The present work aimed to assess the circulating signature and diversity of the circulating blood microbiome of the Southern Gulf of St. Lawrence Atlantic cod, a population that faces extinction following decades of continuous decline. At the phylum level, the blood microbiome signature was dominated by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria. Apart from a few minor differences, particularly concerning the lower prevalence of Firmicutes, this taxonomic structure at the phylum level was similar to that recently described in the circulating microbiome of the Greenland halibut (Reinhardtius hippoglossoides) and Atlantic halibut (Hippoglossus hippoglossus) in the Gulf of St. Lawrence [20]. However, we could distinguish two populations with distinct blood microbiome signatures at the lower ranks. The presence of Alphaproteobacteria primarily dominated the first signature. At the same time, the second showed the dominance of Gammaproteobacteria and a very heterogeneous signature at the order and family levels, a notable difference from the first group dominated by Rhizobiales and Bradyrhizobiaceae. Interestingly, the second group had a signature dominated by the Nitrobacter and Sediminibacterium genera, which are involved in the nitrogen cycle [32]. Finally, we found that the taxonomic and phylogenetic structures of the bacterial community were restricted to specific regions of the SGSL, suggesting that the environment directly impacts the circulating microbiome. The data revealed exciting clinical prospects for using a blood microbiome genetic signature for detecting dysbiosis, risk stratification, and disease surveillance of the cod population in response to environmental changes.
In medicine, the characterization of the peripheral blood-derived microbiome signature, defined as blood microbial DNA, is increasingly used by clinicians to assess an individual's health status, detect dysbiosis and potential pathogens, or as a biomarker to inform disease severity and progression [33–37]. This concept is also gaining momentum in ecology as the circulating microbiome of dogs, bovine, wild birds and wild fish populations were recently studied, showing that the genetic structure of the blood microbiome, just as in humans, is modulated by genetic and spatiotemporal factors, as well as disease conditions [20, 38–41]. In the present study, the observed shift toward the dominance of Nitrobacter and Sediminibacterium suggests that environmental factors severely impact the blood microbiome signature. The presence of Sediminibacterium is not uncommon in aquatic species [42–44]. In trout, the presence of this genus is sensitive to seasonal changes (Savard et al., 2023). Its presence is also not uncommon in dysbiotic microbiome profiles. In humans, for example, its presence is associated with lung cancer diagnosis and is in higher abundance in the circulating microbiome of type 2 diabetes mellitus patients [45, 46]. The presence of Nitrobacter is also not uncommon in dysbiotic microbiomes. The Nitrobacter genus plays a role in the nitrogen cycle, as it can oxidize nitrite (NO2−) to nitrate (NO3−). To our knowledge, however, this dominance of Nitrobacter has not been reported in wild fish populations in the past, although bacteria associated with the metabolism of nitro compounds have been found, albeit at lower levels, in the blood microbiome, gut or skin microbiome of various animals, including bovine and fish [40, 47–49]. Experimentally, however, exposure of goldfish to nitrite has been shown to induce a shift in the gill, nose and skin microbiome toward bacterial communities involved in the nitrogen cycle and the disappearance of taxa generally found in the microbiome [50]. Usually, nitrite, an intermediate stage in the nitrogen balance, should not be detectable in a stable environment. High surface nitrite/nitrate concentrations are not uncommon in marine coastal ecosystems, as it is commonly released in seawater because of agricultural activity [51–53]. Whether this dysbiotic microbiome signature is associated with health issues in cod will require future investigation.
The presence of Nitrobacter and Sediminibacterium in population A contrasted with the microbiome profile of population B, where we found DNA derived from Pseudoalteromonas, a genus of marine bacteria commonly found in marine species, such as sponges, shellfish, macroalgae and fish, including wild fish populations of the Greenland halibut and Atlantic halibut of the Gulf of St. Lawrence [20, 54–57]. Considered a mutualistic bacterium that plays a vital role in the fitness and survival of its host, this genus is known to adapt well to cold environments. It can synthesize bioactive compounds with strong antibacterial and antitumor properties [54, 58, 59].
Our study revealed the existence of two distinct microbiome signatures in cod populations. We found, however, no significant difference in the α-diversity of both microbiomes. Differences in sex, relative condition or maturity classes were neither associated with a specific signature. Similar conclusions were drawn when we looked for temperature, salinity, or depth differences. Our analysis showed, however, that individuals with a Nitrobacter-rich microbiome (group A) were explicitly found in samples collected near the north coast of Cape Breton Island. Whether this is explained by a specific diet, environmental conditions, or distinct migratory patterns combined with seasonal variations is presently unclear. All these factors have been shown to impact the microbiome of marine fish populations [56, 60–65]. Seasonal variations may also explain such variations. For example, during winter, the SGSL contains high concentrations of total nitrate (NO2− + NO3−), which is later consumed in the spring by algal blooms (Figure S3) [66]. The presence of Nitrobacter reflects a high concentration of nitrite, but whether the GSL nitrite composition has been impacted by humans (agricultural and aquacultural waste) or by a natural origin in currents remains unclear. Alternatively, both signatures may reflect distinctive migratory behavior.
It is important to remember that our study is based on DNA sequencing analysis of DNA extracted from blood samples. It does not necessarily reflect the presence of bacteria in the blood. Although the presence of bacteria in the blood of healthy individuals remains debatable, this does not hold in diseased individuals where damaged epithelial membrane integrity is impaired, leading to dysbiotic profiles in the blood microbiome [67]. Such changes in the blood microbiome are increasingly used to delineate the onset, progression and treatment of diseases, not only in the case of infectious diseases but also in a variety of other conditions, including cancer, metabolic, neurological and cardiovascular diseases, as well as for detecting behavioral anomalies[33, 36, 68, 69]. The use of the blood microbiome in marine biology is only in its infancy, but it offers a new perspective to better assess the health status of wild fish populations.