Multivariate analysis of enriched landfill soil consortia provide insight on the community structural perturbation and functioning during low-density polyethylene degradation

Microbiological Research - Tập 274 - Trang 127425 - 2023
Aubrey Dickson Chigwada1, Henry Joseph Oduor Ogola1, Memory Tekere1
1Department of environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort, 1709, South Africa

Tài liệu tham khảo

Andersen, K.S., Kirkegaard, R.H., Albertsen, M., 2018. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. bioRxiv. https://doi.org/10.1371/journal.pone.0132783. Atanasova, 2021, Plastic degradation by extremophilic bacteria, Int. J. Mol. Sci., 22 Bátori, 2018, Anaerobic degradation of bioplastics: a review, Waste Manag., 80, 406, 10.1016/j.wasman.2018.09.040 Bénédicte, 2000, A new two-component regulatory system involved in adhesion, autolysis, and extracellular proteolytic activity of staphylococcus aureus, J. Bacteriol., 182, 3955, 10.1128/JB.182.14.3955-3964.2000 Bhatia, 2014, Implications of a novel Pseudomonas species on low density polyethylene biodegradation: an in vitro to in silico approach, Springerplus, 3, 497, 10.1186/2193-1801-3-497 Brunner, 2018, Ability of fungi isolated from plastic debris floating in the shoreline of a lake to degrade plastics, PLoS One, 13, 1, 10.1371/journal.pone.0202047 Bryant, 2016, Diversity and activity of communities inhabiting plastic debris in the North Pacific gyre, mSystems, 1, 1, 10.1128/mSystems.00024-16 Buchholz, 2022, Plastics degradation by hydrolytic enzymes: the plastics-active enzymes database—PAZy, Proteins Struct. Funct. Bioinforma., 90, 1443, 10.1002/prot.26325 Caporaso, 2010, PyNAST: a flexible tool for aligning sequences to a template alignment, Bioinformatics, 26, 266, 10.1093/bioinformatics/btp636 Chang, 2013, Isolation of biphenyl and polychlorinated biphenyl-degrading bacteria and their degradation pathway, Appl. Biochem. Biotechnol., 170, 381, 10.1007/s12010-013-0191-5 De Cáceres, 2010, Improving indicator species analysis by combining groups of sites, Oikos, 119, 1674, 10.1111/j.1600-0706.2010.18334.x DeAngelis, 2013, Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1, Front. Microbiol., 4, 280, 10.3389/fmicb.2013.00280 Delacuvellerie, 2019, The plastisphere in marine ecosystem hosts potential specific microbial degraders including Alcanivorax borkumensis as a key player for the low-density polyethylene degradation, J. Hazard. Mater., 380, 10.1016/j.jhazmat.2019.120899 Ding, 2019, Metagenomic analysis of zinc surface–associated marine biofilms, Microb. Ecol., 77, 406, 10.1007/s00248-018-01313-3 Douglas, 2018, 169 Dussud, 2018, Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters, Environ. Pollut., 236, 807, 10.1016/j.envpol.2017.12.027 Ekanayaka, 2022, A Review of the Fungi That Degrade Plastic, J. Fungi, 10.3390/jof8080772 Emmanuel-Akerele, 2022, Isolation and identification of plastic degrading bacteria from dumpsites Lagos. Adv, Environ. Technol., 8, 59 Eyheraguibel, 2017, Characterization of oxidized oligomers from polyethylene films by mass spectrometry and NMR spectroscopy before and after biodegradation by a Rhodococcus rhodochrous strain, Chemosphere, 184, 366, 10.1016/j.chemosphere.2017.05.137 Furneaux, 2021, Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities, Mol. Ecol. Resour., 21, 1833, 10.1111/1755-0998.13387 Gajendiran, 2016, Microbial degradation of low-density polyethylene (LDPE) by Aspergillus clavatus strain JASK1 isolated from landfill soil, 3 Biotech, 6, 52, 10.1007/s13205-016-0394-x Gao, 2021, A marine bacterial community capable of degrading poly(ethylene terephthalate) and polyethylene, J. Hazard. Mater., 416, 10.1016/j.jhazmat.2021.125928 Geng, 2015, Paradevosia shaoguanensis gen. nov., sp. nov., Isolated from a Coking Wastewater, Curr. Microbiol., 70, 110, 10.1007/s00284-014-0689-2 Gonnella, 2019, Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2, BMC Genom., 20, 339, 10.1186/s12864-019-5710-5 Haedar, 2019, Selection of plastic degradation indigenous bacteria isolated from tamangapa landfill Macassar City, J. Phys. Conf. Ser., 1341 Hou, 2021, Potential for and distribution of enzymatic biodegradation of polystyrene by environmental microorganisms, Mater. (Basel), 14, 1 Huang, 2019, LDPE microplastic films alter microbial community composition and enzymatic activities in soil, Environ. Pollut., 254, 10.1016/j.envpol.2019.112983 Ilyas, 2017, Microbial Diversity as a Tool for Wastewater Treatment, Adv. Mater. Waste Water Treat., 171 Jogler, 2020, Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago, Antonie Van. Leeuwenhoek, 113, 1889, 10.1007/s10482-020-01424-3 Kawai, 2002, Microbial degradation of polyethers, Appl. Microbiol. Biotechnol., 58, 30, 10.1007/s00253-001-0850-2 Khruengsai, 2021, Low-density polyethylene film biodegradation potential by fungal species from thailand, J. Fungi, 7 Kowalczyk, 2016, Achromobacter xylosoxidans as a new microorganism strain colonizing high-density polyethylene as a key step to its biodegradation, Environ. Sci. Pollut. Res., 23, 11349, 10.1007/s11356-016-6563-y Krause, 2020, Persistence of plastic debris and its colonization by bacterial communities after two decades on the abyssal seafloor, Sci. Rep., 10, 1, 10.1038/s41598-020-66361-7 Kumar, 2021, Landfill microbiome harbour plastic degrading genes: a metagenomic study of solid waste dumping site of Gujarat, India, Sci. Total Environ., 779 Langille, 2013, Analysis predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 31, 814, 10.1038/nbt.2676 Lee, 2021, Biodegradative activities of fungal strains isolated from terrestrial environments in Korea, Mycobiology, 49, 285, 10.1080/12298093.2021.1903131 Li, 2023, The plastisphere of biodegradable and conventional microplastics from residues exhibit distinct microbial structure, network and function in plastic-mulching farmland, J. Hazard. Mater., 442, 10.1016/j.jhazmat.2022.130011 Liang, 2022, Preliminary findings of polypropylene carbonate (PPC) plastic film mulching effects on the soil microbial community, Agric, 12 Lozupone, 2006, UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context, BMC Bioinforma., 7, 1, 10.1186/1471-2105-7-371 Maria, 2022, Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the Ocean, mSystems, 7, e01415 Mohanan, 2020, Microbial and enzymatic degradation of synthetic plastics, Front. Microbiol, 11 Mollasalehi, S., 2013. Fungal biodegradation of polyvinyl alcohol in soil and compost environments. The University of Manchester (United Kingdom). Ndahebwa, 2018, Molecular characterization of low-density polyethene (LDPE) degrading bacteria and fungi from Dandora dumpsite, Nairobi, Kenya, Int. J. Microbiol Ojha, 2017, Evaluation of HDPE and LDPE degradation by fungus, implemented by statistical optimization, Sci. Rep., 7, 1, 10.1038/srep39515 Pathak, 2017, Review on the current status of polymer degradation: a microbial approach, Bioresour. Bioprocessing., 4, 1, 10.1186/s40643-017-0145-9 Pootakham, 2017, High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system, Sci. Rep., 7, 1, 10.1038/s41598-017-03139-4 Puiggené, 2022, Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1, Sci. Rep., 12, 1, 10.1038/s41598-022-06558-0 Qi, 2021, Evaluation of PET degradation using artificial microbial consortia, Front. Microbiol., 12, 10.3389/fmicb.2021.778828 Raaman, 2012, Biodegradation of plastic by Aspergillus spp. isolated from polythene polluted sites around Chennai, J. Acad. Ind. Res, 1, 313 Radwan, 2020, Metagenomic characterization of microbial communities on plasticized fabric materials exposed to harsh tropical environments, Int. Biodeterior. Biodegrad., 154, 10.1016/j.ibiod.2020.105061 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Rüthi, 2020, The “plastisphere” of biodegradable plastics is characterized by specific microbial taxa of alpine and arctic soils, Front. Environ. Sci., 8, 1, 10.3389/fenvs.2020.562263 Salinas, 2023, Development of plastic-degrading microbial consortia by induced selection in microcosms, Front. Microbiol., 14, 1143769, 10.3389/fmicb.2023.1143769 Sangale, 2019, Potential of fungi isolated from the dumping sites mangrove rhizosphere soil to degrade polythene, Sci. Rep., 9, 1, 10.1038/s41598-019-41448-y Sekhohola-Dlamini, 2020, Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing, Biodegradation, 31, 1, 10.1007/s10532-019-09890-x Sekhohola‐Dlamini, 2021, Community diversity metrics, interactions, and metabolic functions of bacteria associated with municipal solid waste landfills at different maturation stages, Microbiologyopen, 10, 10.1002/mbo3.1118 Singh, 2015, Multifarious activities of cellulose degrading bacteria from Koala (Phascolarctos cinereus) faeces, J. Anim. Sci. Technol., 57, 1, 10.1186/s40781-015-0056-2 Skariyachan, 2017, Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions, Environ. Sci. Pollut. Res., 24, 8443, 10.1007/s11356-017-8537-0 Taghavi, 2021, Degradation of plastic waste using stimulated and naturally occurring microbial strains, Chemosphere, 263, 10.1016/j.chemosphere.2020.127975 Vaksmaa, 2021, Microbial communities on plastic polymers in the Mediterranean Sea, Front. Microbiol., 12, 10.3389/fmicb.2021.673553 Wang, 2021, Culture enrichment combined with long-read sequencing facilitates genomic understanding of hadal sediment microbes, Front. Mar. Sci., 8, 10.3389/fmars.2021.754332 Wang, 2020, A polystyrene-degrading Acinetobacter bacterium isolated from the larvae of Tribolium castaneum, Sci. Total Environ., 726, 10.1016/j.scitotenv.2020.138564 Weber, 2018, Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis, Bioinformatics, 34, 1411, 10.1093/bioinformatics/btx617 Whelan, 2020, Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota, Nat. Microbiol., 5, 379, 10.1038/s41564-019-0643-y Wright, 2021, Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere, ISME J., 15, 789, 10.1038/s41396-020-00814-9 Xu, 2017, Aquamicrobium soli sp. nov., a bacterium isolated from a chlorobenzoate-contaminated soil, Antonie Van. Leeuwenhoek, 110, 305, 10.1007/s10482-016-0800-8 Yue, 2021, Biodegradation of bisphenol-A polycarbonate plastic by Pseudoxanthomonas sp. strain NyZ600, J. Hazard. Mater., 416, 10.1016/j.jhazmat.2021.125775 Yukie, 1998, Purification and properties of a polyester polyurethane-degrading enzyme from comamonas acidovorans TB-35, Appl. Environ. Microbiol., 64, 62, 10.1128/AEM.64.1.62-67.1998 Zeghal, 2021, The potential role of marine fungi in plastic degradation – a review, Front. Mar. Sci., 8 Zhang, 2022, Polyvinyl chloride degradation by a bacterium isolated from the gut of insect larvae, Nat. Commun., 13, 5360, 10.1038/s41467-022-32903-y Zheng, 2005, A review of plastic waste biodegradation, Crit. Rev. Biotechnol., 25, 243, 10.1080/07388550500346359 Zhuge, 2020, A novel strain of planomicrobium isolated from paper mill and its capacity of cellulose degradation, BioResources, 15, 1732, 10.15376/biores.15.1.1732-1746