Bacterial metagenome analysis of Mytilus galloprovincialis collected from Istanbul and Izmir coastal stations of Turkey

Efficiency comparison of DNA extraction kits for analysing the cockle gut bacteriome

Cockles play a vital ecological role and provide valuable ecosystem services globally. However, the performance, production, and safe consumption of cockles are significantly influenced by their gut-associated bacteriome. Accurate understanding of gut-bacteriome interactions, and surveillance of pathogenic bacteria loads in cockles, rely on efficient DNA extraction methods that yield high-quality and representative bacterial DNA. Despite this importance, reliable extraction methods for cockles are currently overlooked. Therefore, we evaluated the performance of five DNA extraction kits (E.Z.N.A.® Soil DNA; FastDNA® Spin; DNeasy PowerSoil Pro; QIAamp PowerFecal DNA; ZymoBIOMICS™DNA Miniprep) in terms of DNA quality, yield, bacterial community structure (analysed by using denaturating gradient gel electrophoresis; DGGE), and bacteriome composition (analysed by 16S rRNA gene sequencing) in Cerastoderma edule gut. The DNeasy kit provided the highest purity and quantity of bacterial DNA, while the PowerFecal and Zymo kits exhibited reduced extraction efficiency. DGGE profiles revealed significant variability between the tested kits (R = 0.512; mean P = 0.011), but the FastDNA kit under-represented the bacterial community in cockles' gut. Based on alpha diversity, the DNeasy kit outperformed the others and successfully detected all abundant genera found with the alternative kits. Our findings indicate that the DNeasy kit is an efficient DNA extraction method, enabling a molecular representation of the gut-associated bacteriome in C. edule. These results contribute to the development of effective techniques for studying the cockle gut bacteriome and its ecological implications.

Feeding Behavior, Gut Microbiota, and Transcriptome Analysis Reveal Individual Growth Differences in the Sea Urchin Strongylocentrotus intermedius

Growth differentiation among farmed sea urchins (Strongylocentrotus intermedius) poses a significant challenge to aquaculture, with there being a limited understanding of the underlying molecular mechanisms. In this study, sea urchins with varying growth rates, reared under identical conditions, were analyzed for feeding behavior, gut microbiota, and transcriptomes. Large-sized sea urchins demonstrated significantly higher feeding ability and longer duration than smaller ones. The dominant phyla across all size groups were Campylobacterota, Proteobacteria, and Firmicutes, with Campylobacterota showing the highest abundance in small-sized sea urchins (82.6%). However, the families Lachnospiraceae and Pseudomonadaceae were significantly less prevalent in small-sized sea urchins. Transcriptome analysis identified 214, 544, and 732 differentially expressed genes (DEGs) in the large vs. medium, large vs. small, and medium vs. small comparisons, respectively. Gene Ontology and KEGG pathway analyses associated DEGs with key processes such as steroid biosynthesis, protein processing within the endoplasmic reticulum, and nucleotide sugar metabolism. Variations in phagosomes and signaling pathways indicated that size differences are linked to disparities in energy expenditure and stress responses. These findings provide a foundation for future investigations into the regulatory mechanisms underlying growth differences in S. intermedius and provide clues for the screening of molecular markers useful to improve sea urchin production.

Evaluation of the health of Mediterranean mussels (Mytilus galloprovincialis Lamarck, 1819) distributed in the Çanakkale strait, Turkey

The observation of mortality in Mediterranean mussels (Mytilus galloprovincialis) distributed in the Çanakkale Strait in recent years was influential in developing the research question for this study. In this study, the presence of bacteria (Vibrio spp.) and parasites (Marteilia spp. and Haplosporidium spp.) in mussels collected from Kumkale, Kepez, and Umurbey stations in the Çanakkale Strait was investigated seasonally. Microbiological findings, histopathology, oxidative stress enzymes and their gene expressions, lipid peroxidation, lysosomal membrane stability, and changes in haemolymph were examined. In summer samples, both the defence system and the extent of damage were higher in gill tissue. In winter samples, enzyme activities and lipid peroxidation were found to be predominantly higher in digestive gland tissues. Histological examinations and Hemacolor staining revealed the presence of protozoan cysts, and for bacterial examination, molecular analysis performed after culturing revealed the presence of 7 Vibrio species. While the total numbers of heterotrophic bacteria detected in all samples were at acceptable levels, the predominance of Vibrio spp. numbers among the total heterotrophic bacteria detected in almost all samples were noteworthy. The total hemocyte count was calculated as 5.810(4)±0.58 (cells/mm3) in winter and 7.210(4)±1.03 (cells/mm3) in summer. These factors are considered to be possible causes of mussel mortality.

Microbiome profile of the Antarctic clam Laternula elliptica

The filter feeder clam Laternula elliptica is a key species in the Antarctic ecosystem. As a stenothermal benthic species, it has a poor capacity for adaptation to small temperature variations. Despite their ecological importance and sensitivity to climate change, studies on their microbiomes are lacking. The goal of this study was to characterize the bacterial communities of L. elliptica and the tissues variability of this microbiome to provide an initial insight of host-microbiota interactions. We investigated the diversity and taxonomic composition of bacterial communities of L. elliptica from five regions of the body using high-throughput 16S rRNA gene sequencing. The results showed that the microbiome of L. elliptica tended to differ from that of the surrounding seawater samples. However, there were no significant differences in the microbial composition between the body sites, and only two OTUs were present in all samples, being considered core microbiome (genus Moritella and Polaribacter). No significant differences were detected in diversity indexes among tissues (mean 626.85 for observed OTUs, 628.89 Chao1, 5.42 Shannon, and 0.87 Simpson). Rarefaction analysis revealed that most tissues reached a plateau of OTU number according to sample increase, with the exception of Siphon samples. Psychromonas and Psychrilyobacter were particularly abundant in L. elliptica whereas Fluviicola dominated seawater and siphons. Typical polar bacteria were Polaribacter, Shewanella, Colwellia, and Moritella. We detected the prevalence of pathogenic bacterial sequences, particularly in the family Arcobacteraceae, Pseudomonadaceae, and Mycoplasmataceae. The prokaryotic diversity was similar among tissues, as well as their taxonomic composition, suggesting a homogeneity of the microbiome along L. elliptica body. The Antarctic clam population can be used to monitor the impact of human activity in areas near Antarctic stations that discharge wastewater.

Changes in extractive components and bacterial flora in live mussels Mytilus galloprovincialis during storage at different temperatures

To estimate the quality of mussels during storage, the mortality, succinate dehydrogenase (SDH) activity, extractive components, viable bacterial count (VBC), and bacterial flora of live mussels were investigated. The hierarchical cluster analysis, based on extractive components and VBC, taste active value (TAV), and equivalent umami concentration (EUC), suggested that metabolite composition, bacterial, and taste changing patterns of samples stored at 5 and 10°C differed from those stored at 0°C. The mortality of mussels stored at 5 and 10°C was lower than those at 0°C. The gills of live mussels stored at 0°C for more than 7 days exhibited significantly lower SDH activity than those stored at 5 and 10°C. There was no significant difference in EUC among the samples stored at different temperatures, but a significantly higher TAV of Ala and succinic acid was observed in live mussels after 12 days of storage at 5 and 10°C than in those stored at 0°C. Next-generation sequencing analysis showed that samples stored at 5 and 10°C lost bacterial diversity, and their bacterial flora changed compared to that before storage. Considering these results, the most suitable storage condition to maintain high quality for live mussels is 5°C for less than 7 days.

Predator Presence Alters Intestinal Microbiota in Mussel

Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.

Assessing the Bacterial Community Composition of Bivalve Mollusks Collected in Aquaculture Farms and Respective Susceptibility to Antibiotics

Aquaculture is a growing sector, providing several products for human consumption, and it is therefore important to guarantee its quality and safety. This study aimed to contribute to the knowledge of bacterial composition of Crassostrea gigas, Mytilus spp. and Ruditapes decussatus, and the antibiotic resistances/resistance genes present in aquaculture environments. Two hundred and twenty-two bacterial strains were recovered from all bivalve mollusks samples belonging to the Aeromonadaceae, Bacillaceae, Comamonadaceae, Enterobacteriaceae, Enterococcaceae, Micrococcaceae, Moraxellaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Staphylococcaceae, Streptococcaceae, Vibrionaceae, and Yersiniaceae families. Decreased susceptibility to oxytetracycline prevails in all bivalve species, aquaculture farms and seasons. Decreased susceptibilities to amoxicillin, amoxicillin/clavulanic acid, cefotaxime, cefoxitin, ceftazidime, chloramphenicol, florfenicol, colistin, ciprofloxacin, flumequine, nalidixic acid and trimethoprim/sulfamethoxazole were also found. This study detected six qnrA genes among Shewanella algae, ten qnrB genes among Citrobacter spp. and Escherichia coli, three oqxAB genes from Raoultella ornithinolytica and bla_TEM-1 in eight E. coli strains harboring a qnrB19 gene. Our results suggest that the bacteria and antibiotic resistances/resistance genes present in bivalve mollusks depend on several factors, such as host species and respective life stage, bacterial family, farm’s location and season, and that is important to study each aquaculture farm individually to implement the most suitable measures to prevent outbreaks.

Occurrence and distribution of fecal indicators and pathogenic bacteria in seawater and Perna perna mussel in the Gulf of Annaba (Southern Mediterranean)

The identification of fecal contamination in coastal marine ecosystems is one of the main requirements for evaluation of potential risks to human health. The objective of this study was to investigate the occurrence and distribution of fecal indicators and pathogenic bacteria in seawaters and mussels collected monthly during a period of 1 year from four different sites in Northeastern Algeria (sites S1 to S4), through biochemical and molecular analyses. Our research is the first to use molecular analysis to unambiguously identify the potentially pathogenic bacteria present in Algerian Perna perna mussels. The obtained results revealed that the levels of fecal indicator bacteria (FIB) from both P. perna and seawater samples largely exceeded the permissible limits at S2 and S3. This is mainly related to their location close to industrial and coastal activity zones, which contain a mixture of urban, agricultural, and industrial pollutants. Besides, P. perna collected from all sites were severalfold more contaminated by FIB than seawater samples, primarily during the warm season of the study period. Biochemical and molecular analyses showed that isolated bacteria from both seawater and mussels were mainly potentially pathogenic species such as E. coli, Salmonella spp., Staphylococcus spp., Klebsiella spp., Pseudomonas spp., and Proteus spp.

Biodegradation of Emerging Pharmaceuticals from Domestic Wastewater by Membrane Bioreactor: The Effect of Solid Retention Time

Although conventional biological treatment plants can remove basic pollutants, they are ineffective at removing recalcitrant pollutants. Membrane bioreactors contain promising technology and have the advantages of better effluent quality and lower sludge production compared to those of conventional biological treatment processes. In this study, the removal of pharmaceutical compounds by membrane bioreactors under different solid retention times (SRTs) was investigated. To study the effect of SRT on the removal of emerging pharmaceuticals, the levels of pharmaceuticals were measured over 96 days for the following retention times: 20, 30, and 40-day SRT. It was found that the 40-day SRT had the optimum performance in terms of the pharmaceuticals’ elimination. The removal efficiencies of the chemical oxygen demand (COD) for each selected SRT were higher than 96% at steady-state conditions. The highest degradation efficiency was observed for paracetamol. Paracetamol was the most removed compound followed by ranitidine, atenolol, bezafibrate, diclofenac, and carbamazepine. The microbial community at the phylum level was also analyzed to understand the biodegradability of pharmaceuticals. It was noticed that the Proteobacteria phylum increased from 46.8% to 60.0% after 96 days with the pharmaceuticals. The Actinobacteria class, which can metabolize paracetamol, carbamazepine, and atenolol, was also increased from 9.1% to 17.9% after adding pharmaceuticals. The by-products of diclofenac, bezafibrate, and carbamazepine were observed in the effluent samples.