Evolution of species interactions in a biofilm community

Mixed species biofilm: Structure, challenge and its intricate involvement in hospital associated infections

Hospital associated infections or healthcare associated infections (HAIs) are a major threat to healthcare and medical management, mostly because of their recalcitrant nature. The primary cause of these HAIs is bacterial associations, especially the interspecies interactions. In interspecies interactions, more than one species co-exists in a common platform of extracellular polymeric substances (EPS), establishing a strong interspecies crosstalk and thereby lead to the formation of mixed species biofilms. In this process, the internal microenvironment and the surrounding EPS matrix of the biofilms ensure the protection of the microorganisms and allow them to survive under antagonistic conditions. The communications between the biofilm members as well as the interactions between the bacterial cells and the matrix polymers, also aid in the rigidity of the biofilm structure and allow the microorganisms to evade both the host immune response and a wide range of anti-microbials. Therefore, to design a treatment protocol for HAIs is difficult and it has become a growing point of concern. This review therefore first aims to discuss the role of microenvironment, molecular structure, cell-cell communication, and metabolism of mixed species biofilms in manifestation of HAIs. In addition, we discuss the electrochemical properties of mixed-species biofilms and their mechanism in developing drug resistance. Then we focus on the most dreaded bacterial HAI including oral and gut multi-species infections, catheter-associated urinary tract infections, surgical site infections, and ventilator-associated pneumonia. Further, we highlight the challenges to eradication of the mixed species biofilms and the current and prospective future strategies for the treatment of mixed species-associated HAI. Together, the review presents a comprehensive understanding of mixed species biofilm-mediated infections in clinical scenario, and summarizes the current challenge and prospect of therapeutic strategies against HAI.

Klebsiella pneumoniae AI-2 transporters mediate interspecies interactions and composition in a three-species biofilm community

Biofilms in nature often exist as communities. In this study, an experimental mixed-species community consisting of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was used to investigate how AI-2 transporters affect interspecies interactions and composition. The K. pneumoniae lsrB/lsrD deletion mutants had a 10-25-fold higher concentration of extracellular AI-2 compared to the wild-type. Although these deletion mutants produced monospecies biofilms of similar biomass, the substitution of these mutants for the parental strain significantly altered composition. Dual-species biofilm assays demonstrated that the changes in composition were due to the cumulative effect of pairwise interactions. It was further revealed that K. pneumoniae being present physically in the consortium was important in AI-2 mediating composition in the consortium, and that AI-2 transporters were crucial in achieving maximum biomass in the community. In conclusion, these findings demonstrate that AI-2 transporters mediate interspecies interactions and is important in maintaining the compositional equilibrium of the community.

Cell Membrane-Coated Nanoparticles for Dental, Oral, and Craniofacial Diseases

Dental, oral, and craniofacial diseases can substantially impact the quality of human life, thereby posing a serious public health concern. Although conventional therapies such as surgery have solved these problems largely, the prognosis of patients is not always satisfactory. Cell membrane-coated nanoparticles (CMCNPs) carry nanodrugs with the help of natural cell membranes, therefore utilizing their remarkable ability to interface and interact with their surrounding environment. These nanoparticles have demonstrated substantial advantages in drug targeting, prolonging blood circulation time, penetrating biofilms, and immune escape. With the assistance of CMCNPs, the therapeutic effects of dental, oral, and craniofacial diseases can reach a higher level. CMCNPs have been applied for dental, oral, and craniofacial diseases for various conditions such as head and neck cancer, periodontal disease, and oral biosignal detection. For the therapies of head and neck cancer, CMCNPs have been widely utilized as a tool of chemotherapy, phototherapy, and immunotherapy, while yet to be exploited in imaging technique. In the end, we summarized the challenges and prospectives of CMCNPs for dental, oral, and craniofacial diseases: large-scale production with uniform standards and high quantity, extensive application directions in dental, oral, and craniofacial regions (implant, endodontics), and the promotion of its clinical application.

Can photocatalysis inhibit interspecies bacterial cooperation to quench the formation of robust complex bacterial biofilms in water environments?

Bacterial biofilms pose significant a public health risk as an environmental reservoir for opportunistic aquatic bacterial pathogens. Understanding the interspecies roles of complex bacterial biofilms under different stimuli and regulatory mechanisms of stress responses is the key to controlling their dissemination. Herein, two-species mixture (TSM) biofilms (Staphylococcus aureus and Pseudomonas aeruginosa) were constructed in a flowthrough reactor. Compared with the single-species biofilms, the TSM biofilm had higher growth activity to reach maturity faster, forming a staggered community structure. Moreover, the TSM biofilm exhibited greatly improved resistance to different antibiotics (16-128 times higher), especially to those that act on protein synthesis and cell membrane integrity, when compared to single planktonic microorganisms. In the presence of stimuli, photocatalysis effectively inactivated the TSM biofilm within 10 h, a 4-fold shorter inactivation time compared to UVC irradiation. In addition, photocatalysis effectively depleted the extracellular polymers of the TSM biofilm and inhibited secretion of their interspecies quorum sensing signaling molecule autoinducer-2 (AI-2). However, the expression of AI-2 induced related virulence factors, and biofilm growth-related genes were initially up-regulated 3 - 10 fold for the TSM biofilm within the first 2 - 4 h of photocatalysis, followed by significant down-regulation. Furthermore, the addition of the AI-2 precursor 4,5-dihydroxy-2,3-pentanedione effectively delayed the photocatalytic inactivation efficiency of the TSM biofilm compared to the control. These results suggest that photocatalysis can effectively inactivate biofilms by inhibiting interspecies cooperation by quenching AI-2 in the TSM biofilm. This work sheds light on controlling biofilms in public health engineering systems.

Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities

SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.

Formation of filamentous fungal biofilms in water and the transformation of resistance to chlor(am)ine disinfection

Biofilms are composed of complex multi-species in nature, potentially threatening drinking water safety. In this work, the formation of single- and multi-species fungal biofilms formed by Aspergillus niger (A. niger) and Aspergillus flavus (A. flavus), and the inactivation of mature biofilms using chlor(am)ine were firstly investigated. Results revealed that the antagonistic interaction occurred between A. niger and A. flavus. Chloramination at 20 mg/L for 30 min achieved 74.74 % and 76.04 % inactivation of A. flavus and multi-species biofilm, which were 1.69- and 1.84-fold higher than that of chlorine at the same condition. However, no significant difference was observed in the inactivation of A. niger biofilm between chlorine and monochloramine disinfection due to the lower amount of extracellular polymeric substance produced by it (p > 0.05). The inactivation of biofilm by monochloramine fitted the Weibull model well. According to the Weibull model, the monochloramine resistance of biofilm were as follows: A. flavus > multi-species > A. niger biofilm. Besides, an increase in reactive oxygen levels, damage of cell membrane, and leakage of intracellular substances in biofilms were observed after chlor(am)ination. More intracellular polysaccharides and proteins were leaked in chloramination inactivation (p < 0.05). This study provides important implications for controlling fungal biofilm.

Origin of biogeographically distinct ecotypes during laboratory evolution

Resource partitioning is central to the incredible productivity of microbial communities, including gigatons in annual methane emissions through syntrophic interactions. Previous work revealed how a sulfate reducer (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification in a planktonic context, improving stability, cooperativity, and productivity within 300-1000 generations. Here, we show that mutations in just 15 Dv and 7 Mm genes within a minimal assemblage of this evolved community gave rise to co-existing ecotypes that were spatially enriched within a few days of culturing in a fluidized bed reactor. The spatially segregated communities partitioned resources in the simulated subsurface environment, with greater lactate utilization by attached Dv but partial utilization of resulting H2 by low affinity hydrogenases of Mm in the same phase. The unutilized H2 was scavenged by high affinity hydrogenases of planktonic Mm, producing copious amounts of methane. Our findings show how a few mutations can drive resource partitioning amongst niche-differentiated ecotypes, whose interplay synergistically improves productivity of the entire mutualistic community.

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology

Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.

Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile

Clostridioides difficile can transiently or persistently colonize the human gut, posing a risk factor for infections. This colonization is influenced by complex molecular and ecological interactions with human gut microbiota. By investigating C. difficile dynamics in human gut communities over hundreds of generations, we show patterns of stable coexistence, instability, or competitive exclusion. Lowering carbohydrate concentration shifted a community containing C. difficile and the prevalent human gut symbiont Phocaeicola vulgatus from competitive exclusion to coexistence, facilitated by increased cross-feeding. In this environment, C. difficile adapted via single-point mutations in key metabolic genes, altering its metabolic niche from proline to glucose utilization. These metabolic changes substantially impacted inter-species interactions and reduced disease severity in the mammalian gut. In sum, human gut microbiota interactions are crucial in shaping the long-term growth dynamics and evolutionary adaptations of C. difficile, offering key insights for developing anti-C. difficile strategies.

Parallel evolution of alternate morphotypes of Chryseobacterium gleum during experimental evolution with Caenorhabditis elegans

Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities.

Polar accumulation of pyoverdin and exit from stationary phase

Pyoverdin is a water-soluble metal-chelator synthesized by members of the genus Pseudomonas and used for the acquisition of insoluble ferric iron. Although freely diffusible in aqueous environments, preferential dissemination of pyoverdin among adjacent cells, fine-tuning of intracellular siderophore concentrations, and fitness advantages to pyoverdin-producing versus nonproducing cells, indicate control of location and release. Here, using time-lapse fluorescence microscopy to track single cells in growing microcolonies of Pseudomonas fluorescens SBW25, we show accumulation of pyoverdin at cell poles. Accumulation occurs on cessation of cell growth, is achieved by cross-feeding in pyoverdin-nonproducing mutants and is reversible. Moreover, accumulation coincides with localization of a fluorescent periplasmic reporter, suggesting that pyoverdin accumulation at cell poles is part of the general cellular response to starvation. Compatible with this conclusion is absence of non-accumulating phenotypes in a range of pyoverdin mutants. Analysis of the performance of pyoverdin-producing and nonproducing cells under conditions promoting polar accumulation shows an advantage to accumulation on resumption of growth after stress. Examination of pyoverdin polar accumulation in a multispecies community and in a range of laboratory and natural species of Pseudomonas, including P. aeruginosa PAO1 and P. putida KT2440, confirms that the phenotype is characteristic of Pseudomonas.

Analysis of Spatial and Biochemical Characteristics of In Vitro Cariogenic Biofilms

Background Dental caries is the most common bacterial disease of calcified tissues of teeth. Cariogenic biofilms formed on the tooth surface secrete organic acids and thus result in demineralization. Delving into the depth of biofilms is crucial to understand the pathogenic mechanisms and design improved therapeutic approaches. The aim of the study is to analyze the spatial and biochemical characteristics of cariogenic biofilms. Materials and methods Pulp tissue samples sourced from freshly extracted third molars were incubated with oral cariogenic bacteria namely Streptococcus mutans, Staphylococcus aureus, Escherichia coli, Entamoeba faecalis, and Candida albicans to form the biofilm. Spatial assessment of biofilms was done under FESEM (field emission scanning electron microscope, JSM-IT800, JEOL, Tokyo, Japan). FTIR (Fourier transform infrared spectroscopy, Alpha II, Bruker, Germany) spectra were assessed for chemical molecular interactions in 24- and 48-hour time periods.  Results Morphological assessment with FESEM revealed rapid growth and aggregation within a short time period. FTIR spectra to analyze chemical constituents of biofilm presented with varied peaks of water, amide A, amide I, water, lipids, and phospholipids. Conclusion Further validation with more advanced imaging for an extended time period is vital to derive better conclusive evidence.

Metabolic interactions affect the biomass of synthetic bacterial biofilm communities

IMPORTANCE

Co-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. According to our results, metabolic exchanges and resource competition may partially explain the co-occurrence network analysis results found in synthetic bacterial biofilm communities.

Solving polymicrobial puzzles: evolutionary dynamics and future directions

Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.

Genotypic variations and interspecific interactions modify gene expression and biofilm formation of Xanthomonas retroflexus

Multispecies biofilms are important models for studying the evolution of microbial interactions. Co-cultivation of Xanthomonas retroflexus (XR) and Paenibacillus amylolyticus (PA) systemically leads to the appearance of an XR wrinkled mutant (XRW), increasing biofilm production. The nature of this new interaction and the role of each partner remain unclear. We tested the involvement of secreted molecular cues in this interaction by exposing XR and XRW to PA or its supernatant and analysing the response using RNA-seq, colony-forming unit (CFU) estimates, biofilm quantification, and microscopy. Compared to wild type, the mutations in XRW altered its gene expression and increased its CFU number. These changes matched the reported effects for one of the mutated genes: a response regulator part of a two-component system involved in environmental sensing. When XRW was co-cultured with PA or its supernatant, the mutations effects on XRW gene expression were masked, except for genes involved in sedentary lifestyle, being consistent with the higher biofilm production. It appears that the higher biofilm production was the result of the interaction between the genetic context (mutations) and the biotic environment (PA signals). Regulatory genes involved in environmental sensing need to be considered to shed further light on microbial interactions.

Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates

Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.

Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention

KEY MESSAGE

The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.

Competitive interactions facilitate resistance development against antimicrobials

While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.

ROS generating BODIPY loaded nanoparticles for photodynamic eradication of biofilms

Bacterial biofilms can pose a serious health risk to humans and are less susceptible to antibiotics and disinfection than planktonic bacteria. Here, a novel method for biofilm eradication based on antimicrobial photodynamic therapy utilizing a nanoparticle in conjunction with a BODIPY derivative as photosensitizer was developed. Reactive oxygen species are generated upon illumination with visible light and lead to a strong, controllable and persistent eradication of both planktonic bacteria and biofilms. One of the biggest challenges in biofilm eradication is the penetration of the antimicrobial agent into the biofilm and its matrix. A biocompatible hydrophilic nanoparticle was utilized as a delivery system for the hydrophobic BODIPY dye and enabled its accumulation within the biofilm. This key feature of delivering the antimicrobial agent to the site of action where it is activated resulted in effective eradication of all tested biofilms. Here, 3 bacterial species that commonly form clinically relevant pathogenic biofilms were selected: Escherichia coli, Staphylococcus aureus and Streptococcus mutans. The development of this antimicrobial photodynamic therapy tool for biofilm eradication takes a promising step towards new methods for the much needed treatment of pathogenic biofilms.

Diversity characterization of bacteria and fungi in water, sediments and biofilms from Songhua River in Northeast China

Water, sediments, and biofilms are the typical microbial carriers in natural water environments. However, comparative analysis of the distribution of bacterial and fungal communities in different carriers within the same habitat is relatively lacking. Therefore, this study employed 16 S and ITS rRNA gene sequencing to identify bacterial and fungal community structures in water, sediments, and biofilm. The results show that (1) the OTUs numbers revealed that the bacterial abundance, at the levels of species, genus, and family, followed the order of sediments > water > biofilms, while the fungal abundance order was water > sediments > biofilms. In addition, bacteria were mainly present in sediments, while fungi were mainly present in water. (2) The α diversity index (Shannon, ACE, Simpson, and Chao1) order, for bacteria was: sediments > water > biofilms, indicating that the diversity and homogeneity of bacteria in sediments were relatively higher; for fungi was: water > sediments > biofilms, indicating that the diversity and abundance of fungi in water were high. (3) The core phylum of bacterial in the water, sediments, and biofilms was Cyanobacteria (31.3-46.1%) and Actinobacteria (27.6-36.1%); Proteobacteria (35.0-41.8%), Cyanobacteria (14.7-36.6%); and Proteobacteria (63.3-69.2%), respectively. (4) The mainly colonized fungal phyla in biofilms in the water, sediments, and biofilms were Basidiomycota (29.3-38.7%) and Ascomycota (16.2-27.7%); Zygomycota (13.1-17.5%), Basidiomycota (5.6-17.6%); and Zygomycota (23.8-44.2%). (5) There were significant species differences in bacterial and fungal communities in water, sediments, and biofilm by NMDS analysis. Findings are useful for guiding significance for the Biogeochemical cycle of elements, the environmental fate of pollutants, and the study of water ecosystems.

Becoming settlers: Elements and mechanisms for surface colonization by Pseudomonas putida

Pseudomonads are considered to be among the most widespread culturable bacteria in mesophilic environments. The evolutive success of Pseudomonas species can be attributed to their metabolic versatility, in combination with a set of additional functions that enhance their ability to colonize different niches. These include the production of secondary metabolites involved in iron acquisition or having a detrimental effect on potential competitors, different types of motility, and the capacity to establish and persist within biofilms. Although biofilm formation has been extensively studied using the opportunistic pathogen Pseudomonas aeruginosa as a model organism, a significant body of knowledge is also becoming available for non-pathogenic Pseudomonas. In this review, we focus on the mechanisms that allow Pseudomonas putida to colonize biotic and abiotic surfaces and adapt to sessile life, as a relevant persistence strategy in the environment. This species is of particular interest because it includes plant-beneficial strains, in which colonization of plant surfaces may be relevant, and strains used for environmental and biotechnological applications, where the design and functionality of biofilm-based bioreactors, for example, also have to take into account the efficiency of bacterial colonization of solid surfaces. This work reviews the current knowledge of mechanistic and regulatory aspects of biofilm formation by P. putida and pinpoints the prospects in this field.

A simplified synthetic rhizosphere bacterial community steers plant oxylipin pathways for preventing foliar phytopathogens

Rhizosphere-enriched microbes induced by foliar phytopathogen infection can be assembled into a functional community to enhance plant defense mechanisms. However, the functions of stably-colonizing rhizosphere microbiota are rarely investigated. In this study, Botrytis cinerea infection changed rhizosphere bacterial communities in tomato plants. The phytopathogen-infected plants recruited specific rhizosphere bacterial taxa, while several bacterial taxa stably colonized the rhizosphere, regardless of phytopathogen infection. Through the analysis of the rhizosphere bacterial community, we established a synthetic community harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria species. Furthermore, the 38-species community was simplified into a three-species community, consisting of one phytopathogen-inducible (Asticcacaulis sp.) and two stably-colonizing species (Arachidicoccus sp. And Phenylobacterium sp.). The simplified community provided a durable protection for the host plants by synergistic effects, with the phytopathogen-inducible species triggering plant defense responses and the stably-colonizing species promoting biofilm formation. The simplified community exhibited similar protective effects as the 38-species community. Moreover, the activation of oxylipin pathways in the phytopathogen-infected leaves was significantly intensified by the simplified community. However, the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully abolished the community-induced plant disease resistance. In contrast, transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of divinyl ethers, displayed stronger resistance against B. cinerea compared to wild-type plants. Collectively, these findings provided insights into the utilization of the simplified community for preventing gray mold disease.

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

Artificial selection of communities drives the emergence of structured interactions

Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level functions of interest. These experiments typically involve selection acting on populations of communities, each of which is composed of multiple species. If numerical simulations started to explore the evolutionary dynamics of this complex, multi-scale system, a comprehensive theoretical understanding of the process of artificial selection of communities is still lacking. Here, we propose a general model for the evolutionary dynamics of communities composed of a large number of interacting species, described by disordered generalised Lotka-Volterra equations. Our analytical and numerical results reveal that selection for scalar community functions leads to the emergence, along an evolutionary trajectory, of a low-dimensional structure in an initially featureless interaction matrix. Such structure reflects the combination of the properties of the ancestral community and of the selective pressure. Our analysis determines how the speed of adaptation scales with the system parameters and the abundance distribution of the evolved communities. Artificial selection for larger total abundance is thus shown to drive increased levels of mutualism and interaction diversity. Inference of the interaction matrix is proposed as a method to assess the emergence of structured interactions from experimentally accessible measures.

Efficient clearance of periodontitis pathogens by S. gordonii membrane-coated H2O2 self-supplied nanocomposites in a "Jenga" style

As a key pathogen of periodontitis, P. gingivalis requires support of the initial colonizing bacterium (S. gordonii preferably) to form symbiotic biofilms on gingival tissues with enhanced antibiotic resistance. Here, we report a new strategy to treat periodontitis biofilms with S. gordonii membrane-coated H2O2 self-supplied nanocomposites (ZnO2/Fe3O4@MV NPs) in a "Jenga" style. Integration of our special MV coatings enables selectively enhanced internalization of the cargos in S. gordonii, thus inducing severe damage to the foundational bacterial layer and collapse/clearance of symbiotic biofilms consequently. This strategy allows us to clear the symbiotic biofilms of S. gordonii and P. gingivalis with active hydroxyl radicals (˙OH) derived from ZnO2-Fe3O4@MV NPs in a H2O2 self-supplied, nanocatalyst-assisted manner. This "Jenga-style" treatment provides a cutting-edge proof of concept for the removal of otherwise robust symbiotic biofilms of periodontitis where the critical pathogens are difficult to target and have antibiotic resistance.

Bacterial assemblages imply methylmercury production at the rice-soil system

The plant microbiota can affect plant health and fitness by promoting methylmercury (MeHg) production in paddy soil. Although most well-known mercury (Hg) methylators are observed in the soil, it remains unclear how rice rhizosphere assemblages alter MeHg production. Here, we used network analyses of microbial diversity to identify bulk soil (BS), rhizosphere (RS) and root bacterial networks during rice development at Hg gradients. Hg gradients greatly impacted the niche-sharing of taxa significantly relating to MeHg/THg, while plant development had little effect. In RS networks, Hg gradients increased the proportion of MeHg-related nodes in total nodes from 37.88% to 45.76%, but plant development enhanced from 48.59% to 50.41%. The module hub and connector in RS networks included taxa positively (Nitrososphaeracea, Vicinamibacteraceae and Oxalobacteraceae) and negatively (Gracilibacteraceae) correlating with MeHg/THg at the blooming stage. In BS networks, Deinococcaceae and Paludibacteraceae were positively related to MeHg/THg, and constituted the connector at the reviving stage and the module hub at the blooming stage. Soil with an Hg concentration of 30 mg kg-1 increased the complexity and connectivity of root microbial networks, although microbial community structure in roots was less affected by Hg gradients and plant development. As most frequent connector in root microbial networks, Desulfovibrionaceae did not significantly correlate with MeHg/THg, but was likely to play an important role in the response to Hg stress.

Synergistic effects of biofilm-producing PGPR strains on wheat plant colonization, growth and soil resilience under drought stress

Drought stress substantially impedes crop productivity throughout the world. Microbial based approaches have been considered a potential possibility and are under study. Based on our prior screening examination, two distinct and novel biofilm-forming PGPR strains namely Bacillus subtilis-FAB1 and Pseudomonas azotoformans-FAP3 are encompassed in this research. Bacterial biofilm development on glass surface, microtiter plate and seedling roots were assessed and characterized quantitatively and qualitatively by light and scanning electron microscopy. Above two isolates were further evaluated for their consistent performance by inoculating on wheat plants in a pot-soil system under water stresses. Bacterial moderate tolerance to ten-day drought was recorded on the application of individual strains with wheat plants; however, the FAB1 + FAP3 consortium expressively improved wheat survival during drought. The strains FAB1 and FAP3 displayed distinct and multifunctional plant growth stimulating attributes as well as effective roots and rhizosphere colonization in combination which could provide sustained wheat growth during drought. FAB1 and FAP3-induced alterations cooperatively conferred improved plant drought tolerance by controlling physiological traits (gs, Ci, E, iWUE and P_N), stress indicators (SOD, CAT, GR, proline and MDA content) and also maintained physico-chemical attributes and hydrolytic enzymes including DHA, urease, ALP, protease, ACP and β glucosidase in the soil. Our findings could support future efforts to enhance plant drought tolerance by engineering the rhizobacterial biofilms and associated attributes which requires in-depth exploration and exploiting potential native strains for local agricultural application.

Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes

Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess the magnitude of adaptation. In doing so, proper consideration should be given when determining the appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes in the framework or execution of fitness evaluations significantly impacted the outcomes. The first case illustrates that discrepancies in fitness conclusions can arise depending on the approach to evaluating fitness, the culture vessel used, and the sampling method. The second case reveals that variations in environmental conditions can occur associated with culture vessel material. Specifically, these subtle changes can greatly affect microbial physiology leading to changes in the culture pH and distorting fitness measurements. Finally, the last case reports that heterogeneity in CFU formation time can result in inaccurate fitness conclusions. Based on each case, considerations and recommendations are presented for future adaptive evolution experiments.

Evolutionary repeatability of emergent properties of ecological communities

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Glycerol Droplet Spreading on Growing Bacillus Subtilis Biofilms

Bacterial biofilm is a three-dimensional matrix composed of a large number of living bacterial individuals. The strong bio-interaction between the bacteria and its self-secreted matrix environment strengthens the mechanical integrity of the biofilm and the sustainable resistance of bacteria to antibiotics. As a soft surface, the biofilm is expected to present different dynamical wetting behavior in response to shear stress, which is, however, less known. Here, the spreading of liquid droplet on Bacillus subtilis biofilm at its different growing phases was experimentally investigated. Due to the viscoelastic response of the biofilm to fast spreading of the droplet, three stages were identified as inertial, viscous stages, and a longer transition in between. The physical heterogeneity of growing biofilm correlates with the spreading scaling within the inertial stage, followed by the possible chemical variation after a critical growing time. By using the duration of inertial spreading, the characteristic time scale was successfully linked to the shear modulus of the elastic dissipation of the biofilm. This measurement suggests a facile, non-destructive and in vivo method to understand the mechanical instability of this living matter.

Effects of Disinfectants on Larval Growth and Gut Microbial Communities of Black Soldier Fly Larvae

The use of the black soldier fly has been demonstrated to be effective in the treatment of swine manure. Since the outbreaks of ASFV, prevention procedures, including manure disinfection, have changed dramatically. Glutaraldehyde (GA) and potassium peroxymonosulfate (PPMS) have been shown to be effective in the prevention of this pathogen and are thus widely used in the disinfection of swine manures, etc. However, research on the effects of disinfectants in manures on the growth of BSFL and gut microbiota is scarce. The goal of this study was to determine the effects of GA and PPMS on BSFL growth, manure reduction, and gut microbiota. In triplicate, 100 larvae were inoculated in 100 g of each type of manure compound (manure containing 1% GA treatment (GT1), manure containing 0.5% GA treatment (GT2), manure containing 1% PPMS treatment (PT1), manure containing 0.5% PPMS treatment (PT2), and manure without disinfectant (control)). After calculating the larval weight and waste reduction, the larval gut was extracted and used to determine the microbial composition. According to the results, the dry weights of the larvae fed PT1-2 (PT1: 86.7 ± 4.2 mg and PT2: 85.3 ± 1.3 mg) were significantly higher than those of the larvae fed GT1-2 (GT1: 72.5 ± 2.1 mg and GT2: 70 ± 2.8 mg) and the control (64.2 ± 5.8 mg). There was a 2.8-4.03% higher waste reduction in PT1-2 than in the control, and the waste reduction in GT1-2 was 7.17-7.87% lower than that in the control. In a gut microbiota analysis, two new genera (Fluviicola and Fusobacterium) were discovered in PT1-2 when compared to GT1-2 and the control. Furthermore, the disinfectants did not reduce the diversity of the microbial community; rather, Shannon indices revealed that the diversities of GT1-2 (GT1: 1.924 ± 0.015; GT2: 1.944 ± 0.016) and PT1 (1.861 ± 0.016) were higher than those of the control (1.738 ± 0.015). Finally, it was found that both disinfectants in swine manures at concentrations of 1% and 0.5% may be beneficial to the complexity and cooperation of BSFL gut microbiota, according to an analysis of microbial interactions.

Acinetobacter baumannii Kills Fungi via a Type VI DNase Effector

Many Gram-negative bacteria deploy a type VI secretion system (T6SS) to inject toxins into target cells to promote their survival and replication in complex environments. Here, we report that Acinetobacter baumannii uses its T6SS to kill fungi and that the effector TafE (ACX60_15365) is responsible for such killing. Although ectopically expressed TafE is toxic to both Escherichia coli and Saccharomyces cerevisiae, deletion of tafE only affects the antifungal activity of A. baumannii. We demonstrate that TafE is a DNase capable of targeting the nuclei of yeast cells and that an Ntox15 domain is essential for its ability to degrade DNA. Furthermore, our findings show that A. baumannii is protected from the toxicity of TafE by elaborating the immunity protein TaeI (ACX60_15360), which antagonizes the activity of the effector by direct binding. The discovery of A. baumannii T6SS effectors capable of killing multiple taxonomically distinct microbes has shed light on a mechanism of the high-level fitness of this pathogen in environments characterized by scarce nutrients and the potential presence of diverse microorganisms. IMPORTANCE Acinetobacter baumannii is an increasing important nosocomial pathogen that is difficult to combat due to its ability to survive in harsh environments and the emergence of isolates that are resistant to multiple antibiotics. A better understanding of the mechanism underlying the toughness of A. baumannii may identify its Achilles' heel, which will facilitate the development of novel preventive and treatment measures. In this study, our findings show that A. baumannii kills fungi with the DNase effector TafE injected into competitor cells by its type VI secretion system. A. baumannii is protected from the activity of TafE by the immunity protein TaeI, which inactivates the effector by direct binding. Our results suggest that inactivation of its T6SS or effectors may reduce the fitness of A. baumannii and increase the effectiveness of treatment by means such as antibiotics. Furthermore, our finding suggests that targeted degradation of TaeI may be an effective strategy to kill A. baumannii.

Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community

Species interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this question in a community of yeast Saccharomyces cerevisiae and alga Chlamydomonas reinhardtii that have a net commensal relationship that results from a balance between competitive and mutualistic interactions. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular those that increase and reduce the yields of both species. The presence of the alga does not change which mutations are adaptive in yeast (that is, there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favour yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of the alga, adaptative mutations contending for fixation in yeast are more likely to enhance the mutualism, even though cooperativity is not directly favoured by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.

How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts

Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some of these associations have evolved into obligate relationships with permanent symbiont localization within the host, the majority require colonization of every host generation from the environment or via maternal provisions. Across the broad diversity of host species and tissue types that beneficial bacteria can colonize, there are some highly specialized strategies for establishment yet also some common patterns in the molecular basis of colonization. This review focuses on the mechanisms underlying the early stage of beneficial bacterium-invertebrate associations, from initial contact to the establishment of the symbionts in a specific location of the host's body. We first reflect on general selective pressures that can drive the transition from a free-living to a host-associated lifestyle in bacteria. We then cover bacterial molecular factors for colonization in symbioses from both model and nonmodel invertebrate systems where these have been studied, including terrestrial and aquatic host taxa. Finally, we discuss how interactions between multiple colonizing bacteria and priority effects can influence colonization. Taking the bacterial perspective, we emphasize the importance of developing new experimentally tractable systems to derive general insights into the ecological factors and molecular adaptations underlying the origin and establishment of beneficial symbioses in animals.

Azospirillum baldaniorum Sp245 exploits Pseudomonas fluorescens A506 biofilm to overgrow in dual-species macrocolonies

Biofilms are essential for plant-associated bacteria to colonize their host. In this work, we analysed the interaction of Azospirillum baldaniorum Sp245 and Pseudomonas fluorescens A506 in mixed macrocolony biofilms. We identified certain culture conditions where A. baldaniorum Sp245 exploits P. fluorescens A506 to boost its growth. Azospirillum growth increased proportionally to the initial number of pseudomonads building the biofilm, which in turn were negatively affected in their growth. Physical contact with P. fluorescens A506 was essential for A. baldaniorum Sp245 growth increase. Biofilm ultrastructure analysis revealed that Pseudomonas produces a thick structure that hosts Azospirillum cells in its interior. Additional experimentation demonstrated that Azospirillum growth boost is compromised when interacting with biofilm-deficient Pseudomonas mutants, and that a low oxygen concentration strongly induce A. baldaniorum Sp245 growth, overriding Pseudomonas stimulation. In this line, we used a microaerophilia reporter strain of A. baldaniorum Sp245 to confirm that dual-species macrocolonies contain a higher number of cells under microaerophilic conditions. Taking all the results into consideration, we propose that A. baldaniorum Sp245 can benefit from P. fluorescens A506 partnership in mixed biofilms by taking advantage of the low oxygen concentration and scaffold made up of Pseudomonas-derived matrix, to expand its growth.

'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms

Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.

Assessing the importance of interspecific interactions in the evolution of microbial communities

Interspecific interactions play an important role in the establishment of a community phenotype. Furthermore, the evolution of a community can both occur through an independent evolution of the species composing the community and the interactions among them. In this study, we investigated how important the evolution of interspecific interactions was in the evolutionary response of eight two-bacterial species communities regarding productivity. We found evidence for an evolution of the interactions in half of the studied communities, which gave rise to a mean change of 15% in community productivity as compared to what was expected from the individual responses. Even when the interactions did not evolve themselves, they influenced the evolutionary responses of the bacterial strains within the communities, which further affected community response. We found that evolution within a community often promoted the adaptation of the bacterial strains to the abiotic environment, especially for the dominant strain in a community. Overall, this study suggested that the evolution of the interspecific interactions was frequent and that it could increase community response to evolution.

Toward a unified nomenclature for strains with hyper-biofilm phenotypes

Hyper-biofilm strains form robust biofilms, are highly adaptable, and form highly tolerant subpopulations in biofilms grown in vivo and in vitro. Such subpopulations are formed by a wide range of bacteria and thus have been given different names in different species. This situation calls for the establishment of a unified nomenclature for strains with hyper-biofilm phenotypes.

Biofilm antimicrobial susceptibility through an experimental evolutionary lens

Experimental evolution experiments in which bacterial populations are repeatedly exposed to an antimicrobial treatment, and examination of the genotype and phenotype of the resulting evolved bacteria, can help shed light on mechanisms behind reduced susceptibility. In this review we present an overview of why it is important to include biofilms in experimental evolution, which approaches are available to study experimental evolution in biofilms and what experimental evolution has taught us about tolerance and resistance in biofilms. Finally, we present an emerging consensus view on biofilm antimicrobial susceptibility supported by data obtained during experimental evolution studies.

In vitro visualization and quantitative characterization of Pseudomonas aeruginosa biofilm growth dynamics on polyether ether ketone

Prevention and treatment of orthopedic device-related infection (ODRI) is complicated by the formation of bacterial biofilms. Biofilm formation involves dynamic production of macromolecules that contribute to the structure of the biofilm over time. Limitations to clinically relevant and translational biofilm visualization and measurement hamper advances in this area of research. In this paper, we present a multimodal methodology for improved characterization of Pseudomonas aeruginosa grown on polyether ether ketone (PEEK) as a model for ODRI. PEEK discs were inoculated with P. aeruginosa, incubated for 4-48 h time intervals, and fixed with 10% neutral-buffered formalin. Samples were stained with fluorescent dyes to measure biofilm components, imaged with confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), and quantified. We were able to visualize and quantify P. aeruginosa biofilm growth on PEEK implants over 48 h. Based on imaging data, we propose a generalized growth cycle that can inform orthopedic diagnostic and treatment for this pathogen on PEEK. These results demonstrate the potential of using a combined CLSM and SEM approach for determining biofilm structure, composition, post-adherence development on orthopedic materials. This model may be used for quantitative biofilm analysis for other pathogens and other materials of orthopedic relevance for translational study of ODRI.

The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil

Background

Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study.

Results

In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice.

Conclusions

Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02648-1.

Spatial Structure Formation by RsmE-Regulated Extracellular Secretions in Pseudomonas fluorescens Pf0-1

Cells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures are manifested through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene were repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE's primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identified the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses showed that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community. IMPORTANCE In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces; however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE's paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.

Polymicrobial Biofilm Organization of Staphylococcus aureus and Pseudomonas aeruginosa in a Chronic Wound Environment

Biofilm on the skin surface of chronic wounds is an important step that involves difficulties in wound healing. The polymicrobial nature inside this pathogenic biofilm is key to understanding the chronicity of the lesion. Few in vitro models have been developed to study bacterial interactions inside this chronic wound. We evaluated the biofilm formation and the evolution of bacteria released from this biofilm on the two main bacteria isolated in this condition, Staphylococcus aureus and Pseudomonas aeruginosa, using a dynamic system (BioFlux™ 200) and a chronic wound-like medium (CWM) that mimics the chronic wound environment. We observed that all species constituted a faster biofilm in the CWM compared to a traditional culture medium (p < 0.01). The percentages of biofilm formation were significantly higher in the mixed biofilm compared to those determined for the bacterial species alone (p < 0.01). Biofilm organization was a non-random structure where S. aureus aggregates were located close to the wound surface, whereas P. aeruginosa was located deeper in the wound bed. Planktonic biofilm-detached bacteria showed decreased growth, overexpression of genes encoding biofilm formation, and an increase in the mature biofilm biomass formed. Our data confirmed the impact of the chronic wound environment on biofilm formation and on bacterial lifecycle inside the biofilm.

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Hard-to-heal wounds are a problem for both patients and caregivers. The biofi lm is one of the local factors of delayed healing. Wound hygiene carried out in 4 steps (cleansing, debridement, refashion - care of the edges, and dressing) constitutes the basis of proactive and curative anti-biofi lm strategies.

Nutritional stress induced intraspecies competition revealed by transcriptome analysis in Sphingomonas melonis TY

Bacteria have developed various mechanisms by which they can compete or cooperate with other bacteria. This study showed that in the cocultures of wild-type Sphingomonas melonis TY and its isogenic mutant TYΔndpD grow with nicotine, the former can outcompete the latter. TYΔndpD undergoes growth arrest after four days when cocultured with wild-type TY, whereas the coculture has just entered a stationary phase and the substrate was nearly depleted, and the interaction between the two related strains was revealed by transcriptomic analysis. Analysis of the differential expression genes indicated that wild-type TY inhibited the growth of TYΔndpD mainly through toxin-antitoxin (TA) systems. The four upregulated antitoxin coding genes belong to type II TA systems in which the bactericidal effect of the cognate toxin was mainly through inhibition of translation or DNA replication, whereas wild-type TY with upregulated antitoxin genes can regenerate cognate immunity protein continuously and thus prevent the lethal action of toxin to itself. In addition, colicin-mediated antibacterial activity against closely related species may also be involved in the competition between wild-type TY and TYΔndpD under nutritional stress. Moreover, upregulation of carbon and nitrogen catabolism related-, stress response related-, DNA repair related-, and DNA replication-related genes in wild-type TY showed that it triggered a series of response mechanisms when facing dual stress of competition from isogenic mutant cells and nutritional limitation. Thus, we proposed that S. melonis TY employed the TA systems and colicin to compete with TYΔndpD under nutritional stress, thereby maximally acquiring and exploiting finite resources. KEY POINTS: • Cross-feeding between isogenic mutants and the wild-type strain. • Nutrition stress caused a shift from cooperation to competition. • TYΔndpD undergo growth arrest by exogenous and endogenous toxins.

Biofilm cultivation facilitates coexistence and adaptive evolution in an industrial bacterial community

The majority of ecological, industrial and medical impacts of bacteria result from diverse communities containing multiple species. This diversity presents a significant challenge as co-cultivation of multiple bacterial species frequently leads to species being outcompeted and, with this, the possibility to manipulate, evolve and improve bacterial communities is lost. Ecological theory predicts that a solution to this problem will be to grow species in structured environments, which reduces the likelihood of competitive exclusion. Here, we explored the ability of cultivation in a structured environment to facilitate coexistence, evolution, and adaptation in an industrially important community: Lactococcus lactis and Leuconostoc mesenteroides frequently used as dairy starter cultures. As commonly occurs, passaging of these two species together in a liquid culture model led to the loss of one species in 6 of 20 lineages (30%). By contrast, when we co-cultured the two species as biofilms on beads, a stable coexistence was observed in all lineages studied for over 100 generations. Moreover, we show that the co-culture drove evolution of new high-yield variants, which compared to the ancestor grew more slowly, yielded more cells and had enhanced capability of biofilm formation. Importantly, we also show that these high-yield biofilm strains did not evolve when each species was passaged in monoculture in the biofilm model. Therefore, both co-culture and the biofilm model were conditional for these high-yield strains to evolve. Our study underlines the power of ecological thinking—namely, the importance of structured environments for coexistence—to facilitate cultivation, evolution, and adaptation of industrially important bacterial communities.

Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community

Species loss within a microbial community can increase resource availability and spur adaptive evolution. Environmental shifts that cause species loss or fluctuations in community composition are expected to become more common, so it is important to understand the evolutionary forces that shape the stability and function of the emergent community. Here we study experimental cultures of a simple, ecologically stable community of Saccharomyces cerevisiae and Lactobacillus plantarum, in order to understand how the presence or absence of a species impacts coexistence over evolutionary timescales. We found that evolution in coculture led to drastically altered evolutionary outcomes for L. plantarum, but not S. cerevisiae. Both monoculture- and co-culture-evolved L. plantarum evolved dozens of mutations over 925 generations of evolution, but only L. plantarum that had evolved in isolation from S. cerevisiae lost the capacity to coexist with S. cerevisiae. We find that the evolutionary loss of ecological stability corresponds with fitness differences between monoculture-evolved L. plantarum and S. cerevisiae and genetic changes that repeatedly evolve across the replicate populations of L. plantarum. This work shows how coevolution within a community can prevent destabilising evolution in individual species, thereby preserving ecological diversity and stability, despite rapid adaptation.