The costly disposal of the semisolid residual pomace generated in the two phase extraction used in modern olive mills is causing serious problems to the small oil producers of rural southeastern Spain. Composting may be a viable alternative since complementary residues are usually available in these areas to prepare an adequate starting mixture. In this work, four different combinations of residues (pomace+rabbit manure, pomace+sheep manure, pomace+rabbit manure+rice straw, pomace+rabbit manure+almond shells) were composted in 3 ton piles aerated by turnings, using technology available to any small community of oil producers. During the four long processes (9-10 months), a steady decrease of organic matter and increases in the concentrations of nutrient and humic substances were observed, together with large increases in pH and salinity which may reduce the agronomic value of the final products.

Environmental DNA (eDNA) is increasingly used for biodiversity monitoring, particularly in aquatic systems. However, each step, from sample collection to bioinformatic analysis, can introduce biases and influence the reliability of results. While much effort has been put into the optimization of laboratory methods, less attention has been devoted to estimate the impacts of eDNA capture methods. To address this issue, water samples were collected at nine small ponds and puddles where up to 10 amphibian species occur, using precipitation, disc filters, and capsules. We focused on targeted detection of an amphibian species, Salamandra salamandra, and on the composition of the whole amphibian community. Species detection was performed using a novel qPCR assay for S. salamandra and high‐throughput sequencing, combined with stringent versus relaxed PCR replication thresholds. Filtration techniques (disc filters and capsules) outperformed precipitation, generating a higher number of detections of S. salamandra and higher amounts of captured eDNA, while species detection was identical between disc filters and capsules. There were no significant differences between capture methods regarding amphibian community composition. The variation in detection success associated with capture methods was far higher than that associated with PCR replication, regardless of the detection method used. Our results highlight the importance of choosing a suitable capture method for eDNA studies and suggest that the choice of capture method outweighs the choice of detection method used. To the best of our knowledge, this is the first study to compare high‐capacity capsules with common eDNA methods for water samples, such as precipitation and standard disc filters.

Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with preexisting bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was nonsignificant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.

Enhancing the role of the soil microbiota in plant phosphorus (P) and sulfur (S) supply through application of organic fertilizer could reduce dependencies on non-sustainable synthetic fertilizers. To compare the effects of organic/inorganic fertilizers on the soil microbiota, soil columns with Lolium perenne (ryegrass) were setup in a greenhouse and amended with an inorganic fertilizer, cattle slurry (organic), or urea (P-and S-free control). Ryegrass rhizosphere of the slurry treatment had significantly higher abundances of bacterial-feeding nematodes, mycorrhizal colonization, cultivable heterotrophic bacteria, phosphonate-and sulfonate-utilizing bacteria, arylsulfatase activity, available P and Variovorax asfA gene copies compared to the inorganic and urea treatments. Phosphomonoesterase activities, and gene abundances involved in organic P and S transformations (phoD, phoC, Burkholderia & Polaromonas asfA) were similar in all treatments. Grass dry matter yield, shoot uptake of N, P and S were significantly higher in the inorganic treatment compared to the urea and slurry treatments. Community compositions differed significantly between the three fertilizer treatments and included the bacterial, alkaline phosphomonoesterase-producing bacterial, fungal, AM fungal, and nematode communities. Bacteriodetes were found in higher relative abundance in the organic treatment while Acidobacteria were more abundant in the urea and inorganic fertilizer treatments. These community shifts correlated significantly with grass dry matter yield, uptake of N, P and S, mycorrhizal colonization, enzyme activities, abundances of bacteria and bacterial-feeding nematodes. We concluded that organic fertilization promoted soil microbes and nematodes which have the potential to support sustainable plant growth, provided that the overall nutrient requirements are met.

22Traditional detection of aquatic invasive species, via morphological identification is often time-23 consuming and can require a high level of taxonomic expertise, leading to delayed mitigation 24 responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-25 based sequencing technology have been used to overcome these hindrances, but sample 26 processing is often lengthy. More recently, portable nanopore sequencing technology has 27 become available, which has the potential to make molecular detection of invasive species more 28 widely accessible and to substantially decrease sample turnaround times. However, nanopore-29 sequenced reads have a much higher error rate than those produced by Illumina platforms, 30 which has so far hindered the adoption of this technology. We provide a detailed laboratory 31 protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect 32 invasive species, and we test its application using invasive bivalves. We sampled water from 33 sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve 34 communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a 35 turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference 36 sequences. There were no taxa detected other than those known to occur. The lack of 37 detections of some species at some sites could be explained by their known low abundances. 38

We present the complete genome sequences of two Xanthomonas euroxanthea strains isolated from buds of a walnut tree. The whole-genome sequences of strains CPBF 367 and CPBF 426 consist of two circular chromosomes of 4,923,218 bp and 4,883,254 bp and two putative plasmids of 45,241 bp and 17,394 bp, respectively. These data may contribute to the understanding of Xanthomonas species-specific adaptations to walnut.

The InBIO Barcoding Initiative (IBI) Hemiptera 01 dataset contains records of 131 specimens of Hemiptera. Most specimens have been morphologically identified to species or subspecies level and represent 88 species in total. The species of this dataset correspond to about 7.3% of continental Portuguese hemipteran species diversity. All specimens were collected in continental Portugal. Sampling took place from 2015 to 2019 and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. This dataset increases the knowledge on the DNA barcodes and distribution of 88 species of Hemiptera from Portugal. Six species, from five different families, were new additions to the Barcode of Life Data System (BOLD), with another twenty five species barcodes' added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF). Eutettix variabilis and Fieberiella florii are recorded for the first time for Portugal and Siphanta acuta, an invasive species, previously reported from the Portuguese Azores archipelago, is recorded for the first time for continental Portugal.

The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snakeflies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological analysis. This work is the first to sample and DNA sequence lacewings and snakeflies of Portugal. A reference collection was built with captured specimens that were identified morphologically. DNA barcode sequences of 658 bp were obtained from 243 specimens of 54 species. The results showed that most species can be successfully identified through DNA barcoding, with the exception of seven species of Chrysopidae (Neuroptera). Additionally, the first published distribution data are presented for Portugal for the neuropterans Gymnocnemia variegata (Schneider, 1845) and Myrmecaelurus (Myrmecaelurus) trigrammus (Pallas, 1771).