Fast and accurate mapping of fine scale abundance of a VME in the deep sea with computer vision

With growing anthropogenic pressure on deep-sea ecosystems, large quantities of data are needed to understand their ecology, monitor changes over time and inform conservation managers. Current methods of image analysis are too slow to meet these requirements. Recently, computer vision has become more accessible to biologists, and could help address this challenge. In this study we demonstrate a method by which non-specialists can train a YOLOV4 Convolutional Neural Network (CNN) able to count and measure a single class of objects. We apply CV to the extraction of quantitative data on the density and population size structure of the xenophyophore Syringammina fragilissima, from more than 58,000 images taken by an AUV 1200 m deep in the North-East Atlantic. The workflow developed used open-source tools, cloud-base hardware, and only required a level of experience with CV commonly found among ecologists. The CNN performed well, achieving a recall of 0.84 and precision of 0.91. Individual counts per image and size measurements resulting from model predictions were highly correlated (0.96 and 0.92, respectively) with manually collected data. The analysis could be completed in less than 10 days thus bringing novel insights into the population size structure and fine scale distribution of this Vulnerable Marine Ecosystem. It showed S. fragilissima distribution is patchy. The average density is 2.5 ind.m−2 but can vary from up to 45 ind.m−2 only a few tens of meter away from areas where it is almost absent. The average size is 5.5 cm and the largest individuals (>15 cm) tend to be in areas of low density. This study demonstrates how researchers could take advantage of CV to quickly and efficiently generate large quantitative datasets data on benthic ecosystems extent and distribution. This, coupled with the large sampling capacity of AUVs could bypass the bottleneck of image analysis and greatly facilitate future deep-ocean exploration and monitoring. It also illustrates the future potential of these new technologies to meet the goals set by the UN Ocean Decade

The distribution of deep-sea sponge aggregations (Porifera) in relation to oceanographic processes in the Faroe-Shetland Channel.

Deep-sea sponge aggregations have been identified as potential Vulnerable Marine Ecosystems under United Nations General Assembly Resolution 61/105. Understanding the distribution of these habitats is critical to future spatial management efforts, and central to this understanding are quantitative data on the environmental drivers of that distribution. Accumulations of large suspension feeders are hypothesised to aggregate in regions of internal wave formation. The causal link is thought to be an increase in the supply of food related to the incidence of internal waves, which results in resuspension of particulate organic matter on which the sponges feed. There is, however, almost no empirical evidence to support this hypothesis for deep-sea sponge aggregations, although there is strong circumstantial evidence. We tested the relationship between sponge density and 1) temperature range (as a measure of internal wave presence in this region), and 2) optical backscatter (a measure of particulate flux) for a known sponge aggregation in the Faroe-Shetland Channel where internal wave interaction with the slope is further well-documented. 25 benthic video transects, ranging from 422 to 979 m water depth were conducted in the study region. 225 images were analysed and all taxa identified to morphotypes and quantified. Temperature and optical backscatter data were drawn from archived CTD data, and data from long term (4 months) and 2 seasonal short term (11 days) mooring deployments from the region. A generalised linear model was used to test the relationship between sponge density and temperature range (ΔT), and sponge density and optical backscatter. The results showed a statistically significant positive relationship between sponge density and temperature range, with the highest sponge densities occurring at depths of greatest temperature range. They showed a statistically significant positive relationship between sponge density and optical backscatter for long term and one short term seasonal deployment (Sep–Oct), but a weak negative relationship for the other short term mooring deployment (April-May). We conclude that sponge aggregations in the Faroe-Shetland Channel are associated with slope regions that are subjected to abrupt and pronounced changes in temperature due to intensified internal wave activity over the slope between depths of 400–600 and that lead to intensified near-bed currents and elevated resuspension of particulate. Our data provide empirical evidence of the relationship between internal wave processes and deep-sea sponge aggregations. These data modify current theory on drivers of deep sea sponge aggregation distribution, suggesting aggregations also occur directly within regions of internal wave breaking, rather than simply proximal to these regions

Marine plastics threaten giant Atlantic Marine Protected Areas.

There has been a recent shift in global perception of plastics in the environment, resulting in a call for greater action. Science and the popular media have highlighted plastic as an increasing stressor [1,2]. Efforts have been made to confer protected status to some remote locations, forming some of the world's largest Marine Protected Areas, including several UK overseas territories. We assessed plastic at these remote Atlantic Marine Protected Areas, surveying the shore, sea surface, water column and seabed, and found drastic changes from 2013-2018. Working from the RRS James Clark Ross at Ascension, St. Helena, Tristan da Cunha, Gough and the Falkland Islands (Figure 1A), we showed that marine debris on beaches has increased more than 10 fold in the past decade. Sea surface plastics have also increased, with in-water plastics occurring at densities of 0.1 items m-3; plastics on seabeds were observed at ≤ 0.01 items m-2. For the first time, beach densities of plastics at remote South Atlantic sites approached those at industrialised North Atlantic sites. This increase even occurs hundreds of meters down on seamounts. We also investigated plastic incidence in 2,243 animals (comprising 26 species) across remote South Atlantic oceanic food webs, ranging from plankton to seabirds. We found that plastics had been ingested by primary consumers (zooplankton) to top predators (seabirds) at high rates. These findings suggest that MPA status will not mitigate the threat of plastic proliferation to this rich, unique and threatened biodiversity

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem

Identification of a General O-linked Protein Glycosylation System in Acinetobacter baumannii and Its Role in Virulence and Biofilm Formation

Acinetobacter baumannii is an emerging cause of nosocomial infections. The isolation of strains resistant to multiple antibiotics is increasing at alarming rates. Although A. baumannii is considered as one of the more threatening “superbugs” for our healthcare system, little is known about the factors contributing to its pathogenesis. In this work we show that A. baumannii ATCC 17978 possesses an O-glycosylation system responsible for the glycosylation of multiple proteins. 2D-DIGE and mass spectrometry methods identified seven A. baumannii glycoproteins, of yet unknown function. The glycan structure was determined using a combination of MS and NMR techniques and consists of a branched pentasaccharide containing N-acetylgalactosamine, glucose, galactose, N-acetylglucosamine, and a derivative of glucuronic acid. A glycosylation deficient strain was generated by homologous recombination. This strain did not show any growth defects, but exhibited a severely diminished capacity to generate biofilms. Disruption of the glycosylation machinery also resulted in reduced virulence in two infection models, the amoebae Dictyostelium discoideum and the larvae of the insect Galleria mellonella, and reduced in vivo fitness in a mouse model of peritoneal sepsis. Despite A. baumannii genome plasticity, the O-glycosylation machinery appears to be present in all clinical isolates tested as well as in all of the genomes sequenced. This suggests the existence of a strong evolutionary pressure to retain this system. These results together indicate that O-glycosylation in A. baumannii is required for full virulence and therefore represents a novel target for the development of new antibiotics

New technologies and applications of laparoscopic and robotic surgery in urology

Background: cool and dry gas insufflation during laparoscopy induces hypothermia and cytokine increase, with significant perioperative morbidity. Few studies have suggested that warmed and humidified insufflation leads to an improved body core temperature (BCT) maintenance, a reduction of the inflammatory response and an improved quality of postoperative course, compared with standard insufflation. Objective: to assess if warmed and humidified CO2 insufflation with HumiGard™ device can achieve significant benefits over standard insufflation in terms of risk of hypothermia and cytokine response, in the setting of robot-assisted radical prostatectomy (RARP). Design: prospective, randomized, controlled clinical trial (September, 2015, June, 2016). Setting: single center study in a tertiary hospital. Participants: 64 patients with prostate cancer undergoing RARP were randomized, 32 to the treatment group and 32 to the control group. Intervention: the treatment group (H+WB) received warmed, humidified CO2 insufflation with HumiGard™ device, plus hot air warming blanket; the control group (WB) received standard CO2 insufflation, plus hot air warming blanket. Main outcomes and measures: BCT, plasma levels of cytokines IL-6 and TNF-α, pain scores, and intraoperative parameters. The data were analyzed according to the Bayesian paradigm. Results: intraoperative BCT increased in both groups during surgery, with a statistically significant difference favoring group H+WB, ending at 0.2°C higher on average than group WB. The overall BCT increase was 0.088 degree per hour in the WB group, with an additional 0.064 degree per hour in the H+WB group. No difference across groups, at none of the time points, could be shown as far as mean serum cytokine levels was concerned. No statistical differences were noted for pain scores and the other intraoperative parameters. Conclusions: during RARP, warm and humidified CO2 insufflation with the HumiGard™ device was more effective than the standard CO2 insufflation in maintaining the patient’s heat homeostasis, even if the difference was minimal. No benefit could be shown in terms of cytokine levels and pain scores. Trial registration: Clinicaltrials.gov Identifier: NCT0258697