Current project:

Microbiomes of Zooplankton  

Zooplankton is an important component of aquatic food webs. They keep the water column clear as well as provide significant benefits to other aquatic organisms. Like plants and higher animals, zooplankton harbour a rich community of microbes. Colonization of zooplankton species by microbes has been proposed to provide numerous ecosystem services including nutrient acquisition, stress protection, detoxification and habitat provision. To date, still a lack of understanding in microbiome composition of zooplankton, zooplankton-microbe interactions in the functioning of freshwater aquatic food webs and lake biogeochemistry. We want to investigate the microbial diversity and community composition of zooplankton, phytoplankton, and bacterioplankton in different freshwater lakes. We also want to investigate the microbial community dynamics of Rotifers from resting eggs to the adult stage under sterile and non-sterile conditions using different genetic clones of Rotifers.  This project was funded by the NIOO strategic fund. This research is linked to the NIOO research theme “Microbiomes”.

 

Personal Information

Name: Md Sainur Samad
Present address: Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, NETHERLANDS
E-mail: s.samad@nioo.knaw.nl and sainur24@gmail.com
Personal website: https://sainur.github.io/

Research Interest: Microbiology, Microbial ecology, Molecular biology and Biotechnology

Education:

Doctor of Philosophy (PhD)

  • Year: 2014-2017 
  • Research area: Microbiology (Microbial Ecology)
  • Research department: Microbiology and Immunology
  • Thesis title: N cycling and microbial dynamics in pasture soils
  • Supervisor: Dr Sergio E. Morales
  • Year of completion: 2017 (September)
  • Institute: University of Otago, NEW ZEALAND

Master of Science in Applied Biotechnology (MSc in ABT) (2 years)

  • Year: 2010-2012
  • Supervisor: Professor Stefan Bertilsson 
  • Institute: Uppsala University, SWEDEN

Master of Science in Fisheries Biology & Genetics (MS in FBG) (1.5 years)

  • Year: 2007-2009
  • Supervisor: Professor Rafiqul Islam Sarder
  • Institute: Bangladesh Agricultural University, BANGLADESH

Bachelor of Science in Fisheries (BSc in Fisheries) (4 years)

  • Year: 2003-2007
  • Institute: Bangladesh Agricultural University, BANGLADESH

Research skills
Bioinformatics:
- Programming and statistics: R & Python
- Qiime & R: 16S amplicon sequence data processing and analysis
- MG-RAST & R: metagenomic sequence data processing and analysis
- Phylogenetic analysis
Wetlab:
- Bacteria/archaea: isolation & identification based on culture dependent and culture independent approaches (dilution-to-extinction)
- Nucleic acids: DNA & RNA extraction, purification & quantification; cDNA synthesis; Gel electrophoresis
- Protein: purification & quantification; SDS-PAGE; GFP production from E. coli; protein crystallization
- Gene: cloning & sequencing; gene expression & identification
- Sequencing: sample preparation for next-generation sequencing (NGS)- both amplicon and metagenome
- PCR, qPCR, RT-PCR
- T-RFLP
- Multiple displacement amplification (MDA)
- Flow Cytometry: microbial growth & abundance quantification
- Gas chromatrography: measurement of N2O, N2, O2, CO2, CH4 and other gases
- Water and soil chemistry analysis
- Antibiotics: determination of minimal inhibitory concentrations (MICs)

Research & teaching experience

1. Postdoc (September 2017-): Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, NETHERLANDS
2. Lab Demonstrator (July 2015 to June 2017): Course MICR 221, MICR 222
3. Research Assistant (March 2013 to Dec 2013): Dept. of Ecology & Genetics/ Limnology, Uppsala University, Sweden
Research field: Microbial ecology
Supervisors: Dr Alexander Eiler, Dr Eva Lindström and Dr Silke Langenheder
4. Project Assistance (Oct 2012 to Feb. 2013): Dept. of Ecology & Genetics/ Limnology, Uppsala University, Sweden
Research field: Microbial ecology
Supervisor: Dr Alexander Eiler
5. Summer Work (Feb 2011 to Aug 2011): Catch-up growth study of Atlantic salmon, EBC, Uppsala University, Sweden
Research field: Animal ecology
Supervisor: Dr. Fredrik Sundström
6. Research Assistant (Dec 2007 to July 2009): worked on a project ‘Gene pool conservation and strain improvement of Indian major carps and some indigenous    endangered fish species of Bangladesh’ Funded by UGC and MoSICT, Bangladesh
Research field: Fish breeding and conservation
Supervisor: Dr Md. Rariqul Islam Sarder
 

Publications (Peer-reviewed): 

  1.  Samad, M. S., Johns, C., Richards, K. G., Lanigan, G. J., de Klein, C. A., Clough, T. J., & Morales, S. E. (2017). Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria. Molecular Ecology, 1-15. http://doi.org/10.1111/mec.14275. 
  2.  Clough, T. J., Lanigan, G. J., Klein, C. A., Samad, M. S., Morales, S. E., Rex, D., ... & Richards, K. G. (2017). Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil. Scientific Reports, 7(1), 2185. http://doi.org/10.1038/s41598-017-02278-y.
  3.  Samad, M. S., & Bertilsson, S. (2017). Seasonal variation in abundance and diversity of bacterial methanotrophs in five temperate lakes. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.00142. 
  4. Samad, M. S., Biswas, A., Bakken, L. R., Clough, T. J., De Klein, C. A., Richards, K. G., ... & Morales, S. E. (2016). Phylogenetic and functional potential links pH and N2O emissions in pasture soils. Scientific Reports, 6, 35990. http://doi.org/10.1038/srep35990.
  5.  Samad, M. S., Bakken, L. R., Nadeem, S., Clough, T. J., de Klein, C. A., Richards, K. G., ... & Morales, S. E. (2016). High-resolution denitrification kinetics in pasture soils link N2O emissions to pH, and denitrification to C mineralization. PloS One, 11(3), e0151713. http://doi.org/10.1371/journal.pone.0151713. 
  6. Langenheder, S., Comte, J., Zha, Y., Samad, M. S., Sinclair, L., Eiler, A., & Lindström, E. S. (2016). Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin. Environmental Microbiology Reports, 8(4), 479–485. http://doi.org/10.1111/1758-2229.12392. 
  7. Rex, D., Clough, T. J., Richards, K. G., de Klein, C., Morales, S. E., Samad, M. S., ... & Lanigan, G. J. (2018). Fungal and bacterial contributions to codenitrification emissions of N2O and N2 following urea deposition to soil. Nutrient Cycling in Agroecosystems, 1-15. https://doi.org/10.1007/s10705-017-9901-7