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    A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium

    1.Prabakaran S, Lippens G, Steen H, Gunawardena J. Post‐translational modification: nature’s escape from genetic imprisonment and the basis for dynamic information encoding. Wiley Interdiscip Rev Syst Biol Med. 2012;4:565–83.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Khoury GA, Baliban RC, Floudas CA. Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci Rep. 2011;1:90.CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 
    3.den Ridder M, Daran-Lapujade P, Pabst M. Shot-gun proteomics: why thousands of unidentified signals matter. FEMS Yeast Res. 2020;20:foz088.Article 
    CAS 

    Google Scholar 
    4.Spoel SH. Orchestrating the proteome with post-translational modifications. Oxford University Press UK. 2018;19:4499–4503.5.Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, et al. Essentials of glycobiology. 3rd edition. (Cold Spring Harbor Laboratory Press, New York, 2015–2017).6.Varki A. Evolutionary forces shaping the Golgi glycosylation machinery: why cell surface glycans are universal to living cells. Cold Spring Harb Perspect Biol. 2011;3:a005462.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    7.Varki A, Lowe JB. Biological roles of glycans. In: Varki A. Essentials of glycobiology. 2nd edition (Cold Spring Harbor Laboratory Press, New York, 2009). pp 75–88.8.Herget S, Toukach PV, Ranzinger R, Hull WE, Knirel YA, Von der Lieth C-W. Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. BMC Struct Biol. 2008;8:1–20.Article 
    CAS 

    Google Scholar 
    9.Schäffer C, Messner P. Emerging facets of prokaryotic glycosylation. FEMS Microbiol Rev. 2017;41:49–91.PubMed 
    Article 
    CAS 

    Google Scholar 
    10.Eichler J, Koomey M. Sweet new roles for protein glycosylation in prokaryotes. Trends Microbiol. 2017;25:662–72.CAS 
    PubMed 
    Article 

    Google Scholar 
    11.Eichler J. Extreme sweetness: protein glycosylation in archaea. Nat Rev Microbiol. 2013;11:151.CAS 
    PubMed 
    Article 

    Google Scholar 
    12.Kleikamp HB, Lin YM, McMillan DG, Geelhoed JS, Naus-Wiezer SN, Van Baarlen P, et al. Tackling the chemical diversity of microbial nonulosonic acids–a universal large-scale survey approach. Chem Sci. 2020;11:3074–80.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    13.Boleij M, Kleikamp H, Pabst M, Neu TR, Van Loosdrecht MC, Lin Y. Decorating the anammox house: sialic acids and sulfated glycosaminoglycans in the extracellular polymeric substances of anammox granular sludge. Environ Sci Technol. 2020;54:5218–26.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    14.Bucci M. A gut reaction. Nat Chem Biol. 2020;16:363-.CAS 
    PubMed 
    Article 

    Google Scholar 
    15.Conrad R. The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Rep. 2009;1:285–92.CAS 
    PubMed 
    Article 

    Google Scholar 
    16.Lam P, Lavik G, Jensen MM, van de Vossenberg J, Schmid M, Woebken D, et al. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc Natl Acad Sci. 2009;106:4752–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    17.Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, et al. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature. 2006;440:790.PubMed 
    Article 

    Google Scholar 
    18.Kartal B, Kuenen JV, Van Loosdrecht M. Sewage treatment with anammox. Science. 2010;328:702–3.CAS 
    PubMed 
    Article 

    Google Scholar 
    19.van Niftrik L, Jetten MS. Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Mol Biol Rev. 2012;76:585–96.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    20.Fuerst JA, Sagulenko E. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol. 2011;9:403.CAS 
    PubMed 
    Article 

    Google Scholar 
    21.Van Teeseling MC, Mesman RJ, Kuru E, Espaillat A, Cava F, Brun YV, et al. Anammox Planctomycetes have a peptidoglycan cell wall. Nat Commun. 2015;6:6878.PubMed 
    Article 
    CAS 

    Google Scholar 
    22.Jeske O, Schüler M, Schumann P, Schneider A, Boedeker C, Jogler M, et al. Planctomycetes do possess a peptidoglycan cell wall. Nat Commun. 2015;6:7116.CAS 
    PubMed 
    Article 

    Google Scholar 
    23.van Teeseling MC, Maresch D, Rath CB, Figl R, Altmann F, Jetten MS, et al. The S-layer protein of the anammox bacterium Kuenenia stuttgartiensis is heavily O-glycosylated. Front Microbiol. 2016;7:1721.PubMed 
    PubMed Central 

    Google Scholar 
    24.van Teeseling MC, de Almeida NM, Klingl A, Speth DR, den Camp HJO, Rachel R, et al. A new addition to the cell plan of anammox bacteria:“Candidatus Kuenenia stuttgartiensis” has a protein surface layer as the outermost layer of the cell. J Bacteriol. 2014;196:80–9.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    25.Boleij M, Pabst M, Neu TR, van Loosdrecht MC, Lin Y. Identification of glycoproteins isolated from extracellular polymeric substances of full-scale anammox granular sludge. Environ Sci Technol. 2018;52:13127–35.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    26.Gerbino E, Carasi P, Mobili P, Serradell M, Gómez-Zavaglia A. Role of S-layer proteins in bacteria. World J Microbiol Biotechnol. 2015;31:1877–87.CAS 
    PubMed 
    Article 

    Google Scholar 
    27.Sleytr UB, Schuster B, Egelseer E-M, Pum D. S-layers: principles and applications. FEMS Microbiol Rev. 2014;38:823–64.CAS 
    PubMed 
    Article 

    Google Scholar 
    28.Schuster B, Sleytr UB. Relevance of glycosylation of S-layer proteins for cell surface properties. Acta biomaterialia. 2015;19:149–57.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    29.Tamir A, Eichler J N-Glycosylation is important for proper Haloferax volcanii S-layer stability and function. Appl Environ Microbiol. 2017;83:e03152-16.30.Wang F, Cvirkaite-Krupovic V, Kreutzberger MA, Su Z, de Oliveira GA, Osinski T, et al. An extensively glycosylated archaeal pilus survives extreme conditions. Nat Microbiol. 2019;4:1401–10.31.Li P-N, Herrmann J, Tolar BB, Poitevin F, Ramdasi R, Bargar JR, et al. Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. ISME J. 2018;12:2389–402.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    32.Posch G, Pabst M, Brecker L, Altmann F, Messner P, Schäffer C. Characterization and scope of S-layer protein O-glycosylation in Tannerella forsythia. J Biol Chem. 2011;286:38714–24.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Benz I, Schmidt MA. Never say never again: protein glycosylation in pathogenic bacteria. Mol Microbiol. 2002;45:267–76.CAS 
    PubMed 
    Article 

    Google Scholar 
    34.Sekot G, Posch G, Messner P, Matejka M, Rausch-Fan X, Andrukhov O, et al. Potential of the Tannerella forsythia S-layer to delay the immune response. J Dent Res. 2011;90:109–14.CAS 
    PubMed 
    Article 

    Google Scholar 
    35.Szymanski CM, Burr DH, Guerry P. Campylobacter protein glycosylation affects host cell interactions. Infect Immun. 2002;70:2242.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Drickamer K, Taylor ME. Evolving views of protein glycosylation. Trends Biochem Sci. 1998;23:321–4.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    37.Koomey M. O-linked protein glycosylation in bacteria: snapshots and current perspectives. Curr Opin Struct Biol. 2019;56:198–203.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    38.Wang N, Anonsen JH, Hadjineophytou C, Reinar WB, Børud B, Vik Å, et al. Allelic polymorphisms in a glycosyltransferase gene shape glycan repertoire in the O-linked protein glycosylation system of Neisseria. Glycobiology. 2021;31:477–91.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, et al. Comparative glycoproteomics of stem cells identifies new players in ricin toxicity. Nature. 2017;549:538–42.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    40.Polasky DA, Yu F, Teo GC, Nesvizhskii AI. Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods. 2020;17:1125–32.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    41.Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods. 2020;17:1133–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Fulton KM, Li J, Tomas JM, Smith JC, Twine SM. Characterizing bacterial glycoproteins with LC-MS. Expert Rev Proteom. 2018;15:203–16.CAS 
    Article 

    Google Scholar 
    43.Ahrné E, Müller M, Lisacek F. Unrestricted identification of modified proteins using MS/MS. Proteomics. 2010;10:671–86.PubMed 
    Article 
    CAS 

    Google Scholar 
    44.Bern M, Kil YJ, Becker C. Byonic: advanced peptide and protein identification software. Curr Protoc Bioinforma. 2012;40:13.20. 1-13.20. 14Article 

    Google Scholar 
    45.Na S, Bandeira N, Paek E. Fast multi-blind modification search through tandem mass spectrometry. Mol Cell Proteomics. 2012;11:1–13.46.Devabhaktuni A, Lin S, Zhang L, Swaminathan K, Gonzalez CG, Olsson N, et al. TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nat Biotechnol. 2019;37:469–79.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    47.Izaham ARA, Scott NE. Open database searching enables the identification and comparison of bacterial glycoproteomes without defining glycan compositions prior to searching. Mol Cell Proteom. 2020;19:1561–74.CAS 
    Article 

    Google Scholar 
    48.Ahmad Izaham AR, Ang C-S, Nie S, Bird LE, Williamson NA, Scott NE. What are we missing by using hydrophilic enrichment? improving bacterial glycoproteome coverage using total proteome and FAIMS analyses. J Proteome Res. 2020;20:599–612.49.Kelstrup CD, Frese C, Heck AJ, Olsen JV, Nielsen ML. Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). Mol Cell Proteom. 2014;13:1914–24.CAS 
    Article 

    Google Scholar 
    50.Wuhrer M, Catalina MI, Deelder AM, Hokke CH. Glycoproteomics based on tandem mass spectrometry of glycopeptides. J Chromatogr B 2007;849:115–28.CAS 
    Article 

    Google Scholar 
    51.Hoffmann M, Marx K, Reichl U, Wuhrer M, Rapp E. Site-specific O-glycosylation analysis of human blood plasma proteins. Mol Cell Proteom. 2016;15:624–41.CAS 
    Article 

    Google Scholar 
    52.Singh C, Zampronio CG, Creese AJ, Cooper HJ. Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins. J proteome Res. 2012;11:4517–25.CAS 
    PubMed 
    Article 

    Google Scholar 
    53.Hoffmann M, Pioch M, Pralow A, Hennig R, Kottler R, Reichl U, et al. The fine art of destruction: a guide to in‐depth glycoproteomic analyses—exploiting the diagnostic potential of fragment ions. Proteomics 2018;18:1800282.Article 
    CAS 

    Google Scholar 
    54.Kosma P, Wugeditsch T, Christian R, Zayni S, Messner P. Glycan structure of a heptose-containing S-layer glycoprotein of Bacillus thermoaerophilus. Glycobiology. 1995;5:791–6.CAS 
    PubMed 
    Article 

    Google Scholar 
    55.Faridmoayer A, Fentabil MA, Haurat MF, Yi W, Woodward R, Wang PG, et al. Extreme substrate promiscuity of the Neisseria oligosaccharyl transferase involved in protein O-glycosylation. J Biol Chem. 2008;283:34596–604.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Harding CM, Nasr MA, Scott NE, Goyette-Desjardins G, Nothaft H, Mayer AE, et al. A platform for glycoengineering a polyvalent pneumococcal bioconjugate vaccine using E. coli as a host. Nat Commun. 2019;10:1–11.CAS 
    Article 

    Google Scholar 
    57.Speth DR, Guerrero-Cruz S, Dutilh BE, Jetten MS. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system. Nat Commun. 2016;7:11172.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    58.Lawson CE, Wu S, Bhattacharjee AS, Hamilton JJ, McMahon KD, Goel R, et al. Metabolic network analysis reveals microbial community interactions in anammox granules. Nat Commun. 2017;8:1–12.Article 
    CAS 

    Google Scholar 
    59.Straka LL, Meinhardt KA, Bollmann A, Stahl DA, Winkler M-K. Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria. ISME J. 2019;13:1997–2004.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Hu Z, Wessels HJ, van Alen T, Jetten MS, Kartal B. Nitric oxide-dependent anaerobic ammonium oxidation. Nat Commun. 2019;10:1–7.Article 
    CAS 

    Google Scholar 
    61.Shaw DR, Ali M, Katuri KP, Gralnick JA, Reimann J, Mesman R, et al. Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria. Nat Commun. 2020;11:1–12.Article 
    CAS 

    Google Scholar 
    62.Lewis AL, Desa N, Hansen EE, Knirel YA, Gordon JI, Gagneux P, et al. Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure. Proc Natl Acad Sci. 2009;106:13552–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    63.Fernández L, Rodríguez A, García P. Phage or foe: an insight into the impact of viral predation on microbial communities. ISME J. 2018;12:1171–9.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    64.Wang J, Cheng B, Li J, Zhang Z, Hong W, Chen X, et al. Chemical remodeling of cell‐surface sialic acids through a palladium‐triggered bioorthogonal elimination reaction. Angew Chem Int Ed. 2015;54:5364–8.CAS 
    Article 

    Google Scholar 
    65.Pabst M, Fischl RM, Brecker L, Morelle W, Fauland A, Köfeler H, et al. Rhamnogalacturonan II structure shows variation in the side chains monosaccharide composition and methylation status within and across different plant species. Plant J. 2013;76:61–72.CAS 
    PubMed 

    Google Scholar 
    66.Popa I, Pons A, Mariller C, Tai T, Zanetta J-P, Thomas L, et al. Purification and structural characterization of de-N-acetylated form of GD3 ganglioside present in human melanoma tumors. Glycobiology. 2007;17:367–73.CAS 
    PubMed 
    Article 

    Google Scholar 
    67.Paschinger K, Wilson IB. Anionic and zwitterionic moieties as widespread glycan modifications in non-vertebrates. Glycoconj J. 2020;37:27–40.CAS 
    PubMed 
    Article 

    Google Scholar 
    68.Nothaft H, Scott NE, Vinogradov E, Liu X, Hu R, Beadle B, et al. Diversity in the protein N-glycosylation pathways within the Campylobacter genus. Mol Cell Proteom. 2012;11:1203–19.Article 
    CAS 

    Google Scholar 
    69.Hadjineophytou C, Anonsen JH, Wang N, Ma KC, Viburiene R, Vik Å, et al. Genetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system. PLoS Genet. 2019;15:e1008532.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    70.Oshiki M, Satoh H, Okabe S. Ecology and physiology of anaerobic ammonium oxidizing bacteria. Environ Microbiol. 2016;18:2784–96.CAS 
    PubMed 
    Article 

    Google Scholar 
    71.Kartal B, Geerts W, Jetten MS. Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. Methods in enzymology. 486. Elsevier; 2011. p. 89–108.
    Google Scholar 
    72.Lotti T, Kleerebezem R, Lubello C, Van Loosdrecht M. Physiological and kinetic characterization of a suspended cell anammox culture. Water Res. 2014;60:1–14.CAS 
    PubMed 
    Article 

    Google Scholar 
    73.Kleikamp HB, Pronk M, Tugui C, da Silva LG, Abbas B, Lin YM, et al. Database-independent de novo metaproteomics of complex microbial communities. Cell Syst. 2021;12:375–83.74.Köcher T, Pichler P, Swart R, Mechtler K. Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat Protoc. 2012;7:882.PubMed 
    Article 
    CAS 

    Google Scholar 
    75.Lawson CE, Nuijten GH, de Graaf RM, Jacobson TB, Pabst M, Stevenson DM, et al. Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13 C and 2 H metabolic network mapping. ISME J. 2021;15:673–87.CAS 
    PubMed 
    Article 

    Google Scholar 
    76.Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    77.Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Laczny CC, Kiefer C, Galata V, Fehlmann T, Backes C, Keller A. BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation. Nucleic Acids Res. 2017;45:W171–W9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    79.Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    80.Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    81.Sieber CM, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836–43.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    82.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    83.Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy T, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    84.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. Prokaryotic genome annotation pipeline. In: The NCBI Handbook. 2nd edition. (National Center for Biotechnology Information, US, 2013). pp 131–45.85.Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726–31.CAS 
    PubMed 
    Article 

    Google Scholar 
    86.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

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    Analysis of volatiles from feces of released Przewalski’s horse (Equus przewalskii) in Gasterophilus pecorum (Diptera: Gasterophilidae) spawning habitat

    The volatiles from fresh feces of Przewalski’s horse at the pre-oviposition, oviposition, and post-oviposition stages of G. pecorum
    Throughout the stages of pre-oviposition (PREO), oviposition (OVIP), and post-oviposition (POSO) of G. pecorum, 70 volatiles were identified in fresh feces of Przewalski’s horse. Among them, 46, 48, and 52 volatiles were identified at PREO, OVIP, and POSO, respectively, and 29 volatiles were common at all three stages. In addition, 4, 5, and 9 volatiles were common between PREO and OVIP, OVIP and POSO, as well as PREO and POSO, whereas 4, 10, and 9 volatiles were unique at the single stage of PREO, OVIP, and POSO, respectively (Table 1; Fig. S1). According to relative content, the two main chemical classes of volatiles were aromatic hydrocarbons and alkenes, that is, their respective contents in a sample were both more than 25% of the total content. Except alcohols which exhibited significant difference between PREO and POSO (One-way ANOVA, F = 8.400, df = 2, P = 0.018), there was no significant difference in all other pairwise comparisons among the nine chemical classes at three stages (One-way ANOVA or Kruskal–Wallis test: P  > 0.05) (Fig. 1). Non-metric multidimensional scaling (NMDS) analysis revealed certain extent of overlap (Fig. 2), while one-way analysis of similarity (ANOSIM) indicated that there were significant differences among the three stages (R = 0.5391, P = 0.008).Table 1 The volatiles from fresh feces of Przewalski’s horse at the stages of PREO, OVIP, and POSO of Gasterophilus pecorum.Full size tableFigure 1Volatile classes detected from fresh feces of Przewalski’s horse at the stages of PREO, OVIP, and POSO of Gasterophilus pecorum. PREO, OVIP, and POSO represent fresh feces at the stages of pre-oviposition, oviposition, and post-oviposition of Gasterophilus pecorum, respectively. Data are mean (n = 3) ± SE. Different letters indicate significant differences at P  0.05). Furthermore, acetic acid was common to PREO and POSO, but no difference was observed between them (Independent t test, t = 0.137, df = 4, P = 0.897) (Table 1).Of particular concern among the eight volatiles mentioned above, ammonium acetate and butanoic acid were unique to OVIP, the critical stage of oviposition. Although not one of the five most abundant volatiles, another nine volatiles were also specific to OVIP, of which hexanoic acid, cyclopentasiloxane,decamethyl- and cyclohexene,3-methyl-6-(1-methylethyl)- were higher than 1% in relative content (Table 1).Among the 47 volatiles common to two or three stages, only six volatiles were significantly different in relative contents. Of which, D-limonene was higher at PREO than at OVIP (One-way ANOVA: F = 11.936, df = 2, P = 0.012) or POSO (P = 0.012), and 1-butanol was higher at OVIP than at PREO (One-way ANOVA: F = 8.175, df = 2, P = 0.024) or POSO (P = 0.04). Relative contents of the other four volatiles were less than 1% (Table 1).The volatiles from feces of Przewalski’s horse with different freshness states at the OVIP stage of G. pecorum
    Totally, 83 volatiles were detected from fresh feces (Fresh), semi-fresh feces (Semi-fresh), and dry feces (Dry) at the OVIP stage of G. pecorum. Of which, 48, 41 and 28 volatiles were identified in Fresh, Semi-fresh and Dry, and 7 volatiles were common to all three feces with different freshness states. In addition, 14, 3 and 3, were common between Fresh and Semi-fresh, Semi-fresh and Dry, as well as Fresh and Dry, whereas 24, 17, and 15 were unique to Fresh, Semi-fresh, and Dry, respectively (Table 2; Fig. S2). Aromatic hydrocarbons and alkenes, acids and ketones, as well as alcohols and aldehydes were the two main chemical classes of Fresh, Semi-fresh, and Dry in respective. Except esters and ‘others’ which showed no significant difference in the feces, there were significant differences among other seven classes in at least one pairwise comparison of the three freshness states (One-way ANOVA, Independent t-test or Kruskal–Wallis test: P  More

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    Ecological and health risk assessment of trace metals in water collected from Haripur gas blowout area of Bangladesh

    Physiochemical characteristics of water in the blowout regionThe physiochemical properties of water were measured in the laboratory. The analyzed properties are shown in Table 3.Table 3 The analyzed physiochemical properties of water.Full size tableThe average value of pH is 6.529 indicates water of the study area is slightly acidic in nature. The average value of CO2 (6.5) complied with the lowering tendency of pH. The average ORP value 36 also reflecting the sign of acidic water in the study region. According to WHO standards (2011), the value of conductivity within range 0–800, Total dissolved solids less than 500 ppm, alkalinity 120 ppm, and total hardness less than 300 mg/L are allowable for drinking and domestic purpose37. The average value of conductivity 76.7 µs/cm, total dissolved solids 44.2 ppm, alkalinity 109.1 concurred with the dirking water standard by WHO (2011). The average value of TH is 49 ppm points out that the properties of water are soft.Spatial distribution of trace elements derived from water bodies around the blowout areaThe primary purpose of this study is to understand the concentration level of different Trace metals in the area. In this study, Pb, Ni, Cu, Cd, and Zn were examined (Fig. 3). Besides the toxic metal spatial distribution map is constructed using the inverse distance weighting (IWD) method in Arc GIS (version 10.5). The map (Fig. 4) shows common patterns of hotspots near the Syl-1 blowout area for every metal. This scenario indicates that these metals are originated from the same source46.The contiguous area near Syl-4 well also exhibited a similar pattern to Syl-1 for all metals except Cd. A high concentration of Cd was found closed to the Syl-1 area. The elevated concentration of toxic metals like Ni, Pb, and Cd are found in the adjacent areas of blowout points (Fig. 4). Continuous gas escaping from these abandoned wells might stimulate the trace metal accumulation, especially Pb would be more toxic when it will come to a contact with gasoline (Syl-1 and Syl-4)7. The non-essential toxic metals like Ni, Cd, and Pb in water can pose a serious health threat inthesite47. In addition, these toxic elements can contribute to acute or chronic health issues like high blood pressure, kidney failure, headache, abdominal pain, cancer, nerve damage, and so on for the long-term consumption of such water48.Standard value of Pb in water is 0.01 mg/L, Ni is 0.02 mg/L, Cu is 2 mg/L, Cd is 0.003 mg/L in water37. In this analysis, the average value of Pb = 0.04, Cd = 0.05, Ni = 0.16, Cu = 0.03 mg/L, respectively. The TMs like Zn concentration is about zero or below the detection level for water samples in the study location. The values of Pb, Cd and Ni were higher than the standards level indicates that the water should not be used for any purpose49.Figure 3The concentration of trace elements in the study area.Full size imageFigure 4The spatial distribution map of toxic metals in the area.Full size imageCorrelation coefficient (R) matrix of water quality parameter presented in the blowout areaA Correlation matrix represents the relationship among several variables. It is generated based on the correlation coefficient, which ranges from − 1 to 1. The value of correlation coefficient (1, − 1) indicates perfect correlation, (− 0.9 to − 0.7 or 0.9–0.7) shows strong correlation, (0.4–0.6 either positive or negative) represents moderate correlation, (0.1–0.3 or − 0.1 to − 0.3) displays as weak and 0 indicates no relationship between variables50. The mathematical expressions are described in the article by MacMillan et al.51 to evaluate the correlation coefficient (r).The correlation matrix is shown in Table 4. From the Table 4, it is clear that the pH shows a moderate to strong correlation with CO2 (0.63) and alkalinity (0.69). Whereas, it shows a very strong positive correlation with Total Hardness (TH) and Ca2+ (0.88), respectively. The moderately positive correlation reflects with EC (0.41) and trace elements Ni (0.62). The rest of parameters show a negative correlation. The CO2 exhibits a good correlation with EC (0.72), TH and Ca2+ (0.52). Alkalinity states a good correlation with TH and Calcium ions (0.76). EC shows a maximum correlation with TDS (1.00); maximum correlation also found in the case of TH and Ca2+. Turbidity has a positive correlation for all of the parameters except EC and TDS. TDS shows a strong positive correlation with all of the trace elements, in the case of Pb (0.54), Cd (0.88), Ni (0.68) and for Cu the value is 0.64. All trace elements have a strong correlation with each other. Pb represents a good correlation with Cd (0.65), Ni (0.54) and Cd (0.35). Ni has a strong correlation with Cd (0.61), Cu (0.43). Cu also implies a good correlation with Cd (0.58). In the end, it can be mentioned that a strong positive correlation can be detected among all of the trace elements and also for most of the relative parameters. CO2 established the equilibrium state in the water with ions might be lowering the oxidation. The trace metals Cu and Cd were positively correlated with the turbidity. The washed turbid water from the blow out areas might stimulate these trace metals. The inverse association with oxidation and total hardness indicates the less vegetated areas have higher influx rate of soil materials. It implies the result of the correlation matrix indicated that all of the trace elements and also relevant ions presented in the water of blowout area resultant from the same source46.Table 4 Correlation coefficient matrix of water parameters.Full size tableFactor loading of water parametersThe interrelationship within a set of variables or objects is represented by factor analysis. The factors contain all of the basic information about a wider set of variables or observed objects. It shows how the variables are strongly correlated with the determined factor. Factor analysis is also known as a multivariate approach to reducing data33. Among different types of factor analysis, Principal component analysis account for the maximum variance of observed variables. So, it can be called variance-oriented33. Factor loading shows how certain variables strongly correlate for a given factor. Factor loading varies from − 1 to + 1 where the value of factor loading below − 0.5 or above 0.5 suggested good correlations and value closed to − 1 or + 1, suggesting a more robust correlation32. The Table 5 represented the principal component analysis result of factor solution.Table 5 Principal components analysis results of water parameters.Full size tableFrom analysis (Table 5), it can be realized that the water quality parameters such as Turbidity, TH, Ca2+, Cd, Ni and Cu have a stronger correlation with each other’s reflecting their source of origin might be from the same area14. Factor loading also suggested that more robust interconnection exists among CO2, EC and TDS. In this analysis, the two-factor solution explained approximately 80.6% of the variance. The eigenvalue, total variance explained are represented in Supplementary Table S1. That percentage is high enough to accept the results. It can also be added that the red and yellow colored loading represented strong correlation with each other46,52.Water quality index (WQI)The WQI is one of the best tools for monitoring the surface-groundwater contamination and can be used for water quality improvement programs. The WQI is determined from various  physicochemical parameters like pH, EC, TDS, TH, EC, and so forth. Higher estimation of WQI indicates poor water quality and lower estimation of WQI shows better water quality. During this examination, WQI esteems a range from 0.02633 to 5144.37 and are characterized into five water types shown in Table 6. The noteworthy WQI is recorded in case of (sample-1) which demonstrates an elevated level of contamination. Water sample 2, 5, 8 and 10 are grouped under class-1 which demonstrates there is a lower degree of pollution in water. In addition, WQI calculation for sample 2, 5, 8 and 10 excluded trace elements value and WQI evaluation for sample 1, 3, 4, 6, 7 and 9 included the heavy metals value in water. These results also clarify the association of heavy metals on water quality degradation of the study area.Table 6 Classification of the water quality index for individual parameter of water.Full size tableThe situation of contamination in the areaThe level of contamination has been demonstrated in terms of the CFi, PLI, and also PI analysis of water samples around the blowout area. The values of CFi are indicated the degree of contamination. The intensity of CFi has been determined with some numerical values like 1, 3, and 6. The CFi value is less than 1, which implies low contamination, as the value is > 6 indicated a high degree of contamination36. The Table 7 elucidates that the degree of contamination in the case of trace elements Pb, Cd, and Ni are very high for most of the locations of the research sides. Besides Cu and Zn exhibit that level contamination is low in the area. In other cases, the PLI can be evaluated by using the CFi value. The value of PLI greater than 1 symbolizes polluted and less than 1 represents the unpolluted status36,39. The pollution load index rate of Pb, Cd, and Ni are 2.3, 2.87, and 2.56, respectively (Fig. 5).This result indicates the pollution of water bodies in the sampling sites. The other elements such as Cu and Zn are within the allowable limit are shown in Fig. 5. Moreover, the PI indicates similar results as CFi and PLI.Table 7 Contamination factor of water samples.Full size tableFigure 5Pollution load index of the study area.Full size imageThe state of potential ecological threat in the areaThe ecological potential risk index has been appealed to detect the possible threat to the ecological system in the adjoining area. The calculated RI value provided the risk factor of water for understanding the ecological threat. When the RI value is more than 600, it is considered a polluted case11,14,36. The computed RI value of the study for Pb, Cd, Ni, and Cu are 123.5, 2770, 235, and 0.23, respectively (Table 8). The value of Cd is high enough (RI  > 600). So, the Cd values indicated that the potential threat to the ecological system. Besides, the TMs like Ni and Cu are specified medium to low ecological pollution in the area are shown in Table 8. Moreover, the spatial distribution has been presented to outlook the potential ecological threats around the blow out location of the gas field is shown in Fig. 6.Table 8 Ecological risk index (RI) of the study area.Full size tableFigure 6A map of the spatial distribution of potential ecological risk threats in the study area.Full size imageThe spatial distribution map of RI also pointed out the high ecological risk closed to the blowout areas (Fig. 6). From these results, it can be implied that the use of  this water for domestic or drinking purposes, can be harmful for living beings. Moreover, it can be distressed the ecological system in the site. Hence, the use of the water from this site should be avoided by dwellers near the blowout areas of the gas field.Assessment of noncarcinogenic health risksNoncarcinogenic risk is one of the vital categories of human health risk assessment. It is known that a polluted environment is highly liable for causing a health risk. Toxic metal presents in water also very harmful for public health, including child and adult both. The health risks may be extended through ingestion and skin absorption of water. To know the harmful impacts of trace elements of water on the human body, noncarcinogenic risk evaluation is more important. For that, the value of CDI for ingestion and dermal absorption was evaluated at the beginning to identify such risk index (Supplementary Table S2 and S3). Then the CDI has been divided with the RfD value. From where, the HQ can be acquired separately for ingestion and dermal absorption. The summation of HQingestion and HQdermal expressed the HQtotal. And the HQtotal entirety was used to achieve the HI are shown in Table 9.Table 9 The HQ and hazard index (HI) value of noncarcinogenic analysis of the area.Full size tableThe results elucidate that case of adult, the mean value of CDITotal for Pb is 1.29E-03, Cd is 1.45E-03, Ni is 4.93E-03 and Cu is 4.83E-04, respectively. For the child, the mean value of CDITotal in the case of Pb, Cd, Ni, and CU is4.7544E-03, 5.33E-03, 1.81E-03 and 1.77E-04, correspondingly. Additionally, the order of CDITotal for adults are Ni  > Cd  > Pb  > Cu (Supplementary Table S2) whereas, for child, it is quite different. In the case of children, the order  are Cd  > Pb  > Ni  > Cu are presented in Supplementary Table S3.The mean values of HQTotal of Pb, Cd, Cu, and Ni are ranging from 4.46E−05 to 1.45E−02 for child. Besides, these values for adults are extending from 1.21E−05 to 4.66E−03. These values suggest that the trace elements in the water of the study area are quite harmful to the child than an adult. The children’s HQTotal has been ordered as Cd  > Pb  > Ni  > Cu and for the adult Cu  More

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    Influences of conservation measures on runoff and sediment yield in different intra-event-based flood regimes in the Chabagou watershed

    Effects on intra-event-based flood runoff and sediment characteristicsBetween the 1960s and 1990s, there was no significant change in rainfall in the Chabagou watershed35. The mean values of runoff and sediment transport in the baseline period and measurement period were calculated. Regardless of rainfall influence, the effect of conservation measures was assessed by the time series contrasting method25.Table 1 shows the statistics of the characteristics of event-based flood flows and sediment in 1961–1990 (excluding 1970). Compared with those in the baseline period, T and Tr in the measurement period increased by 16.54% and 29.21%, respectively; however, Tp decreased by 55.52% in the measurement period, which showed that the soil and water conservation measures extended the flood duration while reducing the time of increased discharge. Under identical rainfall conditions, long-duration runoff with less time for increased discharge could cause less erosion than short-duration runoff with more time for increased discharge36. Hence, the conservation measures reduced soil erosion by prolonging the flood duration and reducing the time to peak. In addition, the hydrodynamic indices qp, H and qm were 75.2%, 56.0% and 68.0% lower, respectively, in the measurement period than in the baseline period. Moreover, E in the measurement period was only 10.2% that in the baseline period. The results showed that the conservation measures greatly reduced the hydrodynamic energy and thus soil erosion. In addition, the relative erosion indicators SSY, SCE and MSCE, decreased 69.2%, 33.3%, and 11.9%, respectively, in the measurement period compared with the baseline period, which indicated that the conservation measures significantly reduced soil erosion and decreased the mean sediment concentration, although the reduction in the maximum sediment concentration was relatively small. The conservation measures, especially the engineering measures, reduced the runoff velocity, extended the flood duration, and reduced the peak discharge, which sharply reduced the runoff erosion power37,38. As a consequence of the decrease in erosive energy, soil erosion was diminished.Table 1 Descriptive statistics of the characteristics of event-based flood flows and sediment in 1961–1990 (excluding 1970).Full size tableInfluence on intra-event-based flood regimesClassification of flood events and the characteristics of baseline period flood regimesFigure 2 shows the clustering results of the flood events at the Caoping hydrological station in 1961–1969. The flood events were divided into 4 regimes with a significance level of p  More

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    Assessing the predictability of existing water-to-enamel geolocation models against known human teeth

    1.Bartelink, E. J., Mackinnon, A. T., Prince-Buitenhuys, J. R., Tipple, B. J. & Chesson, L. A. Stable isotope forensics as an investigative tool in missing persons investigations BT. In Handbook of Missing Persons (eds Morewitz, S. J. & Sturdy Colls, C.) 443–462 (Springer, 2016).Chapter 

    Google Scholar 
    2.Ehleringer, J. R. et al. Hydrogen and oxygen isotope ratios in human hair are related to geography. Proc. Natl. Acad. Sci. USA 105, 2788–2793 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    3.Laffoon, J. E., Rojas, R. V. & Hofman, C. L. Oxygen and carbon isotope analysis of human dental enamel from the caribbean: Implications for investigating individual origins. Archaeometry 55, 742–765 (2013).CAS 
    Article 

    Google Scholar 
    4.Glick, P. L. Patterns of enamel maturation. J. Dent. Res. 58, 883–895 (1979).CAS 
    PubMed 
    Article 

    Google Scholar 
    5.Lacruz, R. S., Habelitz, S., Wright, J. T. & Paine, M. L. Dental enamel formation and implications for oral health and disease. Physiol. Rev. 97, 939–993 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Longinelli, A. Oxygen isotopes in mammal bone phosphate: A new tool for paleohydrological and paleoclimatological research?. Geochim. Cosmochim. Acta 48, 385–390 (1984).CAS 
    Article 
    ADS 

    Google Scholar 
    7.Luz, B., Kolodny, Y. & Horowitz, M. Fractionation of oxygen isotopes between mammalian bone-phosphate and environmental drinking water. Geochim. Cosmochim. Acta 48, 1689–1693 (1984).CAS 
    Article 
    ADS 

    Google Scholar 
    8.Levinson, A. A., Luz, B. & Kolodny, Y. Variations in oxygen isotopic compositions of human teeth and urinary stones. Appl. Geochemistry 2, 367–371 (1987).CAS 
    Article 

    Google Scholar 
    9.Dansgaard, W. Stable isotopes in precipitation. Tellus A 16, 436–468 (1964).Article 
    ADS 

    Google Scholar 
    10.Rozanski, K., Araguás-Araguás, L. & Gonfiantini, R. Isotopic patterns in modern global precipitation in Climate Change in Continental Isotopic Records 1–36 (American Geophysical Union, 1993). 11.Terzer, S., Wassenaar, L. I., Araguás-Araguás, L. J. & Aggarwal, P. K. Global isoscapes for δ18O and δ2H in precipitation: Improved prediction using regionalized climatic regression models. Hydrol. Earth Syst. Sci. Discuss. https://doi.org/10.5194/hessd-10-7351-2013 (2013).12.Bowen, G. J. Interpolating the isotopic composition of modern meteoric precipitation. Water Resour. Res. 39, 1–13 (2003).Article 
    CAS 

    Google Scholar 
    13.West, A. G., February, E. C. & Bowen, G. J. Spatial analysis of hydrogen and oxygen stable isotopes (“isoscapes”) in ground water and tap water across South Africa. J. Geochem. Explor. 145, 213–222 (2014).CAS 
    Article 

    Google Scholar 
    14.Ehleringer, J. R. et al. A Framework for the incorporation of isotopes and isoscapes in geospatial forensic investigations in Isoscapes SE-17 (eds. West, J. B., Bowen, G. J., Dawson, T. E. & Tu, K. P.) 357–387 (Springer, 2010).15.Laffoon, J. E. et al. Investigating human geographic origins using dual-isotope (87Sr/86Sr, δ18O) assignment approaches. PLoS ONE 12, e0172562 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    16.Daux, V. et al. Oxygen isotope fractionation between human phosphate and water revisited. J. Hum. Evol. 55, 1138–1147 (2008).PubMed 
    Article 

    Google Scholar 
    17.Dotsika, E. Correlation between δ18Ow and δ18Οen for estimating human mobility and paleomobility patterns. Sci. Rep. 10, 15439 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    18.Chenery, C., Müldner, G., Evans, J., Eckardt, H. & Lewis, M. Strontium and stable isotope evidence for diet and mobility in Roman Gloucester, UK. J. Archaeol. Sci. 37, 150–163 (2010).Article 

    Google Scholar 
    19.Herrmann, N., Li, Z.-H., Warner, M., Weinand, D. & Soto, M. Isotopic and elemental analysis of the William Bass donated skeletal collection and other modern donated collections. Dep. Justice Rep. 1, 248669 (2015).
    Google Scholar 
    20.Keller, A. T., Regan, L. A., Lundstrom, C. C. & Bower, N. W. Evaluation of the efficacy of spatiotemporal Pb isoscapes for provenancing of human remains. Forensic Sci. Int. 261, 83–92 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    21.Pollard, A. M., Pellegrini, M. & Lee-Thorp, J. A. Technical note: some observations on the conversion of dental enamel δ18O(p)values to δ18O(w)to determine human mobility. Am. J. Phys. Anthropol. 145, 499–504 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    22.Posey, R. Development and Validation of a Spatial Prediction Model for Forensic Geographical Provenancing of Human Remains (University of East Anglia, 2011).23.Warner, M. M., Plemons, A. M., Herrmann, N. P. & Regan, L. A. Refining stable oxygen and hydrogen isoscapes for the identification of human remains in Mississippi. J. Forensic Sci. https://doi.org/10.1111/1556-4029.13575 (2018).Article 
    PubMed 

    Google Scholar 
    24.Chenery, C. A., Pashley, V., Lamb, A. L., Sloane, H. J. & Evans, J. A. The oxygen isotope relationship between the phosphate and structural carbonate fractions of human bioapatite. Rapid Commun. Mass Spectrom. 26, 309–319 (2012).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    25.Bell, L. S., Lee-Thorp, J. A. & Elkerton, A. Sailing against the wind. J. Archaeol. Sci. 37, 683–686 (2010).Article 

    Google Scholar 
    26.Pellegrini, M., Pouncett, J., Jay, M., Pearson, M. P. & Richards, M. P. Tooth enamel oxygen “isoscapes’’ show a high degree of human mobility in prehistoric Britain. Sci. Rep. 6, 1–10 (2016).Article 
    CAS 

    Google Scholar 
    27.Podlesak, D. W., Bowen, G. J., O’Grady, S., Cerling, T. E. & Ehleringer, J. R. δ2H and δ18O of human body water: A GIS model to distinguish residents from non-residents in the contiguous USA. Isotopes Environ. Health Stud. https://doi.org/10.1080/10256016.2012.644283 (2012).Article 
    PubMed 

    Google Scholar 
    28.Bowen, G. J. & Wilkinson, B. Spatial distribution of δ18O in meteoric precipitation. Geology 30, 315–318 (2002).Article 
    ADS 

    Google Scholar 
    29.Lee-Thorp, J. Two decades of progress towards understanding fossilization processes and isotopic signals in calcified tissue minerals. Archaeometry 44, 435–446 (2002).CAS 
    Article 

    Google Scholar 
    30.Bryant, D., Koch, P. L., Froelich, P. N., Showers, W. J. & Genna, B. J. Oxygen isotope partitioning between phosphate and carbonate in mammalian apatite. Geochim. Cosmochim. Acta 60, 5145–5148 (1996).CAS 
    Article 
    ADS 

    Google Scholar 
    31.Iacumin, P., Bocherens, H., Mariotti, A. & Longinelli, A. Oxygen isotope analyses of co-existing carbonate and phosphate in biogenic apatite: A way to monitor diagenetic alteration of bone phosphate?. Earth Planet. Sci. Lett. 142, 1–6 (1996).CAS 
    Article 
    ADS 

    Google Scholar 
    32.Wright, L. E., Valdés, J. A., Burton, J. H., Douglas Price, T. & Schwarcz, H. P. The children of Kaminaljuyu: Isotopic insight into diet and long distance interaction in Mesoamerica. J. Anthropol. Archaeol. 29, 155–178 (2010).Article 

    Google Scholar 
    33.Chesson, L. A., Kenyhercz, M. W., Regan, L. A. & Berg, G. E. Addressing data comparability in the creation of combined data sets of bioapatite carbon and oxygen isotopic compositions. Archaeometry 61, 1193–1206 (2019).CAS 
    Article 

    Google Scholar 
    34.International Atomic Energy Agency/World Meteorological Organization. Global Network of Isotopes in Precipitation http://www.iaea.org/water (2020).35.Bowen, G. J. The Online Isotopes in Precipitation Calculator, Version 3.1  https://wateriso.utah.edu/waterisotopes/pages/data_access/oipc.html (2018).36.Tipple, B. J. et al. Stable hydrogen and oxygen isotopes of tap water reveal structure of the San Francisco Bay Area’s water system and adjustments during a major drought. Water Res. 119, 212–224 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    37.Wang, S. et al. Water source signatures in the spatial and seasonal isotope variation of chinese tap waters. Water Resour. Res. 54, 9131–9143 (2018).Article 
    ADS 

    Google Scholar 
    38.Ghassemi, F. & White, I. Inter-Basin Water Transfer: Case Studies from Australia, United States, Canada, China and India (Cambridge University Press, 2007).Book 

    Google Scholar 
    39.World Health Organization. Progress on Sanitation and Drinking Water: 2010 Update http://apps.who.int/iris/bitstream/10665/81245/1/9789241505390_eng.pdf (2013).40.Good, S. P. et al. Patterns of local and nonlocal water resource use across the western U.S. determined via stable isotope intercomparisons. Water Resour. Res. https://doi.org/10.1002/2012WR013085 (2014).Article 

    Google Scholar 
    41.Bowen, G. J., Ehleringer, J. R., Chesson, L. A., Stange, E. & Cerling, T. E. Stable isotope ratios of tap water in the contiguous United States. Water Resour. Res. 43, 1–12 (2007).Article 
    CAS 

    Google Scholar 
    42.Chesson, L. A. et al. Strontium isotopes in tap water from the coterminous USA. Ecosphere 3, 67 (2012).Article 

    Google Scholar 
    43.Ammer, S. T. M., Bartelink, E. J., Vollner, J. M., Anderson, B. E. & Cunha, E. M. Spatial distributions of oxygen stable isotope ratios in tap water from mexico for region of origin predictions of unidentified border crossers. J. Forensic Sci. 65, 1049–1055 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    44.Daux, V. et al. Oxygen and hydrogen isotopic composition of tap waters in France. Geol. Soc. Lond. Spec. Publ. 507, 207 (2021).
    Google Scholar 
    45.Gautam, M. K., Song, B. Y., Shin, W. J., Bong, Y. S. & Lee, K. S. Spatial variations in oxygen and hydrogen isotopes in waters and human hair across South Korea. Sci. Total Environ. 726, 138365 (2020).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    46.Zhao, S. et al. Divergence of stable isotopes in tap water across China. Sci. Rep. 7, 43653 (2017).PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    47.Ueda, M. & Bell, L. S. A city-wide investigation of the isotopic distribution and source of tap waters for forensic human geolocation ground-truthing. J. Forensic Sci. 62, 655–667 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    48.Jameel, Y. et al. Tap water isotope ratios reflect urban water system structure and dynamics across a semiarid metropolitan area. Water Resour. Res. 52, 5891–5910 (2016).CAS 
    Article 
    ADS 

    Google Scholar 
    49.Lee-Thorp, J., Manning, L. & Sponheimer, M. Problems and prospects for carbon isotope analysis of very small samples of fossil tooth enamel. Bull. Geol. Soc. Fr. 168, 767–773 (1997).CAS 

    Google Scholar 
    50.Connan, M. et al. Multidimensional stable isotope analysis illuminates resource partitioning in a sub-Antarctic island bird community. Ecography 42, 1948–1959 (2019).Article 

    Google Scholar 
    51.Coplen, T. B. Guidelines and recommended terms for expression of stable-isotope-ratio and gas-ratio measurement results. Rapid Commun. Mass Spectrom. 25, 2538–2560 (2011).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    52.Metro Vancouver. Water Treatment & Supply  http://www.metrovancouver.org/services/water/Pages/default.aspx (2020).53.International Atomic Energy Agency. International Atomic Energy Agency: RCWIP (Regionalized Cluster-Based Water Isotope Prediction) Model: Gridded precipitation δ18O|δ2H| δ18O and δ2H isoscape data http://www.iaea.org/water (2014).54.Gujarati, D. N. Linear regression: A mathematical introduction. Rapid Commun. Mass Spectrom. https://doi.org/10.4135/9781071802571 (2019).Article 

    Google Scholar 
    55.Coplen, T. B. Normalization of oxygen and hydrogen isotope data. Chem. Geol. Isot. Geosci. Sect. 72, 293–297 (1988).CAS 
    Article 

    Google Scholar 
    56.Kruskal, W. H. & Wallis, W. A. Use of ranks in one-criterion variance analysis. J. Am. Stat. Assoc. 47, 583–621 (1952).MATH 
    Article 

    Google Scholar 
    57.Shapiro, S. S. & Wilk, M. B. An analysis of variance test for normality (complete samples). Biometrika 52, 591–611 (1965).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    58.R Core Team. R: A Language and Environment for Statistical Computing (2020).59.Kobayashi, K. & Salam, M. U. Comparing simulated and measured values using mean squared deviation and its components. Agron. J. 92, 345–352 (2000).Article 

    Google Scholar 
    60.Gauch, H. G., Hwang, J. T. G. & Fick, G. W. Model evaluation by comparison of model-based predictions and measured values. Agron. J. 95, 1442–1446 (2003).Article 

    Google Scholar 
    61.Metro Vancouver. Metro Vancouver Growth Projections: A Backgrounder http://www.metrovancouver.org/services/regional-planning/PlanningPublications/OverviewofMetroVancouversMethodsinProjectingRegionalGrowth.pdf (2018).62.City of Kelowna. City of Kelowna Water http://www.kelowna.ca/cm/page393.aspx (2009).63.City of Prince George. Water and Watersheds  https://www.princegeorge.ca/CityServices/Pages/Environment/WaterAndWatersheds.aspx (2017).64.City of Winnipeg. Water and Waste Department http://www.winnipeg.ca/waterandwaste/water/default.stm (2017).65.City of Toronto. Drinking Water http://www1.toronto.ca/wps/portal/contentonly?vgnextoid=e73cfe4eda8ae310VgnVCM10000071d60f89RCRD (2017).66.Jacklin, J. Assessment of Vanderhoof South Drinking Water Supply: Source Water Characteristics https://www2.gov.bc.ca/assets/gov/environment/air-land-water/water/waterquality/water-quality-reference-documents/dwa-vanderhoof_south.pdf (2005).67.Ministère du Développement durable de l’Environnement et de la Lutte contre les changements climatiques. Summary Profile of the Rivière des Outaouais Watershed http://www.environnement.gouv.qc.ca/eau/bassinversant/bassins/outaouais/portrait-sommaire-en.pdf (2015).68.Municipalité de L’Isle-aux-Allumettes. Municipality of L’Isle-Aux-Allumettes http://www.isle-aux-allumettes.com/index-en.php (2012).69.Mant, M., Nagel, A. & Prowse, T. investigating residential history using stable hydrogen and oxygen isotopes of human hair and drinking water. J. Forensic Sci. 61, 884–891 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    70.Koehler, G. & Hobson, K. A. Tracking cats revisited: Placing terrestrial mammalian carnivores on δ2H and δ18O isoscapes. PLoS ONE 14, e0221876 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    71.Wassenaar, L. I., Athanasopoulos, P. & Hendry, M. J. Isotope hydrology of precipitation, surface and ground waters in the Okanagan Valley, British Columbia, Canada. J. Hydrol. 411, 37–48 (2011).CAS 
    Article 
    ADS 

    Google Scholar 
    72.Cameron, E. M., Hall, G. E. M., Veizer, J. & Krouse, H. R. Isotopic and elemental hydrogeochemistry of a major river system: Fraser River, British Columbia, Canada. Chem. Geol. 122, 149–169 (1995).CAS 
    Article 
    ADS 

    Google Scholar 
    73.Waterisotope Database. http://waterisotopesDB.org (2019).74.Mostapa, R., Ishak, A. K., Mohamad, K. & Demana, R. Identification of bottled zam zam water in Malaysian market using hydrogen and oxygen stable isotope ratios(d2H and d18O). J. Nucl. Relat. Technol. 11, 48–53 (2014).
    Google Scholar 
    75.Thompson, A. H. et al. Stable isotope analysis of modern human hair collected from Asia (China, India, Mongolia, and Pakistan). Am. J. Phys. Anthropol. https://doi.org/10.1002/ajpa.21162 (2010).Article 
    PubMed 

    Google Scholar 
    76.Katebe, R., Musukwa, G., Mweetwa, B., Shaba, P. & Njovu, E. Assessment of Uranium in Drinking Water in Kitwe, Chambeshi and Chingola in the Copperbelt Region of Zambia (IAEA, 2015).77.Zurbrügg, R., Wamulume, J., Kamanga, R., Wehrli, B. & Senn, D. B. River-floodplain exchange and its effects on the fluvial oxygen regime in a large tropical river system (Kafue Flats, Zambia). J. Geophys. Res. Biogeosci. 117, 1–10 (2012).Article 
    CAS 

    Google Scholar 
    78.The Government of the Hong Kong Special Administrative Region. Water Supplies Department https://www.wsd.gov.hk/en/publications-and-statistics/pr-publications/the-facts/index.html (2019).79.Demény, A., Gugora, A. D., Kesjár, D., Lécuyer, C. & Fourel, F. Stable isotope analyses of the carbonate component of bones and teeth: The need for method standardization. J. Archaeol. Sci. 109, 104979 (2019).Article 
    CAS 

    Google Scholar 
    80.Wunder, M. B. Using Isoscapes to Model probability surfaces for determining geographic origins BT: Isoscapes: Understanding movement, pattern, and process on Earth through isotope mapping in (eds. West, J. B., Bowen, G. J., Dawson, T. E. & Tu, K. P.) 251–270 (Springer, 2010).81.Graul, C. leafletR: Interactive Web-Maps Based on the Leaflet JavaScript Library (2016).82.Pye, K. Isotope and trace element analysis of human teeth and bones for forensic purposes. Geol. Soc. Lond. Spec. Publ. 232, 215–236 (2004).CAS 
    Article 
    ADS 

    Google Scholar  More

  • in

    MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology

    1.Sohn, H. B. et al. Barcode system for genetic identification of soybean [Glycine max (L.) Merrill] cultivars using InDel markers specific to dense variation blocks. Front. Plant Sci. 8, 520 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Korir, N. K. et al. Plant variety and cultivar identification: advances and prospects. Crit. Rev. Biotechnol. 33, 111–125 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.Jamali, S. et al. Identification and distinction of soybean commercial cultivars using morphological and microsatellite markers., Iranian. J. Crop Sci. 13, 131–145 (2011).
    Google Scholar 
    4.Wu, K. et al. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers. BMC Genet. 15, 35 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    5.Lee, S. H. et al. How deep learning extracts and learns leaf features for plant classification. Pattern Recognit. 71, 1–13 (2017).Article 

    Google Scholar 
    6.Zhao, C., Chan, S. S. F., Cham, W.-K. & Chu, L. M. Plant identification using leaf shapes: a pattern counting approach. Pattern Recognit. 48, 3203–3215 (2015).Article 

    Google Scholar 
    7.Price, C. A. et al. Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles. Plant Physiol. 155, 236–245 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.De Vylder, J., Vandenbussche, F. & Hu, Y. et al. Rosette tracker: an open source image analysis tool for automatic quantification of genotype effects[J]. Plant physiology 160, 1149–1159 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Zhou, J. et al. Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat. Plant Methods 13, 117 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    10.Biot, E. et al. Multi-scale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development 143, 3417–3428 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    11.Minervini, M. et al. Phenotiki: an open software and hardware platform for affordable and easy image-based phenotyping of rosette-shaped plants. Plant J. 90, 204–216 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Neto, J. C. et al. Plant species identification using Elliptic Fourier leaf shape analysis. Computers Electron. Agriculture 50, 121–134 (2006).Article 

    Google Scholar 
    13.Cope, J. S. et al. in International Symposium on Visual Computing (eds Bebis, G. et al.) 669–677 (Springer, 2010).14.Chaki, J. & Parekh, R. Plant leaf recognition using shape based features and neural network classifiers, Int. J. Adv. Comp. Sci. Appl. 2, 41–47 (2011).15.Naresh, Y. & Nagendraswamy, H. Classification of medicinal plants: an approach using modified LBP with symbolic representation. Neurocomputing 173, 1789–1797 (2016).Article 

    Google Scholar 
    16.Pradeep Kumar, T., Veera Prasad Reddy, M. & Bora, P. K. Leaf identification using shape and texture features. Proceedings of International Conference on Computer Vision and Image Processing (eds Raman B., Kumar S., Roy P. P., Sen D.) 531–541 (Springer Singapore, 2017).17.Tharwat, A., Gaber, T., Awad, Y. M., Dey, N. & Hassanien, A. E. Plants identification using feature fusion technique and bagging classifier. (eds Gaber T., Hassanien A. E., El-Bendary N., Dey N.). The 1st International Conference on Advanced Intelligent System and Informatics (AISI2015), November 28–30, 2015, Beni Suef, Egypt. 461–471 (Springer International Publishing, 2016).18.Codizar, A. L. & Solano, G. Plant leaf recognition by venation and shape using artificial neural networks. In: 2016 7th International Conference on Information,Intelligence, Systems & Applications (IISA). 1–4 (IEEE, 2016).19.Yang, C. Plant leaf recognition by integrating shape and texture features. Pattern Recognit. 112, 107809 (2021).Article 

    Google Scholar 
    20.Liu, C. et al. A novel identification method for apple (Malus domestica Borkh.) cultivars based on a deep convolutional neural network with leaf image input. Symmetry 12, 217 (2020).Article 

    Google Scholar 
    21.Baldi, A. et al. A leaf-based back propagation neural network for oleander (Nerium oleander L.) cultivar identification. Computers Electron. Agriculture 142, 515–520 (2017).Article 

    Google Scholar 
    22.X. Yu, et al. Patchy image structure classification using multi-orientation region transform. in Proceedings of the AAAI Conference on Artificial Intelligence. 12741–12748 (AAAI, 2020).23.Edelsbrunner, H & Harer, J. in Persistent Homology—a Survey (eds Goodman, J. E., Pach, J., Pollack, R.). 257–282 (Contemporary Mathematics American Mathematical Society, 2008).24.Li, M. et al. Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Front. Plant Sci. 9, 553 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    25.Reininghaus, J. et al. A stable multi-scale kernel for topological machine learning, in: 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 4741–4748 (IEEE, Boston, MA, USA, 2015).26.Li, C., Ovsjanikov, M. & Chazal, F. Persistence-based structural recognition. in Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 1995–2002 (IEEE Computer Society, 2014).27.Dey, T., Mandal, S. & Varcho, W. Improved image classification using topological persistence. in Proceedings of the Conference on Vision, Modeling and Visualization. 161–168 (Eurographics Association, 2017).28.MacLane, S. Homology. Bull. Am. Math. Soc. 70, 329–331 (1964).Article 

    Google Scholar 
    29.Qaiser, T. et al. Tumor segmentation in whole slide images using persistent homology and deep convolutional features. in Annual Conference on Medical Image Understanding and Analysis. 320–329 (Springer, 2017).30.Qaiser, T. et al. Fast and accurate tumor segmentation of histology images using persistent homology and deep convolutional features. Med. Image Anal. 55, 1–14 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Zeppelzauer, M. et al. A study on topological descriptors for the analysis of 3d surface texture. Computer Vis. Image Underst. 167, 74–88 (2018).Article 

    Google Scholar 
    32.Chollet, F. Xception: Deep learning with depthwise separable convolutions. in Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 1251–1258 (IEEE Computer Society, 2017).33.Hofer, C. et al. Deep learning with topological signatures. In: Advances in Neural Information Processing Systems. 1634–1644 (Curran Associates Inc., 2017).34.Turner, K., Mukherjee, S. & Boyer, D. M. Persistent homology transform for modeling shapes and surfaces. Inf. Inference.: A J. IMA 3, 310–344 (2014).Article 

    Google Scholar 
    35.Deng, J. et al. Imagenet: a large-scale hierarchical image database. in 2009 IEEE Conference on Computer Vision and Pattern Recognition. 248–255 (IEEE, 2009).36.Adams, H. et al. Persistence images: A stable vector representation of persistent homology. J. Mach. Learn. Res. 18, 218–252 (2017).
    Google Scholar 
    37.Bubenik, P. Statistical topological data analysis using persistence landscapes. J. Mach. Learn. Res. 16, 77–102 (2015).
    Google Scholar 
    38.Wang, B. et al. From species to cultivar: Soybean cultivar recognition using joint leaf image patterns by multi-scale sliding chord matching. Biosyst. Eng. 194, 99–111 (2020).Article 

    Google Scholar 
    39.Heiberger, R. M., & Neuwirth E. One-way ANOVA. In: R through Excel. 165–191 (Springer, 2009).40.Ling, H. & Jacobs, D. W. Shape classification using the inner-distance. IEEE Trans. Pattern Anal. Mach. Intell. 29, 286–299 (2007).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    41.Wang, B. & Gao, Y. Hierarchical string cuts: a translation, rotation, scale, and mirror invariant descriptor for fast shape retrieval. IEEE Trans. Image Process 23, 4101–4111 (2014).42.Kaya, A. et al. Analysis of transfer learning for deep neural network-based plant classification models. Computers Electron. Agriculture 158, 20–29 (2019).Article 

    Google Scholar 
    43.Yanping, Z. & Liu, W. WeizhenLiuBioinform/mfcis: source code of mfcis. (Version 1.0.2). Zenodo https://doi.org/10.5281/zenodo.4739746 (2021).44.Barré, P. et al. LeafNet: a computer vision system for automatic plant species identification. Ecol. Inform. 40, 50–56 (2017).Article 

    Google Scholar 
    45.Beghin, T. et al. Shape and texture-based plant leaf classification. in International Conference on Advanced Concepts for Intelligent Vision Systems, 345–353 (Springer, 2010).46.Blonder, B. et al. X-ray imaging of leaf venation networks. N. Phytologist 196, 1274–1282 (2012).Article 

    Google Scholar 
    47.Gan, Y. et al. Automatic hierarchy classification in venation networks using directional morphological filtering for hierarchical structure traits extraction. Computational Biol. Chem. 80, 187–194 (2019).CAS 
    Article 

    Google Scholar 
    48.Cui, F. & Yang, G. Score level fusion of fingerprint and finger vein recognition. J. Computational Inf. Syst. 7, 5723–5731 (2011).
    Google Scholar 
    49.Park, H.-A. & Park, K. R. Iris recognition based on score level fusion by using SVM. Pattern Recognit. Lett. 28, 2019–2028 (2007).Article 

    Google Scholar 
    50.Ghosh, S. et al. Software for systems biology: from tools to integrated platforms. Nat. Rev. Genet. 12, 821–832 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    51.Smulders, M., Booy, I. & Vosman, B. Use of molecular and biochemical methods for identification of plant varieties throughout the agri-chain. (eds Trienekens, J. H. & Zuurbier, P. J. P.) In Proceedings of the 2nd International Conference on Chain Management in Agri-and Food Business. 591–600 (Department of Management studies Wageningen Agricultural University, May 1996).52.Park, H. et al. Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs. J. Plant Biotechnol. 47, 124–130 (2020).Article 

    Google Scholar 
    53.Fufa, H. et al. Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars. Euphytica 145, 133–146 (2005).CAS 
    Article 

    Google Scholar 
    54.Kim, M. et al. Genome-wide SNP discovery and core marker sets for DNA barcoding and variety identification in commercial tomato cultivars. Sci. Horticulturae 276, 109734 (2021).CAS 
    Article 

    Google Scholar 
    55.Patzak, J., Henychová, A., Paprštein, F. & Sedlák, J. Evaluation of S-incompatibility locus, genetic diversity and structure of sweet cherry (Prunus avium L.) genetic resources by molecular methods and phenotypic characteristics. J. Horticultural Sci. Biotechnol. 95, 84–92 (2020).CAS 
    Article 

    Google Scholar 
    56.Pourkhaloee, A. et al. Molecular analysis of genetic diversity, population structure, and phylogeny of wild and cultivated tulips (Tulipa L.) by genic microsatellites. Horticulture Environ. Biotechnol. 59, 875–888 (2018).CAS 
    Article 

    Google Scholar 
    57.Cho, K. H. et al. Sequence-characterized amplified region markers and multiplex-polymerase chain reaction assays for kiwifruit cultivar identification. Horticulture Environ., Biotechnol. 61, 395–406 (2020).CAS 
    Article 

    Google Scholar 
    58.Agarwal, M., Shrivastava, N. & Padh, H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27, 617–631 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    59.Nadeem, M. A. et al. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnological Equip. 32, 261–285 (2018).CAS 
    Article 

    Google Scholar 
    60.Yamaç, S. S. & Todorovic, M. Estimation of daily potato crop evapotranspiration using three different machine learning algorithms and four scenarios of available meteorological data. Agric. Water Manag. 228, 105875 (2020).Article 

    Google Scholar 
    61.Reisi Gahrouei, O., McNairn, H., Hosseini, M. & Homayouni, S. Estimation of crop biomass and leaf area index from multitemporal and multispectral imagery using machine learning approaches. Can. J. Remote Sens. 46, 84–99 (2020).Article 

    Google Scholar 
    62.Colmer, J. et al. SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination. N. Phytologist 228, 778–793 (2020).CAS 
    Article 

    Google Scholar 
    63.Danner, M., Berger, K., Wocher, M., Mauser, W. & Hank, T. Efficient RTM-based training of machine learning regression algorithms to quantify biophysical & biochemical traits of agricultural crops. ISPRS J. Photogramm. Remote Sens. 173, 278–296 (2021).Article 

    Google Scholar 
    64.Zeiler, M. D. & Fergus R. in Visualizing and Understanding Convolutional Networks (eds Fleet D., Pajdla T., Schiele B., Tuytelaars T.). Computer Vision–ECCV 2014. 818–833 (Springer International Publishing, 2014).65.Erhan, D., Bengio, Y., Courville, A. & Vincent, P. Visualizing higher-layer features of a deep network. Univ. Montr. 1341, 1 (2009).
    Google Scholar 
    66.Simonyan, K., Vedaldi, A. & Zisserman, A. Deep inside convolutional networks: Visualising image classification models and saliency maps[C]//InWorkshop at International Conference on Learning Representations. (2014).67.Islam, M. R. Feature and score fusion based multiple classifier selection for iris recognition. Computational Intell. Neurosci. 2014, e380585 (2014).Article 

    Google Scholar 
    68.Yang, J. et al. Feature fusion: parallel strategy vs. serial strategy. Pattern Recognit. 36, 1369–1381 (2003).Article 

    Google Scholar 
    69.Bryson, A. E. et al. Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves. Preprint at bioRxiv https://doi.org/10.1101/2020.06.22.163899 (2020). More

  • in

    Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor

    1.Heil M, Karban R. Explaining evolution of plant communication by airborne signals. Trends Ecol Evol. 2010;25:137–44.Article 

    Google Scholar 
    2.Rubin IN, Ellner SP, Kessler A, Morrell KA. Informed herbivore movement and interplant communication determine the effects of induced resistance in an individual-based model. J Anim Ecol. 2015;84:1273–85.Article 

    Google Scholar 
    3.Kalske A, Shiojiri K, Uesugi A, Sakata Y, Morrell K, Kessler A. Insect herbivory selects for volatile-mediated plant-plant communication. Curr Biol. 2019;29:3128–33.CAS 
    Article 

    Google Scholar 
    4.Frisen ML, Porter SS, Stark SC, von Wettberg EJ, Sachs JL, Martinez-Romero E. Microbially mediated plant functional traits. Ann Rev Ecol Evol Syst. 2011;42:23–46.Article 

    Google Scholar 
    5.Lebeis SL, Herrera Paredes S, Lundberg DS, Breakfield N, Gehrin J, McDonald M, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015;349:860–4.CAS 
    Article 

    Google Scholar 
    6.Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, et al. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12:1496–507.CAS 
    Article 

    Google Scholar 
    7.Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Van Wees SCM, Bakker PAHM. Induced systemic resistance by beneficial microbes. Ann Rev Phytopathol. 2014;52:347–75.CAS 
    Article 

    Google Scholar 
    8.Frank L, Wenig M, Ghirardo A, van der Krol A, Vlot AC, Schnitzler J-P, et al. Isoprene and β-caryophyllene confer plant resistance via different plant internal signaling pathways. Plant Cell Environ. 2021;44:1151–64.CAS 
    Article 

    Google Scholar 
    9.Kong HG, Song GC, Sim H-J, Ryu C-M. Achieving similar root microbiota composition in neighbouring plants through airborne signalling. ISME J. 2021;15:397–408.CAS 
    Article 

    Google Scholar 
    10.Dicke M, Bruin J. Chemical information transfer between plants: back to the future. Biochem Syst Ecol. 2001;29:981–94.CAS 
    Article 

    Google Scholar 
    11.Peacher MD, Meiners SJ. Inoculum handling alters the strength and direction of plant-microbe interactions. Ecology. 2020;4:e02994.
    Google Scholar 
    12.Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM. Hormonal modulation of plant immunity. Ann Rev Cell Dev Biol. 2012;28:489–521.CAS 
    Article 

    Google Scholar 
    13.Erb M. Volatiles as inducers and suppressors of plant defense and immunity—origins, specificity, perception, and signalling. Curr Opin Plant Biol. 2018;44:117–21.CAS 
    Article 

    Google Scholar 
    14.Nagashima A, Higaki T, Koeduka T, Ishigami K, Hosokawa S, Watanabe H, et al. Transcriptional regulators involved in responses to volatile organic compounds in plants. J Biol Chem. 2019;294:2256–66.CAS 
    Article 

    Google Scholar 
    15.Khorassani R, Hettwer U, Ratzinger A, Steingrobe B, Karlovsky P, Claassen N. Citramalic acid and salicylic acid in sugar beet root exudates solubilize soil phosphorus. BMC Plant Biol. 2011;11:21.Article 

    Google Scholar 
    16.Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci. 2018;115:E1157–65.CAS 
    Article 

    Google Scholar 
    17.Crawford KM, Bauer JT, Comita LS, Eppinga MB, Johnson DJ, Mangan SA, et al. When and where plant-soil feedback may promote plant coexistence: a meta-analysis. Ecol Lett. 2019;22:1274–84.Article 

    Google Scholar 
    18.Tidbury HJ, Best A, Boots M. The epidemiological consequences of immune priming. Proc R Soc B: Biol Sci. 2015;279:4505–12.Article 

    Google Scholar 
    19.Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Natural soil microbiomes alter flowering phenology and the intensity of selection of flowering time in a wild Arabidopsis relative. Ecol Lett. 2014;17:717–26.Article 

    Google Scholar 
    20.Petipas RH, Geber MA, Lau JA. Microbe-mediated adaptation in plants. Ecol Lett. 2021;24:1302–17. More

  • in

    Lytic archaeal viruses infect abundant primary producers in Earth’s crust

    1.Flemming, H. C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    2.Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).CAS 
    Article 
    ADS 

    Google Scholar 
    3.Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    4.Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    5.Castelle, C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    6.Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    7.Probst, A. J. et al. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat. Commun. 5, 5497 (2014).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    8.Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    9.Weinbauer, M. G. & Rassoulzadegan, F. Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6, 1–11 (2004).PubMed 
    Article 

    Google Scholar 
    10.Engelhardt, T., Kallmeyer, J., Cypionka, H. & Engelen, B. High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments. ISME J. 8, 1503–1509 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    11.Danovaro, R. et al. Virus-mediated archaeal hecatomb in the deep seafloor. Sci. Adv. 2, e1600492 (2016).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    12.Kyle, J. E., Eydal, H. S., Ferris, F. G. & Pedersen, K. Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden. ISME J. 2, 571–574 (2008).PubMed 
    Article 

    Google Scholar 
    13.Labonté, J. M. et al. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front. Microbiol. 6, 349 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    14.Hylling, O. et al. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci. Rep. 10, 11879 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    15.Daly, R. A. et al. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat. Microbiol. 4, 352–361 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    16.Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167–170 (2010).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    17.Pauly, M. D., Bautista, M. A., Black, J. A. & Whitaker, R. J. Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 374, 20180093 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    18.Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3, 328–336 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Henneberger, R., Moissl, C., Amann, T., Rudolph, C. & Huber, R. New insights into the lifestyle of the cold-loving SM1 euryarchaeon: natural growth as a monospecies biofilm in the subsurface. Appl. Environ. Microbiol. 72, 192–199 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    20.Probst, A. J. et al. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. ISME J. 7, 635–651 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    21.Bird, J. T., Baker, B. J., Probst, A. J., Podar, M. & Lloyd, K. G. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Front. Microbiol. 7, 1221 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Hernsdorf, A. W. et al. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J. 11, 1915–1929 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Moissl, C., Rachel, R., Briegel, A., Engelhardt, H. & Huber, R. The unique structure of archaeal ‘hami’, highly complex cell appendages with nano-grappling hooks. Mol. Microbiol. 56, 361–370 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    24.Rudolph, C., Wanner, G. & Huber, R. Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology. Appl. Environ. Microbiol. 67, 2336–2344 (2001).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    25.Rudolph, C., Moissl, C., Henneberger, R. & Huber, R. Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springs. FEMS Microbiol. Ecol. 50, 1–11 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    26.Schwank, K. et al. An archaeal symbiont-host association from the deep terrestrial subsurface. ISME J. 13, 2135–2139 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    27.Probst, A. J. & Moissl-Eichinger, C. “Altiarchaeales”: uncultivated archaea from the subsurface. Life 5, 1381–1395 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    28.Makarova, K. S. et al. Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles 18, 877–893 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    29.Vik, D. R. et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ 5, e3428 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    30.Anderson, R. E., Brazelton, W. J. & Baross, J. A. The deep viriosphere: assessing the viral impact on microbial community dynamics in the deep subsurface. Carbon Earth 75, 649–675 (2013).CAS 
    Article 

    Google Scholar 
    31.Rodrigues, R. A. L. et al. An anthropocentric view of the virosphere-host relationship. Front. Microbiol. 8, 1673 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    32.Munson-McGee, J. H., Snyder, J. C. & Young, M. J. Archaeal viruses from high-temperature environments. Genes 9, 128 (2018).PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 
    33.Paez-Espino, D. et al. Uncovering Earth’s virome. Nature 536, 425–430 (2016).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    34.Philosof, A. et al. Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota. Curr. Biol. 27, 1362–1368 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Ahlgren, N. A., Fuchsman, C. A., Rocap, G. & Fuhrman, J. A. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J. 13, 618–631 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    36.Gudbergsdottir, S. R., Menzel, P., Krogh, A., Young, M. & Peng, X. Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. Environ. Microbiol. 18, 863–874 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    37.Munson-McGee, J. H., Rooney, C. & Young, M. J. An uncultivated virus infecting a nanoarchaeal parasite in the hot springs of Yellowstone National Park. J. Virol. 94, e01213-19 (2020).38.Zablocki, O., van Zyl, L. J., Kirby, B. & Trindade, M. Diversity of dsDNA viruses in a South African hot spring assessed by metagenomics and microscopy. Viruses 9, 348 (2017).PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 
    39.Emerson, J. B. et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat. Microbiol. 3, 870–880 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    40.Trubl, G. et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems 3, 338103 (2018).Article 

    Google Scholar 
    41.Hochstein, R. A., Amenabar, M. J., Munson-McGee, J. H., Boyd, E. S. & Young, M. J. Acidianus tailed spindle virus: a new archaeal large tailed spindle virus discovered by culture-independent methods. J. Virol. 90, 3458–3468 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Jahn, M. T. et al. Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. ISME J. 15, 1–11 (2021).43.Anderson, R. E., Brazelton, W. J. & Baross, J. A. Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front. Microbiol. 2, 219 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Chen, I. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    45.Bornemann, T. L. V. et al. Geological degassing enhances microbial metabolism in the continental subsurface. https://doi.org/10.1101/2020.03.07.980714 (2020).46.Sharrar, A. M. et al. Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron Basin. Front. Microbiol. 8, 791 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    47.Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M. B. VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    48.Kieft, K. et al. Virus-associated organosulfur metabolism in human and environmental systems. Cell Reports, in press (2021).49.Allers, E. et al. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environ. Microbiol. 15, 2306–2318 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    50.Roux, S. et al. Minimum information about an uncultivated virus genome (MIUViG). Nat. Biotechnol. 37, 29–37 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    51.Breitbart, M. & Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    52.Short, C. M. & Suttle, C. A. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl. Environ. Microbiol. 71, 480–486 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    53.Bautista, M. A., Black, J. A., Youngblut, N. D. & Whitaker, R. J. Differentiation and structure in Sulfolobus islandicus rod-shaped virus populations. Viruses 9, 120 (2017).PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 
    54.Held, N. L. & Whitaker, R. J. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ. Microbiol. 11, 457–466 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    55.Baquero, D. P. et al. New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities. ISME J. 14, 1821–1833 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Molnár, J. et al. Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLoS ONE 15, e0231864 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    57.Prangishvili, D., Garrett, R. A. & Koonin, E. V. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 117, 52–67 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    58.Deng, L., Garrett, R. A., Shah, S. A., Peng, X. & She, Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088–1099 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    59.Silas, S. et al. Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. Elife 6, e27601 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Guo, T., Han, W. & She, Q. Tolerance of Sulfolobus SMV1 virus to the immunity of IA and III-B CRISPR-Cas systems in Sulfolobus islandicus. RNA Biol. 16, 549–556 (2019).PubMed 
    Article 

    Google Scholar 
    61.Athukoralage, J. S. et al. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 577, 572–575 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    62.Bhoobalan-Chitty, Y., Johansen, T. B., Di Cianni, N. & Peng, X. Inhibition of type III CRISPR-Cas immunity by an archaeal virus-encoded anti-CRISPR protein. Cell 179, 448–458 e411 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    63.Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microbiol. Ecol. 13, 19–27 (1997).Article 

    Google Scholar 
    64.Wilhelm, S. W. & Suttle, C. A. Viruses and nutrient cycles in the sea—viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49, 781–788 (1999).Article 

    Google Scholar 
    65.Probst, A. J. et al. Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME J. 14, 1547–1560 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Dong, X. et al. Fermentative spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME J. 12, 2039–2050 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Vidakovic, L., Singh, P. K., Hartmann, R., Nadell, C. D. & Drescher, K. Dynamic biofilm architecture confers individual and collective mechanisms of viral protection. Nat. Microbiol. 3, 26–31 (2018).CAS 
    PubMed 
    Article 

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

    Google Scholar 
    69.Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    70.Probst, A. J. et al. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species. PLoS ONE 9, e99801 (2014).71.John, S. G. et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ. Microbiol. Rep. 3, 195–202 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    72.Joshi, N. & Fass, J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle (2011).73.Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

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

    Google Scholar 
    75.Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282–1288 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    76.Bornemann, T. L. V., Esser, S. P., Stach, T. L., Burg, T. & Probst, A.J. uBin—a manual refining tool for metagenomic bins designed for educational purposes. https://doi.org/10.1101/2020.07.15.204776 (2020).77.Couvin, D. et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 46, W246–W251 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Medvedeva, S. et al. Virus-borne mini-CRISPR arrays are involved in interviral conflicts. Nat. Commun. 10, 5204 (2019).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    79.Iranzo, J., Faure, G., Wolf, Y. I. & Koonin, E. V. Game-theoretical modeling of interviral conflicts mediated by mini-CRISPR arrays. Front. Microbiol. 11, 381 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    80.Denman, R. B. Using Rnafold to predict the activity of small catalytic RNAs. Biotechniques 15, 1090-& (1993).
    Google Scholar 
    81.Lange, S. J., Alkhnbashi, O. S., Rose, D., Will, S. & Backofen, R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 41, 8034–8044 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    82.Moller, A. G. & Liang, C. MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ 5, e3788 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    83.Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    84.Bischoff, V. et al. Cobaviruses—a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J. 13, 1404–1421 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    85.Boratyn, G. M. et al. Domain enhanced lookup time accelerated BLAST. Biol. Direct 7, 12 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    86.Grazziotin, A. L., Koonin, E. V. & Kristensen, D. M. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45, D491–D498 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    87.Remmert, M., Biegert, A., Hauser, A. & Söding, J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173–175 (2011).PubMed 
    Article 
    CAS 

    Google Scholar 
    88.Marz, M. et al. Challenges in RNA virus bioinformatics. Bioinformatics 30, 1793–1799 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    89.Finn, R. D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 45, D190–D199 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    90.Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    91.Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    92.Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    93.Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, W200–W204 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    94.Meier-Kolthoff, J. P. & Göker, M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 33, 3396–3404 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    95.Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 14, 60 (2013).Article 

    Google Scholar 
    96.Göker, M., Garcia-Blazquez, G., Voglmayr, H., Telleria, M. T. & Martin, M. P. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS ONE 4, e6319 (2009).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    97.Bin Jang, H. et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632–639 (2019).Article 
    CAS 

    Google Scholar 
    98.Bolduc, B. et al. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect archaea and bacteria. PeerJ 5, e3243 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    99.Brister, J. R., Ako-Adjei, D., Bao, Y. & Blinkova, O. NCBI viral genomes resource. Nucleic Acids Res. 43, D571–D577 (2015).CAS 
    Article 

    Google Scholar 
    100.Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    101.Moraru, C., Varsani, A. & Kropinski, A. M. VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12, 1268 (2020).102.Guy, L., Kultima, J. R. & Andersson, S. G. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334–2335 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    103.Team RC. R: a language and environment for statistical computing. (R Foundation for Statistical Computing, 2019). https://www.R-project.org/.104.Papadopoulos, J. S. & Agarwala, R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23, 1073–1079 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    105.Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113 (2004).Article 
    CAS 

    Google Scholar 
    106.Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    107.Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    108.Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    109.Rambaut, A. FigTree, a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. http://tree.bio.ed.ac.uk/software/figtree/ (2006).110.Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    111.Barrero-Canosa, J. & Moraru, C. Linking microbes to their genes at single cell level with direct-geneFISH. In: An Overview of FISH Concepts and Protocols for Microbial Cells (eds Almeida, C. & Azevedo, N.). (Springer Nature, 2020).112.Barrero-Canosa, J., Moraru, C., Zeugner, L., Fuchs, B. M. & Amann, R. Direct-geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms. Environ. Microbiol. 19, 70–82 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    113.Perras, A. K. et al. S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Front. Microbiol. 6, 543 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    114.Wallner, G., Amann, R. & Beisker, W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14, 136–143 (1993).CAS 
    PubMed 
    Article 

    Google Scholar 
    115.Moissl, C., Rudolph, C., Rachel, R., Koch, M. & Huber, R. In situ growth of the novel SM1 euryarchaeon from a string-of-pearls-like microbial community in its cold biotope, its physical separation and insights into its structure and physiology. Arch. Microbiol. 180, 211–217 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    116.Flechsler, J. et al. 2D and 3D immunogold localization on (epoxy) ultrathin sections with and without osmium tetroxide. Microsc. Res. Tech. 83, 691–705 (2020).117.Schlitzer, R. Data Analysis and Visualization with Ocean Data View, CMOS Bulletin SCMO. 43, 9–13 (2015). More