Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation

As motivation to address environmental dissemination of antimicrobial resistance (AMR) is mounting, there is a need to characterize mechanisms by which AMR can propagate under environmental conditions. Here we investigated the effect of temperature and stagnation on the persistence of wastewater-associated antibiotic resistance markers in riverine biofilms and the invasion success of genetically-tagged Escherichia coli. Biofilms grown on glass slides incubated in-situ downstream of a wastewater treatment plant effluent discharge point were transferred to laboratory-scale flumes fed with filtered river water under potentially stressful temperature and flow conditions: recirculation flow at 20 °C, stagnation at 20 °C, and stagnation at 30 °C. After 14 days, quantitative PCR and amplicon sequencing were used to quantify bacteria, biofilms diversity, resistance markers (sul1, sul2, ermB, tetW, tetM, tetB, blaCTX-M-1, intI1) and E. coli. Resistance markers significantly decreased over time regardless of the treatment applied. Although invading E. coli were initially able to colonize the biofilms, its abundance subsequently declined. Stagnation was associated with a shift in biofilm taxonomic composition, but there was no apparent effect of flow conditions or the simulated river-pool warming (30 °C) on AMR persistence or invasion success of E. coli. Results however indicated that antibiotic resistance markers in the riverine biofilms decreased under the experimental conditions in the absence of exposure to external inputs of antibiotics and AMR.

Organic pulses and bacterial invasion alleviated by the resilience of soil microbial community

Biogas slurry is a nutrient-rich secondary product of livestock feces digestion which is recycled as a crop plantation fertilizer and provides exogenous microbes to the soil. However, the effects of biogas slurry microbes on the soil resident community remain unknown. In this study, we examined the ecological consequences of long-term biogas slurry pulse on the soil resident community and found that it promoted crop yield and altered soil characteristics. The soil microbial ecosystem was altered as a result of organic amendments due to the exogenous input of microbes and nutrients. Nevertheless, the soil resident communities were highly resilient to long-term organic pulses, as evidenced by community diversity and composition. The two dominant bacterial species in biogas slurry were Sterolibacterium and Clostridium. Notably, the abundance of Clostridium in biogas slurry increased following long-term amendments, while other species such as GP1 and Subdivision3_genera_incertae_sedis decreased; which was consistent with the results of module-eigengene analysis. Long-term organic pulses shifted the balance of microbial community assembly from stochastic to deterministic processes. Overall, our findings indicated that organic pulses accompanied with bacterial invasion could be alleviated by the resilience of soil microbial communities, thereby emphasizing the importance of microbiota assemblage and network architecture.

Inter-basin water diversion homogenizes microbial communities mainly through stochastic assembly processes

Inter-basin water transfer is an effective manner to achieve the optimal allocation of water resources, while accompanied by some ecological effects. The responses of microorganisms to water diversion and the ecological processes in regulating the community assembly are still unclear. Taking the eastern route of South-to-North Water Diversion Project as the study area, we investigated the microbial community patterns and the underlying assemblage processes in habitats with different hydrological connectivity, including isolated lakes, connected lakes and man-made canal. The results showed that microbial communities in the canal had higher diversity, lower dissimilarity, weaker compositional variation, and stronger co-occurrence patterns compared with that in the connected and isolated lakes. These findings suggested that the increase of connectivity among natural aquatic habitats due to water diversion can homogenize microbial communities and reduce microbial heterogeneity. The neutral and null models demonstrated the importance of stochastic processes in shaping microbial community assembly. Dispersal limitation and variable selection were the predominant mechanisms structuring microbial communities in the isolated lakes. Due to the homogenized environmental condition and the enhanced hydrologic connectivity in the canal and the connected lakes, microbial communities had higher dispersal capability and ecological drift occurred more frequently in these lotic habitats. The variations in microbial community structure were mainly driven by biotic ecological succession than abiotic factors, with positive and negative cohesion explained 63% and 25% of variability, respectively. Six taxa were considered as the potential introduced microorganisms, which may favor the nutrient biogeochemical cycling and the organic matter degradation, but may also bring ecological risks. Overall, this study provides a deeper understanding of the ecological consequences of inter-basin water diversion, and helps the regulation and management of these projects.

Comparative evaluation of package types in alleviating textural softening and package-swelling of Paocai during storage: Insight into microbial invasion, cell wall pectinolysis and alteration in sugar and organic acid profiles

The present study aimed to investigate the effect of initial vacuum package (VP), air package (AP) and salt-solution package (NP) on texture softening and package-swelling of Paocai by comparing the changes in physicochemical properties, pectinolysis, microstructure, microbial profile, as well as sugar and organic acid profiles during storage. Results showed that, when compared with AP and NP, with suppressive microbial invasion and less total pectinase activity, VP could retain more soluble pectin and induce more compact microstructure of Paocai, leading to higher hardness of Paocai during storage. As for package-swelling, VP mitigated gas-production in package by changing the microbial composition and metabolic patterns of sugar and organic acid in Paocai, especially targeted regulating the abundance of genus Kazachstania. This study provided a perspective for appropriate packaging technology to control the pectinase activity as well as cell-invading and gas-producing microorganisms for manufacturing fermented vegetable with better texture and non-package-swelling.

Study of invasion and colonization of E. faecalis in microtubes by a novel device

Enterococcus faecalis (E. faecalis) is a species that has frequently been isolated from root canal of patients suffering from persistent periodontitis. To a great degree, the resistance of E. faecalis to irrigating solutions and intracanal medicaments is due to its invasion into the dentinal tubules. In this study, we developed a device to observe the dynamic process of the bacterial invasion into microtubes. According to the diameter of the dentinal tubules and other microstructures in the root canals, we designed four different size microtubes with different lengths in this device. As expected, E. faecalis is able to steadily grow in this device and penetrate into the microtubes, and a continuous observation is achieved. We found that the depth and speed of bacterial penetration, the extent of colonization and the arrangement of the bacteria in the microtubes are strongly influenced by the size of the microtube. The length of the microtube also influences the speed and depth of the bacterial invasion. Bacteria in microtubes with a similar diameter to the real dentinal tubules showed a discontinuous distribution, which is consistent with the final bacterial distribution in the native dentinal tubules. Considering the device's advantages such as its ability to provide real-time observations, its ability to be modified as necessary, and its standardized operation, it has great potential to be widely used as a platform for the observation of the interaction of different bacteria during an invasion course and to test the efficacy of new antibacterial agents in dentistry.

Fungal communities as an experimental approach to Darwin's naturalization hypothesis

Darwin's naturalization hypothesis suggests that the success of an invasive species will be lower when colonizing communities are formed by phylogenetically related rather than unrelated species due to increased competition. Although microbial invasions are involved in both natural and anthropogenic processes, factors affecting the success of microbial invaders are unknown. A biological invasion assay was designed using Trichoderma cf. harzianum as the invader and two types of recipient communities assembled in microcosm assays: communities phylogenetically related to the invader, and communities phylogenetically unrelated to it. Both types of communities were invaded by T. cf. harzianum, and the success of colonization was monitored by qPCR; its effect on the genetic structure of recipient fungal communities was then assessed by DGGE profiles. T. cf. harzianum established itself in both communities, reaching 1000-10,000 times higher copy numbers in the non-related communities. However, invader establishment does not affect the structure of the invaded communities. These results suggest that the composition of recipient communities and their phylogenetic relationship to the invader affect the success of colonization by T. cf. harzianum. While this approach represents a very simplified assay, these microcosms enable an experimental test of Darwin's hypothesis in order to understand the biological invasion process in microbial communities.