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Fulltext A metagenomic comparison of clearwater, probiotic, and Rapid BFTTM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures

Waiho K, Abd Razak MS, Abdul Rahman MZ, Zaid Z, Ikhwanuddin M, Fazhan H, et al.

PeerJ, 2023;11:e15758.
PMID: 37790619 DOI: 10.7717/peerj.15758

Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture.
Fulltext Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Shi X, Waiho K, Li X, Ikhwanuddin M, Miao G, Lin F, et al.

BMC Genomics, 2018 Dec 29;19(1):981.
PMID: 30594128 DOI: 10.1186/s12864-018-5380-8

BACKGROUND: Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals.
RESULTS: Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively.
CONCLUSIONS: Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.
Fulltext Aquaponics production of catfish and pumpkin: Comparison with conventional production systems

Oladimeji SA, Okomoda VT, Olufeagba SO, Solomon SG, Abol-Munafi AB, Alabi KI, et al.

Food Sci Nutr, 2020 May;8(5):2307-2315.
PMID: 32405388 DOI: 10.1002/fsn3.1512

Aquaponics is known to be a smart way of producing fish and crops simultaneously; however, there is a paucity of information about the extents of this system's efficiency over other conventional methods of food production. Thus, this study was designed to evaluate the performance of a catfish-pumpkin aquaponics system in comparison with recirculatory and static aquaculture systems (for fish performance), as well as irrigated and nonirrigated systems (for pumpkin performance). Results obtained showed that the production of fish in the aquaponics system was 29% and 75% more efficient than recirculatory and static aquaculture systems, respectively. The survival of the fish was also significantly improved probably due to better water quality in the aquaponics system. With respect to pumpkin production, yield in the aquaponics system was about five times the performance in irrigated land and eleven times those in nonirrigated land. This study gives definitive evidence to support the efficiency of the aquaponics system over other conventional food production methods.
High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crabs

Zhang Y, Yuan Y, Zhang M, Yu X, Qiu B, Wu F, et al.

BMC Biol, 2024 Nov 07;22(1):255.
PMID: 39511558 DOI: 10.1186/s12915-024-02054-1

BACKGROUND: Evolutionary adaptation drives organismal adjustments to environmental pressures, exemplified in the diverse morphological and ecological adaptations seen in Decapoda crustaceans, particularly brachyuran crabs. Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Despite their ecological importance, the genetic mechanisms underpinning their developmental processes, reproductive strategies, and nutrient acquisition remain poorly understood.
RESULTS: Here, we report a comprehensive genomic analysis of the green mud crab Scylla paramamosain using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. The genome exhibits 33,662 protein-coding genes, enriched in various pathways related to development and environmental adaptation. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, investigation into Hox gene regulation sheds light on their role in pleopod development, with the Abd-A gene identified as a linchpin. Post-transcriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the potential role of fru gene in ovarian development and the identification of novel-miR35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neo-functionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation.
CONCLUSIONS: Our findings shed light on various aspects of crab biology, including genome sequencing, assembly, and annotation, as well as gene family expansion, contraction, and regulatory mechanisms governing crucial developmental processes such as metamorphosis, reproductive strategies, and fatty acid metabolism.
Moulting Performances Evaluation of Female Orange Mud Crab, Scylla olivacea (Herbst, 1796) In-Captivity: Effects of Water Salinity and Limb Autotomy

Adnan AS, Gamburud LC, Mohd Affendi IS, Mohd Pauzi M, Mahsol HH, Muhammad T, et al.

Trop Life Sci Res, 2024 Mar;35(1):197-217.
PMID: 39262870 DOI: 10.21315/tlsr2024.35.1.11

Female Scylla olivacea has become more popular in Malaysia as emerging species mainly for soft-shell crabs and crab fattening (to increase weight, size and ovary maturation so that they can be sold at a higher price). To harvest crabs in soft-shell conditions and fattening, both conditions depend mostly on moulting events. To accelerate the moulting process, the manipulation of water parameter (salinity) and autotomy of the limb is commonly used. In this study, the evaluation of the moulting performances of full limb autotomy (the removal of all the appendages except for the swimming legs) and non-ablated (control) using immature S. olivacea cultured in three different salinity treatments (10 ppt, 20 ppt and 30 ppt) were performed. Results indicate there were significant differences between mud crab's culture duration, BW increments, growth performances and feeding efficiency with salinity. However, CW increments and survival indicate no significant effect with salinity. Meanwhile, limb autotomy proved to affect the culture duration, BW increments, survival and feeding efficiency of S. olivacea. The study concludes that both salinity and limb autotomy play significant roles in moulting performances of S. olivacea, with 20 ppt being the best salinity to stimulate S. olivacea moulting and development compared with the other two treatments (10 ppt and 30 ppt). Limb autotomy also indicates promising results as this technique proved to accelerate the moulting duration of S. olivacea with a 100% moulting percentage within 30 days. Therefore, the outcome would certainly benefit in the aquaculture production of this species of commercial importance mainly on soft-shell crabs production and also emerge as crabs fattening technique.