Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress

Beyond biogeographic patterns: Processes shaping the microbial landscape in soils and sediments along the Yangtze River

Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives. However, ecological processes shaping distribution patterns of microorganisms across large spatial-scale watersheds remain largely unknown. Using Illumina sequencing and multiple statistical methods, we characterized distribution patterns and maintenance diversity of microorganisms (i.e., archaea, bacteria, and fungi) in soils and sediments along the Yangtze River. Distinct microbial distribution patterns were found between soils and sediments, and microbial community similarity significantly decreased with increasing geographical distance. Physicochemical properties showed a larger effect on microbial community composition than geospatial and climatic factors. Archaea and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments, but opposite for bacteria. Archaea, bacteria, and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments, suggesting stronger environmental adaptation. Stochasticity dominated community assemblies of archaea and fungi in soils and sediments, whereas determinism dominated bacterial community assembly. Our results have therefore highlighted distinct microbial distribution patterns and diversity maintenance mechanisms between soils and sediments, and emphasized important roles of species replacement, environmental adaptability, and ecological assembly processes on microbial landscape. Our findings are helpful in predicting loss of microbial diversity in the Yangtze River Basin, and might assist the establishment of environmental policies for protecting fragile watersheds.

Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces

Background

To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements.

Results

We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells.

Conclusions

The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01406-z.

NaCl salinity enhances tetracycline bioavailability to Escherichia coli on agar surfaces

Soil salinity is a worldwide problem and is damaging soil functions. Meanwhile, increasing amounts of anthropogenic antibiotics are discharged to agricultural soils. Little is known about how soil salinity (e.g., NaCl) could influence the bioavailability of antibiotics to bacteria. In this study, a tetracycline-responsive Escherichia coli bioreporter grew on the surfaces of agar microcosms at the same tetracycline concentration (200 μg/L), but various NaCl concentrations (0.5-19.2 g/L) with estimated osmotic potential of -0.18 to -1.80 MPa, and agar content (0.3%-5%) with estimated intrinsic permeability of 38 to 32,928 nm². These agar microcosms mimicked very fine textured soils with a range of NaCl salinity. Increasing agar content lowered the intrinsic permeability hence decreasing tetracycline bioavailability to E. coli, due likely to the reduced mass transfer of tetracycline via water flow. Intriguingly, tetracycline bioavailability increased with increasing NaCl concentration which caused the increase in osmotic stress. This is contradictory to the notion that osmotic stress reduces bacterial chemical uptake. Further analysis of E. coli membrane integrity demonstrated that the enhanced tetracycline bioavailability to bacteria could result from the compromised cell membranes and enhanced membrane permeability at higher NaCl salinity. Overall, this study suggests that high soil salinity (NaCl) may enhance the selection pressure exerted by antibiotics on bacteria.

Electric Field Effects on Bacterial Deposition and Transport in Porous Media

Bacterial deposition and transport are key to microbial ecology and biotechnological applications. We therefore tested whether electrokinetic forces (electroosmotic shear force ( F_EOF), electrophoretic drag force ( F_EP)) acting on bacteria may be used to control bacterial deposition during transport in laboratory percolation columns exposed to external direct current (DC) electric fields. For different bacteria, yet similar experimental conditions we observed that DC fields either enhanced or reduced bacterial deposition efficiencies (α) relative to DC-free controls. By calculating the DLVO force of colloidal interactions, F_EOF, F_EP, and the hydraulic shear forces acting on single cells at a collector surface we found that DC-induced changes of α correlated to | F_EOF| to | F_EP| ratios: If | F_EOF| > | F_EP|, α was clearly increased and if | F_EOF| < | F_EP| α was clearly decreased. Our findings allow for better prediction of the forces acting on a bacterium at collector surface and, hence, the electrokinetic control of microbial deposition in natural and manmade ecosystems.

Ecology of Contaminant Biotransformation in the Mycosphere: Role of Transport Processes

Fungi and bacteria often share common microhabitats. Their co-occurrence and coevolution give rise to manifold ecological interactions in the mycosphere, here defined as the microhabitats surrounding and affected by hyphae and mycelia. The extensive structure of mycelia provides ideal "logistic networks" for transport of bacteria and matter in structurally and chemically heterogeneous soil ecosystems. We describe the characteristics of the mycosphere as a unique and highly dynamic bacterial habitat and a hot spot for contaminant biotransformation. In particular, we emphasize the role of the mycosphere for (i) bacterial dispersal and colonization of subsurface interfaces and new habitats, (ii) matter transport processes and contaminant bioaccessibility, and (iii) the functional stability of microbial ecosystems when exposed to environmental fluctuations such as stress or disturbances. Adopting concepts from ecological theory, the chapter disentangles bacterial-fungal impacts on contaminant biotransformation in a systemic approach that interlinks empirical data from microbial ecosystems with simulation data from computational models. This approach provides generic information on key factors, processes, and ecological principles that drive microbial contaminant biotransformation in soil. We highlight that the transport processes create favorable habitat conditions for efficient bacterial contaminant degradation in the mycosphere. In-depth observation, understanding, and prediction of the role of mycosphere transport processes will support the use of bacterial-fungal interactions in nature-based solutions for contaminant biotransformation in natural and man-made ecosystems, respectively.

Spatiotemporal disturbance characteristics determine functional stability and collapse risk of simulated microbial ecosystems

Terrestrial microbial ecosystems are exposed to many types of disturbances varying in their spatial and temporal characteristics. The ability to cope with these disturbances is crucial for maintaining microbial ecosystem functions, especially if disturbances recur regularly. Thus, understanding microbial ecosystem dynamics under recurrent disturbances and identifying drivers of functional stability and thresholds for functional collapse is important. Using a spatially explicit ecological model of bacterial growth, dispersal, and substrate consumption, we simulated spatially heterogeneous recurrent disturbances and investigated the dynamic response of pollutant biodegradation – exemplarily for an important ecosystem function. We found that thresholds for functional collapse are controlled by the combination of disturbance frequency and spatial configuration (spatiotemporal disturbance regime). For rare disturbances, the occurrence of functional collapse is promoted by low spatial disturbance fragmentation. For frequent disturbances, functional collapse is almost inevitable. Moreover, the relevance of bacterial growth and dispersal for functional stability also depends on the spatiotemporal disturbance regime. Under disturbance regimes with moderate severity, microbial properties can strongly affect functional stability and shift the threshold for functional collapse. Similarly, networks facilitating bacterial dispersal can delay functional collapse. Consequently, measures to enhance or sustain bacterial growth/dispersal are promising strategies to prevent functional collapses under moderate disturbance regimes.

Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem

Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how this is related to the bacterial biomass abundance. In this paper, we use a numerical simulation approach to systematically analyze the dynamic response of a microbial population to recurrent disturbances of different spatial distribution. The spatially explicit model considers microbial degradation, growth, dispersal, and spatial networks that facilitate bacterial dispersal mimicking effects of mycelial networks in nature. We find: (i) There is a certain capacity for high resistance of biodegradation performance to recurrent disturbances. (ii) If this resistance capacity is exceeded, spatial zones of different biodegradation performance develop, ranging from no or reduced to even increased performance. (iii) Bacterial biomass and biodegradation dynamics respond inversely to the spatial fragmentation of disturbances: overall biodegradation performance improves with increasing fragmentation, but bacterial biomass declines. (iv) Bacterial dispersal networks can enhance functional resistance against recurrent disturbances, mainly by reactivating zones in the core of disturbed areas, even though this leads to an overall reduction of bacterial biomass.