Information retrieval from marine soundscape by using machine learning-based source separation

In remote sensing of the marine ecosystem, visual information retrieval is limited by the low visibility in the ocean environment. Marine soundscape has been considered as an acoustic sensing platform of the marine ecosystem in recent years. By listening to environmental sounds, biological sounds, and human-made noises, it is possible to acoustically identify various geophysical events, soniferous marine animals, and anthropogenic activities. However, the sound detection and classification remain a challenging task due to the lack of underwater audio recognition database and the simultaneous interference of multiple sound sources. To facilitate the analysis of marine soundscape, we have employed information retrieval techniques based on non-negative matrix factorization (NMF) to separate different sound sources with unique spectral-temporal patterns in an unsupervised approach. NMF is a self-learning algorithm which decomposes an input matrix into a spectral feature matrix and a temporal encoding matrix. Therefore, we can stack two or more layers of NMF to learn the spectral-temporal modulation of k sound sources without any learning database [1]. In this presentation, we will demonstrate the application of NMF in the separation of simultaneous sound sources appeared on a long-term spectrogram. In shallow water soundscape, the relative change of fish chorus can be effectively quantified even in periods with strong mooring noise [2]. In deep-sea soundscape, cetacean vocalizations, an unknown biological chorus, environmental sounds, and systematic noises can be efficiently separated [3]. In addition, we can use the features learned in procedures of blind source separation as the prior information for supervised source separation. The self-adaptation mechanism during iterative learning can help search the similar sound source from other acoustic dataset contains unknown noise types. Our results suggest that the NMF-based source separation can facilitate the analysis of the soundscape variability and the establishment of audio recognition database. Therefore, it will be feasible to investigate the acoustic interactions among geophysical events, soniferous marine animals, and anthropogenic activities from long-duration underwater recordings. REFERENCES: 1. Lin, T.-H., Fang, S.-H., Tsao. Y. 2017. Improving biodiversity assessment via unsupervised separation of biological sounds from long-duration recordings. Sci Rep, 7: 4547. 2. Lin, T.-H., Tsao. Y., Akamatsu, T. 2018. Comparison of passive acoustic soniferous fish monitoring with supervised and unsupervised approaches. J. Acoust. Soc. Am. Express Letters, 143: EL278. 3. Lin, T.-H., Tsao. Y. 2018. Listening to the deep: Exploring marine soundscape variability by information retrieval techniques. OCEANS'18 MTS/IEEE Kobe / Techno-Ocean 2018, in press

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidiwn diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.Japan Society for the Promotion of ScienceJapan Agcy Marine Earth Sci & Technol, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2370061, JapanUniv Vale Itajal, Dept Biol Sci, CTTMar, R Uruguai 458, BR-88302202 Itajal, SC, BrazilUniv Fed Sao Paulo, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, BrazilUniv Sao Paulo, Inst Oceanog, 191 Praca Oceanog, BR-05508120 Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, BrazilJSPS: 23770098JSPS: 15K18601Web of Scienc

In situ fluorochrome calcein marking of deep-sea molluscs using a new growth chamber

Abstract A new instrument designed for in situ chemical marking experiments was developed and applied to the deep-sea seep clams Calyptogena soyoae and Calyptogena okutanii. Fluorochrome calcein was used for vital staining of four living clams kept in a specially designed in situ growth chamber that was placed on the seafloor at a coldseep site off Hatsushima Island, Sagami Bay, central Japan. The shell margins of both C. soyoae and C. okutanii were clearly stained, forming a thin fluorescent band. This method will be useful for age and growth-rate determinations of many other marine organisms with accretionary growing skeletons

Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific

Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P.  clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities

Marine Biodiversity in Japanese Waters

To understand marine biodiversity in Japanese waters, we have compiled information on the marine biota in Japanese waters, including the number of described species (species richness), the history of marine biology research in Japan, the state of knowledge, the number of endemic species, the number of identified but undescribed species, the number of known introduced species, and the number of taxonomic experts and identification guides, with consideration of the general ocean environmental background, such as the physical and geological settings. A total of 33,629 species have been reported to occur in Japanese waters. The state of knowledge was extremely variable, with taxa containing many inconspicuous, smaller species tending to be less well known. The total number of identified but undescribed species was at least 121,913. The total number of described species combined with the number of identified but undescribed species reached 155,542. This is the best estimate of the total number of species in Japanese waters and indicates that more than 70% of Japan's marine biodiversity remains un-described. The number of species reported as introduced into Japanese waters was 39. This is the first attempt to estimate species richness for all marine species in Japanese waters. Although its marine biota can be considered relatively well known, at least within the Asian-Pacific region, considering the vast number of different marine environments such as coral reefs, ocean trenches, ice-bound waters, methane seeps, and hydrothermal vents, much work remains to be done. We expect global change to have a tremendous impact on marine biodiversity and ecosystems. Japan is in a particularly suitable geographic situation and has a lot of facilities for conducting marine science research. Japan has an important responsibility to contribute to our understanding of life in the oceans

Open Ocean Deep Sea

The deep sea comprises the seafloor, water column and biota therein below aspecified depth contour. There are differences in views among experts and agencies regarding the appropriate depth to delineate the “deep sea”. This chapter uses a 200 metre depth contour as a starting point, so that the “deep sea” represents 63 per cent of the Earth’s surface area and about 98.5 per cent of Earth’s habitat volume (96.5 per cent of which is pelagic). However, much of the information presented in this chapter focuses on biodiversity of waters substantially deeper than 200 m. Many of the other regional divisions of Chapter 36 include treatments of shelf and slope biodiversity in continental-shelf and slope areas deeper than 200m. Moreover Chapters 42 and 45 on coldwater corals and vents and seeps, respectively, and 51 on canyons, seamounts and other specialized morphological habitat types address aspects of areas in greater detail. The estimates of global biodiversity of the deep sea in this chapter do include all biodiversity in waters and the seafloor below 200 m. However, in the other sections of this chapter redundancy with the other regional chapters is avoided, so that biodiversity of shelf, slope, reef, vents, and specialized habitats is assessed in the respective regional or thematic chapters. AB - The deep sea comprises the seafloor, water column and biota therein below aspecified depth contour. There are differences in views among experts and agencies regarding the appropriate depth to delineate the “deep sea”. This chapter uses a 200 metre depth contour as a starting point, so that the “deep sea” represents 63 per cent of the Earth’s surface area and about 98.5 per cent of Earth’s habitat volume (96.5 per cent of which is pelagic). However, much of the information presented in this chapter focuses on biodiversity of waters substantially deeper than 200 m. Many of the other regional divisions of Chapter 36 include treatments of shelf and slope biodiversity in continental-shelf and slope areas deeper than 200m. Moreover Chapters 42 and 45 on coldwater corals and vents and seeps, respectively, and 51 on canyons, seamounts and other specialized morphological habitat types address aspects of areas in greater detail. The estimates of global biodiversity of the deep sea in this chapter do include all biodiversity in waters and the seafloor below 200 m. However, in the other sections of this chapter redundancy with the other regional chapters is avoided, so that biodiversity of shelf, slope, reef, vents, and specialized habitats is assessed in the respective regional or thematic chapters.https://nsuworks.nova.edu/occ_facbooks/1050/thumbnail.jp

Mucus glycoproteins selectively secreted from bacteriocytes in gill filaments of the deep-sea clam Calyptogena okutanii

The deep-sea clam Calyptogena okutanii possesses a large gill containing vertically transmitted symbiotic sul-fur-oxidizing bacteria. It produces large amounts of highly viscoelastic mucus from the gill, which is thought to be a physical and chemical barrier. The mucus collected from the gill was shown to be composed of glycoproteins having the following sugar composition: Man (17.4%), GlcNAc (16.6%), GalNAc (15%), Glc (1.1%), Gal (29.9%), Xyl (3.0%), Fuc (14.4%), and unknown (2.6%), indicating that it contained mucin-like glycoproteins. In a monoclonal antibody li-brary against the gill tissue, we found a monoclonal antibody (mAb), CokG-B3C10, reacting to the mucus. Western blot analysis using the mAb showed that it reacted to several glycoproteins in the mucus from the gill tissue, but not with those of other tissues such as the mantle, foot, and ovary, where mucus production has been reported in bivalves. Fur-ther, immunohistochemical analysis showed the CokG-B3C10 mAb reacting to glycoproteins was detected in the inner area of the gill, which was occupied by many bacteriocytes in the row of gill filaments. Strong mAb signals were found on the outer surface of the bacteriocytes facing the interfilamental space, and in the interfilamental spaces between filaments. Weaker signals were also observed in the bacteriocyte cells. These results indicate that the CokG-B3C10 mAb-binding mucus glycoproteins were produced from cells including bacteriocytes and nonbacteriocyte cells in the inner area of the gill filaments.http://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt09-06_leg1/ehttp://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt10-01/ehttp://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt10-08/

Nationwide surveillance of bacterial respiratory pathogens conducted by the surveillance committee of Japanese Society of Chemotherapy, the Japanese Association for Infectious Diseases, and the Japanese Society for Clinical Microbiology in 2010: General view of the pathogens\u27 antibacterial susceptibility

The nationwide surveillance on antimicrobial susceptibility of bacterial respiratory pathogens from patients in Japan, was conducted by Japanese Society of Chemotherapy, Japanese Association for Infectious Diseases and Japanese Society for Clinical Microbiology in 2010.The isolates were collected from clinical specimens obtained from well-diagnosed adult patients with respiratory tract infections during the period from January and April 2010 by three societies. Antimicrobial susceptibility testing was conducted at the central reference laboratory according to the method recommended by Clinical and Laboratory Standard Institutes using maximum 45 antibacterial agents.Susceptibility testing was evaluable with 954 strains (206 Staphylococcus aureus, 189 Streptococcus pneumoniae, 4 Streptococcus pyogenes, 182 Haemophilus influenzae, 74 Moraxella catarrhalis, 139 Klebsiella pneumoniae and 160 Pseudomonas aeruginosa). Ratio of methicillin-resistant S.aureus was as high as 50.5%, and those of penicillin-intermediate and -resistant S.pneumoniae were 1.1% and 0.0%, respectively. Among H.influenzae, 17.6% of them were found to be β-lactamase-non-producing ampicillin (ABPC)-intermediately resistant, 33.5% to be β-lactamase-non-producing ABPC-resistant and 11.0% to be β-lactamase-producing ABPC-resistant strains. Extended spectrum β-lactamase-producing K.pneumoniae and multi-drug resistant P.aeruginosa with metallo β-lactamase were 2.9% and 0.6%, respectively.Continuous national surveillance of antimicrobial susceptibility of respiratory pathogens is crucial in order to monitor changing patterns of susceptibility and to be able to update treatment recommendations on a regular basis