Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data

The decline in wild-caught fisheries paired with increasing global seafood demand is pushing the need for seafood sustainability to the forefront of national and regional priorities. Validation of species identity is a crucial early step, yet conventional monitoring and surveillance tools are limited in their effectiveness because they are extremely time-consuming and require expertise in fish identification. DNA barcoding methods are a versatile tool for the genetic monitoring of wildlife products; however, they are also limited by requiring individual tissue samples from target specimens which may not always be possible given the speed and scale of seafood operations. To circumvent the need to individually sample organisms, we pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds on industrial and artisanal fishing vessels in Ecuador. Fish identified genetically as present were compared to target species reported by each vessel’s crew. Additionally, we contrasted the geographic range of identified species against the satellite-based fishing route data of industrial vessels to determine if identified species could be reasonably expected in the catch.publishedVersio

Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data

The decline in wild-caught fisheries paired with increasing global seafood demand is pushing the need for seafood sustainability to the forefront of national and regional priorities. Validation of species identity is a crucial early step, yet conventional monitoring and surveillance tools are limited in their effectiveness because they are extremely time-consuming and require expertise in fish identification. DNA barcoding methods are a versatile tool for the genetic monitoring of wildlife products; however, they are also limited by requiring individual tissue samples from target specimens which may not always be possible given the speed and scale of seafood operations. To circumvent the need to individually sample organisms, we pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds on industrial and artisanal fishing vessels in Ecuador. Fish identified genetically as present were compared to target species reported by each vessel’s crew. Additionally, we contrasted the geographic range of identified species against the satellite-based fishing route data of industrial vessels to determine if identified species could be reasonably expected in the catch

Participatory Boat Tracking Reveals Spatial Fishing Patterns in an Indonesian Artisanal Fishery

The Spermonde Archipelago holds one of the largest artisanal fisheries in Indonesia, providing livelihoods for local communities and many other people involved in international trade networks of seafood. High demand and a lack of enforcement of existing fisheries regulations turn into high pressure for the coral reef ecosystem, contributing to its overall degradation. Estimations on the ecological impacts of different levels of fishing pressure, as well as fisheries stock assessments and marine resource management require precise information of the spatial distribution of fishing effort, which involves great uncertainty when only anecdotal information is considered. We explored the feasibility of applying participatory boat tracking to complement fisheries data during the NW monsoon season 2014–2015. We conducted interviews, measured catch landings, and distributed GPS data loggers among hook and line fishermen to identify fishing grounds by gear-dependent patterns of boat movement. Most of the fishing activities involved two gears (octopus bait and trolling line for live groupers) and three fishing grounds. The mass of catch landings was dominated by Octopoda (CPUE = 10.1 kg boatday−1) while the most diverse group was the fish family Serranidae, with Plectropomus leopardus being the main target species. In conclusion, boat tracking combined with interviews and catch surveys has proven a useful tool to reduce uncertainty in information on spatial resource use, while allowing a high level of participation by fishermen

Fishers' local ecological knowledge to support mangrove research in the Galapagos

Mangroves provide multiple ecosystem services to coastal communities and their fisheries. In the Galapagos, mangroves have been primarily prized for their role as nursery grounds; though, the importance of cultural benefits, including the development of knowledge systems among fishers, needs to be further explored. Fishers' local ecological knowledge (LEK) has been employed in the past to answer questions about the marine environment; not yet about mangroves. In such regard, this ethnoecological approach can contribute to unveil mangrove habitat-dependence relationships among fishery taxa across the life cycle, connectivity among habitats, and productivity spatial patterns across the archipelago. To access fishers' LEK, we conducted 35 semi-structured interviews and 2 facilitated community workshops comprising 3 activities. A photo-elicitation method allowed us to extract values given to mangroves (i.e., ecosystem services), from which indirect use values were considered more relevant for fisheries. As such, the accumulation of LEK might have been crucial for the establishment of these values among fishers. By using a species-habitat association method, we revealed a high perceived connectivity between mangroves and other coastal and marine habitats in the Galapagos. Although this suggests an overall weak dependence to the ecosystem, fishers' anecdotes allowed us to recognize novel species occurrences and exclusive habitat uses (e.g., spawning in Centropomus viridis). By applying Social Network Analysis to species-habitat association results, we learned that certain migratory commercial species (e.g., Lutjanus argentiventris, Seriola rivoliana) might constitute critical links in marine trophic webs and across seascapes. Finally, through scoring and participatory mapping methods, we revealed the prominence of western islands' mangroves for fishery productivity, which were linked to biophysical attributes, like forest canopy and freshwater. Yet, other locations in central and southeastern islands might also be important, as they hold similar attributes. Interviews to other mangrove users (e.g., naturalist guides, park rangers, scientists; N = 33), and past scientific studies allowed us to triangulate LEK and to find complementarity among knowledge sources. Despite having an explorative focus, our work already showcases the potential of fishers' LEK in improving mangrove research in the Galapagos, and the arising opportunities for ecosystem-based fisheries management and mangrove protection

5 - Coral reef social–ecological systems under pressure in Southern Sulawesi

Abstract Ecological and social processes of the Spermonde Archipelago, South Sulawesi, Indonesia, have been intensively studied during the Science for the Protection of Indonesian Coastal Ecosystems (SPICE) program. The archipelago is of specific interest to better understand how intensive exploitation of marine resources results in the degradation of reef systems. The projects specifically targeted (1) ecological processes in coral reefs, (2) genetic structure of populations, and (3) social–ecological dynamics relating to resource use, social networks, and governance structures. A modeling component emphasized (4) the integration of different ecological, social, and environmental components. Results indicated that reef resources in the Spermonde Archipelago are intensively exploited and further stressed by pollution effluents from hinterland processes. The lack of alternative livelihoods perpetuates dependencies within the patron–client system of the artisanal fisheries and supports high exploitation and also destructive resource uses. Greater inclusion of local stakeholders in the governance may result in better conservation practices, sustainable resource use, and improved livelihoods for the people. Abstrak Selama proyek SPICE, aspek ekologis dan sosial di perairan Kepulauan Spermonde, Sulawesi Selatan, Indonesia, dipelajari secara intensif. Kepulauan dan perairan ini mengundang banyak perhatian untuk lebih memahami bagaimana tingkat pemanfaatan sumber daya laut yang intensif berakibat pada degradasi sistem terumbu karang. Kerangka kerja proyek penelitian SPICE, secara khusus, menargetkan kajian-kajian mengenai (a) proses ekologis dalam sistem terumbu karang, (b) struktur genetik populasi untuk menentukan konektifitasnya, dan (c) dinamika sosial-ekologi yang berkaitan dengan penggunaan sumber daya, jejaring sosial dan struktur tata kelola. Komponen pemodelan juga dimasukkan kedalam kajian mengenai (d) integrasi berbagai komponen ekologi, sosial dan lingkungan dalam karakterisasi sistem sosial-ekologis. Hasil-hasil penelitian menunjukkan bahwa sumber daya terumbu karang di Kepulauan Spermonde sangat tereksploitasi dan terancam juga oleh limbah polusi dari proses di daratan. Kurangnya mata pencaharian alternatif memperkuat ketergantungan para nelayan tradisional pada sistem patron-klien dan meningkatkan penggunaan sumber daya yang tidak berkelanjutan dan merusak. Keikutsertaan pemangku kepentingan lokal yang lebih erat dalam tata kelola sumber daya alam Kepulauan Spermonde sangat memungkinkan hasil praktik konservasi yang lebih baik, penggunaan sumber daya berkelanjutan, dan peningkatan mata pencaharian bagi masyarakat

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.Funding: the Tri-I Program in Computational Biology and Medicine (CBM) funded by NIH grant 1T32GM083937; GitHub; Philip Blood and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by NSF grant number ACI-1548562 and NSF award number ACI-1445606; NASA (NNX14AH50G, NNX17AB26G), the NIH (R01AI151059, R25EB020393, R21AI129851, R35GM138152, U01DA053941); STARR Foundation (I13- 0052); LLS (MCL7001-18, LLS 9238-16, LLS-MCL7001-18); the NSF (1840275); the Bill and Melinda Gates Foundation (OPP1151054); the Alfred P. Sloan Foundation (G-2015-13964); Swiss National Science Foundation grant number 407540_167331; NIH award number UL1TR000457; the US Department of Energy Joint Genome Institute under contract number DE-AC02-05CH11231; the National Energy Research Scientific Computing Center, supported by the Office of Science of the US Department of Energy; Stockholm Health Authority grant SLL 20160933; the Institut Pasteur Korea; an NRF Korea grant (NRF-2014K1A4A7A01074645, 2017M3A9G6068246); the CONICYT Fondecyt Iniciación grants 11140666 and 11160905; Keio University Funds for Individual Research; funds from the Yamagata prefectural government and the city of Tsuruoka; JSPS KAKENHI grant number 20K10436; the bilateral AT-UA collaboration fund (WTZ:UA 02/2019; Ministry of Education and Science of Ukraine, UA:M/84-2019, M/126-2020); Kyiv Academic Univeristy; Ministry of Education and Science of Ukraine project numbers 0118U100290 and 0120U101734; Centro de Excelencia Severo Ochoa 2013–2017; the CERCA Programme / Generalitat de Catalunya; the CRG-Novartis-Africa mobility program 2016; research funds from National Cheng Kung University and the Ministry of Science and Technology; Taiwan (MOST grant number 106-2321-B-006-016); we thank all the volunteers who made sampling NYC possible, Minciencias (project no. 639677758300), CNPq (EDN - 309973/2015-5), the Open Research Fund of Key Laboratory of Advanced Theory and Application in Statistics and Data Science – MOE, ECNU, the Research Grants Council of Hong Kong through project 11215017, National Key RD Project of China (2018YFE0201603), and Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) (L.S.

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)