Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates

Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.This work was supported by the "Contrato-Programa" UIDB/04050/2020 and the project NIS-DNA (PTDC/BIA-BMA/29754/2017) funded by national funds through the FCT I.P (Foundation for Science and Technology). Financial support granted by the FCT to S.D. (CEECIND/00667/2017) and B.R.L. (PD/BD/127994/2016) is also acknowledged. A.F.F. was supported by the project FRESHING founded by the FCT and COMPETE (PTDC/AAGMAA/2261/2014-POCI-01-0145-FEDER356016824). M.J.F. was supported by FCT through MARE strategic project UIDB/04292/2020 and Norma Transitoria-DL57/2016

The global EPTO database: Worldwide occurrences of aquatic insects

Motivation: Aquatic insects comprise 64% of freshwater animal diversity and are widely used as bioindicators to assess water quality impairment and freshwater ecosystem health, as well as to test ecological hypotheses. Despite their importance, a comprehensive, global database of aquatic insect occurrences for mapping freshwater biodiversity in macroecological studies and applied freshwater research is missing. We aim to fill this gap and present the Global EPTO Database, which includes worldwide geo-referenced aquatic insect occurrence records for four major taxa groups: Ephemeroptera, Plecoptera, Trichoptera and Odonata (EPTO). Main type of variables contained: A total of 8,368,467 occurrence records globally, of which 8,319,689 (99%) are publicly available. The records are attributed to the corresponding drainage basin and sub-catchment based on the Hydrography90m dataset and are accompanied by the elevation value, the freshwater ecoregion and the protection status of their location. Spatial location and grain: The database covers the global extent, with 86% of the observation records having coordinates with at least four decimal digits (11.1 m precision at the equator) in the World Geodetic System 1984 (WGS84) coordinate reference system. Time period and grain: Sampling years span from 1951 to 2021. Ninety-nine percent of the records have information on the year of the observation, 95% on the year and month, while 94% have a complete date. In the case of seven sub-datasets, exact dates can be retrieved upon communication with the data contributors.Major taxa and level of measurement: Ephemeroptera, Plecoptera, Trichoptera and Odonata, standardized at the genus taxonomic level. We provide species names for 7,727,980 (93%) records without further taxonomic verification. Software format: The entire tab-separated value (.csv) database can be downloaded and visualized at https://glowa bio.org/proje ct/epto_datab ase/. Fifty individual datasets are also available at https://fred.igb-berlin. de, while six datasets have restricted access. For the latter, we share metadata and the contact details of the authors

Fish and macroinvertebrate assemblages reveal extensive degradation of the world's rivers

Rivers suffer from multiple stressors acting simultaneously on their biota, but the consequences are poorly quantified at the global scale. We evaluated the biological condition of rivers globally, including the largest proportion of countries from the Global South published to date. We gathered macroinvertebrate- and fish-based assessments from 72,275 and 37,676 sites, respectively, from 64 study regions across six continents and 45 nations. Because assessments were based on differing methods, different systems were consolidated into a 3-class system: Good, Impaired, or Severely Impaired, following common guidelines. The proportion of sites in each class by study area was calculated and each region was assigned a Köppen-Geiger climate type, Human Footprint score (addressing landscape alterations), Human Development Index (HDI) score (addressing social welfare), % rivers with good ambient water quality, % protected freshwater key biodiversity areas; and % of forest area net change rate. We found that 50% of macroinvertebrate sites and 42% of fish sites were in Good condition, whereas 21% and 29% were Severely Impaired, respectively. The poorest biological conditions occurred in Arid and Equatorial climates and the best conditions occurred in Snow climates. Severely Impaired conditions were associated (Pearson correlation coefficient) with higher HDI scores, poorer physico-chemical water quality, and lower proportions of protected freshwater areas. Good biological conditions were associated with good water quality and increased forested areas. It is essential to implement statutory bioassessment programs in Asian, African, and South American countries, and continue them in Oceania, Europe, and North America. There is a need to invest in assessments based on fish, as there is less information globally and fish were strong indicators of degradation. Our study highlights a need to increase the extent and number of protected river catchments, preserve and restore natural forested areas in the catchments, treat wastewater discharges, and improve river connectivity

Répteis em fragmentos de Cerrado e Mata Atlântica no Campo das Vertentes, Estado de Minas Gerais, Sudeste do Brasil

Os dados sobre a fauna reptiliana em Minas Gerais são pontuais e revelam carência de informações sobre esse grupo, principalmente em regiões de transição entre a Mata Atlântica e o Cerrado. A área do estudo está situada no município de Ritápolis (21° 01' 37.07" S e 44° 19' 11.84" O), microrregião Campo das Vertentes, Estado de Minas Gerais, Sudeste do Brasil. Pretendeu-se com a presente pesquisa conhecer a composição da fauna de répteis local. As observações, capturas e coletas foram realizadas quinzenalmente, durante dois dias consecutivos, de agosto de 2005 a julho de 2006. As capturas foram realizadas por meio de armadilhas de interceptação e queda, distribuídas em oito sítios, sendo quatro em área de mata de galeria e quatro em área aberta, perfazendo um esforço amostral de 6.912 horas-balde. Foi também realizada procura ativa e encontros ocasionais com registros fotográficos dos espécimes, e, no caso de serpentes, alguns exemplares foram entregues por terceiros quando encontradas mortos. Registrou-se a presença de 31 espécies de répteis, sendo duas espécies de cágados, nove de lagartos, duas de anfisbenas e 18 de serpentes. Apenas os lagartos Cercosaura ocellata, Enyalius bilineatus e Tupinambis merianae e as serpentes Leptodeira annulata e Apostolepis assimilis foram capturados nas armadilhas de queda. Os lagartos mais comuns foram Ameiva ameiva e Mabuya frenata, e as serpentes mais abundantes foram Oxyrhophus guibei e Sibynomorphus mikanii. Os lagartos estão bem representados na área, com espécies típicas de mata, como Enyalius bilineatus, e de áreas aberta de cerrado, como Ameiva ameiva e Mabuya frenata. A fauna de serpentes possui representantes típicos de áreas abertas do Cerrado, como O. guibei e Micrurus frontalis, e de regiões florestadas, como Liophis poecilogyrus e Philodryas olfersii. A diversidade de espécies de répteis e o registro prévio de Amphisbaena dubia e Hydromedusa tectifera para o Estado de Minas Gerais indicam a grande potencialidade do Campo das Vertentes em revelar a ocorrência de espécies novas ou a ampliação na distribuição de outras

Lipid profile and cardiovascular risk in two Amazonian populations Perfil lipídico e risco cardiovascular em amazônidas

OBJECTIVE: To compare the lipid profiles and coronary heart disease risks of 2 Brazilian Amazonian populations as follows: a riverside population (village of Vigia) and an urban population (city of Belém in the state of Pará). METHODS: Fifty individuals controlled for age and sex were assessed in each region, and the major risk factors for coronary heart disease were analyzed. RESULTS: According to the National Cholesterol Education Program (NCEP III) and using the Framingham score, both populations had the same absolute risk of events (Vigia = 5.4 ± 1 vs Belém = 5.7 ± 1), although the population of Vigia had a lower consumption of saturated fat (P<0.0001), a greater consumption of mono- and polyunsaturated fat (P<0.03), in addition to lower values for body mass index (25.4± 0.6 vs 27.6 ± 0.7 kg/m², P<0.02), of biceps skin fold (18.6 ± 1.1 vs 27.5 ± 1.3 mm, P<0.0001), of triceps skin fold (28.7 ± 1.2 vs 37.3 ± 1.7 mm, P<0.002), and of total cholesterol (205 ± 5 vs 223 ± 6 mg/dL, P< 0.03) and triglycerides (119 ± 9 vs 177 ± 18 mg/dL, P<0.005). Both populations did not differ in regard to HDL-C (46 ± 1 vs 46 ± 1 mg/dL), LDL-C (135 ± 4 vs 144 ± 5 mg/dL) and blood pressure (SBP 124 ± 3 vs 128 ± 3 mmHg; DBP 80 ± 2 vs 82 ± 2 mmHg). CONCLUSION: The riverside and urban populations of Amazonia had similar cardiovascular risks. However, the marked difference in the variables studied suggests that different strategies of prevention should be applied.<br>OBJETIVO: Comparar o perfil lipídico e risco coronariano de uma população ribeirinha (Vigia) ao de uma população urbana (Belém). MÉTODOS: Foram avaliados 50 indivíduos de cada região, controlados por idade e sexo, examinando-se os principais fatores de risco para a doença coronariana. RESULTADOS: Segundo o Programa Nacional de Educação sobre o Colesterol (NCEP III) e determinando-se o escore de Framingham, ambas as populações expressaram o mesmo risco absoluto de eventos (Vigia 5,4 ± 1 vs. Belém 5,7 ± 1), a despeito da população de Vigia apresentar menor consumo de gordura saturada (p<0,0001), maior de mono e poliinsaturada (p<0,03), além de menores valores do índice de massa corpórea (25,4±0,6 vs. 27,6±0,7kg/m², p<0,02), da prega biceptal (18,6±1,1 vs. 27,5±1,3mm, p<0,0001) e triceptal (28,7±1,2 vs. 37,3±1,7mm, p<0,002), de colesterol total (205±5 vs. 223±6mg/dL, p< 0,03) e triglicérides (119 ± 9 vs. 177±18mg/dL, p<0,005), não diferindo no HDL-c (46±1 vs. 46±1mg/dL), LDL-c (135 ± 4 vs. 144 ± 5mg/dL) e pressão arterial (PAS 124 ± 3 vs. 128 ± 3mmHg; PAD 80 ± 2 vs. 82 ± 2mmHg). CONCLUSÃO: A população ribeirinha e urbana da Amazônia apresentaram risco cardiovascular semelhante. Entretanto, a marcante diferença entre as variáveis estudadas sugere que devam ser aplicadas diferentes estratégias de prevenção

Women in limnology in the Iberian Peninsula: biases, barriers and recommendations

12 páginas, 5 figuras, 2 tablasGender biases in science have received increasing attention in recent years. Underrepresentation at the highest academic levels and bias in publication are some of the factors affecting women in science. In this study, we assessed the situation of women in Limnology, a specific field of natural sciences, within the geographic context of the Iberian Peninsula.We used a multi-faceted approach to diagnose the situation, and we propose guidelines to reduce gender gaps in Limnology. The database of members of the Iberian Limnological Association (AIL) was used to analyse the variability between genders at different professional stages. Data was also compiled on plenary speakers who attended conferences organized by different associations (AIL, SEFS and ASLO) to assess women’s visibility. A published data set was used to identify leadership patterns in publications with respect to gender. Finally, a survey of AIL memberswas conducted to understand their perception of the barriers in science that result in differences between the genders. This study recognized differences at the recruitment level (more tenured positions are held by men), visibility at conferences (fewer women are invited as plenary speakers) and publication as team leaders (men have more publications as first and last authors). Survey participants recognised the scarcity of grants/funding, difficulties in balancing life and career, and the scarcity of job opportunities as the three main barriers in science, regardless of gender. Yet, women identified family-related barriers such as having children and gender biases more frequently. Overall, our study indicates that there is a general gender bias in the field of Limnology in the Iberian Peninsula; however, it is slightly lower than the reported levels in Europe and for other disciplines in Spain. Finally, we provide a list of recommendations to balance the current biases based on suggestions made by the participants of a round table held at the XVII Congress of the AIL (Santander, July 2014). We encourage associations in natural sciences and the AIL in particular to use this study as a guideline for best practices as well as a baseline for future analysis of gender biases.M. M. Sánchez- Montoya was supported with the MC-Intra European Fellowship (CLITEMP Project-330466), M. Bartrons with the European Research Council Synergy grant (ERC-2013-SyG 610028- IMBALANCE-P), B. Gallardo with a Severo Ochoa Program for Centres of Excellence in R+D+I (SEV-2012-0262), E. Chappuis with an Intramural CSIC project (ref. 0065) and N. Catalán with a studentship from the Wenner-Gren foundation (Sweden).Peer reviewe

Global concerns related to water biology and security: The need for language and policies that safeguard living resources versus those that dilute scientific knowledge

Increasingly, scientists and non-scientists, especially employees of government agencies, tend to use weak or equivocal language when making statements related to science policy and governmental regulation. We use recent publications to provide examples of vague language versus examples of strong language when authors write about regulating anthropogenic pressures on natural resources. Lifeless language is common in agency reports, policy documents, and even scientific papers published by academics. Such language limits success in regulating anthropogenic pressures on natural resources. This challenge must be recognized and countered as a driver of the condition of water and associated resources. We also list sources of vague wording, provide global examples of how ambiguous language and political influences have contributed to water resource degradation, discuss the recent history of science censorship, and offer possible solutions for more direct scientific discourse. We found that: (1) equivocal language was especially common in concluding statements and not only by government employees; (2) authors discussed confusing language concerns in an agency publication; and (3) agency employees sometimes used active, strong language. Key drivers of weak language include: (1) holding on to old paradigms and resisting new knowledge; (2) scientific uncertainty; (3) institutional manuscript review policies; (4) employment and funding insecurity; and (5) avoiding the appearance of advocacy. Examples associated with euphemistic language included climate change, flow and physical habitat alteration, dams, agriculture, mining, forestry, and fisheries, as well as resistance towards monitoring, assessing, and reporting ecological conditions. Suggestions for mitigating equivocal language involve employment protections and greater focus on scientific ethics. We conclude that natural resource scientists should resist calls to employ imprecise language. Instead, they should be strong advocates for prescriptive and protective natural resource actions—based on their science—to halt and reverse the systemic degradation of those resources

Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers

DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be thoroughly quantified before it can be mainstreamed into biomonitoring programmes. Here, we used 80 unsorted macroinvertebrate samples collected in Portugal under a Water Framework Directive monitoring programme, to compare community diversity and taxonomic composition metrics estimated through morphotaxonomy versus metabarcoding from storage ethanol using three markers (COI-M19BR2, 16S-Inse01 and 18S-Euka02) and a multimarker approach. A preliminary in silico analysis showed that the three markers were adequate for the target taxa, with detection failures related primarily to the lack of adequate barcodes in public databases. Metabarcoding of ethanol samples retrieved far less taxa per site (alpha diversity) than morphotaxonomy, albeit with smaller differences for COI-M19BR2 and the multimarker approach, while estimates of taxa turnover (beta diversity) among sites were similar across methods. Using generalized linear mixed models, we found that after controlling for differences in read coverage across samples, the probability of detection of a taxon was positively related to its proportional abundance, and negatively so to the presence of heavily sclerotized exoskeleton (e.g., Coleoptera). Overall, using our experimental protocol with different template dilutions, the COI marker showed the best performance, but we recommend the use of a multimarker approach to detect a wider range of taxa in freshwater macroinvertebrate samples. Further methodological development and optimization efforts are needed to reduce biases associated with body armouring and rarity in some macroinvertebrate taxainfo:eu-repo/semantics/publishedVersio