MSc. Clafy Fernandes, PhD
Job Position: Postdoc - Department of Aquatic Microbial Ecology (AME)
Phone:
+420 38777 5127
E-mail:
clafy.fernandes@hbu.cas.cz
Room:
C220
My research explores the genomics and biogeography of abundant freshwater prokaryotes, particularly genome-streamlined lineages that numerically dominate lake bacterioplankton but remain poorly understood. The central focus of my doctoral research was the SAR11-IIIb lineage (genus Fontibacterium). This freshwater bacterial genus is a globally ubiquitous group that originated from one of the most successful marine-to-freshwater transitions in microbial evolution. They are genome-streamlined aerobic chemoheterotrophs characterized by small cell sizes and reduced metabolic complexity. Besides cultivation and cultivation-based experiments, I used comparative genomics, single-cell techniques such as CARD-FISH and metagenomic analyses to advance our understanding this group. My current work focuses on the genetic diversity and abundance of rhodopsin genes in Fontibacterium. Proteorhodopsins are light-driven proton pumps potentially central to the energy metabolism in carbon-limited systems, yet their diversity, expression patterns, and ecological role in freshwater SAR11 remain largely unexplored. Through periodic sampling of three oligotrophic systems combined with metagenomic and transcriptomics analyses, these results will allow us to evaluate how their expression varies along environmental gradients and seasonal cycles.
Positions
- 2026-present : Postdoctoral researcher, Institute of Hydrobiology, Biology Centre CAS, Czech Republic
- 2020-2025 : Doctoral researcher (Limnology), Institute of Hydrobiology, Biology Centre CAS & University of South Bohemia, Czech Republic
- 2017-2020 : Researcher (Marine Microbial Ecology), National Institute of Oceanography, Goa, India
Education
- PhD in Limnology - University of South Bohemia & Institute of Hydrobiology, Czech Republic (2020- 2025)
- M.Sc. in Biotechnology - Mangalore University, India (2015-2017)
- B.Sc. in Biotechnology - Goa University, India (2012-2015)
Awards and Grants
- Assessing the genetic diversity and abundance of proteorhodopsin genes related to ‘Ca. Fonsibacter’ (LD12) in freshwater lakes. Individual research project, grant agency of University of South Bohemia, 032/P/2023.
- PhD scholarship 022/2020/P, grant agency of University of South Bohemia,032/P/2023.
- Grant Programme BC (Biology Centre CAS) for abroad stay for early-stage researchers.
| Total found: 4 records
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Chiriac M.,
Layoun P., Fernandes C.,
Szöke-Nagy T.,
Kasalický V., Okazaki Y., Woodhouse J.N., Grossart H., Piwosz K.,
Znachor P., Sonntag B., Callieri C., Orlić S., Sommaruga R., Lepère C., Biderre-Petit C., Tammert H., Herlemann D.P.R., Ślusarczyk M., Bednarska A., Banciu H.L., Zalewski M., Woźniczka A.,
Ghai R.,
Salcher M.,
Haber M. (2026) Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order. Microbiome
14
: 27. DOI: 10.1186/s40168-025-02272-x |
|
Fernandes C.,
Haber M.,
Layoun P.,
Chiriac M.,
Bulzu P.,
Ghai R.,
Kasalický V.,
Shabarova T., Grossart H., Woodhouse J., Piwosz K., Alonso C., Zanetti J., Hamilton D.P., Ngochera M., Nakano S., Okazaki Y.,
Salcher M. (2025) Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium. Nature Microbiology
10
: 2194–2206. DOI: 10.1038/s41564-025-02091-8 |
|
Salcher M.,
Layoun P., Fernandes C.,
Chiriac M.,
Bulzu P.,
Ghai R.,
Shabarova T., Lanta V., Callieri C., Sonntag B., Posch T., Lepori F. ,
Znachor P.,
Haber M. (2025) Bringing the uncultivated microbial majority of freshwater ecosystems into culture. Nature Communications
16
: 7971. DOI: 10.1038/s41467-025-63266-9 |
|
Boukheloua R.,
Mukherjee I.,
Park H.,
Šimek K.,
Kasalický V., Ngochera M., Grossart H., Picazo-Mozo A., Camacho A. , Cabello-Yeves P.J., Rodriguez-Valera F. , Callieri C., Andrei A.S., Pernthaler J., Posch T., Alfreider A., Sommaruga R., Hahn M., Sonntag B., López-García P., Moreira D., Jardillier L., Lepère C., Biderre-Petit C., Bednarska A., Ślusarczyk M., Tóth V.R., Banciu H.L., Kormas K., Orlić S., Śantić D., Muyzer G., Herlemann D.P.R., Tammert H., Bertilsson S., Langenheder S., Zechmeister T. , Salmaso N., Storelli N., Capelli C., Lepori F. , Lanta V.,
Henriques Vieira H.,
Kostanjšek F.,
Kabeláčová K.,
Chiriac M.,
Haber M.,
Shabarova T.,
Rychtecký P., Fernandes C.,
Znachor P.,
Szöke-Nagy T.,
Layoun P.,
Wong H., Kavagutti V.,
Bulzu P.,
Salcher M., Piwosz K.,
Ghai R. (2024) Global freshwater distribution of Telonemia protists. The ISME Journal
18
: wrae177. DOI: 10.1093/ismejo/wrae177 |
