Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
Sci Rep. 2017 Nov 28;7(1):16483. doi: 10.1038/s41598-017-16633-6.
Microbial biofilms are omnipresent in nature and relevant to a broad spectrum of industries ranging from bioremediation and food production to biomedical applications. To date little is understood about how multi-species biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we apply a meta-proteomics approach to investigate the mechanisms influencing biofilm formation in a model consortium of four bacterial soil isolates; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. Protein abundances in community and single species biofilms were compared to describe occurring inter-species interactions and the resulting changes in active metabolic pathways. To obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for generating reduced reference proteomes for spectral database searches. Meta-proteomics profiling indicated that community development is dependent on cooperative interactions between community members facilitating cross-feeding on specific amino acids. Opposite regulation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, indicate that competition for limited resources also affects community development. Overall our results demonstrate the multitude of pathways involved in biofilm formation in mixed communities.
微生物生物膜在自然界中无处不在，与生物修复和食品生产到生物医学应用等广泛的行业都有关联。由于这些生物系统的复杂性，目前对于多物种生物膜群落如何在分子水平上发展和发挥功能，人们知之甚少。在这里，我们应用宏蛋白质组学方法来研究影响四种土壤分离细菌模型群落生物膜形成的机制；产碱杆菌、反硝化黄色单胞菌、微杆菌和解淀粉芽孢杆菌。将群落和单种生物膜中的蛋白质丰度进行比较，以描述发生的种间相互作用以及活跃代谢途径的变化。为了在密切相关的物种之间获得完整的分类分辨率，并支持正确的蛋白质定量，我们开发了一种新的方法来生成简化参考蛋白质组，用于光谱数据库搜索。宏蛋白质组学分析表明，群落的发展依赖于群落成员之间的合作相互作用，促进了特定氨基酸的交叉喂养。然而，解淀粉芽孢杆菌和反硝化黄色单胞菌中发酵和氮代谢途径的相反调节模式可能表明，对有限资源的竞争也会影响群落的发展。总的来说，我们的结果表明，混合群落中生物膜形成涉及多种途径。
