Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation

The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification.

Enhancing reef fish diversity using artificial reef-building: A case study of coral reef rehabilitation on Nyamuk Island, Anambas Islands

CCMRS-IPB conducted coral reef rehabilitation at damaged coral reefs around Nyamuk Island. Those artificial reef buildings for rehabilitation gave shelter spaces for reef fish. This research aims to calculate the effect of coral reef-building, which enhances rugosity to the reef fish diversity around the rehabilitation sites. The study was conducted on Nyamuk Island in the Anambas Islands. Reef fish were sampled annually from 2014 to 2019 using the underwater visual census. The Diversity index and non-Metric Multidimensional Scaling were built to discover reef fish diversity, and reef fish species were affected the most. Yearly data shows an escalation number of reef fish abundance and richness at the end of 2019. The major reef fish group is found to have constant diversity throughout the year compared to other functional groups. The target reef fish group came to this rehabilitation ecosystem primarily attracted by nourishment availability. There is a shift in the reef fish diversity from the early year to the project end. Generally, major reef fish groups will be refuged first around the rehabilitation sites, especially territorial types. Target fish groups from herbivorous and carnivorous types will mostly come along after their food availability and location to get around.

Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus

Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.

Variasi Temporal Kelompok Ikan Terumbu Karang di Pulau Tidung Kecil Menggunakan eDNA Metabarkoding dan Sensus Visual

Coral reef fish are play key role in coral reef ecosystem. The presence of reef fish affected by antrophogenic and natural factors, such seasonal changes. This study aimed to asess the temporal variation of coral reef fish group in Tidung Kecil Island using eDNA metabarcoding and Undewater Visual Census. This research was conducted at December 2019 (West season) and August 2020 (East season). Target group are dominated in west season (64.1%) and east season (59.25%) using eDNA metabarcoding. While, major group fish are the highest relative abundance in both season by using Underwater Visual Census. Family Carangidae are the highest species richness (15 species) in wet season and Serranidae (3 species) in east season, respectively. Futhermore, famili Pomacentridae are the most richness species in west and east seasons 10 and 11 species respectively. Thus, it can be concluded these two methods are effective for monitoring structure or abundance of coral reef fish based on seasonal variation. Ikan karang menjadi indikator dalam menilai keanekaragaman hayati di ekosistem tersebut. Keberadaan ikan di ekosistem terumbu karang dapat dipengaruhi oleh faktor antropogenik dan faktor alam salah satunya perubahan musim. Penelitian ini bertujuan untuk menganalisis kelimpahan kelompok ikan terumbu karang di Pulau Tidung Kecil menggunakan eDNA metabarkoding dan Sensus Visual. Pengambilan data dilakukan pada bulan Desember 2019 (musim barat) dan Agustus 2020 (musim timur). Ikan target mendominasi pada musim barat dan timur dengan persentase sebesar 64.11% dan 59.25%. Sensus visual berhasil mendeteksi ikan mayor dengan persentase tertinggi 62.5% di musim barat dan 82.8% di musim timur. Famili Carangidae merupakan famili dengan jumlah spesies tertinggi di musim barat (15 species) dan Siganidae di musim timur menggunakan eDNA metabarkoding (3 species). Hasil UVC menunjukkan famili Pomcentridae memilki jumlah spesies tertinggi di kedua musim (11 dan 10 spesies) menggundakan sensus visual. Dapat disimpulkan bahwa kedua metode tersebut dapat menjadi pendekatan dalam monitoring struktur atau kelimpahan ikan terumbu karang berdasarkan musim.

Substitution of fishmeal with solid-state fermented pigeon pea and effects on growth and gut microbiomes of Nile Tilapia

Solid state fermented pigeon pea meal (FPP) was used in substituting fish meal (FM) in diets of Oreochromis niloticus. Five diets varying in inclusion levels of FM: FPP as followed: Feed 1, 250:50; Feed 2, 200:100; Feed 3, 150:150; Feed 4, 100:200 and Feed 5, 50:250 were made. A commercial feed (Feed 6), was used as a control. Triplicate groups of tilapia fingerling were stocked in plastic aquaria at six fish per unit and fed ad libitum for 60days. Results showed that specific growth rate (SGR) of tilapia fed Feed 5 (2.60±0.12% day-1) was better (p<0.05) than those recorded in Feed 1 (2.36±.07 % day-1). Similarly, food conversion ratio (FCR) (1.13±0.01) and mean weight gain (60.00±0.04g) were higher (p<0.05) in Feed 5 when compared with those in Feed 1 where FCR was 1.19±0.02 and MWG (50.96±0.04g). The results of Aspartate amino transferase (AST) and alanine amino transferase (ALT) decreased with increasing inclusion level of FPP. Gut microbial load increased with increasing level of FPP. The fish group fed Feed 5 had the highest foregut (2.60 x 10-5 CFU/ml), midgut (3.98 x 10-5 CFU/ml) and hindgut (4.52 x 10-5 CFU/ml) micrbiota. In general, gut microbiomes were dominated by cellulose and carbohydrate utilizing bacteria: Citrobacter fruendi, Bacillus subtilis and Staphylococcus aureus. Inference from the study revealed that O. niloticus was able to utilize the diets due to the presence of probiotics in them.

Analysis of Income Disparity of Coastal and Non-Coastal Communities in Banten Province, Indonesia

This study aims to analyze the large income disparity in coastal and non-coastal areas in Banten Province and to analyze whether the fisheries sub-sector has become the economic base in Banten Province in 2015 – 2019. January until May 2021. The method is carried out by survey method then analyzed quantitatively and presented descriptively. The data of this study were sourced from secondary data and primary data. Data were obtained from BPS Banten Province, BPS West Java Province, Marine and Fisheries Service Banten Province, Marine and Fisheries Service West Java Province and through questionnaires from coastal and non-coastal communities. Data analysis includes analysis of Williamson index, Gini coefficient and Location Quotient (LQ). based on the results of research conducted, it can be concluded that the income disparity in the coastal areas of Banten Province is greater than in the non-coastal areas. The Gini ratio analysis shows that the value of the Gini ratio has decreased from year to year, which means that income distribution is more evenly distributed until in 2019 it reaches 0. The fisheries sector in Banten Province is included in the non-base sector because it has a value of 0.5671. Production of catch commodities that get superior commodities: small pelagic fish group (mean LQ=1.81) and demersal fish group (mean LQ=0.84). The fisheries sector in Banten Province is included in the non-base sector because it has a value of 0.5671. Production of catch commodities that get superior commodities: small pelagic fish group (mean LQ=1.81) and demersal fish group (mean LQ=0.84). The fisheries sector in Banten Province is included in the non-base sector because it has a value of 0.5671. Production of catch commodities that get superior commodities: small pelagic fish group (mean LQ=1.81) and demersal fish group (mean LQ=0.84).

KOMPOSISI HASIL TANGKAPAN PERIKANAN PAYANG DAN BAGAN TANCAP SEBELUM REKLAMASI TELUK JAKARTA (GIANT SEA WALL)

Payang merupakan alat tangkap dengan laju tangkap relatif tinggi di Teluk Jakarta, sedangkan bagan tancap dikenal kurang selektif karena hasil tangkapannya didominasi oleh ikan berukuran kecil baik jenis pelagis maupun demersal. Penelitian ini dilaksanakan dengan metode fishing experiment pada payang dan bagan tancap. Hasil penelitian menunjukkan bahwa hasil tangkapan payang dan bagan tancap didominasi oleh jenis ikan demersal namun proporsi tangkapannya tidak jauh berbeda dengan jenis ikan pelagis. Komposisi ikan hasil tangkapan payang pada Agustus dan Oktober didominasi oleh jenis ikan pelagis, sedangkan pada bulan Desember didominasi oleh jenis ikan demersal. Nilai laju tangkap payang untuk jenis ikan pelagis ditemukan tinggi pada Agustus dan Oktober disebabkan oleh dominasi ikan cekong (Sardinella lemuru) dalam jumlah besar. Komposisi ikan hasil tangkapan bagan tancap pada Mei didominasi oleh jenis ikan demersal, sedangkan pada Oktober didominasi oleh jenis ikan pelagis. Daerah penangkapan payang meliputi perairan Pulau Damar, Pulau Bendera, Muara Pecah, Muara Angke, Pulau Onrust, Pulau Putri, Kronjo, sedangkan daerah penangkapan bagan tancap terkonsentrasi di sebelah barat perairan Teluk Jakarta, sekitar Pulau Kayangan, Pulau Bidadari dan Pulau Onrust. ABSTRACT Payang, a mini danish seine, is an artisanal fishing gear that has high catchability rate. Like payang, another dominant fishing gear in Jakarta Bay, the lift net, is also known as unselective fishing gear since small fish dominate its catch. This research uses the fishing experiment method with payang and lift net to figure out the gears' catch composition and catch rate. The result shows both fishing gears predominately caught the demersal fish group, but its proportion does not much from the pelagic group. During August and October, the catch composition of payang was dominated by pelagic fish, while demersal fish was caught mostly in December. The high catch rate for pelagic fish was recorded in August and October since cekong fish (Sardinella lemuru) dominated the cath. The catch composition of lift net was dominated by demersal fish during May, while pelagic fish were mostly captured in October. Payang’s fishing ground includes Pulau Damar waters, Pulau Bendera, Muara Pecah, Muara Angke, Pulau Onrust, Pulau Putri, and Kronjo, while the lift net dominates the western part of part of Jakarta Bay including Pulau Kayangan, Pulau Bidadari, and Pulau Onrust.

Freshwater-adapted sea bass Dicentrarchus labrax feeding frequency impact in a lettuce Lactuca sativa aquaponics system

The aim of this study is to investigate the effect of three daily fish feeding frequencies, two, four and eight times per day (FF2, FF4, and FF8, respectively) on growth performance of sea bass (Dicentrarchus labrax)and lettuce plants (Lactuca sativa) reared in aquaponics. 171 juvenile sea bass with an average body weight of 6.80 ± 0.095 g were used, together with 24 lettuce plants with an average initial height of 11.78 ± 0.074 cm over a 45-day trial period. FF2 fish group showed a significantly lower final weight, weight gain and specific growth rate than the FF4 and FF8 groups. Voluntary feed intake was similar for all the three feeding frequencies treatmens (p > 0.05). No plant mortality was observed during the 45-day study period. All three aquaponic systems resulted in a similar leaf fresh weight and fresh and dry aerial biomass. The results of the present study showed that the FF4 or FF8 feeding frequency contributes to the more efficient utilization of nutrients for better growth of sea bass adapted to fresh water while successfully supporting plant growth to a marketable biomass.

Prolactin induced cyto-architectural changes in the corpuscles of Stannius of stinging catfish, Heteropneustes fossilis acclimated to different calcium media

Adult fish Heteropneustes fossilis were divided into 4 groups –(i) Group A: kept in artificial freshwater and daily injected intraperitoneally with vehicle; (ii) Group B: kept in artificial freshwater and were daily injected intraperitoneally with 0.1 mg/100 g body wt of oProlactin; (iii) Group C: maintained in calcium-deficient freshwater and daily injected intraperitoneally with vehicle; (iv) Group D: kept in calcium-deficient freshwater and daily injected intraperitoneally with 0.1 mg/100 g body wt of oProlactin. Blood samples were taken 2 h after the last injection on 1, 3, 5, 10 and 15 days of the treatment. Plasma calcium levels were analyzed. The corpuscles of Stannius (CS) were fixed for histological studies. Artificial freshwater: The plasma calcium levels of vehicle-injected specimens (group A) remained unaltered throughout the experiment. Following prolactin treatment (group B) the plasma calcium levels progressively increased from day 3 to day 5. The values became normocalcemic at day 10 and day 15. After day 5 following prolactin administration (group B), the nuclear volume of AF-positive cells increased and the cells were seen degranulated. After day 10, there was an increased dilatation of sinusoids and the nuclear volume of AF-positive cells showed further increase. On day 15, these changes were exaggerated. The AFnegative cells of the corpuscles of Stannius of prolactin-treated fish (group B) showed no change in their histological structure and nuclear volume. Calcium-deficient freshwater: The plasma calcium level decreased in vehicle-injected fish (group C) from day 1 to day 3 (as compared to level of the fish kept in artificial freshwater). Thereafter, the level increased from day 5 resulting in hypercalcemia at day 10 and day 15. In prolactin treated fish (group D) the plasma calcium level indicated progressive increase from day 5 to day 15. In the vehicle-injected fish (group C) the AF-positive cells of corpuscles of Stannius showed accumulati