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The ICES Workshop on ICES reference points (WKREF2) was tasked review the WKREF1 report and based on the outcome develop updated guidelines for the ICES reference points system and recommendations for ACOM consideration. The WKREF1 report has suggested 5 key recom- mendations to simplify and harmonise the ICES reference points framework representing a ma- jor change to the current guidelines. At WKREF2, we detailed discussions and four key concerns were raised about the proposed approach. The first related to the simplification of rules to define Blim. Around two thirds of category 1 stocks would end up as WKREF1 “Blim Type 2” where Blim would be set as a fraction of B0. The Allee effect or “depensation” maybe more important than previously thought and should be furthered explored for ICES stocks since it has important consequences for Blim. A number of challenges and issues around defining Blim using the current guidelines were documented. Some suggestions on improvement criteria were discussed including using classifiers to define spas- modic stocks and using change point algorithms to address non-stationary productivity regimes. However, further work is need to make these approaches operational and there was no consen- sus that the WKREF1 Blim types should replace the current guidelines. WKREF1 recommended that the FMSY proxy should be based on a biological proxies and should be less than the deterministic FMSY. It was pointed out that the stochastic FMSY estimated in EqSim for example, is lower than the deterministic FMSY and that the current guidelines ensure that the FMSY should not pose a more than 5% risk to Blim. A large amount of work described in WD 1 was carried out to develop an MSE framework to consistency and robustness test a candidate refer- ence point system for North East Atlantic stocks. However, WKREF2 recommended that further work needs to be carried out to condition and test the simulation framework before the conclu- sions could be adopted by ICES and incorporated into the guidelines. A number of considerations for defining MSY related reference points were discussed including using model validation and prediction skill to ensure that ICES provide robust and credible ad- vice. There is evidence that density dependence (DD) is important in the majority of ICES stocks (68% in recruitment and 54% in growth). The correct prediction of the shape and strength of density-dependence in productivity is key to predicting future stock development and providing the best possible long-term fisheries management advice. A suggested approach to use surplus production models (SPMs) to account for DD in FMSY was suggested and discussed but there was no consensus on whether that approach was appropriate. There was consensus that the FECO approach as a means of adapting target fishing mortality to medium-term changes in productiv- ity should be included in the guidelines subject to a benchmark and ACOM approval. While WKREF1 and 2 focused mainly on Category 1 stocks ToR c) called for a “simplified and harmonised set of guidelines for estimating MSY and precautionary reference points applicable in the advice framework across various ICES stock categories.” Ideally the ICES assessment cat- egories should provide equivalent risk across all stocks. This issue was discussed but no recom- mendations emerged. There was no consensus a revised reference point framework was proposed at WKREF2. How- ever, it was agreed that it should be presented here for further discussion at ACOM and other fora. The key feature of the suggested approach is that the stock status evaluation is treated in- dependent of the Advice Rule (AR). The main feature of the system is that the biomass trigger is not linked to a stock status evaluation, it is linked to the expected biomass when fishing at the target fishing mortality, in contrast to the current ICES approach. It also entailed that FMSY would also become an upper limit of fishing mortality and that the advised fishing mortality would be set at or lower than that level. WKREF2 did not discuss what to do in situations where SSB< Blim or alternative forms of HCR for the advice rule. Building community understanding and con- sensus around simplified and harmonised guidelines has yet to be achieved. A further workshop WKREF3 will be required to achieve that aim. The report includes 6 recommendations for ACOM consideration. ICES The main objective of the workshop was to review the recommendations of WKREF1 and con- sider how these might feed into a new reference points framework and guidelines for ICES. There were a number of presentations on the wider issues of best practice for reference points, the Allee effect, density dependence and the WKIRISH approach. The starting point was to try and develop a set of simplified and harmonised guidelines based on the WKREF1 report rather than evolving the current guidelines to include the WKREF1 conclusions. A key aspect of the meeting was to allow for discussions in order to build a shared understanding of the strengths and weakness of the current framework and of the new framework emerging from WKREF1. Published Non Refereed

Additional file 1. Result S1. Analysis of rhizosheath sand composition. Result S2. Analysis of cultivable bacteria. Table S1. Climatic conditions throughout the year in Ksar Ghilane, Sahara Desert (Tunisia); data elaborated from https://www.worldweatheronline.com ; data as reported as monthly average measurement from January 2019 to now. Table S2. List of FISH probes used and conditions applied; probe sequence (5’-3’), attached fluorochrome (fluor.), bacterial target group, percentage of formaldehyde (FA) used during treatment, and references are also reported. Table S3. Number of KTUs and sequences used for each sample. RH: rhizosphere, RS: rhizosheath, RT: root tissue, BS: bulk sand. Table S4. Humidity (RH%) and temperature (T°C) measured in summer (June, 2016) and winter (November, 2016) for bulk sand and belowground speargrasses (i.e., plant rhizosheath–root system, RS). Table S5. Physico-chemical analyses conducted on bulk sand (BS) and rhizosheath matrix (RS) collected in summer (S) and winter (W). Table S6. PERMANOVA pair-wise comparison test of physico-chemical conditions (Table S5) in rhizosheath (RS) and bulk sand (BS) collected during summer (S) and winter (W) seasons. Table S7. Multivariate test (pairwise comparison) of beta-diversity associated with root tissue, rhizosheath, rhizosphere, and bulk sand. Table S8. Mean and standard error of multivariate dispersions from centroid calculated for each compartment (within-betadiversity). Table S9. Relative importance of different ecological processes in the assembly of bacterial community associated with the rhizosheath-root system compartments and bulk sand in two contrasting seasons. Table S10. Generalized linear model univariate test indicates the KTUs contributing to the difference in bulk soil among summer and winter. Table S11. Tukey’s honest significance difference (TukeyHSD) pairwise comparison tests for the degree, betweenness and keystone species detected across the four co-occurrence networks, namely bulk sand winter, bulk sand winter summer, rhizosheath–root system winter and rhizosheath–root system summer. Table S12. List of bacterial isolates, PGP activity, and abiotic resistance tested in vitro. Figure S1. Stipagrostis pungens rhizosheath-root system. Figure S2. Rarefaction curves of bacterial reads obtained by pair-ends MiSeq Illumina sequencing in bulk sand, rhizosheath, rhizosphere, and root tissues. Figure S3. Visualization of Stipagrostis pungens rhizosheath with scanning electron microscopy (SEM). Figure S4. SEM images and electron micrographs of the sand grains and root tissue within the rhizosheath of Stipagrostis pungens using environmental scanning electron microscopy (ESEM) to reveal chemical composition. Figure S5. Localization of bacteria in rhizosheath-root system by confocal laser-scanning microscopy (CLSM) and fluorescence in situ hybridization (FISH). Figure S6. Bacterial KTUs distribution across samples. Figure S7. Venn diagram shows the distribution of bacterial KTUs across compartment categories. Figure S8. Alpha diversity expressed as richness (number of KTUs) and Shannon diversity across the compartment categories. Figure S9. Quantification of betadiversity components in bulk sand bacterial communities across seasons (summer and winter). Figure S10. Alpha diversity expressed as richness (number of KTUs) and Shannon diversity across the compartments in summer and winter. Figure S11. Venn diagrams showing the number of KTUs present in summer and/or in winter in each compartment category. Figure S12. Analysis of 2-fold change was performed to evaluate the KTUs that had a significantly (p < 0.01) different relative abundance (2-fold change) over summer and winter. Figure S13. Taxonomy of co-occurrence network degrees in bulk sand and rhizosheath matrix across seasons. Figure S14. Microcosms to evaluate sand wettability in vitro. Evaluation of sand weight at 48 h and along the entire incubation (0, 24 and 48 h).

The Workshop on use of Ageing and Maturity Staging Error Matrices in Stock Assessment (WKAMEMSA) aimed to compile previous experiences with incorporating age and maturity error information in the assessment and scientific advice process within ICES, create protocols to quantify the observation error in age and maturity data used as input data in the assessment models, identify the lines of development required to incorporate that information, and select candidate stocks and models to be used as case studies and progress in each of the steps related to age and maturity error that affect the final uncertainty in the assessment. The approaches followed by three of the main assessment models used in ICES (SAM, SS3 and Gadget) to incorporate ageing errors in the assessment, data requirements, as well as the steps to consider in the organization of age reading and maturity staging exchange events were addressed during the workshop.The revision of previous research studies showed that not accounting for ageing error in stock assessment produces bias in the estimation of the Spawning-Stock Biomass (SSB) and smoothed estimates of annual recruitment, which can lead to under/overestimation of fishing mortality in the short-term forecast. Another group of studies proposed different approaches to incorporate ageing errors in stock assessment by using use the information from exchange events to calculate model-based Ageing Error Matrices (AEM) that could be incorporated into stock assessment models.SAM, SS3 and Gadget can use and incorporate ageing error information in the stock assessment, however none of these assessment models include the possibility of considering errors in the maturity process at this stage. These models can use the output from age exchange events to produce internally model-based AEMs during the model optimization. The results of preliminary studies with these assessment models were presented. Alternative approaches to use the exchange event information and produce AEM inside and outside the assessment models were discussed.The need of increasing the communication between coordinators of calibration exercises and stock assessors was highlighted; in order to assess if a given stock requires a tailored design of exchange events, data input format and model structure. The organization of regular calibration exercises with adequate sample size is required to assess the potential changes in ageing errors over time.Finally, a selection of stocks was suggested to be used as case studies for SAM, SS3 and gadget. It is expected that these case studies serve to set guidance on the best practices throughout the entire process, from the organization of exchange events to the use of their outputs in the stock assessment during the benchmark process.

The Scientific, Technical and Economic Committee for Fisheries (STECF) hold its 60th plenary on 25-29 March 2019at JRC, Ispra, Italy.-- 159 pages, Commission Decision of 25 February 2016 setting up a Scientific, Technical and Economic Committee for Fisheries, C(2016) 1084, OJ C 74, 26.2.2016, p. 4–10. The Commission may consult the group on any matter relating to marine and fisheries biology, fishing gear technology, fisheries economics, fisheries governance, ecosystem effects of fisheries, aquaculture or similar disciplines

The eastern Baltic (EB) cod (Gadus morhua) stock was depleted and overexploited for decades until the mid-2000s, when fishing mortality rapidly declined and biomass started to increase, as shown by stock assessments. These positive developments were partly assigned to effective management measures, and the EB cod was considered one of the most successful stock recoveries in recent times. In contrast to this optimistic view, the analytical stock assessment failed in 2014, leaving the present stock status unclear. Deteriorated quality of some basic input data for stock assessment in combination with changes in environmental and ecological conditions has led to an unusual situation for cod in the Baltic Sea, which poses new challenges for stock assessment and management advice. A number of adverse developments such as low nutritional condition and disappearance of larger individuals indicate that the stock is in distress. In this study, we (i) summarize the knowledge of recent changes in cod biology and ecosystem conditions, (ii) describe the subsequent challenges for stock assessment, and (iii) highlight the key questions where answers are urgently needed to understand the present stock status and provide scientifically solid support for cod management in the Baltic Sea.

Cardinale, Massimiliano ... et al.-- This report was reviewed by the STECF during its spring plenary meeting held from 13 to 17 April 2015 in Brussels, Belgium.-- 394 pages, The STECF expert working group >EWG 1419 - Mediterranean assessment part 2>, has convened in Rome during 19-23 January 2015 and addressed a series of issues as requested by DG MARE in the correspomnding terms of references. The detailed output of this working group efforts is included in the following report

Cardinale, Massimiliano ... et al.-- This report was reviewed by the STECF during its 50TH plenary meeting held from 9 to 13 November 2015 in Brussels.-- 409 pages, The Expert Working Group meeting of the Scientific, Technical and Economic Committee for Fisheries EWG 15-11 was held from 31 Aug - 04 Sep 2015 in Palma de Mallorca, Spain to assess the status of demersal and small pelagic stocks in the Mediterranean Sea against the proposed FMSY reference points

Cardinale, Massimiliano ... et al.-- The report was reviewed by the STECF during its winter plenary held from 10 to 14 November 2014 in Brussels, Belgium.-- 393 pages, The Expert Working Group meeting of the Scientific, Technical and Economic Committee for Fisheries EWG 14-09 was held from 14 - 18 July 2014 in Rome, Italy to assess the status of demersal and small pelagic stocks in the Mediterranean Sea against the proposed FMSY reference point

Cardinale, Massimiliano ... et al.-- This report was reviewed by the STECF during its 44th plenary meeting held from 4 to 8 November 2013 in Brussels, Belgium.-- 399 pages, The Expert Working Group meeting of the Scientific, Technical and Economic Committee for Fisheries EWG 13-09 was held from 15 – 19 July 2013 in Ispra, Italy to assess the status of demersal and small pelagic stocks in the Mediterranean Sea against the proposed FMSY reference points. The report was reviewed and endorsed by the STECF during its plenary meeting held from 4 to 8 November 2013 in Brussels (Belgium)

Cardinale, Massimiliano ... et al.-- The report was reviwed and adopted by the STECF during its 39th plenary held from 16 to 20 April 2012 in Brussels, Belgium.-- 404 pages, The Expert Working Group meeting of the Scientific, Technical and Economic Committee for Fisheries EWG 11-20 was held from 16 - 20 January in Madrid, Spain, to assess the status of demersal and small pelagic stocks in the Mediterranean Sea against the proposed FMSY reference point and to carry out short and medium term forecasts. The report was reviwed and adopted by the STECF during its 39th plenary held from 16 to 20 April 2012 in Brussels (Belgium)

Cardinale, Massimiliano ... et al.-- This report was reviewed by the STECF during its 41st plenary meeting held from 5 to 9 November, 2012 in Brussels, Belgium.-- 498 pages, The Expert Working Group meeting of the Scientific, Technical and Economic Committee for Fisheries EWG 12-10 was held from 16 - 20 July in Sete, France, to assess the status of demersal and small pelagic stocks in the Mediterranean Sea against the proposed FMSY reference point. The report was reviewed and endorsed by the STECF during its 41st plenary held from 5 to 9 November 2012 in Brussels (Belgium)

Cardinale, Massimiliano ... et al.-- Report of the SGMED-10-03 Working Group on the Mediterranean, 13-17 December 2010, Mazara del Vallo, Sicily, Italy.-- 645 pages, SGMED-10-03 was held during 13 - 17 December 2010, Mazara del Vallo, Sicily (Italy). The report is a compilation of information on existing fisheries and stock data in order to update the status of the main demersal and small pelagic stocks. The report deals with assessment of historic and recent trends in stock parameters (stock size, recruitment and exploitation), short and medium term forecasts of stock size and catch under different management scenatios, as well as determination of limit and precautious reference points and relevant scientific advice. STECF reviewed the report during its Plenary meeting on 11-15 April 2011

21 pages, 7 figures, 1 table, supporting information may be found in the online version of this article: http://onlinelibrary.wiley.com/doi/10.1111/j.1467-2979.2011.00453.x/suppinfo, In Mediterranean European countries, 85% of the assessed stocks are currently overfished compared to a maximum sustainable yield reference value (MSY) while populations of many commercial species are characterized by truncated size- and age-structures. Rebuilding the size- and age-structure of exploited populations is a management objective that combines single species targets such as MSY with specific goals of the ecosystem approach to fisheries management (EAF), preserving community size-structure and the ecological role of different species. Here, we show that under the current fishing regime, stock productivity and fleet profitability are generally impaired by a combination of high fishing mortality and inadequate selectivity patterns. For most of the stocks analysed, a simple reduction in the current fishing mortality (Fcur) towards an MSY reference value (FMSY), without any change in the fishing selectivity, will allow neither stock biomass nor fisheries yield and revenue to be maximized. On the contrary, management targets can be achieved only through a radical change in fisheries selectivity. Shifting the size of first capture towards the size at which fish cohorts achieve their maximum biomass, the so-called optimal length, would produce on average between two and three times higher economic yields and much higher biomass at sea for the exploited stocks. Moreover, it would contribute to restore marine ecosystem structure and resilience to enhance ecosystem services such as reservoirs of biodiversity and functioning food webs. © 2011 Blackwell Publishing Ltd.

Mc 2009. Microscopy Conference, Graz, Austria. 30 August - 4 September 2009. First Joint Meeting Of Dreiländertagung And Multinational Congress On Microscopy.

The bacterial communities associated with 11 different lichen samples (belonging to eight different species) from different habitats were investigated. The culturable aerobic-heterotrophic fraction of the bacterial communities was isolated from nine lichen samples on protein-rich and sugar-rich/N-free media. Thirty-four bacterial isolates were purified and pooled into groups (phylotypes) by analysis of the ribosomal internal transcribed spacer polymorphism. Twenty five phylotypes were identified, each comprising between one and three isolates. One isolate of each phylotype was partially sequenced and the resulting 16S rRNA gene sequences were compared in a phylogenetic analysis. Three genera of Firmicutes, four of Actinobacteria and three of Proteobacteria were identified. Two phylotypes, belonging to the phyla Actinobacteria and Proteobacteria, respectively, were not identified at genus level. Some bacterial taxa were retrieved frequently in different lichen species sampled in the same or different sites. Paenibacillus and Burkholderia phylotypes seem to be common in lichens. Luteibactor rhizovicina was found in three different lichens of two different regions. In a cultivation-independent approach, total DNA was extracted from 11 lichen samples. Molecular fingerprints of the bacterial communities were obtained by PCR-amplification of the internal transcribed spacer region, and sequencing of selected bands indicated the presence of additional bacteria.

Sensitization to pollen allergens has been increasing in Europe every year. Most studies in this field are related to climate change, phenology, allergens associated with different pollens, and allergic disorders. As a plant microhabitat, pollen is colonized by diverse microorganisms, including endotoxin-producing bacteria which may contribute to pollen allergy (pollinosis). Therefore, bacteria isolated from high allergenic and low allergenic plant pollen, as well as the pollen itself with all microbial inhabitants, were used to assess the effect of the pollen by measuring the endotoxins lipopolysaccharides (LPS) and lipoteichoic acid (LTA) concentrations and their effect on chemokine and cytokine release from transwell cultured epithelial A549 cells as a model of epithelial lung barrier. High allergenic pollen showed a significantly higher level of bacterial endotoxins; interestingly, the endotoxin level found in the bacterial isolates from high allergenic pollen was significantly higher compared to that of bacteria from low allergenic pollen. Moreover, bacterial LPS concentrations across different pollen species positively correlated with the LPS concentration across their corresponding bacterial isolates. Selected bacterial isolates from hazel pollen (HA5, HA13, and HA7) co-cultured with A549 cells induced a potent concentration-dependent release of the chemokine interleukin-8 and monocyte chemotactic protein-1 as well as the cytokine TNF-alpha and interleukin-2 to both apical and basal compartments of the transwell model. This study clearly shows the role of bacteria and bacterial endotoxins in the pollen allergy as well as seasonal allergic rhinitis.

AimsClimate change imposes adaptation of viticulture in risk areas, such as the Mediterranean. Mycorrhization is a valid tool to reduce the impact of the expected temperature/drought increase. Aim of this work was to test the effects of mycorrhization on grapevine vegetative growth, element composition of soil/leaves, and microbiota of bulk soil/rhizosphere/endorhiza, in the field, under exacerbated summer stress conditions obtained by planting the rootstocks in June.Methods118 rooted cuttings of 1103-Paulsen (Vitis berlandieri×Vitis rupestris) were planted in Salento (Apulia, Southern Italy); about half of them were mycorrhized. Leaf Area Index, shoot growth and survival rate were monitored across two growing seasons. Leaf/shoot weight, chemical analysis of 25 elements, and 16S rRNA gene metabarcoding of bulk soil/rhizosphere/endorhiza were performed on subsamples.ResultsMycorrhized plants showed significantly higher survival rate and growth, and accumulated significantly higher amounts of 18 elements. 27 endorhizal OTUs (representing ~20% of total sequences) were differently distributed (20 OTUs more abundant in mycorrhized plants); in the rhizosphere, instead, 12 OTUs (~2.5% of total sequences) were differently distributed. A few Actinobacterial OTUs were enriched by mycorrhization in the root endosphere; the same OTUs were the most correlated with the chemical elements, suggesting a role in element dynamics. These OTUs were not hub taxa of the co-occurrence network.ConclusionsThis work shed light onto the interactions between mycorrhiza and microbiome, in the context of plant element dynamics, which is useful to identify potential target candidates for biotechnological applications, thus moving towards a more sustainable, ecosystem-based viticulture.

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.

Background In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath–root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert. Results The belowground rhizosheath–root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath–root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath–root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment. Conclusions Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions.