Royal Netherlands Institute for Sea Research
Royal Netherlands
Institute for Sea Research
Phone number
+31 (0)222 369 427
Location
Texel
Function
Postdoc
Expertise
  • Improved cultivation of previously uncultivated microbes.
  • Physiological characterization of novel microorganisms.
  • Microbial diversity analysis.
  • Microbial genome and metagenome annotation.

Dr. Subhash Yadav

Postdoc

Research Interest:

My major research interest includes the cultivation of novel putative lineages of procaryotes from marine habitats by adopting the ‘meta-omics’ technologies. At present, the DNA sequencing technology and the innovative sampling methods have revealed a plethora of novel procaryotic lineages in various marine habitats. However, their physiology and metabolic functions are largely unknown. We mainly assume their functions by implementing the single cell sequencing and by metagenome assembled genomes (MAGs). Nevertheless, there are several complex functional attributes of microorganisms which cannot be deduced from genome alone. They require culture-based physiological and metabolic analyses to confirm such attributes.

I adopt the improved culturing methods (i.e. genome informed physiology, medium compositions mimicking in-situ physicochemical properties, diffusion chambers, high pressure cultivation etc.) for the enrichments and isolation of uncultivated members. These approcahes are very helpful to bring the uncultivated microbial majority in cultured form which consequently, helps in the better understanding of their role in the biogeochemical cycling, in addition, to access their novel bioactivities for various biotechnological applications. I am also interested to develop the high-throughput cultivation devices to capture the new microorganisms from various marine habitats. I am excited to learn about the requirements of uncultivated microorganisms to grow them in pure form. Currently, I am cultivating and characterizing the physiology of unknown microbial members (anaerobic bacteria and archaea) from deep sulfidic waters of the Black Sea.

Research Experience:

Postdoctoral Researcher at Korean Environmental Microorganisms Bank (KEMB), College of Life Science, Kyonggi University, South Korea, from November, 2015 to June, 2017. Supervisor: Prof. Sang-Seob Lee

Senior Research Fellow (SRF) at National Bureau of Agriculturally Important Microorganisms, India (Indian Council of Agricultural Research) from Sept. 2007 to August, 2010. Supervisor: Dr. Anil K Saxena

Educational\Academic:

PhD (2010-2015) “Estimates of bacterial diversity of three coastal habitats of India and description of few new bacterial taxa” University of Hyderabad, India. Supervisor: Prof. Ch. Venkata Ramana  

Fellowships/award:

PhD Gold medal (Best PhD thesis of Department of Plant Sciences, University of Hyderabad, India - session 2014-2015).

DAAD (The German Academic Exchange Service) fellowship from July, 2011 to Oct, 2011 (University of Muenster, Germany).

Council of Scientific and Industrial Research (CSIR)-SRF from April 2013 to July, 2015.

List of Publications:

2020

Laura Villanueva, F. A. Bastiaan von Meijenfeldt, Alexander B. Westbye, Subhash Y., Ellen C. Hopmans, Bas E. Dutilh, and Jaap S. Sinninghe Damsté (2020) Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids. The ISME Journal. https://doi.org/10.1038/s41396-020-00772-2.

Subhash Y., Laura Villanueva,Nicole Bale, Michel Koenen, Ellen C. Hopmans and Jaap S. Sinninghe Damsté (2020) Physiological, chemotaxonomic and genomic characterization of two novel piezotolerant bacteria of the family Marinifilaceae isolated from sulfidic waters of the Black Sea. Syst. Appl. Microbiol. https://doi.org/10.1016/j.syapm.2020.126122

Subhash Y., Jin-Soo Kim, Sang-Seob Lee (2020) Alkanindiges hydrocarboniclasticus sp. nov. isolated from crude oil contaminated sands and emended description of the genus Alkanindiges. Curr. Microbiol. https://doi.org/10.1007/s00284-020-02266-y.

Nicole Bale, Michel Koenen, Subhash Y., Ellen C. Hopmans, Laura Villanueva, Jaap S. Sinninghe Damsté and Stefan Schouten (2020) Diagnostic amide products of amino lipids detected in the microaerophilic bacteria Lutibacter during routine fatty acid analysis using gas chromatography. Org. Geochem. https://doi.org/10.1016/j.orggeochem.2020.104027.

2018

Subhash Y., Radha V., Srinivas S., Ramaprasad E.V.V., Shivani Y., Ojha R., Tushar L., Sasikala Ch. and Venkata Ramana Ch. (2018) Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis. J. Antibiot.  71, 575-583.

Subhash Y., Sang-Seob Lee (2018) Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand. Int. J. Syst. Evol. Microbiol. 68, 675-680.

2017

Da-Hye Jin, Subhash Y., Sang-Seob Lee (2017) Psedoduganella eburnea sp. nov. isolated from lagoon sediments.  Int. J. Syst. Evol. Microbiol. 67, 5268-5272.

Subhash Y. and Sang-Seob Lee (2017) Description of Oceanispirochaeta sediminicola gen. nov., sp. nov., an obligate anaerobic bacterium isolated from coastal marine sediments and reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov. Int. J. Syst. Evol. Microbiol. 67, 3403-3409.

Subhash Y., Hye-Ji Kim, and Sang-Seob Lee (2017) Description of Aneurinibacillus sediminis sp. nov. isolated from a lagoon sediments. Int. J. Syst. Evol. Microbiol. 67, 2544-2548.

Subhash Y. and Sang-Seob Lee (2017) Roseomonas suffusca sp. nov. isolated from lagoon sediments. Int. J. Syst. Evol. Microbiol. 67, 2390-2396. 

Subhash Y., Da-Hye Eoon and Sang-Seob Lee (2017) Description of Skermanella mucosa sp. nov. isolated from crude oil contaminated soils. Antonie van Leeuwenhoek. 110, 1053-1060.

Shivani Y, Subhash Y., Sasikala Ch. and Ramana Ch.V (2017) Characterisation of a newly isolated member of a candidatus lineage, Marispirochaeta aestuarii gen. nov. sp. nov. Int. J. Syst. Evol. Microbiol. 67, 3929-3936.

Shivani Y., Subhash Y., Dave Bharti P, Sasikala Ch, Venkata Ramana Ch (2017) Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp. Int. J. Syst. Evol. Microbiol. 67, 87-93.

2016

Subhash Y., John J Bang, Taek H You, Sang-Seob Lee (2016) Description of Comamonas sediminis sp. nov., isolated from lagoon sediments. Int. J. Syst. Evol. Microbiol. 66, 2735-2739. 

Subhash Y. and Sang-Seob Lee (2016) Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int. J. Syst. Evol. Microbiol. 66, 2935-2970.

Subhash Y. and Sang-Seob Lee (2016) Skermanella rosea sp. nov., isolated from hydrocarbon contaminated soils. Int. J. Syst. Evol. Microbiol. 66, 3951-3956. 

Subhash Y., John J Bang, Taek H You, Sang-Seob Lee (2016) Roseomonas rubra sp. nov., isolated from lagoon sediments. Int. J. Syst. Evol. Microbiol. 66, 3821-3827. 

Subhash Y. and Sang-Seob Lee (2016) Shinella curvata sp. nov., isolated from hydrocarbon contaminated desert sands. Int. J. Syst. Evol. Microbiol. 66, 3929-3934.

Subhash Y., Min-Jeong Park. and Sang-Seob Lee (2016) Microvirgula curvata sp. nov., isolated from hydrocarbon contaminated soils. Int. J. Syst. Evol. Microbiol. 66, 5309-5313.

Shivani, Y., Subhash, Y., Sasikala Ch. and Ramana Ch.V (2016) Description of "Candidatus Marispirochaeta associata" and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov. Int. J. Syst. Evol. Microbiol. 66, 5485-5492.

2015

Shivani, Y., Subhash, Y., Sasikala Ch. and Ramana Ch.V (2015) Spirochaeta lutea sp. nov., isolated from marine habitats and emended description of the genus Spirochaeta. Syst. Appl. Microbiol. 38, 110-114.

Azmatunnisa M, Rahul K, Subhash Y, Sasikala Ch, Venkata Ramana Ch (2015) Bacillus oleivorans sp. nov., a diesel-oil degrading and solvent tolerant bacterium. Int. J. Syst. Evol. Microbiol. 65, 1310-1315.

Shivani Y, Subhash Y, Dave Bharti P, Sasikala Ch, Venkata Ramana Ch (2015) Bacillus crescens sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 65, 2531-2536. 

2014

Subhash, Y., Sasikala Ch. and Ramana Ch.V (2014) Pontibacter ruber sp. nov., and Pontibacter deserti sp. nov., isolated from desert. Int. J. Syst. Evol. Microbiol. 64, 1006-1011. 

Subhash, Y., Sasikala Ch. and Ramana Ch.V (2014) Salinimicrobium sediminis sp. nov. isolated from a deep sea sediments. Int. J. Syst. Evol. Microbiol. 64, 984-988. 

Subhash, Y., Sasikala Ch. & Ramana Ch.V (2014). Bacillus luteus sp. nov. isolated from a soil. Int. J. Syst. Evol. Microbiol. 64, 1580-1586. 

Subhash, Y., Sasikala Ch. and Ramana Ch.V (2014) Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish. Int. J. Syst. Evol. Microbiol. 64, 2238-2243. 

Subhash, Y., Sasikala Ch. and Ramana Ch.V (2014) Hymenobacter roseus isolated from sands. Int. J. Syst. Evol. Microbiol. 64, 4129-4133. 

2013 

Subhash, Y., Shivani Yadav, Rajeev Kaushik, Anil K Saxena, Dilip K Arora (2013) Genetic and functional diversity of fluorescent Pseudomonas from rhizospheric soils of wheat crop. J Basic Microbiol. 54, 425-437.

Subhash, Y., Tushar, L., Sasikala Ch. and Ramana Ch.V (2013) Falsirhodobacter halotolerans gen. nov. sp. nov., isolated from a dry soil of a solar saltern. Int. J. Syst. Evol. Microbiol. 63, 2132-2137.

Subhash, Y., Tushar, L., Sasikala Ch. and Ramana Ch.V (2013) Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from a dry soil of a solar saltern. Int. J. Syst. Evol. Microbiol. 63, 4524-4532.

Subhash, Y., Tushar, L., Sasikala Ch. and   Ramana, Ch.V. (2013). Mongoliicoccus alkaliphilus sp. nov. and Litoribacter alkaliphilus sp. nov. isolated from salt pans. Int. J. Syst. Evol. Microbiol. 63, 3457-3462.

Subhash, Y., Sasikala Ch. & Ramana Ch.V (2013). Flavobacterium aquaticum sp. nov.,  isolated  from  a  water  sample  of  a  rice  field. Int. J. Syst. Evol. Microbiol. 63, 3463-3469.

Subhash, Y., Tushar, L., Sasikala Ch. and Ramana Ch.V (2013) Vogesella alkaliphila sp. nov., isolated from an alkaline soil. Int. J. Syst. Evol. Microbiol. 63, 2338-2343.

Ramana, Ch.V., Srinivas, A., Subhash, Y., Tushar, L., Mukherjee, T., Usha, P. and Sasikala,   Ch.   (2013)   Salinicoccus   halitifaciens   sp.   nov.,   a   novel   bacterium participating in halite formation. Antonie van Leeuwenhoek. 103, 885-898.

Shalem Raj, P., Sasikala, Ch., Ramaprasad, E.V.V., Subhash, Y., Busse, H.-J., Schumann, P., and Ramana, Ch.V. (2013) Chryseomicrobium amylolyticum sp. nov., isolated from a semi-arid tropical soil of India and emended descriptions of the genus Chryseomicrobium and Chyseomicrobium imtechense. Int. J. Syst. Evol. Microbiol. 63, 2612-2617. 

2011 

Subhash, Y., Rajeev Kaushik, Anil K Saxena, Dilip K Arora (2011) Genetic and functional diversity of Bacillus strains in the soils long term irrigated with paper and pulp mill effluent. J. Gen. Appl. Microbiol. 57, 183-195.

Subhash, Y., Rajeev Kaushik, Anil K. Saxena and Dilip K. Arora (2011) Diversity and phylogeny of plant growth promoting bacilli from moderately acidic soil. J. Basic Microbiol. 51, 98-106. 

A, Srinivas, K.  Rahul, Ch.  Sasikala, Subhash, Y., E.  V.  V.  Ramprasad, Ch.  V. Ramana (2011) Georgenia satyanarayanai sp. nov., an alkaliphilic and thermotolerant amylase producing actinobacterium isolated from a soda lake. Int. J. Syst. Evol. Microbiol. 62, 2405-2409.

 

 

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