Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

Yuchen Zhang; Andrew Plymale; Jiyoung Son; Qiaoyun Huang; Wenli Chen; Xiao-Ying Yu

doi:10.3389/fchem.2023.1203314

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

Front Chem. 2023 May 25:11:1203314. doi: 10.3389/fchem.2023.1203314. eCollection 2023.

Authors

Yuchen Zhang^{1

2}, Andrew Plymale³, Jiyoung Son³, Qiaoyun Huang², Wenli Chen², Xiao-Ying Yu⁴

Affiliations

¹ National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.
² State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
³ Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, United States.
⁴ Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, TN, United States.

Abstract

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

Keywords: ToF-SIMS; biofilms; flow-cell culture; matrix effects; principal component analhysis (PCA).

Grants and funding

The manuscript preparation for X-YY was supported by the strategic Laboratory Directed Research and Development (LDRD) of the Physical Sciences Directorate of the Oak Ridge National Laboratory (ORNL).