Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data

IntroductionMicrobes are increasingly (re)considered for environmental assessments because they are powerful indicators for the health of ecosystems. The complexity of microbial communities necessitates powerful novel tools to derive conclusions for environmental decision-makers, and machine learning is a promising option in that context. While amplicon sequencing is typically applied to assess microbial communities, metagenomics and total RNA sequencing (herein summarized as omics-based methods) can provide a more holistic picture of microbial biodiversity at sufficient sequencing depths. Despite this advantage, amplicon sequencing and omics-based methods have not yet been compared for taxonomy-based environmental assessments with machine learning.MethodsIn this study, we applied 16S and ITS-2 sequencing, metagenomics, and total RNA sequencing to samples from a stream mesocosm experiment that investigated the impacts of two aquatic stressors, insecticide and increased fine sediment deposition, on stream biodiversity. We processed the data using similarity clustering and denoising (only applicable to amplicon sequencing) as well as multiple taxonomic levels, data types, feature selection, and machine learning algorithms and evaluated the stressor prediction performance of each generated model for a total of 1,536 evaluated combinations of taxonomic datasets and data-processing methods.ResultsSequencing and data-processing methods had a substantial impact on stressor prediction. While omics-based methods detected a higher diversity of taxa than amplicon sequencing, 16S sequencing outperformed all other sequencing methods in terms of stressor prediction based on the Matthews Correlation Coefficient. However, even the highest observed performance for 16S sequencing was still only moderate. Omics-based methods performed poorly overall, but this was likely due to insufficient sequencing depth. Data types had no impact on performance while feature selection significantly improved performance for omics-based methods but not for amplicon sequencing.DiscussionWe conclude that amplicon sequencing might be a better candidate for machine-learning-based environmental stressor prediction than omics-based methods, but the latter require further research at higher sequencing depths to confirm this conclusion. More sampling could improve stressor prediction performance, and while this was not possible in the context of our study, thousands of sampling sites are monitored for routine environmental assessments, providing an ideal framework to further refine the approach for possible implementation in environmental diagnostics

The future depends on what we do today – projecting Europe’s surface water quality into three different future scenarios

There are infinite possible future scenarios reflecting the impacts of anthropogenic multiple stress on our planet. These impacts include changes in climate and land cover, to which aquatic ecosystems are especially vulnerable. To assess plausible developments of the future state of European surface waters, we considered two climate scenarios and three storylines describing land use, management and anthropogenic development (‘Consensus’, ‘Techno’ and ‘Fragmented’, which in terms of environmental protection represent best-, intermediate- and worst-case, respectively). Three lake and four river basins were selected, representing a spectrum of European conditions through a range of different human impacts and climatic, geographical and biological characteristics. Using process-based and empirical models, freshwater total nitrogen, total phosphorus and chlorophyll-a concentrations were projected for 2030 and 2060. Under current conditions, the water bodies mostly fail good ecological status. In future predictions for the Techno and Fragmented World, concentrations further increased, while concentrations generally declined for the Consensus World. Furthermore, impacts were more severe for rivers than for lakes. Main pressures identified were nutrient inputs from agriculture, land use change, inadequately managed water abstractions and climate change effects. While the basins in the Continental and Atlantic regions were primarily affected by land use changes, in the Mediterranean/Anatolian the main driver was climate change. The Boreal basins showed combined impacts of land use and climate change and clearly reflected the climate-induced future trend of agricultural activities shifting northward. The storylines showed positive effects on ecological status by classical mitigation measures in the Consensus World (e.g. riparian shading), technical improvements in the Techno World (e.g. increasing wastewater treatment efficiency) and agricultural extensification in the Fragmented World. Results emphasize the need for implementing targeted measures to reduce anthropogenic impacts and the importance of having differing levels of ambition for improving the future status of water bodies depending on the societal future to be expected

A Synthesis of Marine Monitoring Methods With the Potential to Enhance the Status Assessment of the Baltic Sea

Highlights - We rated novel methods regarding their ability to improve the Baltic Sea monitoring. - Methods were assessed with respect to their costs and applicability. - All methods can potentially increase data resolution or monitor novel ecosystem elements. - We recommend several novel methods for the Baltic status assessment.A multitude of anthropogenic pressures deteriorate the Baltic Sea, resulting in the need to protect and restore its marine ecosystem. For an efficient conservation, comprehensive monitoring and assessment of all ecosystem elements is of fundamental importance. The Baltic Marine Environment Protection Commission HELCOM coordinates conservation measures regulated by several European directives. However, this holistic assessment is hindered by gaps within the current monitoring schemes. Here, twenty-two novel methods with the potential to fill some of these gaps and improve the monitoring of the Baltic marine environment are examined. We asked key stakeholders to point out methods likely to improve current Baltic Sea monitoring. We then described these methods in a comparable way and evaluated them based on their costs and applicability potential (i.e., possibility to make them operational). Twelve methods require low to very low costs, while five require moderate and two high costs. Seventeen methods were rated with a high to very high applicability, whereas four methods had moderate and one low applicability for Baltic Sea monitoring. Methods with both low costs and a high applicability include the Manta Trawl, Rocket Sediment Corer, Argo Float, Artificial Substrates, Citizen Observation, Earth Observation, the HydroFIA®pH system, DNA Metabarcoding and Stable Isotope Analysis

A Temporal Gate for Viral Enhancers to Co-opt Toll-Like-Receptor Transcriptional Activation Pathways upon Acute Infection

Viral engagement with macrophages activates Toll-Like-Receptors (TLRs) and viruses must contend with the ensuing inflammatory responses to successfully complete their replication cycle. To date, known counter-strategies involve the use of viral-encoded proteins that often employ mimicry mechanisms to block or redirect the host response to benefit the virus. Whether viral regulatory DNA sequences provide an opportunistic strategy by which viral enhancer elements functionally mimic innate immune enhancers is unknown. Here we find that host innate immune genes and the prototypical viral enhancer of cytomegalovirus (CMV) have comparable expression kinetics, and positively respond to common TLR agonists. In macrophages but not fibroblasts we show that activation of NFκB at immediate-early times of infection is independent of virion-associated protein, M45. We find upon virus infection or transfection of viral genomic DNA the TLR-agonist treatment results in significant enhancement of the virus transcription-replication cycle. In macrophage time-course infection experiments we demonstrate that TLR-agonist stimulation of the viral enhancer and replication cycle is strictly delimited by a temporal gate with a determined half-maximal time for enhancer-activation of 6 h; after which TLR-activation blocks the viral transcription-replication cycle. By performing a systematic siRNA screen of 149 innate immune regulatory factors we identify not only anticipated anti-viral and pro-viral contributions but also new factors involved in the CMV transcription-replication cycle. We identify a central convergent NFκB-SP1-RXR-IRF axis downstream of TLR-signalling. Activation of the RXR component potentiated direct and indirect TLR-induced activation of CMV transcription-replication cycle; whereas chromatin binding experiments using wild-type and enhancer-deletion virus revealed IRF3 and 5 as new pro-viral host transcription factor interactions with the CMV enhancer in macrophages. In a series of pharmacologic, siRNA and genetic loss-of-function experiments we determined that signalling mediated by the TLR-adaptor protein MyD88 plays a vital role for governing the inflammatory activation of the CMV enhancer in macrophages. Downstream TLR-regulated transcription factor binding motif disruption for NFκB, AP1 and CREB/ATF in the CMV enhancer demonstrated the requirement of these inflammatory signal-regulated elements in driving viral gene expression and growth in cells as well as in primary infection of neonatal mice. Thus, this study shows that the prototypical CMV enhancer, in a restricted time-gated manner, co-opts through DNA regulatory mimicry elements, innate-immune transcription factors to drive viral expression and replication in the face of on-going pro-inflammatory antiviral responses in vitro and in vivo and; suggests an unexpected role for inflammation in promoting acute infection and has important future implications for regulating latency

Marine monitoring in transition : On the verge of technological revolution?

Efforts to renew marine ecosystem monitoring to include advanced technology and cost-effective methods have been repeatedly called for. The current environmental legislation in European Union (EU) requires also ecosystem monitoring beyond the scope of conventional methods and sampling strategies. Despite several studies showing the benefits of new methods, the progress to adopt the methods in national monitoring programmes under legal requirements has been slow. In this study, we have reviewed the current use of a set of methods in marine monitoring programmes under the EU marine strategy framework directive (MSFD), which calls for a holistic view of the marine environment and thus requires tens of monitoring parameters by different methods. Here we assess how widely the new methods are being adopted in the EU member states implementing the MSFD. Our results show a relatively high adoption rate for certain methods, while others are widely ignored. We compare the results also with the monitoring strategies of the four regional sea conventions. We argue that the adoption of methods in European and regional programmes may positively influence the national use of new methods

Gaps in current Baltic Sea environmental monitoring - Science versus management perspectives

Legislations and commitments regulate Baltic Sea status assessments and monitoring. These assessments suffer from monitoring gaps that need prioritization. We used three sources of information; scientific articles, project reports and a stakeholder survey to identify gaps in relation to requirements set by the HELCOM's Baltic Sea Action Plan, the Marine Strategy Framework Directive and the Water Framework Directive. The most frequently mentioned gap was that key requirements are not sufficiently monitored in space and time. Biodiversity monitoring was the category containing most gaps. However, whereas more than half of the gaps in reports related to biodiversity, scientific articles pointed out many gaps in the monitoring of pollution and water quality. An important finding was that the three sources differed notably with respect to which gaps were mentioned most often. Thus, conclusions about gap prioritization for management should be drawn after carefully considering the different viewpoints of scientists and stakeholders.publishedVersio

Perceived multiple stressor effects depend on sample size and stressor gradient length

Multiple stressors are continuously deteriorating surface waters worldwide, posing many challenges for their conservation and restoration. Combined effect types of multiple stressors range from single-stressor dominance to complex interactions. Identifying prevalent combined effect types is critical for environmental management, as it helps to prioritise key stressors for mitigation. However, it remains unclear whether observed single and combined stressor effects reflect true ecological processes unbiased by sample size and length of stressor gradients. Therefore, we examined the role of sample size and stressor gradient lengths in 158 paired-stressor response cases with over 120,000 samples from rivers, lakes, transitional and marine ecosystems around the world. For each case, we split the overall stressor gradient into two partial gradients (lower and upper) and investigated associated changes in single and combined stressor effects. Sample size influenced the identified combined effect types, and stressor interactions were less likely for cases with fewer samples. After splitting gradients, 40 % of cases showed a change in combined effect type, 30 % no change, and 31 % showed a loss in stressor effects. These findings suggest that identified combined effect types may often be statistical artefacts rather than representing ecological processes. In 58 % of cases, we observed changes in stressor effect directions after the gradient split, suggesting unimodal stressor effects. In general, such non-linear responses were more pronounced for organisms at higher trophic levels. We conclude that observed multiple stressor effects are not solely determined by ecological processes, but also strongly depend on sampling design. Observed effects are likely to change when sample size and/or gradient length are modified. Our study highlights the need for improved monitoring programmes with sufficient sample size and stressor gradient coverage. Our findings emphasize the importance of adaptive management, as stress reduction measures or further ecosystem degradation may change multiple stressor-effect relationships, which will then require associated changes in management strategies.Scenarios of Biodiversity and Ecosystem Services II programme, jointly supported by Belmont Forum, Biodiversa and the European Commission; Deutsche Forschungsgemeinschaft; Fénix Programme, Government of Cantabria; Augusto González de Linares, Programa de ayudas de la Universidad de Cantabria para contratos posdoctorales, grant number: POS-UC-2020-07; Environmental Protection Agency (Ireland); Marine Institute (Ireland); Basque Water Agency (URA) and Consorcio de Aguas Bilbao-Bizkaia (Spain); Cawthron Institute, New Zealand; Ministry for the Environment, New Zealand; Oranga Taiao Oranga Tangata research programme, New Zealand Ministry of Business, Innovation and Employment grant number MAUX1502; The project FRESHABIT LIFE IP (LIFE14/IPE/FI/023); USA National Science Foundation, Dimensions of Biodiversity Program (1831096); Irish Research Council Laureate Award (IRCLA/2017/112)