DNA barcoding and morphological identification of spiny lobsters in South Korean waters: a new record of Panulirus longipes and Panulirus homarus homarus

To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.

Yes, we can use it: A formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics + barcoding research using the Caribbean spiny lobster Panulirus argus

Whole mitogenomes or short fragments (e.g., 300-700 bp of the cox1 gene) are markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or low-coverage whole genome (LCWGS) sequencing with or without prior mitochondrial enrichment and Illumina sequencing. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I tested first if mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a 'gold' standard reference mitogenome retrieved from the same individualusing Illumina sequencing. LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines did retrieve a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not 'perfect', phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads can reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other closely and distantly related species in the same genus, family, and superorder. This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION so to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income and developing countries.

Predatory bacteria in the haemolymph of the cultured spiny lobster Panulirus ornatus

Bdellovibrio and like organisms (BALOs) are Gram-negative obligate predators of other bacteria in a range of environments. The recent discovery of BALOs in the circulatory system of cultured spiny lobster P. ornatus warrants more investigation. We used a combination of co-culture agar and broth assays and transmission electron microscopy to show a Halobacteriovorax sp. strain Hbv preyed upon the model prey bacterium Vibrio sp. strain Vib. The haemolymph microbiome of juvenile P. ornatus was characterised following injection of phosphate buffered saline (control) or prey and/or predator bacteria for 3 d. The predator Hbv had no effect on survival compared to the control after 3 d. However, when compared to the prey only treatment group, lobsters injected with both prey and predator showed significantly lower abundance of genus Vibrio in the haemolymph bacterial community composition. This study indicates that predatory bacteria are not pathogenic and may assist in controlling microbial population growth in the haemolymph of lobsters.

Size Distribution, Length-Weight Relationship, and Size at Morphometric Maturity of the Mud Spiny Lobster Panulirus polyphagus (Herbst, 1793) in the Johor Strait

Spiny lobsters of the genus Panulirus are economically important and support local fishing communities. However, mud spiny lobster Panulirus polyphagus is among the least known species within this genus in terms of their biological information. This study relates to the size distribution, length-weight relationship, and size at morphometric maturity of P. polyphagus in the Johor Strait. Within the year 2010, 300 specimens were collected off the coast of Johor Strait, Malaysia. There was no significant difference in body size (cephalothorax length, CL) and body weight (BW) between sexes. CL and BW were highly correlated and males of P. polyphagus displayed positive growth allometry, whereas the opposite was observed in females. Based on the merus (ML) and carpus length (CPL) of the third right walking leg, the piecewise linear regression analysis estimated that the size at maturity for male was 6.58 cm CL (based on ML) and 7.58 cm CL (based on CPL), whereas it was 8.18 cm CL (based on ML) and 6.75 cm (based on CPL) for females. Two discriminant functions of high classification and revalidation rates (> 98.6% in males and > 98.7% in females) that can discern maturation status in males and females of P. polyphagus were derived using the discriminant function analysis. Biological information derived from this study serves as an essential baseline for future fishery management and conservation of P. polyphagus.

Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

Partial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169–23.880% for COI, 1.336–23.434% for 12S, and 7.897–71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.

The U.S. Caribbean Region

This chapter describes the Caribbean region and the major issues facing this marine fisheries ecosystem, and presents some summary statistics related to the 90 indicators of ecosystem-based fisheries management (EBFM) criteria. While containing the highest number of managed taxa among the eight regional U.S. marine ecosystems, including over 200 distinctly managed coral reef species, this region has been challenged by historical exploitation of its important fisheries, particularly Caribbean spiny lobster, queen conch, and its snapper-grouper complex. The U.S. Caribbean has been affected by above average natural and human stressors that include the nationally second-highest rate of SST increase over the past 70 years, increasing frequency and intensity of hurricanes, high coastal development, and concentrated historical fishing pressure. Although ranked low overall regarding the status of its marine socioeconomics, the U.S. Caribbean leads nationally in terms of aspects of its marine tourism, particularly cruise ship destinations, which contribute heavily to its local economy. Overall, EBFM progress has been made in terms of implementing ecosystem-level planning, advancing knowledge of ecosystem principles, and in assessing risks and vulnerabilities to ecosystems through ongoing investigations into climate vulnerability and species prioritizations for stock and habitat assessments.

The effect of probiotic and prebiotic-MOS on the survival, growth and immune competence on spiny lobster Panulirus homarus culture

The use of probiotics and prebiotic to improve growth and health status of spiny lobster has been evaluated. The purpose of this study was to obtain the effect of probiotics and prebiotics for the culture of spiny lobster Panulirus homarus. The method was initiated with culturing of probiotics (4 strains) and supplemented it in a moist diets. Spiny lobster was collected from Jembrana-Bali waters with an initial body weight of 70.34 ± 4.5 g and cultured in concrete tanks with volume of 4 m3. Initial stock density for each treatment was 15 pcs / m3. The treatments tested were supplemented on moist diets with (A) probiotics, (B) probiotics and prebiotics-MOS (Mannan Oligo Sacharida) and (C) Controle (without probiotics and prebiotic) and each treatment with three replication. The results obtained that the survival rate of spiny lobster was not significantly different (P> 0.05), i.e. (A) 92.70%, (B) 93.33 (%) and (C) 93.33% respectively. However, the results of probiotics supplementation as well as a combination of probiotics and prebiotics showed growth differences compared to control (P<0.05), namely (A) 156.97 ± 6.17 g, (B) 153.75 ± 9.17 g, while (C) control 131.47 ± 7.91 g. The probiotics supplementation on moist diets could increased health status of spiny lobsters, this was expressed by target genes related to immunity (ALFHa-1, ALFHa-4, SAA, ProPO, Tgase and CP). Spiny lobster immunity increased by 2.60 to 42.7 times after challenging with MHD (Milky Haemolymph Disease). The supplementation of probiotics and prebiotics (MOS) could increase immune response by 2.10 to 25.75 times, respectively after challenging with MHD.

Effect of shelter net sizes on growth, survivality, and health of scalloped spiny lobster, Panulirus homarus (Linnaeus 1758) reared in fiberglass tank

Scalloped spiny lobster (Panulirus homarus) is an export commodity with high economic value in Asian-Pacific markets. Addition of artificial shelter for spiny lobster grow out reduces cannibalism while addition of net in spiny lobster rearing tank can increase mobility space. This study aimed to determine the optimum of shelter net size on growth, survival rate and health of spiny lobster grow out. This study used completely randomized design with three treatments and three replications; analyzed by ANOVA. The rearing was conducted using 9 fiberglass tank 1000 liter in volume. This research used scalloped spiny lobster, with average body weight (BW) 8.56±1.23 g and total length (TL) 7.39±0.114 cm, in stocking density 50 lobster/tank. Three shelter net sizes as treatments, i.e.: A: shelter net size of 4 time of bottom area (4 m2), B: size of 2 time of bottom area (2 m2) and C: without net addition. Feeding were twice a day, with dry pellet 1% biomass/day and trash fish and mussel meat (2:1) 10% biomass/day. The sampling of survival rate, total length and body weight were conducted every 15 days; while total haemocyte (THC) and BRIX index on the end of experiment. For supporting data was observed of water quality parameters: salinity, temperature, pH, DO, nitrite and ammonia. The result show that the survival rate on experiment during 75 days rearing, was significant different (P<0.05) among treatments. The best survival rate was on treatment A (4 time of bottom area) with survival rate (93.94±2.62%), followed by treatment B (2 time of bottom area) (80.56±2.88%: and treatment C (without net addition) (68.78±4.67 %). The grow of body weight and total length show that highest on treatment B with body weight and total length in the end of experiment was 37.77±1.896 g and 10.30 ±0.361a cm; followed by treatment A (35.58±0.405 g and 10.15 ±0.146 cm) and lowest in C (35.34±2.061 g and 10.04 ±0.265 cm); but from statistic analyze not significant different among treatment (p>0.05). Addition for shelter net size of 4 time of bottom area net more suitable for scallop spiny lobster reared in fiberglass tank; because can increased the survival rate and reduced the cannibalism.

Population structure and biological aspects of lobster (Panulirus spp.) of the Madura Strait landed in Situbondo of East Java, Indonesia

Lobster is an important economic fishery resource in domestic and international trade. The high economic value of lobster due to increasing market demand has led to its intensive exploitation. The enactment of specific regulations on lobster proves the urgency of its management. Madura Strait is one of the unique biogeographical sea regions of East Java. This research was conducted in January-March 2021 at Pasir Hitam Beach, Situbondo. The purpose of this study was to determine the species composition of lobsters, the frequency distribution and the growth form, and the sex ratio. The analysis applied is class distribution of length and weight classes, regression analysis, and chi-square. The lobster catches consist of 4 species, namely Scalloped spiny lobster (Panulirus homarus), Ornate spiny lobster (P. ornatus), Painted spiny lobster (P. versicolor), and Mud spiny lobster (P. polyphagus). P. homarus is the most dominant species. The frequency distribution of carapace length and weight of P. homarus, P. ornatus, and P. versicolor has met the minimum size limits rules. The length and weight relationship of P. Homarus and P. ornatus were negative allometric, while P. versicolor isometric. Lobster sex ratio is in a balanced condition.