在污水处理厂(WWTP)中,复杂的微生物群落处理污水中的各种化学物质。分泌的蛋白质是关键的,因为许多蛋白质首先与外部(宏)分子相互作用或降解。为了更好地了解污水处理厂中的微生物功能,我们预测了来自23个丹麦WWTP的1,000多个具有生物营养去除功能的高质量宏基因组组装基因组(MAG)的WWTP微生物群的分泌蛋白质组。重点放在检查靶向主要类型的大分子的分泌的分解代谢外切酶上。我们证明,拟杆菌具有很高的消化复杂多糖的潜力,还有蛋白质和核酸.对酸性细菌和Gemmatimonadota的活性污泥成员了解不足,也具有很高的细胞外多糖消化能力。分泌的核酸酶由61%的MAG编码,表明对于WWTP中的细胞外DNA和/或RNA消化的重要性。分泌的脂肪酶是预测的最不常见的大分子靶向酶,主要由γ变形菌和粘液菌编码。相比之下,不同的类群编码胞外肽酶,表明蛋白质是广泛使用的营养素。多种分泌的多血红素细胞色素表明各种分类单元具有胞外电子转移的能力,包括一些编码具有>100血红素结合基序的未描述的细胞色素的类杆菌。粘液菌有异常大的分泌蛋白补体,可能与掠夺性生活方式和/或复杂的细胞周期有关。许多γ变形杆菌MAG(主要是前β变形杆菌)编码很少或没有分泌的水解酶,但是许多周质底物结合蛋白和ABC-和TRAP-转运蛋白,表明它们主要由小分子维持。一起,这项研究全面概述了污水处理厂微生物如何与环境相互作用,为他们的功能和利基划分提供新的见解。污水处理厂(WWTP)是清洁废水的关键生物技术系统,允许水重新进入环境,限制富营养化和污染。它们对于资源的回收也越来越重要。它们主要通过微生物的活动发挥作用,充当“活海绵”,“吸收和转化营养,有机材料,和污染物。尽管有很多研究,污水处理厂中的许多微生物是未经培养的,特征不佳,限制了我们对其功能的理解。这里,我们分析了来自WWTP的大量高质量宏基因组组装的基因组中编码的分泌酶和蛋白质,特别强调那些用来降解有机材料的。该分析表明,在微生物的不同主要系统发育群体中,分泌的蛋白质组分布高度不同。从而为不同群体在活性污泥中如何发挥作用和共存提供了新的见解。这些知识将有助于更好地了解如何有效地管理和利用WWTP微生物组。
In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme
cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed
cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a \"living sponge,\" taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.