Philippa Kaur

von Wintersdorff, C. J. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).
Google Scholar 
Suay-García, B. & Pérez-Gracia, M. T. Present and future of carbapenem-resistant Enterobacteriaceae (CRE) infections. Antibiotics 8, 122 (2019).PubMed Central 
Article 
CAS 

Google Scholar 
Blair, J. M., Webber, M. A., Baylay, A. J., Ogbolu, D. O. & Piddock, L. J. Molecular mechanisms of antibiotic resistance. Nat. Rev. Microbiol. 13, 42–51 (2015).CAS 
PubMed 
Article 

Google Scholar 
Codjoe, F. S. & Donkor, E. S. Carbapenem resistance: a review. Med Sci. 6, 1 (2017).
Google Scholar 
Schechner, V. et al. Asymptomatic rectal carriage of blaKPC producing carbapenem-resistant Enterobacteriaceae: who is prone to become clinically infected? Clin. Microbiol. Infect. 19, 451–456 (2013).CAS 
PubMed 
Article 

Google Scholar 
Penders, J., Stobberingh, E. E., Savelkoul, P. H. & Wolffs, P. F. The human microbiome as a reservoir of antimicrobial resistance. Front Microbiol. 4, 87 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Nordmann, P., Naas, T. & Poirel, L. Global spread of Carbapenemase-producing Enterobacteriaceae. Emerg. Infect. Dis. 17, 1791–1798 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tooke, C. L. et al. β-Lactamases and β-lactamase inhibitors in the 21st century. J. Mol. Biol. 431, 3472–3500 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sun, X. et al. Microbiota-derived metabolic factors reduce campylobacteriosis in mice. Gastroenterology 154, 1751–1763.e2 (2018).CAS 
PubMed 
Article 

Google Scholar 
Ichinohe, T. et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl Acad. Sci. USA 108, 5354–5359 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).CAS 
PubMed 
Article 

Google Scholar 
Lieberman, T. D. et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat. Genet. 43, 1275–1280 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Chu, N. D., Smith, M. B., Perrotta, A. R., Kassam, Z. & Alm, E. J. Profiling living bacteria informs preparation of fecal microbiota transplantations. PLoS ONE 12, e0170922 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Ferreiro, A., Crook, N., Gasparrini, A. J. & Dantas, G. Multiscale evolutionary dynamics of host-associated microbiomes. Cell 172, 1216–1227 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Mo, Y. et al. Duration of carbapenemase-producing Enterobacteriaceae carriage in hospital patients. Emerg. Infect. Dis. 26, 2182–2185 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Haverkate, M. R. et al. Duration of colonization with Klebsiella pneumoniae carbapenemase-producing bacteria at long-term acute care hospitals in Chicago, Illinois. Open Forum Infect. Dis. 3, ofw178 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Korach-Rechtman, H. et al. Intestinal dysbiosis in carriers of carbapenem-resistant Enterobacteriaceae. mSphere 5, e00173–20 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yoshida, N. et al. Bacteroides vulgatus and Bacteroides dorei reduce gut microbial lipopolysaccharide production and inhibit atherosclerosis. Circulation 138, 2486–2498 (2018).CAS 
PubMed 
Article 

Google Scholar 
Lenoir, M. et al. Butyrate mediates anti-inflammatory effects of. Gut Microbes 12, 1–16 (2020).PubMed 
Article 
CAS 

Google Scholar 
Riedel, C. U. et al. Anti-inflammatory effects of bifidobacteria by inhibition of LPS-induced NF-κB activation. World J. Gastroenterol. 12, 3729–3735 (2006).PubMed 
PubMed Central 
Article 

Google Scholar 
Zeng, M. Y., Inohara, N. & Nuñez, G. Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunol. 10, 18–26 (2017).CAS 
PubMed 
Article 

Google Scholar 
Winter, S. E. & Bäumler, A. J. A breathtaking feat: to compete with the gut microbiota, Salmonella drives its host to provide a respiratory electron acceptor. Gut Microbes 2, 58–60 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Rivera-Chávez, F., Lopez, C. A. & Bäumler, A. J. Oxygen as a driver of gut dysbiosis. Free Radic. Biol. Med. 105, 93–101 (2017).PubMed 
Article 
CAS 

Google Scholar 
Chng, K. R. et al. Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut. Nat. Ecol. Evol. 4, 1256–1267 (2020).PubMed 
Article 

Google Scholar 
Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207–217 (2010).CAS 
PubMed 
Article 

Google Scholar 
Stacy, A. et al. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell 184, 615–627.e17 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Barreto, H. C., Sousa, A. & Gordo, I. The landscape of adaptive evolution of a gut commensal bacteria in aging mice. Curr. Biol. 30, 1102–1109.e5 (2020).CAS 
PubMed 
Article 

Google Scholar 
Ernst, C. M. et al. Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nat. Med. 26, 705–711 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhao, S. et al. Adaptive evolution within gut microbiomes of healthy people. Cell Host Microbe 25, 656–667.e8 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Warsi, O. M., Andersson, D. I. & Dykhuizen, D. E. Different adaptive strategies in E. coli populations evolving under macronutrient limitation and metal ion limitation. BMC Evol. Biol. 18, 72 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Hickman, R. A., Munck, C. & Sommer, M. O. A. Time-resolved tracking of mutations reveals diverse allele dynamics during Escherichia coli antimicrobial adaptive evolution to single drugs and drug pairs. Front. Microbiol. 8, 893 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Auriol, C., Bestel-Corre, G., Claude, J. B., Soucaille, P. & Meynial-Salles, I. Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity. Proc. Natl Acad. Sci. USA 108, 1278–1283 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Juers, D. H., Matthews, B. W. & Huber, R. E. LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci. 21, 1792–1807 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rogers, A. W. L., Tsolis, R. M. & Bäumler, A. J. Salmonella versus the microbiome. Microbiol. Mol. Biol. Rev. 85, e00027–19 (2021).CAS 
PubMed 
Article 

Google Scholar 
Hughes, E. R. et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis. Cell Host Microbe 21, 208–219 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gupta, S., Allen-Vercoe, E. & Petrof, E. O. Fecal microbiota transplantation: in perspective. Ther. Adv. Gastroenterol. 9, 229–239 (2016).Article 

Google Scholar 
Wortelboer, K., Nieuwdorp, M. & Herrema, H. Fecal microbiota transplantation beyond Clostridioides difficile infections. EBioMedicine 44, 716–729 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426–429 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Martinson, J. N. V. et al. Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults. ISME J. 13, 2306–2318 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Woyke, T., Doud, D. F. R. & Schulz, F. The trajectory of microbial single-cell sequencing. Nat. Methods 14, 1045–1054 (2017).CAS 
PubMed 
Article 

Google Scholar 
Domingo, E. & Perales, C. Viral quasispecies. PLoS Genet. 15, e1008271 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yamada, C. et al. Molecular insight into evolution of symbiosis between breast-fed infants and a member of the human gut microbiome Bifidobacterium longum. Cell Chem. Biol. 24, 515–524.e5 (2017).CAS 
PubMed 
Article 

Google Scholar 
Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gao, S., Bertrand, D., Chia, B. K. & Nagarajan, N. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biol. 17, 102 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Gao, S., Bertrand, D. & Nagarajan, N. FinIS: improved in silico finishing using an exact quadratic programming formulation. Lect. Notes Comput. Sci. 7534, 314–325 (2012).Article 

Google Scholar 
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997v2 (2013).Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Franzosa, E. A. et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15, 962–968 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Hawinkel, S., Mattiello, F., Bijnens, L. & Thas, O. A broken promise: microbiome differential abundance methods do not control the false discovery rate. Brief. Bioinformatics 20, 210–221 (2019).PubMed 
Article 

Google Scholar 
Morton, J. T. et al. Establishing microbial composition measurement standards with reference frames. Nat. Commun. 10, 2719 (2019).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Inouye, M. et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6, 90 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517–D525 (2020).CAS 
PubMed 
Article 

Google Scholar 
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).PubMed 
PubMed Central 
Article 

Google Scholar 
Wilm, A. et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 40, 11189–11201 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hinrichs, A. S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590–D598 (2006).CAS 
PubMed 
Article 

Google Scholar 
Pracana, R., Priyam, A., Levantis, I., Nichols, R. A. & Wurm, Y. The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB. Mol. Ecol. 26, 2864–2879 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Quinlan, A. R. BEDTools: the Swiss-Army tool for genome feature analysis. Curr. Protoc. Bioinformatics 47, 11.12.1–34 (2014).Article 

Google Scholar 
Spedicato, G. Discrete time Markov chains with R. R J. 9.2, 84 (2017).Article 

Google Scholar 
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hahsler, M., Piekenbrock, M. & Doran, D. dbscan: fast density-based clustering with R. J. Stat. Softw. 91, 1–30 (2019).Article 

Google Scholar 
Galata, V., Fehlmann, T., Backes, C. & Keller, A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res. 47, D195–D202 (2019).CAS 
PubMed 
Article 

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

Google Scholar 
Quan, S. et al. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet. 8, e1002444 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tsuchido, T., VanBogelen, R. A. & Neidhardt, F. C. Heat shock response in Escherichia coli influences cell division. Proc. Natl Acad. Sci. USA 83, 6959–6963 (1986).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Trubetskoy, D., Proux, F., Allemand, F., Dreyfus, M. & Iost, I. SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo. Nucleic Acids Res. 37, 6540–6549 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Garoff, L., Huseby, D. L., Praski Alzrigat, L. & Hughes, D. Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli. J. Antimicrob. Chemother. 73, 3285–3292 (2018).CAS 
PubMed 
Article 

Google Scholar 
Aponte, R. A., Zimmermann, S. & Reinstein, J. Directed evolution of the DnaK chaperone: mutations in the lid domain result in enhanced chaperone activity. J. Mol. Biol. 399, 154–167 (2010).CAS 
PubMed 
Article 

Google Scholar 
Mundhada, H. et al. Increased production of l-serine in Escherichia coli through adaptive laboratory evolution. Metab. Eng. 39, 141–150 (2017).CAS 
PubMed 
Article 

Google Scholar 
Conrad, T. M. et al. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc. Natl Acad. Sci. USA 107, 20500–20505 (2010).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li, Y. et al. LPS remodeling is an evolved survival strategy for bacteria. Proc. Natl Acad. Sci. USA 109, 8716–8721 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar  More

Coffaro, G. & Bocci, M. Resources competition between Ulva rigida and Zostera marina: A quantitative approach applied to the Lagoon of Venice. Ecol. Model. 102(1), 81–95 (1997).CAS 
Article 

Google Scholar 
Araújo, C. V. et al. Feeding niche preference of the mudsnail Peringia ulvae. Mar. Freshw. Res. 66(7), 573–581 (2015).Article 

Google Scholar 
Whitfield, A. K. The role of seagrass meadows, mangrove forests, salt marshes and reed beds as nursery areas and food sources for fishes in estuaries. Rev. Fish Biol. Fish. 27(1), 75–110 (2017).Article 

Google Scholar 
Su, L. et al. The occurrence of microplastic in specific organs in commercially caught fishes from coast and estuary area of east China. J. Hazard. Mater. 365, 716–724 (2019).CAS 
PubMed 
Article 

Google Scholar 
Benassai, G. Introduction to Coastal Dynamics and Shoreline Protection (Wit Press, 2006).
Google Scholar 
Decho, A. W. Microbial biofilms in intertidal systems: An overview. Cont. Shelf Res. 20(10–11), 1257–1273 (2000).ADS 
Article 

Google Scholar 
Thompson, C. E., Amos, C. L. & Umgiesser, G. A comparison between fluid shear stress reduction by halophytic plants in Venice Lagoon, Italy and Rustico Bay, Canada—Analyses of in situ measurements. J. Mar. Syst. 51(1–4), 293–308 (2004).Article 

Google Scholar 
Neumeier, U. & Amos, C. L. Turbulence reduction by the canopy of coastal Spartina salt-marshes. J. Coast. Res. 53, 433–439 (2006).
Google Scholar 
Black, K. S., Tolhurst, T. J., Paterson, D. M. & Hagerthey, S. E. Working with natural cohesive sediments. J. Hydraul. Eng. 128(1), 2–8 (2002).Article 

Google Scholar 
Paterson, D. M. Short-term changes in the erodibility of intertidal cohesive sediments related to the migratory behavior of epipelic diatoms. Limnol. Oceanogr. 34(1), 223–234 (1989).ADS 
Article 

Google Scholar 
Tolhurst, T.J., Jesus, B., Brotas, V. & Paterson, D.M. Diatom migration and sediment armouring—An example from the Tagus Estuary, Portugal. in Migrations and Dispersal of Marine Organisms. 183–193. (Springer, 2003).Tinoco, R. O. & Coco, G. Observations of the effect of emergent vegetation on sediment resuspension under unidirectional currents and waves. Earth Surf. Dyn. 2(1), 83 (2014).ADS 
Article 

Google Scholar 
Chen, Y. et al. Differential sediment trapping abilities of mangrove and saltmarsh vegetation in a subtropical estuary. Geomorphology 318, 270–282 (2018).ADS 
Article 

Google Scholar 
Cozzolino, L., Nicastro, K. R., Zardi, G. I. & Carmen, B. Species-specific plastic accumulation in the sediment and canopy of coastal vegetated habitats. Sci. Total Environ. 723, 138018 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Widdows, J., Pope, N. D. & Brinsley, M. D. Effect of Spartina anglica stems on near-bed hydrodynamics, sediment erodability and morphological changes on an intertidal mudflat. Mar. Ecol. Prog. Ser. 362, 45–57 (2008).ADS 
Article 

Google Scholar 
Marion, C., Anthony, E. J. & Trentesaux, A. Short-term (≤ 2 yrs) estuarine mudflat and saltmarsh sedimentation: High-resolution data from ultrasonic altimetery, rod surface-elevation table, and filter traps. Estuar. Coast. Shelf Sci. 83(4), 475–484 (2009).ADS 
Article 

Google Scholar 
Coulombier, T., Neumeier, U. & Bernatchez, P. Sediment transport in a cold climate salt marsh (St. Lawrence Estuary, Canada), the importance of vegetation and waves. Estuar. Coast. Shelf Sci. 101, 64–75 (2012).ADS 
Article 

Google Scholar 
Neumeier, U. & Ciavola, P. Flow resistance and associated sedimentary processes in a Spartina maritima salt-marsh. J. Coast. Res. 20(2), 435–447 (2002).
Google Scholar 
Yao, W. et al. Micro-and macroplastic accumulation in a newly formed Spartina alterniflora colonized estuarine saltmarsh in southeast China. Mar. Pollut. Bull. 149, 110636 (2019).CAS 
Article 

Google Scholar 
Fok, L. & Cheung, P. K. Hong Kong at the Pearl River Estuary: A hotspot of microplastic pollution. Mar. Pollut. Bull. 99(1–2), 112–118 (2015).CAS 
PubMed 
Article 

Google Scholar 
Weinstein, J. E., Crocker, B. K. & Gray, A. D. From macroplastic to microplastic: Degradation of high-density polyethylene, polypropylene, and polystyrene in a salt marsh habitat. Environ. Toxicol. Chem. 35(7), 1632–1640 (2016).CAS 
PubMed 
Article 

Google Scholar 
Willis, K. A., Eriksen, R., Wilcox, C. & Hardesty, B. D. Microplastic distribution at different sediment depths in an urban estuary. Front. Mar. Sci. 4, 419 (2017).Article 

Google Scholar 
Stead, J. L. et al. Identification of tidal trapping of microplastics in a temperate salt marsh system using sea surface microlayer sampling. Sci. Rep. 10(1), 1–10 (2020).Article 
CAS 

Google Scholar 
Friend, P. L., Ciavola, P., Cappucci, S. & Santos, R. Bio-dependent bed parameters as a proxy tool for sediment stability in mixed habitat intertidal areas. Cont. Shelf Res. 23(17–19), 1899–1917 (2003).ADS 
Article 

Google Scholar 
Hurley, R., Woodward, J. & Rothwell, J. J. Microplastic contamination of river beds significantly reduced by catchment-wide flooding. Nat. Geosci. 11(4), 251–257 (2018).ADS 
CAS 
Article 

Google Scholar 
Ockelford, A., Cundy, A. & Ebdon, J. E. Storm response of fluvial sedimentary microplastics. Sci. Rep. 10(1), 1–10 (2020).Article 
CAS 

Google Scholar 
Wang, J. Q. et al. Bioturbation of burrowing crabs promotes sediment turnover and carbon and nitrogen movements in an estuarine salt marsh. Ecosystems 13(4), 586–599 (2010).CAS 
Article 

Google Scholar 
Soulsby, R.L.. The bottom boundary layer of shelf seas. in Elsevier Oceanography Series. Vol. 35. 189–266. (Elsevier, 1983).Thompson, C. E., Amos, C. L., Lecouturier, M. & Jones, T. E. R. Flow deceleration as a method of determining drag coefficient over roughened flat beds. J. Geophys. Res. Oceans 109, C3 (2004).
Google Scholar 
Chirol, C. et al. The influence of bed roughness on turbulence: Cabras Lagoon, Sardinia, Italy. J. Mar. Sci. Eng. 3(3), 935–956 (2015).Article 

Google Scholar 
Kassem, H., Sutherland, T. F. & Amos, C. L. Hydrodynamic controls on the particle size of resuspended sediment from sandy and muddy substrates in British Columbia, Canada. J. Coast. Res. 37, 691 (2021).CAS 
Article 

Google Scholar 
Nepf, H. M. Flow and transport in regions with aquatic vegetation. Annu. Rev. Fluid Mech. 44, 123–142 (2012).ADS 
MathSciNet 
MATH 
Article 

Google Scholar 
Bouma, T. J. et al. Density-dependent linkage of scale-dependent feedbacks: A flume study on the intertidal macrophyte Spartina anglica. Oikos 118(2), 260–268 (2009).Article 

Google Scholar 
Amos, C. L. et al. The stability of tidal flats in Venice Lagoon—The results of in-situ measurements using two benthic, annular flumes. J. Mar. Syst. 51(1–4), 211–241 (2004).Article 

Google Scholar 
Amos, C. L., Feeney, T., Sutherland, T. F. & Luternauer, J. L. The stability of fine-grained sediments from the Fraser River Delta. Estuar. Coast. Shelf Sci. 45(4), 507–524 (1997).ADS 
CAS 
Article 

Google Scholar 
Tolhurst, T.J., Gust, G., & Paterson, D.M. The influence of an extracellular polymeric substance (EPS) on cohesive sediment stability. in Proceedings in Marine Science. Vol. 5. 409–425. (Elsevier, 2002).Brückner, M. Z. et al. Benthic species as mud patrol-modelled effects of bioturbators and biofilms on large-scale estuarine mud and morphology. Earth Surf. Proc. Land. 46(6), 1128–1144 (2021).ADS 
Article 

Google Scholar 
Ferdowsi, B., Ortiz, C. P., Houssais, M. & Jerolmack, D. J. River-bed armouring as a granular segregation phenomenon. Nat. Commun. 8(1), 1–10 (2017).CAS 
Article 

Google Scholar 
Andersen, T. J., Jensen, K. T., Lund-Hansen, L., Mouritsen, K. N. & Pejrup, M. Enhanced erodibility of fine-grained marine sediments by Hydrobia ulvae. J. Sea Res. 48(1), 51–58 (2002).ADS 
Article 

Google Scholar 
Orvain, F., Sauriau, P. G., Sygut, A., Joassard, L. & Le Hir, P. Interacting effects of Hydrobia ulvae bioturbation and microphytobenthos on the erodibility of mudflat sediments. Mar. Ecol. Prog. Ser. 278, 205–223 (2004).ADS 
Article 

Google Scholar 
Orvain, F., Sauriau, P. G., Bacher, C. & Prineau, M. The influence of sediment cohesiveness on bioturbation effects due to Hydrobia ulvae on the initial erosion of intertidal sediments: A study combining flume and model approaches. J. Sea Res. 55(1), 54–73 (2006).ADS 
Article 

Google Scholar 
Widdows, J. et al. Inter-comparison between five devices for determining erodability of intertidal sediments. Cont. Shelf Res. 27(8), 1174–1189 (2007).ADS 
Article 

Google Scholar 
Amos, C. L. et al. The stability of a mudflat in the Humber estuary, South Yorkshire, UK. Geol. Soc. Lond. Spec. Publ. 139(1), 25–43 (1998).ADS 
Article 

Google Scholar 
Tolhurst, T. J., Black, K. S. & Paterson, D. M. Muddy sediment erosion: Insights from field studies. J. Hydraul. Eng. 135(2), 73–87 (2009).Article 

Google Scholar 
Quaresma, V. D. S., Bastos, A. C. & Amos, C. L. Sedimentary processes over an intertidal flat: A field investigation at Hythe flats, Southampton Water (UK). Mar. Geol. 241(1–4), 117–136 (2007).ADS 
Article 

Google Scholar 
Helcoski, R., Yonkos, L. T., Sanchez, A. & Baldwin, A. H. Wetland soil microplastics are negatively related to vegetation cover and stem density. Environ. Pollut. 256, 113391 (2020).CAS 
PubMed 
Article 

Google Scholar 
Rochman, C. M. et al. Classify plastic waste as hazardous. Nature 494(7436), 169–171 (2013).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Barboza, L. G. A., Vethaak, A. D., Lavorante, B. R., Lundebye, A. K. & Guilhermino, L. Marine microplastic debris: An emerging issue for food security, food safety and human health. Mar. Pollut. Bull. 133, 336–348 (2018).CAS 
PubMed 
Article 

Google Scholar 
de Barros, M. S. F., dos Santos Calado, T. C., Silva, A. S. & dos Santos, E. V. Ingestion of plastic debris affects feeding intensity in the rocky shore crab Pachygrapsus transversus Gibbes 1850 (Brachyura: Grapsidae). Int. J. Biodivers. Conserv. 12(1), 113–117 (2020).
Google Scholar 
Villagran, D. M., Truchet, D. M., Buzzi, N. S., Lopez, A. D. F. & Severini, M. D. F. A baseline study of microplastics in the burrowing crab (Neohelice granulata) from a temperate southwestern Atlantic estuary. Mar. Pollut. Bull. 150, 110686 (2020).CAS 
PubMed 
Article 

Google Scholar 
Townend, I. A Conceptual Model of Southampton Water. Vol 1. (Tech. Rep.). ABPmer report.. http://www.estuary-guide.net/pdfs/southampton_water_case_study.pdf. Accessed 21 May 2008 (ABP Marine Environmental Research Ltd., 2008).Amos, C. L., Grant, J., Daborn, G. R. & Black, K. Sea carousel—A benthic, annular flume. Estuar. Coast. Shelf Sci. 34(6), 557–577 (1992).ADS 
Article 

Google Scholar 
Thompson, C. E., Amos, C. L., Jones, T. E. R. & Chaplin, J. The manifestation of fluid-transmitted bed shear stress in a smooth annular flume-a comparison of methods. J. Coast. Res. 1, 1094–1103 (2003).
Google Scholar 
Buls, T., Anderskouv, K., Friend, P. L., Thompson, C. E. & Stemmerik, L. Physical behaviour of Cretaceous calcareous nannofossil ooze: Insight from flume studies of disaggregated chalk. Sedimentology 64(2), 478–507 (2017).Article 

Google Scholar 
Tuprakay, S., Usahanunth, N. & Tuprakay, S. R. A study bakelite plastics waste from industrial process in concrete products as aggregate. Int. J. Struct. Civ. Eng. Res. 6(4), 7 (2017).
Google Scholar 
Thompson, C. E. L., Couceiro, F., Fones, G. R. & Amos, C. L. Shipboard measurements of sediment stability using a small annular flume—Core mini flume (CMF). Limnol. Oceanogr. Methods 11(11), 604–615 (2013).Article 

Google Scholar 
Kassem, H., Thompson, C. E., Amos, C. L. & Townend, I. H. Wave-induced coherent turbulence structures and sediment resuspension in the nearshore of a prototype-scale sandy barrier beach. Cont. Shelf Res. 109, 78–94 (2015).ADS 
Article 

Google Scholar 
Kassem, H. et al. Observations of nearbed turbulence over mobile bedforms in combined, collinear wave-current flows. Water 12(12), 3515 (2020).CAS 
Article 

Google Scholar 
Elgar, S., Raubenheimer, B. & Guza, R. T. Quality control of acoustic Doppler velocimeter data in the surfzone. Meas. Sci. Technol. 16(10), 1889 (2005).ADS 
CAS 
Article 

Google Scholar 
Goring, D. G. & Nikora, V. I. Despiking acoustic Doppler velocimeter data. J. Hydraul. Eng. 128(1), 117–126 (2002).Article 

Google Scholar 
Mori, N., Suzuki, T. & Kakuno, S. Noise of acoustic Doppler velocimeter data in bubbly flows. J. Eng. Mech. 133(1), 122–125 (2007).
Google Scholar 
Stapleton, K. R. & Huntley, D. A. Seabed stress determinations using the inertial dissipation method and the turbulent kinetic energy method. Earth Surf. Proc. Land. 20(9), 807–815 (1995).ADS 
Article 

Google Scholar 
Dyer, K. Estuaries, A Physical Introduction. 2nd edn. https://doi.org/10.2307/1797104 (Wiley, 1997). More

Sewage and TSE quantity characteristicsThe WWT facilities have been implemented for Zabol with a capacity of 39,000 m3/day. Table 1 shows the volume of water consumption and sewage production based on the sewage coefficient in urban communities of the study area.Table 1 Water consumption, TSE volume and receiving resources in the study area—2019.Full size tableAs shown in Table 1, the total water consumption in the study area is 22.538 mcm/year while based on the development conditions. Afterward, the sewage volume was calculated to 16.194 mcm/year, considering the sewage coefficient and water consumption.Continuously, the sewage data obtained from the Water and Wastewater Organization of Zabol city, Iran, showed that the sewage entrance to the treatment plants of the study area is about 19,000 m3/day and 137 working days. Therefore, the TSE volume of the WWT plant was calculated based on the following scenarios of (1) data obtained from the Water and Wastewater Organization, Iran, and (2) based on the capacity of WWT plant. Note that the working days for both scenarios will be 137. The calculation is based on Eq. (1). The total TSE volume for scenarios 1 and 2 is 2.8 and 5.1 mcm/year, respectively.The difference between the calculation based on capacity and the existing data is due to the removal of raw sewage before entering the treatment plant, which has caused health and environmental problems in the region. Data obtained from Iran Department of Environment34 showed that 1.68 mcm/y of sewage were extracted for the farms. Previous studies in the same study area also reported the significant (P  5. Note that typical abundance of total and fecal coliforms (FC) in raw sewage are 107–109 and 106–108 100/mL, respectively, and were reduced by 1–5 orders of magnitude in treated TSE, depending on the type of treatment39,40. Classical treatments, which do not include any specific disinfection step, reduce fecal micro-organisms densities by 1–3 orders of magnitude40, but because of their high abundance in raw sewage, they are still discharged in large numbers with treated TSEs in the environment.Figure 6The results of the abundance of total coliforms (TC) and fecal coliforms (FC).Full size imageAdditionally, the results of yearly values of physicochemical factors of Zabol TSE (mg/L) including BOD5, COD, TDS, TH, and EC in the period of 2017–2019, showed in Fig. 7. The yearly results suggested that the values through the years of investigation did not show significant changes. In the following parts, the possibility of TSE evaluated considering various standards.Figure 7The results of yearly values of physicochemical factors of Zabol TSE.Full size imagePotential application of TSEComparing the quality of the TSE and sewage are based on various regulations showed in Table 3. It includes the food and agriculture organization (FAO), US environmental protection agency (USEPA), the Canadian water quality index (CWQI), and Iran’s national standards (INS), considering the irrigation and recreational application.Table 3 Guidelines for interpretations of water quality of sewage and TSE of Zabol WWT plants (average in the period of 2017–2019) compared to the standards of regulations.Full size tableAccording to the FAO Guide41 for Classifying Agricultural Water Quality, as shown in Table 3, the most crucial parameters for the application of TSE in irrigation include electrical conductivity (EC), sodium uptake ratio (SAR), chlorine, BOD, COD, and FC. However, three out of seven parameters namely BOD, COD, and FC in the TSE are largely erratic with the limits recommended in the standards.Based on USEPA42, the value of total suspended solids in TSE of Zabol WWT plant largely inconsistent with the limits recommended in the standards for TSE reuse. However, TDS, EC, and pH, met the criteria. Moreover, except TSS and pH, the other chemical parameters of sewage also meet the criteria. It is worth mentioning that EPA does not require or restrict any types of water reuse. Generally, states maintain primary regulatory authority (i.e., primacy) in allocating and developing water resources. Some US states have established programs to specifically address reuse, and some have incorporated water reuse into their existing programs. EPA, states, tribes, and local governments implement programs under the Safe Drinking Water Act and the Clean Water Act to protect the quality of drinking water source waters, community drinking water, and waterbodies like rivers and lakes.According to INS regulations for irrigation and recreation reuse of TSE33, the value parameters tested for the TSE of the Zabol WWT plant are following the limits recommended in the standards for consumption as irrigation (except chlorine) and recreation projects.Finally, the CWQI is a means to provide consistent procedures for Canadian jurisdictions to report water quality information to both management and the public. The CWQI value ranges between 1 and 100, and the result is further simplified by assigning it to a descriptive category in Table 4.Table 4 The CWQI value and descriptive.Full size tableThe results of CWQI software for analyzing the TSE of the WWT plant in the study area, as shown in Table 5 and Fig. 8, indicated its poor quality for drinking, and aquatic. While it is fair for livestock and marginal for irrigation. However, considering the purpose of this study for irrigation of the native plants, it met the criteria. Note that the input data set is based on the period of 2017–2019.Table 5 The results of TSE in various applications assessed by CWQI.Full size tableFigure 8CWQI tets results for TSE of WWT plant in the study area.Full size imageThe results of this section indicated the consideration of various parameters due to various regulations and demonstrated that the treatment technology upgrade was significantly better than those of urban miscellaneous water and agriculture water standards, indicating this system can be widely used for urban landscape hydration. Moreover, squeezing the sewage treatment process for being cost effective could be recommended considering the measurements of FC, BOD, and COD.Optimal area suggestion for project executionConsidering three steps of wind erosion which are detachment, transportation, and deposition, the sand fixation methods have to be done in the detachment area to be more effective. Hence, the most advantageous regions for project execution were selected based on the factors of (a) discovering the dust origins, and (b) vegetation cover. Regarding the first concern, it was shown that the dry sediments of the Farah river43, and the presence of dunes between the two sand movements corridors in Sistan, namely Jazinak (near Zabol city) and Tasuki corridors (shown in Fig. 9), was increased the dust concentration in Zabol city37,44 while the agricultural lands, and other infrastructures such as roads, and irrigation canals developed in the area between Zahedan and Zabol city.Figure 9Locations and names of Hamuns lake and sand movement corridors in the study area © 2022 by Springer Nature Limited is licensed under Attribution 4.0 International (created by ArcMap 10.5).Full size imageSubsequently, based on a guide that 30% of vegetation cover has a significant effect on the process of soil detachment45,46, and soil protection in the desert areas47, the regions with less than 30% vegetation cover in the study area based on field observation was investigated and showed in Fig. 10. Field observation demonstrated that most areas along with the Jazinak sand corridor and Zabol city have 1–15% and 15–30%36, which are in the priority for stabilization.Figure 10The critical dust hotspot and dust origins in the study area © 2022 by Springer Nature Limited is licensed under Attribution 4.0 International (created by ArcMap 10.5).Full size imageThe results are consistent with Abbasi et al.37, reported that the Hamun Baringak Lake plays a crucial role in the aeolian mobilization of sediments in the Sistan region because of the hydrological droughts that led to the gradual decline of the wetland vegetation cover. Notably, Jahantigh48, in the same study area, reported that the average forage yield of Aeluropus lagopoides in Hamun Hirmand lake in the condition of the water inflow and during drought, was estimated to be 8869 and 173 kg/ha, respectively. It can be explained by the effect of water presence on plant production and cover. However, the average of bare soil of Hamun lake was estimated to be 7.5% and 84.2% in the two periods of water inflow and drought, respectively48. It indicated the impact of dusty days. Therefore, the mentioned areas with the vegetation cover below 30% prioritized for stabilization techniques to dust reduction or mitigation.The detailed field investigation of the land use and vegetation cover, as shown in Fig. 12, indicated the presence of native plants such as A. lagopoides and Tamarix spp. Based on Fig. 11, among the Tamarix genus, the three species of T. aphylla, T. stricta, and T.hispida were observed in the study area. T. stricta is a native species to Iran with benefits including, traditional therapeutic uses in Persian Medicine49,50. Also, the soil EC in the habitat of T. aphylla (15.70 mhos/cm) is almost the same as the control area (15.80 mhos/cm) in the depth of 0–30 cm; while the available potassium in T. aphylla habitat (460 mg/l) was also more than the control area (180 mg/l)51. Hence, the afforestation of Tamarix spp. has caused the addition of soil amendments and increased the clods.Figure 11The most land use/cover in the study area.Full size imageConsequently, the water requirement of the plants in the desert area consisting of T.aphylla, is reported in Table 6. The water requirement of T. stricta was estimated based on Table 6 to be 580 m3/ha for 500 plants no./ha with a vegetation cover of 10–30%.Table 6 Annual water requirement of the T. aphylla for irrigation in the early stages of establishment in terms of planting density (Rad, 2018).Full size tableMoreover, Fig. 12 shows the vast (50% more) soil coverage of T. stricta in the collar area compared to T. aphylla. Therefore, it is more appropriate to cultivate T. stricta than T. aphylla for the biological restoration of the region. Note that the introduced dust mitigation technique using TSE of Zabol WWT can play a specific role in the rehabilitation of soil cover in the mentioned area due to the low water need of native plants. Consequently, it has a significant impact on dust reduction in Zabol city.Figure 12The picture of (a) T. stricta and (b) T. aphylla in the study area.Full size imageHence, based on the hotspots of dust origins in the study area, the most appropriate sites for the project executions of TSE were selected, as shown in Fig. 13. Investigations indicated that a total of 27,500 ha are suitable for the project excision. Hence, considering the water requirement of 500 m3/ha/year, TSE volume of 5.1 mcm/year, vegetation cover of below 30%, and other observations such as the soil coverage in the collar area, the native plant of T. stricta selected for the afforestation of 10,000 ha on the west part of Zabol. This region has the priority in stabilization due to companionship to the corridors with a vegetation cover of 16–30%.Figure 13Area suggested for the dust mitigation project execution by the application of TSE © 2022 by Springer Nature Limited is licensed under Attribution 4.0 International (created by ArcMap 10.5).Full size imageCost analysisFinally, due to the vast area of TSE application, the total of 27,500 ha, with the puprose of dust mitigation, the project execution costs must have been addressed. Hence, Fig. 13 shows the distance of Zabol city to Hamun Hirmand and Baringak lake for transportation calculation. Accordingly, the distance from Zabol to Hamun Hirmand and Baringak lake is 14 and 33 km, respectively. The whole area around Zabol city to Hammon Hirmand lake is cultivated lands; hence, the existing roads reduced construction costs.The two main modes of transportation are trucks and pipelines. There are various pros and cons to both methods. Truck transportation is favored for low volume and short distances, while its costs rapidly increase for large-scale transportation. On the other hand, pipeline transportation is appropriate for large volumes, and long travel distances as it has a positive impact on reducing greenhouse gas emissions. Using pipelines also reduces noise, reduces highway traffic, and improves highway safety.Based on the literature, the variable and fixed transportation cost components depend on the type of product shipped, design requirements, and other decisions related to facility planning. For the sewage sludge with a pH level of 7.0 ± 0.1; hence, a low-cost PVC pipe suggested. Moreover, for cost optimization, as the WWT facilities in the study area do not generate enough volume daily, it makes economical sense to store sewage for a few days to increase the shipped volume. However, reducing the storage to a single day condenses these investment costs drastically52.It was estimated that the total costs for a facility-owned and rented single trailer truck with a capacity of 30 m3 to be $5.6/m3 and 7.4/m3/km, respectively53. Hence, the variable unit transportation cost along a pipeline with a capacity of 480 m3/day is estimated to be $0.144/m3/km. In despite of previous studies mentioning that it is more economical to use a pipeline rather than a rented single trailer truck if the volume shipped is greater than 700 m3/day, in the study area, it is more economical to use a facility-owned single trailer truck, while the shipped volume is 1200 m3/day due to the low cost of petroleum and very close distance of the suggested area. More

Hawkes, C. V., Bull, J. J. & Lau, J. A. Symbiosis and stress: how plant microbiomes affect host evolution. Philos. T. R. Soc. B. 375, 20190590 (2020).CAS 
Article 

Google Scholar 
Leopold, D. R. & Busby, P. E. Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function. Curr. Biol. 30, 3260–3266 (2020).CAS 
PubMed 
Article 

Google Scholar 
Morella, N. M. et al. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proc. Natl Acad. Sci. USA 117, 1148–1159 (2020).CAS 
PubMed 
Article 

Google Scholar 
Garcia, J. & Kao-Kniffin, J. Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling. Front. Plant Sci. 9, 1516 (2018).Article 

Google Scholar 
Marschner P. Plant-Microbe Interactions in the Rhizosphere and Nutrient Cycling in Nutrient Cycling in Terrestrial Ecosystems (eds. Marschner, P. & Rengel, Z.) 159–183 (Springer, 2007).Vannier, N., Agler, M. & Hacquard, S. Microbiota-mediated disease resistance in plants. PLoS Pathog. 15, e1007740 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, 6584 (2019).
Google Scholar 
Bender, S. F., Wagg, C. & van der Heijden, M. G. A. An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability. Trends Ecol. Evol. 31, 440–452 (2016).PubMed 
Article 

Google Scholar 
Dessaux, Y., Grandclemént, C. & Faure, D. Engineering the Rhizosphere. Trends Plant Sci. 21, 266–278 (2016).CAS 
PubMed 
Article 

Google Scholar 
Swenson, W., Wilson, D. S. & Elias, R. Artificial ecosystem selection. Proc. Natl Acad. Sci. USA 97, 9110–9114 (2000).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Panke-Buisse, K., Poole, A., Goodrich, J., Ley, R. E. & Kao-Kniffin, J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J. 9, 980–989 (2015).CAS 
PubMed 
Article 

Google Scholar 
van den Bergh, B. et al. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol. Mol. Biol. Rev. 82, e00008–e00018 (2018).PubMed 
PubMed Central 

Google Scholar 
Garcia, J. & Kao-Kniffin, J. Can dynamic network modelling be used to identify adaptive microbiomes? Funct. Ecol. 34, 2065–2074 (2020).Article 

Google Scholar 
Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).CAS 
PubMed 
Article 

Google Scholar 
Wilson, D. & Wilson, E. Evolution “for the good of the group”. Am. Sci. 96, 380–389 (2008).Article 

Google Scholar 
de la Fuente Cantó, C. et al. An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness. Plant J. 103, 951–964 (2020).PubMed 
Article 
CAS 

Google Scholar 
Sachs, J., Mueller, U., Wilcox, T. & Bull, J. The evolution of cooperation. Q. Rev. Biol. 79, 135–160 (2004).PubMed 
Article 

Google Scholar 
Harrington, K. & Sanchez, A. Eco-evolutionary dynamics of complex social strategies in microbial communities. Commun. Integr. Biol. 7, e28230 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Rauch, J., Kondev, J. & Sanchez, A. Cooperators trade off ecological resilience and evolutionary stability in public goods games. J. R. Soc. Interface 14, 20160967 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Sexton, D. & Schuster, M. Nutrient limitation determines the fitness of cheaters in bacterial siderophore cooperation. Nat. Commun. 8, 230 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Schmidt, J. E., Kent, A. D., Brisson, V. L. & Gaudin, A. C. M. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome 7, 146 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Turner, T. et al. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere. microbiome plants ISME J. 7, 2248–2258 (2013).CAS 
PubMed 

Google Scholar 
Jones, D. L., Nguyen, C. & Finlay, R. D. Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant Soil 321, 5–33 (2009).CAS 
Article 

Google Scholar 
George, E., Marschner, H. & Jakobsen, I. Role of Arbuscular Mycorrhizal Fungi in Uptake of Phosphorus and Nitrogen From Soil. Crit. Rev. Biotechnol. 15, 257–270 (1995).Article 

Google Scholar 
Hodge, A. & Fitter Alastair, H. Substantial nitrogen acquisition by arbuscular mycorrhizal fungi from organic material has implications for N cycling. Proc. Natl Acad. Sci. USA 107, 13754–13759 (2010).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lambers, H. & Teste, F. P. Interactions between arbuscular mycorrhizal and non-mycorrhizal plants: do non-mycorrhizal species at both extremes of nutrient availability play the same game. Plant Cell Environ. 36, 1911–1915 (2013).PubMed 

Google Scholar 
Delaux, P. M. et al. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet. 10, e1004487 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Anas, M. et al. Fate of nitrogen in agriculture and environment: agronomic, eco-physiological and molecular approaches to improve nitrogen use efficiency. Biol. Res. 53, 47 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Madhaiyan, M. et al. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int. J. Syst. Evol. Microbiol. 65, 578–586 (2015).CAS 
PubMed 
Article 

Google Scholar 
Song, H. et al. Environmental filtering of bacterial functional diversity along an aridity gradient. Sci. Rep. 9, 866 (2019).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Xia, L. C. et al. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst. Biol. 5, S15 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Kuntal, B. K., Chandrakar, P., Sadhu, S. & Mandhi, S. S. ‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets. ISME J. 13, 442–454 (2019).PubMed 
Article 

Google Scholar 
Layeghifard, M., Hwang, D. M. & Guttman, D. S. Disentangling Interactions in the Microbiome: A Network Perspective. Trends Microbiol. 25, 217–228 (2017).CAS 
PubMed 
Article 

Google Scholar 
Hu, Q. et al. Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria. NPJ Biofilms Microbiomes 6, 8 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Faust, K. et al. Cross-biome comparison of microbial association networks. Front. Microbiol. 6, 1200 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Rengel, Z. & Marschner, P. Nutrient availability and management in the rhizosphere: exploiting genotypic differences. N. Phytol. 168, 305–312 (2005).CAS 
Article 

Google Scholar 
Marschner, P. The Role of Rhizosphere Microorganisms in Relation to P Uptake by Plants in The Ecophysiology of Plant-Phosphorus Interactions (eds. White, P. & Hammond, J.) 165–167 (Springer, 2008).Repert, D., Underwood, J., Smith, R. & Song, B. Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station. J. Geophys. Res. Biogeosci. 119, 2328–2344 (2014).CAS 
Article 

Google Scholar 
Rolletschek, H. et al. Ectopic expression of an amino acid transporter (VfAAP1) in seeds of Vicia narbonensis and pea increases storage proteins. Plant Physiol. 137, 1236–1249 (2005).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sanders, A. et al. AAP1 regulates import of amino acids into developing Arabidopsis embryos. Plant J. 59, 540–552 (2009).CAS 
PubMed 
Article 

Google Scholar 
Carter, A. M. & Tegeder, M. Increasing nitrogen fixation and seed development in soybean requires complex adjustments of nodule nitrogen metabolism and partitioning processes. Curr. Biol. 26, 2044–2051 (2016).CAS 
PubMed 
Article 

Google Scholar 
Meier, I. C. et al. Root exudation of mature beech forests across a nutrient availability gradient: the role of root morphology and fungal activity. N. Phytol. 226, 583–594 (2020).CAS 
Article 

Google Scholar 
Xu, Y., He, J., Cheng, W., Xing, X. & Li, L. Natural 15N abundance in soils and plants in relation to N cycling in a rangeland in Inner Mongolia. J. Plant Ecol. 3, 201–207 (2010).Article 

Google Scholar 
Henneron, L. et al. Rhizosphere control of soil nitrogen cycling: a key component of plant economic strategies. N. Phytol. 228, 1269–1282 (2020).CAS 
Article 

Google Scholar 
Hobbie, E. A. & Högberg, P. Nitrogen isotopes link mycorrhizal fungi and plants to nitrogen dynamics. N. Phytol. 196, 367–382 (2012).CAS 
Article 

Google Scholar 
Zhou, S. et al. Assessing nitrification and denitrification in a paddy soil with different water dynamics and applied liquid cattle waste using the 15N isotopic technique. Sci. Total Environ. 430, 93–100 (2012).CAS 
PubMed 
Article 

Google Scholar 
Fuertes-Mendizábal, T. et al. 15N Natural Abundance Evidences a Better Use of N Sources by Late Nitrogen Application in Bread Wheat. Front. Plant Sci. 9, 853 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Yoneyama, T., Omata, T., Nakata, S. & Yazaki, J. Fractionation of Nitrogen Isotopes during the Uptake and Assimilation of Ammonia by Plants. Plant Cell Physiol. 32, 1211–1217 (1991).CAS 

Google Scholar 
Vacheron, J. et al. Plant growth-promoting rhizobacteria and root system functioning. Front. Plant Sci. 4, 356 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Granada, C., Passaglia, L., de Souza, E. & Sperotto, R. Is Phosphate Solubilization the Forgotten Child of Plant Growth-Promoting Rhizobacteria? Front. Microbiol. 9, 2054 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Compant, S., Duffy, B., Nowak, J., Clément, C. & Barka, E. Use of Plant Growth-Promoting Bacteria for Biocontrol of Plant Diseases: Principles, Mechanisms of Action, and Future Prospects. Appl. Environ. Microbiol. 71, 4951 (2005).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Berges, J.A., & Mulholland, M.R. Enzymes and nitrogen cycling in Nitrogen in the marine environment (eds. Capone, D., Bronk, D., Mulholland, M., & Carpenter, E.) 1385–1444 (Elsevier 2008).DeAngelis, K. M., Lindow, S. E. & Firestone, M. Bacterial quorum sensing and nitrogen cycling in rhizosphere soil. FEMS Microb. Ecol. 66, 197–207 (2008).CAS 
Article 

Google Scholar 
Evans, S., Martiny, J. & Allison, S. Effects of dispersal and selection on stochastic assembly in microbial communities. ISME J. 11, 176–185 (2017).PubMed 
Article 

Google Scholar 
Ron, R., Fragman-Sapir, O. & Kadmon, R. (2018). Dispersal increases ecological selection by increasing effective community size. Proc. Natl Acad. Sci. USA. 115, 11280–11285 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Busby, P. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, e2001793 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Sergaki, C., Lagunas, B., Lidbury, I., Gifford, M. & Schäfer, P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. Front. Plant Sci. 9, 1205 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Herlemann, D. P. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Garcia, J. et al. Selection pressure on the rhizosphere microbiome alters nitrogen use efficiency and seed yield in Brassica rapa. National Center for Biotechnology Information Repository. https://www.ncbi.nlm.nih.gov/sra/PRJNA833111 (2022).Ruan, Q. et al. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22, 2532–2538 (2006).CAS 
PubMed 
Article 

Google Scholar 
Pollet, T. et al. Prokaryotic community successions and interactions in marine biofilms: the key role of Flavobacteria. FEMS Microbiol. Ecol. 94, fiy083 (2018).
Google Scholar 
Durno, W. E. et al. Expanding the boundaries of local similarity analysis. BMC Genomics 14, S3 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Garcia, J. et al. Selection pressure on the rhizosphere microbiome alters nitrogen use efficiency and seed yield in Brassica rapa. https://doi.org/10.5281/zenodo.6800595 (2022). More

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 
Inagaki, F. et al. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349, 420–424 (2015).CAS 
PubMed 
Article 

Google Scholar 
Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
D’Hondt, K. et al. Microbiome innovations for a sustainable future. Nat. Microbiol. 6, 138–142 (2021).PubMed 
Article 
CAS 

Google Scholar 
Lloyd, K. G., Steen, A. D., Ladau, J., Yin, J. & Crosby, L. Phylogenetically novel uncultured microbial cells dominate earth microbiomes. mSystems 3, e00055-18 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Lewis, W. H., Tahon, G., Geesink, P., Sousa, D. Z. & Ettema, T. J. G. Innovations to culturing the uncultured microbial majority. Nat. Rev. Microbiol. 19, 225–240 (2021).CAS 
PubMed 
Article 

Google Scholar 
Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).CAS 
PubMed 
Article 

Google Scholar 
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).CAS 
PubMed 
Article 

Google Scholar 
Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, REVIEWS0003 (2002).PubMed 
PubMed Central 
Article 

Google Scholar 
Engelen, B. & Imachi, H. Cultivation of subseafloor prokaryotic life in developments in marine geology. In Earth and Life Processes Discovered from Subseafloor Environment. Vol. 7 (eds. Stein, R., Blackman, D., Inagaki, F. & Larsen, H.-L.) 197–209 (Elsevier, 2014).Baker, B. J., Appler, K. E. & Gong, X. New microbial biodiversity in marine sediments. Annu. Rev. Mar. Sci. 13, 161–175 (2021).Article 

Google Scholar 
Hoshino, T. et al. Global diversity of microbial communities in marine sediment. Proc. Natl Acad. Sci. USA 117, 27587–27597 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tahon, G., Geesink, P. & Ettema, T. J. G. Expanding archaeal diversity and phylogeny: past, present, and future. Annu. Rev. Microbiol. 75, 359–381 (2021).PubMed 
Article 
CAS 

Google Scholar 
Bhattarai, S., Cassarini, C. & Lens, P. N. L. Physiology and distribution of archaeal methanotrophs that couple anaerobic oxidation of methane with sulfate reduction. Microbiol. Mol. Biol. Rev. 83, e00074-18 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Krukenberg, V. et al. Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia. Environ. Microbiol. 20, 1651–1666 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wegener, G., Krukenberg, V., Ruff, S. E., Kellermann, M. Y. & Knittel, K. Metabolic capabilities of microorganisms involved in and associated with the anaerobic oxidation of methane. Front. Microbiol. 7, 46 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Agrawal, L. K. et al. Treatment of raw sewage in a temperate climate using a UASB reactor and the hanging sponge cubes process. Water Sci. Technol. 36, 433–440 (1997).CAS 
Article 

Google Scholar 
Tyagi, V. K. et al. Future perspectives of energy saving down-flow hanging sponge (DHS) technology for wastewater valorization—a review. Rev. Environ. Sci. Biotechnol. 20, 389–418 (2021).Article 

Google Scholar 
Namita Maharjan, N. et al. Downflow hanging sponge system: a self-sustaining option for wastewater treatment. In Wastewater Treatment (IntechOpen, London, UK, 2020) Available at https://www.intechopen.com/online-first/74120Nurmiyanto, A. & Ohashi, A. Downflow hanging sponge (DHS) reactor for wastewater treatment—a short review. MATEC Web Conf. 280, 05004 (2019).CAS 
Article 

Google Scholar 
Hatamoto, M., Okubo, T., Kubota, K. & Yamaguchi, T. Characterization of downflow hanging sponge reactors with regard to structure, process function, and microbial community compositions. Appl. Microbiol. Biotechnol. 102, 10345–10352 (2018).CAS 
PubMed 
Article 

Google Scholar 
Tandukar, M., Uemura, S., Ohashi, A. & Harada, H. Combining UASB and the ‘fourth generation’ down-flow hanging sponge reactor for municipal wastewater treatment. Water Sci. Technol. 53, 209–218 (2006).CAS 
PubMed 
Article 

Google Scholar 
Chuang, H.-P. et al. Microbial community that catalyzes partial nitrification at low oxygen atmosphere as revealed by 16S rRNA and amoA genes. J. Biosci. Bioeng. 104, 525–528 (2007).CAS 
PubMed 
Article 

Google Scholar 
Imachi, H. et al. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J. 5, 1913–1925 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Aoki, M. et al. A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor. PLoS ONE 9, e105356 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Kato, S. et al. Biotic manganese oxidation coupled with methane oxidation using a continuous-flow bioreactor system under marine conditions. Water Sci. Technol. 76, 1781–1795 (2017).CAS 
PubMed 
Article 

Google Scholar 
Imachi, H. et al. Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Sci. Rep. 9, 2305 (2019).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Imachi, H. et al. Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment. Int. J. Syst. Evol. Microbiol. 64, 812–818 (2014).CAS 
PubMed 
Article 

Google Scholar 
Imachi, H. et al. Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino-acid-utilizing bacterium isolated from marine subsurface sediment. Int. J. Syst. Evol. Microbiol. 66, 1293–1300 (2016).CAS 
PubMed 
Article 

Google Scholar 
Imachi, H. et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577, 519–525 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Miyazaki, M. et al. Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. Int. J. Syst. Evol. Microbiol. 64, 4147–4154 (2014).PubMed 
Article 
CAS 

Google Scholar 
Miyazaki, M. et al. Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta. Int. J. Syst. Evol. Microbiol. 64, 2798–2804 (2014).CAS 
PubMed 
Article 

Google Scholar 
Nakahara, N. et al. Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi. Int. J. Syst. Evol. Microbiol. 69, 1185–1194 (2019).CAS 
PubMed 
Article 

Google Scholar 
Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015).CAS 
PubMed 
PubMed Central 
Article 

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

Google Scholar 
Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021).CAS 
PubMed 
Article 

Google Scholar 
Ruff, S. E. et al. Global dispersion and local diversification of the methane seep microbiome. Proc. Natl Acad. Sci. USA 112, 4015–4020 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chadwick, G. et al. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol. 20, e3001508 (2022).PubMed 
PubMed Central 
Article 

Google Scholar 
Cario, A., Oliver, G. C. & Rogers, K. L. Exploring the deep marine biosphere: challenges, innovations, and opportunities. Front. Earth Sci. 7, 225 (2019).Article 

Google Scholar 
Jørgensen, B. B. & Boetius, A. Feast and famine—microbial life in the deep-sea bed. Nat. Rev. Microbiol. 5, 770–781 (2007).PubMed 
Article 
CAS 

Google Scholar 
Hoehler, T. M. & Jørgensen, B. B. Microbial life under extreme energy limitation. Nat. Rev. Microbiol. 11, 83–94 (2013).CAS 
PubMed 
Article 

Google Scholar 
Schink, B. & Stams, A. J. M. Syntrophism among prokaryotes. In The Prokaryotes: Prokaryotic Communities and Ecophysiology (eds. Rosenberg, E. et al.) 471–493 (Springer, 2013).de Bok, F. A. M. et al. The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum. Int. J. Syst. Evol. Microbiol. 55, 1697–1703 (2005).PubMed 
Article 
CAS 

Google Scholar 
Imachi, H. et al. Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic, propionate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 57, 1487–1492 (2007).PubMed 
Article 

Google Scholar 
Qiu, Y.-L. et al. Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl. Environ. Microbiol. 74, 2051–2058 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Matsushita, S. et al. Anti-bacterial effects of MnO2 on the enrichment of manganese-oxidizing bacteria in downflow hanging sponge reactors. Microbes Environ. 35, ME20052 (2020).PubMed Central 

Google Scholar 
Momper, L. et al. Rectinema subterraneum sp. nov, a chemotrophic spirochaete isolated from the deep terrestrial subsurface. Int. J. Syst. Evol. Microbiol. 70, 4739–4747 (2020).CAS 
PubMed 
Article 

Google Scholar 
Chuang, H.-P., Ohashi, A., Imachi, H., Tandukar, M. & Harada, H. Effective partial nitrification to nitrite by down-flow hanging sponge reactor under limited oxygen condition. Water Res. 41, 295–302 (2007).CAS 
PubMed 
Article 

Google Scholar 
Hatamoto, M., Koshiyama, Y., Kindaichi, T., Ozaki, N. & Ohashi, A. Enrichment and identification of methane-oxidizing bacteria by using down-flow hanging sponge bioreactors under low methane concentration. Ann. Microbiol. 61, 683–687 (2010).Article 
CAS 

Google Scholar 
Hatamoto, M., Yamamoto, H., Kindaichi, T., Ozaki, N. & Ohashi, A. Biological oxidation of dissolved methane in effluents from anaerobic reactors using a down-flow hanging sponge reactor. Water Res. 44, 1409–1418 (2010).CAS 
PubMed 
Article 

Google Scholar 
Hatamoto, M., Miyauchi, T., Kindaichi, T., Ozaki, N. & Ohashi, A. Dissolved methane oxidation and competition for oxygen in down-flow hanging sponge reactor for post-treatment of anaerobic wastewater treatment. Bioresour. Technol. 102, 10299–10304 (2011).CAS 
PubMed 
Article 

Google Scholar 
Hatamoto, M. et al. Potential of nitrous oxide conversion in batch and down-flow hanging sponge bioreactor systems. Sustain. Environ. Res. 24, 117–128 (2014).
Google Scholar 
Cao, L. T. T. et al. Biological oxidation of Mn(II) coupled with nitrification for removal and recovery of minor metals by downflow hanging sponge reactor. Water Res. 68, 545–553 (2015).CAS 
PubMed 
Article 

Google Scholar 
Yamaguchi, T. et al. A novel approach for toluene gas treatment using a downflow hanging sponge reactor. Appl. Microbiol. Biotechnol. 102, 5625–5634 (2018).CAS 
PubMed 
Article 

Google Scholar 
Matsushita, S. et al. Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater. Water Res. 130, 224–233 (2018).CAS 
PubMed 
Article 

Google Scholar 
Onodera, T. et al. Characterization of the retained sludge in a down-flow hanging sponge (DHS) reactor with emphasis on its low excess sludge production. Bioresour. Technol. 136, 169–175 (2013).CAS 
PubMed 
Article 

Google Scholar 
Miyaoka, Y., Hatamoto, M., Yamaguchi, T. & Syutsubo, K. Eukaryotic community shift in response to organic loading rate of an aerobic trickling filter (down-flow hanging sponge reactor) treating domestic sewage. Microb. Ecol. 73, 801–814 (2016).PubMed 
Article 
CAS 

Google Scholar 
Park, M.-O., Ikenaga, H. & Watanabe, K. Phage diversity in a methanogenic digester. Microb. Ecol. 53, 98–103 (2006).PubMed 
Article 
CAS 

Google Scholar 
Wu, Q. & Liu, W.-T. Determination of virus abundance, diversity and distribution in a municipal wastewater treatment plant. Water Res. 43, 1101–1109 (2009).CAS 
PubMed 
Article 

Google Scholar 
Chien, I.-C., Meschke, J. S., Gough, H. L. & Ferguson, J. F. Characterization of persistent virus-like particles in two acetate-fed methanogenic reactors. PLoS One 8, e81040 (2013).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Girguis, P. R., Orphan, V. J., Hallam, S. J. & DeLong, E. F. Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Appl. Environ. Microbiol. 69, 5472–5482 (2003).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang, Y., Maignien, L., Zhao, X., Wang, F. & Boon, N. Enrichment of a microbial community performing anaerobic oxidation of methane in a continuous high-pressure bioreactor. BMC Microbiol. 11, 137 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sauer, P., Glombitza, C. & Kallmeyer, J. A system for incubations at high gas partial pressure. Front. Microbiol. 3, 25 (2012).PubMed 
PubMed Central 
Article 

Google Scholar 
Bhattarai, S. et al. Enrichment of sulfate reducing anaerobic methane oxidizing community dominated by ANME-1 from Ginsburg Mud Volcano (Gulf of Cadiz) sediment in a biotrickling filter. Bioresour. Technol. 259, 433–441 (2018).CAS 
PubMed 
Article 

Google Scholar 
Cassarini, C. et al. Enrichment of anaerobic methanotrophs in biotrickling filters using different sulfur compounds as electron acceptor. Environ. Eng. Sci. 36, 431–443 (2018).Article 
CAS 

Google Scholar 
Cassarini, C. et al. Anaerobic methane oxidation coupled to sulfate reduction in a biotrickling filter: reactor performance and microbial community analysis. Chemosphere 236, 124290 (2019).CAS 
PubMed 
Article 

Google Scholar 
Adams, M. M., Hoarfrost, A. L., Bose, A., Joye, S. B. & Girguis, P. R. Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity. Front. Microbiol. 4, 110 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Machdar, I., Sekiguchi, Y., Sumino, H., Ohashi, A. & Harada, H. Combination of a UASB reactor and a curtain type DHS (downflow hanging sponge) reactor as a cost-effective sewage treatment system for developing countries. Water Sci. Technol. 42, 83–88 (2000).CAS 
Article 

Google Scholar 
Judd, S. The status of membrane bioreactor technology. Trends Biotechnol. 26, 109–116 (2008).CAS 
PubMed 
Article 

Google Scholar 
Smith, A. L. et al. Perspectives on anaerobic membrane bioreactor treatment of domestic wastewater: a critical review. Bioresour. Technol. 122, 149–159 (2012).CAS 
PubMed 
Article 

Google Scholar 
Meulepas, R. J. W. et al. Enrichment of anaerobic methanotrophs in sulfate-reducing membrane bioreactors. Biotechnol. Bioeng. 104, 458–470 (2009).CAS 
PubMed 
Article 

Google Scholar 
Jagersma, G. C. et al. Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment. Environ. Microbiol. 11, 3223–3232 (2009).CAS 
PubMed 
Article 

Google Scholar 
Lettinga, G., van Velsen, A. F. M., Hobma, S. W., de Zeeuw, W. & Klapwijk, A. Use of the upflow sludge blanket (USB) reactor concept for biological wastewater treatment, especially for anaerobic treatment. Biotechnol. Bioeng. 22, 699–734 (1980).CAS 
Article 

Google Scholar 
Sekiguchi, Y., Kamagata, Y., Nakamura, K., Ohashi, A. & Harada, H. Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl. Environ. Microbiol. 65, 1280–1288 (1999).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tawfik, A., Ohashi, A. & Harada, H. Sewage treatment in a combined up-flow anaerobic sludge blanket (UASB)-down-flow hanging sponge (DHS) system. Biochem. Eng. J. 29, 210–219 (2006).CAS 
Article 

Google Scholar 
Onodera, T. et al. Development of a sixth-generation down-flow hanging sponge (DHS) reactor using rigid sponge media for post-treatment of UASB treating municipal sewage. Bioresour. Technol. 152, 93–100 (2014).CAS 
PubMed 
Article 

Google Scholar 
Tandukar, M., Ohashi, A. & Harada, H. Performance comparison of a pilot-scale UASB and DHS system and activated sludge process for the treatment of municipal wastewater. Water Res. 41, 2697–2705 (2007).CAS 
PubMed 
Article 

Google Scholar 
Hallam, S. J. et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457–1462 (2004).CAS 
PubMed 
Article 

Google Scholar 
Nauhaus, K., Albrecht, M., Elvert, M., Boetius, A. & Widdel, F. In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ. Microbiol. 9, 187–196 (2007).CAS 
PubMed 
Article 

Google Scholar 
Wegener, G., Niemann, H., Elvert, M., Hinrichs, K. & Boetius, A. Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane. Environ. Microbiol. 10, 2287–2298 (2008).CAS 
PubMed 
Article 

Google Scholar 
Hu, H., Natarajan, V. P. & Wang, F. Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods. Mar. Life Sci. Technol. 3, 231–242 (2021).Article 
CAS 

Google Scholar 
Balch, W. E., Fox, G. E., Magrum, L. J., Woese, C. R. & Wolfe, R. S. Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 43, 260–296 (1979).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yokooji, Y. et al. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J. Biol. Chem. 284, 28137–28145 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Moench, T. & Zeikus, J. G. An improved preparation method for a titanium (III) media reductant. J. Microbiol. Methods 1, 199–202 (1983).CAS 
Article 

Google Scholar 
Miyashita, A. et al. Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs (ANMEs). FEMS Microbiol. Lett. 297, 31–37 (2009).CAS 
PubMed 
Article 

Google Scholar 
Sekiguchi, Y. et al. Sequence-specific cleavage of 16S rRNA for rapid and quantitative detection of particular groups of anaerobes in bioreactors. Water Sci. Technol. 52, 107–113 (2005).CAS 
PubMed 
Article 

Google Scholar 
Meechan, P. J. & Wilson, C. Use of ultraviolet lights in biological safety cabinets: a contrarian view. Appl. Biosaf. 11, 222–227 (2006).Article 

Google Scholar 
Imachi, H., Sekiguchi, Y., Kamagata, Y., Ohashi, A. & Harada, H. Cultivation and in situ detection of a thermophilic bacterium capable of oxidizing propionate in syntrophic association with hydrogenotrophic methanogens in a thermophilic methanogenic granular sludge. Appl. Environ. Microbiol. 66, 3608–3615 (2000).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stams, A. J., Grolle, K. C., Frijters, C. T. & van Lier, J. B. Enrichment of thermophilic propionate-oxidizing bacteria in syntrophy with Methanobacterium thermoautotrophicum or Methanobacterium thermoformicicum. Appl. Environ. Microbiol. 58, 346–352 (1992).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Uchino, Y. & Suzuki, K. A simple preparation of liquid media for the cultivation of strict anaerobes. J. Pet. Environ. Biotechnol. S3, 001 (2011).
Google Scholar 
Akinyemi, T. S., Shao, N. & Whitman, W. B. Genus Methanothrix. In Bergey’s Manual of Systematics of Archaea and Bacteria (John Wiley & Sons, 2020). More

Deli, J., Matus, Z. & Tóth, G. Carotenoid composition in the fruits of asparagus officinalis. J. Agric. Food Chem. 48, 2793–2796 (2000).CAS 
PubMed 

Google Scholar 
Howard, L. R., Talcott, S. T., Brenes, C. H. & Villalon, B. Changes in phytochemical and antioxidant activity of selected pepper cultivars (Capsicum species) as influenced by maturity. J. Agric. Food Chem. 48, 1713–1720 (2000).CAS 
PubMed 

Google Scholar 
Odgerel, B. & Tserendulam, D. Effect of Chlorella as a biofertilizer on germination of wheat and barley grains. P. Mongolian Acad. Sci. 56(4), 26–31 (2016).
Google Scholar 
Sun, R. B., Guo, X. S., Wang, D. Z. & Chua, H. Y. Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle. Appl. Soil Ecol. 95(6), 171–178 (2015).
Google Scholar 
Yu, Y. Q., Luo, Z. B., Fu, H. & Jin, Y. Effect of balanced nutrient fertilizer: A case study in Pinggu District, Beijing China. Sci. Total Environ. 754, 1–8 (2021).
Google Scholar 
Ahmad, P. et al. Role of transgenic plants in agriculture and biopharming. Biotech. Adv. 30, 524–540 (2012).CAS 

Google Scholar 
Sherlock, R. & Morrey, J. D. Ethical Issues in Biotechnology (Rowman and Littlefield. Publishers, Inc., 2002).
Google Scholar 
Schiavon, M., Ertani, A. & Nardi, S. Effects of an alfalfa protein hydrolysate on the gene expression and activity of enzymes of TCA cycle and N metabolism in Zea mays L. J. Agric. Food Chem. 56, 11800–11808 (2008).CAS 
PubMed 

Google Scholar 
Muscolo, A., Sidari, M. & Nardi, S. Humic substance: relationship between structure and activity. Deeper information suggests univocal findings. J. Geochem. Explor. 129, 57–63 (2013).CAS 

Google Scholar 
Nardi, S., Carletti, P., Pizzeghello, D., Muscolo, A. Biological activities of humic substances. In Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems. PART I. Fundamentals and Impact of Mineral-Organic-Biota Interactions on the Formation, Transformation, Turnover, and Storage of Natural Nonliving Organic Matter (NOM). (Ed. Senesi, N., Xing, B., Huang, P.M.) 301–335 (John Wiley and Sons, Hoboken, 2009).Ertani, A., Nardi, S. & Altissimo, A. Review: long-term research activity on the biostimulant properties of natural origin compounds. Acta Hort. 1009, 181–188 (2013).
Google Scholar 
Ertani, A. et al. Biostimulant activity of two protein hydrolysates on the growth and nitrogen metabolism in maize seedlings. J. Plant Nutr. Soil Sci. 172, 237–244 (2009).CAS 

Google Scholar 
Vaccaro, S. et al. Effect of a compost and its water-soluble fractions on key enzymes of nitrogen metabolism in maize seedlings. J. Agric. Food Chem. 57, 11267–11276 (2009).CAS 
PubMed 

Google Scholar 
Azcona, I. et al. Growth and development of pepper are affected by humic substances derived from composted sludge. J. Plant Nutr. Soil Sci. 174, 916–924 (2011).CAS 

Google Scholar 
Schiavon, M. et al. High molecular size humic substances enhance phenylpropanoid metabolism in maize (Zea mays L.). J. Chem. Ecol. 36, 662–669 (2010).CAS 
PubMed 

Google Scholar 
Ertani, A., Schiavon, M., Muscolo, A. & Nardi, S. Alfalfa plant-derived biostimulant stimulates short-term growth of salt stressed Zea mays L. plants. Plant Soil 364, 145–158 (2013).CAS 

Google Scholar 
Pascual, I., Azcona, I., Morales, F., Aguirreolea, J. & Sanchez-Diaz, M. Growth, yield and physiology of verticillium-inoculated pepper plants treated with ATAD and composted sewage sludge. Plant Soil 319, 291–306 (2009).CAS 

Google Scholar 
Pascual, I. et al. Growth, yield and fruit quality of pepper plants amended with two sanitized sewage sludges. J. Agric. Food Chem. 58, 6951–6959 (2010).CAS 
PubMed 

Google Scholar 
Kim, M. J., Shim, C. K., Kim, Y. K., Ko, B. G. & Kim, B. H. Effect of Biostimulator Chlorella fusca on improving growth and qualities of Chinese Chives and Spinach in organic farm. Plant Pathol. J. 34(6), 567–574 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Pulz, O. & Gross, W. Valuable products from biotechnology of microalgae. Appl. Microbiol. Biot. 65, 635–648 (2004).CAS 

Google Scholar 
Kim, S. J., Ko, E. J., Hong, J. K. & Jeun, Y. C. Ultrastructures of Colletotrichum orbiculare in cucumber leaves expressing systemic acquired resistance mediated by Chlorella fusca. Plant Pathol. J. 34(2), 113–120 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Faheed, F. A. & Abd-El Fattah, Z. Effect of Chlorella vulgaris as bio-fertilizer on growth parameters and metabolic aspects of Lettuce Plant. J. Agri. Soc. Sci. 4, 165–169 (2008).
Google Scholar 
Agwa, O. K., Ogugbue, C. J. & Williams, E. E. Field evidence of Chlorella vulgaris potentials as a biofertilizer for Hibiscus esculentus. Int. J. Agric. Res. 12(4), 181–189 (2017).CAS 

Google Scholar 
Ördög, V. et al. Screening microalgae for some potentially useful agricultural and pharmaceutical secondary metabolites. J. Appl. Physicol. 16, 309–401 (2004).
Google Scholar 
Stirk, W. A., Novák, O., Strnad, M. & van Staden, J. Cytokinins in macroalgae. Plant Growth Regul. 41, 13–24 (2003).CAS 

Google Scholar 
Kholssi, R., Marks, E. A. N., Montero, J. M. O., Debdoubi, A. & Rad, C. Biofertilizing effect of Chlorella sorokiniana suspensions on wheat growth. J. Plant Growth Regul. 38, 644–649 (2019).CAS 

Google Scholar 
Stirk, W. A., Ördög, V., Van Staden, J. & Jäger, K. Cytokinin-and auxin-like activity in Cyanophyta and microalgae. J. Appl. Phycol. 14, 215–221 (2002).CAS 

Google Scholar 
Park, E. R., Jo, J. O., Kim, S. M., Lee, M. Y. & Kim, K. S. Volatile flavor component of leek (Allium tuberosum Rotter). J. Korean Soc. Food Sci. Nutr. 27, 563–567 (1998) ((in Korean)).CAS 

Google Scholar 
Jin, H. et al. Ultrahigh-cell-density heterotrophic cultivation of the unicellular green microalga Scenedesmus acuminatus and application of the cells to photoautotrophic culture enhance biomass and lipid production. Biotechnol. Bioeng. 117, 96–108 (2020).CAS 
PubMed 

Google Scholar 
Kim, M. J., Shim, C. K., Kim, Y. K., Hong, S. J. & Kim, S. C. Isolation and morphological identification of fresh water green algae from organic farming habitats in Korea. Korean J. Org. Agric. 22, 743–760 (2014).
Google Scholar 
Li, L., Tian, S. L., Jiang, J. & Wang, Y. Regulation of nitric oxide to Capsicum under lower light intensities. S. Afr. J. Bot. 132, 268–276 (2020).CAS 

Google Scholar 
Cho, Y. Y., Oh, S. B., Oh, M. M. & Son, J. E. Estimation of individual leaf area, fresh weight, and dry weight of hydroponically grown cucumbers (Cucumis sativus L.) using leaf length, width, and SPAD value. Sci. Hortic-Amst. 111, 330–334 (2007).
Google Scholar 
Oster, U., Tanaka, R., Tanaka, A. & Rudiger, W. Cloning and functional expression of gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. Plant J. 21(3), 305–310 (2000).CAS 
PubMed 

Google Scholar 
Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72(1–2), 248–254 (1976).CAS 
PubMed 

Google Scholar  More

Mack, R. N. et al. Biotic invasions: Causes, epidemiology, global consequences, and control. Ecol. Appl. 10, 689–710 (2000).
Google Scholar 
Turbelin, A. J., Malamud, B. D. & Francis, R. A. Mapping the global state of invasive alien species: Patterns of invasion and policy responses. Glob. Ecol. Biogeogr. 26, 78–92 (2017).
Google Scholar 
Jackson, M. C. Interactions among multiple invasive animals. Ecology 96, 2035–2041 (2015).CAS 
PubMed 

Google Scholar 
Rodriguez, L. F. Can invasive species facilitate native species? Evidence of how, when, and why these impacts occur. Biol. Invasions 8, 927–939 (2006).
Google Scholar 
Duenas, M. A. et al. The role played by invasive species in interactions with endangered and threatened species in the United States: A systematic review. Biodivers. Conserv. 27, 3171–3183 (2018).
Google Scholar 
Weidenhamer, J. D. & Callaway, R. M. Direct and indirect effects of invasive plants on soil chemistry and ecosystem function. J. Chem. Ecol. 36, 59–69 (2010).CAS 
PubMed 

Google Scholar 
Bajwa, A. A., Chauhan, B. S., Farooq, M., Shabbir, A. & Adkins, S. W. What do we really know about alien plant invasion? A review of the invasion mechanism of one of the world’s worst weeds. Planta 244, 39–57 (2016).CAS 
PubMed 

Google Scholar 
Tallamy, D. W., Narango, D. L. & Mitchell, A. B. Do non-native plants contribute to insect declines?. Ecol. Entomol. 46, 729–742. https://doi.org/10.1111/een.12973 (2021).Article 

Google Scholar 
Bezemer, T. M., Harvey, J. A. & Cronin, J. T. Response of native insect communities to invasive plants. Annu. Rev. Entomol. 59, 119 (2014).CAS 
PubMed 

Google Scholar 
Cheng, F. & Cheng, Z. Research progress on the use of plant allelopathy in agriculture and the physiological and ecological mechanisms of allelopathy. Front. Plant Sci. 6, 1020 (2015).PubMed 
PubMed Central 

Google Scholar 
Kalisz, S., Kivlin, S. N. & Bialic-Murphy, L. Allelopathy is pervasive in invasive plants. Biol. Invasions 23, 367–371 (2021).
Google Scholar 
Pyšek, P. et al. A global assessment of invasive plant impacts on resident species, communities and ecosystems: The interaction of impact measures, invading species’ traits and environment. Glob. Change Biol. 18, 1725–1737 (2012).ADS 

Google Scholar 
Zhang, P., Li, B., Wu, J. & Hu, S. Invasive plants differentially affect soil biota through litter and rhizosphere pathways: A meta-analysis. Ecol. Lett. 22, 200–210 (2019).ADS 
PubMed 

Google Scholar 
Dudareva, N., Klempien, A., Muhlemann, J. K. & Kaplan, I. Biosynthesis, function and metabolic engineering of plant volatile organic compounds. New Phytol. 198, 16–32 (2013).CAS 
PubMed 

Google Scholar 
Clavijo McCormick, A. Can plant–natural enemy communication withstand disruption by biotic and abiotic factors?. Ecol. Evol. 6, 8569–8582 (2016).PubMed 
PubMed Central 

Google Scholar 
Bruce, T. J., Wadhams, L. J. & Woodcock, C. M. Insect host location: A volatile situation. Trends Plant Sci. 10, 269–274 (2005).CAS 
PubMed 

Google Scholar 
Clavijo McCormick, A., Unsicker, S. B. & Gershenzon, J. The specificity of herbivore-induced plant volatiles in attracting herbivore enemies. Trends Plant Sci. 17, 303–310 (2012).CAS 
PubMed 

Google Scholar 
Baldwin, I. T., Halitschke, R., Paschold, A., Von Dahl, C. C. & Preston, C. A. Volatile signaling in plant–plant interactions: “Talking trees” in the genomics era. Science 311, 812–815 (2006).ADS 
CAS 
PubMed 

Google Scholar 
Kegge, W. & Pierik, R. Biogenic volatile organic compounds and plant competition. Trends Plant Sci. 15, 126–132 (2010).CAS 
PubMed 

Google Scholar 
Effah, E., Holopainen, J. K. & Clavijo McCormick, A. Potential roles of volatile organic compounds in plant competition. Perspect. Plant Ecol. Evol. Syst. 38, 58–63 (2019).
Google Scholar 
Kigathi, R. N., Weisser, W. W., Reichelt, M., Gershenzon, J. & Unsicker, S. B. Plant volatile emission depends on the species composition of the neighboring plant community. BMC Plant Biol. 19, 1–17 (2019).
Google Scholar 
Karban, R., Wetzel, W. C., Shiojiri, K., Pezzola, E. & Blande, J. D. Geographic dialects in volatile communication between sagebrush individuals. Ecology 97, 2917–2924 (2016).PubMed 

Google Scholar 
Wheeler, G. S., David, A. S. & Lake, E. C. Volatile chemistry, not phylogeny, predicts host range of a biological control agent of Old-World climbing fern. Biol. Control 159, 104636 (2021).CAS 

Google Scholar 
Li, N. et al. Manipulating two olfactory cues causes a biological control beetle to shift to non-target plant species. J. Ecol. 105, 1534–1546 (2017).CAS 

Google Scholar 
Buddenhagen, C. E. Broom Control Monitoring at Tongariro National Park (Department of Conservation Wellington, 2000).
Google Scholar 
Hayes, L. et al. Biocontrol of Weeds: Achievements to Date and Future Outlook. Ecosystem services in New Zealand-conditions and trends Vol. 2, 375–385 (Manaaki Whenua Press, 2013).
Google Scholar 
Bagnall, A. Heather at Tongariro. A study of a weed introduction. Tussock Grasslands Mt. Lands Inst. Rev 41, 17–21 (1982).
Google Scholar 
Chapman, H. M. & Bannister, P. The spread of heather, Calluna vulgaris (L.) Hull, into indigenous plant communities of Tongariro National Park. N. Z. J. Ecol. 7–16 (1990).Effah, E. et al. Effects of two invasive weeds on arthropod community structure on the Central Plateau of New Zealand. Plants 9, 919 (2020).CAS 
PubMed Central 

Google Scholar 
Keesing, V. F. Impacts of invasion on community structure: habitat and invertebrate assemblage responses to Calluna vulgaris (L.) Hull invasion, in Tongariro National Park, New Zealand, Massey University Palmerston North, New Zealand, (1995).Peterson, P. G., Fowler, S. V. & Barrett, P. Is the poor establishment and performance of heather beetle in Tongariro National Park due to the impact of parasitoids predators or disease. N. Z. Plant Prot. 57, 89–93. https://doi.org/10.30843/nzpp.2004.57.6977 (2004).Article 

Google Scholar 
Ajpark. The brands and the bees: trade marks and the mānuka challenge for honey businesses, https://www.ajpark.com/insights/the-brands-and-the-bees-trade-marks-and-the-manuka-challenge-for-honey-businesses/#:~:text=M%C4%81nuka%20is%20a%20taonga%20species,may%20be%20offensive%20to%20M%C4%81ori (2021).Effah, E. et al. Seasonal and environmental variation in volatile emissions of the New Zealand native plant Leptospermum scoparium in weed-invaded and non-invaded sites. Sci. Rep. 10, 1–11 (2020).
Google Scholar 
Effah, E., Min Tun, K., Rangiwananga, N. & Clavijo McCormick, A. Mānuka clones differ in their volatile profiles: Potential implications for plant defence, pollinator attraction and bee products. Agronomy 12, 169 (2022).CAS 

Google Scholar 
Effah, E. et al. Natural variation in volatile emissions of the invasive weed Calluna vulgaris in New Zealand. Plants 9, 283 (2020).CAS 
PubMed Central 

Google Scholar 
Team, R. C. R: A language and environment for statistical computing (R Foundation for Statistical Computing, 2021).Ripley, B. et al. Package ‘mass’. Cran r 538, 113–120 (2013).
Google Scholar 
Chen, B. M., Liao, H. X., Chen, W. B., Wei, H. J. & Peng, S. L. Role of allelopathy in plant invasion and control of invasive plants. Allelopathy J 41, 155–166 (2017).
Google Scholar 
Ninkovic, V., Markovic, D. & Rensing, M. Plant volatiles as cues and signals in plant communication. Plant Cell Environ. 44, 1030–1043 (2021).CAS 
PubMed 

Google Scholar 
Holopainen, J. K. Multiple functions of inducible plant volatiles. Trends Plant Sci. 9, 529–533 (2004).CAS 
PubMed 

Google Scholar 
Rhoades, D. F. Responses of alder and willow to attack by tent caterpillars and webworms: evidence for pheromonal sensitivity of willows. In Plant Resistance to Insects (ed. Hedin, P. A.) 55–68 (American Chemical Society, 1983).
Google Scholar 
Hedin, P. A. Plant Resistance to Insects (American Chemical Society, 1983).
Google Scholar 
Heil, M. & Karban, R. Explaining evolution of plant communication by airborne signals. Trends Ecol. Evol. 25, 137–144 (2010).PubMed 

Google Scholar 
Barbosa, P. et al. Associational resistance and associational susceptibility: Having right or wrong neighbors. Annu. Rev. Ecol. Evol. Syst. 40, 1 (2009).
Google Scholar 
Kigathi, R. N., Weisser, W. W., Veit, D., Gershenzon, J. & Unsicker, S. B. Plants suppress their emission of volatiles when growing with conspecifics. J. Chem. Ecol. 39, 537–545 (2013).CAS 
PubMed 

Google Scholar 
Peñuelas, J. & Llusià, J. Influence of intra-and inter-specific interference on terpene emission by Pinus halepensis and Quercus ilex seedlings. Biol. Plant. 41, 139–143 (1998).
Google Scholar 
Ormeno, E., Fernandez, C. & Mévy, J.-P. Plant coexistence alters terpene emission and content of Mediterranean species. Phytochemistry 68, 840–852 (2007).CAS 
PubMed 

Google Scholar 
Himanen, S. J. et al. Birch (Betula spp.) leaves adsorb and re-release volatiles specific to neighbouring plants—A mechanism for associational herbivore resistance?. New Phytol. 186, 722–732 (2010).CAS 
PubMed 

Google Scholar 
Kessler, A. & Kalske, A. Plant secondary metabolite diversity and species interactions. Annu. Rev. Ecol. Evol. Syst. 49, 115–138 (2018).
Google Scholar 
Quintana-Rodriguez, E. et al. Plant volatiles cause direct, induced and associational resistance in common bean to the fungal pathogen Colletotrichum lindemuthianum. J. Ecol. 103, 250–260 (2015).CAS 

Google Scholar 
Loreto, F. & D’Auria, S. How do plants sense volatiles sent by other plants? Trends Plant Sci. (2021).Giordano, D., Facchiano, A., D’Auria, S. & Loreto, F. A hypothesis on the capacity of plant odorant-binding proteins to bind volatile isoprenoids based on in silico evidences. Elife 10, e66741 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Ninkovic, V., Markovic, D. & Dahlin, I. Decoding neighbour volatiles in preparation for future competition and implications for tritrophic interactions. Perspect. Plant Ecol. Evol. Syst. 23, 11–17 (2016).
Google Scholar 
Kegge, W. et al. Red: far-red light conditions affect the emission of volatile organic compounds from barley (Hordeum vulgare), leading to altered biomass allocation in neighbouring plants. Ann. Bot. 115, 961–970 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Gershenzon, J. Metabolic costs of terpenoid accumulation in higher plants. J. Chem. Ecol. 20, 1281–1328 (1994).CAS 
PubMed 

Google Scholar 
Anderson, P., Sadek, M., Larsson, M., Hansson, B. & Thöming, G. Larval host plant experience modulates both mate finding and oviposition choice in a moth. Anim. Behav. 85, 1169–1175 (2013).
Google Scholar 
Cunningham, J. P., Moore, C. J., Zalucki, M. P. & West, S. A. Learning, odour preference and flower foraging in moths. J. Exp. Biol. 207, 87–94 (2004).PubMed 

Google Scholar 
McCormick, A. C., Reinecke, A., Gershenzon, J. & Unsicker, S. B. Feeding experience affects the behavioral response of polyphagous gypsy moth caterpillars to herbivore-induced poplar volatiles. J. Chem. Ecol. 42, 382–393 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Proffit, M., Khallaf, M. A., Carrasco, D., Larsson, M. C. & Anderson, P. ‘Do you remember the first time?’ Host plant preference in a moth is modulated by experiences during larval feeding and adult mating. Ecol. Lett. 18, 365–374 (2015).PubMed 

Google Scholar 
Mayhew, P. J. Herbivore host choice and optimal bad motherhood. Trends Ecol. Evol. 16, 165–167 (2001).PubMed 

Google Scholar 
Jackson, T. et al. Anticipating the unexpected–managing pasture pest outbreaks after large-scale land conversion (New Zealand Grassland Association, 2012).Townsend, R. J., Dunbar, J. E. & Jackson, T. A. Flight behaviour of the manuka chafers, Pyronota festiva (Fabricius) and Pyronota setosa (Given) (Coleoptera: Melolonthinae), on the flipped soils of Cape Foulwind on the West Coast of New Zealand. N. Z. Plant Prot. 71, 255–261. https://doi.org/10.30843/nzpp.2018.71.175 (2018).Article 

Google Scholar 
Ferguson, C. M. et al. Quantifying the economic cost of invertebrate pests to New Zealand’s pastoral industry. N. Z. J. Agric. Res. 62, 255–315 (2019).
Google Scholar 
Cunningham, J. Can mechanism help explain insect host choice?. J. Evol. Biol. 25, 244–251 (2012).CAS 
PubMed 

Google Scholar 
Syrett, P., Smith, L. A., Bourner, T. C., Fowler, S. V. & Wilcox, A. A European pest to control a New Zealand weed: Investigating the safety of heather beetle, Lochmaea suturalis (Coleoptera: Chrysomelidae) for biological control of heather, Calluna vulgaris. Bull. Entomol. Res. 90, 169–178. https://doi.org/10.1017/S0007485300000286 (2000).CAS 
Article 
PubMed 

Google Scholar 
Fowler, S., Harman, H., Memmott, J., Peterson, P. & Smith, L. In Proceedings of the XII International Symposium on Biological Control of Weeds (eds Julien, M. H. et al.) 495–502.Fowler, S. V. et al. Investigating the poor performance of heather beetle, Lochmaea suturalis (Thompson) (Coleoptera: Chrysomelidae), as a weed biocontrol agent in New Zealand: Has genetic bottlenecking resulted in small body size and poor winter survival?. Biol. Control 87, 32–38 (2015).
Google Scholar 
Effah, E. et al. Herbivory and attenuated UV radiation affect volatile emissions of the invasive weed Calluna vulgaris. Molecules 25, 3200 (2020).CAS 
PubMed Central 

Google Scholar 
Pearson, D. E. & Callaway, R. M. Indirect nontarget effects of host-specific biological control agents: Implications for biological control. Biol. Control 35, 288–298 (2005).
Google Scholar 
Rand, T. A. & Louda, S. M. Exotic weed invasion increases the susceptibility of native plants to attack by a biocontrol herbivore. Ecology 85, 1548–1554. https://doi.org/10.1890/03-3067 (2004).Article 

Google Scholar  More

Falkowski PG. The role of phytoplankton photosynthesis in global biogeochemical cycles. Photosynth Res. 1994;39:235–58.CAS 
PubMed 
Article 

Google Scholar 
Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science. 1998;281:237.CAS 
PubMed 
Article 

Google Scholar 
Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76:667–84.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bell W, Mitchell R. Chemotactic and growth response of marine bacteria to algal extracellular products. Biol Bull. 1972;143:265–77.Article 

Google Scholar 
Seymour JR, Amin SA, Raina J-B, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat Microbiol. 2017;2:17065.CAS 
PubMed 
Article 

Google Scholar 
Azam F, Malfatti F. Microbial structuring of marine ecosystems. Nat Rev Microbiol. 2007;5:782–91.CAS 
PubMed 
Article 

Google Scholar 
Meyer N, Bigalke A, Kaulfuß A, Pohnert G. Strategies and ecological roles of algicidal bacteria. FEMS Microbiol Rev. 2017;41:880–99.CAS 
PubMed 
Article 

Google Scholar 
Windler M, Bova D, Kryvenda A, Straile D, Gruber A, Kroth PG. Influence of bacteria on cell size development and morphology of cultivated diatoms. Phycol Res. 2014;62:269–81.Article 

Google Scholar 
Buhmann MT, Schulze B, Forderer A, Schleheck D, Kroth PG. Bacteria may induce the secretion of mucin-like proteins by the diatom Phaeodactylum tricornutum. J Phycol. 2016;52:463–74.CAS 
PubMed 
Article 

Google Scholar 
van Tol HM, Amin SA, Armbrust EV. Ubiquitous marine bacterium inhibits diatom cell division. ISME J. 2017;11:31–42.PubMed 
Article 
CAS 

Google Scholar 
Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, et al. Interaction and signaling between a cosmopolitan phytoplankton and associated bacteria. Nature 2015;522:98–101.CAS 
PubMed 
Article 

Google Scholar 
Durham BP, Sharma S, Luo H, Smith CB, Amin SA, Bender SJ, et al. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc Natl Acad Sci. 2015;112:453–7.CAS 
PubMed 
Article 

Google Scholar 
Durham BP, Dearth SP, Sharma S, Amin SA, Smith CB, Campagna SR, et al. Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. Environ Microbiol 2017;19:3500–13.CAS 
PubMed 
Article 

Google Scholar 
Grossart H-P, Levold F, Allgaier M, Simon M, Brinkhoff T. Marine diatom species harbour distinct bacterial communities. Environ Microbiol. 2005;7:860–73.CAS 
PubMed 
Article 

Google Scholar 
Crenn K, Duffieux D, Jeanthon C. Bacterial epibiotic communities of ubiquitous and abundant marine diatoms are distinct in short- and long-term associations. Front Microbiol. 2018;9:2879.PubMed 
PubMed Central 
Article 

Google Scholar 
Behringer G, Ochsenkühn MA, Fei C, Fanning J, Koester JA, Amin SA. Bacterial communities of diatoms display strong conservation across strains and time. Front Microbiol. 2018;9:659.PubMed 
PubMed Central 
Article 

Google Scholar 
Schäfer H, Abbas B, Witte H, Muyzer G. Genetic diversity of ‘satellite’ bacteria present in cultures of marine diatoms. FEMS Microbiol Ecol 2002;42:25–35.PubMed 

Google Scholar 
Shibl AA, Isaac A, Ochsenkühn MA, Cárdenas A, Fei C, Behringer G, et al. Diatom modulation of select bacteria through use of two unique secondary metabolites. Proc Natl Acad Sci. 2020;117:27445–55.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Fu H, Uchimiya M, Gore J, Moran MA. Ecological drivers of bacterial community assembly in synthetic phycospheres. Proc Natl Acad Sci. 2020;117:3656–3662.Stock W, Blommaert L, De Troch M, Mangelinckx S, Willems A, Vyverman W, et al. Host specificity in diatom-bacteria interactions alleviates antagonistic effects. FEMS Microbiol Ecol. 2019;95:fiz171.Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, et al. Dynamic metabolic exchange governs a marine algal-bacterial interaction. Elife. 2016;5:e17473.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, et al. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker’s guide to life in the sea. ISME J. 2010;4:61–77.PubMed 
Article 
CAS 

Google Scholar 
Frank O, Michael V, Päuker O, Boedeker C, Jogler C, Rohde M, et al. Plasmid curing and the loss of grip – the 65-kb replicon of Phaeobacter inhibens DSM 17395 is required for biofilm formation, motility and the colonization of marine algae. Syst Appl Microbiol. 2015;38:120–7.CAS 
PubMed 
Article 

Google Scholar 
Paul C, Pohnert G. Interactions of the algicidal bacterium Kordia algicida with diatoms: regulated protease excretion for specific algal lysis. PLoS One. 2011;6:e21032.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stock F, Bilcke G, De Decker S, Osuna-Cruz CM, Van den Berge K, Vancaester E, et al. distinctive growth and transcriptional changes of the diatom Seminavis robusta in response to quorum sensing related compounds. Front Microbiol. 2020;11:1240.PubMed 
PubMed Central 
Article 

Google Scholar 
Guillard RRL Culture of Phytoplankton for Feeding Marine Invertebrates. In: Smith WL, Chanley MH, editors. Culture of marine invertebrate animals: proceedings — 1st conference on culture of marine invertebrate animals greenport. Boston, MA: Springer US; 1975. p. 29–60.Rasband WS (2016). ImageJ, U.S. National Institutes of Health, Bethesda, MD, USA. Available at: http://imagej.nih.gov/ij/, 1997–2015.DuBois M, Gilles KA, Hamilton JK, Rebers PA, Smith F. Colorimetric method for determination of sugars and related substances. Anal Chem. 1956;28:350–6.CAS 
Article 

Google Scholar 
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 
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.CAS 
PubMed 
Article 

Google Scholar 
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559.Article 
CAS 

Google Scholar 
Alexa A, Rahnenfuhrer J (2021). topGO: Enrichment analysis for gene ontology. R package version 2.46.0.Csardi G, Nepusz T (2006). “The igraph software package for complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org.Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D. NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. BMC Bioinform. 2017;18:177.Article 
CAS 

Google Scholar 
Shapiro HM (2003). Physical parameters and their uses. In: Shapiro HM (ed). Practical Flow Cytometry. John Wiley & Sons, Inc.: New York, NY, USA, pp. 273-85.Clercq AD, Inzé D. Cyclin-dependent kinase inhibitors in yeast, animals, and plants: a functional comparison. Crit Rev Biochem Mol Biol. 2006;41:293–313.PubMed 
Article 
CAS 

Google Scholar 
Zinser ER. The microbial contribution to reactive oxygen species dynamics in marine ecosystems. Environ Microbiol Rep. 2018;10:412–27.CAS 
PubMed 
Article 

Google Scholar 
Whalen KE, Kirby C, Nicholson RM, O’Reilly M, Moore BS, Harvey EL. The chemical cue tetrabromopyrrole induces rapid cellular stress and mortality in phytoplankton. Sci Rep. 2018;8:15498.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Sheyn U, Rosenwasser S, Ben-Dor S, Porat Z, Vardi A. Modulation of host ROS metabolism is essential for viral infection of a bloom-forming coccolithophore in the ocean. ISME J. 2016;10:1742–54.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Finkel ZV, Irwin AJ, Schofield O. Resource limitation alters the ¾ size scaling of metabolic rates in phytoplankton. Mar Ecol Prog Ser. 2004;273:269–80.Article 

Google Scholar 
De Troch M, Chepurnov V, Gheerardyn H, Vanreusel A, Ólafsson E. Is diatom size selection by harpacticoid copepods related to grazer body size? J Exp Mar Biol Ecol. 2006;332:1–11.Article 

Google Scholar 
Finkel ZV. Light absorption and size scaling of light-limited metabolism in marine diatoms. Limnol Oceanogr. 2001;46:86–94.CAS 
Article 

Google Scholar 
Wilhelm T, Said M, Naim V. DNA replication stress and chromosomal instability: dangerous liaisons. Genes. 2020;11:642.CAS 
PubMed Central 
Article 

Google Scholar 
Gelot C, Magdalou I, Lopez BS. Replication stress in mammalian cells and its consequences for mitosis. Genes. 2015;6:267–98.Vogt E, Kirsch-Volders M, Parry J, Eichenlaub-Ritter U. Spindle formation, chromosome segregation and the spindle checkpoint in mammalian oocytes and susceptibility to meiotic error. Mutat. Res. – Genet. Toxicol. Environ. Mutagen. 2008;651:14–29.CAS 

Google Scholar 
Van de Meene AML, Pickett-Heaps JD. Valve morphogenesis in the centric diatom Rhizosolenia setigera (Bacillariophyceae, Centrales) and its taxonomic implications. Eur J Phycol. 2004;39:93–104.Article 

Google Scholar 
Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, et al. Bacterial quorum-sensing signal arrests phytoplankton cell division and impacts virus-induced mortality. mSphere. 2021;6:e00009–21.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Von Dassow P, Petersen TW, Chepurnov VA, Virginia Armbrust E. Inter- and intraspecific relationships between nuclear DNA content and cell size in selected members of the centric diatom genus Thalassiosira (Bacillariophyceae). J Phycol. 2008;44:335–49.Article 
CAS 

Google Scholar 
Pokrzywinski KL, Tilney CL, Warner ME, Coyne KJ. Cell cycle arrest and biochemical changes accompanying cell death in harmful dinoflagellates following exposure to bacterial algicide IRI-160AA. Sci Rep. 2017;7:45102.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Durkin CA, Mock T, Armbrust EV. Chitin in diatoms and its association with the cell wall. Eukaryot Cell. 2009;8:1038.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wildermuth MC. Modulation of host nuclear ploidy: a common plant biotroph mechanism. Curr Opin Plant Biol. 2010;13:449–58.CAS 
PubMed 
Article 

Google Scholar 
Cho J-C, Giovannoni SJ. Croceibacter atlanticus gen. nov., sp. nov., A Novel Marine Bacterium in the Family Flavobacteriaceae. Syst Appl Microbiol. 2003;26:76–83.CAS 
PubMed 
Article 

Google Scholar 
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607–21.CAS 
PubMed 
Article 

Google Scholar 
Morris JJ, Lenski RE, Zinser ER. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio. 2012;3:e00036–12.PubMed 
PubMed Central 
Article 

Google Scholar 
Ndhlovu A, Durand PM, Ramsey G. Programmed cell death as a black queen in microbial communities. Mol Ecol. 2021;30:1110–9.CAS 
PubMed 
Article 

Google Scholar 
Schreiber F, Littmann S, Lavik G, Escrig S, Meibom A, Kuypers MMM, et al. Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments. Nat Microbiol. 2016;1:16055.CAS 
PubMed 
Article 

Google Scholar 
Sengupta A, Carrara F, Stocker R. Phytoplankton can actively diversify their migration strategy in response to turbulent cues. Nature 2017;543:555–8.CAS 
PubMed 
Article 

Google Scholar 
Levy SF, Ziv N, Siegal ML. Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant. PLoS Biol. 2012;10:e1001325.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ackermann M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat Rev Microbiol. 2015;13:497–508.CAS 
PubMed 
Article 

Google Scholar 
Blair PM, Land ML, Piatek MJ, Jacobson DA, Lu T-YS, Doktycz MJ, et al. Exploration of the biosynthetic potential of the populus microbiome. mSystems. 2018;3:e00045–18.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Helfrich EJN, Vogel CM, Ueoka R, Schäfer M, Ryffel F, Müller DB, et al. Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat Microbiol. 2018;3:909–19.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Long RA, Qureshi A, Faulkner DJ, Azam F. 2-n-Pentyl-4-quinolinol produced by a marine Alteromonas sp. and its potential ecological and biogeochemical roles. Appl Environ Microbiol. 2003;69:568–76.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Calabrese EJ. Hormesis: from mainstream to therapy. Cell Commun Signal. 2014;8:289–91.Article 

Google Scholar 
Chen WM, Sheu FS, Sheu SY. Novel l-amino acid oxidase with algicidal activity against toxic cyanobacterium Microcystis aeruginosa synthesized by a bacterium Aquimarina sp. Enzym Microb Technol. 2011;49:372–9.CAS 
Article 

Google Scholar 
El-Aouar Filho RA, Nicolas A, De Paula Castro TL, Deplanche M, De Carvalho Azevedo VA, Goossens PL, et al. Heterogeneous family of cyclomodulins: smart weapons that allow bacteria to hijack the eukaryotic cell cycle and promote infections. Front Cell Infect Microbiol. 2017;7:364.Ricci V, Giannouli M, Romano M, Zarrilli R. Helicobacter pylori gamma-glutamyl transpeptidase and its pathogenic role. World J Gastroenterol. 2014;20:630–8.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Teeling H, Fuchs Bernhard M, Becher D, Klockow C, Gardebrecht A, Bennke Christin M, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 2012;336:608–11.CAS 
PubMed 
Article 

Google Scholar  More