TY - BOOK
T1 - Community dispersal
T2 - Developing and applying a novel method to explore the dispersal potential of bacterial communities from environmental samples
AU - Krüger, Urse Scheel
N1 - The research was carried out in the Department of Geochemistry, The National Geological Survey of Denmark and Greenland (GEUS) during the period of 2013-2018 in collaboration with the Section for Microbial Ecology and Biotechnology at the Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. [Publ. as: Danmarks og Grønlands Geologiske Undersøgelse, Rapport 2018/27]
PY - 2018
Y1 - 2018
N2 - Dispersal has been considered an essential aspect of microbial life since the very first studies of bacteria in the17th century. Traditionally, dispersal is divided into passive modes (caused, e.g. by weather phenomena orhuman activities) and activemodes, also termed motility, which requiremetabolic energy often using dedicatedcellular appendages such as flagella. In the soil environment active dispersal presumably ensures bacterialfitness in a heterogeneous world of limited resources and plays an important role for community dynamics,interactions and ecology but also in other contexts such as bioremediation and plant protection.One of the challenges to bacterial dispersal in soil, different to those experienced by microbes in liquid cultures,is the unsaturated conditions that are common in soil. More specifically the thickness and connectivity of theliquid films between soil particles have a huge impact on bacterial motility at the microscale. Under unsaturatedconditions, when the soil becomes dryer, the matric potential becomes increasingly negative and the liquidfilms become thinner and disconnected, which has been shown to restrict bacterial flagellar motility to arelatively narrow range of water potentials (0 to -2 kPa). Due to these known restrictions, the importance ofactive dispersal in soil has been debated for years, with some claiming that motility is limited to transientfavorable periods following irrigation and rainfall. However, this theory might be based on a rather simplifiedview of soil. In clayey tills, which cover more than 40% of the Danish land area, the well-structured soil profileis divided into clearly different soil compartments. In these soils the water, primarily from rainfalls, movesfrom the plow layer through preferential flow paths towards groundwater reservoirs. The preferential flowpaths are made up of a complex system of biopores (mainly earthworm burrows and plant root channels) thatare connected to tectonic fractures in deeper layers. These can provide bacterial habitats with vastly differentphysical and chemical compositions as well as hydration conditions, compared to the matrix sediments. Whilepreferential flow paths are considered a potential major route for the passive transport of bacteria trough soil,the contribution of active dispersal in these compartments has never been explored.Previous knowledge on bacterial motility is mostly based on pure culture studies using a few carefully selectedstrains in highly artificial laboratory settings, while the role of active dispersal for natural communities remainsessentially unknown. This knowledge gap is largely caused by the lack of methods for mass assessment ofdispersal potential of bacteria in environmental samples, as very few attempts have been made to assessbacterial dispersal at the community level.The overall objective of this thesis was therefore to develop a method for assessing community motility undercontrolled hydration conditions, apply the method to uncover the dispersal potential of environmental bacterialcommunities and to identify the bacterial dispersers. Furthermore, the aim was to apply the method to explorethe dispersal potential of bacterial communities from a well-structured clay till depth profile, targetingpreferential flow paths and matrix sediments. Revealing the potential role of active dispersal in theheterogeneous environment.In Manuscript I, a method that provides profiles of community-level surface dispersal from environmentalsamples under controlled hydration conditions was developed. This enabled us to isolate and uncover thediversity of the fastest bacterial dispersers. The method was based on the Porous Surface Model (PSM),previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porousceramic disc. The novel procedure targeted complex communities, capturing the dispersed bacteria on a solidmedium for growth and detection. The method was first validated by distinguishing motile flagellatedPseudomonas putida and gliding Flavobacterium johnsoniae strains from their nonmotile mutants. Applyingthe method to soil and lake water bacterial communities showed that community-scale dispersal declined asconditions became drier. However, for both communities, dispersal was detected even under low-hydrationconditions (matric potential, -3.1 kPa), previously proven too dry for flagellar motility. We were then able tospecifically recover and characterize the fastest dispersers from the inoculated communities. For both soil andlake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially lessdiverse than the total communities. The dispersing fraction of the soil microbial community was dominated byPseudomonas, which increased in abundance under low-hydration conditions, while the dispersing fraction ofthe lake community was dominated by Aeromonas.In Manuscript II we applied the novel method to assess the dispersal of five bacterial communities derivedfrom contrasting compartments along a fractured clay till depth profile, including plow layer soil, preferentialflow paths and matrix sediments down to 350 cm below surface. In agreement with the results fromManuscript I, we found bacteria capable of active dispersal at -3.1 kPa in all communities. Further testing ofthe plow layer community uncovered active dispersal even at matric potentials of -6.3 to -8.4 kPa, which washitherto thought too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, we found thedispersing communities to be less diverse compared to corresponding total communities, supporting andextending the results in Manuscript I. The dominant dispersers in most compartments belonged to the genusPseudomonas, and, in plow layer soil, also Rahnella. The dispersing community in the matrix sediment at 350cm below surface was an exception and was dominated by Pantoea. An increased proportion of sharedAmplicon Sequence Variants of the dispersing communities, compared to non-dispersers, between thehydrologically connected compartments of plow layer, biopores and tectonic fractures suggest that activedispersal is important for colonization of these compartments. These results highlight the importance ofaddressing soil heterogeneity when exploring the role of active dispersal in soil and bring us a step closer toassessing the importance of bacterial dispersal under environmentally relevant conditions.
AB - Dispersal has been considered an essential aspect of microbial life since the very first studies of bacteria in the17th century. Traditionally, dispersal is divided into passive modes (caused, e.g. by weather phenomena orhuman activities) and activemodes, also termed motility, which requiremetabolic energy often using dedicatedcellular appendages such as flagella. In the soil environment active dispersal presumably ensures bacterialfitness in a heterogeneous world of limited resources and plays an important role for community dynamics,interactions and ecology but also in other contexts such as bioremediation and plant protection.One of the challenges to bacterial dispersal in soil, different to those experienced by microbes in liquid cultures,is the unsaturated conditions that are common in soil. More specifically the thickness and connectivity of theliquid films between soil particles have a huge impact on bacterial motility at the microscale. Under unsaturatedconditions, when the soil becomes dryer, the matric potential becomes increasingly negative and the liquidfilms become thinner and disconnected, which has been shown to restrict bacterial flagellar motility to arelatively narrow range of water potentials (0 to -2 kPa). Due to these known restrictions, the importance ofactive dispersal in soil has been debated for years, with some claiming that motility is limited to transientfavorable periods following irrigation and rainfall. However, this theory might be based on a rather simplifiedview of soil. In clayey tills, which cover more than 40% of the Danish land area, the well-structured soil profileis divided into clearly different soil compartments. In these soils the water, primarily from rainfalls, movesfrom the plow layer through preferential flow paths towards groundwater reservoirs. The preferential flowpaths are made up of a complex system of biopores (mainly earthworm burrows and plant root channels) thatare connected to tectonic fractures in deeper layers. These can provide bacterial habitats with vastly differentphysical and chemical compositions as well as hydration conditions, compared to the matrix sediments. Whilepreferential flow paths are considered a potential major route for the passive transport of bacteria trough soil,the contribution of active dispersal in these compartments has never been explored.Previous knowledge on bacterial motility is mostly based on pure culture studies using a few carefully selectedstrains in highly artificial laboratory settings, while the role of active dispersal for natural communities remainsessentially unknown. This knowledge gap is largely caused by the lack of methods for mass assessment ofdispersal potential of bacteria in environmental samples, as very few attempts have been made to assessbacterial dispersal at the community level.The overall objective of this thesis was therefore to develop a method for assessing community motility undercontrolled hydration conditions, apply the method to uncover the dispersal potential of environmental bacterialcommunities and to identify the bacterial dispersers. Furthermore, the aim was to apply the method to explorethe dispersal potential of bacterial communities from a well-structured clay till depth profile, targetingpreferential flow paths and matrix sediments. Revealing the potential role of active dispersal in theheterogeneous environment.In Manuscript I, a method that provides profiles of community-level surface dispersal from environmentalsamples under controlled hydration conditions was developed. This enabled us to isolate and uncover thediversity of the fastest bacterial dispersers. The method was based on the Porous Surface Model (PSM),previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porousceramic disc. The novel procedure targeted complex communities, capturing the dispersed bacteria on a solidmedium for growth and detection. The method was first validated by distinguishing motile flagellatedPseudomonas putida and gliding Flavobacterium johnsoniae strains from their nonmotile mutants. Applyingthe method to soil and lake water bacterial communities showed that community-scale dispersal declined asconditions became drier. However, for both communities, dispersal was detected even under low-hydrationconditions (matric potential, -3.1 kPa), previously proven too dry for flagellar motility. We were then able tospecifically recover and characterize the fastest dispersers from the inoculated communities. For both soil andlake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially lessdiverse than the total communities. The dispersing fraction of the soil microbial community was dominated byPseudomonas, which increased in abundance under low-hydration conditions, while the dispersing fraction ofthe lake community was dominated by Aeromonas.In Manuscript II we applied the novel method to assess the dispersal of five bacterial communities derivedfrom contrasting compartments along a fractured clay till depth profile, including plow layer soil, preferentialflow paths and matrix sediments down to 350 cm below surface. In agreement with the results fromManuscript I, we found bacteria capable of active dispersal at -3.1 kPa in all communities. Further testing ofthe plow layer community uncovered active dispersal even at matric potentials of -6.3 to -8.4 kPa, which washitherto thought too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, we found thedispersing communities to be less diverse compared to corresponding total communities, supporting andextending the results in Manuscript I. The dominant dispersers in most compartments belonged to the genusPseudomonas, and, in plow layer soil, also Rahnella. The dispersing community in the matrix sediment at 350cm below surface was an exception and was dominated by Pantoea. An increased proportion of sharedAmplicon Sequence Variants of the dispersing communities, compared to non-dispersers, between thehydrologically connected compartments of plow layer, biopores and tectonic fractures suggest that activedispersal is important for colonization of these compartments. These results highlight the importance ofaddressing soil heterogeneity when exploring the role of active dispersal in soil and bring us a step closer toassessing the importance of bacterial dispersal under environmentally relevant conditions.
M3 - Ph.D. thesis
BT - Community dispersal
PB - Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen
ER -