“Microorganisms and their Functioning in Changing Environment”

“Microorganisms and their Functioning in
Changing Environment”
Winter Internship Certificate Program -2023 Organised by the
Gujarat Ecological Education & Research (GEER) Foundation,
Gandhinagar
05 January 2024
Prof. Satya P. Singh
Guest Faculty & PhD Supervisor ( Dec 2023- Continue)
UGC BSR Faculty (Nov 2020-Nov 2023)
Professor & Head (2003-2020)
UGC-CAS Department of Biosciences
Saurashtra University
Rajkot, Gujarat, India

Contents
 Integration and convergence in Science
 Microorganisms and Ecosystem: An Overview
 Extremity and Microbial diversity
 Adaptations to Extreme Conditions
 Natural –Artificial Evolution
 Climate Change- Microorganisms/Plants/Animals –
Impact on Environment

Science: Towards Integration of Conventional
Disciplines
Multidisciplinary Approaches
Quest for new Knowledge: Among biological sciences as well
as across the boundaries
Answers for basics questions and mysteries of life and nature
Search for New potentials: Agriculture, Medicine, Industries,
Storage and transmission of data, Biosensors
Unconventional thinking : Leads to revolutionary ideas

CELL TYPES
 Electron Microscopy
 Cellular Architecture: Eukaryotes VS Prokaryotes
 Compartmentalization & Multiplicity of the unit
membranes
 Archaea
 Organelles and Ultrastructure's

Microbes: The Master Chemists
Anton van Leeuwenhoek
Pasteur
Watson &Crick
Genetic Engineering & Molecular
Biology
Microbes
Versatility
Diversity
Fast Growth
Easy to manipulate
Impact & Applications
Medicine : Disease, Vaccines,
Health& Hygiene
Agriculture: Soil Fertility& disease
Control
Industries : Production of value
based products
Environment : Monitoring &
Management

Microorganisms, Environment and Climate Change
Biological systems are highly dynamic
Changing climate/Extremity/Nutritional Status
Microorganisms
Environment
Animals/Plants/Human Being

PROGRESSION OF DIMENSIONS IN
BIOLOGICAL SCIENCES
 Whole organisms- Fundamentals genetics /Biochemistry
 Tissues
 Cell
 Organelles
 Molecular levels-Single gene/Single protein
 Cloning – Expression of Single gene
 Genomics Proteomics
 Metagenomics- Biomes

Evolution: Natural Vs Artificial

How Some Species Will Survive Climate Change
(Ref: Daniel Rubinoff on August 15, 2022, Scientific American
Hybrids/ the organisms containing DNA from more than one species- Referred as
unlucky reproductive-wise and lacked some Darwinian common sense
New genomic data & analysis suggest that the closely unrelated species- which have
swapped genes defy evolutionary common sense- BUT are NOT vanishingly rare.
Are relatively ecologically stable and better equipped against the climate change: in the
face of adversaries: droughts, floods and heat waves
This shuffle of DNA: Confer serious benefits, like disease resistance or adaptations to
new environments.
Homo sapiens is a great example of this:
Thanks to genomic technology, 2-4% of most Eurasian people’s DNA is
directly traced to Neandertals
Genomes of most of us- equipped with a package of non–Homo sapiens genes-
conferring benefits to our species.
Habit of exchanging genes: An unexpected way to dodge extinction

Mutations, Horizontal gene transfer, and survival of the
organisms/ Ancient animals in adverse conditions such
as climate changes
• Steve Palumbi and Elora López-Nandam, Hopkins Marine Station, Stanford University
• Some corals have Long lives of hundreds/thousands of years
• Acquiring and filtering of mutations in Giant corals appears: A base for future adaptation
• Animals function with a set of virtually unchanged genes throughout their lifetime. But, long-
lived animals have constantly been changing genes
• Organisms with DNA from more than one species- Ecologically stable, better equipped, and
powerful against the adversaries of climate changes; droughts, floods, and heat waves.
• In the Homo sapiens, a comparative example, 2-4% of most Eurasian people’s DNA is
directly traced to Neandertals. Thus, our genomes consist of non–Homo sapiens genes- setting a
solid ground for our benefits
• Exchanging genes provides a powerful way to dodge extinction.
Elora H. López-Nandam et al., Proceedings of the Royal Society B: Biological Sciences (2023).
DOI: 10.1098/rspb.2022.1766
Rubinoff, D. 2022,
https://www.scientificamerican.com/article/here-rsquo-s-how-some-species-will-survive-climate-change/

2022 Nobel Prize in Physiology or Medicine has been awarded for
pioneering studies of human evolution
•That harnessed precious snippets of DNA found in fossils tens of thousands years old.
•Svante Pääbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology
(MPI-EVA) in Leipzig, Germany
•The sequencing of the Neanderthal genome and the discovery of a new group of
hominins called the Denisovans, and also spawned the fiercely competitive field of
palaeogenomics.
•How genes flowed between ancient hominin
populations, to trace these Groups’ migrations
•Origins of some aspects of modern human physiology: including features of the
immune system and mechanisms of adaptation to life at high altitudes.
•

Genetic Plasticity of the Microorganisms
Ability to change/evolve new potential
• Depends on the susceptibility of the organism to
Alteration & Exchange of genetic information
• Genetic Adaptation to Pollutants
• Horizontal Transfer of Catabolic Plasmids

Frances H. Arnold
Linus Pauling Professor of Chemical Engineering, Bioengineering
and Biochemistry; Director, Donna and Benjamin M. Rosen
Bioengineering Center
Nobel Prize-2018: Chemistry
B.S., Mechanical and Aerospace Engineering, Princeton University,
1979; Ph.D., Chemical Engineering, University of California,
Berkeley, 1985; Postdoctoral, UC Berkeley, Chemistry, 1985;
Postdoctoral, Caltech, Chemistry, 1986
Nobel Prize-2018: Chemistry
Shared with: George P Smith and
Gregory P Winter

Directed evolution: Like climbing a hill on a 'fitness landscape'
Elevation represents the desired property. Each round of selection samples mutants on all
sides of the starting template (1) and selects the mutant with the highest elevation, thereby
climbing the hill. This is repeated until a local summit is reached (2).
Thomas Shafee- Thomas, Shafee, (2014). "Evolvability of a viral protease: experimental
evolution of catalysis, robustness and specificity". PhD Thesis. University of Cambridge.
Performing multiple rounds of directed evolution is useful not only because a new library of
mutants is created in each round but also because each new library uses better mutants as
templates.

“Microorganisms and their Functioning in Changing Environment”

Microbial World-Its Limitations-Extremity

Microbial World & Its Limitations
Microbial activities only under limited set of conditions
Only fraction (1-5%) of microbial world known and explored
Biocatalysts from microbes able to function only under delicate &
defined set of Conditions
Applications under Natural Environmental Conditions are limited

Need of the Hour
Exploration of newer habitats: Particularly extremes ones-
Environmental, Ecological and Biotechnological applications
Evolving Molecular & Microbial Potential: Gene shuffling and
Directed evolution
Microbial Interactions: with plants and animals
Evolving unique & novel biocatalytic capabilities: for industrial &
Environmental applications

Extreme Environments & Extremophiles
Evolution-Diversity-Commercial Interest
Living Fossils & Evolutionary Relics
Moderate VS Ultra Extreme Environment
Hyper-extremity & Limits - Life on Other planets

Thomas Brock, a famous professor of microbial ecology, was visiting Yellowstone
National Park in July 1964
Bacterial mats, golden brown in color, seen on the outer edges of 2 different
chromatic Beauty Pool’s in Upper Geyser Basin of Yellowstone caldera,
Wyoming.Source: ASM Microbe Library
Temperature Zonation &
Discovery of Hyperherophiles
Thermus aquaticus, 60-80℃.-
Taq Pol-PCR

The pool of microorganisms formed by water
seeping from a hot pool. Cyanobacteria and
other microorganisms living in the pool of hot
water
Zonation of microorganisms in the
seep from a hot pool. The temperature
gradient decreases from right to left of the
image, where the temperature is low enough
to enable plants to grow

A large channel draining from a hot pool, containing carotenoid-rich microorganisms. The
temperature of this channel in the foreground is about 60 o
C. Layers of white-coloured
limestone (forming a rock deposit known as travertine) can also be seen. Note the footprints
of buffalo in the foreground. These animals often seek the warmth of thermal areas in the
winter months

Some Other
Extreme
Environments

Samples were collected from…
• Water samples from
• the two hot spring reservoirs (Kunds) for Men
• Soil samples from the bank of the river (discharged
water from all reservoirs) & near by area.
 Soil Type: A
 Soil Type: B
 Soil Type: C
• Physicochemical analysis of samples including
temperature, pH and TDS
Seasonal Diversity (Year 2008-09)

Adaptations to the Extremity
At Various levels
 Cell Morphology
 Cell envelops & Appendages: CW, CM, Flagella, Capsule
 Membrane Transport
 Metabolism
 Structure & Stability of Macromolecules
 Thermodynamic adaptations
 Molecular levels: Replication, Transcription, Translation,
Protein folding

•Kikani, B.A. Patel, R.K., Thumar, J.T. Bhatt, H.B., Rathore, Dalip, Koladiya, Gopi,
and Singh S.P. 2023, Solvent tolerant enzymes in extremophiles: Adaptations and
Applications”, International Journal of Biological Macromolecules (IJBIOMAC)
(IF 8.10) (Elsevier), https://doi.org/10.1016/j.ijbiomac.2023.124051

Dimensions of the Diversity Assessment
Morphological and Growth Characteristics
Biochemical/Metabolic
Enzymatic Profiling
Molecular Characteristics

Media characterization of seasonal actinomycetes on ISP media

Light microscopic examinations (1000x)
of isolates form Okha Madhi after
Gram’s staining
SEM analysis of actinomycetes from
different sites demonstrating a) vegetative
mycelia of OM-4; b, c, d)
Sheikh, M., Rathore, D.S., Gohel, S.D. and Singh
S.P. 2019. Indian Journal of Geo-Marine Sciences
(CSIR-NISCARE),
Gohel, S. D. and Singh S.P. 2018. Geomicrobiology
Journal, 35:9, 775-789
Thumar, J.T. and Singh S.P. 2011. Biotechnology
Bioprocess Engineering, 16, 6:1180-1186

Cell morphology and Gram reaction Cultural characterization
Pigmentation profile

H2S Production
Indole
Oxidase
Nitrate
Catalase
Urea Utilization
MR
VP
Phenyl alanine
0 5 10 15 20 25 30 35 40 45
Biochemical fingerprinting
Isolates
Arabinose
Rhamnose
Xylose
Raffinose
Mannose
Inositol
Lactose
Fructose
Trehalose
Cellobiose
Maltose
Mannitol
0 5 10 15 20 25 30 35
Isolates
Sugar utilization profile

Antibiotics sensitivity & resistance profile
Antimicrobial activityiesagainst pathogens
Strains
No. of antibiotics
Resistant (a) Tested (b) MAR index (a/b)
Ok-1 12 31 0.387
Ok-2 7 31 0.225
Ok-4 7 31 0.225
Ok-6 12 31 0.387
Ok-8 6 31 0.193
Ok-10 6 31 0.193
Ok-13 9 31 0.290
Ok-14 12 31 0.387
Ok-17 9 31 0.290
Ok-18 14 31 0.451
Ok-19 15 31 0.483
Ok-20 12 31 0.387
Ok-22 12 31 0.387
Ok-23 10 31 0.322
Ok-24 13 31 0.419
D-2 13 31 0.419
D-5 19 31 0.612
D-8 11 31 0.354
S-1 11 31 0.354
S-2 25 31 0.806
Sampling site wise MAR Indices
Total
strains (c)
Aggregate
antibiotic resistance
score (a)
No. of antibiotics
tested (b)
MAR index
a/(b × c)
Okha
Port (15)
143 31 0.307
Dwarka
beach (3)
43 31 0.462
Somnath
beach (2)
36 31 0.580
MAR (Multiple Antibiotic Resistances) Indices of different marine actinomycetes

Antibiotic sensitivity profile on the basis of mode of action (a:
U- I, b: U- II and c: U- III)

Molecular Approaches to study Actinomycetes
Dangar, K. G., Kalasava,A. B., Dave, A. V. and Singh S.P.
2018. Journal of Cell &Tissue Research, 18(3) 6559-6570
Gohel, S. D. and Singh S.P. 2018. Geomicrobiology Journal,
35:9, 775-789
Sharma, A.K. Kikani, B.A. and Singh S.P. 2020,
Geomicrobiology Journal, DOI: 10.1080/01490451.2020.1860165
Gohel, S. D. Vaishali, M. and Singh S.P. 2023. Geomicrobiology
( Taylor & Francis), (IF 2.40), 40(6): 59--604
, DOI: 10.1080/01490451.2023.2218383

F243 &
R513
F984 &
R1378
U1F & R U2F& R NF & R
0
5
10
15
20
25
Total
no.
of
isolates
Chemotaxonomic features
16S rRNA gene amplification profile
Sharma, A.K. Kikani, B.A. and Singh S.P. 2020, Geomicrobiology Journal, DOI:
10.1080/01490451.2020.1860165

Primer Denaturation Annealing Extension No. of
cycles
F243 &
R513
94ºC - 5 min 94ºC-30s
56ºC-30s
72ºC-1min
72ºC-10 min 30
F984 &
R1378
94ºC - 5 min 96ºC-45s
56ºC-30s
72ºC-2min
72ºC-10 min 35
U1F & R 94ºC-10 min 94ºC-30s
56ºC-30s
72ºC-1min
72ºC-10 min 30
U2F & R 94ºC-10 min 94ºC-30s
56ºC-30s
72ºC-1min
72ºC-10 min 30
NF & R 94ºC - 5 min 94ºC-30s
60ºC-30s
72ºC-1min
72ºC-10 min 30
PCR amplification conditions

0.8% agarose gel show PCR products of isolates from Okha Madhi amplified with (a) U1
primer at 52.3°C 55.3°C 59.4°C: lane-1 Medium range DNA ruler lane-2,3,4 OM-3, lane-5,6,7
OM-4 lane-8,9,10 OM-5 lane-11,12,13 OM-6 lane-14 Super Mix DNA ladder, lane-15,16,17
OM-8 lane-18,19,20 OM-9 lane-21,22,23 OM-11 (b) U2 primer at 52.7°C, 55.9°C, 59.2°C:
lane-1 High range DNA ruler lane-2,3,4 OM-1 lane-5,6,7 OM-3 lane-8,9,10 OM-4 lane-11
Super Mix DNA ladder, lane-12,13,14 OM-6 lane-15,16,17 OM-7 lane-18 High range DNA
ruler lane-19,20,21 OM-8 lane-22,23,24 OM-9 lane-25,26,27 OM-11
Gohel, S. D. and Singh S.P. 2018. Molecular. Geomicrobiology Journal, 35:9, 775-789

0.8% agarose gel show PCR products of isolates Okha Madhi amplified with (a) StrepB/E
(Lane 2-24) at 50.7°C, 53.9°C, 56.7°C and StrepB/F (Lane 26-28) at 54.1°C, 58.1°C, 60.0°C
lane-1 High range marker (10 kb), lane-2,3,4 OM-3 lane-5,6,7 OM-4 lane-8 High range
marker, lane-9,10,11 OM-5 lane-12 High range marker, lane-13,14,15 OM-8 lane-16,17,18 OM-
9 lane-19,20,21 OM-10 lane-22,23,24 OM-11 lane-25: High range marker, lane-26,27,28 OM-2
(b) N F/R primer at 53.3°C, 56.4°C, 60.0°C lane-1 high range marker (10 kb), lane-2,3,4 OM-6
lane-5,6,7 OM-8 lane-8,9,10 OM-9 lane-11,12,13 OM-11 lane-14,15,16 OM-12

16S rRNA amplification profile
of isolates from A) Okha Madhi
and B) Okha site
U1
U2
StrepB/E
StrepB/F
N-F/R
OK-1
OK-2
OK-3
OK-4
OK-5
OK-6
OK-7
OK-8
OK-9
OK-10
U1
U2
StrepB/E
StrepB/F
N-F/R
OM-1
OM-2
OM-3
OM-4
OM-5
OM-6
OM-7
OM-8
OM-9
OM-10
OM-11
OM-12

Amplified ribosomal DNA restriction analysis (ARDRA)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 1 2 3 4 5 6 7
A B
Abbreviations:
A: 1- Marker, 2-D2, 3-OK-24, 4-OK-4, 5-OK-17,
6-OK-18, 7-OK-8, 8-D8, 9-OK-19, 10-OK-13, 11-
OK-22, 12-OK-20, 13-OK-1, 14-S1, 15-D-5
B: 1-Marker, 2-S2, 3-OK-23, 4-OK-10, 5-OK-2, 6-
OK-6, 7-OK-14 (Left to right position)
Sharma, A.K. Kikani, B.A. and Singh S.P. 2020, Geomicrobiology Journal, DOI:
10.1080/01490451.2020.1860165

Bhatt, H.B. and Singh S.P. 2022, Frontiers in Marine Science, doi:
10.3389/fmars.2022.769043
Saline Desert- LRK” Distribution of Bacterial Genera

AL1 AL3 KH1 KH3 AL KH
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100% Others
Unclassified
[Thermi]
Crenarchaeota
Nitrospirae
Cyanobacteria
Euryarchaeota
OD1
Chloroflexi
Acidobacteria
Actinobacteria
Planctomycete
s
Bacteroidetes
Firmicutes
Proteobacteria
Phylum
Relative
abundance
(%)
Nirali Raiyani & S P Singh Raiyani, Nirali and Singh S.P. 2020, Extraction of environmental
DNA, construction of metagenomic libraries and functional screening of enzymes from salt pan soil,
Indian Journal of Geo-Marine Sciences, Accepted (NISCARE, CSIR, IF 0.50),

AL1 AL3 KH1 KH3 AL KH
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100% Unclassified
Others
Fulvivirga
Idiomarina
Anaerospora
Rhodococcus
4-29
Bradyrhizobium
Deinococcus
Janibacter
Brevundimonas
Kaistobacter
Psychrobacter
Pseudomonas
Sediminibacterium
Methanosaeta
Acidiphilium
Sphingomonas
Hyphomicrobium
Gramella
Methylobacterium
Mycobacterium
Genus
Relative
abundance
(%)
Raiyani, Nirali and Singh S.P. 2020, Taxonomic and functional profiling of the microbial
communities of Arabian Sea: A Metagenomics approach Journal: Genomics (Elsevier, IF
6.20), 112:4361- 4369 https://doi.org/10.1016/j.ygeno.2020.07.024

Salient Features of Halophilic/Haloalkaliphilic Bacteria
and Their Enzymes
•Wide occurrence of bacteria with variable levels of salt tolerance and salt needs
• Vasavada, S. Thumar, J. and Singh, S. P.2006.Current Science 91 (10): 1393-1397
• Sheikh, M., Rathore, D.S., Gohel, S.D. and Singh S.P. 2019. Indian Journal of Geo-Marine Sciences
(CSIR-NISCARE),
• Gohel, S. D. and Singh S.P. 2018. Geomicrobiology Journal, 35:9, 775-789
• Thumar, J.T. and Singh S.P. 2011. Biotechnology Bioprocess Engineering, 16, 6:1180-1186
•Homology based on 16 S rRNA gene sequencing indicated presence of some novel
strains
• Rawal, C. M.,et al.,, Journal of Bacteriology, J. Bacteriol. 194(17): 4775 (IF 3.82).
• Gohel, S. D. and Singh S.P. 2018. Geomicrobiology Journal, 35:9, 775-789
• Sharma, A.K. Kikani, B.A. and Singh S.P. 2020, Geomicrobiology Journal, DOI:
10.1080/01490451.2020.1860165
• Dangar, K. G., Kalasava,A. B., Dave, A. V. and Singh S.P. 2018. Journal of Cell &Tissue Research, 18(3)
6559-6570
• Bhatt, H.B., Begum, M.A., Chintalapati, S., Chintalapati, V.R. and Singh, S.P. 2017. International Journal
of Systematic & Evolutionary Microbiology (IJSEM), 67(11):4435-4442 (IF 2.1)
• Nowlan B., Dodia, M.S., Singh, S.P and Patel, B. K. C. 2006. Int J Syst Evol. Microbiol 56:1073-1077
• Bhatt, H.B., Gohel, S.D. and Singh, S.P. 2017. 3 Biotech, 8,53, https://doi.org/10.1007/s13205-017-1075-

and Their Enzymes
•Denaturation of proteins- Extremely resistant against denaturation
•In-vitro protein folding: Renaturation varies and affected by pH, Salt,
Temperature
•Salt -Dependence temperature profile and thermostability
• Dodia M. S., Rawal C. M., Bhimani H. G., Joshi R. H., Khare, S. K. and Singh, S. P. 2008. Journal of
Industrial Microbiology & Biotechnology 35(2):121-132
• Raval, V. Rawal, C.M., Pillai, S. and Singh S.P. 2014. Process Biochemistry 49 (6): 955-962 (IF 2.63)
• Gupta, A., Roy, I., Patel, R.K., Singh, S.P., Khare, S.K. and M.N. Gupta. 2005. Journal of
Chromatography A 1075: 103-108
• Kinetics & Thermodynamic Adaptations: Catalytic efficienct,
Entropy/Entahlpy/Kd/Half Life
• Dodia M. S., Rawal C. M., Bhimani H. G., Joshi R. H., Khare, S. K. and Singh, S. P. 2008. Journal of
Industrial Microbiology & Biotechnology 35(2):121-132

and Their Enzymes
•Heterologous gene expression of salt/Temperatures
•Thakrar Foram, Koladiya Gopi and Singh S. P. 2023 Applied Biochemistry and Biotechnology (IF 3.10)
(Springer), Published Online on 15 April 2023, https://doi.org/10.1007/s12010-023-04472-3
•Bhatt, H.B. and Singh S.P. 2020Frontiers in Microbiology (IF 4.25), 11:1-16,
https://doi.org/10.3389/fmicb.2020.00941
•Purohit, M. and Singh S.P. 2014Process Biochemistry 49: 61-68, (IF 2.63).
•Gohel, S. and Singh S.P. 2012. International Journal of Biological Macromolecules (IJBIOMAC) 50: 664–
671 (IF 8.10). PMID: 22327111, DOI: 10.1016/j.ijbiomac.2012.01.039
•Metagenomics-Exploration of novel genes
•Raiyani, Nirali, and Singh S.P. 2023, https://doi.org/10.1007/s11356-023-25196-1
•Purohit M.K, --------and Singh S. P., 2022, Environmental Science and Pollution Research (IF 5.10) (Springer),
https://doi.org/10.1007/s11356-022-21411-7
•Raiyani, Nirali and Singh S.P. 2020, Genomics (Elsevier, IF 6.20), 112:4361- 4369
https://doi.org/10.1016/j.ygeno.2020.07.024
•Raiyani, Nirali and Singh S.P. 2020, Indian Journal of Geo-Marine Sciences, Accepted (NISCARE, CSIR, IF 0.50),
•Purohit, M. and Singh S.P. 2013. International Journal of Biological Macromolecules (IJBIOMAC) 53: 138–
143 (IF 8.10). 10.1016/j.ijbiomac.2012.10.032

Rhizosphere Microbiome: Salinity and Other
Abiotic Stress

Rhizosphere microbiome: Important in the
functioning of plant ecosystems
 Only Limited Knowledge
 Coupling traditional approaches with NGS techniques- to corelate community ecology and
physiology in the rhizosphere
 Identification of the chemical and microbial markers on how plants recruit and stimulate
beneficial microorganisms
 Microbiome highly significant to improve crop protection under stress and pathogenic
conditions
 To identify unknown soil microorganisms, functions, and genes
 To control plant and human pathogens
 To redirect rhizosphere microbiome to prevent pathogens
FEMS Microbiology Reviews, Volume 37, Issue 5, September 2013, Pages 634–663,
https://doi.org/10.1111/1574-6976.12028
Rodrigo Mendes, Paolina Garbeva, Jos M. Raaijmakers

Microbiome under Stress
Abiotic Stresses Shift Belowground Populus-Associated Bacteria
Toward a Core Stress Microbiome Adverse growth conditions can lead to
decreased plant growth, productivity, and survival, result
 “Common stress microbiome” Suggest a tightly controlled relationships between the
plant host and bacterial Community
 A conserved structure in bacterial communities associated with poplar trees under
different growth conditions.
 Change in Microbial community under Stress: Enhanced Water utilization & nutrient
uptake
 Ability of the microbiome to buffer the plant from extreme environmental conditions
 An opportunity for modulating the microbiome to optimize plant growth
ASM, mSystems, 2018 Collin M. Timm et al.

Core Microbiome and Minimal
Microbiome
A set of core microorganisms that effectively protect plants from soilborne
pathogens and stress conditions
What would be core microbiome?? Same for all cases??
How many traits required to protect plants from pathogens remains???
‘Minimal Microbiome’ To avoid antagonism and functional redundancy
‘Minimal microbiome’ would have minimal set of microbial traits for a
specific ecosystem
Control of different pathogens on different crops requires a different subset of
antagonistic microorganisms!!!
Core Microbiomes- Judged functionally rather than taxonomic considerations
FEMS Microbiology Reviews, Volume 37, Issue 5, September 2013, Pages 634–663,
https://doi.org/10.1111/1574-6976.12028 Rodrigo Mendes, Paolina Garbeva, Jos M.
Raaijmakers

Interwoven-Interactive action
Global warming-Enhanced melting of Antarctica- Sea Level
 Ocean circulation around Antarctica- the global network of currents-
shift heat, oxygen, and nutrients around the globe
 Reduced Overturning - Due to dilution of the salinity- less dense-
Lowering of sinking force
 Changes in Antarctica- Global influence: as waters move
throughout the planet
 Modelling (Matthew England, UNSW, Sydney): If global carbon
emissions continue at the current rate- Antarctic overturning will slow by more
than 40 percent in the next 30 years
David Fogarty, Climate Change Editor, Nature, Mar 30, 2023
Adele Morrison, Earth Sciences, ANU, Canberra
Matthew England, UNSW, Sydney

CO2 Generation and its removal/ Consumption
 Need for shift in the narrative
 Emissions Very High
 Radical, immediate emission cuts
 Suitability/effectiveness of the method/s- Would require long time to
judge its impact on environment
 CO2 Removal likely to fail at larger scale: Hence rely on the
environment to stabilize atmospheric CO2 over thousands of years
 A burning argument for rapid decarbonization????
Nature 616, 9 (2023) doi: https://doi.org/10.1038/d41586-023-00953-x

Microorganisms & Climate change
 Microorganisms-highly diverse & most abundant: Greatly affected by a
changing climate
 Major drivers of elemental cycles
 Key producers and consumers of greenhouse gases
 Yet, remotely attended for the threats of climate change
 Pertinent to understand the changing climate and its effect on microbes,
consequently influencing environment
Microbes and Climate Change – Science, People & Impacts Report on an American Academy of
Microbiology Virtual Colloquium held on November 5, 2021

Avian Community Structure and Forest
Habitat in Achanakmar Tiger Reserve
Birds are among the best indicators of environmental quality
• Interaction between the biological and non-biological
factors
• Nature and Nutritional status
Dynamics of the Avian population --- Migration of the Birds
• Increasing anthropogenic activities
Enhanced forest degradation and deforestation
Conversion of forest to agricultural land
Greenhouse gases, Temperature change, and climate change
Mark Anthony and Dr. Garima Tiwari, GGV- Bilaspur studied Deciduous forest, 2023

Diu, India, On the Beaches of Diu Nov 2023
Report on an American Academy of
Microbiology Virtual Colloquium held on
November 5, 2021
NEWS 10 June 2019 Nature
World’s largest plant survey reveals alarming extinction rate
Since 1900, nearly 3 species of seed-bearing plants have disappeared per
year ― 500 times faster than they would naturally.

Conclusion/Research Recommendations
Extremophiles
 Diversity & Novel strains-Cultural, Biochemical. Metabolic and Molecular Traits
 Wide occurrence and variation in enzyme level
 Variation in Biochemical traits of the enzymes for the catalysis and stability
 Extremity-driven Enzymatic features
Extremophiles & Climate change
 Interdisciplinary research: To understand microbial activities and metabolic flux as
altered by the changing climate
 Global elemental cycles and impact on pathogens
 Data building on microbial diversity- their activities related to greenhouse gases
 Linking microbes with the earth climate models: to improve the current and
predictive performance of models

Policy and Regulations on Climate Change
Enhanced research investments
Generation of knowledge on how microbes are significant
Innovation and development of Microbial based approaches for cleaner energy
generation

‘Disruptive’ science has declined’
Disruptive VS Incremental Science
Nature NEWS- 04 January 2023. Nature 613, 225 (2023) Park, M., Leahey, E. & Funk,
R. J. Nature 613, 138–144 (2023), doi: https://doi.org/10.1038/d41586-022-04577-5
A sharp decline in ‘Disruptive Science’ over the period of 1945- 2010.
A similar thought was also expressed a few years ago by Sydney Brenner, a Nobel
Laureate in 2002

Biology must generate ideas as well as data
Paul Nurse WORLD VIEW Nature 13 September 2021
Sydney Brenner: Nobel Laureate– ematode worm Caenorhabditis
elegans as a model organism
Data should be a means to knowledge, not an end in themselves.
“Drowning in a sea of data and starving for knowledge,”
Framing is neglected, Why the data are being collected; What is
the hypotheses ; what ideas are emerging.
Lack of biological conclusions or present new ideas.

Richard Feynman
https://en.wikipedia.org/wiki/Richard_Feynman
Richard Phillips Feynman, an American theoretical physicist, known for
his work in the path integral formulation of quantum mechanics,

Financial Support
DBT, UGC, DST, MoES, GSBTM,
Saurashtra University, Rajkot
Research Collaborations
•IIT Delhi, New Delhi: Prof. S. K.Khare
•DUSC, New Delhi: Prof. Sanjay Kapoor
•NFRI, Tsukuba, Japan: Dr. Kiyoshi Hayashi ( Now at
Toyo University, Japan)
•Griffith University, Australia
•JNTU Hyderabad, Prof. Ch. Sasikala
•Central University of Hyderabad, Prof. Ch. Rama Rao

Research Team
Dr. Sangeeta Gohel, Assistant Professor
Dr. Vikram Raval, DST Young Scientist (Now at Gujarat University)
Dr. Aparna Singh, DST Women Scientist ( Now Asstt. Prof, Surat)
Dr. Kalpana Rakholiya, SERB- National Post-Doctoral Fellow
Ms. Kruti Dangar, DST Women Scientist (Now Asstt. prof,
Saurashtra University)
&
Ph.D./M.Phil/M.Sc. Students

Dr. Bharat Joshi (Canada)
Dr. Manish Bhatt ( Canada)
Dr. Rajesh K. Patel ( Professor, VNUSG, Surat)
Dr. Anju Mittal ( Scientist, USA)
Dr. Mital Dodia ( Scientist, Canada)
 Dr.. Jignasha Thumar ( Asstt. Prof. Gandhinagar)
Dr. Rupal Joshi (ZRC, Ahmedabad)
Dr. Chetna Rajyaguru (Associate Prof. Rajkot)
Ms. Geera Mankad ( Associate Prof. Rajkot)
Dr. Chirantan Raval ( Asst Prof., Govt College)
 Dr. Megha Purohit ( Scientist and Entrepreneur, Canada)
Dr. Himanshu Bhimani ( Associate Prof. Navsari Ag Univ,)
Dr. Bhavtosh Kikani (Asstt Prof. CHARUSAT)
Dr. Amit Sharma (Scientist, ZRC, Ahmedabad)
Dr. Kruti Dangar (Asstt Prof. Saurashtra University)
Dr. Atman Vaidya ( Biology Teacher & Entrepreneur)
Dr.r. Hitarth Bhatt (Asstt Prof. Virani College, Rajkot)
Dr. Rupal Pandya (USA)
Dr. Foram Thakrar ( Ahmedabad)
Dr. Dalip Singh Rathore ( GBRC, Gandhinagar)
Dr Mahejbin Sheikh (Visiting Faculty)
Acknowledgements : Ph.D. Students

Patents applied and application published
1 202121018804 TEMP/E-1/20844/2021-MUM 9667 FORM1 Full
PATENT APPLICATION PUBLICATION
Application No.202121018803, INDIA
Dat of filing of Application:23/04/2021
Publication Date: 28/10/2022
2 202121018805 TEMP/E-1/20852/2021-MUM 9667 FORM1 Ful
Application No.202121018804 A, INDIA (22)
Date of filing of Application:23/04/2021
3 202121018803 TEMP/E-1/20823/2021-MUM 9667 FORM1 Full
Application No.202121018805 A, INDIA (22)
Date of filing of Application:23/04/2021

Recent Publications
( Cumulative Impact factor : 240, H-Index: 35)
2023
Gohel, S.D., Majithiya, Vaishali, and Singh S.P. 2023, Genetic and physiological diversity of marine
Actinobacteria isolated from Okha coastline, Gujarat, India-”,
Geomicrobiology (Taylor & Francis) (IF 2.40), 40 (6), 590–604 DOI:
10.1080/01490451.2023.2218383
Shukla, Rushit and Singh S.P. 2023, Purification and Characterization of an Amylase From a Newly
Isolated Geobacillus Thermoleovorans TTIO4 From Hot Spring of Tuwa-Timba”, ‘Starch’ (Wiley)
(IF 2.688) Accepted for publication on 05 May 2023, DPI:
https://doi.org/10.1002/star.202200254
•Thakrar Foram, Koladiya Gopi and Singh S. P. 2023 “Heterologous Expression and Structural elucidation
of a highly thermostable alkaline serine protease from haloalkaliphilic actinobacterium, Nocardiopsis sp.
Mit-7”, Applied Biochemistry and Biotechnology (IF 3.10) (Springer), Published Online on 15 April
2023, https://doi.org/10.1007/s12010-023-04472-3

•Kikani, B.A. Patel, R.K., Thumar, J.T. Bhatt, H.B., Rathore, Dalip,
Koladiya, Gopi, and Singh S.P. 2023, Solvent tolerant enzymes in
extremophiles: Adaptations and Applications”, International Journal
of Biological Macromolecules (IJBIOMAC) (IF 8.10) (Elsevier),
https://doi.org/10.1016/j.ijbiomac.2023.124051
•Dobariya Ankita, Mankad Gira, Ramavat Hasti, and Singh S. P. 2023
“Efficacy of the fruit and vegetable peels as substrates for the growth
and production of α-Amylases in Marine Actinobacteria”, Applied
Biochemistry and Biotechnology (IF 3.10) (Springer), Published
Online on 17 April 2023, https://doi.org/10.1007/s12010-023-04422-z
•Raiyani, Nirali, and Singh S.P. 2023, Microbial community and
predictive functionalities associated with the marine sediment of
Coastal Gujarat, Environmental Science & Pollution Research
(IF 5.10) (Springer), Published On-Line 18 January 2023,
https://doi.org/10.1007/s11356-023-25196-1

2022
Purohit, M.K, Rathore Dalip Singh, Koladiya Gopi, Pandey Sandip and Singh S. P., 2022, Comparative
analysis of the catalysis and stability of the native, recombinant and metagenomic alkaline proteases in
organic solvents, Environmental Science and Pollution Research (IF 4.30) (Springer), accepted for
published, 07 June 2022
Thakur Nagendra, Singh Satya P. and Zhang, Changyi, 2022. Microorganisms under extreme environments
and their applications, Current Research in Microbial Sciences (2022), doi:
https://doi.org/10.1016/j.crmicr.2022.100141
Joshi Rupal, Raval Vikram, Bhatt Hitarth and Singh S. P., 2022 “Phenotypic characteristics, phylogenetic
analysis and characterization of alkaline proteases of marine bacteria Geomicrobium halophilum,
Oceanobacillus oncorhynchi, and Oceanobacillus khimchii”, BIOLOGIA (IF 1.34), 10.1007/s11756-022-
01095-7
Raval Vikram, Rathore Dalip Singh and Singh S. P., 2022 “Comparative studies of the characteristics of
two alkaline proteases from Haloalkaliphilic bacterium D-15-9 and Oceanobacillus onchorynchii Mi-10-
54”, APPLIED BIOCHEMISTRY AND MICROBIOLOGY (IF 0.95) (Springer),
Bhatt, H.B. and Singh S.P. 2022, Diversity of cultivable bacteria in a saline desert of Little Rann of Kutch,
India: a phylogenetic perspective , Frontiers in Marine Science (IF 4.90), doi:
10.3389/fmars.2022.769043

2021
Dwivedi, Purna, Sharma, A. K. and Singh, S.P. 2021. Biochemical properties and repression
studies of an alkaline serine protease from a haloalkaliphilic actinomycete, Nocarpdiopsis
dassonvillei subsp. albirubida OK-14. Biocatalysis and Agricultural Biotechnology,
Accepted. 07 June 2021 (Elsevier; IF: 0.90)
Kikani, B.A. and Singh, S.P. 2021. Amylases from thermophilic bacteria: Structure and
Function Relationship. Critical Reviews in Biotechnology, In Press, 30 April 2021 (Taylor &
Francis; IF: 8.102)
Rathore, D. R., Sheikh, M., Gohel G.D, and Singh, S.P. 2021. Genetic and phenotypic
heterogeneity of the Nocardiopsis alba strains of sea water. Current Microbiology, 78: 1377-
1387 (Springer; IF: 1.75), DOI: 10.1007/s00284-021-02420-0
Chauhan, J.V., Mathukiya, R. Singh, S.P. and Gohel, S.D. 2021. Two steps purification,
biochemical characterization, thermodynamics and structure elucidation of thermostable
alkaline serine protease from Nocardiopsis alba strain OM-5. International Journal of
Biological Macromolecules (IJBIOMAC), 169: 39-50 (Elsevier; IF: 5.16),
https://doi.org/10.1016/j.ijbiomac.2020.12.061 , Available On-Line 12 Dec 2020.
Rathore, D R and Singh, S.P. 2021. Kinetics of growth and co-production of amylase and
protease in novel marine actinomycete, Streptomyces lopnurensis KaM5. Folia Microbiologica
(Springer; IF: 1.70), https://doi.org/10.1007/s12223-020-00843-z

2020
Sharma, A.K. Kikani, B.A. and Singh S.P. 2020, Diversity and Phylogeny of Actinomycetes of
Arabian Sea along the Gujarat Coast. Geomicrobiology Journal (Taylor & Francis, IF 1.90),
DOI: 10.1080/01490451.2020.1860165
Raiyani, Nirali and Singh S.P. 2020, Extraction of environmental DNA, construction of
metagenomic libraries and functional screening of enzymes from salt pan soil, Indian Journal
of Geo-Marine Sciences, Accepted (NISCARE, CSIR, IF 0.50),
Raiyani, Nirali and Singh S.P. 2020, Taxonomic and functional profiling of the microbial
communities of Arabian Sea: A Metagenomics approach
Journal: Genomics (Elsevier, IF 6.20), 112:4361- 4369
https://doi.org/10.1016/j.ygeno.2020.07.024
Bhatt, H.B. and Singh S.P. 2020,
Cloning, Expression and structural elucidation of a biotechnologically potential alkaline serine
protease from a newly isolated Haloalkaliphilic
Bacillus lehensis JO-26, Frontiers in Microbiology (IF 4.25), 11:1-16,
https://doi.org/10.3389/fmicb.2020.00941

2020
Sharma, A.K. Kikani, B.A. and Singh S.P. 2020,
Biochemical, thermodynamic and structural characteristics of a biotechnologically compatible a
lkaline protease from a haloalkaliphilic,
Nocardiopsis dassonvillei OK-18 International Journal of Biological Macromolecules
(IJBIOMAC), 153:680-696, DOI: 10.1016/j.ijbiomac.2020.03.006 (IF 5.16)
Pandya, Rupal D. and Singh S.P. 2020, Pigment production by an extreme halophilic archaeon
on Halorubrum sp. J4.2.2 from little Rann of Kutch, Gujarat, India. Research Journal of
Biotechnology, 15(1):88-100. E-ISSN: 2278-4535 Print ISSN: 0973-6263
2019
Thakrar, F.J. and Singh S.P. 2019. Catalytic, thermodynamic and structural properties of an
immobilized and highly thermostable alkaline protease from a haloalkaliphilic actinobacteria,
Nocardiopsis alba Tata-5. Bioresource Technology, 278:150-158 (IF 5.802)
Sheikh, M., Rathore, D.S., Gohel, S.D. and Singh S.P. 2019. Cultivation and characteristics of
the Marine Actinobacterial from the Sea water of Alang, Bhavnagar. Indian Journal of Geo-
Marine Sciences (CSIR-NISCARE), 48(12), 1896-1901(IF 0.4).
Rathore, D.S., Sheikh, M.A., Gohel, S.D. and Singh, S.P. (2019) Isolation strategies, abundance
and characteristics of the marine actinomycetes of Kachhighadi, Gujarat, India. Journal of
Marine Biological Association of India (JMBAI), CMFRI Cochin, India 61(1): 21-27

2018
Gohel, S. D. and Singh S.P. 2018. Thermodynamics of a Ca2+
dependent, highly thermostable
and detergent compatible purified alkaline serine protease from Nocardiopsis xinjiangensis
strain OM-6. International Journal of Biological Macromolecules (IJBIOMAC),
https://doi.org/10.1016/j.ijbiomac.2018.02.157, 113:565-574 (IF 3.00)
Gohel, S. D. and Singh S.P. 2018. Molecular phylogeny and diversity of the salt-tolerant
alkaliphilic actinobacteria inhabiting Coastal Gujarat, India. Geomicrobiology Journal, DOI:
10.1080/01490451.2018.1471107, 35:9, 775-789 (IF 1.5)
Thakrar, F.J., Kikani, B.A., Sharma, A.K. and Singh S.P. 2018. Stability of alkaline proteases
from haloalkaliphilic actinobacteria probed by circular dichroism spectroscopy. Applied
Biochemistry and Microbiology (Russia), 54(6), 591-602 (IF 0.68)
Sheikh, M., Rathore, D. S., Gohel, S. D. and Singh S.P. 2018. Marine actinobacteria associated
with the invertebrate hosts: a rich source of bioactive compounds: A Review. (Invited
contribution) Journal of Cell &Tissue Research, 18 (01), 6361-6374.

2018
Dangar, K. G., Kalasava, A. B., Dave, A. V. and Singh S.P. 2018. Molecular diversity of
Nocardiopsis alba sp. isolated from the coastal region of Gujarat, India. Journal of Cell
&Tissue Research, 18(3) 6559-6570
Vaidya A., Nair, V. S., Georrge, J. and Singh S.P. 2018. Comparative analysis of
thermophilic proteases, Research Journal of Life Sciences, Bioinformatics, Pharaceutical
and Chemical Sciences (RJLBPCS) 4(6), P. 66. DOI: 10.26479/2018.0406.05
Pandey, S. Sharma, A.K., Solanki, Kiran P. and Singh S.P. January 2018. Catalysis and
stability of an extracellular α- amylase from a haloalkaliphilic bacterium as a function of the
organic solvents at different pH, salt concentrations and temperatures. Indian Journal of
Geo-Marine Sciences (CSIR-NISCARE), 47 (01), 240-248 (IF 0.4).

2017
Bhatt, H.B., Gohel, S.D. and Singh, S.P. 2017. Phylogeny, Novel bacterial lineage and
enzymatic potential of haloalkaliphilic bacteria from the saline coastal desert of Little Rann of
Kutch, Gujarat, India. 3 Biotech, 8,53, https://doi.org/10.1007/s13205-017-1075-0 (IF 1.36)
Bhatt, H.B., Begum, M.A., Chintalapati, S., Chintalapati, V.R. and Singh, S.P.
2017. Desertibacillus haloalkaliphilus gen. nov.sp. nov., isolated from a salt desert.
International Journal of Systematic & Evolutionary Microbiology (IJSEM), 67(11):4435-
4442 (IF 2.1)
Kikani, B.A., Sharma, A.K. & Singh, S.P. 2017. Metagenomic and Culture-Dependent
Analysis of the Bacterial Diversity of a Hot Spring Reservoir as a Function of the Seasonal
Variation. International Journal of Environmental Research, 11: 25-38.
DOI:10.1007/s41742-017-0003-9 (IF 1.0).
Datta, A., Sharma, A., Kundu, R.S. and Singh S.P. 2017. Diversity and enzymatic profile of
bacterial flora in the gut of an estuarine fish, Mugil jerdoni. Indian Journal of Geo-Marine
Sciences (CSIR-NISCARE), 46(06): 1116-1127 (IF 0.4)

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