Environmental bacteria are most often endowed with native surface-attachment programs that frequently conflict with efforts to engineer biofilms and synthetic communities with given tridimensional architectures. In this work we report the editing of the genome of Pseudomonas putida KT2440 for stripping the cells of most outer-facing structures of the bacterial envelope that mediate motion, binding to surfaces and biofilm formation. To this end, 23 segments of the P. putida chromosome encoding a suite of such functions were deleted, resulting in the surface-naked strain EM371, the physicochemical properties of which changed dramatically in respect to the wild type counterpart. As a consequence, surface-edited P. putida cells were unable to form biofilms on solid supports and because of the swimming deficiency and other physicochemical alterations showed a much faster sedimentation in liquid media. Surface-naked bacteria were then used as carriers of interacting partners (e.g. Jun-Fos domains) ectopically expressed by means of an autotransporter display system on the now easily accessible cell envelope. Abstraction of individual bacteria as adhesin-coated spherocylinders enabled rigorous quantitative description of the multi-cell interplay brought about by thereby engineered physical interactions. The model was then applied to parameterize the data extracted from automated analysis of confocal microscopy images of the experimentally assembled bacterial flocks for analyzing their structure and distribution. The resulting data not only corroborated the value of P. putida EM371 over the parental strain as a platform for display artificial adhesins but also provided a strategy for rational engineering of distributed biocatalysis.

中文翻译：

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裸细胞：表面简化的恶臭假单胞菌菌株的新兴特性

环境细菌最常具有天然的表面附着程序，这些程序经常与工程生物膜和具有给定三维结构的合成群落的工作相冲突。在这项工作中，我们报告了恶臭假单胞菌KT2440的基因组编辑，用于剥离介导运动，结合表面和生物膜形成的细菌包膜最外层结构的细胞。为此，删除了编码一系列这样的功能的恶臭假单胞菌染色体的23个片段，产生了表面裸露的菌株EM371，其菌株的理化性质相对于野生型对应物而言发生了巨大变化。结果，经过表面编辑的P。恶臭菌细胞无法在固体支持物上形成生物膜，并且由于游泳不足和其他理化改变，在液体培养基中的沉积要快得多。然后，将表面裸露的细菌用作通过现在容易接近的细胞包膜上的自动转运展示系统异位表达的相互作用伴侣（例如Jun-Fos域）的载体。将单个细菌提取为粘附素涂层的球形圆柱体，可以对由此设计的物理相互作用带来的多细胞相互作用进行严格的定量描述。然后将该模型应用于参数化从实验组装的细菌群的共聚焦显微镜图像的自动分析中提取的数据，以分析其结构和分布。