1) Soil viruses are abundant, with concentrations of 107 to 109 viruses per gram of soil. They play important roles in nutrient cycles and gene transfer. The majority are bacteriophages. 2) Presentations highlighted soil viral metagenomics approaches, ecological impacts of viral replication cycles, and existing knowledge gaps. Examples of predicted virus-host interactions and impacts on plant pathogens were discussed. 3) Knowledge gaps include using bacteriophages against insect endosymbionts, using viral abundance for insect pest control through metagenomics, and how phages can regulate soil nutrient status and insect pest metabolism. Investigating soil viral diversity could transform understanding of their role in ecosystem processes and microbial

1. SOIL VIRUSES
A NEW HOPE
SUBMITTED BY
KISHOR PUJAR
FIRST Ph.D.
PALB 9014
University of Agricultural Sciences Bangalore

2. IMPORTANCE
Abundance
• Soil viruses are abundant 107 to 109 viruses per
gram
• Abundance appears to be strongly influenced by
water availability and temperature,
Role
• Nutrient cycles, food web interactions, gene
transfer,
• Viruses impact global ocean food webs, carbon
cycling, and climate
Diversity
• The majority of viruses found in soils are
believed to be bacteriophages

3. HIGHLIGHTS OF PRESENTATION
Soil viral metagenomic approaches
Ecological impacts of different viral replication
Existing knowledge gaps that we can begin to fill

4. Examples of predicted virus-host interactions, potential feedback between viruses and
biogeochemistry, and possible viral impacts on plant pathogens that are ripe for
further investigation in a variety of natural and agricultural soils;
Williamson KE et al. (2017)

5. (a) Soil aggregate. Mineral grains (sand, silt, clay) are held together by organic matter
and microorganisms, including fungal mycelia, plant root exudates, and bacterial
exopolymers.
(b) Increased magnification shows bacterial biofilm attached to mineral grain, organic
matter, and air-water interface within the soil pore.
(c) Increased magnification shows size of typical bacteriophage (50–60-nm capsid
diameter) in relation to typical bacterial cell (1–2 μm) within a water film coating
the soil pore.
K.E. Williamson (2017)

6. VIRAL ABUNDANCE ACROSS SOILS
Hot desert [Mojave (United States), Sonoran (United States), Chihuahuan (United
States), Saharan (Africa), Namib (Africa), Arabian (Middle East), and Registan
(Afghanistan) Deserts]
Agricultural soils [England , Scotland , the United States, China, and Vietnam.
Forest soils include samples from Delaware and Virginia.]
Wetland soils [ Delaware and Virginia]
Cold desert soils [McMurdo Dry Valleys, Antarctica.
Field soils include samples from Virginia.]
Duboise SM et al. (1979)

7. VIRAL DIVERSITY IN SOILS
Green JC et al. (2015)
Bacteria
Hosts
• Archaea, protists, fungi, nematodes, annelids, arthropods, plants and burrowing
animals
2,000 phages -11 bacterial and 2 archaeal phyla,
85% of these viruses infecting hosts within the 3 phyla
Gammaproteobacteria, Firmicutes, and Actinobacteria
Host range
• Soil viruses that infect insects and plants - Knowledge is incomplete and tends
to focus on crop pests or viral biological control agents for pests.
532 to 129,000 for marine samples,
400 to 40,000 for freshwaters.
Richness

8. Morphological Diversity
• Extraction through density gradient centrifugation and
visualization under TEM (Transmission electron microscopy)
• International Committee on Taxonomy of Viruses (ICTV)- Based
on tail morphology
Morphotypes including tailed, polyhedral (spherical), rod-shaped,
filamentous and bacilliform particles.
• Agricultural soils was dominated by spherical, non tailed particles
(56%),
• Tailed phages (80%) in other soils.
Gerba CP. (1984)
Podoviridae
• Short
• Noncontractile
tails
Myoviridae
• Long
• Contractile
tails
Siphoviridae
• Long
• Non tailed
particles

9. Viral Genetic Diversity
• The lack of a universally conserved phylogenetic marker.
• g23 marker gene has been used to assess the genetic diversity of T4-
like phages in rice paddy soils in Japan and China, wetlands in China
and upland agricultural fields in China.
• Viral Genetic Diversity Is Constrained Or Selected By
environmental Conditions
Paddy soils
• Sharply defined
cluster
Fresh waters
• Distinct but more
diffuse cluster
Soils
• Forming a third
distinct cluster
• Sharing some
overlap with the
freshwater/paddy
grouping

10. Genomics
• To improve understanding of the genetic and functional diversity
of viruses within soils.
• Genome data base - 7,148 virus genomes had been sequenced
• With specific regard to soils, many of the sequenced viral genomes
belong to crop pests.
• Much less is known regarding the genome contents of viruses that
infect (micro)organisms living within the soil matrix
• Viral genomics has given rise to genetic prospecting, these arch for
genes with utility in specific applications ex. phage lysins as anti
bacterials.
Constraints
Isolation -most microbial hosts are not amenable to cultivation
Bioinformatics -bioinformatics analysis and annotation of the
resulting sequence data are laborious and time consuming

11. Mycobacteriums
megmatis strain
mc2 155
Sequenced >1,300
distinct viral
genomes isolated
High level of genetic
mosaicism
Gene transfer among
mycobacteriophages
New genes entering the pool
from outside sources as
well.
Genetic exchange and
the evolutionary
biology of their hosts
Viral genomes represent the
largest pool of possibilities
when it comes to solving
biological problems, revealing
a multitude of different ways
to encode proteins that share
a particular function.
Allen LZ et al. (2011)

12. Meta genomics
Currently
only 8
soil viromes
soils are dominated by
tailed, dsDNA phages
Constraints
Problem Bioinformatics bottleneck
Contain a high proportion of reads not affiliated
with known sequences
54.5–97.3% of all reads cannot be matched with a
specific taxonomic source, a specific protein function,
or both, rendering these reads unusable in most
downstream analyses
Kim K. et al.(2008)
study of genetic
material recovered
directly
from environmental
samples.

13. IMPACTS OF VIRAL REPLICATION
IN SOIL ECOSYSTEMS
Lytic Impacts
 In the lytic cycle, viral infection leads to near-immediate viral
replication inside the host cell and results in cell lysis upon the
release of progeny viruses
Lysogenic Impacts
 In the lysogenic cycle, viral DNA is inserted into the host
chromosome or maintained extra chromosomally and replicated
passively with the host, unless/until the virus is induced to
undergo the lytic cycle

14. Lytic Impacts Atmospheric CO2 fixed by plant
photosynthesis provides fresh organic C
inputs into soils
, converting some into and some into more,
Increase the amount of labile C and reduce the
proportion of C going to more stable, mineral-
associated or pore-controlled organic matter
Serve to increase microbial production and
respiration in soils
LYSIS
SOIL MICROBES
Decompose convert
Biomass
with respiratory
losses
some Recalcitrant and
Mineral-
bound
forms
Golchin A et al. (1994)

15. Application of rhizobiophages to crop soils
1. Can reduce nodulation by phage-sensitive rhizobia
2. Nitrogen flux
3. Influence nodulation competition, especially when phage
resistant rhizobia are used in combination with lytic phages
4. persistence or loss of effective N-fixing rhizobia strains,
5. success or failure of nodulation events, and, ultimately,
symbiotic effectiveness and nitrogen fixation rate.

16. Lytic Impacts
• Temperate phages may integrate their genomes into the host genome,
where the phage genome is maintained as a prophage, replicating as the
host cell grows and divides
Regulation of host metabolism.
• Regulatory proteins bind to homologous sequences in the host
chromosome, down regulating metabolic functions in host bacteria and
reducing energy expenditures.
Host survival
• This phage-controlled suppression of particular metabolic operons
directly contributes to host survival when nutrients are scarce or very
slowly available.
Superinfection immunity
• Protect bacterial hosts from additional phage infection or change host
phenotype (lysogenic conversion), sometimes resulting in significant
changes in host fitness and also bacterial survival in the presence of
multiple viral threats
Feiner R. et.al.(2015)

17. Novel viral species of Soils
 SpaA1 from Antarctic soils.
 It is morphologically similar to phages of the family
Siphoviridae.
 The 42,784 bp genome of the phage encodes 63 genes
which cluster within three regions of the genomes, each of
apparently different origin, in a mosaic pattern.
 Remarkably, one of the regions contains an almost
complete genome of a distinct bacteriophage, MZTP02.
 These data suggest that MZTP02 can be exchanged
between genomes of other bacteriophages, leading to the
formation of chimeric genomes.
 The insertion of a complete phage genome into
the genome of another phage has not been described
previously and might represent a novel ’fast track’ route
for virus evolution and horizontal gene transfer.

18. Existing knowledge gaps that we can begin to fill
1. Use of bacteriophages against endo symbionts
• Southern chinch bug, Blissus insularis, possesses
specialized midgut crypts that harbour e exocellular
symbiont Burkholderia
• Oral administration of antibiotics suppressed the gut
symbionts in B. insularis and negatively impacted insect
host fitness, as reflected by retarded development,
smaller body size, and higher susceptibility to an
insecticide, bifenthrin
• Soil-lytic phages BiBurk16MC_R active against he
cultures of specific Burkholderia ribotypes
• Characterization of the phage determined its specificity
to the Bi16MC_R_vitro ribotype and placed it within the
family Podoviridae

19. 2. Use of viral abundance for in control of insect pest (by meta
genomic study)
3. Use of phages leads to sustainable agriculture (reduce inputs)
4. Phages control the nutrient status of soil intern regulate the soil
dwelling insect pests
5. Phages have potential to regulate the host metabolism (ex- can
affect the function of endosymbiotic bacteria in insect pests)

20. Target species Disease/issue Animal/plant
1 Clostridium perfringens Necrotic enteritis Poultry
2 Escherichia coli Respiratory infection Poultry
3 Salmonella enterica serovar
typhimurium
Zoonotic Swin
4 Xanthomonas axonopodis pv.
Citri
Canker Citrus
5 Erwinia amylovora Fire blight Apple/pear
6 Ralstonia solanacearum Bacterial wilt Tomato
7 Vibrio anguillarum Vibriosis Fish
Use of phages in various fields

21. References
1. Emersona, J. B. (2019) Soil Viruses: A New Hope. mSystems.
4:3.
2. Svircev, A., Roach D. and Castle, A (2018). Framing the Future
with Bacteriophages in Agriculture. Viruses. 10:218.
3. Trubl,G., Jang,H.B., Roux,S.,Emerson, J.B., Solonenko,N.,
Vik,D.R., Solden,L., Ellenbogen,J., Runyon,A.T.,
Bolduc,B.,Woodcroft, B.J.,Saleska, SR., Tyson,G.W.,
Wrighton,K.C., Sullivan,M.B. and Rich,V.I. 2018. Soil viruses
are under explored players in ecosystem carbon processing.
mSystem. 3:5
4. Xu Y., Buss, E. A. and Boucias D. G. (2016). Impacts of
Antibiotic and Bacteriophage Treatments on the Gut-Symbiont-
Associated Blissus insularis (Hemiptera: Blissidae). Insects. 7:
61.

22. Conclusion
Investigating this largely unexplored diversity of
soil viruses has the potential to transform our
understanding of the role of viruses in global
ecosystem processes and the evolution of
microbial life itself.

23. Thank
you