MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

Organic matter degradation by microorganisms from Amazon river: metagenomics and population genomes

Microbes from Amazon river basin represent an unexplored biodiversity, with a huge metabolic potential. This ecosystem receives large amounts of terrestrial organic matter (OM), which promotes heterotrophic microbial growth. Microbial populations have been exposed for millennia to a complex OM derived from plants, and these communities must have developed metabolic pathways to degrade it. In the present work, 106 metagenomes from 30 sampling stations of rivers and lakes of the Amazon river basin were analyzed, covering the freshwater and coastal ocean areas. Using the gold standard techniques for assembly and gene prediction, the first gene catalog of freshwater microorganisms was generated, containing more than 3.7 million non-redundant genes, predominantly those of bacterial origin (35.73%). The present work comprises the hugest biodiversity ever sampled in Amazon river until now. As an auxiliary system, the AGSSY program was created to assist in the data mining of this catalog, proving to be fast and efficient in this process. The analysis of k-mers diversity suggests that these genes originate from local evolutionary processes. In addition, there is a stratification of the OM processing in the water column, possibly regulated by a sophisticated system of alternative carbon sources use, mainly based on tricarboxylates. The spatial structure of the OM processing genes suggests a zonation of lignin, cellulose and hemicellulose degradation. Using hybrid binning methods, taking into account contigs composition and abundance, it was possible to reconstruct 51 non-redundant population genomes. Through the analysis of them, it was possible to verify abundant endemic species belonging to Bacteria and Archaea, with a predominance of the Proteobacterium phylum (39%). Population genome analyzes, together with the gene catalog data, suggest a sophisticated priming model for the degradation of terrestrial OM in the Amazon River. Such a model would be based on the retroinhibition undergone by organisms that oxidize lignin, and in a community of microorganisms using alternative carbon sources that blocks this effect.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Os micróbios da bacia do rio Amazonas representam uma biodiversidade inexplorada, com grande potencial metabólico. Este ecossistema recebe grandes quantidades de matéria orgânica (organic matter, OM) terrestre, o que promove o crescimento microbiano heterotrófico. Populações microbianas foram expostas durante milênios a uma OM complexa derivada de plantas, e essas comunidades devem ter desenvolvido vias metabólicas para degradá-la. No presente trabalho, foram analisados 106 metagenomas provenientes de 30 estações de amostragem de rios e lagos da bacia Amazônica, cobrindo as zonas de água doce e costeira. Utilizando-se as técnicas padrão ouro para montagem e predição gênica, foi gerado o primeiro catálogo de genes de microrganismos de água doce, contendo mais de 3,7 milhões de genes não redundantes, com predominância daqueles de origem bacteriana (35,73%). Este estudo compreendeu até então a maior biodiversidade de microrganismos aquáticos amostrados no rio Amazonas. Como um sistema auxiliar, foi criado o programa AGSSY que auxilia na mineração de dados deste catálogo, mostrando-se rápido e eficiente neste processo. A análise de diversidade dos k-mers sugere que esses genes tem origem a partir de processos evolutivos locais. Além disso, há uma estratificação do processamento da OM na coluna de água, possivelmente regulada por um sistema sofisticado de uso alternativo de fontes de carbono, principalmente baseado em tricarboxilatos. A estrutura espacial dos genes de processamento de OM sugere uma substituição dos metabolismos de lignina e hemi-celulose, pelo metabolismo de celulose no oceano. Utilizando-se os métodos de binning híbridos, levando em conta composição e abundância dos contigs foi possível a reconstrução de 51 genomas populacionais não-redundantes. Por meio da análise destes, foi possível verificar espécies endêmicas abundantes pertencentes a Bactérias e Arquéias, com um predomínio do filo Proteobactéria (39%). Análises dos genomas populacionais, em conjunto com os dados do catálogo de genes, sugerem um sofisticado modelo de priming para a degradação de OM terrestre no rio Amazonas. Tal modelo seria baseado na retroinibição sofrida pelos organismos que oxidam a lignina, e numa comunidade de microrganismos utilizadores de fontes alternativas de carbono, que bloqueiam este efeito.CAPES: 88881.131637/2016-01CNPq: 141112/2016-

Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters

14 pages, 5 figures, 1 table, supporting Information https://doi.org/10.1111/mec.16222.-- This article has earned Open Data and Open Materials badges. The data is available at https://doi.org/10.21203/rs.3.rs-32535/v2 and https://doi.org/10.5281/zenodo.1484509.-- Data availability statement: This manuscript has been made available as a preprint at Research Square (https://doi.org/10.21203/rs.3.rs-32535/v2). Metagenomes used to construct the Amazon River PGs have been made available at NCBI-SRA database as projects SRP044326, PRJEB25171 and SRP039390. The PG nucleotide sequences have been deposited at the European Nucleotide Archive (ENA) in the project: PRJEB25176. The PG annotations are available at Zenodo (https://doi.org/10.5281/zenodo.1484509).-- This is the pre-peer reviewed version of the following article: [Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters; Molecular Ecology 31(1): 206-219 (2022)], which has been published in final form at https://doi.org/10.1111/mec.16222. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsRivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a complex microbial consortium could explain the quick turnover of TeOM previously observed in this ecosystemWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Tollip or not Tollip: what are the evolving questions behind it?

Tollip plays an important role in the interleukin-1 receptor IL-1R and Toll pathways. As a modulator of the immune pathway, it indirectly controls the amount of antimicrobial peptides. This could indicate a vital step in maintaining animal immune systems and preventing infection. Evolutionary questions are crucial to understanding the conservation and functioning of the biochemical pathways like the Tollip-mediated one. Through an analysis of 36 sequences of the Tollip protein from different animal taxa, downloaded from Kyoto Encyclopedia of Genes and Genomes (KEGG) databank, we inferred diverse evolutionary parameters, such as molecular selection and structure conservation, by analyzing residue by residue, beyond the canonical parameters to this type of study, as maximum likelihood trees. We found that Tollip presented different trends in its evolving history. In primates, the protein is becoming more unstable, just the opposite is observed in the arthropod group. The most interesting finding was the concentration of positively selected residues at amino terminal ends. Some observed topological incongruences in maximum likelihood trees of complete and curated Tollip data sets could be explained through horizontal transfers, evidenced by recombination detection. These results suggest that there is more to be researched and understood about this protein

Tollip or not Tollip: what are the evolving questions behind it?

Tollip plays an important role in the interleukin-1 receptor IL-1R and Toll pathways. As a modulator of the immune pathway, it indirectly controls the amount of antimicrobial peptides. This could indicate a vital step in maintaining animal immune systems and preventing infection. Evolutionary questions are crucial to understanding the conservation and functioning of the biochemical pathways like the Tollip-mediated one. Through an analysis of 36 sequences of the Tollip protein from different animal taxa, downloaded from Kyoto Encyclopedia of Genes and Genomes (KEGG) databank, we inferred diverse evolutionary parameters, such as molecular selection and structure conservation, by analyzing residue by residue, beyond the canonical parameters to this type of study, as maximum likelihood trees. We found that Tollip presented different trends in its evolving history. In primates, the protein is becoming more unstable, just the opposite is observed in the arthropod group. The most interesting finding was the concentration of positively selected residues at amino terminal ends. Some observed topological incongruences in maximum likelihood trees of complete and curated Tollip data sets could be explained through horizontal transfers, evidenced by recombination detection. These results suggest that there is more to be researched and understood about this protein

Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

18 pages, 7 figures, 1 table, supplementary information https://doi.org/10.1186/s40168-020-00930-wBackground. The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. Results. We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. Conclusions. Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical riversCDSJ was supported by a PhD scholarship from Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq #141112/2016-6). FHS and HS work was supported by Research Productivity grants from CNPq (Process # 311746/2017-9 and #309514/2017-7, respectively). RL was supported by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain). This work was supported by Petróleo Brasileiro S.A. (Petrobras), as part of a research agreement (#0050.0081178.13.9) with the Federal University of São Carlos, SP, Brazil, within the context of the Geochemistry Thematic Network. Additionally, this work was supported by the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain) and MicroEcoSystems (240904, RCN, Norway) to RL and Fundação de Amparo à Pesquisa do Estado de São Paulo – FAPESP (Process #2014/14139-3) to HS. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 (CAPES #88881.131637/2016-01)With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)Peer reviewe

Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome

19 pages, 6 figures, 1 table, supporting information https://doi.org/10.1111/1462-2920.16367.-- Data Availability Statement: All the code used for the analyses can be found in the following repository: https://github.com/adriaaulaICM/key_biogem_genes. The data to reproduce the analyses can be found in the same repository. The reader can find in the data folder a FASTA file for all the gene variants, the abundance count table, the taxonomic assignation (both with GTDB and Uniref databases), the functional annotation for each variant, and the seasonality testMicrobes drive the biogeochemical cycles of marine ecosystems through their vast metabolic diversity. While we have a fairly good understanding of the spatial distribution of these metabolic processes in various ecosystems, less is known about their seasonal dynamics. We investigated the annual patterns of 21 biogeochemical relevant functions in an oligotrophic coastal ocean site by analysing the presence of key genes, analysing high-rank gene taxonomy and the dynamics of nucleotide variants. Most genes presented seasonality: photoheterotrophic processes were enriched during spring, phosphorous-related genes were dominant during summer, coinciding with potential phosphate limitation, and assimilatory nitrate reductases appeared mostly during summer and autumn, correlating negatively with nitrate availability. Additionally, we identified the main taxa driving each function at each season and described the role of underrecognized taxa such as Litoricolaceae in carbon fixation (rbcL), urea degradation (ureC), and CO oxidation (coxL). Finally, the seasonality of single variants of some families presented a decoupling between the taxonomic abundance patterns and the functional gene patterns, implying functional specialization of the different genera. Our study unveils the seasonality of key biogeochemical functions and the main taxonomic groups that harbour these relevant functions in a coastal ocean ecosystemThis research was funded by grants REMEI (CTM2015-70340-R), MIAU (RTI2018-101025-B-I00), and ECLIPSE (PID2019-110128RB-100) from the Spanish Ministry of Science and Innovation, and received support from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000924-S). Adrià Auladell was supported by a Spanish FPI grant from the Ministry of Science and Innovation. Isabel Ferrera had the support of a ‘2019 Leonardo Grant for Researchers and Cultural Creators’ from the BBVA FoundationPeer reviewe

Seasonality of biogeochemically relevant genes in the NW Mediterranean coastal microbiome

16 Symposium of Aquatic Microbial Ecology (SAME16), “From Boat to Bench”- Integrating field observation with lab experiments, 1-6 September 2019, Potsdam, Germany.-- 1 pageMarine biogeochemical processes are mediated by microorganisms through protein encoding genes, some being solely present in prokaryotes. During the last decade, genomic site-specific and large-scale expeditions have discovered millions of genes, unveiling new putative functions and large gene heterogeneity. Nonetheless, little still is known about the genomic basis of key biogeochemical processes, the taxonomic groups mediating them and whether seasonal patterns occur across taxonomic levels. For these reasons, we conducted temporal analyses of the functional diversity for 18 key functional genes in a model coastal marine microbiome. We analyzed a 7- year metagenomic time-series from the Blanes Bay Microbial Observatory (NW Mediterranean Sea) through state-of-the-art omics’ tools and time series statistics. This dataset allowed us to explore the seasonal trends and gene heterogeneity in various key genes involved in the four major marine biogeochemical cycles (carbon, phosphorus, sulfur and nitrogen). Preliminary results show some key functions as seasonal, although with heterogeneity across the different taxonomical ranks. Our results define the seasonality of gene presence in that coastal environment and are the basis to discuss the implications of the seasonality of such genes for ecosystem functioningPeer Reviewe