The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria

The rich diversity of secondary metabolites produced by soil bacteria has been appreciated for over a century, and advances in chemical analysis and genome sequencing continue to greatly advance our understanding of this biochemical complexity. However, we are just at the beginning of understanding the physicochemical properties of bacterial metabolites, the factors that govern their production and ecological roles. Interspecific interactions and competitor sensing are among the main biotic factors affecting the production of bacterial secondary metabolites. Many soil bacteria produce both volatile and soluble compounds. In contrast to soluble compounds, volatile organic compounds can diffuse easily through air- and gas-filled pores in the soil and likely play an important role in long-distance microbial interactions. In this review we provide an overview of the most important soluble and volatile classes of secondary metabolites produced by soil bacteria, their ecological roles, and their possible synergistic effects

No Apparent Costs for Facultative Antibiotic Production by the Soil Bacterium Pseudomonas fluorescens Pf0-1

Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures. Methodology and Principal Findings: We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibioticproducing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either. Significance: Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.

The role of macrophage-inducible C-type lectin in different stages of chronic liver disease

The macrophage-inducible C-type lectin (mincle) is part of the innate immune system and acts as a pattern recognition receptor for pathogen-associated molecular patterns (PAMPS) and damage-associated molecular patterns (DAMPs). Ligand binding induces mincle activation which consequently interacts with the signaling adapter Fc receptor, SYK, and NF-kappa-B. There is also evidence that mincle expressed on macrophages promotes intestinal barrier integrity. However, little is known about the role of mincle in hepatic fibrosis, especially in more advanced disease stages. Mincle expression was measured in human liver samples from cirrhotic patients and donors collected at liver transplantation and in patients undergoing bariatric surgery. Human results were confirmed in rodent models of cirrhosis and acute-on-chronic liver failure (ACLF). In these models, the role of mincle was investigated in liver samples as well as in peripheral blood monocytes (PBMC), tissues from the kidney, spleen, small intestine, and heart. Additionally, mincle activation was stimulated in experimental non-alcoholic steatohepatitis (NASH) by treatment with mincle agonist trehalose-6,6-dibehenate (TDB). In human NASH, mincle is upregulated with increased collagen production. In ApoE deficient mice fed high-fat western diet (NASH model), mincle activation significantly increases hepatic collagen production. In human cirrhosis, mincle expression is also significantly upregulated. Furthermore, mincle expression is associated with the stage of chronic liver disease. This could be confirmed in rat models of cirrhosis and ACLF. ACLF was induced by LPS injection in cirrhotic rats. While mincle expression and downstream signaling via FC receptor gamma, SYK, and NF-kappa-B are upregulated in the liver, they are downregulated in PBMCs of these rats. Although mincle expressed on macrophages might be beneficial for intestinal barrier integrity, it seems to contribute to inflammation and fibrosis once the intestinal barrier becomes leaky in advanced stages of chronic liver disease

Janus kinase 2 inhibition by pacritinib as potential therapeutic target for liver fibrosis

anus kinase 2 (JAK2) signaling is increased in human and experimental liver fibrosis with portal hypertension. JAK2 inhibitors, such as pacritinib, are already in advanced clinical development for other indications and might also be effective in liver fibrosis. Here, we investigated the antifibrotic role of the JAK2 inhibitor pacritinib on activated hepatic stellate cells (HSCs) in vitro and in two animal models of liver fibrosis in vivo.Jonel Trebicka is supported by the German Research Foundation project ID 403224013–SFB 1382 (A09); by the German Federal Ministry of Education and Research (BMBF) for the DEEP‐HCC project; by the Hessian Ministry of Higher Education, Research, and the Arts (HMWK) for the ENABLE cluster project; and by Eurostars (Grant ID 12350). The MICROB‐PREDICT (project ID 825694), DECISION (project ID 847949), GALAXY (project ID 668031), LIVERHOPE (project ID 731875), and IHMCSA (project ID 964590) projects have received funding from the European Union's Horizon 2020 research and innovation program. The manuscript reflects only the authors' views, and the European Commission is not responsible for any use that may be made of the information it contains. The funders had no influence on study design, data collection and analysis, decision to publish, or preparation of the manuscript

Mining into interspecific bacterial interactions

In terrestrial ecosystems bacteria live in close proximity with many different microbial species and form complex multi-species networks. Within those networks bacteria are constantly interacting with each other and produce a plethora of secondary metabolites like antibiotics, enzymes, volatiles and other compounds from diverse chemical classes. Several independent studies revealed that the production of secondary metabolites by soil bacteria can be influenced by the interaction with other microorganisms in their vicinity. In this thesis we show how interspecific interactions between soil bacteria influence the production of soluble and volatile secondary metabolites, gene expression and fitness. To elucidate the effect of interspecific interactions on antimicrobial activity in soil bacteria a high-through-put screening method was developed and applied on a collection of 146 rhizobacterial isolates obtained from similar habitats. In addition we examined if the production of volatile organic compounds is influenced by interspecific interactions. Thus, the identity and antimicrobial activity of volatiles produced by bacteria cultivated in monoculture as well in interaction were examined. Furthermore a sand microcosm approach was applied to investigate how Pseudomonas fluorescens strain Pf0-1 responded to the presence of monocultures and mixtures of a Gram-negative (Pedobacter sp. V48) and a Gram-positive (Bacillus sp. V102) bacterial strain under two nutritional conditions. The interaction between a gram-negative Burkholderia and a gram-positive Paenibacillus isolate was subjected to detailed metabolome, volatolome and transcriptome analysis. One distinct volatile and one non-volatile compound produced only during interspecific interaction but not in the monoculture were identified. The activity of the interacting bacteria and the compounds produced during interaction were tested against a range of human and plant pathogens. In summary, this thesis extends the knowledge about the effect of interspecific bacterial interactions on secondary metabolites production (soluble and volatiles), gene expression and fitness in bacteria. The exploitation of such bacterial interspecific interactions can be an important “tool” for the discovery of novel antimicrobial and agro-chemical compounds. The obtained knowledge can help in selecting the right players in synthetic communities that fulfil important ecosystem services like disease suppression in agricultural crop systems

Volatiles in inter-specific bacterial interactions

The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities

Numbers of CFUs of Bacillus sp. V102 and Pedobacter sp. V48 in monoculture and in mixed cultures (with strain Pf0-1) at day 6 under nutrient rich conditions (A) and under nutrient poor conditions (B).

<p>Significant differences between the CFUs in monoculture and in mixed cultures are indicated with an asterisk (p≤0.05). Error bars are indicating standard deviation (SD) between the triplicates. Abbreviations: Pf0-1: <i>Pseudomonas fluorescens</i> Pf0-1, BAC: <i>Bacillus</i> sp. V102, PB: <i>Pedobacter</i> sp. V48.</p

The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom

Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.</p

Bacterial strains and used antibiotics / selection method applied in the selective cell counting.

<p>Bacterial strains and used antibiotics / selection method applied in the selective cell counting.</p