“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

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).

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).

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.

Loss of SOC due to OM oxidation, soil erosion, OM mineralization etc

Fig: SOC sequestration decreases by conventional agricultural practices (Brevik, 2012)

Carbon dioxide concentration in the atmosphere

Source: NASA (climate change guide, 2014)

The highest CO2 level in earth’s history

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

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).

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)

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

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

UnSaturated 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)

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)

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.

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).

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.

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.

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.