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Maliheh Mehrshad

Maliheh Mehrshad
I am a group leader at the Department of Aquatic Sciences and Assessment, SLU. My main research interest is to understand the functional and evolutionary aspects of parasitic interactions among aquatic microbes, specifically multipartite interactions. I combine multi-omics analyses, experimental manipulations of the natural community, enrichment cultures, and cultivated multi-trophic model systems to understand these interactions.


Ongoing Projects:

1- ERC starting grant - Phage co-infection: a missing link in deciphering phage coevolutionary dynamics-MULTIPHAGE

2- VR grant - Virus-virus interaction strategies: Understanding functional strategies when multiple viruses co-infect a single host (mVish)

3- Formas grant - How do parasitic interactions modulate the fate of phytoplankton biomass during lake eutrophication

4- STINT mobility grant - Cultural mutuality; elucidating the adaptation strategies of freshwater microbes to eutrophication by combining high throughput cultivation and omics analyses (CUALITY)

5- EasiGenomics grant - Exploring the molecular basis of parasitic chytrid-phytoplankton interactions

To check the full list of our projects and progress of our research on each project check our research webpage 


Group leader Position          Fall 2020-ongoing

Department of Aquatic Sciences and Assessment, SLU

Post-DOC Positions          Summer 2016-Fall2020                                   

-Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden (Winter 2019-Fall 2020)

-Department of Aquatic Microbial Ecology, Biology Centre CAS, Ceske Budejovice, Czech Republic (Summer 2016-Fall 2018)

PhD in Microbiology , University of Tehran, Tehran, Iran                

Thesis Title: Metagenomic survey of prokaryotes in the photic zone of the Caspian Sea



Bionomics Team members:

PostDoc: Dr. Vinicius Kavagutti (SLU, May 2024-ongoing) working on virus-bacteria interactions and virus co-infection

PhD student: Zahra Goodarzi M. Sc., (SLU, November 2023-ongoing) Thesis project: “Impact of viruses on freshwater phytoplankton”

Check this link for the complete list of mentees



Selected publications

For full list of publications check Google Scholar  &   ORCID

1- Zahiri. Z., Mehrshad. N., Mehrshad. M. (2023) DF-Phos: Prediction of Protein phosphorylation Sites by Deep Forest The Journal of Biochemistry, mvad116

2- Jurdzinski. KT., Mehrshad. M., Delgado. LF., Deng. Z., Bertilsson. S., Andersson. AF. (2023) Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. Science Advances 9, 21 (Shared first authorship)

3- Meriggi. C, Mehrshad. M., Johnson. R.K., Laugen. A.T., Drakare. S. (2023) Challenges in supplying empirical proof for predictions derived from Species Distribution Models (SDMs): the case of an invasive cyanobacterium. ISME communications 3, 56

4- Kavagutti. V.S., Bulzu. P.A., Chiriac. C.M., Salcher. M.M., Mukherjee. I., Shabarova.T., Grujčić. V., Mehrshad. M., Kasalický. V., Andrei. A.S., Jezberová. J., Seďa. J., Rychtecký. P., Znachor. P., Šimek. K., Ghai. R. (2023) High-resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome 11, 15 

5- Kheiri. R., Mehrshad. M., Pourbabaee. A.A., Ventosa. A., Amoozegar M.A. (2023) Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation. Scientific Reports 13, 374 

6- Goodarzi. Z., Asad. S., Mehrshad. M. (2022) Genome-resolved insight into the reservoir of antibiotic resistance genes in an aquatic microbial community. Scientific Reports 12, 21047 

7- Rezaei Somee. M., Amoozegar, M.A., Dastgheib, S.M.M. Shavandi. M., Ghanbari Maman. L., Bertilsson. S., Mehrshad. M. (2022) Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea. BMC Genomics 23, 690 (2022). 

8- Buck. M., Mehrshad. M., Bertilsson. S. (2022) mOTUpan: a robust Bayesian approach to leverage metagenome assembled genomes for core-genome estimation. NAR genomics and bioinformatics 4 (3), lqac060 (Shared last authorship)

9- Westmeijer. G., Mehrshad. M., Turner. S., Alakangas. L., Sachpazidou. V., Bunse. C., Pinhassi. J., Ketzer. M., Åström. M., Bertilsson. S, Dopson. M. (2022) Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities. Communications biology. 5. 37.  

10- Rodríguez-Gijón. A., Nuy. JK., Mehrshad. M., Buck. M., Schulz. F., Woyke. T., Garcia. SL. (2022) A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy. Frontiers in Microbiology 

11- Mehrshad. M., Lopez-Fernandez. M., Sundh, S., Bell. E., Simone. D., Buck. M., Bernier-Latmani. R., Bertilsson. S., Dopson. M. (2021) Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nature Communications. 12, 4253. 

12- Rezaei Somee. M., Dastgheib. SMM., Shavandi. M., Ghanbari Maman. L., Kavousi. K., Amoozegar. M. A., Mehrshad. M. (2021) Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents. Scientific Reports 11, 11316. 

13-  Sobat. M., Asad. S., Kabiri. M., Mehrshad. M. (2021) Metagenomic discovery and functional validation of L-asparaginases with anti-leukemic effect from the Caspian Sea.  iScience. 24 (1), 101973. 

14-  Garcia. SL., Mehrshad. M., Buck. M., Tsuji. J., Neufeld. JD., McMahon. KD., Bertilsson. S., Greening. C., Peura. S. (2021) Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations. mSystems. 6:e01196-20 (Shared first authorship)

15- Cabello-Yeves. P. J., Callieri. C., Picazo. A., Mehrshad. M., Haro-Moreno. J.M., Roda-Garcia. J., Dzhembekova. N., Slabakova. V., Slabakova. N., Moncheva. S., Rodriguez-Valera. F. (2021) Microbiome of the Black Sea water column analyzed by genome centric metagenomics. Environmental Microbiome. 16, 5. 

16-  Martin. G., Rissanen. AJ., Garcia. SL., Mehrshad. M., Buck. M., Peura. S. (2021) Candidatus Methylumidiphilus drives peaks in methanotrophic relative abundance in stratified lakes and ponds across Northern landscapes. Frontiers in Microbiology 12:669937.

17-  Šimek. K., Grujcic. V., Mukherjee. I., Kasalický. V., Nedoma. J., Posch. T., Mehrshad. M., Salcher. MM., (2020) Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes. 96 (10),  fiaa121. FEMS Microbiology Ecology fiaa121. 

18-  Vavourakis. CD., Mehrshad. M., Balkema. C., Hall. RV., Andrei. AS., Ghai. R., Sorokin. DY., Muyzer. G. (2019) Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biology 17 (1), 1-20. 

19-  Kavagutti. VS., Andrei. AS., Mehrshad. M., Salcher. MM., Ghai. R. (2019) Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome 7, 135. 

20-  Bulzu. PA., Andrei. AS., Salcher. MM., Mehrshad. M., Inoue. K., Kandori. H., Beja. O., Ghai. R., Banciu. HL. (2019) Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nature microbiology 4, 1129–1137. 

21-  Andrei. AS., Salcher. MM., Mehrshad. M., Rychtecký. P., Znachor. P., Ghai. R.  (2019) Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. ISME journal 13, 1056–1071. 

22-  Mehrshad. M., Salcher. MM., Okazaki. Y., Nakano. S., Šimek. K., Andrei. AS., Ghai. R. (2018) Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi. Microbiome 6 (1), 176. 

23-  Vavourakis. CD., Andrei. AS., Mehrshad. M., Ghai. R., Sorokin. D., Muyzer. G. (2018) A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome 6 (1), 168 (Shared second authorship)

24-  Mehrshad. M., Rodriguez-Valera. F., Amoozegar. M. A., López-García. P., Ghai. R. (2018) The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME Journal 12, 655–668. 

25-  Cabello-Yeves. P. J., Ghai. R., Mehrshad. M., Picazo. A., Camacho. A., Rodriguez-Valera. F. (2017) Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs. Frontiers in Microbiology 8:2131. 

26-  Amoozegar. M. A., Khansha. J., Mehrshad. M., Shahzadeh Fazeli. S. A., Ramezani. M., Rafael. R., Sánchez-Porro. C., Ventosa. A. (2017) Soortia roseihalophila gen. nov., sp. nov., a new taxon in the order Balneolales isolated from a travertine spring, and description of Soortiaceae fam. nov. Int J Syst Evol Microbiol 67:113120. 

27-  Ghai. R., Mehrshad. M., Mizuno. C., Rodriguez-Valera. F. (2016) Metagenomic Recovery of Phage Genomes of Uncultured Freshwater Actinobacteria. ISME Journal 11: 304-308. 

Book chapters

1- Amoozegar, M.A. and Mehrshad. M. (2022). Alteribacillus. In Bergey's Manual of Systematics of Archaea and Bacteria (eds M.E. Trujillo, S. Dedysh, P. DeVos, B. Hedlund, P. Kämpfer, F.A. Rainey and W.B. Whitman). 

2- Amoozegar, M.A. and Mehrshad. M. (2022). Saliterribacillus. In Bergey's Manual of Systematics of Archaea and Bacteria (eds M.E. Trujillo, S. Dedysh, P. DeVos, B. Hedlund, P. Kämpfer, F.A. Rainey and W.B. Whitman). 

3- Bertilsson. S., Mehrshad. M. (2021) Diversity and Dynamics of Bacterial Communities in Freshwater Lakes. Diversity and Dynamics of Bacterial Communities in Freshwater Lakes, this article is a chapter for the Encyclopedia of Inland Waters, Second Edition. 

4- Amoozegar, M.A. and Mehrshad. M. (2019). Salinithrix. In Bergey's Manual of Systematics of Archaea and Bacteria (eds M.E. Trujillo, S. Dedysh, P. DeVos, B. Hedlund, P. Kämpfer, F.A. Rainey and W.B. Whitman). 

5-      Amoozegar, M.A. and Mehrshad. M. (2019). Aquibacillus. In Bergey's Manual of Systematics of Archaea and Bacteria (eds M.E. Trujillo, S. Dedysh, P. DeVos, B. Hedlund, P. Kämpfer, F.A. Rainey and W.B. Whitman). 

6-      Amoozegar. M. A., Mehrshad. M., Akhoondi. H. (2015) Microbial Degradation of Synthetic Dyes in Wastewaters, book chapter: Application of Extremophilic Microorganisms in Decolorization and Biodegradation of Textile Wastewater: pages 267-295; Springer.


Want to know more about our research and work? Check Bionomics Team research webpage


Researcher at the Department of Aquatic Sciences and Assessment; Division of Microbial Ecology
Postal address:
Institutionen för vatten och miljö
Box 7050
750 07 UPPSALA
Visiting address: Lennart Hjelms väg 9, Uppsala