Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits

The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.

Vertical distribution of microplastic along the main gate of Indonesian Throughflow pathways

Even though Pacific - Indian Ocean exchange [Indonesian Throughflow (ITF)] has been measured for the last three decades, the measurements of microplastic in the region is very limited. This study was the initial investigation of the vertical distribution of microplastic in the deep-sea areas across the ITF Pathway. Niskin water samples were utilized to obtain the samples from a water column in a range of 5 to 2450 m. A total of 924 microplastic particles with an average abundance of 1.062 ± 0.646. n/L were found in the water column. Our findings indicate that water temperature and water density are the most significant factors correlated to the microplastic concentration. This study will be the first report discussing the distribution of microplastics in the deep-sea water column that could be highly significant in determining the fate and transport of microplastic within Indonesian waters that exits into the Indian Ocean.

Physical oceanography of the present day Indonesian Throughflow

The Indonesian Throughflow (ITF) transfers c. 15 Sv (1 Sv=106 m3s−1) of relatively cool, fresh water from the tropical Pacific Ocean to the tropical Indian Ocean. Additionally, the ITF is a key interocean component of the global ocean warm water route, which returns water from the Pacific Ocean to the Atlantic Ocean to close the loop of the thermohaline overturning circulation associated with North Atlantic Deep Water. That flow consequently freshens the Indian Ocean and transports heat between basins. The ITF can also be described by the island rule, which relates the winds over the entire South Pacific Ocean to the magnitude of the ITF. El Niño-Southern Oscillation (ENSO) dominates the regional variability in the Pacific Ocean and exerts a strong control over the variability of ITF transport. The Indian Ocean responds to the ENSO signal as well, but is also influenced by the Indian Ocean Dipole, a climate phenomenon that may act independently of ENSO to affect the ITF.

Phylogeography and limited genetic connectivity in the endangered boring giant clam across the Coral Triangle

The Coral Triangle is the global center of marine biodiversity; however, its coral reefs are critically threatened. Because of the bipartite life history of many marine species with sedentary adults and dispersive pelagic larvae, designing effective marine protected areas requires an understanding of patterns of larval dispersal and connectivity among geographically discrete populations. We used mtDNA sequence data to examine patterns of genetic connectivity in the boring giant clam (Tridacna crocea) in an effort to guide conservation efforts within the Coral Triangle. We collected an approximately 485 base pair fragment of mtDNA cytochrome c oxidase 1 (CO1) from 414 individuals at 26 sites across Indonesia. Genetic structure was strong between regions (phi(ST)=0.549, p < 0.00001) with 3 strongly supported clades: one restricted to western Sumatra, another distributed across central Indonesia, and a third limited to eastern Indonesia and Papua. Even within the single largest clade, small but significant genetic structure was documented (phi(ST)=0.069, p < 0.00001), which indicates limited gene flow within and among phylogeographic regions. Significant patterns of isolation by distance indicated an average dispersal distance of only 25-50 km, which is far below dispersal predictions of 406-708 km derived from estimates of passive dispersal over 10 days via surface currents. The strong regional genetic structure we found indicates potent limits to genetic and demographic connectivity for this species throughout the Coral Triangle and provides a regional context for conservation planning. The recovery of 3 distinct evolutionarily significant units within a well-studied taxonomic group suggests that biodiversity in this region may be significantly underestimated and that Tridacna taxa may be more endangered than currently recognized.