Use of viruses and virus-resistant microorganisms for controlling microorganism populations

Abstract

A lytic virus specific for a target strain of a microorganism and substantially free of undesirable genes may be utilized in processes including control of populations of microorganisms. The virus may include a host-range mutant, or “h-mutant.” A method for generating virus includes growing virus-resistant variants of a target strain of a microorganism in the presence of viruses that are specific for the target strain. Only h-mutant viruses will proliferate. Wild-type virus-resistant and virus-resistant variants of a microorganism are also disclosed, as are methods generating such variants. Methods for controlling target strain microorganisms include introducing virus into a treatment site where control of a population of a target strain microorganism is desired or introducing virus-resistant variants of a microorganism into treatment sites where the presence of the microorganism is desired.

1 . A composition for controlling populations of a microorganism, comprising: 
 a virus: 
 incapable of: 
 infecting a multicellular organism; and  
 transferring undesired genes to an infected host microorganism; and  
 
 capable of: 
 infecting a virus-resistant variation of a target strain of the microorganism.  
 
   
   
   
       2 . The composition of  claim 1 , wherein the virus comprises a lytic virus.  
   
   
       3 . The composition of  claim 2 , wherein the lytic virus is incapable of converting from a lytic state to a temperate state.  
   
   
       4 . The composition of  claim 1 , further comprising a wild-type virus specific for the target strain.  
   
   
       5 . The composition of  claim 4 , wherein the wild-type virus comprises a lytic virus.  
   
   
       6 . The composition of  claim 1 , further comprising a carrier microorganism infected with the virus.  
   
   
       7 . The composition of  claim 6 , wherein the carrier microorganism comprises an avirulent microorganism.  
   
   
       8 . The composition of  claim 1 , further comprising: 
 an antimicrobial agent specific for the microorganism.    
   
   
       9 . A composition for controlling a population of a beneficial microorganism, comprising a virus-resistant variation of the beneficial microorganism.  
   
   
       10 . The composition of  claim 9 , wherein the virus-resistant variation comprises resistance to a wild-type of a virus specific for the beneficial microorganism.  
   
   
       11 . The composition of  claim 9 , wherein the virus-resistant variation comprises resistance to an h-mutant virus specific for the beneficial microorganism.  
   
   
       12 . The composition of  claim 9 , further comprising: 
 an h-mutant virus specific for an undesirable microorganism.    
   
   
       13 . The composition of  claim 9 , wherein the beneficial microorganism comprises at least one of  Pantoea annanus, Serratia entomophilia, Enterobacter aerogenes, T. ferroxidans , a member of the genus  Acidiphilium , a member of the genus  Rhodococcus , a member of the genus  Sulfobus , and a member of the genus  Thiobacillus.    
   
   
       14 . A method of controlling a population of a target strain of a microorganism, comprising: 
 introducing a virus that is: 
 incapable of infecting a multicellular organism or transferring undesired genes to an infected host microorganism; and  
 capable of infecting a virus-resistant variation of a target strain of the microorganism; and  
   permitting the virus to infect the target strain.    
   
   
       15 . The method according to  claim 14 , wherein introducing comprises introducing a lytic virus.  
   
   
       16 . The method according to  claim 14 , wherein introducing comprises introducing an h-mutant virus.  
   
   
       17 . The method according to  claim 14 , wherein introducing comprises introducing a wild-type virus.  
   
   
       18 . The method according to  claim 14 , further comprising: 
 introducing an antimicrobial agent into a treatment site.    
   
   
       19 . The method according to  claim 14 , wherein introducing comprises administering the virus to a live animal.  
   
   
       20 . The method according to  claim 14 , wherein introducing comprises treating a food product with the virus.  
   
   
       21 . The method according to  claim 20 , wherein treating the food product comprises treating raw meat or raw poultry.  
   
   
       22 . The method according to  claim 14 , wherein the virus is selective for the target strain microorganism over a beneficial microorganism.  
   
   
       23 . A method of controlling a population of a beneficial microorganism, comprising introducing a virus-resistant variation of the beneficial microorganism into a treatment site.  
   
   
       24 . The method according to  claim 23 , wherein introducing comprises exposing a toxic chemical or other pollutant to the virus-resistant variation of the beneficial microorganism.  
   
   
       25 . The method according to  claim 23 , wherein introducing comprises introducing at least one of  Pantoea ananus, Serratia entomophilia, Enterobacter aerogenes, T. ferroxidans , a member of the genus  Acidiphilium , a member of the genus  Rhodococcus , a member of the genus  Sulfobus , and a member of the genus  Thiobacillus  into the treatment site.  
   
   
       26 . The method according to  claim 23 , wherein introducing is effected to control growth of fungi.  
   
   
       27 . The method according to  claim 23 , wherein introducing is effected to control the proliferation or spread of an insect population.  
   
   
       28 . The method according to  claim 27 , wherein introducing is effected to control the proliferation or spread of insect populations as exemplified by New Zealand grass grub and locusts.  
   
   
       29 . The method according to  claim 27 , wherein introducing includes applying the virus-resistant variation of the beneficial microorganism to a plant.  
   
   
       30 . The method according to  claim 23 , wherein introducing is effected to oxidize sulfide to sulfuric acid.  
   
   
       31 . The method according to  claim 23 , wherein introducing is effected to release petroleum and petroleum-related substances from bituminous shale.  
   
   
       32 . The method according to  claim 23 , wherein introducing is effected to acidify sulfur.  
   
   
       33 . The method according to  claim 23 , wherein introducing effects at least one of acidifying alkaline soil, decomposing rubber products, bioremediating hazardous chemicals or pollutants, treating sewage or wastewater, treating odors or sources of odors, fermentation processes.  
   
   
       34 . A method of generating h-mutant virus, comprising: 
 isolating a target strain of a microorganism;    isolating a virus-resistant variant of the target strain by growing the target strain in the presence of a wild-type virus specific for the target strain;    isolating the h-mutant virus by growing the virus-resistant variant in the presence of the wild-type virus;    isolating an h-mutant virus-resistant variant of the target strain by growing the virus-resistant variant of the target strain in the presence of the h-mutant virus; and    isolating a second h-mutant virus by growing the h-mutant virus-resistant variant in the presence of the h-mutant virus.    
   
   
       35 . The method according to  claim 34 , further comprising: 
 screening at least one of the target strain and the h-mutant virus-resistant variant for undesirable genes.    
   
   
       36 . The method according to  claim 34 , wherein isolating the second h-mutant virus comprises isolating an h-mutant virus having specificity for a plurality of h-mutant virus-resistant variants of the target strain.  
   
   
       37 . The method according to  claim 34 , further comprising: 
 screening for and excluding any temperate viruses.    
   
   
       38 . The method according to  claim 34 , further comprising: 
 screening at least one of the h-mutant virus and the second h-mutant virus for undesirable genes.    
   
   
       39 . A method of generating a virus-resistant variant of a microorganism, comprising: 
 isolating an h-mutant virus by exposing a wild-type microorganism to a virus specific for the wild-type microorganism;    isolating a virus-resistant variant of the microorganism by exposing the wild-type microorganism to the h-mutant virus;    isolating at least one second h-mutant virus by exposing the virus-resistant variant of the microorganism to the at least one h-mutant virus; and    isolating at least one second virus-resistant variant of the microorganism by exposing at least one of the wild-type microorganism and at least one type of virus-resistant variant of the microorganism to the at least one second h-mutant virus.    
   
   
       40 . The method according to  claim 39 , wherein at least one of isolating the virus-resistant variant and isolating the at least one second virus-resistant variant comprises growing at least one of the wild-type microorganism and the virus-resistant variant in the presence of an h-mutant virus specific for the microorganism.  
   
   
       41 . The method according to  claim 40 , wherein isolating the at least one second virus-resistant variant comprises isolating at least one second virus-resistant variant having resistance to infection by a plurality of h-mutant viruses.  
   
   
       42 . A composition for controlling populations on food products of a microorganism that is pathogenic to a mammal, comprising an h-mutant virus specific for and capable of infecting a virus-resistant variation of a target strain of the microorganism.  
   
   
       43 . The composition of  claim 42 , wherein the microorganism are enteric pathogens, as exemplified by  Salmonella, Campylobacter , or  E. coli.    
   
   
       44 . The composition of  claim 42 , wherein the target strain comprises  E. coli  0157:H7.  
   
   
       45 . A method of controlling a population on a food product of a target strain of a microorganism that is pathogenic to a mammal, comprising: 
 applying to the food product a lytic virus that is specific for the target strain and that is not capable of infecting a multi-cellular organism or transferring undesired genes to a host microorganism; and    permitting the lytic virus to infect the target strain.    
   
   
       46 . The method according to  claim 45 , wherein the lytic virus comprises an h-mutant virus.  
   
   
       47 . The method according to  claim 45 , wherein the lytic virus comprises a wild-type virus.  
   
   
       48 . The method according to  claim 45 , wherein the allowing comprises allowing the lytic virus to infect the target strain of enteric pathogens, as exemplified by the genera  Salmonella, Campylobacter , or  Escherichia.    
   
   
       49 . The method according to  claim 45 , wherein the target strain comprises  E. coli  0157:H7.  
   
   
       50 . A method of treating a host infected with a microorganism, comprising: 
 administering a composition including a lytic virus substantially free of any undesirable genes and specific for the microorganism to the host so that the virus contacts the microorganism; and    allowing the lytic virus to infect the microorganism.    
   
   
       51 . The method according to  claim 50 , wherein the lytic virus comprises an h-mutant virus.  
   
   
       52 . The method according to  claim 50 , wherein the lytic virus comprises a wild-type virus.  
   
   
       53 . The method according to  claim 50 , wherein the composition further includes an antimicrobial agent.  
   
   
       54 . A method of disinfecting a target strain of a microorganism from an object, comprising: 
 exposing the object to a composition comprising a lytic h-mutant virus specific for the target strain; and    allowing the lytic h-mutant virus to infect the target strain.    
   
   
       55 . A method of preventing a microorganism from infecting a potential host, comprising: 
 administering a composition including an h-mutant virus to the potential host such that the h-mutant virus will contact the microorganism during the course of infecting the potential host.    
   
   
       56 . A method of preventing the transfer of undesirable genes from a first microorganism to a second microorganism, comprising: 
 exposing at least one of the first microorganism and the second microorganism to a lytic virus that is substantially free of any undesirable genes and is specific for the first microorganism; and    permitting the lytic virus to infect the first microorganism.    
   
   
       57 . The method according to  claim 56 , wherein the undesirable genes are selected from genes which encode virulence factors, toxin production, or antibiotic resistance.  
   
   
       58 . A method for increasing water oxygen levels, comprising: 
 exposing microorganisms that reduce water oxygen levels to viruses that will infect and lyse them.    
   
   
       59 . The method according to  claim 58 , wherein exposing comprises exposing the microorganisms to viruses including h-mutant virus that will infect and lyse at least some virus-resistant strains of the microorganism.  
   
   
       60 . The method according to  claim 58 , wherein exposing comprises applying the viruses to algae.  
   
   
       61 . The method according to  claim 58 , wherein exposing comprises introducing the viruses into the water.  
   
   
       62 . A composition for increasing oxygen levels in water, comprising virus and h-mutant virus that will infect and lyse bacteria that reduce water oxygen levels.  
   
   
       63 . A method for reducing or preventing acid mine drainage, comprising: 
 introducing viruses that will infect and lyse  T. ferroxidans  into environments where acid mine drainage originates or may originate.    
   
   
       64 . The method according to  claim 63 , wherein introducing comprises introducing the viruses into a coal mine.  
   
   
       65 . The method according to  claim 63 , wherein introducing includes introducing h-mutant viruses that will infect and lyse virus-resistant strains of  T. ferroxidans  into the environments where acid mine drainage originates or may originate.  
   
   
       66 . A composition for reducing or preventing acid mine drainage, comprising h-mutant virus that will infect and lyse  T. ferroxidans.