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There are gaps in our understanding of sturgeon's response to anthropogenic sounds and the spatial scales at which they occur. We measured spatial displacement of Atlantic sturgeon in the St. Lawrence River at various distances of approaching merchant ships. This fish population is designated as "threatened," although anthropogenic noise is not currently considered a direct threat. For several years, Atlantic sturgeon migrations have been monitored by the Quebec government using acoustic transmitters and a network of telemetry receivers in the St. Lawrence River. We combined fish telemetry data with merchant ship positions to detect co-occurrences between Atlantic sturgeons that remained in the vicinity of the receivers and approaching ships. Numerical simulations reveal that the probability of masking of transmitters (69 kHz) by ship noise was infinitesimal and that the disappearance of the transmitter signal was related to fish movement. When the ships approached, a significant spatial displacement was detected with ships at distances between 0.5 and 5 km from the receivers. After emitter signal loss, over 61% of sturgeons took at least 30 min to be detected again or did not return at all in the vicinity of the receivers. Furthermore, the median time to redetection after a ship transit was longer than when no ship was approaching (31 vs. 18 min). Our results show that sturgeons alter their position due to approaching ships at greater trigger distances than previously documented, which are too far away to be attributed to visual cues alone. We also found that the long-distance propagation of low-frequency sounds from large ships through water should not be heard by Atlantic sturgeon at distances of 1 km and longer based on current knowledge of sturgeons hearing. These results suggest that behavioral responses in Atlantic sturgeons are modulated not only by visual cues but can also be triggered by underwater sounds at relatively long distances, although the precise mechanism is still unknown., (© 2024 The Author(s). Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

The endangered beluga whale (Delphinapterus leucas) of the St. Lawrence Estuary (SLEB) faces threats from a variety of anthropogenic factors. Since belugas are a highly social and vocal species, passive acoustic monitoring has the potential to deliver, in a non-invasive and continuous way, real-time information on SLEB spatiotemporal habitat use, which is crucial for their monitoring and conservation. In this study, we introduce an automatic pipeline to analyze continuous passive acoustic data and provide standard and accurate estimations of SLEB acoustic presence and vocal activity. An object detector extracted vocalizations of beluga whales from an acoustic recording of beluga vocal activity. Then, two deep learning classifiers discriminated between high-frequency call types (40-120 kHz) and the presence of low-frequency components (0-20 kHz), respectively. Different algorithms were tested for each step and their main combinations were compared in time and performance. We focused our work on a high residency area, Baie Sainte-Marguerite (BSM), used for socialization and feeding by SLEB. Overall, this project showed that accurate continuous analysis of SLEB vocal activity at BSM could provide valuable information to estimate habitat use, link beluga behavior and acoustic activity within and between herds, and quantify beluga presence and abundance., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

Anthropogenic noise from navigation is a major contributor to the disturbance of the acoustic soundscape in underwater environments containing noise-sensitive life forms. While previous studies mostly developed protocols for the empirical determination of noise source levels associated with the world's commercial fleet, this work explores the radiated noise emitted by small recreational vessels that thrive in many coastal waters, such as in the St. Lawrence Estuary beluga population's summer habitat. Hydrophone-based measurements in the Saguenay River (QC, Canada) were carried out during the summers of 2021 and 2022. Shore-based observations identified 45 isolated transits of small, motorized vessels and were able to track their displacement during their passage near the hydrophone. Received noise levels at the hydrophone typically fell below the hearing audiogram of the endangered St. Lawrence Estuary beluga. Monopole source levels at low frequencies (0.1-≲2 kHz) held on average twice the acoustic power compared to their mid-frequency (≳2-30 kHz) counterparts. The speed over ground of recreational vessel showed a positive correlation with the back-propagated monopole source levels. Estimations of the mid-frequency noise levels based on low-frequency measurements should be used moderately.

Exposure to anthropogenic noise from the commercial fleet is one of the primary constituents of the acoustic pollution perturbing the environment of aquatic life. Merchant ships (e.g. bulkers, tankers) have been the focus of numerous studies for underwater noise source level determination and modeling. This work extends pre-existing studies to the ferry ship class. Hydrophone-based measurements of the N.M. Trans-Saint-Laurent ferry near the Rivière-du-Loup harbor (Rivière-du-Loup, QC CANADA) were obtained for 186 transits between 2020 July 22th and 2020 September 5th. For each transit, monopole source levels are estimated for two (2) different modes of operation i.e., the low-speed phases of acceleration/deceleration when the ferry launches/docks at Rivière-du-Loup and the passages at quasi-operational speed at the hydrophone's closest-point-of-approach. Relative differences between the two (2) modes of operation are presented here in the low-frequency domain between 141 and 707 Hz. An average excess of 8 to 11.5 dB indicates that the ferry is likely one order of magnitude noisier, within this frequency band, during acceleration/deceleration when compared to passages at operational speed. This highlights that, in terms of marine mammal conservation, a significant reduction of the noise pollution could be achieved, for instance, by avoiding sudden speed changes in the vicinity of whales., (© 2022. The Author(s).)

A key aspect of ocean protection consists in estimating the abundance of marine mammal population density within their habitat, which is usually accomplished using visual inspection and cameras from line-transect ships, small boats, and aircraft. However, marine mammal observation through vessel surveys requires significant workforce resources, including for the post-processing of pictures, and is further challenged due to animal bodies being partially hidden underwater, small-scale object size, occlusion among objects, and distracter objects (e.g., waves, sun glare, etc.). To relieve the human expert's workload while improving the observation accuracy, we propose a novel system for automating the detection of beluga whales ( Delphinapterus leucas ) in the wild from pictures. Our system relies on a dataset named Beluga-5k, containing more than 5.5 thousand pictures of belugas. First, to improve the dataset's annotation, we have designed a semi-manual strategy for annotating candidates in images with single (i.e., one beluga) and multiple (i.e., two or more belugas) candidate subjects efficiently. Second, we have studied the performance of three off-the-shelf object-detection algorithms, namely, Mask-RCNN, SSD, and YOLO v3-Tiny, on the Beluga-5k dataset. Afterward, we have set YOLO v3-Tiny as the detector, integrating single- and multiple-individual images into the model training. Our fine-tuned CNN-backbone detector trained with semi-manual annotations is able to detect belugas despite the presence of distracter objects with high accuracy (i.e., 97.05 mAP@0.5). Finally, our proposed method is able to detect overlapped/occluded multiple individuals in images (beluga whales that swim in groups). For instance, it is able to detect 688 out of 706 belugas encountered in 200 multiple images, achieving 98.29% precision and 99.14% recall.

Estimating the impacts of anthropogenic disturbances requires an understanding of the habitat-use patterns of individuals within a population. This is especially the case when disturbances are localized within a population's spatial range, as variation in habitat use within a population can drastically alter the distribution of impacts.Here, we illustrate the potential for multilevel binomial models to generate spatial networks from capture-recapture data, a common data source used in wildlife studies to monitor population dynamics and habitat use. These spatial networks capture which regions of a population's spatial distribution share similar/dissimilar individual usage patterns, and can be especially useful for detecting structured habitat use within the population's spatial range.Using simulations and 18 years of capture-recapture data from St. Lawrence Estuary (SLE) beluga, we show that this approach can successfully estimate the magnitude of similarities/dissimilarities in individual usage patterns across sectors, and identify sectors that share similar individual usage patterns that differ from other sectors, that is, structured habitat use. In the case of SLE beluga, this method identified multiple clusters of individuals, each preferentially using restricted areas within their summer range of the SLE.Multilevel binomial models can be effective at estimating spatial structure in habitat use within wildlife populations sampled by capture-recapture of individuals, and can be especially useful when sampling effort is not evenly distributed. Our finding of a structured habitat use within the SLE beluga summer range has direct implications for estimating individual exposures to localized stressors, such as underwater noise from shipping or other activities., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Vessel underwater noise (VUN) is one of the main threats to the recovery of the endangered St. Lawrence Estuary Beluga population (SLEB). The 1% yearly population decline indicates that the cumulative threats are already beyond sustainable limits for the SLEB. However, a potential threefold increase in shipping traffic is expected within its critical habitat in the coming years resulting from proposed port-industrial projects in the Saguenay River. Current data indicate that SLEB typically use multiple sectors within their summer range, likely leading to differential VUN exposure among individuals. The degree of displacement and spatial mixing among habitats are not yet well understood but can be simulated under different assumptions about movement patterns at the individual and population levels. Here, we propose using an agent-based model (ABM) to explore the biases introduced when estimating exposure to stressors such as VUN, where individual-centric movement patterns and habitat use are derived from different spatial behaviour assumptions. Simulations of the ABM revealed that alternative behavioural assumptions for individual belugas can significantly alter the estimation of instantaneous and cumulative exposure of SLEB to VUN. Our simulations also predicted that with the projected traffic increase in the Saguenay River, the characteristics making it a quiet zone for SLEB within its critical habitat would be nullified. Whereas spending more time in the Saguenay than in the Estuary allows belugas to be exposed to less noise under the current traffic regime, this relationship is reversed under the increased traffic scenario. Considering the importance of the Saguenay for SLEB females and calves, our results support the need to understand its role as a possible acoustic refuge for this endangered population. This underlines the need to understand and describe individual and collective beluga behaviours using the best available data to conduct a thorough acoustic impact assessment concerning future increased traffic., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Lethal collisions with ships are limiting the recovery of several at-risk whale species worldwide. In the St. Lawrence Estuary (Quebec, Canada), the endangered blue whale and of special concern fin whale are among the migratory species subject to collisions with large ships. In 2011, a working group composed of representatives from the maritime industry, the government, non-governmental organizations, and academia was created to explore solutions to mitigate ship-whale collisions in the St. Lawrence Estuary. Adopting an adaptive risk management framework, the working group took advantage of the best available scientific data and tools to co-construct realistic collision mitigation options and evaluate their likely benefits for whale conservation and costs for the industry. In 2013, the working group recommended the implementation of voluntary measures to mitigate collision risks, consisting of a slow-down area, a no-go area, and a caution area; a recommended route was added in 2014. Along with the voluntary framework, the working group agreed to continuously monitor compliance with and assess effectiveness of these mitigation measures. After the fourth year of implementation, voluntary measures showed encouraging results, with a reduction of up to 40% of lethal collision risks with fin whales in the highest density area. This reduction in risk is mainly related to ship speed reduction in the slow-down area from 14.1 ± 2.6 knots in 2012 to 11.3 ± 1.7 knots since 2014. The presence of a mandatory pilotage area overlapping with the slow-down area was instrumental to facilitate communication about the mitigation measures, with the pilotage corporation sitting as a regular member of the working group. This resulted in significantly slower speeds in the slow-down area for ships with a pilot from the pilotage corporation onboard compared to those without (-0.8 knots, p-value < 0.001). It is also likely to explain the weaker compliance of the maritime industry with the no-go area located outside of the mandatory pilotage area. Other factors of success include: the continuous dedication of the government to a voluntary and transparent participatory process; the use of available data, tools and institutions; the presence of an environmental certification program representative in the working group; and the adoption by consensus of an adaptive risk management approach. The traditional regulatory approach to conservation is often blamed for its focus on deterring negative behaviors, doing nothing to encourage and reward positive ones. In agreement with other case studies, the benefits of the voluntary measures implemented in the St. Lawrence Estuary include the pro-active commitment from the industry (which is likely to reduce conflicts with regulators), the greater flexibility and freedom that allowed to come up with cost-effective and tailored-made mitigation measures, and the fast achievement of conservation gains. More importantly perhaps, the human and working capital built throughout the concertation process have the potential to be a fundamental cornerstone in dealing with more complex issues such as the chronically increasing level of underwater noise in whale habitats., Competing Interests: The authors have declared that no competing interests exist.

The genes encoding the six polypeptide components of the alkene monooxygenase from Xanthobacter strain Py2 (Xamo) have been located on a 4.9-kb fragment of chromosomal DNA previously cloned in cosmid pNY2. Sequencing and analysis of the predicted amino acid sequences indicate that the components of Xamo are homologous to those of the aromatic monooxygenases, toluene 2-, 3-, and 4-monooxygenase and benzene monooxygenase, and that the gene order is identical. The genes and predicted polypeptides are aamA, encoding the 497-residue oxygenase alpha-subunit (XamoA); aamB, encoding the 88-residue oxygenase gamma-subunit (XamoB); aamC, encoding the 122-residue ferredoxin (XamoC); aamD, encoding the 101-residue coupling or effector protein (XamoD); aamE, encoding the 341-residue oxygenase beta-subunit (XamoE); and aamF, encoding the 327-residue reductase (XamoF). A sequence with >60% concurrence with the consensus sequence of sigma54 (RpoN)-dependent promoters was identified upstream of the aamA gene. Detailed comparison of XamoA with the oxygenase alpha-subunits from aromatic monooxygenases, phenol hydroxylases, methane monooxygenase, and the alkene monooxygenase from Rhodococcus rhodochrous B276 showed that, despite the overall similarity to the aromatic monooxygenases, XamoA has some distinctive characteristics of the oxygenases which oxidize aliphatic, and particularly alkene, substrates. On the basis of the similarity between Xamo and the aromatic monooxygenases, Xanthobacter strain Py2 was tested and shown to oxidize benzene, toluene, and phenol, while the alkene monooxygenase-negative mutants NZ1 and NZ2 did not. Benzene was oxidized to phenol, which accumulated transiently before being further oxidized. Toluene was oxidized to a mixture of o-, m-, and p-cresols (39.8, 18, and 41.7%, respectively) and a small amount (0.5%) of benzyl alcohol, none of which were further oxidized. In growth studies Xanthobacter strain Py2 was found to grow on phenol and catechol but not on benzene or toluene; growth on phenol required a functional alkene monooxygenase. However, there is no evidence of genes encoding steps in the metabolism of catechol in the vicinity of the aam gene cluster. This suggests that the inducer specificity of the alkene monooxygenase may have evolved to benefit from the naturally broad substrate specificity of this class of monooxygenase and the ability of the host strain to grow on catechol.

The epoxide hydrolase (EH) from Corynebacterium sp. C12, which grows on cyclohexene oxide as sole carbon source, has been purified to homogeneity in two steps, involving anion exchange followed by hydrophobic-interaction chromatography. The purified enzyme is multimeric (probably tetrameric) with a subunit size of 32,140 Da. The gene encoding Corynebacterium EH was located on a 3.5-kb BamHI fragment of C12 chromosomal DNA using a DNA probe generated by PCR using degenerate primers based on the N-terminal and an internal amino acid sequence. Sequencing and database comparison of the predicted amino acid sequence of Corynebacterium EH shows that it is similar to mammalian and plant soluble EH, and the recently published sequence of epichlorohydrin EH from Agrobacterium radiobacter AD1 [Rink, R., Fennema, M., Smids, M., Dehmel, U. & Janssen, D. B. (1997) J. Biol. Chem. 272, 14650- 14657), particularly around the catalytic site. All of these proteins belong to the alpha/beta-hydrolase-fold family of enzymes. Similarity to the mammalian microsomal EH is weaker.

Epoxypropane isomerase from Xanthobacter Py2 has been resolved into at least two components (A and B) by ion-exchange chromatography. Both components were required for the degradation of epoxypropane and were purified further. Component A was apparently homohexameric with a subunit M(r) of about 44,000, and possessed NAD(+)-dependent dihydrolipoamide dehydrogenase activity and lipoamide reductase activity. It was sensitive to inhibition by o-phenanthroline and the thiol-specific reagents N-ethylmaleimide(NEM)and p-chloromercuribenzoate. Component B was homodimeric with a subunit M(r), of 62,170 and contained 2 mol.mol-1 FAD. It had an NADPH-dependent lipoamide reductase activity which was sensitive to NEM and p-chloromercuribenzoate. The N-terminal amino acid sequences and monomer sizes of components A and B correspond to those of ORF1 and ORF3 respectively (ORF = open reading frame) of a recently published sequence of a clone which complements mutants unable to degrade epoxypropane. NADPH was found to replace the need for a low-M(r), fraction in epoxypropane degradation assays containing components A and B and NAD+. The predicted amino acid sequence of component A (ORF1) has been analysed and shown to contain a potential ADP binding site near the N-terminus and putative cofactor binding domain near the C-terminus, with sequence similarity to the biotinyl and lipoyl binding domains of biotin-dependent carboxylases and 2-oxoacid dehydrogenases respectively. A reaction mechanism for epoxypropane degradation, incorporating recent evidence for combined isomerization and carboxylation to acetoacetate, is discussed.

The cat reporter gene was used to assess expression of two promoters, previously strongly expressed in Escherichia coli, in Brevibacterium sp. R312 strain. The tac promoter (de Boer et al., 1983, Proc. Natl. Acad. Sci. USA 80, 21-25) was poorly expressed in Brevibacterium sp. In contrast, the AatII-SalI fragment of plasmid pYEJ001 (Pharmacia LKB Biotechnology, Sweden) containing two lac operators, a consensus sequence promoter and the cat structural gene clearly revealed chloramphenicol acetyltransferase activity and the presence of a 25,600-kDa protein, corresponding to the monomeric CAT protein, in cell extracts.

Promoter sequences recognized by Escherichia coli RNA polymerase were isolated from Brevibacterium sp. R312, a coryneform strain producing nitrile hydratase and amidase. Ten Escherichia coli clones containing promoter sequences were selected for their ability to grow with chloramphenicol concentrations of up to 1500 micrograms/ml. The strength of these promoter sequences was determined. We carried out a preliminary study of the strongest promoter having a chloramphenicol acetyl-transferase/beta-lactamase activities ratio of 18.4.

A wide-spectrum amidase from Brevibacterium sp. R312 was partially purified. The enzyme subunit was purified by reversed phase HPLC and the N-terminal amino acid sequence was found to be identical to that of Pseudomonas aeruginosa aliphatic amidase.

Replication of several cryptic plasmids from coryneform strains was investigated in Brevibacterium sp. R312. Only the Corynebacterium glutamicum pSR1 replicon was found to be suitable for establishing a host-vector system. Two pSR1 derivatives, pRPCG200 and pHYCG1, were used as cloning vectors. They carry a neomycin-resistance-encoding and a tetracycline-resistance-encoding gene, respectively.