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Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates
Microorganisms ( IF 4.5 ) Pub Date : 2021-01-16 , DOI: 10.3390/microorganisms9010186
Fons A de Vogel 1, 2 , Cathleen Schlundt 3 , Robert E Stote 4 , Jo Ann Ratto 4 , Linda A Amaral-Zettler 1, 3, 5
Affiliation  

Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases.

中文翻译:

来自历史上定义的具有生物降解聚羟基脂肪酸酯能力的塑料生物降解联盟的海洋细菌的比较基因组学

随着化石燃料塑料对环境的影响逐渐显现,可生物降解和可堆肥塑料受到越来越多的关注。在适当的条件下,微生物可以消耗这些塑料并在几周到几个月内将其生物降解。生物基聚羟基脂肪酸酯 (PHA) 聚合物系列因其理化特性以及在土壤、水生和堆肥环境中的生物降解性而成为一种有吸引力的替代品。标准测试方法可用于生物降解,使用天然接种物或确定的群落,后者由于标准化和可比性而受到青睐。最初的海洋生物降解标准测试方法ASTM D6691采用了这样一个定义的联盟来测试PHA生物降解性。然而,该联盟的分类组成和代谢潜力从未使用 DNA 测序技术得到证实。为此,我们复活了该联盟的可用成员,并确定了他们的系统发育位置、基因组序列内容和代谢潜力。复活的成员属于芽孢杆菌科红杆菌科弧菌科。使用比较基因组学方法,我们在大多数成员中发现了 PHA 生产和利用所需的所有酶。在透明区测定中,三个分离株也显示出细胞外解聚酶活性。然而,我们没有发现经典的 PHA 解聚酶,但鉴定了两种潜在的新细胞外解聚酶,类似于三酰甘油脂肪酶。
更新日期:2021-01-18
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