAR) had no significant relationships with PP, while longitude, depth, surface salinity, chlorophyll a (Chl a) and transparency were significantly correlated with PP. Overall, the results presented herein indicate that monsoonal changes and terrestrial and offshore water systems have crucial effects on environmental factors that are associated with PP changes.

Based on oceanographic survey data in June 2012 in the Lembeh Strait, the zooplankton ecological characteristics such as species composition, individual abundance, dominant species and distribution were analyzed. The results showed that 183 species (including 4 sp.) had been recognized, most of them belonged to copepoda. Cnidaria followed with 43 species (including 1 sp.) were identified. The average abundance of zooplankton was (150.47±58.91) ind./m³. As to the horizontal distribution, the abundance of the zooplankton was higher in the southern waters than in the northern waters. The dominant species in the study area were Lensia subtiloides, Sagitta enflata, Lucifer intermedius, Oikopleura rufescens, Diphyes chamissoni, Creseis acicula, Subeucalanus subcrassus, Temora discaudata, Aglaura hemistoma, Doliolum denticulatum, Canthocalanus pauper, Oikopleura longicauda and Nanomia bijuga. Zooplankton biodiversity indexes were higher in study area than previous study in the other regions. The findings from this study provide important baseline information for future research and monitoring programs.

Water samples were collected in order to study the spatial variation of photosynthetic pigments and phytoplankton community composition in the Lembeh Strait (Indonesia) and the Kelantan River Estuary (Malaysia) during July and August 2016, respectively. Phytoplankton photosynthetic pigments were detected using high performance liquid chromatography combining with the CHEMTAX software to confirm the Chl a biomass and community composition. The Chl a concentration was low at surface in the Lembeh Strait, which it was 0.580–0.682 μg/L, with the average (0.620±0.039) μg/L. Nevertheless, the Chl a concentration fluctuated violently at surface in the Kelantan River Estuary, in which the biomass was 0.299–3.988 μg/L, with the average (0.922±0.992) μg/L. The biomass at bottom water was higher than at surface in the Kelantan River Estuary, in which the Chl a concentration was 0.704–2.352 μg/L, with the average (1.493±0.571) μg/L. Chl b, zeaxanthin and fucoxanthin were three most abundant pigments in the Lembeh Strait. As a consequence, phytoplankton community composition was different in the two study areas. In the Lembeh Strait, prasinophytes (26.48%±0.83%) and Synechococcus (25.73%±4.13%) occupied ~50% of the Chl a biomass, followed by diatoms (20.49%±2.34%) and haptophytes T8 (15.13%±2.42%). At surface water in the Kelantan River Estuary, diatoms (58.53%±18.44%) dominated more than half of the phytoplankton biomass, followed by Synechococcus (27.27%±14.84%) and prasinophytes (7.00%±4.39%). It showed the similar status at the bottom water in the Kelantan River Estuary, where diatoms, Synechococcus and prasinophytes contributed 64.89%±15.29%, 16.23%±9.98% and 8.91%±2.62%, respectively. The different phytoplankton community composition between the two regions implied that the bottom up control affected the phytoplankton biomass in the Lembeh Strait where the oligotrophic water derived from the West Pacific Ocean. The terrigenous nutrients supplied the diatoms growing, and pico-phytoplankton was grazed through top down control in the Kelantan River Estuary.

Specific bacterial communities interact with phytoplankton in laboratory algal cultures. These communities influence phytoplankton physiology and metabolism by transforming and exchanging phytoplankton-derived organic matter. Functional bacterial groups may participate in various critical nutrients fluxes within these associations, including nitrogen (N) metabolism. However, it is unclear how bacterial communities and the associated algae respond to changes of phycosphere N conditions. This response may have far-reaching implications for global nutrient cycling, algal bloom formation, and ecosystem function. Here, we identified changes in the bacterial communities associated with Phaeodactylum tricornutum when co-cultured with different forms and concentrations of N based on the Illumina HiSeq sequencing of 16S rRNA amplicons. Phylogenetic analysis identified Proteobacteria and Bacteroidetes as the dominant phyla, accounting for 99.5% of all sequences. Importantly, bacterial abundance and community structure were more affected by algal abundance than by the form or concentration of inorganic N. The relative abundance of three gammaproteobacterial genera (Marinobacter, Algiphilus and Methylophaga) markedly increased in N-deficient cultures. Thus, some bacterial groups may play a role in the regulation of N metabolism when co-cultured with P. tricornutum.

Recent studies have highlighted the valuable role played by mangrove forests in carbon sequestration and storage. Although Indonesia accounts for a large proportion of global mangrove area, knowledge on the carbon stock and sources in the Indonesian mangrove is still limited. In this study, we quantified the ecosystem organic carbon (OC) stock and its spatial variation at an oceanic mangrove in Wori, North Sulawesi, Indonesia. The sources of soil OC were also investigated. The results showed that the mangrove soil had a substantial OC stock containing 15.4 kg/m² (calculated by carbon) in the top 50 cm soil, and represented the majority of the ecosystem OC stock at the Wori mangrove. The mangrove biomass and ecosystem OC stock were 8.3 kg/m² and 23.7 kg/m², respectively. There was no significantly difference in the soil OC stock among the stations with difference distances offshore, while the highest mangrove biomass OC stock was found at the seaward station. Isotope mixing calculations showed that the rich OC in mangrove soils was attributed to the accumulated autochthonous mangrove source while the suspended organic matter in tidal water and the mangrove-adjacent seagrass contributed less than 20% to the soil OC. The results further demonstrated the importances of the oceanic mangrove in carbon storage and the mangrove plants in contributing OC to their soils.

Upwelling occurs on the coast of Java between June and October, forced by local alongshore winds associated with the southeasterly monsoon. This causes variations in phytoplankton community composition in the upwelling zone compared with the surrounding offshore area. Based on pigments analysis with subsequent calculations of group contributions to total chlorophyll a (Chl a) using CHEMTAX, we studied the distribution and composition of phytoplankton assemblages in the subsurface chlorophyll maximum along the south coast of Java and the influence of upwelling. Nineteen phytoplankton pigments were identified using high-performance liquid chromatography, and CHEMTAX analysis associated these to ten major phytoplankton groups. The phytoplankton community in the coastal area influenced by upwelling was characterized by high Chl a and fucoxanthin concentrations, indicating the dominance of diatoms. In contrast, in the offshore area, the Chl a and fucoxanthin concentrations declined to very low levels and the community was dominated by haptophytes represented by 19′-Hexanoyloxyfucoxanthin. Accordingly, microphytoplankton was found to be the major size class in the coastal area influenced by upwelling, while nanophytoplankton was most abundant in the offshore area. Low concentrations of other accessory pigments indicated less contribution from dinoflagellates, prasinophytes, chlorophytes and cryptophytes. Photo-pigment indices revealed that photosynthetic carotenoids (PSCs) were the largest component of the pigment pool, exceeding the proportion of Chl a, with the average PSC_TP up to 0.62. These distribution trends can mainly be explained by phytoplankton adaption strategies to upwelling and subsurface conditions by changing species composition and adjusting the pigment pool.

Bacterial diseases affecting corals pose an enormous threat to the health of coral reefs. The relationship between certain bacterial species and coral diseases remain largely unknown. Pigment abnormalities are common in Porites lutea. Here we used Illumina 16S rRNA gene sequencing to analyze the bacterial communities associated with healthy P. lutea and P. lutea with pigment abnormalities. We observed an increase of alpha diversity of the bacterial community of P. lutea with pigment abnormalities, relative to healthy corals. We then identified changes in the abundance of individual operational taxonomic units (OTUs) between pigmented and healthy corals. We were able to identify eight OTUs associated with pigment abnormalities, which are possibly the causative agents of pigment abnormalities.