More stories

  • in

    A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

    Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003).Article 
    CAS 
    PubMed 

    Google Scholar 
    Timmer-Ten Hoor, A. A new type of thiosulphate oxidizing, nitrate reducing microorganism: Thiomicrospira denitrificans sp. nov. Neth. J. Sea Res. 9, 344–350 (1975).Article 
    CAS 

    Google Scholar 
    Cai, L., Shao, M. & Zhang, T. Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment. Stand. Genom. Sci. 9, 1302–1310 (2014).Article 

    Google Scholar 
    Wang, S., Jiang, L., Liu, X., Yang, S. & Shao, Z. Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas. Int. J. Syst. Evol. Microbiol. 70, 2657–2663 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Takai, K. et al. Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int. J. Syst. Evol. Microbiol. 56, 1725–1733 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Hu, Q., Wang, S., Lai, Q., Shao, Z. & Jiang, L. Sulfurimonas indica sp. nov., a hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal sulfide chimney in the Northwest Indian Ocean. Int. J. Syst. Evol. Microbiol. 71, 1466–5034 (2021).Article 

    Google Scholar 
    Wang, S. et al. Sulfurimonas sediminis sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal vent at the Longqi system, southwestern Indian ocean. Antonie Van Leeuwenhoek 114, 813–822 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Wang, S. et al. Characterization of Sulfurimonas hydrogeniphila sp. nov., a novel bacterium predominant in deep-sea hydrothermal vents and comparative genomic analyses of the genus Sulfurimonas. Front. Microbiol. 12, 626705 (2021).Labrenz, M. et al. Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas. Int. J. Syst. Evol. Microbiol. 63, 4141–4148 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Henkel, J. V. et al. Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea. Syst. Appl. Microbiol. 44, 126155 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ratnikova, N. M. et al. Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano. Int. J. Syst. Evol. Microbiol. 70, 487–492 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Han, Y. & Perner, M. The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines. Front. Microbiol. 6, 989 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    López-garcía, P. et al. Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ. Microbiol. 5, 961–976 (2003).Article 
    PubMed 

    Google Scholar 
    Nakagawa, S. et al. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ. Microbiol. 7, 1619–1632 (2005).Article 
    CAS 
    PubMed 

    Google Scholar 
    Huber, J. A. et al. Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. FEMS Microbiol. Ecol. 73, 538–549 (2010).CAS 
    PubMed 

    Google Scholar 
    Meier, D. V. et al. Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. ISME J. 11, 1545–1558 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mino, S. et al. Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents. ISME J. 11, 909–919 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Akerman, N. H., Butterfield, D. A., Huber, J. A., Huber, J. A. & Paul, J. B. Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids. Front. Microbiol. 4, 185 (2013).Rogge, A., Vogts, A., Voss, M. & Labrenz, M. Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r -strategists. Environ. Microbiol. 19, 2495–2506 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    German, C. R. et al. Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise. Proc. Natl Acad. Sci. USA 107, 14020–14025 (2010).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sylvan, J. B., Pyenson, B. C., Rouxel, O., German, C. R. & Edwards, K. J. Time-series analysis of two hydrothermal plumes at 9°50’ N East Pacific Rise reveals distinct, heterogeneous bacterial populations. Geobiology 10, 178–192 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Perner, M. et al. In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field. Environ. Microbiol. 15, 1551–1560 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Haalboom, S. et al. Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge. Biogeosciences 17, 2499–2519 (2020).Article 
    CAS 

    Google Scholar 
    Li, J. et al. Distribution and succession of microbial communities along the dispersal pathway of hydrothermal plumes on the Southwest Indian Ridge. Front. Mar. Sci. 7, 581381 (2020).Article 

    Google Scholar 
    Dick, G. J. et al. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front. Microbiol. 4, 124 (2013).Dick, G. J. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat. Rev. Microbiol. 17, 271–283 (2019).Article 
    CAS 
    PubMed 

    Google Scholar 
    German, C. R. & Seyfried, W. E. in Treatise on Geochemistry 2nd edn (eds Holland, H. D. & Turekian, K. K.), 8, 191–233 (Elsevier, 2014).Kadko, D., Baross, J. & Alt, J. The magnitude and global implications of hydrothermal flux. Geophys. Monogr. Ser. 91, 446–466 (1995).
    Google Scholar 
    German, C. R. et al. Volcanically hosted venting with indications of ultramafic influence at Aurora hydrothermal field on Gakkel Ridge. Nat. Commun. 13, 6517 (2022).Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Konstantinidis, K. T., Rosselló-móra, R. & Amann, R. Uncultivated microbes in need of their own taxonomy. ISME J. 11, 2399–2406 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Murray, A. E. et al. Roadmap for naming uncultivated Archaea and Bacteria. Nat. Microbiol. 5, 987–994 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Eren, A. M. et al. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 9, 968–979 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Dick, G. J. & Tebo, B. M. Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume. Environ. Microbiol. 12, 1334–1347 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lesniewski, R. A., Jain, S., Anantharaman, K., Schloss, P. D. & Dick, G. J. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J. 6, 2257–2268 (2012).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sheik, C. S. et al. Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin. ISME J. 9, 1434–1445 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Reed, D. C. et al. Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents. ISME J. 9, 1857–1869 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Han, Y. & Perner, M. The role of hydrogen for Sulfurimonas denitrificans’ metabolism. PLoS ONE 9, 8–14 (2014).
    Google Scholar 
    Ilbert, M. & Bonnefoy, V. Insight into the evolution of the iron oxidation pathways. Biochim. Biophys. Acta 1827, 161–175 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Yu, H. & Leadbetter, J. R. Bacterial chemolithoautotrophy via manganese oxidation. Nature 583, 453–458 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Andrews, S. C. Iron storage in bacteria. Adv. Microb. Physiol. 40, 281–351 (1998).Article 
    CAS 
    PubMed 

    Google Scholar 
    Pitcher, R. S. & Watmough, N. J. The bacterial cytochrome cbb 3 oxidases. Biochim. Biophys. Acta 1655, 388–399 (2004).Article 
    CAS 
    PubMed 

    Google Scholar 
    Sousa, F. L. et al. The superfamily of heme–copper oxygen reductases: types and evolutionary considerations. Biochim. Biophys. Acta 1817, 629–637 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Park, B. et al. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl. Environ. Microbiol. 76, 7575–7587 (2010).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658 (2011).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bayer, B. et al. Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. ISME J. 15, 1025–1039 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Yamamoto, M., Arai, H., Ishii, M. & Igarashi, Y. Role of two 2-oxoglutarate: ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions. FEMS Microbiol. Lett. 263, 189–193 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Yamamoto, M., Ikeda, T., Arai, H., Ishii, M. & Igarashi, Y. Carboxylation reaction catalyzed by 2-oxoglutarate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus. Extremophiles 14, 79–85 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Berg, I. A. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl. Environ. Microbiol. 77, 1925–1936 (2011).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    French, C. E., Bell, J. M. L. & Ward, F. B. Diversity and distribution of hemerythrin-like proteins in prokaryotes. FEMS Microbiol. Lett. 279, 131–145 (2008).Article 
    CAS 
    PubMed 

    Google Scholar 
    Isaza, C. E., Silaghi-dumitrescu, R., Iyer, R. B., Kurtz, D. M. & Chan, M. K. Structural basis for O2 sensing by the hemerythrin-like domain of a bacterial chemotaxis protein: substrate tunnel and fluxional n terminus. Biogeochemistry 45, 9023–9031 (2006).Article 
    CAS 

    Google Scholar 
    Kendall, J. J., Barrero-tobon, A. M., Hendrixson, D. R. & Kelly, D. J. Hemerythrins in the microaerophilic bacterium Campylobacter jejuni help protect key iron–sulphur cluster enzymes from oxidative damage. Environ. Microbiol. 16, 1105–1121 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nariya, S. & Kalyuzhnaya, M. G. Hemerythrins enhance aerobic respiration in Methylomicrobium alcaliphilum 20Z R, a methane-consuming bacterium. FEMS Microbiol. Lett. 367, fnaa003 (2020).Sheng, Y. et al. Superoxide dismutases and superoxide reductases. Chem. Rev. 114, 3854–3918 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Anantharaman, K., Breier, J. A., Sheik, C. S. & Dick, G. J. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc. Natl Acad. Sci. USA 110, 330–335 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Dede, B. et al. Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes. ISME J. 16, 1479–1490 (2022).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schlindwein, V. (ed.) The Expedition of the Research Vessel ‘Polarstern’ to the Antarctic in 2013 (ANT-XXIX/8). Reports on polar and marine research, Bremerhaven, Alfred Wegener Institute for Polar and Marine Research, 672, 111 (2014); https://doi.org/10.2312/BzPM_0672_2014Boetius, A. The Expedition PS86 of the Research Vessel POLARSTERN to the Arctic Ocean in 2014. Reports on polar and marine research, Bremerhaven, Alfred Wegener Institute for Polar and Marine Research, 685, 133 (2015); https://doi.org/10.2312/BzPM_0685_2015Boetius, A. & Purser, A. The Expedition PS101 of the Research Vessel POLARSTERN to the Arctic Ocean in 2016. Reports on polar and marine research, Bremerhaven, Alfred Wegener Institute for Polar and Marine Research, 706, 230 (2017); https://doi.org/10.2312/BzPM_0706_2017Varliero, G., Bienhold, C., Schmid, F., Boetius, A. & Molari, M. Microbial diversity and connectivity in deep-sea sediments of the South Atlantic Polar Front. Front. Microbiol. 10, 665 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pernthaler, A., Pernthaler, J. & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68, 3094–3101 (2002).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Alm, E. W., Oerther, D. B., Larsen, N., Stahl, D. A. & Raskin, L. The oligonucleotide probe database. Appl. Environ. Microbiol. 62, 3557–3559 (1996).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919–1925 (1990).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).Article 

    Google Scholar 
    Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).Hassenrück, C., Quast, C., Rapp, J. & Buttigieg, P. Amplicon (GitHub, accessed 15 April 2019); https://github.com/chassenr/NGS/tree/master/AMPLICONMahé, F., Rognes, T., Quince, C., de Vargas, C. & Dunthorn, M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2, e593 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bushnell, B. BBMap: A Fast, Accurate, Splice-Aware Aligner. United States (2014). https://www.osti.gov/servlets/purl/1241166Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kopylova, E., Noe, L. & Touzet, H. Sequence analysis SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Gruber-vodicka, H. R., Seah, B. K. & Pruesse, E. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems 5, e00920 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. https://doi.org/10.14806/ej.17.1.200 (2011).Zhang, J., Kobert, K., Fluori, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li, D., Liu, C., Luo, R., Sadakane, K. & Lam, T. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761–6771 (2015).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wheeler, T. J. & Eddy, S. R. nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487–2489 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108 (2007).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Preprint at bioRxiv https://doi.org/10.1101/2022.07.11.499243 (2022).Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: assessing genomic data quality and beyond. Curr. Protoc. 1, e323 (2021).Article 
    PubMed 

    Google Scholar 
    Laslett, D. & Canback, B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32, 11–16 (2004).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).Article 
    CAS 
    PubMed 

    Google Scholar 
    Haft, D. H. et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29, 41–43 (2001).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kanehisa, M., Sato, Y. & Morishima, K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 248, 726–731 (2015).
    Google Scholar 
    Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kristensen, D. M. et al. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26, 1481–1487 (2010).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. L. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    Søndergaard, D., Pedersen, C. N. S. & Greening, C. HydDB: a web tool for hydrogenase classification and analysis. Sci. Rep. 6, 34212 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Garber, A. I. et al. FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies. Front. Microbiol. 11, 37 (2020).Passardi, F. et al. PeroxiBase: the peroxidase database. Phytochemistry 68, 1605–1611 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lucchetti-miganeh, C., Goudenège, D., Thybert, D., Salbert, G. & Barloy-hubler, F. SORGOdb: superoxide reductase gene ontology curated database. BMC Microbiol. 11, 105 (2011).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 4–8 (2016).
    Google Scholar 
    Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Tu, Q., Lin, L., Cheng, L., Deng, Y. & He, Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 35, 1040–1048 (2019).Article 
    CAS 
    PubMed 

    Google Scholar 
    Li, H. et al. A cross-species alignment tool (CAT). BMC Bioinformatics 8, 349 (2007).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil, 314–324, doi: 10.1109/IPDPS.2019.00041 (2019); https://ieeexplore.ieee.org/document/8820962Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E. & Zanini, F. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics 38, 2943–2945 (2022).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jalili, V. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res. 48, 395–402 (2020).Article 

    Google Scholar 
    Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44, W232–W235 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kalyaanamoorthy, S. et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Berger, S. A., Krompass, D. & Stamatakis, A. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol. 60, 291–302 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2, W256–W259 (2019).Article 

    Google Scholar 
    Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    van Dongen, S. & Abreu-goodger, C. in Bacterial Molecular Networks: Methods and Protocols, Methods in Molecular Biology (eds van Helden, J. et al.) 281–295 (Springer, 2012).Altschup, S. F., Gish, W., Pennsylvania, T. & Park, U. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).Article 

    Google Scholar 
    Nguyen, L., Schmidt, H. A., Haeseler, A., Von & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chernomor, O., von Haeseler, A. & Minh, B. Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 65, 997–1008 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Delmont, T. O. & Eren, A. M. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 6, e4320 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jensen, L. J. et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 36, 250–254 (2008).Article 

    Google Scholar 
    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–360 (2012).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2013).Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.6-4. https://CRAN.R-project.org/package=vegan (2022).Robinson, M. D., Mccarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Reiner-Benaim, A. FDR control by the BH procedure for two-sided correlated tests with implications to gene expression data analysis. Biom. J. 49, 107–126 (2007).Article 
    PubMed 

    Google Scholar 
    Villanueva, R. A. M. & Chen, Z. J. ggplot2: elegant graphics for data analysis (2nd ed.). Meas. Interdiscip. Res. Perspect. 17, 160–167 (2019).Diepenbroek, M. et al. Towards an integrated biodiversity and ecological research data management and archiving platform: the German Federation for the Curation of Biological Data (GFBio). In Informatik 2014 – Big Data Komplexität meistern Proc. 232 (eds Plödereder, E. et al.) 1711–1725 (Gesellschaft für Informatik, 2014).Schmidt, K., Koschinsky, A., Garbe-Schönberg, D., de Carvalho, L. M. & Seifert, R. Geochemistry of hydrothermal fluids from the ultramafic-hosted Logatchev hydrothermal field, 15°N on the Mid-Atlantic Ridge: temporal and spatial investigation. Chem. Geol. 242, 1–21 (2007).Article 
    CAS 

    Google Scholar 
    Perner, M. et al. The influence of ultramafic rocks on microbial communities at the Logatchev hydrothermal field, located 15 degrees N on the Mid-Atlantic Ridge. FEMS Microbiol. Ecol. 61, 97–109 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Douville, E. et al. The rainbow vent fluids (36°14’N, MAR): the influence of ultramafic rocks and phase separation on trace metal content in Mid-Atlantic Ridge hydrothermal fluids. Chem. Geol. 184, 37–48 (2002).Article 
    CAS 

    Google Scholar 
    Ji, F. et al. Geochemistry of hydrothermal vent fluids and its implications for subsurface processes at the active Longqi hydrothermal field, Southwest Indian Ridge. Deep Sea Res. I 122, 41–47 (2017).Article 
    CAS 

    Google Scholar  More

  • in

    Large sinuous rivers are slowing down in a warming Arctic

    Gillet, N. et al. Canada’s Changing Climate Report (Government of Canada, 2019).Bintanja, R. The impact of Arctic warming on increased rainfall. Sci. Rep. 8, 6–11 (2018).Article 

    Google Scholar 
    Camill, P. Permafrost thaw accelerates in boreal peatlands during late-20th century climate warming. Clim. Change 68, 135–152 (2005).Article 
    CAS 

    Google Scholar 
    Hollesen, J., Matthiesen, H., Møller, A. B. & Elberling, B. Permafrost thawing in organic Arctic soils accelerated by ground heat production. Nat. Clim. Change 5, 574–578 (2015).Article 

    Google Scholar 
    Walvoord, M. A. & Striegl, R. G. Increased groundwater to stream discharge from permafrost thawing in the Yukon River basin: potential impacts on lateral export of carbon and nitrogen. Geophys. Res. Lett. 34, L12402 (2007).Pearson, R. G. et al. Shifts in Arctic vegetation and associated feedbacks under climate change. Nat. Clim. Change 3, 673–677 (2013).Article 

    Google Scholar 
    Heijmans, M. M. P. D. et al. Tundra vegetation change and impacts on permafrost. Nat. Rev. Earth Environ. 3, 68–84 (2022).Article 

    Google Scholar 
    Tape, K., Sturm, M. & Racine, C. The evidence for shrub expansion in Northern Alaska and the Pan-Arctic. Glob. Change Biol. 12, 686–702 (2006).Article 

    Google Scholar 
    Mekonnen, Z. A. et al. Arctic tundra shrubification: a review of mechanisms and impacts on ecosystem carbon balance. Environ. Res. Lett. 16, 053001 (2021).Article 
    CAS 

    Google Scholar 
    Shevtsova, I. et al. Strong shrub expansion in tundra-taiga, tree infilling in taiga and stable tundra in central Chukotka (north-eastern Siberia) between 2000 and 2017. Environ. Res. Lett. 15, 085006 (2020).Article 

    Google Scholar 
    Wild, B. et al. Rivers across the Siberian Arctic unearth the patterns of carbon release from thawing permafrost. Proc. Natl Acad. Sci. USA 116, 10280–10285 (2019).Article 
    CAS 

    Google Scholar 
    Rowland, J. C. et al. Arctic landscapes in transition: responses to thawing permafrost. Eos 91, 229–230 (2010).Article 

    Google Scholar 
    Walcker, R., Corenblit, D., Julien, F., Martinez, J. M. & Steiger, J. Contribution of meandering rivers to natural carbon fluxes: evidence from the Ucayali River, Peruvian Amazonia. Sci. Total Environ. 776, 146056 (2021).Article 
    CAS 

    Google Scholar 
    Torres, M. A. et al. Model predictions of long-lived storage of organic carbon in river deposits. Earth Surf. Dyn. 5, 711–730 (2017).Article 

    Google Scholar 
    Allen, J. R. Sedimentary structures: their character and physical basis. Dev. Sedimentol. 30B, 1–593 (1982).
    Google Scholar 
    Howard, A. D. & Knutson, T. R. Sufficient conditions for river meandering: a simulation approach. Water Resour. Res. 20, 1659–1667 (1984).Article 

    Google Scholar 
    Chassiot, L., Lajeunesse, P. & Bernier, J. F. Riverbank erosion in cold environments: review and outlook. Earth-Sci. Rev. 207, 103231 (2020).Article 

    Google Scholar 
    Constantine, J. A., Dunne, T., Ahmed, J., Legleiter, C. & Lazarus, E. D. Sediment supply as a driver of river meandering and floodplain evolution in the Amazon Basin. Nat. Geosci. 7, 899–903 (2014).Article 
    CAS 

    Google Scholar 
    Horton, A. J. et al. Modification of river meandering by tropical deforestation. Geology 45, 511–514 (2017).Article 

    Google Scholar 
    Ielpi, A. & Lapôtre, M. G. A. A tenfold slowdown in river meander migration driven by plant life. Nat. Geosci. 13, 82–86 (2020).Article 
    CAS 

    Google Scholar 
    Kokelj, S. V., Lantz, T. C., Tunnicliffe, J., Segal, R. & Lacelle, D. Climate-driven thaw of permafrost preserved glacial landscapes, northwestern Canada. Geology 45, 371–374 (2017).Article 

    Google Scholar 
    Zhang, T. et al. Warming-driven erosion and sediment transport in cold regions. Nat. Rev. Earth Environ. 3, 832–851(2022).Brown, D. R. N. et al. Implications of climate variability and changing seasonal hydrology for subarctic riverbank erosion. Clim. Change 162, 385–404 (2020).Article 

    Google Scholar 
    Gautier, E. et al. Fifty-year dynamics of the Lena River islands (Russia): spatio-temporal pattern of large periglacial anabranching river and influence of climate change. Sci. Total Environ. 783, 147020 (2021).Article 
    CAS 

    Google Scholar 
    Piliouras, A., Lauzon, R. & Rowland, J. C. Unraveling the combined effects of ice and permafrost on Arctic delta morphodynamics. J. Geophys. Res. Earth Surf. 126, e2020JF005706 (2021).Matsubara, Y. et al. Geomorphology river meandering on Earth and Mars: a comparative study of Aeolis Dorsa meanders, Mars and possible terrestrial analogs of the Usuktuk River, AK, and the Quinn River, NV. Geomorphology 240, 102–120 (2015).Article 

    Google Scholar 
    Lininger, K. B. & Wohl, E. Floodplain dynamics in North American permafrost regions under a warming climate and implications for organic carbon stocks: a review and synthesis. Earth-Sci. Rev. 193, 24–44 (2019).Article 
    CAS 

    Google Scholar 
    Treat, C. C. & Jones, M. C. Near-surface permafrost aggradation in Northern Hemisphere peatlands shows regional and global trends during the past 6000 years. Holocene 28, 998–1010 (2018).Article 

    Google Scholar 
    Lapôtre, M. G. A., Ielpi, A., Lamb, M. P., Williams, R. M. E. & Knoll, A. H. Model for the formation of single-thread rivers in barren landscapes and implications for pre-Silurian and martian fluvial deposits. J. Geophys. Res. Earth Surf. 124, 2757–2777 (2019).Article 

    Google Scholar 
    Wang, G., Hu, H. & Li, T. The influence of freeze-thaw cycles of active soil layer on surface runoff in a permafrost watershed. J. Hydrol. 375, 438–449 (2009).Article 

    Google Scholar 
    Tananaev, N. & Lotsari, E. Defrosting northern catchments: fluvial effects of permafrost degradation. Earth-Sci. Rev. 228, 103996 (2022).Article 

    Google Scholar 
    Tarnocai, C., Nixon, M. F. & Kutny, L. Circumpolar-active-layer-monitoring (CALM) sites in the Mackenzie Valley, northwestern Canada. Permafr. Periglac. Process. 15, 141–153 (2004).Article 

    Google Scholar 
    Nguyen, T.-N., Burn, C. R., King, D. J. & Smith, S. L. Estimating the extent of near-surface permafrost using remote sensing, Mackenzie Delta, Northwest Territories. Permafr. Periglac. Process. 20, 141–153 (2009).Article 

    Google Scholar 
    Stephani, E., Drage, J., Miller, D., Jones, B. M. & Kanevskiy, M. Taliks, cryopegs, and permafrost dynamics related to channel migration, Colville River Delta, Alaska. Permafr. Periglac. Process. 31, 239–254 (2020).Article 

    Google Scholar 
    Walvoord, M. A. & Kurylyk, B. L. Hydrologic impacts of thawing permafrost—a review. Vadose Zo. J. 15, vzj2016.01.0010 (2016).Article 

    Google Scholar 
    Leopold, L. B., Wolman, M. G. & Miller, J. P. Fluvial Processes in Geomorphology (Dover, 1964).Sylvester, Z., Durkin, P. & Covault, J. A. High curvatures drive river meandering. Geology 47, 263–266 (2019).Article 

    Google Scholar 
    Lageweg, W. I. van de et al. Bank pull or bar push: what drives scroll-bar formation in meandering rivers? Geology 42, 319–322 (2014).Liljedahl, A. K., Timling, I., Frost, G. V. & Daanen, R. P. Arctic riparian shrub expansion indicates a shift from streams gaining water to those that lose flow. Commun. Earth Environ. 1, 50 (2020).Article 

    Google Scholar 
    Parker, G. et al. A new framework for modeling the migration of meandering rivers. Earth Surf. Process. Landf. 36, 70–86 (2011).Article 

    Google Scholar 
    Blanckaert, K. Topographic steering, flow recirculation, velocity redistribution, and bed topography in sharp meander bends. Water Resour. Res. 46, W09506 (2010).
    Google Scholar 
    Ielpi, A. & Lapôtre, M. G. A. Biotic forcing militates against river meandering in the modern Bonneville Basin of Utah. Sedimentology 66, 1896–1929 (2019).Article 

    Google Scholar 
    Fox, G. A. et al. Measuring streambank erosion due to ground water seepage: correlation to bank pore water pressure, precipitation and stream stage. Earth Surf. Process. Landf. 1573, 1558–1573 (2007).Article 

    Google Scholar 
    O’Neill, H. B., Smith, S. L. & Duchesne, C. Long-term permafrost degradation and thermokarst subsidence in the Mackenzie Delta Area indicated by thaw tube measurements. In 18th International Conference on Cold Regions Engineering and 8th Canadian Permafrost Conference (eds Bilodeau, J.-P. et al.) 643–651 (ASCE, 2019).Qiu, J. Thawing permafrost reduces river runoff. Nature https://doi.org/10.1038/nature.2012.9749 (2012).Zheng, L., Overeem, I., Wang, K. & Clow, G. D. Changing Arctic river dynamics cause localized permafrost thaw. J. Geophys. Res. Earth Surf. 124, 2324–2344 (2019).Article 

    Google Scholar 
    Jorgenson, M. T. et al. An Ecological Land Survey for the Colville River Delta, Alaska, 1996 (ABR, Inc., 1997).Park, H., Yoshikawa, Y., Yang, D. & Oshima, K. Warming water in arctic terrestrial rivers under climate change. J. Hydrometeorol. 18, 1983–1995 (2017).Article 

    Google Scholar 
    Roy-Leveillee, P. & Burn, C. R. Near-shore talik development beneath shallow water in expanding thermokarst lakes, Old Crow Flats, Yukon. J. Geophys. Res. Earth Surf. 122, 1070–1089 (2017).Article 

    Google Scholar 
    Langer, M. et al. Rapid degradation of permafrost underneath waterbodies in tundra landscapes—toward a representation of thermokarst in land surface models. J. Geophys. Res. Earth Surf. 121, 2446–2470 (2016).Article 

    Google Scholar 
    O’Neill, H. B., Roy-Leveillee, P., Lebedeva, L. & Ling, F. Recent advances (2010–2019) in the study of taliks. Permafr. Periglac. Process. 31, 346–357 (2020).Article 

    Google Scholar 
    French, H. The Periglacial Environment (Wiley, 2017).Prowse, T. D. River-ice ecology. I: Hydrologic, geomorphic, and water-quality aspects. J. Cold Reg. Eng. 15, 1–16 (2001).Article 
    CAS 

    Google Scholar 
    Yang, X., Pavelsky, T. M. & Allen, G. H. The past and future of global river ice. Nature 577, 69–73 (2020).Article 
    CAS 

    Google Scholar 
    Brown, J., Ferrians, O. J. Jr, Heginbottom, J. A. & Melkinov, E. S. Circum-Arctic Map of Permafrost and Ground-Ice Conditions (USGS, 1997); https://pubs.usgs.gov/cp/45/report.pdfIelpi, A., Lapotre, M. G. A., Finotello, A. & Roy-Léveillée, P. Large sinuous rivers are slowing down in a warming Arctic. Zenodo https://doi.org/10.5281/zenodo.7556050 (2023).Leopold, L. B. & Maddock, T. J. The Hydraulic Geometry of Stream Channels and Some Physiographic Implications (USGS, 1953).Giorgino, T. Computing and visualizing dynamic time warping alignments in R: the dtw package. J. Stat. Softw. 31, 1–24 (2009).Article 

    Google Scholar 
    Donovan, M., Belmont, P. & Sylvester, Z. Evaluating the relationship between meander-bend curvature, sediment supply, and migration rates. J. Geophys. Res. Earth Surf. 126, e2020JF006058 (2021).Article 

    Google Scholar 
    Sylvester, Z., Durkin, P. R., Hubbard, S. M. & Mohrig, D. Autogenic translation and counter point bar deposition in meandering rivers. GSA Bull. 133, 2439–2456 (2021).Titov, M. Code for dynamic time warping analysis. GitHub http://mlt.github.io/QGIS-Processing-tools/tags/dtw.html (2015).Finotello, A., D’Alpaos, A., Lazarus, E. D. & Lanzoni, S. High curvatures drive river meandering: COMMENT. Geology 47, e485 (2019).Finotello, A. et al. American Geophysical Union, Fall Meeting Abstracts (AGU, 2020).Congedo, L. Semi-automatic classification plugin: a Python tool for the download and processing of remote sensing images in QGIS. J. Open Source Softw. 6, 3172 (2021).Article 

    Google Scholar  More

  • in

    The extent of windfarm infrastructures on recognised European blanket bogs

    When studying windfarm developments at the European region scale, the high densities of windfarm developments on blanket bog in Galicia and Greater Manchester (north England) are influenced by the total extent of the recognised blanket bog which is lower in Spain (31.2 km2 total extent) and in Greater Manchester (40.8 km2 total extent) in comparison to other regions (Fig. 1), although no relationship between the total extent of recognised blanket bog and the windfarm developments (wind turbines, tracks and total affected area) was found. Although the rest of the European regions across Spain showed lower densities of windfarm infrastructures (Fig. 2), the total extent of recognised blanket bogs across those regions was under 1 km2 (Fig. 1) meaning that the majority of recognised Spanish blanket bogs could be under threat due to their small size and the potential impact of windfarm infrastructures, if installed. In addition to this, previously unrecognised Spanish blanket bogs that have now been reported17 that could also be under pressure as the lack of formal recognition and protection leaves this habitat exposed to a range of anthropogenic activities, including windfarm developments. In fact, some examples of blanket bogs with extensive damage have been identified and reported in Galicia25, and more recently in Cantabrian blanket bogs17.Spanish unmapped areas of blanket bog at the edge-of-range of this habitat in the south of Europe are, therefore, particularly at risk from windfarm developments, and may disappear before their extent and importance can be defined40. Currently, new renewable energy regulations have been developed as a result of the climate emergency, and several windfarm developments have been proposed in ecologically sensitive areas, where blanket bogs have been reported (e.g. Sierra del Escudo, Spain) increasing the pressure on this habitat. Spanish blanket bogs also have specific characteristics, such as their small size as a consequence of the topographical limitations (e.g. slope) for their development26, meaning that they usually only cover the hill summits, where wind energy potential is at its greatest. Since blanket bogs are small and the windfarm development may cover all of the hill summit for their installation, many blanket bogs will be irrevocably damaged40.Most of the Galician blanket bogs were protected in 1999, under the Natura 2000 network and were declared as Special Area of Conservation (SAC) in 2014. However, between 1999 and 2012, Galician blanket bogs underwent severe and significant alterations in the peatland surface as a consequence of the large number of windfarm developments41 that were established during the period (Table A—Supplementary information), even when the site was incorporated into the Natura 2000 network (Table B—Supplementary information). Despite available scientific evidence that showed the potential environmental risks for these vulnerable ecosystems, windfarms were installed in what this work found to be the most extensive windfarm infrastructures across recognised European blanket bogs (Fig. 2).The incomplete current understanding of the extent of Spanish blanket bogs highlights the need to improve the completeness and representativeness of their current records across the Spanish Atlantic biogeographical region to include, within Natura 2000, a sufficient cover of their occupied area, in proportion to the representation of this natural habitat type in the Member state, for which it could therefore be concluded that the network is complete. Due to the increasing evidence highlighting how important the transitional areas are within the blanket bog complex42, other peatland types and wet heaths should be also considered when recognising and protecting blanket bogs. Mapping unrecorded blanket bogs must be a priority to fully understand the geographical and climatic range of this habitat, and obligatory protection under the Habitats Directive (92/43/EEC) is key to protecting the southern edge-of-range of this habitat.In addition to the lack of protection and updated inventories, the priority status included in the Habitats Directive, key to promoting their protection and restoration, is only for active blanket bogs, excluding other degraded blanket bogs with the potential to be active (carbon sinks), if they are restored. An approach similar to that of Scotland, where degraded blanket bogs are included33,39, could promote blanket bog restoration across Europe and improve the protection of this natural carbon storage.Many countries have also misinterpreted the active status of the blanket bog meaning that it is difficult to define whether the recognised blanket bog habitat is classed as a priority or not. Some countries, such as the Republic of Ireland, have classified as 7130 only active blanket bogs36, meaning that degraded blanket bogs lack appropriate classification and incorrectly applying the Habitat Directive designation as not all blanket bogs are included. The priority status is given when the habitat is particularly vulnerable or unique to the EU and necessitates additional measures for their protection and surveillance; however, whilst some blanket bogs may not act currently as carbon sinks, they still contain large amounts of carbon, and when restored they can recover their carbon sink function1, and then act to mitigate climate change.The issue of windfarm developments across the Republic of Ireland has been previously reported using a peat map43. However, despite researchers highlighting the importance of excluding vulnerable peatland ecosystems in future developments44, new areas of windfarms have been built affecting further recognised blanket bogs. At least 79 wind turbines have been installed in the Republic of Ireland since 2008 on recognised blanket bogs (Table A—Supplementary information) representing the 9.8% of the total onshore turbines installed in the country (Table 3), highlighting the importance of this conflict. The contribution of wind energy production to electricity supply was predicted to be up to 30% by 202044. In 2020, wind energy consumed in the Republic of Ireland represented 36%45. This represented an average annual increase of wind energy consumption of 16.9%45 between 2005 and 2020, which may explain part of the increase of 42% in wind turbines since 2008 (Table A—Supplementary information).Table 3 Total % of turbines on blanket bog (recognised/national inventories) in relation with the total turbines installed by country.Full size tableAcross Europe, several governments have developed climate action plans that over the next decade promote renewable energies to reduce carbon emissions. The government of the Republic of Ireland is aiming to generate up to 80% of electricity from renewable energy by 2030, providing support for onshore windfarm developments with an increase of up to 32% of the renewable energy production by 2030, but with a favourable preference for offshore wind energy production (up to 52% of the renewable energy production)46. This may help to reduce the conflict between blanket bogs and windfarm developments. Currently, windfarm annual energy production on blanket bogs accounts for 263.4 MW, 6.1% of the total production of wind energy in the Republic of Ireland47.The promotion of onshore wind energy production46 and the lack of protection of the full extent of blanket bogs are also threats that need to be considered in the Republic of Ireland. In 2008, a peat map was published showing the distribution of blanket bogs and raised bogs across the Republic of Ireland43. However, the inventory of current recognised blanket bogs under the Habitats Directive does not cover the full extent reported in this research43. While the total extent of recognised blanket bogs under the Habitats Directive 92/43/ECC reported a total of 3621 km2 of blanket bogs36, the real extent of blanket bogs across the country could be up to 2.5 times more (9202 km2)43, highlighting the lack of protection and the potential further increase of the windfarms and peatlands conflict in the Republic of Ireland as it happens in Spain and Scotland.The lack of recognition of blanket bog habitat in combination with the promotion of wind energy production across the island of Ireland could affect further areas of blanket bog, increasing the degradation of blanket bogs. An urgent review of inventories needs to be promoted in both countries, the Republic of Ireland and Northern Ireland, to fully assess the impact of the extensive areas of windfarms across the whole island.In Scotland, the pressure of windfarm developments on blanket bogs is also evident, where the Scottish Planning Policy considers classes 1 and 2 as areas of significant protection; although, windfarm developments may be possible under some circumstances48 as is permitted under the Habitats Directive across the EU29. However, to assess the impacts of windfarms on peatlands in a consistent way and evaluate the environmental impact of potential new developments on carbon-rich soils, a carbon calculator has been developed by the Scottish Government49. The carbon calculator allows users to estimate the carbon savings of windfarms installed on peatlands, although they highlight the importance of long-term management in relation to the final net carbon calculation49. Nonetheless, installing windfarms on non-degraded peatlands has been reported as unlikely to reduce carbon emissions even when the management has been considered carefully and it should be avoided 30. Therefore, peatlands under classes 1 and 2 considered by the Scottish government as a priority should be excluded from any windfarm developments (currently representing over 16% of onshore turbines, Table 3); especially considering the current policy of increasing onshore windfarms in Scotland50. Long-term research is needed to fully assess the impacts before new windfarm developments are installed.The difference between the recognised blanket bogs included in the EU Habitats Directive and the Scottish national inventory highlights the importance of updating and defining the complete extent of blanket bogs to facilitate their protection and restoration.In this novel research, the extent of windfarm developments across all recognised European blanket bogs under the Habitats Directive have been assessed. Large extents of blanket bogs have already been damaged, concentrated in the edge-of-range of this habitat and directly affecting hundreds of hectares of blanket bog across the rest of Europe. The full potential long-term damage to the habitat functionality is still unclear, but scientific evidence supports the negative impacts of windfarm developments on this critical habitat. European blanket bogs need further scientific evidence to demonstrate the real benefit of incentivising the reduction of carbon emissions by installing onshore windfarm infrastructures on peatlands which are causing the degradation of the most important long-term natural carbon sink and storage ecosystems. A strategic restoration plan and appropriate relevant legislation would be beneficial to promote the safeguarding of blanket bogs in the UK after Brexit. An urgent revision and compliance of the legislation regarding the protection of blanket bogs needs to be implemented, especially under the current trend of promotion and increasing legislation on renewable energy to reduce carbon emissions. An improvement of the national inventories across the EU and UK protected area networks is critical to implement the recognition, protection, and restoration of this habitat, in order to guarantee its favourable conservation status and its function as a long-term carbon sink to mitigate climate change. More

  • in

    Competition’s role

    Decline in organism size is seen as a major biological response to climate change, and can be particularly pronounced in aquatic ectotherms such as fish, with subsequent implications for fishery yield and food security. However, as well as being modulated by climate factors, the fish population size structure can also be impacted by biotic (competition, predation) and other human factors (harvesting). For migrating species such as salmon, while smaller size may represent reduced size at maturity, it may also indicate faster maturation. More

  • in

    Future riverine impact

    Shuang Gao from Bjerkens Center for Climate Research in Norway, and colleagues from Germany and the United States explored future changes in marine primary production and carbon uptake under climate scenarios using the Norwegian Earth-system model, with four river transport configurations incorporating established future economic development and nutrient-use efficiency pathways. The researchers find that riverine nutrient inputs lessen nutrient limitation under warmer conditions. In the future, the effect of increased riverine carbon may be larger than the effect of nutrient inputs on the projections of ocean carbon uptake. In the historical period, increased nutrient inputs are considered the most prominent driver of carbon uptake. The results of this study are subject to model limitations, and high-resolution models should be used to assess the future impact. More

  • in

    Simultaneous sulfate and nitrate reduction in coastal sediments

    Boudreau BP, Huettel M, Forster S, Jahnke RA, McLachlan A, Middelburg JJ, et al. Permeable marine sediments: Overturning an old paradigm. Eos, Trans Am Geophys Union. 2001;82:133–6.Article 

    Google Scholar 
    Cook PL, Wenzhöfer F, Rysgaard S, Galaktionov OS, Meysman FJ, Eyre BD, et al. Quantification of denitrification in permeable sediments: Insights from a two‐dimensional simulation analysis and experimental data. Limnol Oceanogr Methods. 2006;4:294–307.Article 
    CAS 

    Google Scholar 
    Evrard V, Glud RN, Cook PL. The kinetics of denitrification in permeable sediments. Biogeochemistry. 2013;113:563–72.Article 

    Google Scholar 
    Huettel M, Berg P, Kostka JE. Benthic exchange and biogeochemical cycling in permeable sediments. Ann Rev Marine Sci. 2014;6:23–51.Article 

    Google Scholar 
    Rao AMF, McCarthy MJ, Gardner WS, Jahnke RA. Respiration and denitrification in permeable continental shelf deposits on the South Atlantic Bight: Rates of carbon and nitrogen cycling from sediment column experiments. Continental Shelf Res. 2007;27:1801–19.Article 

    Google Scholar 
    Billerbeck M, Werner U, Polerecky L, Walpersdorf E, de Beer D, Huettel M Surficial and deep pore water circulation governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Marine Ecol Progr Series. 2006;326:61–76.Jansen S, Walpersdorf E, Werner U, Billerbeck M, Böttcher ME, de Beer D. Functioning of intertidal flats inferred from temporal and spatial dynamics of O2, H2S and pH in their surface sediment. Ocean Dyn. 2009;59:317–32.Article 

    Google Scholar 
    de Beer D, Wenzhöfer F, Ferdelman TG, Boehme SE, Huettel M, van Beusekom JEE, et al. Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Rømø Basin, Wadden Sea. Limnol Oceanogr. 2005;50:113–27.Article 

    Google Scholar 
    Gao H, Matyka M, Liu B, Khalili A, Kostka JE, Collins G, et al. Intensive and extensive nitrogen loss from intertidal permeable sediments of the Wadden Sea. Limnol Oceanogr. 2012;57:185–98.Article 
    CAS 

    Google Scholar 
    Gao H, Schreiber F, Collins G, Jensen MM, Kostka JE, Lavik G, et al. Aerobic denitrification in permeable Wadden Sea sediments. ISME J. 2009;4:417.Article 
    PubMed 

    Google Scholar 
    Elliott AH, Brooks NH. Transfer of nonsorbing solutes to a streambed with bed forms: Theory. Water Resour Res. 1997;33:123–36.Article 
    CAS 

    Google Scholar 
    Precht E, Huettel M. Advective pore‐water exchange driven by surface gravity waves and its ecological implications. Limnol Oceanogr. 2003;48:1674–84.Article 

    Google Scholar 
    Ahmerkamp S, Marchant HK, Peng C, Probandt D, Littmann S, Kuypers MM, et al. The effect of sediment grain properties and porewater flow on microbial abundance and respiration in permeable sediments. Sci Rep. 2020;10:1–12.Article 

    Google Scholar 
    Ahmerkamp S, Winter C, Krämer K, Beer DD, Janssen F, Friedrich J, et al. Regulation of benthic oxygen fluxes in permeable sediments of the coastal ocean. Limnol Oceanogr. 2017;62:1935–54.Article 
    CAS 

    Google Scholar 
    Cardenas MB, Wilson JL Dunes, turbulent eddies, and interfacial exchange with permeable sediments. Water Resour Res. 2007;43:W08412.Santos IR, Eyre BD, Huettel M. The driving forces of porewater and groundwater flow in permeable coastal sediments: a review. Estuarine, Coastal Shelf Sci. 2012;98:1–15.Article 

    Google Scholar 
    Probandt D, Eickhorst T, Ellrott A, Amann R, Knittel K. Microbial life on a sand grain: from bulk sediment to single grains. ISME J. 2018;12:623–33.Article 
    PubMed 

    Google Scholar 
    Marchant HK, Ahmerkamp S, Lavik G, Tegetmeyer HE, Graf J, Klatt JM, et al. Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously. ISME J. 2017;11:1799.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marchant HK, Holtappels M, Lavik G, Ahmerkamp S, Winter C, Kuypers MMM. Coupled nitrification–denitrification leads to extensive N loss in subtidal permeable sediments. Limnol Oceanogr. 2016;61:1033–48.Article 

    Google Scholar 
    Marchant HK, Tegetmeyer HE, Ahmerkamp S, Holtappels M, Lavik G, Graf J, et al. Metabolic specialization of denitrifiers in permeable sediments controls N2O emissions. Environ Microbiol. 2018;20:4486–502.Article 
    CAS 
    PubMed 

    Google Scholar 
    Laverman AM, Pallud C, Abell J, Van, Cappellen P. Comparative survey of potential nitrate and sulfate reduction rates in aquatic sediments. Geochimica et Cosmochimica Acta. 2012;77:474–88.Article 
    CAS 

    Google Scholar 
    Fenchel T, Jørgensen B. Detritus food chains of aquatic ecosystems: the role of bacteria. Adv Microb Ecol. 1977;1:1–58.Article 
    CAS 

    Google Scholar 
    Canfield DE, Kristensen E, Thamdrup B Aquatic Geomicrobiology: Elsevier Science; 2005.Froelich PN, Klinkhammer G, Bender ML, Luedtke N, Heath GR, Cullen D, et al. Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis. Geochimica et cosmochimica Acta. 1979;43:1075–90.Article 
    CAS 

    Google Scholar 
    Eckford RE, Fedorak PM. Chemical and microbiological changes in laboratory incubations of nitrate amendment “sour” produced waters from three western Canadian oil fields. J Ind Microbiol Biotechnol. 2002;29:243–54.Article 
    CAS 
    PubMed 

    Google Scholar 
    Grigoryan AA, Cornish SL, Buziak B, Lin S, Cavallaro A, Arensdorf JJ, et al. Competitive oxidation of volatile fatty acids by sulfate- and nitrate-reducing bacteria from an oil field in Argentina. Appl Environ Microbiol. 2008;74:4324.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hubert C, Nemati M, Jenneman G, Voordouw G. Containment of biogenic sulfide production in continuous up-flow packed-bed bioreactors with nitrate or nitrite. Biotechnol Progr. 2003;19:338–45.Article 
    CAS 

    Google Scholar 
    Greene EA, Hubert C, Nemati M, Jenneman GE, Voordouw G. Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria. Environ Microbiol. 2003;5:607–17.Article 
    CAS 
    PubMed 

    Google Scholar 
    Wolfe BM, Lui SM, Cowan JA. Desulfoviridin, a multimeric-dissimilatory sulfite reductase from Desulfovibrio vulgaris (Hildenborough) Purification, characterization, kinetics and EPR studies. Eur J Biochem. 1994;223:79–89.Article 
    CAS 
    PubMed 

    Google Scholar 
    Fossing H, Gallardo VA, Jørgensen BB, Hüttel M, Nielsen LP, Schulz H, et al. Concentration and transport of nitrate by the mat-forming sulphur bacterium Thioploca. Nature. 1995;374:713–15.Article 
    CAS 

    Google Scholar 
    Jørgensen BB. Big sulfur bacteria. ISME J. 2010;4:1083.Article 
    PubMed 

    Google Scholar 
    Marzocchi U, Trojan D, Larsen S, Louise Meyer R, Peter Revsbech N, Schramm A, et al. Electric coupling between distant nitrate reduction and sulfide oxidation in marine sediment. ISME J. 2014;8:1682.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Londry KL, Suflita JM. Use of nitrate to control sulfide generation by sulfate-reducing bacteria associated with oily waste. J Ind Microbiol Biotechnol. 1999;22:582–9.Article 
    CAS 
    PubMed 

    Google Scholar 
    McInerney MJ, Bhupathiraju VK, Sublette KL. Evaluation of a microbial method to reduce hydrogen sulfide levels in a porous rock biofilm. J Ind Microbiol. 1992;11:53–8.Article 
    CAS 

    Google Scholar 
    Schwermer CU, Ferdelman TG, Stief P, Gieseke A, Rezakhani N, Van Rijn J, et al. Effect of nitrate on sulfur transformations in sulfidogenic sludge of a marine aquaculture biofilter. FEMS Microbiol Ecol. 2010;72:476–84.Article 
    CAS 
    PubMed 

    Google Scholar 
    Thamdrup B, Fossing H, Jørgensen BB. Manganese, iron and sulfur cycling in a coastal marine sediment, Aarhus Bay, Denmark. Geochimica et Cosmochimica Acta. 1994;58:5115–29.Article 
    CAS 

    Google Scholar 
    Al-Raei AM, Bosselmann K, Böttcher ME, Hespenheide B, Tauber F. Seasonal dynamics of microbial sulfate reduction in temperate intertidal surface sediments: controls by temperature and organic matter. Ocean Dyn. 2009;59:351–70.Article 

    Google Scholar 
    Dyksma S, Pjevac P, Ovanesov K, Mussmann M. Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments. Environ Microbiol. 2018;20:450–61.Article 
    CAS 
    PubMed 

    Google Scholar 
    Musat N, Werner U, Knittel K, Kolb S, Dodenhof T, van Beusekom JEE, et al. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst Appl Microbiol. 2006;29:333–48.Article 
    PubMed 

    Google Scholar 
    Mußmann M, Ishii K, Rabus R, Amann R. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ Microbiol. 2005;7:405–18.Article 
    PubMed 

    Google Scholar 
    Dyksma S, Lenk S, Sawicka JE, Mußmann M. Uncultured gammaproteobacteria and desulfobacteraceae account for major acetate assimilation in a coastal marine sediment. Front Microbiol. 2018;9:3124Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chen J, Hanke A, Tegetmeyer HE, Kattelmann I, Sharma R, Hamann E, et al. Impacts of chemical gradients on microbial community structure. ISME J. 2017;11:920.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Saad S, Bhatnagar S, Tegetmeyer HE, Geelhoed JS, Strous M, Ruff SE. Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations. Environ Microbiol. 2017;19:4866–81.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brunet RC, Garcia-Gil LJ. Sulfide-induced dissimilatory nitrate reduction to ammonia in anaerobic freshwater sediments. FEMS Microbiol Ecol. 1996;21:131–8.Article 
    CAS 

    Google Scholar 
    Murphy AE, Bulseco AN, Ackerman R, Vineis JH, Bowen JL. Sulphide addition favours respiratory ammonification (DNRA) over complete denitrification and alters the active microbial community in salt marsh sediments. Environ Microbiol. 2020;22:2124–39.Article 
    CAS 
    PubMed 

    Google Scholar 
    Krekeler D, Cypionka H. The preferred electron acceptor of Desulfovibrio desulfuricans CSN. FEMS Microbiol Ecol. 1995;17:271–7.Article 
    CAS 

    Google Scholar 
    Seitz H-J, Cypionka H. Chemolithotrophic growth of Desulfovibrio desulfuricans with hydrogen coupled to ammonification of nitrate or nitrite. Arch Microbiol. 1986;146:63–7.Article 
    CAS 

    Google Scholar 
    Dalsgaard T, Bak F. Nitrate reduction in a sulfate-reducing bacterium, Desulfovibrio desulfuricans, isolated from rice paddy soil: sulfide inhibition, kinetics, and regulation. Appl Environ Microbiol. 1994;60:291–7.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marietou A. Nitrate reduction in sulfate-reducing bacteria. FEMS Microbiol Lett. 2016;363:fnw155.Article 
    PubMed 

    Google Scholar 
    Marietou A, Griffiths L, Cole J. Preferential reduction of the thermodynamically less favorable electron acceptor, sulfate, by a nitrate-reducing strain of the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774. J Bacteriol. 2009;191:882–889.Article 
    CAS 
    PubMed 

    Google Scholar 
    Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Environ Sci Technol. 2015;49:924–931.Article 
    CAS 
    PubMed 

    Google Scholar 
    Pereira IA, LeGall J, Xavier AV, Teixeira M. Characterization of a heme c nitrite reductase from a non-ammonifying microorganism, Desulfovibrio vulgaris Hildenborough. Biochimica et Biophysica Acta (BBA)-Protein Struct Mol Enzymol. 2000;1481:119–130.Article 
    CAS 

    Google Scholar 
    Werner U, Billerbeck M, Polerecky L, Franke U, Huettel M, van Beusekom JEE, et al. Spatial and temporal patterns of mineralization rates and oxygen distribution in a permeable intertidal sand flat (Sylt, Germany). Limnol Oceanogr. 2006;51:2549–63.Article 
    CAS 

    Google Scholar 
    Marchant HK, Lavik G, Holtappels M, Kuypers MMM. The fate of nitrate in intertidal permeable sediments. PLOS ONE. 2014;9:e104517.Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Canfield DE. Reactive iron in marine sediments. Geochimica et cosmochimica acta. 1989;53:619–632.Article 
    CAS 
    PubMed 

    Google Scholar 
    Billerbeck M, Werner U, Bosselmann K, Walpersdorf E, Huettel M. Nutrient release from an exposed intertidal sand flat. Marine Ecol Progr Series. 2006;316:35–51.Article 
    CAS 

    Google Scholar 
    Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF, et al. A cryptic sulfur cycle in oxygen-minimum–zone waters off the Chilean Coast. Science. 2010;330:1375.Article 
    CAS 
    PubMed 

    Google Scholar 
    Jørgensen BB, Findlay AJ, Pellerin A. The biogeochemical sulfur cycle of marine sediments. Front Microbiol. 2019;10:849.Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Nemati M, Mazutinec TJ, Jenneman GE, Voordouw G. Control of biogenic H2S production with nitrite and molybdate. J Ind Microbiol Biotechnol. 2001;26:350–355.Article 
    CAS 
    PubMed 

    Google Scholar 
    Haveman SA, Greene EA, Stilwell CP, Voordouw JK, Voordouw G. Physiological and Gene Expression Analysis of Inhibition of Desulfovibrio vulgaris Hildenborough by Nitrite. J Bacteriol. 2004;186:7944–7950.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Behrendt A, de Beer D, Stief P. Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments. Biogeosciences. 2013;10:7509–23.Article 

    Google Scholar 
    Findlay AJ, Pellerin A, Laufer K, Jørgensen BB. Quantification of sulphide oxidation rates in marine sediment. Geochimica et Cosmochimica Acta. 2020;280:441–52.Article 
    CAS 

    Google Scholar 
    Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evolut Microbiol. 2020;70:5972–6016.Article 
    CAS 

    Google Scholar 
    Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, et al. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J. 2016;10:1939–1953.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lenk S, Arnds J, Zerjatke K, Musat N, Amann R, Mußmann M. Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment. Environ Microbiol. 2011;13:758–774.Article 
    CAS 
    PubMed 

    Google Scholar 
    An S, Gardner W S. Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas). Marine Ecol Progr Series. 2002;237:41–50.Article 
    CAS 

    Google Scholar 
    Wankel SD, Ziebis W, Buchwald C, Charoenpong C, de Beer D, Dentinger J, et al. Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments. Nat Commun. 2017;8:15595.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Moura I, Bursakov S, Costa C, Moura JJ. Nitrate and nitrite utilization in sulfate-reducing bacteria. Anaerobe. 1997;3:279–290.Article 
    CAS 
    PubMed 

    Google Scholar 
    Song G, Liu S, Zhang J, Zhu Z, Zhang G, Marchant HK, et al. Response of benthic nitrogen cycling to estuarine hypoxia. Limnol Oceanogr. 2021;66:652–66.Article 
    CAS 

    Google Scholar 
    Tiedje JM, Sexstone AJ, Myrold DD, Robinson JA. Denitrification: ecological niches, competition and survival. Antonie van Leeuwenhoek. 1983;48:569–583.Article 

    Google Scholar 
    Strohm TO, Griffin B, Zumft WG, Schink B. Growth yields in bacterial denitrification and nitrate ammonification. Appl Environ Microbiol. 2007;73:1420–1424.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rütting T, Boeckx P, Müller C, Klemedtsson L. Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle. Biogeosciences. 2011;8:1779–91.Article 

    Google Scholar 
    Røy H, Lee JS, Jansen S, de Beer D. Tide-driven deep pore-water flow in intertidal sand flats. Limnol Oceanogr. 2008;53:1521–30.Article 

    Google Scholar 
    Cline JD. Spectrophotometric determination of hydrogen sulfide in natural waters 1. Limnol Oceanogr. 1969;14:454–458.Article 
    CAS 

    Google Scholar 
    Viollier E, Inglett P, Hunter K, Roychoudhury A, Van, Cappellen P. The ferrozine method revisited: Fe (II)/Fe (III) determination in natural waters. Appl Geochem. 2000;15:785–90.Article 
    CAS 

    Google Scholar 
    Røy H, Weber HS, Tarpgaard IH, Ferdelman TG, Jørgensen BB. Determination of dissimilatory sulfate reduction rates in marine sediment via radioactive 35S tracer. Limnol Oceanogr Methods. 2014;12:196–211.Article 

    Google Scholar 
    García-Robledo E, Corzo A, Papaspyrou S. A fast and direct spectrophotometric method for the sequential determination of nitrate and nitrite at low concentrations in small volumes. Marine Chem. 2014;162:30–36.Article 

    Google Scholar 
    Miranda KM, Espey MG, Wink DA. A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide. 2001;5:62–71.Article 
    CAS 
    PubMed 

    Google Scholar 
    Holtappels M, Lavik G, Jensen MM, Kuypers MMM Chapter ten – 15N-Labeling Experiments to Dissect the Contributions of Heterotrophic Denitrification and Anammox to Nitrogen Removal in the OMZ Waters of the Ocean. In: Klotz MG, editor. Methods in Enzymology. 486: Academic Press; 2011. p. 223-251.Preisler A, De Beer D, Lichtschlag A, Lavik G, Boetius A, Jørgensen BB. Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment.ISME J. 2007;1:341–353.Article 
    CAS 
    PubMed 

    Google Scholar 
    Warembourg FR 5 – Nitrogen fixation in soil and plant systems. In: Knowles R, Blackburn TH, editors. Nitrogen Isotope Techniques. San Diego: Academic Press; 1993. p. 127-156.Orellana LH, Rodriguez-R LM, Konstantinidis KT. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Res. 2016;45:e14–e14.PubMed Central 

    Google Scholar 
    Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7:11257.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, et al. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J. 2018;12:1715–28.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Watanabe T, Kojima H, Fukui M. Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase. Sci Rep. 2016;6:36262.Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar  More

  • in

    Preparation of aluminium-hydroxide-modified diatomite and its fluoride adsorption mechanism

    Scanning electron microscopy and energy spectrum analysisThe SEM images show the morphological structures of DA and Al-DA before and after adsorption (Fig. 1). DA and Al-DA have disk-like microstructures29 with sur-faces containing both large and small pores, that is, DA and Al-DA have unique multi-level pore structures. The main component of DA and Al-DA is silica, which has a large specific surface area, good thermal stability, and is a natural green material for use as a water treatment agent with a porous structure31. The micrographs show that before adsorption, the DA surface is smooth with a distinct pore structure, whereas modification with aluminium hydroxide makes DA coarse and loose because of the formation of amorphous aluminium hydroxide colloids32. After adsorption, the surface pore structure is covered over for DA and completely covered over for Al-DA, which indicates that F− reacts with Al3+ to form nanoscale precipitates22. The results of the EDS analysis (Fig. 2) show that the content of elemental Al increased from 3.96 to 12.74% after DA was modified with aluminium hydroxide, indicating that Al adhered effectively to the modified DA surface. After adsorption, the content of elemental Al decreased from 3.96 to 1.36% for DA and from 12.74 to 2.03% for Al-DA, which fully confirmed that fluorine preferentially combined with Al to form aluminium precipitates during adsorption, thereby decreasing the Al content.Figure 1SEM images of DA and Al-DA before and after adsorption. (A) Before DA adsorption. (B) After DA adsorption. (C) Before Al-DA adsorption. (D) After Al-DA adsorption.Full size imageFigure 2EDS graphs of DA and Al-DA before and after adsorption. (A) Before DA adsorption. (B) After DA adsorption. (C) Before Al-DA adsorption. (D) After Al-DA adsorption.Full size imageXRD analysisThe surface mineral composition and crystallinity of the materials before and after adsorption were analyzed by XRD (Fig. 3). In the DA and Al-DA patterns, the wide diffraction peaks at approximately 22.0°, 26.0°, and 50.0° mainly correspond to amorphous SiO2, and the diffraction peak at approximately 35° mainly corresponds to amorphous Al2O3, indicating that the material is polycrystalline29. It has been re-ported that amorphous materials may be good adsorbents because of a large specific surface area and numerous active sites33. Many Al(OH)3 peaks and NaCl peaks appear in the XRD pattern of Al-DA, indicating the successful modification of DA by aluminium hydroxide. After adsorption, Na3AlF6 peaks appear in the DA pattern, and Na3AlF6 and AlF3 peaks appear in the Al-DA pattern, whereas the characteristic peaks of NaCl are absent in the Al-DA pattern, which indicates the participation of NaCl in the adsorption process. It has been demonstrated that in the presence of excess sodium fluoride in the reaction solution, the generated aluminium fluoride combines with sodium fluoride to form a NaAlF4 intermediate, which is subsequently converted to cryolite complexes by further adsorption of sodium fluoride34. This result confirms the XRD mapping results.Figure 3XRD patterns of DA and Al-DA before and after adsorption.Full size imageInfrared analysisFigure 4 shows the FTIR spectra of DA and Al-DA before and after adsorption: peaks at 3418, 1635, 1096, 791, and 538 cm−1 appear in the spectrum of DA spectrum before adsorption, and peaks at 3630, 3449, 1637, 1094, 913, 793, and 538 cm−1, appear in the Al-DA spectrum before adsorption. The strong and broad band centered at 3418 cm−1 is due to the stretching vibration of the adsorbed water hydroxyl group (O–H) and the surface hydroxyl group, the vibrational peak at approximately 1635 cm−1 is probably from bound water or the surface hydroxyl group; the peaks at 1096 cm−1 and 538 cm−1 correspond to siloxane groups (Si–O–Si–) and an Al–O absorption band, respectively; and the strong oscillations at 791 cm−1 may be attributed to inorganic Al salts35,36,37. The original absorption peak in the DA spectrum is shifted in the spectrum of DA modified with aluminium hydroxide, confirming the successful modification of DA. The shift of the band at 3418 cm−1 in the DA spectrum to a higher frequency at 3623 cm−1 in the DA spectrum after fluoride absorption is caused by fluoride bonding and has been previously reported38. Another noticeable change in the spectra of DA and Al-DA before and after adsorption is the increase or decrease in the intensity of bending vibrations of specific peaks because the highly electronegative fluoride may have an inductive effect on the respective groups that leads to a blueshift, and the formation of hydrogen bonds leads to a redshift and broadening of the spectral band. The shifts and changes of these peaks indicate the interaction of fluoride with the respective groups29. The new peak at approximately 1170 cm−1 in the spectra of DA and Al-DA with adsorbed fluoride may be due to the formation of Al-F bonds6. The IR spectra show that the formation of a new bonding electronic structure by surface complexation with F− is one of the main mechanisms for the adsorption of F−.Figure 4FTIR spectra of DA and Al-DA before and after adsorption.Full size imageZeta potential analysisThe zeta potential of the material surface plays a very key role in the adsorption process, which reflects the surface charge properties of the material under different pH conditions, and also reflects the surface properties of the material. To obtain the zero charge point of the material, we studied the potential change of the material under different pH values. The results are shown in Fig. 5. In the range of pH 3–11, the zeta potential of the two adsorbents decreased linearly with the increase in pH, and the pHzpc of DA and Al-DA were 9.84 and 10.61, respectively. When pH  More

  • in

    Vole outbreaks may induce a tularemia disease pit that prevents Iberian hare population recovery in NW Spain

    Study siteOur study site is in an intensive agricultural landscape in NW Spain known as “Tierra de Campos”, which occupies part of three out of nine provinces of Castilla-y-León region (Palencia, Valladolid, and Zamora). This area is considered the main “hot-spot” of tularemia in Spain and Southern Europe16 and is characterized by higher-than-average vole abundances during outbreaks17.Iberian hare abundance indexYearly occurrence of vole outbreaks in NW Spain between 1996 and 2020 (i.e., 1997, 1998, 2007, 2008, 2014, 2019) were identified based on reports in the news (historical reconstruction18) and more recently (from 2009 onward) using common vole abundance indices obtained from live-trapping monitoring (i.e.4,19).To study the Iberian hare population trends we used regional hunting statistics available from the regional government (Junta de Castilla-y-León, CAZDATA Project, https://medioambiente.jcyl.es/web/es/caza-pesca/cazdata-banco-datos-actividad.html [Cited 2022 Sep 23]), which included hunting records as well as the number of hunting licences from 1974 to 2020. We used the number of hunted hares divided by the number of hunting licences each year as an abundance index for hares in “Tierra de Campos” (compiling data from the provinces of Palencia, Zamora and Valladolid). CAZDATA Project is an initiative proposed by the Hunting Federation of Castilla y León, which has the support of the regional government and, more importantly, the commitment of almost 60% of the hunting societies in the community to implement a system for monitoring hunting activity. Since this information is gathered by hunters for the benefit of the hunting activity, we are confidence on its reliability to carry out the present study.
    Francisella tularensis prevalence in Iberian haresWe compiled data on F. tularensis prevalence in Iberian hares from 2007 to 2016 using previously published information from a passive surveillance program carried out by the “Regional Network of Epidemiological Surveillance” (Red de Vigilancia Epidemiológica de la Dirección General de Salud Pública) of Castilla-y-León region20. This provided us with information on hare tularemia prevalence (amount of positives/number of screened individual) each year within the three provinces from “Tierra de Campos”.Statistical analysesTo study Iberian hare population trends, we calculated an index of yearly hare population instantaneous growth rate (PGR) using the hunting bag data (hare abundance index) from 1996 to 2020. Hare PGR was calculated as follows:$$PGR= lnleft(frac{{AI}_{t}}{{AI}_{t+1}}right)$$where ln stands for natural logarithm, AIt is Iberian hare abundance index on year t. and AIt+1 is the Iberian hare abundance index on year t + 1. PGRs were estimated yearly from 1996 to 2019. This dependent variable was fitted to a Generalized Linear Mixed Model using the glmmTMB function (GLMMTMB, package glmmTMB21) and a gaussian family distribution and identity link function. The categorical variable vole outbreak year (i.e., with two levels: years with (1) or without vole outbreak (0), hereafter “Vole”) and “Province” (i.e., with three levels: Palencia, Valladolid and Zamora), and their interaction were used as explanatory variables. “Year” of sampling was included as a random factor (i.e., 1996–2019). Significance of the fixed effects in the models was calculated with Type II tests using the function Anova in the car package22. We previously checked the model for overdispersion and distribution fitting using function simulateResiduals (package DHARMa23, simulations = 999). The variable PGR expresses the change between year t and t + 1. We included AI at t as a covariate in the model, in order to take into account density-dependence in hare PGR (the extent to which the abundance changes in between year t and t + 1 depends on the abundance during year t). For this to make biological sense, we rescaled the covariable AI so that it has mean equal to zero. Thus, the effect of the other predictor variables in the model (i.e., “Vole” and “Province”) was interpreted as the effect that these variables have on PGR when the abundance value is at 0. Thus, the effect of “Vole” and “Province” on PGR will be obtained by the mean value of abundance.We assessed the effect of vole outbreak years on the Iberian hare’s population PGR by running a multiple Pearson correlation (function ggscatter) between PGR and AI, considering both, PGR for all the years of the study period (i.e., 1996–2019) and only those years where vole outbreaks were detected (i.e., 1997, 1998, 2007, 2008, 2014, 2019).Finally, we tested for difference in the prevalence of F. tularensis on Iberian hare’s during years with or without vole outbreaks using a GLMMTMB21 with a binomial family distribution and a logit link function, where prevalence of F. tularensis in hares was the dependent variable, and “Vole” outbreak years and “Province” (i.e. Palencia, Valladolid and Zamora) were the responses variables. In this case, the variable “Vole” outbreak years included three levels (i.e. 0 = no vole outbreak, 1 = vole outbreak year, 2 = one year after vole outbreak), to assess if F. tularensis prevalence in hare also persist one year after a vole outbreak. “Year” of sampling was included as a random factor (i.e., 2007–2016). Due to the limited sample size, we did not include the interaction between “Vole” and “Province” to not overfit the model. We also previously checked the model for overdispersion and distribution fitting using function simulateResiduals (package DHARMa23, simulations = 999). All analysis were carried out using the R statistical computing environment24. More