Phage Predation Promotes Filamentous Bacterium Piscinibacter Colonization and Improves Structural and Hydraulic Stability of Microbial Aggregates

Phage-based biocontrol of Porphyromonas gingivalis through indirect targeting

Bacteriophages offer an opportunity for chemical-free, precise control of problematic bacteria, but this approach can be limited when lytic phages are difficult to obtain for the target host. In such cases, phage-based targeting of cooperating or cross-feeding bacteria (e.g., Streptococcus gordonii) can be an effective approach to control the problematic bacteria (e.g., Porphyromonas gingivalis). Using a dual-species biofilm system, phage predation of S. gordonii (108 PFU·mL-1) decreased the abundance of pathogenic P. gingivalis by >99% compared with no-treatment controls, while also inhibiting the production of cytotoxic metabolic end products (butyric and propionic acids). Phage treatment upregulated genes associated with interspecies co-adhesion (5- to 8-fold) and quorum sensing (10-fold) in residual P. gingivalis, which is conducive to increased potential to bind to S. gordonii. Counterintuitively, lower-titer phage applications (104 PFU·mL-1) increased the production of extracellular polymeric substance (EPS) by 22% and biofilm biomass by 50%. This overproduction of EPS may contribute to the phenomenon where the biofilm separated into two distinct species layers, as observed by confocal laser scanning microscopy. Although more complex mixed-culture systems should be considered to delineate the merits and limitations of this novel biocontrol approach (which would likely require the use of phage cocktails), our results offer proof of concept that indirect phage-based targeting can expand the applicability of phage-based control of pathogenic bacteria for public health protection.

IMPORTANCE

Lytic phages are valuable agents for targeted elimination of bacteria in diverse applications. Nevertheless, lytic phages are difficult to isolate for some target pathogens. We offer proof of concept that this limitation may be overcome via indirect phage targeting, which involves knocking out species that interact closely with and benefit the primary problematic target bacteria. Our target (P. gingivalis) only forms a periodontal pathogenic biofilm if the pioneer colonizer (S. gordonii) offers its surface for P. gingivalis to attach. Phage predation of the co-adhesive S. gordonii significantly reduced abundance of the target pathogen by >99%, decreased the total biofilm biomass by >44%, and suppressed its production of cytotoxic metabolic byproducts. Thus, this research extends the scope of phage-based biocontrol for public health protection.

Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations

Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.

Adaptive strategies and ecological roles of phages in habitats under physicochemical stress

Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.

Joining the bacterial conversation: increasing the cultivation efficiency of soil bacteria with acyl-homoserine lactones and cAMP

IMPORTANCE

Microorganisms are a repository of interesting metabolites and functions. Therefore, accessing them is an important exercise for advancing not only basic questions about their physiology but also to advance technological applications. In this sense, increasing the culturability of environmental microorganisms remains an important endeavor for modern microbiology. Because microorganisms do not live in isolation in their environments, molecules can be added to the cultivation strategies to "inform them" that they are present in growth-permissive environmental conditions. Signaling molecules such as acyl-homoserine lactones and 3',5'-cyclic adenosine monophosphate belong to the plethora of molecules used by bacteria to communicate with each other in a phenomenon called quorum sensing. Therefore, including quorum sensing molecules can be an incentive for microorganisms, specifically soil bacteria, to increase their numbers on solid media.

Effective abatement of ammonium and nitrate release from sediments by biochar coverage

Inorganic forms of N from sediments and runoff water, among others, remain some of the key sources of pollution of water bodies. However, the release of NH4+-N from sediment to water can be effectively reduced by biochar coverage due to high adsorption capacity, unlike NO3-N, where biochar has a low affinity. The feasibility of biochar coverage to abate NO3--N release needs to be evaluated. This study collected four sediments from Lake Taihu (China). Three types of biochar pyrolyzed from ordinary wastes, coconut shell (coBC), algal and excess sludge, were prepared to cover them and were incubated for 90 days. Results showed that the terminal total nitrogen (TN) and NO3--N concentrations decreased from 5.35 to 2.31-3.04 mg/L, 3.05 to 0.34-1.11 mg/L, respectively. CoBC coverage showed the best performance for reducing NO3--N release flux from 26.99 ± 0.19 to 9.30 ± 0.02 mg/m2·d (63.6 %). Potential denitrifiers, such as Flavobacterium and Exiguobacterium, were enriched in the biochar-coverage layer, and the absolute abundance of N-related functional genes (narG, nirS, nosZ and anammox) was increased by 1.76-4.21 times (p < 0.05). Jar tests by 15N isotope labeling further indicated that biochar addition increased the denitrification and anammox rates by 53.5-83.4 %. Experiments combining exogenous organic‑carbon addition and 15N labeling demonstrated that biochar's key role was regulating organic matter's bioavailability. Analysis with partial least square path modeling (PLS-PM) implied biochar with higher adsorption enhanced the denitrification and anammox processes in sediments via modifying the niche with suitable DOC, TN, and pH. This study suggested that biochar coverage could effectively abate NO3--N release from sediments by affecting the denitrification and anammox processes.