1) Soil microbes play an important role in global carbon and nitrogen cycles by driving processes like organic matter decomposition, nitrogen fixation, and methane/nitrous oxide emissions. 2) Changing environmental conditions due to climate change, like increased temperature and altered precipitation, can impact soil microbial communities and gene expression. 3) Horizontal gene transfer between soil microbes may be a natural adaptation strategy to environmental changes, allowing microbes to acquire new genes that help them survive. Studying this process of natural transformation could provide insights into molecular-level climate change adaptation.

1. “Soil gene transfer – A new approach of climate
change adaptation”
REVIEW
Author/Presenter
Roshan Babu Ojha
Asst. Prof. (Soil Science), HICAST
Co-author: Deepa Devkota

2. Introduction: Climate change
There is no any arguments that climate is changing (Corfee-Morlot
et. al., 2007; Cooney, 2010).
Nepal accounts 0.01% in global carbon-dioxide emission but ranked
as 13th most vulnerable country for climate change effects (Global
Climate Risk Index, 2014).
Carbon-dioxide is major concern in today's global warming context
as it is more than 80 percent of total green house gases emission
(other GHGs: nitrous oxide, methane).
Carbon emissions: Various routes - microbial respiration (OM
oxidation – CO2 emission) in agriculture (Lal et.al., 1998).

3. Introduction: Soil Genes
Soil microbes are mostly responsible for carbon
turnover (Eglin et. al., 2011).
There is declining trend of soil organic carbon
(Carney et. al., 2007) observed with increased
microbial activity and more CO2 emitted (Kirkham,
2011).
Loss of soil organic matter as a result of more
microbial respiration and decomposition finally
alter the soil physical, chemical and biological
properties (Wolf and Synder, 2003; Brevik, 2009).

4. Introduction...contd...
Microbes also plays important role in nitrogen mineralization
which is also affected by C:N ratio. Reduction in soil nitrogen
mineralization occurs when CO2 level increases as C:N ratio
increases (Gill et. al., 2002; Hungate et. al., 2003).
Under elevated CO2 soil C:N ratio increases up to 4.1% with no
added effect of soil N (De Graff et. al., 2006).
Various nitrifiers (N2-fixers) and denitrifiers (conversion of nitrate
to free nitrogen as nitrous oxide as intermediate product) alter
their roles in changing soil atmosphere.
So, microbes plays important role in GHGs emissions, their
sequestration and hence, their integral role in global carbon and
nitrogen cycle.

5. Loss of SOC due to OM oxidation,
soil erosion, OM mineralization
etc
Fig: SOC sequestration decreases by conventional agricultural practices (Brevik, 2012)

6. Carbon dioxide concentration in the atmosphere
Source: NASA (climate change guide, 2014)
The highest CO2 level in
earth’s history

7. Fig: Mode of CO2 emissions and sequestration as illustrated in C-cycle (NASA)

8. Fig: Methane formation and emission in paddy field (Zayer, 2012)
Major sources of CH4 emission
•Anaerobic decomposition of soil
organic matter in the wetlands esp.
paddy fields (Schutz et. al., 1990;
Heilig, 1994; Stepniewski et.al., 2011)
• melting of permafrost soil (Barbar et
al., 2008).

9. Nitrous oxide – next potential green house gas – 300 times
more warming potential than CO2
-N20 emission is triggered by the enhanced microbial activity in
manure and fertilized soil (Lokupitiya and Paustian, 2006; Foster et.
al., 2007).
-When NO3
- converts to NO, N20 or N2 the ideal condition for N2O
emission is soil moisture constant reaches to field capacity during
which biological reaction of nitrate conversion occurs (Mullen,
2011).
-Agriculture accounts 58 % of anthropogenic N2O emission (Smith
et. al., 2007)

10. Fig: Nitrous oxide emission as a part of N2-Cycle (NASA)

11. Soil temperature
pH
Redox potential
Soil nutrient levels
Soil bulk density
Soil porosity
Increasing
temperature
Altered precipitation
Increasing GHGs
concentration
Warmer and shorter
winters
Rising seas levels
Increase gene transfer
rate
Increased virulent
pathogens
P
L
A
N
T
S
CH4 O2
CO2 N2O N2
UnSaturat
ed soil
Saturated soil
Soil physical
and chemical
properties
Biological
Properties
Climate change
effects
Microbial
Community
Fig: soil microbes in changing climatic scenario (French et.al., 2009)

12. Soil Genes: Isolation
Microbes in the soil are isolated with various methods:
Free-air carbon dioxide enrichment (FACE) system and Open top chambers (OTC)
are used to determine the microbial respiration. De Graaff et. al. (2006)
Phospholipid fatty acid profile analysis (Zak et. al., 1996), community DNA
hybridization and %G+C profiling (Griffiths et. al., 1998) are certain techniques to
observe the rhizosphere bacterial community
Power soil DNA kit was used by Santos Freire et. al., (2013) to extract soil DNA
from soil microorganisms and quantification of extracted DNA was done by using
spectrophotometer and 16S rRNA gene for phylogenetic inference of
microorganisms.
For the determination of composition of complex soil inhabiting microbial
communities meta-genomic molecular technologies have been used that detects
the DNA sequence of soil microbes (Urich et. al., 2008)

13. Soil Gene: Isolation contd....
Several methods are available to measure gene expression in soil
by characterizing mRNA (Metcalfe et. al., 2002; Krsek et. al., 2006).
Many of the microbes like ammonia oxidizing bacteria, CO2 fixers,
N2-fixers, the enzymes involved during the biochemical process of
such microbes were quantified with different tags like cDNArRNA-
tags and mRNA-tags were produced when direct pyro-sequencing
of RNA meta transcriptome involves extraction of both mRNA and
rRNA from a sandy soil, with reverse transcription to cDNA (Urich
et. al., 2008).
In soil, microbial nitrogen covers 4% of organic nitrogen whereas
most of the total organic nitrogen is present as extracellular
protein which was stabilized by soil colloids (Nannipieri, 2006)
which was the major consideration of proteomics.

14. Soil gene transfer: Instances and adaptation strategies
Horizontal gene transfer is very common in soil bacteria which plays
crucial role in evolution of bacterial genome and speciation
(Ochman et. al, 2000) influenced by changing climate.
In a soil system, a competent bacterial cell takes up free extracellular
DNA (plasmid or chromosomal) and acquires genes required for
survival which is very important for adaptation also called as natural
transformation (Barkay et. al., 1993; Lilley and Bailey, 1997; Ochman
and Moran, 2001) well documented in Pseudomonas sps (Carlson et.
al., 1983).
Natural transformation occurs at high temperature, high
transformation frequency of Azotobacter vinelandii occurs between
26-370C and Pseudomonas stutzeri occurred between 20-370C but
optimum temperature is 300C (Pages and Sadoff, 1976; Lorenz and
Wackernagel, 1992).

15. Contd...
However, in this temperature range degradation of extracellular DNA
i.e. plasmid DNA may degenerate (French et. al., 2009). There is
necessity of verification of soil temperature for further genetic
exchange between soil microbes in this environment.
There lots of literatures talking about the bacterial gene transfer
through conjugation and transduction (Reanney et. al., 1982;
Stotzky, 1986; Stotzky et. al., Trevors et. al., 1987; Bashan and
Levanony, 1988; Kingmuller et. al., 1990; Levy and Miller, 1992).
But in-situ transduction in soil environment is not well documented
(Trevors et. al., 1987). Study on natural gene transformation is now
rapid which might be the corner stone of climate change adaptation
in future.

16. Contd...
With the changing soil environmental condition (elevated CO2,
increased temperature, altered precipitation), either gene
transformation will occur in the soil naturally or induced
transformation is possible in lab.
Horizontal transformation of bacteria which are a part of the global
carbon and nitrogen cycles viz. nitrifying bacteria, denitrifying
bacteria, methanotrophs, ammonia oxidizing bacteria, N2 fixers
(symbiotic-asymbiotic), CO2 fixers etc is possible which should be
verified in future.
Lorenz and Wackernagel, (1994) also suggested in their review
paper about further study of physiology and genetics of the
process of the natural transformation should be done. If such
transformation is possible, a molecular basis of climate change
adaptation will be established.

17. CONCLUSION
Microbes are ubiquitous organisms present in diverse environmental
condition of soil. Their role in global gaseous cycle is crucial - affected
with changing environment.
Recent advancement in the molecular technology is helpful to identify
and isolate the microbes types is possible - still total genetic
information of a handful of soil is not available.
They have their own genetic expression ability to adopt with changing
circumstances - the chance of negative gene expression (pathogen) is
also equally high.
So, to enhance the positive gene expression, i.e. gene expression for
more N2 fixers, CO2 fixers, methane oxidizers, ammonia oxidizers, this
molecular technique will be milestone for creating a natural balance
and mitigate dreadful effect of climate change.