Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremedi...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.757856/full |
| _version_ | 1818405151839354880 |
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| author | Suzanne M. Kosina Peter Rademacher Kelly M. Wetmore Markus de Raad Marcin Zemla Grant M. Zane Jennifer J. Zulovich Romy Chakraborty Benjamin P. Bowen Benjamin P. Bowen Judy D. Wall Manfred Auer Adam P. Arkin Adam M. Deutschbauer Trent R. Northen Trent R. Northen |
| author_facet | Suzanne M. Kosina Peter Rademacher Kelly M. Wetmore Markus de Raad Marcin Zemla Grant M. Zane Jennifer J. Zulovich Romy Chakraborty Benjamin P. Bowen Benjamin P. Bowen Judy D. Wall Manfred Auer Adam P. Arkin Adam M. Deutschbauer Trent R. Northen Trent R. Northen |
| author_sort | Suzanne M. Kosina |
| collection | DOAJ |
| description | Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics. |
| first_indexed | 2024-12-14T08:51:30Z |
| format | Article |
| id | doaj.art-db98e15f90b94a45b99446edcfdaee62 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-14T08:51:30Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-db98e15f90b94a45b99446edcfdaee622022-12-21T23:09:02ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-12-011210.3389/fmicb.2021.757856757856Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture BiofilmsSuzanne M. Kosina0Peter Rademacher1Kelly M. Wetmore2Markus de Raad3Marcin Zemla4Grant M. Zane5Jennifer J. Zulovich6Romy Chakraborty7Benjamin P. Bowen8Benjamin P. Bowen9Judy D. Wall10Manfred Auer11Adam P. Arkin12Adam M. Deutschbauer13Trent R. Northen14Trent R. Northen15Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesDepartment of Biochemistry, University of Missouri, Columbia, MO, United StatesDepartment of Biochemistry, University of Missouri, Columbia, MO, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United StatesDepartment of Biochemistry, University of Missouri, Columbia, MO, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United StatesPseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.https://www.frontiersin.org/articles/10.3389/fmicb.2021.757856/fullbiofilmmass spectrometrymutant fitness profilingconsortiamorphologymicrobial interaction |
| spellingShingle | Suzanne M. Kosina Peter Rademacher Kelly M. Wetmore Markus de Raad Marcin Zemla Grant M. Zane Jennifer J. Zulovich Romy Chakraborty Benjamin P. Bowen Benjamin P. Bowen Judy D. Wall Manfred Auer Adam P. Arkin Adam M. Deutschbauer Trent R. Northen Trent R. Northen Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms Frontiers in Microbiology biofilm mass spectrometry mutant fitness profiling consortia morphology microbial interaction |
| title | Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms |
| title_full | Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms |
| title_fullStr | Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms |
| title_full_unstemmed | Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms |
| title_short | Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms |
| title_sort | biofilm interaction mapping and analysis bima of interspecific interactions in pseudomonas co culture biofilms |
| topic | biofilm mass spectrometry mutant fitness profiling consortia morphology microbial interaction |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.757856/full |
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