Analysis of microbial populations in plastic–soil systems after exposure to high poly(butylene succinate-co-adipate) load using high-resolution molecular technique

Emadian SM, Onay TT, Demirel B (2017) Biodegradation of bioplastics in natural environments. Waste Manage 59:526–536. https://doi.org/10.1016/j.wasman.2016.10.006 Li Y, Sarkanen S (2003) Biodegradable kraft lignin-based thermoplastics. In: Chiellini E, Solaro R (eds) Biodegradable polymers and plastics. Springer, Boston, pp 121–139 Rahman MH, Bhoi PR (2021) An overview of non-biodegradable bioplastics. J Clean Prod 294:126218. https://doi.org/10.1016/j.jclepro.2021.126218 Haider TP, Völker C, Kramm J et al (2019) Plastics of the future? The impact of biodegradable polymers on the environment and on society. Angew Chem Int Ed 58:50–62. https://doi.org/10.1002/anie.201805766 Brizga J, Hubacek K, Feng K (2020) The unintended side effects of bioplastics: carbon, land, and water footprints. One Earth 3:45–53. https://doi.org/10.1016/j.oneear.2020.06.016 DeVetter L, Liu H, Miles C, Ghimire S (2020) Soil-biodegradable mulches: workshop-Deterioration, degradation and tillage of soil-biodegradable mulch. https://s3.wp.wsu.edu/uploads/sites/2181/2020/11/6.-Deterioration-and-degradation.pdf. Accessed 9 July 2021 Ciriminna R, Pagliaro M (2019) Biodegradable and compostable plastics: a critical perspective on the dawn of their global adoption. ChemistryOpen 9:8–13. https://doi.org/10.1002/open.201900272 Puchalski M, Szparaga G, Biela T et al (2018) Molecular and supramolecular changes in polybutylene succinate (PBS) and polybutylene succinate adipate (PBSA) copolymer during degradation in various environmental conditions. Polymers 10:251. https://doi.org/10.3390/polym10030251 Gigli M, Negroni A, Soccio M et al (2012) Influence of chemical and architectural modifications on the enzymatic hydrolysis of poly(butylene succinate). Green Chem 14:2885–2893. https://doi.org/10.1039/C2GC35876J Mizuno S, Maeda T, Kanemura C, Hotta A (2015) Biodegradability, reprocessability, and mechanical properties of polybutylene succinate (PBS) photografted by hydrophilic or hydrophobic membranes. Polym Degrad Stab 117:58–65. https://doi.org/10.1016/j.polymdegradstab.2015.03.015 Babu RP, O’Connor K, Seeram R (2013) Current progress on bio-based polymers and their future trends. Prog Biomater 2:8. https://doi.org/10.1186/2194-0517-2-8 Bandopadhyay S, Martin-Closas L, Pelacho AM, DeBruyn JM (2018) Biodegradable plastic mulch films: impacts on soil microbial communities and ecosystem functions. Front Microbiol. https://doi.org/10.3389/fmicb.2018.00819 Brunner CT, Baran ET, Pinho ED et al (2011) Performance of biodegradable microcapsules of poly(butylene succinate), poly(butylene succinate-co-adipate) and poly(butylene terephthalate-co-adipate) as drug encapsulation systems. Colloids Surf B 84:498–507. https://doi.org/10.1016/j.colsurfb.2011.02.005 Serrano-Ruiz H, Martin-Closas L, Pelacho AM (2021) Biodegradable plastic mulches: impact on the agricultural biotic environment. Sci Total Environ 750:141228. https://doi.org/10.1016/j.scitotenv.2020.141228 Barron A, Sparks TD (2020) Commercial Marine-Degradable Polymers for Flexible Packaging. iScience. 23:101353. https://doi.org/10.1016/j.isci.2020.101353 Ritchie H, Roser M (2018) Plastic Pollution. Our World in Data. https://ourworldindata.org/plastic-pollution. Accessed 9 July 2021 Kyrikou I, Briassoulis D (2007) Biodegradation of agricultural plastic films: a critical review. J Polym Environ 15:125–150. https://doi.org/10.1007/s10924-007-0053-8 Koitabashi M, Noguchi MT, Sameshima-Yamashita Y et al (2012) Degradation of biodegradable plastic mulch films in soil environment by phylloplane fungi isolated from gramineous plants. AMB Express 2:40. https://doi.org/10.1186/2191-0855-2-40 van Emmerik T, Schwarz A (2020) Plastic debris in rivers. WIREs. Water 7:e1398. https://doi.org/10.1002/wat2.1398 Yu Y, Flury M (2021) Current understanding of subsurface transport of micro- and nanoplastics in soil. Vadose Zone J 20:e20108. https://doi.org/10.1002/vzj2.20108 Shah AA, Eguchi T, Mayumi D et al (2013) Degradation of aliphatic and aliphatic–aromatic co-polyesters by depolymerases from Roseateles depolymerans strain TB-87 and analysis of degradation products by LC-MS. Polym Degrad Stab 98:2722–2729. https://doi.org/10.1016/j.polymdegradstab.2013.10.003 Lee JW, Han M-S, Choi S et al (2011) 3.15—Organic acids: succinic and malic acids. In: Moo-Young M (ed) Comprehensive biotechnology, 2nd edn. Academic Press, Burlington, pp 149–161 Hoshino A, Sawada H, Yokota M et al (2001) Influence of weather conditions and soil properties on degradation of biodegradable plastics in soil. Soil Sci Plant Nutr 47:35–43. https://doi.org/10.1080/00380768.2001.10408366 Gan Z, Zhang H (2019) PMBD: a comprehensive plastics microbial biodegradation database. Database. https://doi.org/10.1093/database/baz119 Moore-Kucera J, Cox SB, Peyron M et al (2014) Native soil fungi associated with compostable plastics in three contrasting agricultural settings. Appl Microbiol Biotechnol 98:6467–6485. https://doi.org/10.1007/s00253-014-5711-x Adhikari D, Mukai M, Kubota K et al (2016) Degradation of bioplastics in soil and their degradation effects on environmental microorganisms. J Agric Chem Environ 5:23–34. https://doi.org/10.4236/jacen.2016.51003 Crawford SE, Hartung T, Hollert H et al (2017) Green toxicology: a strategy for sustainable chemical and material development. Environ Sci Eur 29:16. https://doi.org/10.1186/s12302-017-0115-z Francioli D, Schulz E, Lentendu G et al (2016) Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front Microbiol. https://doi.org/10.3389/fmicb.2016.01446 Schädler M, Buscot F, Klotz S et al (2019) Investigating the consequences of climate change under different land-use regimes: a novel experimental infrastructure. Ecosphere 10:e02635. https://doi.org/10.1002/ecs2.2635 Belete F, Dechassa N, Molla A, Tana T (2018) Effect of nitrogen fertilizer rates on grain yield and nitrogen uptake and use efficiency of bread wheat (Triticum aestivum L.) varieties on the Vertisols of central highlands of Ethiopia. Agric Food Sec 7:78. https://doi.org/10.1186/s40066-018-0231-z Zebarth BJ, Bowen PA, Toivonen PMA (1995) Influence of nitrogen fertilization on broccoli yield, nitrogen accumulation and apparent fertilizer-nitrogen recovery. Can J Plant Sci 75:717–725. https://doi.org/10.4141/cjps95-122 Cosgrove L, McGeechan PL, Robson GD, Handley PS (2007) Fungal communities associated with degradation of polyester polyurethane in soil. Appl Environ Microbiol 73:5817–5824. https://doi.org/10.1128/AEM.01083-07 Caporaso JG, Lauber CL, Walters WA et al (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 108:4516–4522. https://doi.org/10.1073/pnas.1000080107 Ihrmark K, Bödeker ITM, Cruz-Martinez K et al (2012) New primers to amplify the fungal ITS2 region—evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 82:666–677. https://doi.org/10.1111/j.1574-6941.2012.01437.x White TJ, Bruns TD, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322 Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12. https://doi.org/10.14806/ej.17.1.200 Callahan BJ, McMurdie PJ, Rosen MJ et al (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. https://doi.org/10.1038/nmeth.3869 Weißbecker C, Schnabel B, Heintz-Buschart A (2020) Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology. Gigascience. https://doi.org/10.1093/gigascience/giaa135 Kõljalg U, Nilsson RH, Abarenkov K et al (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277. https://doi.org/10.1111/mec.12481 Callahan BJ, McMurdie PJ, Holmes SP (2017) Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J 11:2639–2643. https://doi.org/10.1038/ismej.2017.119 Nilsson RH, Larsson K-H, Taylor AFS et al (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res 47:D259–D264. https://doi.org/10.1093/nar/gky1022 Nguyen NH, Song Z, Bates ST et al (2016) FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol 20:241–248. https://doi.org/10.1016/j.funeco.2015.06.006 Sansupa C, Wahdan SFM, Hossen S et al (2021) Can we use functional annotation of prokaryotic taxa (FAPROTAX) to assign the ecological functions of soil bacteria? Appl Sci 11:688. https://doi.org/10.3390/app11020688 Amend AS, Seifert KA, Bruns TD (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 19:5555–5565. https://doi.org/10.1111/j.1365-294X.2010.04898.x Oksanen J, Blanche FG, Friendly M, et al (2016) Vegan: Community Ecology Package. R-package version 2.4-0 Akutsu-Shigeno Y, Teeraphatpornchai T, Teamtisong K (2003) Cloning and sequencing of a poly(dl-lactic acid) depolymerase gene from Paenibacillus amylolyticus strain TB-13 and its functional expression in Escherichia coli. Appl Environ Microbiol 69(5):2498–2504. https://doi.org/10.1128/AEM.69.5.2498-2504.2003 Abe M, Kobayashi K, Honma N, Nakasaki K (2010) Microbial degradation of poly(butylene succinate) by Fusarium solani in soil environments. Polym Degrad Stab 95:138–143. https://doi.org/10.1016/j.polymdegradstab.2009.11.042 Maia MMD, Heasley A, Camargo de Morais MM et al (2001) Effect of culture conditions on lipase production by Fusarium solani in batch fermentation. Biores Technol 76:23–27. https://doi.org/10.1016/S0960-8524(00)00079-1 Purahong W, Wahdan SFM, Heinz D, et al (2021) Back to the future: decomposability of a bio-based and biodegradable plastic in field soil environments and its microbiome under ambient and future climates. Environmental Science and Technology. (in press) Song Y, Laureijssen-van de Sande WWJ, Moreno LF et al (2017) Comparative ecology of capsular Exophiala species causing disseminated infection in humans. Front Microbiol. https://doi.org/10.3389/fmicb.2017.02514 Fageria NK, dos Santos AB, Moraes MF (2010) Influence of urea and ammonium sulfate on soil acidity indices in lowland rice production. Commun Soil Sci Plant Anal 41:1565–1575. https://doi.org/10.1080/00103624.2010.485237 Zhang X, Liu W, Zhang G et al (2015) Mechanisms of soil acidification reducing bacterial diversity. Soil Biol Biochem 81:275–281. https://doi.org/10.1016/j.soilbio.2014.11.004 Lehtovirta-Morley LE, Ross J, Hink L et al (2016) Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiol Ecol. https://doi.org/10.1093/femsec/fiw057 Su J, Liang D, Lian T (2018) Comparison of denitrification performance by bacterium Achromobacter sp. A14 under different electron donor conditions. Chem Eng J 333:320–326. https://doi.org/10.1016/j.cej.2017.09.129 Meena M, Swapnil P, Zehra A et al (2017) Beneficial microbes for disease suppression and plant growth promotion. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives. Microbial interactions and agro-ecological impacts, vol 2. Springer, Singapore, pp 395–432 Seth HK (1970) A Monograph of the genus Chaetomium. Beihefte zur Nova Hedwigia 37:1–133 Alam MW, Malik A, Rehman A, et al (2021) First record of Chaetomium globosum causing leaf spot of pomegranate in Pakistan. Plant Disease. https://doi.org/10.1094/PDIS-01-21-0200-PDN Guo J-W, Cheng J-S, Yang L-F et al (2015) First report of a leaf spot disease caused by Chaetomium globosum on pomegranate from Yunnan China. Plant Dis 100:223. https://doi.org/10.1094/PDIS-03-15-0243-PDN Soytong K, Kanokmedhakuf S, Kanokmedhakul S et al (2001) Application of Chaetomium species (Ketomium R) as a new broad spectrum biological fungicide for plant disease control. Fungal Divers 7:1–15 Marwah RG, Fatope MO, Deadman ML et al (2007) Musanahol: a new aureonitol-related metabolite from a Chaetomium sp. Tetrahedron 63:8174–8180. https://doi.org/10.1016/j.tet.2007.05.119 Zhang H, Yang Q (2007) Expressed sequence tags-based identification of genes in the biocontrol agent Chaetomium cupreum. Appl Microbiol Biotechnol 74:650–658. https://doi.org/10.1007/s00253-006-0701-2 Tomilova OG, Shternshis MV (2006) The effect of a preparation from Chaetomium fungi on the growth of phytopathogenic fungi. Appl Biochem Microbiol 42:67–71. https://doi.org/10.1134/S0003683806010108 Shanthiyaa V, Saravanakumar D, Rajendran L et al (2013) Use of Chaetomium globosum for biocontrol of potato late blight disease. Crop Prot 52:33–38. https://doi.org/10.1016/j.cropro.2013.05.006 Wallach JC, Samartino LE, Efron A, Baldi PC (1997) Human infection by Brucella melitensis: an outbreak attributed to contact with infected goats. FEMS Immunol Med Microbiol 19:315–321. https://doi.org/10.1111/j.1574-695X.1997.tb01102.x Brandt J, Albertsen M (2018) Investigation of detection limits and the influence of DNA extraction and primer choice on the observed microbial communities in drinking water samples using 16S rRNA gene amplicon sequencing. Front Microbiol. https://doi.org/10.3389/fmicb.2018.02140 Coleman JJ (2016) The Fusarium solani species complex: ubiquitous pathogens of agricultural importance. Mol Plant Pathol 17:146–158. https://doi.org/10.1111/mpp.12289 Wang J, Zhang Y, Gong S et al (2018) Effects of straw mulching on microclimate characteristics and evapotranspiration of drip-irrigated winter wheat in North China Plain. Int J Agric Biol Eng 11:122–131. https://doi.org/10.25165/ijabe.v11i2.3192 Wahdan SFM, Hossen S, Tanunchai B et al (2020) Future climate significantly alters fungal plant pathogen dynamics during the early phase of wheat litter decomposition. Microorganisms 8:908. https://doi.org/10.3390/microorganisms8060908 Tofanelli MBD, Wortman SE (2020) Benchmarking the agronomic performance of biodegradable mulches against polyethylene mulch film: a meta-analysis. Agronomy 10:1618. https://doi.org/10.3390/agronomy10101618 Moore JC, Wszelaki AL (2019) The use of biodegradable mulches in pepper production in the Southeastern United States. HortScience 54:1031–1038. https://doi.org/10.21273/HORTSCI13942-19 Hartman K, van der Heijden MGA, Wittwer RA et al (2018) Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome 6:14. https://doi.org/10.1186/s40168-017-0389-9 Chernov TI, Zhelezova AD (2020) The dynamics of soil microbial communities on different timescales: a review. Eurasian Soil Sc 53:643–652. https://doi.org/10.1134/S106422932005004X Bennett JA, Koch AM, Forsythe J et al (2020) Resistance of soil biota and plant growth to disturbance increases with plant diversity. Ecol Lett 23:119–128. https://doi.org/10.1111/ele.13408 Qi Y, Yang X, Pelaez AM et al (2018) Macro- and micro- plastics in soil-plant system: effects of plastic mulch film residues on wheat (Triticum aestivum) growth. Sci Total Environ 645:1048–1056. https://doi.org/10.1016/j.scitotenv.2018.07.229 Sforzini S, Oliveri L, Chinaglia S, Viarengo A (2016) Application of biotests for the determination of soil ecotoxicity after exposure to biodegradable plastics. Front Environ Sci. https://doi.org/10.3389/fenvs.2016.00068 Xochitl Q-P, María del Consuelo H-B, María del Consuelo M-S et al (2021) Degradation of plastics in simulated landfill conditions. Polymers 13:1014. https://doi.org/10.3390/polym13071014