University of Groningen
The ecology and evolution of bacteriophages of mycosphere-inhabiting Paraburkholderia spp.
Pratama, Akbar Adjie
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Publication date:
2018
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Pratama, A. A. (2018). The ecology and evolution of bacteriophages of mycosphere-inhabiting
Paraburkholderia spp. Rijksuniversiteit Groningen.
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Propositions Associated with the PhD thesis
The ecology and evolution of bacteriophages of mycosphere-inhabiting Paraburkholderia spp.
Akbar Adjie Pratama
1. The mycosphere may have served as a meltingpot of horizontal gene transfer (HGT) processes in soil, as indicated by the fact that the mycosphere dweller Paraburkholderia terrae has an expanded genome, littered with repeat sequences (as an indicator of HGT), containing the genetic repertoire necessary for adaptation to diverse niches
This thesis 2. Species circumscriptions based on 16S rRNA gene sequences do not offer high taxonomic
resolution; hence, the strict division between P. terrae and P. hospita should be reconsidered. This thesis 3. Soil virus metagenomics (viromics) will need to focus on the impact viruses have as modulators
of key soil processes; in particular, their roles as activity and population size modulators needs attention.
This thesis 4. The novel prophage ɸ437, that uniquely infects P. terrae strain BS437, appears consistently, at
high abundance, in mycosphere consortia; its sequence reveals only remote relatedness to any currently recognized phage in the public database.
This thesis 5. Coevolution between P. terrae and its prophage ɸ437 may provide the host bacterium with an
ecological advantage of fungal interactivity, in the form of enhancement of biofilm strength. This thesis 6. Soil bacteriophages impact the ecology and evolution of their hosts. However, the vast biodiversity of hosts and phages, and the extent to which the latter impact soil functioning and microbial interactivity, is yet to be unearthed.
This thesis 7. Concluding that viral predation and lysis are unimportant factors that influence the composition
of soil bacterial communities is very premature.
8. The potential of the plethora of proteins that can be encoded by soil (pro)phages is theoretically unlimited; some of these could be taken to applications such as in medicine, molecular biology, genetics, agriculture and industry.
9. Next time you hear about viruses, you should challenge your view of them being parasitic to their host; rather, viruses can directly advance host fitness and thus constitute “public goods” in a host population.
10. I challenge microbial ecologists not to overlook, and to always integrate, viruses as significant players in their ecosystem models.
11. Global warming will shift the impact of phages in topsoil by the increased induction of host prophages, resulting in enhanced possibilities of phage-driven horizontal gene transfer and/or population size control. This phage-mediated loop will affect mycosphere communities and have a bearing on global element cycling processes in the soil.
12. So which of the favors of your Lord would you deny?
Propositions
Associated with the PhD thesis
The ecology and evolution of bacteriophages of mycosphere-inhabiting Paraburkholderia spp. Akbar Adjie Pratama
1. The mycosphere may have served as a meltingpot of horizontal gene transfer (HGT) processes in soil, as indicated by the fact that the mycosphere dweller Paraburkholderia terrae has an expanded genome, littered with repeat sequences (as an indicator of HGT), containing the genetic repertoire necessary for adaptation to diverse niches
This thesis 2. Species circumscriptions based on 16S rRNA gene sequences do not offer high taxonomic resolution;
hence, the strict division between P. terrae and P. hospita should be reconsidered.
This thesis 3. Soil virus metagenomics (viromics) will need to focus on the impact viruses have as modulators of key soil
processes; in particular, their roles as activity and population size modulators needs attention.
This thesis 4. The novel prophage ɸ437, that uniquely infects P. terrae strain BS437, appears consistently, at high abundance, in mycosphere consortia; its sequence reveals only remote relatedness to any currently recognized phage in the public database.
This thesis 5. Coevolution between P. terrae and its prophage ɸ437 may provide the host bacterium with an ecological
advantage of fungal interactivity, in the form of enhancement of biofilm strength.
This thesis 6. Soil bacteriophages impact the ecology and evolution of their hosts. However, the vast biodiversity of hosts and phages, and the extent to which the latter impact soil functioning and microbial interactivity, is yet to be unearthed.
This thesis 7. Concluding that viral predation and lysis are unimportant factors that influence the composition of soil
bacterial communities is very premature.
8. The potential of the plethora of proteins that can be encoded by soil (pro)phages is theoretically unlimited; some of these could be taken to applications such as in medicine, molecular biology, genetics, agriculture and industry.
9. Next time you hear about viruses, you should challenge your view of them being parasitic to their host; rather, viruses can directly advance host fitness and thus constitute “public goods” in a host population. 10. I challenge microbial ecologists not to overlook, and to always integrate, viruses as significant players in
their ecosystem models.
11. Global warming will shift the impact of phages in topsoil by the increased induction of host prophages, resulting in enhanced possibilities of phage-driven horizontal gene transfer and/or population size control. This phage-mediated loop will affect mycosphere communities and have a bearing on global element cycling processes in the soil.
12. So which of the favors of your Lord would you deny? َبِأَىِِّ َالَ ِٓءِا رِبِّكَمِا ُِّ َذرِمَنِك
Qur’an, Ar-Rahman 55:38 Qur’an, Ar-Rahman 55:38
