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The Science of the Total Environment Jan 2021In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we... (Review)
Review
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.
Topics: Biodiversity; DNA; DNA Barcoding, Taxonomic; DNA, Environmental; Ecosystem
PubMed: 32889465
DOI: 10.1016/j.scitotenv.2020.141729 -
Marine Environmental Research Dec 2022Reef environments are rapidly transforming worldwide, and these changes are causing major impacts to the reef ecosystem. Scientific knowledge is strategic for marine... (Review)
Review
Reef environments are rapidly transforming worldwide, and these changes are causing major impacts to the reef ecosystem. Scientific knowledge is strategic for marine conservation and management in these scenarios. Aiming to contribute to this subject, a systematic review from 1967 to 2020 was conducted, in order to identify gaps in studies regarding reef fish species, ecosystem components and processes. Multidisciplinary sciences concerning reef fish have been rising, mainly in the fields of basic biology and ecology. Besides that, phase shifts and ecosystem services were absent terms in the analyzes of co-occurrence. Research in the ethnosciences needs to be increased, and will improve access to local ecological knowledge, which can be used as a tool to address issues in reef environments. Socio-ecological systems are components of this landscape that has had few publications. The participation in the elaboration of public policies can be a new avenue to foster the biodiversity of reef environments.
Topics: Animals; Ecosystem; Coral Reefs; Anthozoa; Conservation of Natural Resources; Biodiversity; Fishes
PubMed: 36272222
DOI: 10.1016/j.marenvres.2022.105769 -
Viruses Jul 2022Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other... (Review)
Review
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host-pathogen-environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
Topics: Animals; Animals, Wild; Arctic Regions; Birds; Canada; Ecosystem; Influenza A virus; Influenza in Birds; Mammals
PubMed: 35891510
DOI: 10.3390/v14071531 -
Biological Reviews of the Cambridge... Aug 2022Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean...
Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.
Topics: Biodiversity; Caves; Conservation of Natural Resources; Ecology; Ecosystem; Fresh Water
PubMed: 35315207
DOI: 10.1111/brv.12851 -
The Science of the Total Environment Jan 2023Chronic exposure of coral reefs to elevated nutrient conditions can modify the performance of the coral holobiont and shift the competitive interactions of reef... (Meta-Analysis)
Meta-Analysis Review
Chronic exposure of coral reefs to elevated nutrient conditions can modify the performance of the coral holobiont and shift the competitive interactions of reef organisms. Many studies have now quantified the links between nutrients and coral performance, but few have translated these studies to directly address coastal water quality standards. To address this management need, we conducted a systematic review of peer-reviewed studies, public reports, and gray literature that examined the impacts of dissolved inorganic nitrogen (DIN: nitrate, nitrite, and ammonium) and dissolved inorganic phosphorus (DIP: phosphate) on scleractinian corals. The systematic review resulted in 47 studies with comparable data on coral holobiont responses to nutrients: symbiont density, chlorophyll a (chl-a) concentration, photosynthesis, photosynthetic efficiency, growth, calcification, adult survival, juvenile survival, and fertilization. Mixed-effects meta-regression meta-analyses were used to determine the magnitude of the positive or negative effects of DIN and DIP on coral responses. Zooxanthellae density (DIN & DIP), chl-a concentration (DIN), photosynthetic rate (DIN), and growth (DIP) all exhibited positive responses to nutrient addition; maximum quantum yield (DIP), growth (DIN), larval survival (DIN), and fertilization (DIN) exhibited negative responses. In lieu of developing specific thresholds for the management of nutrients as a stressor on coral reefs, we highlight important inflection points in the magnitude and direction of the effects of inorganic nutrients and identify trends among coral responses. The responses of corals to nutrients are complex, warranting conservative guidelines for elevated nutrient concentrations on coral reefs.
Topics: Animals; Anthozoa; Chlorophyll A; Coral Reefs; Nitrogen; Nutrients
PubMed: 36183766
DOI: 10.1016/j.scitotenv.2022.159093 -
Journal of Microbiological Methods Dec 2022Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are... (Review)
Review
Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.
Topics: Animals; Bacteria; Fishes; Food Microbiology; Meat; Proteomics; RNA, Ribosomal, 16S
PubMed: 36243229
DOI: 10.1016/j.mimet.2022.106599 -
Philosophical Transactions of the Royal... Aug 2023Many bird species incorporate anthropogenic materials (e.g. sweet wrappers, cigarette butts and plastic strings) into their nests. Anthropogenic materials have become... (Review)
Review
Many bird species incorporate anthropogenic materials (e.g. sweet wrappers, cigarette butts and plastic strings) into their nests. Anthropogenic materials have become widely available as nesting materials in marine and terrestrial environments globally. These human-made objects can provide important benefits to birds such as serving as reliable signals to conspecifics or protecting against ectoparasites, but they can also incur fundamental survival and energetic costs via offspring entanglement and reduced insulative properties, respectively. From an ecological perspective, several hypotheses have been proposed to explain the use of anthropogenic nest materials (ANMs) by birds but no previous interspecific study has tried to identify the underlying mechanisms of this behaviour. In this study, we performed a systematic literature search and ran phylogenetically controlled comparative analyses to examine interspecific variation in the use of ANM and to examine the influence of several ecological and life-history traits. We found that sexual dimorphism and nest type significantly influenced the use of ANMs by birds providing support for the 'signalling hypothesis' that implies that ANMs reflect the quality of the nest builder. However, we found no support for the 'age' and 'new location' hypotheses, nor for a phylogenetic pattern in this behaviour, suggesting that it is widespread throughout birds. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.
Topics: Animals; Humans; Phylogeny; Nesting Behavior; Birds; Life History Traits
PubMed: 37427475
DOI: 10.1098/rstb.2022.0156 -
Journal of Health, Population, and... Nov 2022A balanced and optimized amount of nutrients in bread, which is the main food in many countries, is necessary to maintain human health. Considering the importance of...
BACKGROUND
A balanced and optimized amount of nutrients in bread, which is the main food in many countries, is necessary to maintain human health. Considering the importance of nutritional values of bread in the food basket of Iranian households, the purpose of this study was to determine the nutrients and their concentrations in breads consumed in Iran.
METHODS
This systematic review study was performed to determine the types of nutrients in breads consumed in Iran by searching reputable international databases including Scopus and Google scholar, PubMed, Science direct, ISI (Web of Science). Data were collected according to inclusion and exclusion criteria and by searching for relevant keywords, emphasizing the types of nutrients in breads consumed in Iran. Qualitative data were collected using the standard PRISMA checklist (preferential reporting items for systematic reviews and meta-analysis). After verifying the quality of the articles, the information was entered into a checklist such as the name of the first author and year of publication of the research, type of study, number of samples, type of nutrition, type of bread and amount of nutrition measured.
RESULTS
After reviewing the information and quality of articles, 10 articles were qualified for systematic review. The review of the articles showed that different breads were experimented, including: Sangak, Barbari, Taftoon, Lavash, French and local bread. The highest number of experimented bread samples was Sangak. Examination of the articles showed that 6 nutrients were experimented in different breads such as Fe, K, Mg, Ca, Cu and Zn. The highest number of experimented in breads was related to the amount of Zn (13 times) and Cu (10 times), respectively. The results of quality assessment of articles showed that most of the studies were of good quality. The results of articles on the amount of nutrients measured in different breads showed that only in two articles the amount of nutrients was reported to be desirable. In most articles, the amount of nutrients in breads was reported to be lower or higher than standard.
CONCLUSION
The results of this study showed that the concentration of nutrients in most articles was undesirable. It is suggested that optimal methods of enrichment of breads and flours be done with interdisciplinary cooperation between food hygiene, environmental health, nutrition, farmers and bakers. It is recommended that food hygiene and environmental health researchers investigate other nutrients (including phosphorus, selenium, manganese, boron and molybdenum) in breads and other staple foods used by people to constructive and practical measures to increase public health.
Topics: Humans; Bread; Flour; Iran; Nutrients; Nutritive Value
PubMed: 36376938
DOI: 10.1186/s41043-022-00329-3 -
Nature Ecology & Evolution Nov 2022Animal migration plays a central role in many ecological and evolutionary processes, yet migratory populations worldwide are increasingly threatened. Adjusting migration... (Review)
Review
Animal migration plays a central role in many ecological and evolutionary processes, yet migratory populations worldwide are increasingly threatened. Adjusting migration timing to match ecosystem phenology is key to survival in dynamic and changing ecosystems, especially in an era of human-induced rapid environmental change. Social cues are increasingly recognized as major components of migratory behaviour, yet a comprehensive understanding of how social cues influence the timing of animal migrations remains elusive. Here, we introduce a framework for assessing the role that social cues, ranging from explicit (for example, active cueing) to implicit (for example, competition), play in animals' temporal migration decisions across a range of scales. By applying this theoretical lens to a systematic review of published literature, we show that a broad range of social cues frequently mediate migration timing at a range of temporal scales and across highly diverse migratory taxa. We further highlight that while rarely documented, several social cue mechanisms (for example, social learning and density dependency) play important adaptive roles in matching migration timing with ecosystem dynamics. Thus, social cues play a fundamental role in migration timing, with potentially widespread ecological consequences and implications for the conservation of migratory species. Furthermore, our analysis establishes a theoretical basis on which to evaluate future findings on the role of both conspecific and interspecific social cues in this intersection of behavioural ecology and global change biology.
Topics: Animals; Humans; Animal Migration; Ecosystem; Cues; Biological Evolution
PubMed: 36280783
DOI: 10.1038/s41559-022-01866-0 -
Marine Drugs Apr 2022Fucoxanthin, belonging to the xanthophyll class of carotenoids, is a natural antioxidant pigment of marine algae, including brown macroalgae and diatoms. It represents... (Review)
Review
Fucoxanthin, belonging to the xanthophyll class of carotenoids, is a natural antioxidant pigment of marine algae, including brown macroalgae and diatoms. It represents 10% of the total carotenoids in nature. The plethora of scientific evidence supports the potential benefits of nutraceutical and pharmaceutical uses of fucoxanthin for boosting human health and disease management. Due to its unique chemical structure and action as a single compound with multi-targets of health effects, it has attracted mounting attention from the scientific community, resulting in an escalated number of scientific publications from January 2017 to February 2022. Fucoxanthin has remained the most popular option for anti-cancer and anti-tumor activity, followed by protection against inflammatory, oxidative stress-related, nervous system, obesity, hepatic, diabetic, kidney, cardiac, skin, respiratory and microbial diseases, in a variety of model systems. Despite much pharmacological evidence from in vitro and in vivo findings, fucoxanthin in clinical research is still not satisfactory, because only one clinical study on obesity management was reported in the last five years. Additionally, pharmacokinetics, safety, toxicity, functional stability, and clinical perspective of fucoxanthin are substantially addressed. Nevertheless, fucoxanthin and its derivatives are shown to be safe, non-toxic, and readily available upon administration. This review will provide pharmacological insights into fucoxanthin, underlying the diverse molecular mechanisms of health benefits. However, it requires more activity-oriented translational research in humans before it can be used as a multi-target drug.
Topics: Carotenoids; Humans; Neoplasms; Seaweed; Xanthophylls
PubMed: 35621930
DOI: 10.3390/md20050279