More stories

  • in

    Ecological niche modeling based on ensemble algorithms to predicting current and future potential distribution of African swine fever virus in China

    Galindo, I. & Alonso, C. African swine fever virus: A review. Viruses 9, 103 (2017).PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Blome, S., Franzke, K. & Beer, M. African swine fever: A review of current knowledge. Virus Res. 2020, 198099 (2020).Article 
    CAS 

    Google Scholar 
    Li, X. & Tian, K. African swine fever in China. Vet. Rec. 183, 300 (2018).PubMed 
    Article 

    Google Scholar 
    Wang, T., Sun, Y. & Qiu, H. J. African swine fever: An unprecedented disaster and challenge to China. Infect. Dis. Poverty 7, 66–70 (2018).Article 

    Google Scholar 
    Gaudreault, N. N., Madden, D. W., Wilson, W. C., Trujillo, J. D. & Richt, J. A. African swine fever virus: An emerging DNA arbovirus. Front. Vet. Sci. 7, 215 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ge, S. et al. Molecular characterization of African swine fever virus, China, 2018. Emerg. Infect. Dis. 24, 2131–2133 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mason-D’Croz, D. et al. Modelling the global economic consequences of a major African swine fever outbreak in China. Nat. Food 1, 221–228 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Woonwong, Y., Do, T. D. & Thanawongnuwech, R. The future of the pig industry after the introduction of African swine fever into Asia. Anim. Front. 10, 30–37 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mulieri, P. R. & Patitucci, L. D. Using ecological niche models to describe the geographical distribution of the myiasis-causing Cochliomyia hominivorax (Diptera: Calliphoridae) in southern South America. Parasitol. Res. 118, 1077–1086 (2019).PubMed 
    Article 

    Google Scholar 
    Escobar, L. E. Ecological niche modeling: An introduction for veterinarians and epidemiologists. Front. Vet. Sci. 7, 519059 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bosso, L. et al. The rise and fall of an alien: why the successful colonizer Littorina saxatilis failed to invade the Mediterranean Sea. Biol. Invasions https://doi.org/10.1007/s10530-022-02838-y (2022).Article 

    Google Scholar 
    Wen, X. et al. Prediction of the potential distribution pattern of the great gerbil (Rhombomys opimus) under climate change based on ensemble modelling. Pest Manag. Sci. 78, 3128–3134 (2022).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cheng, Y. et al. Evaluating the risk for Usutu virus circulation in Europe: Comparison of environmental niche models and epidemiological models. Int. J. Health Geogr. 17, 1–14 (2018).Article 

    Google Scholar 
    Naimi, B. & Araújo, M. B. Sdm: A reproducible and extensible R platform for species distribution modelling. Ecography 39, 368–375 (2016).Article 

    Google Scholar 
    Georges, D. & Thuiller, W. An example of species distribution modeling with biomod2. https://r-forge.r-project.org/…/inst/doc/Simple_species_modelling.pdf?root=biomod (2013).Thuiller, W. BIOMOD: Optimizing predictions of species distributions and projecting potential future shifts under global change. Glob. Change Biol. 9, 1353–1362 (2003).ADS 
    Article 

    Google Scholar 
    Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M. B. BIOMOD: A platform for ensemble forecasting of species distributions. Ecography 32, 369–373 (2009).Article 

    Google Scholar 
    Thuiller, W. Editorial commentary on “BIOMOD: Optimizing predictions of species distributions and projecting potential future shifts under global change”. Glob. Change Biol. 20, 3591–3592 (2014).ADS 
    Article 

    Google Scholar 
    Navarro-Cerrillo, R. M., Duque-Lazo, J., Manzanedo, R. D., Sánchez-Salguero, R. & Palacios-Rodriguez, G. Climate change may threaten the southernmost Pinus nigra subsp. salzmannii (Dunal) Franco populations: An ensemble niche-based approach. iForest Biogeosci. For. 11, 396–405 (2018).Article 

    Google Scholar 
    Assefa, A., Tibebu, A., Bihon, A., Dagnachew, A. & Muktar, Y. Ecological niche modeling predicting the potential distribution of African horse sickness virus from 2020 to 2060. Sci. Rep. 12, 1748 (2022).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Raffini, F. et al. From nucleotides to satellite imagery: Approaches to identify and manage the invasive pathogen Xylella fastidiosa and its insect vectors in Europe. Sustainability 12, 4508 (2020).CAS 
    Article 

    Google Scholar 
    Wani, I. A. et al. Predicting habitat suitability and niche dynamics of Dactylorhiza hatagirea and Rheum webbianum in the Himalaya under projected climate change. Sci. Rep. 12, 13205 (2022).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Boulanger-Lapointe, N. et al. Herbivore species coexistence in changing rangeland ecosystems: First high resolution national open-source and open-access ensemble models for Iceland. Sci. Total Environ. 845, 157140 (2022).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Sillero, N. & Barbosa, A. M. Common mistakes in ecological niche models. Int. J. Geogr. Inf. Sci. 35, 213–226 (2020).Article 

    Google Scholar 
    Varela, S., Anderson, R. P., García-Valdés, R. & Fernández-González, F. Environmental filters reduce the effects of sampling bias and improve predictions of ecological niche models. Ecography 37, 1084–1091 (2014).
    Google Scholar 
    Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: How, where and how many?. Methods Ecol. Evol. 3, 327–338 (2010).Article 

    Google Scholar 
    Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: Prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).Article 

    Google Scholar 
    Xiao-Ge, X. et al. Introduction of BCC models and its participation in CMIP6. Clim. Change Res. 5, 533–539 (2019).
    Google Scholar 
    Wu, T. et al. The Beijing Climate Center Climate System Model (BCC-CSM): The main progress from CMIP5 to CMIP6. Geosci. Model Dev. 12, 1573–1600 (2019).ADS 
    Article 

    Google Scholar 
    Thomson, A. M. et al. RCP4.5: A pathway for stabilization of radiative forcing by 2100. Clim. Change 109, 77–94 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    Assefa, A., Tibebu, A., Bihon, A. & Yimana, M. Global ecological niche modelling of current and future distribution of peste des petits ruminants virus (PPRv) with an ensemble modelling algorithm. Transbound Emerg. Dis. 68, 3601–3610 (2021).PubMed 
    Article 

    Google Scholar 
    Jori, F. & Bastos, A. D. Role of wild suids in the epidemiology of African swine fever. EcoHealth 6, 296–310 (2009).PubMed 
    Article 

    Google Scholar 
    Teklue, T., Sun, Y., Abid, M., Luo, Y. & Qiu, H. J. Current status and evolving approaches to African swine fever vaccine development. Transbound Emerg. Dis. 67, 529–542 (2020).PubMed 
    Article 

    Google Scholar 
    Arias, M. et al. Approaches and perspectives for development of African swine fever virus vaccines. Vaccines 5, 35 (2017).PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Chenais, E. et al. Epidemiological considerations on African swine fever in Europe 2014–2018. Porcine Health Manag. 5, 1–10 (2019).Article 

    Google Scholar 
    Quembo, C. J., Jori, F., Vosloo, W. & Heath, L. Genetic characterization of African swine fever virus isolates from soft ticks at the wildlife/domestic interface in Mozambique and identification of a novel genotype. Transbound Emerg. Dis. 65, 420–431 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Torres, J. R. et al. Chikungunya fever: Atypical and lethal cases in the Western hemisphere: A Venezuelan experience. IDCases 2, 6–10 (2015).PubMed 
    Article 

    Google Scholar 
    Nuanualsuwan, S. et al. Persistence of African swine fever virus on porous and non-porous fomites at environmental temperatures. Porc. Health Manag. 8, 34 (2022).Article 

    Google Scholar 
    Davies, K. et al. Survival of African swine fever virus in excretions from pigs experimentally infected with the Georgia 2007/1 isolate. Transbound Emerg. Dis. 64, 425–431 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Carlson, J. et al. Stability of African swine fever virus in soil and options to mitigate the potential transmission risk. Pathogens 9, 977 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Salari, L. S., Vatandoost, H., Telmadarraiy, Z., Entezar, M. R. & Kia, E. Seasonal activity of ticks and their importance in tick-borne infectious diseases in West Azerbaijan, Iran. J. Arthropod. Borne Dis. 2, 28–34 (2008).
    Google Scholar 
    Vial, L. Biological and ecological characteristics of soft ticks (Ixodida: Argasidae) and their impact for predicting tick and associated disease distribution. Parasite 16, 191–202 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jian, L. et al. WANG potential adaptability of soft tick vectors of African swine fever to China. Chin. J. Vect. Biol. Control 21, 317–320 (2010).
    Google Scholar 
    Cwynar, P., Stojkov, J. & Wlazlak, K. African swine fever status in Europe. Viruses 11, 310 (2019).PubMed Central 
    Article 

    Google Scholar 
    Marmion, M., Parviainen, M., Luoto, M., Heikkinen, R. K. & Thuiller, W. Evaluation of consensus methods in predictive species distribution modelling. Divers. Distrib. 15, 59–69 (2009).Article 

    Google Scholar  More

  • in

    Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

    Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Boyce, D. G., Lewis, M. R. & Worm, B. Global phytoplankton decline over the past century. Nature 466, 591–596 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Henson, S. A., Cael, B. B., Allen, S. R. & Dutkiewicz, S. Future phytoplankton diversity in a changing climate. Nat. Commun. 12, 5372 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vaulot, D., Eikrem, W., Viprey, M. & Moreau, H. The diversity of small eukaryotic phytoplankton (≤3 μm) in marine ecosystems. FEMS Microbiol. Rev. 32, 795–820 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Agawin, N. S. R., Duarte, C. M. & Agustí, S. Nutrient and temperature control of the contribution of picoplankton to phytoplankton biomass and production. Limnol. Oceanogr. 45, 591–600 (2000).CAS 
    Article 

    Google Scholar 
    Morán, X. A. G., López-Urrutia, Á., Calvo-Díaz, A. & Li, W. K. W. Increasing importance of small phytoplankton in a warmer ocean. Glob. Change Biol. 16, 1137–1144 (2010).Article 

    Google Scholar 
    Li, W. K. W., McLaughlin, F. A., Lovejoy, C. & Carmack, E. C. Smallest algae thrive as the arctic ocean freshens. Science 326 https://doi.org/10.1126/science.1179798 (2009).Benner, I., Irwin, A. J. & Finkel, Z. V. Capacity of the common Arctic picoeukaryote Micromonas to adapt to a warming ocean. Limnol. Oceanography Lett. 5, 221–227 (2020).Sunda, W. G. & Huntsman, S. A. Iron uptake and growth limitation in oceanic and coastal phytoplankton. Mar. Chem. 50, 189–206 (1995).CAS 
    Article 

    Google Scholar 
    Raven, J. A. The twelfth Tansley Lecture. Small is beautiful: the picophytoplankton. Funct. Ecol. 12, 503–513 (1998).Article 

    Google Scholar 
    Morel, F. M. M. & Price, N. M. The biogeochemical cycles of trace metals in the oceans. Science 300, 944–947 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gao, X., Bowler, C. & Kazamia, E. Iron metabolism strategies in diatoms. J. Exp. Bot. 72, 2165–2180 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Caputi, L. et al. Community-level responses to iron availability in open ocean plankton ecosystems. Glob. Biogeochemical Cycles 33, 391–419 (2019).CAS 
    Article 

    Google Scholar 
    Carradec, Q. et al. A global ocean atlas of eukaryotic genes. Nat. Commun. 9, 373 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Morrissey, J. et al. A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake. Curr. Biol. 25, 364–371 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Moore, C. M. et al. Processes and patterns of oceanic nutrient limitation. Nat. Geosci. 6, 701–710 (2013).CAS 
    Article 

    Google Scholar 
    Kumar, A. & Bera, S. Revisiting nitrogen utilization in algae: a review on the process of regulation and assimilation. Bioresour. Technol. Rep. 12, 100584 (2020).Article 

    Google Scholar 
    Smith, S. R. et al. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nat. Commun. 10, 4552 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Berg, G. M., Glibert, P. M., Lomas, M. W. & Burford, M. A. Organic nitrogen uptake and growth by the chrysophyte Aureococcus anophagefferens during a brown tide event. Mar. Biol. 129, 377–387 (1997).CAS 
    Article 

    Google Scholar 
    Andersen, R. A., Saunders, G. W., Paskind, M. P. & Sexton, J. P. Ultrastructure and 18s rRNA gene sequence for Pelagomonas calceolata gen. et sp. nov. and the description of a new algal class, the pelagophyceae classis nov. J. Phycol. 29, 701–715 (1993).CAS 
    Article 

    Google Scholar 
    Choi, C. J. et al. Seasonal and geographical transitions in eukaryotic phytoplankton community structure in the Atlantic and Pacific Oceans. Front. Microbiol. 11, 542372 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Duerschlag, J. et al. Niche partitioning by photosynthetic plankton as a driver of CO2-fixation across the oligotrophic South Pacific Subtropical Ocean. ISME J 1–12 https://doi.org/10.1038/s41396-021-01072-z (2021).Worden, A. Z. et al. Global distribution of a wild alga revealed by targeted metagenomics. Curr. Biol. 22, R675–R677 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Dimier, C. é, Brunet, C., Geider, R. & Raven, J. Growth and photoregulation dynamics of the picoeukaryote Pelagomonas calceolata in fluctuating light. Limnol. Oceanogr. 54, 823–836 (2009).CAS 
    Article 

    Google Scholar 
    Dupont, C. L. et al. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 9, 1076–1092 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Kang, Y. et al. Transcriptomic responses of four pelagophytes to nutrient (N, P) and light stress. Front. Mar. Sci. 8, 636699 (2021).Huff, J. T., Zilberman, D. & Roy, S. W. Mechanism for DNA transposons to generate introns on genomic scales. Nature 538, 533–536 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543–548 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Nambiar, M. & Smith, G. R. Repression of harmful meiotic recombination in centromeric regions. Semin Cell Dev. Biol. 54, 188–197 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pessia, E. et al. Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol. Evol. 4, 675–682 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chi, J., Mahé, F., Loidl, J., Logsdon, J. & Dunthorn, M. Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway. Mol. Biol. Evol. 31, 660–672 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ramesh, M. A., Malik, S.-B. & Logsdon, J. M. A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis. Curr. Biol. 15, 185–191 (2005).CAS 
    PubMed 

    Google Scholar 
    Schurko, A. M. & Logsdon, J. M. Using a meiosis detection toolkit to investigate ancient asexual ‘scandals’ and the evolution of sex. Bioessays 30, 579–589 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ibarbalz, F. M. et al. Global trends in marine plankton diversity across kingdoms of life. Cell 179, 1084–1097.e21 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Frémont, P. et al. Restructuring of plankton genomic biogeography in the surface ocean under climate change. Nat. Clim. Chang. 12, 393–401 (2022).Article 

    Google Scholar 
    Ward, D. M. & Kaplan, J. Ferroportin-mediated iron transport: expression and regulation. Biochim Biophys. Acta 1823, 1426–1433 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gobler, C. J., Lonsdale, D. J. & Boyer, G. L. A review of the causes, effects, and potential management of harmful brown tide blooms caused by Aureococcus anophagefferens (Hargraves et sieburth). Estuaries 28, 726–749 (2005).Article 

    Google Scholar 
    Agusti, S., Lubián, L. M., Moreno-Ostos, E., Estrada, M. & Duarte, C. M. Projected changes in photosynthetic picoplankton in a warmer subtropical ocean. Front. Mar. Sci. 5, 506 (2019).Article 

    Google Scholar 
    Anderson, S. I., Barton, A. D., Clayton, S., Dutkiewicz, S. & Rynearson, T. A. Marine phytoplankton functional types exhibit diverse responses to thermal change. Nat. Commun. 12, 6413 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Martin, J. H. et al. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature 371, 123–129 (1994).CAS 
    Article 

    Google Scholar 
    Shi, D., Xu, Y., Hopkinson, B. M. & Morel, F. M. M. Effect of ocean acidification on iron availability to marine phytoplankton. Science 327, 676–679 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    McQuaid, J. B. et al. Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature 555, 534–537 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Turnšek, J. et al. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 10, e52770 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Urzica, E. I. et al. Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage[W][OA]. Plant Cell 24, 3921–3948 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mao, X. et al. Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms. ISME J. 16, 602–605 (2022).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ou, L., Cai, Y., Jin, W., Wang, Z. & Lu, S. Understanding the nitrogen uptake and assimilation of the Chinese strain of Aureococcus anophagefferens (Pelagophyceae). Algal Res. 34, 182–190 (2018).Article 

    Google Scholar 
    Shu, C. J., Ulrich, L. E. & Zhulin, I. B. The NIT domain: a predicted nitrate-responsive module in bacterial sensory receptors. Trends Biochem Sci. 28, 121–124 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wu, S. Q., Chai, W., Lin, J. T. & Stewart, V. General nitrogen regulation of nitrate assimilation regulatory gene nasR expression in Klebsiella oxytoca M5al. J. Bacteriol. 181, 7274–7284 (1999).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Alberti, A. et al. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci. Data 4, 170093 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

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

    Google Scholar 
    Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. https://doi.org/10.1101/gr.210641.116 (2016).Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vaser, R. & Šikić, M. Yet another de novo genome assembler. BioRxiv. https://doi.org/10.1101/656306 (2019).Liu, H. et al. SMARTdenovo: a de novo assembler using long noisy reads. Gigabyte 2021, 1–9 (2021).Article 

    Google Scholar 
    Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wick, R. R., Schultz, M. B., Zobel, J. & Holt, K. E. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31, 3350–3352 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27, 737–746 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aury, J.-M. & Istace, B. Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads. NAR Genomics Bioinform. 3, lqab034 (2021).Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Morgulis, A., Gertz, E. M., Schäffer, A. A. & Agarwala, R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput Biol. 13, 1028–1040 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker. http://repeatmasker.org/ (2013).Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351–i358 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867–868 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Schulz, M. H., Zerbino, D. R., Vingron, M. & Birney, E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086–1092 (2012).CAS 
    PubMed 
    PubMed Central 
    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 
    Li, H. et al. The sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Marchler-Bauer, A. et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 43, D222–D226 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Niang, G. et al. METdb: A genomic reference database for marine species. F1000Research, https://doi.org/10.7490/f1000research.1118000.1 (2020).Kent, W. J. BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).CAS 
    PubMed 
    Article 

    Google Scholar 
    Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dubarry, M. et al. Gmove a tool for eukaryotic gene predictions using various evidences. F1000Research, https://doi.org/10.7490/f1000research.1111735.1 (2016).Sibbald, S. J., Lawton, M. & Archibald, J. M. Mitochondrial genome evolution in pelagophyte algae. Genome Biol. Evol. 13, evab018 (2021).Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Delmont, T. O. et al. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genomics 2, 100123 (2022).CAS 
    Article 

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

    Google Scholar 
    Pesant, S. et al. Open science resources for the discovery and analysis of Tara Oceans data. Sci. Data 2, 150023 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aumont, O., Ethé, C., Tagliabue, A., Bopp, L. & Gehlen, M. PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies. Geoscientific Model Dev. 8, 2465–2513 (2015).CAS 
    Article 

    Google Scholar 
    Clayton, S. et al. Biogeochemical versus ecological consequences of modeled ocean physics. Biogeosciences 14, 2877–2889 (2017).CAS 
    Article 

    Google Scholar 
    Ravindra, K., Rattan, P., Mor, S. & Aggarwal, A. N. Generalized additive models: building evidence of air pollution, climate change and human health. Environ. Int. 132, 104987 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Günther, F. & Fritsch, S. neuralnet: training of neural networks. R. J. 2, 30–38 (2010).Article 

    Google Scholar 
    Gobler, C. J. et al. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc. Natl Acad. Sci. USA 108, 4352–4357 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Guo, L. et al. Genome assembly of Nannochloropsis oceanica provides evidence of host nucleus overthrow by the symbiont nucleus during speciation. Commun. Biol. 2, 1–12 (2019).CAS 
    Article 

    Google Scholar 
    Bowler, C. et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456, 239–244 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Armbrust, E. V. et al. The genome of the diatom thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306, 79–86 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    Worden, A. Z. et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes micromonas. Science 324, 268–272 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Palenik, B. et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PNAS 104, 7705–7710 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Moreau, H. et al. Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biol. 13, R74 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Read, B. A. et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209–213 (2013).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Recapping and mite removal behaviour in Cuba: home to the world’s largest population of Varroa-resistant European honeybees

    We confirm that Cuba is home to the world’s largest European honeybee population that has naturally become Varroa-resistant, with an estimated 220,000 colonies being maintained without any form of chemical treatment for over two decades19 although some drone-trapping occurred during the early years of the transition period This is despite the presence of the K-haplotype of the mite20 and the widespread occurrence of DWV19 throughout Cuba. Hence, the Cuban honeybee population is the first major case of Varroa-resistant European bees occupying an entire country of a large size (109,884 km2). In Europe the proportion of varroa-resistant honeybee populations in each country is highly variable21,22, but they still consist of small, isolated populations within any country. For example, the second largest known area of European Varroa-resistant honeybees is in North Wales, UK where 104 beekeepers have managed around 500 honey bee colonies over an area of 2500 km2 without treatment for over a decade23.It has long been established that sub-Sharan African and Africanised honeybees are Varroa-resistant and both populations cover much larger areas than Cuba, but these honeybee races are not capable of thriving in temperate regions or are rejected by beekeepers in Northern hemispheres. However, previous studies on African/Africanised and European honeybees4,5,6,9 all appear to have evolved with the same resistance mechanism7 and Cuban honeybees follow this pattern showing high recapping behaviour, high mite removal behaviour and low mite reproduction (Figs. 1, 4, Table 1).The strongest evidence that increased recapping behaviour is a direct response to the presence of Varroa, is the very low recapping rates in Varroa-naïve colonies. This is evidenced by the recapping baseline data that has now been collected from four different Varroa-naïve (Varroa free) honeybee populations (Australia, UK [two populations] and Hawaii [this study]) all producing similar results (Fig. 1). Across the four populations, a total of 9542 worker cells from 15 colonies have been studied with an average recapping rate of 2.0% (+ SD 3.2). Interestingly, only two of the colonies had atypical recapping rates of 8.5% and 10.7%, from Australia and Kauai respectively. This may suggest increased sensitivity in these colonies as no obvious causes e.g., wax moth or dead pupa, were detected in either colony. The data summary in Fig. 1 indicates that even in Varroa-treated populations the workers are still able to detect mite infested cells, but the average consistently falls significantly below that found in resistant populations. That is, in non-infested worker cells recapping rates are significantly higher in resistant populations in comparison to susceptible populations (Fig. 1) t4, 5 = − 4.185, p = 0.0023 as well as for infested cells t4, 5 = − 6.905, p = 0.00007.The ability of Cuban honeybees to detect infested cells causes not only high recapping levels but also high removal rates of artificially mite-infested cells. A mean removal rate of 81% is among one of the highest recorded in Apis mellifera7. The average control rate of 45% is driven by three colonies that all removed more than 75% of the controls, while the average of the remaining seven colonies was 28%. During the mite-removal studies in March 2022 natural Varroa infestation was 23%, whereas in December 2021 it was only 13%. This is due to decreasing worker brood rearing, caused by a shortage of nectar during the annual dry season. During this time there is an increase in hygienic behaviour in the colonies24, which could help explain the higher-than-expected removal of control cells.The reproductive ability of Varroa to produce viable i.e., mated, female offspring (r) in infested worker cells in resistant colonies in South Africa4 (r = 0.9), Brazil4 (r = 0.8), Mexico18 (r = 0.73), Europe3 (r = 0.84) is similar to the 0.87 found in Cuba (this study). In Cuba ‘r’ reduces to 0.77 when both single and multiple infested cells are considered. This reduction in mite reproduction, relative to susceptible colonies that have values of r greater than one, is directly linked to the increased ability of resistant workers to both detect and remove, by cannibalisation, the infested pupa. Hence, this ensures the invading mite fails to reproduce7 or reduces mite fertility due to the recapping process4. Although, in this study no significant difference was found in the reproduction of Varroa in recapped or non-recapped cells, supporting the findings of two previous studies5,9. Therefore, recapping may be playing a minor role in resistance. However, recapping remains the best indicator or ‘proxy’ of resistance within the vast majority of honeybee populations since it’s easier, quicker, and it requires less skill to measure recapping rates than mite removal rates. However, recapping is a highly variable trait7, hence both many cells (200–300) per colony and many colonies ( > 10) per population ideally need to be studied to help reduce the variablity, also in temperate countries measuring recapping when mite-infestation rates peak in autumn maximises detecting infested cells since the recapping of cells is spatially associated with infested cells11.Despite the current focus on what is happening in worker cells, studies focusing on the role of recapping in drone brood are still in their infancy with. Currently, data is only available from South Africa9 (Fig. 1) and now Cuba (this study). Interestingly, both studies indicate no significant difference in recapping rates between infested and non-infested brood. This is caused by some colonies performing no recapping of drone brood, while some colonies do recap cells but in a non-targeted manner. Whereas there is a significant increase in the size of the recapped area between infested (3.1 mm) and non-infested (2.3 mm) worker cells (Fig. 3), this does not occur in drone brood, as it appears that the holes are entirely exploratory. However, the lack of removal of infested drone brood may be playing an important role in mite-resistance (see below).The mite infestation of worker cells currently varies between 23 and 13% in Cuba (this study), roughly 25 years after it was first detected (1996). Whereas, in Mexico and Brazil, infestation rates of worker brood have fallen from around 20% in 1996/1999 down to 4% in 2018/197. Although, Varroa was first detected in Brazil much earlier, in 197225 and the Africanised honeybees adapted to the mite and spread northward replacing the susceptible European colonies. Therefore, we predict that the worker infestation rate in Cuba will continue to fall over the next 20 years, especially if high mite-removal rates persist. Correspondingly, we would expect to see the infestation rates of the drone brood (currently at 40%) to remain high as mites potentially avoid reproduction in worker cells. This potentially is a key, but currently overlooked part, of the resistance mechanism. Since an empirical model26 indicated that negative mite population growth occurs in (resistant) Africanised honeybee colonies only when the initial drone cells are present. This is thought to arise because mites also show a tenfold preference to reproduce in drone cells (which comprises only 1–5% of all the honeybee brood) and they soon become overcrowded as the mite population increases. This leads to inter-mite competition for the limited food and space, causing an increase in mite mortality27, resulting in negative reproductive success for mites entering these overcrowded drone cells. Thus, mite population growth in drone brood cells is limited by a density-dependent mechanism. In Cuba it has been observed that strong colonies typically with drone brood do not weaken during the drought season, whereas colonies without drone brood are weak and often die during the drought (APP personal comm).Although Cuban beekeepers have been aware of their mite-resistant honeybees for 15 to 20 years’, Cuba’s situation has only recently come to light16,18. The main reason for Varroa-resistance in Cuba is due to the centralised decision to allow natural resistance to evolve, as also was done successfully in South Africa3, rather than becoming locked into using miticides, as has happened throughout the Northern hemisphere. The CIAPI and Veterinarian Services central decision to ‘not treat’ was greatly assisted by all Cuban beekeepers being professional, registered and embedded within a strong locally based beekeeping community where colony movement and exchange of queens is within each province.There is also a large feral population and due to Cuba’s sub-tropical climate, queens are replaced annually in managed colonies because of almost continuous egg-laying, similar to honeybees in Hawaii. This rapid queen turnover speeds up natural selection relative to honeybee populations in more temperate climates. Finally, Cuba’s 60-year ban on honeybee importation has helped isolate the country from been invaded by Africanised bees which has occurred in many nearby regions (eg. Mexico, Southern USA, Puerto Rico, neighbouring Dominican Republic13 and Haiti (D. Macdonald, Apiary Inspector, Min. of Agi BC, Canada, pers. Comm.). Cuba has many managed European colonies coupled with many queen rearing stations. These colonies are productive and mild mannered. Thus, Cuba is an excellent example of the power of natural selection in honeybees when they are allowed to adapt naturally to Varroa with minimal human interference. More

  • in

    Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

    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

  • in

    Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system

    Iron and carbon dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms a synthetic phototrophic communityThe synthetic microalgal-bacterial community based on the active exchange of iron and carbon was developed by screening multiple siderophore producer bacteria and dye decolorizer algae (Fig. 1; refer to Supplementary Data S1 for detailed results). Out of seven bacterial isolates obtained from untreated textile wastewater, five showed relatively high siderophore production in CAS agar plates and broth (Fig. S1). In broth, Serratia plymuthica PW1, Serratia liquefaciens PW71, and Ralstonia pickettii PW2 produced siderophores in decreasing order of concentration, i.e., 15.26 ± 1.3  > 13.28 ± 0.9  > 10.85 ± 0.7 µMmL−1 (Table 1). Arnow’s assay confirmed that S. plymuthica PW1 (81.10 ± 9.8 µMmL−1), R. pickettii PW2 (97.43 ± 16.8 µMmL−1), and S. liquefaciens PW71 (103.1 ± 8.3 µMmL−1) produced catecholate-type siderophores. On the other hand, Csaky’s assay confirmed that Stenotrophomonas maltophilia PW5 (37.86 ± 0.4 µMmL−1) and Stenotrophomonas maltophilia PW6 (17.73 ± 0.2 µMmL−1) produced hydroxamate-type of siderophores. Out of the five algal species, only freshwater microalgae Chlorella sorokiniana and Scenedesmus sp. showed the highest dye degradation potential; therefore, they were selected for further experiments (Data S1).Fig. 1: The study design explains different stages of experiments to develop a phototrophic community of previously non-associated algae and bacteria.The stages include (A) isolation of bacterial strains from textile wastewater collected from Panipat Industrial area, Haryana (India); B cultivation of freshwater and marine algal strains; C assessment of siderophore production in bacterial strains using Schwyn and Neilands’s universal Chrome Azurol S (CAS) assay; D assessment of dye degradation potential of algae strains using Acid Black 1 (AB1) dye; E interaction study between siderophore producing bacteria and dye degrader microalgae to identify bacterial strains that could sustain on algae-derived DOM secreted in algal exudates; F algal-bacterial co-culturability assessment to study different types of microbial interactions viz. antagonism, mutualism, or no interaction between the two organisms, and G identification of algal-bacterial model phototrophic community based on the active exchange of iron and DOM (refer to Data S1 for detailed results).Full size imageTable 1 Characterization of siderophore production in bacterial strains isolated from textile wastewater.Full size tableAfter that, the sterile exudates from C. sorokiniana and Scenedesmus sp. were used as the sole source of dissolved organic matter for bacterial growth and selection of appropriate microalgal-bacterial partners comprising the phototrophic community (Fig. 1E; Data S2). All five bacterial isolates grew well on the exudate of C. sorokiniana as a sole source of carbon. On the contrary, on exudates of Scenedesmus sp., S. plymuthica PW1 showed moderate growth in 20 h, while the growth of R. pickettii PW2 and S. liquefaciens PW71 remained insignificant. S. maltophilia PW5 and PW6 failed to grow in the exudate of Scenedesmus sp. (Fig. S2B).Finally, the compatibility between the phototrophic community of selected microalgae (C. sorokiniana/ Scenedesmus sp.) and siderophore-producer bacteria (S. plymuthica PW1/ R. pickettii PW2/ S. liquefaciens PW71) was tested by co-culturing them in iron limiting BBM media (BBM-Fe; without EDTA) (Fig. 1F). In the absence of EDTA, Fe precipitates rapidly as iron oxyhydroxides and becomes unavailable to microbes. Microalgal growth curves in co-culture assays were used to measure and compare population characteristics such as carrying capacity ‘k’, growth rate ‘r’, etc., in axenic and consortium setups. Algal growth parameters in co-culture with a bacterial partner were used to categorize their interaction as putative mutualistic, antagonistic, and neutral (Data S1, Tables S1 and S2) [42]. Under iron-limiting conditions, axenic C. sorokiniana experienced iron stress as the cell growth was 4.2 ± 0.4 × 106 cells mL−1 after 200 h incubation. On the other hand, axenic Scenedesmus sp. showed a significantly higher growth (11.3 ± 1.2 × 106 cells mL−1) than C. sorokiniana suggesting an effective iron uptake mechanism under iron-limiting conditions (k; t-test, p = 0.001) (Table S1). In contrast to the axenic microalgal culture, C. sorokiniana in co-culture with R. pickettii PW2 showed a significant increase in cell count at 200 h (6.2 ± 0.85 × 106 cells mL−1) (auc; p = 0.000). However, S. plymuthica PW1 exerted a negative effect on C. sorokiniana (Fig. 2A), as indicated by its significant increase in doubling time (p = 0.009) and reduction in auc (p = 0.001) (Fig. 3A). While S. liquefaciens PW71 remained neutral to C. sorokiniana (auc; p = 0.430) (Fig. 2A, Table 2). On the other hand, the interaction of Scenedesmus sp. with both R. pickettii PW2 and S. liquefaciens PW71 was neutral, while S. plymuthica PW1 showed a negative effect (Figs. 2A and 3A).Fig. 2: Assessment of algal and bacterial growth in co-culture experiments.A The growth curves represent the difference in the growth of C. sorokiniana when grown axenically or in co-culture with S. plymuthica PW1, R. pickettii PW2, and S. liquefaciens PW71 under iron limiting conditions. Whereas, the effect of bacteria on the growth of Scenedesmus sp. was less prominent. The difference in the CFUs of bacterial strains in axenic culture and co-culture suggests the growth-promoting effect of C. sorokiniana on S. plymuthica PW1 and R. pickettii PW2. B Anion-exchange chromatography suggests a difference in the glycosyl composition in the EPS of C. sorokiniana and Scenedesmus sp. C The area under curve (auc) of S. plymuthica PW1 and R. pickettii PW2 obtained after growth curves in different sugars. Here, ‘a’, ‘b’, etc., represent grouping after Tukey’s post hoc test.Full size imageFig. 3: Assessment of algal growth parameters in the algal-bacterial phototrophic community under iron-limiting conditions.A The confidence interval plots represent the significant difference in the growth parameters i.e., growth rate ‘r’, carrying capacity ‘k’, doubling time ‘Dt’, and area under curve ‘auc’, of C. sorokiniana (left panel) and Scenedesmus sp. (right panel) in algal-bacterial co-cultures w.r.t. to axenic culture (horizontal blue dashed line). The symbols ‘*’ and ‘**’ represent p values with statistical significance of ‘p  More

  • in

    Maladaptive evolution or how a beneficial mutation may get lost due to nepotism

    Our model results indicate that in species with a strict social dominance hierarchy where social rank is determined by nepotism, a beneficial mutation occurring in a low-ranking female is not very likely to get established. This outcome emerged despite the immense advantage of the modeled mutation, which doubled its carrier’s survival probability. Moreover, the reproductive skew in our model (see Supplementary Fig. 1) was less radical than the skew reported for the spotted hyena females21, which means that in the model, low-ranking females had a relatively higher reproductive success potential than in reality. In other words, our model may be underestimating the severity of the negative selection a low rank induces.It is reasonable to assume that a low-ranking mutant female in a female dominant society would produce very few surviving offspring due to her low rank and ensuing lack of access to resources. Thus, this female would have only a slight chance to transmit the mutation to the next generation. If this female does reproduce successfully and produces a female which also inherits the mutation, chances of this daughter to pass on the mutation are also slim, as her rank would be even lower than that of her mother. However, if the young produced is a male and has inherited the mutation, chances of transmitting the mutation may increase depending on the male’s reproduction odds. As demonstrated by the four scenarios, the reduction in mutation establishment with decreasing mutant female’s rank became more and more prominent with increasing restrictions on male reproduction. In all four scenarios, the mutation establishment rate median was zero for the lowest ranking mutants, and in all cases but Scenario I, it was 41. Although female dominance hierarchy exists in a few of these species (e.g., Peruvian squirrel monkey41, ring-tailed lemur (Lemur catta)39,42, Verreaux’s sifaka (Propithecus verreauxi))13,25, we did not find any studies indicating female reproductive skew in any of them. Holekamp and Engh25, who reviewed the more classical female dominant species, also reported no evidence for female reproductive skew.This seemingly lack of female reproductive skew among most female dominant species is quite surprising in light of the rather common correlation between social rank and female reproductive success in male dominant species. To mention a few, considerable female reproductive skew is found in baboons (Papio spp), macaques (macaca spp.), feral horses (Equus caballus) and plains zebras (Equus burchelli)8,15,19.Holekamp and Smale28 state that “reproductive skew among female spotted hyenas appears to be greater than that documented among females of male-dominated species characterized by plural breeding”. They suggest that the key determinant of reproductive success among females in this species is rank-related priority of access to food resources. This high priority is reinforced by female dominance over males and is particularly important as this species resides in an environment in which prey availability is seasonal and scarce at times21. Our study suggests that this extreme difference in reproductive success, which, unlike in male-dominated species, is determined by nepotism rather than by physical characters, may induce a handicap on the entire population preventing the establishment of beneficial mutations. This may also hinder adaptation to a changing environment. However, our study results indicate that male equal access to females may, at least partially, counter the inhibition effect on a beneficial mutation establishment. More research is necessary in order to investigate female reproductive skew in species with a social structure similar to that of the spotted hyena, which is characterized by female dominance over males, plural breeding, and a strict female linear social hierarchy determined by nepotism.One intriguing possibility for testing this model’s validity would be an empirical study, provided that the value of some adaptive trait can be measured. In the case of the spotted hyena such a trait may refer to hunting success or physical capabilities. It is well established that adult female spotted hyenas are larger and more aggressive than adult males21, but little attention has been allocated to the study of individual physical differences among females of different ranks. Smith et al.43 studied within clan aggression in the context of the fission-fusion behavior characterizing the spotted hyena clans. Their results indicate more frequent aggression and resulting fissions occurring during times of food shortage. Rank was found to be the major correlate of an aggressive incident result. If it is possible to identify low-ranking females with some beneficial trait (independent of rank), it would be interesting to follow such females’ inclusive reproductive success along time, and even more so, the reproductive success of their sons.Another possible path around the conflict this model suggests would be through the selection of male admission into new clans. Male admission into clans is often constrained by severe aggression of resident immigrant males which may prevent or delay male admission21,26. Such behavior may in fact promote mutant male chances, at least in the case of a mutation that improves physical capabilities.One last, though not very likely possible detour around this difficulty is the occurrence of dominance rank exchanges. Such rank improvements are not very common among female dominated societies, except for in the case of aging females who may clear the way for their daughters44. However, Straus and Holekamp44 found that individuals who repeatedly form coalitions with their top allies are likely to improve their position, and, according to Strauss and Holekamp44, “facilitate revolutionary social change”. It should be kept in mind that not only are such incidents rather rare, but they are unlikely to turn a very low-ranking female into a high-ranking one, especially not when group size is large.More empirical and theoretical research should shed more light on this intriguing question of possible maladaptive evolution. Our model, in line with a few other models such as that of Holman31, suggests that evolution may not always lead to the best solution. As in every process, a local optimum may get evolution trapped and prevent further advance to better optima. More

  • in

    Social Support and Network Formation in a Small-Scale Horticulturalist Population

    Human evolutionary research has historically conceptualised social support as a purely dyadic phenomenon (e.g., see Refs. 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16). That is, given some trait pertaining to two persons i and j — e.g., their genetic relatedness, history of helping each other, physical proximity, or difference in wealth — does i help j? Both elegant and tractable, this dyad-centric view of social support evokes classic theoretical models of cooperation as a “Prisoner’s Dilemma” within a void consisting only of ego (i) and alter (j)17. Yet it also belies the fact that aid relationships (i.e., who helps who) constitute complex networks of supportive social bonds that emanate throughout entire human communities.Members of such networks may, in principle, unilaterally help whomever they wish. And their decisions to help — or to not help — specific others comprise a dynamic, supra-dyadic relational context that shapes one’s plausible set of aid targets at the micro level18,19,20,21,22. Put simply, in social support networks, aid is targeted and interdependent across dyads such that the patterning of cooperation among multiple alters jointly affects whom any one network member helps. This sociocentric (i.e., whole network) view of social support is distinct from the perspective taken by evolutionary graph theorists who study the emergence of cooperation on network structure and other spatial substrates (e.g., square grids) that may be fixed or dynamic (e.g., see Refs. 23,24,25). And it is distinct from the perspective taken by analysts of egocentric (i.e., personal) networks who study how the arrangement of intimate relationships exclusively between one’s closest contacts (e.g., the extent to which one’s friends are also friends) eases access to help (e.g., see Martí, Bolíbar, and Lozares26).Differences between the dyad-centric and the sociocentric perspectives on social support are not merely cosmetic. Indeed, the dyad-centric stance of human evolutionary research has led to a situation wherein the relational context of helping behaviour is underexplored. And this has, in turn, impaired understanding of the relative importance of fundamental evolutionary mechanisms to the structuring of cooperative relationships in human communities.Specifically, human evolutionary research on helping behaviour generally takes the theories of kin selection and reciprocal altruism as lodestars. In so doing, sociometric data from subsistence societies across the globe have been used to investigate whether consanguinity (i.e., genetic kinship) and reciprocity govern aid unconditionally and in relation to multiple social and demographic factors. These include affinity (i.e., marriage-based kinship), physical proximity, relative need, homophily (e.g., based on age and gender), social closeness, friendship, religiosity, reputation, conflict, status, and anthropometric measurements such as size, height, and strength. And, on balance, evidence1,2,3,4,5,6,7,8,9,10,13,14,16,27,28,29,30,31,32,33 suggests that helping family and responding in kind when helped are the primary mechanisms by which humans informally distribute resources vital to day-to-day survival (e.g., advice, information, food, money, durables, and physical assistance).However, despite laudable exceptions2,7,15,28,29,30,31,32,33,34 and perhaps due to the influence of methodological trends in the wider behavioural ecology literature on relationships between animals (see Refs. 35,36,37), human evolutionary studies of real helping behaviour have typically relied on non-network methods — namely, monadic regression, dyadic regression, and permutation tests (e.g., see Refs. 1,2,3,5,6,8,9,10,11,12,13,14,16,27). Respectively, these techniques treat the supra-dyadic structure of social support networks as ignorable, reducible to dyads, or a nuisance to be corrected for38. Yet, sociocentric research by sociologists39,40,41,42,43,44,45,46,47,48,49 firmly establishes that humans create and maintain relationships in accordance with factors intrinsic to the supra-dyadic arrangement of network structure itself (e.g., processes of degree-reinforcement and group formation involving at least three persons). And this sociological research makes clear that network-structure-related dynamics can operate simultaneously and independently of non-network factors (e.g., age and kinship).Ultimately, reliance on methods that disregard complex interdependences between aid obscures the extent to which helping family and responding in kind when helped outrank the dynamics of the cooperative system within which decisions to assist specific individuals take place. This uncertainty represents a substantial gap in our scientific understanding of altruism. Accordingly, here I tackle a major point of interest in evolutionary anthropology and human behavioural ecology50 specifically through the lens of the sociology of social networks18,21,51, asking:RQ: How important is helping family and responding in kind when helped relative to supra-dyadic, network-structure-related constraints on the provision of aid?The Current StudyTo answer my research question, I use Koster’s27 recently-released cross-sectional data on genetic relatedness and the habitual provision of tangible aid (e.g., firewood, food, valuable items, and/or physical assistance). Re-analysed here due to their exceptional detail and measurement quality in addition to their broad relevance to the scientific community (see Methods), these data were collected in 2013 and concern a complete population. Specifically, they cover all 108 adult (18+) residents (11,556 ordered dyads) of the 32 households of Arang Dak — a remote village of 279 indigenous Mayangna and Miskito swidden (i.e., “slash-and-burn”) horticulturalists. Arang Dak sits on the Lakus River in Nicaragua’s Bosawás Biosphere Reserve, a neotropical forest in the Department of Jinotega.In total, the tangible aid network that I analyse — i.e., x(t2013)— consists of 1,485 asymmetric aid relationships between the adult residents of Arang Dak. Of the 1,485 aid relationships, 1,422 are verified by the source and the recipient of help. That is, xij(t2013) = 1 if villager i reported in 2013 that they give tangible aid to villager j at least once per month and villager j reported in 2013 that they receive tangible aid from villager i at least once per month. Still, note that Koster’s27 data document self-reported resource flows as opposed to observed transfers. Named sources and targets of aid are based on the village roster — not freely recalled from memory. See Methods for a summary of the data and details on the measurement of the network and kinship.Modelling StrategyTo analyse tangible aid in relation to supra-dyadic network structure (Fig. 1), I use generative network models following Redhead and von Rueden32 and von Rueden et al.33, amongst other human evolutionary scientists2,7,15,28,29,30,31,32,33,34. Specially, I rely on Stochastic Actor-Oriented Models (SAOMs) which are used for observational (i.e., non-causal) analyses of the temporal evolution of networks.Put simply, SAOMs are akin to multinomial logistic regression. More formally, SAOMs are simulations of individual network members’ choices between outgoing relationships with different rewards and costs. These simulations are calibrated or “tuned” to the observed network data. That is, conditional on x (i.e., the observed states of a dynamic network), SAOMs simulate network evolution between successive observations or “snapshots” of the network at (M) discrete time points — i.e., (xleft({t}_{m}right)to xleft({t}_{m+1}right)) — as a continuous-time, Markovian process of repeated, asynchronous, and sequential tie changes. The Markovian process is defined on the space of all possible directed graphs for a set of N = {1, …, n} network members40,42,44,52,53,54,55.SAOMs decompose change between successive network observations into its smallest possible unit. Specifically, “change” means creating one outgoing tie if it does not exist, dropping one outgoing tie if it does, or doing nothing (i.e., maintaining the status quo network). More formally, during a SAOM simulation, focal actors i (ego) myopically modify just one of their outgoing relationships with some alter j in the set of network members N (i.e., j ∈ N, j ≠ i). The change made by i is the change that maximises a utility or “evaluation” function. In this respect, the evaluation function captures the “attractiveness”44 of tie changes — where “attraction” means “…something like ‘sending a tie to [an actor j] with a higher probability if all other circumstances are equal.’” (Snijders and Lomi56, p. 5).The evaluation function itself is a weighted sum of parameter estimates (widehat{beta }) and their associated covariates k (i.e., SAOM “effects”44) plus a Gumbel-distributed variable used to capture random influences55. The simulated tie changes or “ministeps”44 made by i shift the network between adjacent (unobserved) states. These states differ, at most, by the presence/absence of a single tie40,42. And the probabilities of the ministeps — a large number of which are required to bring one observation of the network to the next (i.e., (xleft({t}_{m}right)to xleft({t}_{m+1}right))) — are given by a multinomial logit which uses the evaluation function as the linear predictor.Each covariate k used to specify the evaluation function summarises some structural (i.e., purely network-related) feature or non-structural feature of i’s immediate (i.e., local) network — e.g., the sum of the in-degrees of i’s alters, the number of reciprocated dyads that i is embedded in, or i’s number of outgoing ties weighted by genetic relatedness. These features correspond to theoretical mechanisms of interest (e.g., preferential attachment, reciprocal altruism, or kin selection) and generally take the form of unstandardised sums.SAOM parameter estimates (widehat{beta }) (log odds ratios) summarise the association between the covariates and the simulated tie changes or “ministeps”. Specifically, should a focal actor i have the opportunity to make a ministep in departure from some current (i.e., status-quo) network state x in transit to a new network state x±ij — i.e., the adjacent network defined by i’s addition/subtraction of the tie xij to/from x — ({widehat{beta }}_{k}) is the log odds of choosing between two different versions of x±ij in relation to some covariate k. For example, ({widehat{beta }}_{{rm{Reciprocity}}}=1.7) would indicate that the log odds of i creating and maintaining the supportive relation xij is, conditional on the other covariates k, larger by 1.7 when xij reciprocates a tie (i.e., xji) compared to when xij does not reciprocate a tie (i.e., reciprocated ties are more “attractive”). In contrast, ({widehat{beta }}_{{rm{Reciprocity}}}=-1.7) would indicate that the log odds of xij is, conditional on the other effects, smaller by −1.7 when xij reciprocates a tie compared to when xij does not reciprocate a tie (i.e., reciprocated ties are less “attractive”).Given the longitudinal nature of the model, the gain in the evaluation function for a ministep is determined by the difference Δ in the value of the statistic s for a covariate k — i.e., Δk,ij(x, x±ij) = sk,i(x±ij) − sk,i(x) — incurred through the addition/subtraction of xij to/from x (see Block et al.42 and Ripley et al.44 on “change statistics”). Accordingly, ({widehat{beta }}_{{rm{Reciprocity}}}=1.7), for example, is the value that xij positively contributes to the evaluation function when xij increases the network statistic sk,i(x) underlying the Reciprocity effect by the value of one (i.e., ΔReciprocity,ij (x, x±ij) = sReciprocity,i(x±ij) − sReciprocity,i (x) = 1 − 0 = 1).The probabilities of network members being selected for a ministep is governed by a separate “rate” function. And the baseline rate parameter λ is a kind of intercept for the amount of network change between successive observations of the analysed network. Larger baseline rates indicate that, on average, more simulated tie changes were made to bring one observation of the network to the next (i.e., (xleft({t}_{m}right)to xleft({t}_{m+1}right))).However, as the data from Nicaragua are from a single point in time (i.e., 2013), I use the cross-sectional or stationary Stochastic Actor-Oriented Model (cf. von Rueden et al.33). Accordingly, Arang Dak’s tangible aid network is assumed to be in “short-term dynamic equilibrium.” As Snijders and Steglich40 (p. 265) discuss in detail, “this ‘short-term equilibrium’ specification of the SAOM is achieved by requiring that the observed network is both the centre and the starting value of a longitudinal network evolution process in which the number of change opportunities per actor [i.e., λ] is fixed to some high (but not too high) value.”Practically speaking, this means that the cross-sectionally observed network is used as the beginning and the target state for a SAOM simulation — i.e., (xleft({t}_{2013}right)to xleft({t}_{2013}right)) — during which actors are allowed to make, on average, very many changes (i.e., λ) to their portfolio of outgoing ties. These simulated tie changes produce a distribution of synthetic networks with properties that are, on average, similar to those of the cross-sectionally observed network in a converged SAOM — where the target properties correspond to the researcher-chosen SAOM effects k. Put simply, “[cross-sectional] SAOMs assume that the network structure, although changing, is in a stochastically stable state.” (Krause, Huisman, and Snijders57, p. 36–37). Thus, the estimated parameters (widehat{beta }) continue to summarise the rules by which ministeps unfold. However, the asynchronous, sequential, simulated tie changes, in a sense, “cancel out” and thus hold the network in “short-term dynamic equilibrium”40,42. Formally, the cross-sectional SAOM is defined as a stationary distribution of a Markov Chain with transition probabilities given by the multinomial logit used to model change between adjacent network states40,42.The rate parameter λ is fixed at 36 for my analysis. The value of 36 is the maximum observed out-degree in the source-recipient-verified tangible aid network x(t2013). Accordingly, under λ = 36, all members of the tangible aid network have, on average, at least one opportunity to modify their entire portfolio of outgoing ties during the simulations. Nevertheless, to ensure the robustness of my results, I also fit a second set of models for which λ was fixed to 108 (i.e., thrice the maximum out-degree).Model SpecificationTo assess the importance of kinship and reciprocity to hypothetical decisions to help others (i.e., ministeps), I use four archetypal specifications of the SAOM’s evaluation function. These model specifications feature nested sets of covariates (i.e., the SAOM “effects”44). And, using language found in prior evolutionary studies3,5, I refer to these archetypal specifications as the “Conventional Model” (Model 1) of aid, the “Extended Model” (Model 2) of aid, the “Networked Aid Model (Limited)” (Model 3), and the “Networked Aid Model (Comprehensive)” (Model 4).The first specification (i.e., Model 1) comes from Hackman et al.3 and Kasper and Borgerhoff Mulder5 who respectively label it the “Human Behavioural Ecology” and “Conventional” model. This specification is comprised of just four dyadic covariates — one each for consanguinity (i.e., Wright’s coefficient of genetic relatedness), affinity (i.e., Wright’s coefficient of genetic relatedness between i’s spouse s and his/her blood relative j), the receipt of aid, and geographic distance. The first three covariates are used to test long-standing predictions of helping in order to reap indirect and direct fitness benefits in line with the theories of kin selection and reciprocal altruism (see Refs. 1,5,27,58,59 for primers). And the fourth covariate is used to adjust for tolerated scrounging — i.e., what Jaeggi and Gurven4 (p. 2) define as aid resulting from one’s inability to monopolise resources due to costs imposed by the resource-poor — where a covariate for distance operationalises pressure to help imposed by those who are spatially close4.The second specification (i.e., Model 2) reflects Kasper and Borgerhoff Mulder’s5 and Thomas et al.’s9 extensions to the conventional model (see also Page et al.16). Specifically, and following important work by Allen-Arave, Gurven, and Hill1, Hooper et al.14, and Nolin7, it is distinguished by nuanced tests of kin selection and reciprocal altruism via interactions between: (i) consanguinity and the receipt of aid; (ii) consanguinity and relative need; and (iii) consanguinity and geographic distance. Furthermore, Kasper and Borgerhoff Mulder’s5 and Thomas et al.’s9 extended model includes covariates for the non-network-related attributes of individuals (e.g., gender, wealth, and physical size), thus adjusting for homophily, trait-based popularity, trait-based activity, and local context (e.g., results from a gift-giving game9 or, in the present case, infidelity and discrimination based on skin-tone27).The third specification (i.e., Model 4) is my revision of the second. It is geared to make the relational context of aid explicit. This is done using nine covariates that account for the breadth of sociologists’ contemporary understanding of supra-dyadic interdependence between positive-valence (i.e., not based on disliking or aggression), asymmetric social relationships39,40,41,42,43,44,45,46,47,48,49. In keeping with the nature of the SAOM, each of these covariates summarises some structural feature of a villager’s immediate (i.e., local) network (e.g., the number of transitive triads that she is embedded in). Accordingly, each structural covariate is used to capture a form of self-organisation — i.e., network formation driven by an individual’s selection of alters in response to network structure itself (Lusher et al.49, p. 10–11 and 23–27).Specifically, the covariates added in the third specification reflect predictions derived from three fundamental sociological theories of the emergence of non-romantic relationships. The first is structural balance theory which posits that individuals create and maintain ties that move groups of three people from an intransitive to a transitive state (i.e., transitive closure), the latter of which is understood to be more psychologically harmonious or “balanced” (see Refs. 39,43,47,48,60,61,62 for primers). The second is Simmelian tie theory which posits that, once formed, individuals will maintain relationships embedded in maximally-cohesive groups of three people such that 3-cliques (i.e., fully-reciprocated triads) are resistant to dissolution (see Refs. 43,48,63 for primers). The third is social exchange theory (as it relates to structured reciprocity) which posits that individuals will unilaterally give benefits to others in response to benefits received such that indirect reciprocity (i.e., returns to generosity) and generalised reciprocity (i.e. paying-it-forward) in groups of three people encourage cyclic closure — i.e., the simplest form of chain-generalised exchange (see Refs. 19,20,43 for primers). Furthermore, the third specification reflects the broad prediction that individuals vary in their propensity to send and receive relationships based on their structural position alone (e.g., popularity-biased attachment) leading to dispersion in the distribution of in-degrees and out-degrees (see Refs. 39,44,49 for primers) — especially for ties with an inherent cost to their maintenance39,42.Last, I consider a fourth specification (i.e., Model 3) that uses a subset of the nine network-structure-related covariates included in Model 4. This limited set of structural effects typifies the specifications used in prior human evolutionary studies of empirical help that present generative models of entire networks2,7,15,28,29,30,31,32,33,34. Specifically, the fourth specification features just three network-structure-related covariates to account for structural balance theory, self-reinforcing in-degree (i.e., popularity-bias), and the interplay between in-degree and out-degree.Descriptive statistics for the relevant attributes of the 108 residents of Arang Dak appear in Table 1. Formulae used to calculate the network statistics sk,i(x) underlying each effect k used to specify my SAOMs, alongside verbal descriptions to aid reader interpretation, appear in Online-Only Table 1. See Methods for additional rationale behind the third specification.Table 1 Descriptive statistics for the monadic and dyadic attributes of the residents of Arang Dak.Full size tableModel ComparisonCompared to prior human evolutionary research on social support networks, I take two novel approaches to gauging the importance of kinship and reciprocity to help. First, I use a technique41 specifically designed to measure the relative importance of individual effects in SAOMs (see Methods). And second, I evaluate each specification’s ability to produce synthetic graphs with topologies representative of the structure of the analysed tangible aid network64.Judging model specifications using topological properties reflects one of the core purposes of methods such as the SAOM and the Exponential Random Graph Model (ERGM) — i.e., to explain the emergence of global network structure (see Refs. 40,42,46,47,49 also Refs. 18,48), not simply the state of individual dyads (i.e., is aid given or not?). Admittedly, explaining global network structure is not a stated primary aim of dyadic-centric or sociocentric studies of help by human evolutionary scientists, including those wherein authors rely on SAOMs or ERGMs2,7,15,28,29,30,31,32,33,34. Still, topological reproduction is an important, strong test of the relative quality of the four archetypal specifications as each encodes the set of rules presumed to govern network members’ decisions about whom to help.To clarify, recall that here it is assumed, a priori, that network members can, in principle, cooperate with whomever they wish, that their cooperative decisions are intertwined across multiple scales, and that their micro-level decisions ultimately give rise to macro-level patterns of supportive social bonds (see Refs. 18,19,20,21,22). The macro-level patterns generated by SAOMs and ERGMs can differ dramatically based on specification40,46,47,49,64,65. Thus, the empirical relevance of a candidate model rests with its ability to produce synthetic graphs similar to the observed structure40,42,46,47,48,49,64. Ultimately, divergence between the real and simulated graphs suggests that a candidate specification is suspect as it does not describe how some network of interest could have formed. More

  • in

    Dust mitigation by the application of treated sewage effluent (TSE) in Iran

    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