FaRLiP in the Environment

Environmental Distribution and Diversity of FaRLiP Cyanobacteria

Where are FaRLiP cyanobacteria distributed in the natural environment? Field collection, laboratory analysis, and the establishment of a database are among our crucial tasks. Additionally, we are intrigued by how FaRLiP cyanobacteria interact with other cyanobacteria in the natural environment and discover their ecological niche.

Relative Publication:

Ko J-T, Li Y-Y, Chen P-Y, Liu P-Y#, Ho M-Y#. (2023) Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13871 (#co-corresponding author)

Establish our FaRLiP Cyanobacteria Database

By utilizing publicly available sequencing data on the internet, we can gain insights into whether FaRLiP cyanobacteria exist in various regions worldwide. This not only helps us understand the environments in which these cyanobacteria may thrive but also allows us to consolidate and incorporate the data of these FaRLiP cyanobacteria into our database.

Relative Publications:

Ko J-T, Li Y-Y, Chen P-Y, Liu P-Y#, Ho M-Y#. (2023) Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13871 (#co-corresponding author)

Sample Collection

The samples collected from the field undergo various treatments and analyses. We use different cultivation conditions, such as employing FRL or antibiotics, to screen and purify FaRLiP cyanobacteria. Flow cytometry is also a valuable tool for our selection process. Furthermore, we analyze the pigment composition by HPLC to understand whether they absorb far-red light. Additionally, we conduct 16S rRNA gene sequencing for the microbial community analysis of the samples.

Relative Publications:

Ko J-T, Li Y-Y, Chen P-Y, Liu P-Y#, Ho M-Y#. (2023) Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13871 (#co-corresponding author)
Behrendt L, Trampe EL, Nord NB, Nguyen J, Kühl M, Lonco, D., Nyarko, A., Dhinojwala, A., Hershey, O. S., & Barton, H. (2020) Life in the dark: far-red absorbing cyanobacteria extend photic zones deep into terrestrial caves. Environ. Microbiol. 22(3), 952–963. https://doi.org/10.1111/1462-2920.14774

Microbial Composition in the Samples

The samples collected from the wild environment can undergo 16S rRNA gene sequencing to understand the bacterial species present in the samples, including the cyanobacteria of interest. Furthermore, by comparing the microbial compositions at different sampling points, we can gain insights into the preferred growth locations for FaRLiP cyanobacteria. Throughout our analytical process, we apply a range of data analysis and programming skills.

Relative Publications:

Nien T-S, Bryant DA, Ho M-Y. (2022) Use of quartz sand columns to study far-red light photoacclimation (FaRLiP) in cyanobacteria. Appl. Environ. Microbiol. 88, e00562-22. https://doi.org/10.1128/aem.00562-22
Ohkubo S, and Miyashita H. (2017) A niche for cyanobacteria producing chlorophyll f within a microbial mat. ISME J. 11(10), 2368–2378. https://doi.org/10.1038/ismej.2017.98

Simulating Terrestrial Environments

Why do FaRLiP cyanobacteria, even when capable of using visible light for photosynthesis, sometimes choose to utilize far-red light for photosynthesis? By coculturing FaRLiP cyanobacteria with non-FaRLiP cyanobacteria in an artificial terrestrial environment established on a quartz sand substrate, and utilizing techniques such as spectroscopy analysis and fluorescence microscopy, we can gain a better understanding of the conditions under which FaRLiP cyanobacteria utilize far-red light. Additionally, we can explore the impact of non-FaRLiP cyanobacteria on their distribution, thereby enhancing our comprehension of the ecological niche selection of FaRLiP cyanobacteria.

Relative Publications:

Nien T-S, Chan T-H, Li Y-Y, Liu T-S, Shiau Y-J, Ho M-Y# (2024) Two cyanobacterial species exhibit stress responses when grown together in visible light or far-red light. mSphere. e00251-24 (link)

Cyanobacterial Interaction

FaRLiP cyanobacteria and non-FaRLiP cyanobacteria may inhabit the same environment in nature. To explore whether they influence each other or engage in interactions for competing limited resources, transcriptional analysis is employed. This analysis helps identify which genes in cyanobacteria exhibit altered expression levels under coculture conditions, allowing us to infer how cyanobacteria may mutually influence and interact with each other. Additionally, we are working on utilizing CRISPR/Cpf1 to explore the function of these coculture-related genes.

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