In vitro selection of a microbial consortium predictive of synergistic functioning along multiple ecosystem scales

AbstractSoil microbes form complex interactive networks throughout the soil and plant rhizosphere. These interactions can result in emergent properties for consortia that are not predictable from the phenotypes of constituents in isolation. We used a four-species consortium to assess the capacity of individual microbial species versus different consortia permutations of the four species to contribute to increased P-solubilization using soil incubations and plant growth experiments. We found that as different combinations of bacterial species were assembled into differing consortia, they demonstrated differing abilities to stimulate soil P cycling and plant growth. The combination of all four microbes in the consortia were much more effective at solubilizing P and stimulating plant growth than any of the individual bacterial species alone. This suggests that in vivo functionally synergistic soil microbial consortia can be adept at performing specific ecosystem functions in situ. Improving our understanding of the mechanisms that facilitate synergistic functioning examined in this study is important for maximizing future food production and agroecosystem sustainability.

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Metabolic Exchange and Energetic Coupling between Nutritionally Stressed Bacterial Species: Role of Quorum-Sensing Molecules

mBio ◽

10.1128/mbio.02758-20 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

David Ranava ◽

Cassandra Backes ◽

Ganesan Karthikeyan ◽

Olivier Ouari ◽

Audrey Soric ◽

...

Keyword(s):

Quorum Sensing ◽

Bacterial Species ◽

Emergent Properties ◽

Desulfovibrio Vulgaris ◽

Interspecies Interactions ◽

Content Type ◽

Bacterial Communication ◽

Metabolic Exchange

ABSTRACT Formation of multispecies communities allows nearly every niche on earth to be colonized, and the exchange of molecular information among neighboring bacteria in such communities is key for bacterial success. To clarify the principles controlling interspecies interactions, we previously developed a coculture model with two anaerobic bacteria, Clostridium acetobutylicum (Gram positive) and Desulfovibrio vulgaris Hildenborough (Gram negative, sulfate reducing). Under conditions of nutritional stress for D. vulgaris, the existence of tight cell-cell interactions between the two bacteria induced emergent properties. Here, we show that the direct exchange of carbon metabolites produced by C. acetobutylicum allows D vulgaris to duplicate its DNA and to be energetically viable even without its substrates. We identify the molecular basis of the physical interactions and how autoinducer-2 (AI-2) molecules control the interactions and metabolite exchanges between C. acetobutylicum and D. vulgaris (or Escherichia coli and D. vulgaris). With nutrients, D. vulgaris produces a small molecule that inhibits in vitro the AI-2 activity and could act as an antagonist in vivo. Sensing of AI-2 by D. vulgaris could induce formation of an intercellular structure that allows directly or indirectly metabolic exchange and energetic coupling between the two bacteria. IMPORTANCE Bacteria have usually been studied in single culture in rich media or under specific starvation conditions. However, in nature they coexist with other microorganisms and build an advanced society. The molecular bases of the interactions controlling this society are poorly understood. Use of a synthetic consortium and reducing complexity allow us to shed light on the bacterial communication at the molecular level. This study presents evidence that quorum-sensing molecule AI-2 allows physical and metabolic interactions in the synthetic consortium and provides new insights into the link between metabolism and bacterial communication.

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Production of Novel Bioactive Compounds by the Bacteria Associated with Some Marine Sponges of Gulf of Mannar and Palk Bay, Southeast Coast of India

International Journal of Emerging Research in Management and Technology ◽

10.23956/ijermt.v6i8.136 ◽

2018 ◽

Vol 6 (8) ◽

pp. 183

Author(s):

V. Ramadas ◽

G. Chandralega

Keyword(s):

Bioactive Compounds ◽

Bacterial Species ◽

Marine Sponges ◽

Marine Organisms ◽

Gulf Of Mannar ◽

Bacterial Symbionts ◽

Palk Bay ◽

Excellent Source

Sponges, exclusively are aquatic and mostly marine, are found from the deepest oceans to the edge of the sea. There are approximately 15,000 species of sponges in the world, of which, 150 occur in freshwater, but only about 17 are of commercial value. A total of 486 species of sponges have been identified in India. In the Gulf of Mannar and Palk Bay a maximum of 319 species of sponges have been recorded. It has been proved that marine organisms are excellent source of bioactive secondary metabolites and number of compounds of originated from marine organisms had been reported to possess in-vitro and in-vivo immuno stimulatory activity. Extracts from 20 sponge species were tested for bacterial symbionts and bioactive compounds were isolated from such associated bacterial species in the present study.

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Crude Citric Acid of Trichoderma asperellum: Tomato Growth Promotor and Suppressor of Fusarium oxysporum f. sp. lycopersici

Plants ◽

10.3390/plants10020222 ◽

2021 ◽

Vol 10 (2) ◽

pp. 222

Author(s):

Abdulaziz A. Al-Askar ◽

WesamEldin I. A. Saber ◽

Khalid M. Ghoneem ◽

Elsayed E. Hafez ◽

Amira A. Ibrahim

Keyword(s):

Citric Acid ◽

Plant Growth ◽

Organic Acid ◽

Wilt Disease ◽

Growth And Yield ◽

Total Phenolic ◽

Growth Promoters ◽

Chlorophyll Pigments

Presently, the bioprocessing of agricultural residues to various bioactive compounds is of great concern, with the potential to be used as plant growth promoters and as a reductive of various diseases. Lycopersiconesculentum, one of the most consumed crops in the human diet, is attacked by Fusarium wilt disease, so the main aim is to biocontrol the pathogen. Several fungal species were isolated from decayed maize stover (MS). Trichodermaasperellum was chosen based on its organic acid productivity and was molecularly identified (GenBank accession number is MW195019). Citric acid (CA) was the major detected organic acid by HPLC. In vitro, CA of T.asperellum at 75% completely repressed the growth of Fusariumoxysporum f. sp. lycopersici (FOL). In vivo, soaking tomato seeds in CA enhanced the seed germination and vigor index. T. asperellum and/or its CA suppressed the wilt disease caused by FOL compared to control. There was a proportional increment of plant growth and yield, as well as improvements in the biochemical parameters (chlorophyll pigments, total phenolic contents and peroxidase, and polyphenol oxidase activities), suggesting targeting both the bioconversion of MS into CA and biological control of FOL.

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Identification of Resistance Determinants for a Promising Antileishmanial Oxaborole Series

Microorganisms ◽

10.3390/microorganisms9071408 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1408

Author(s):

Magali Van den Kerkhof ◽

Philippe Leprohon ◽

Dorien Mabille ◽

Sarah Hendrickx ◽

Lindsay B. Tulloch ◽

...

Keyword(s):

Drug Exposure ◽

In Vitro Selection ◽

Selection Procedure ◽

Cosmid Library ◽

Neglected Diseases ◽

Chromosome 2 ◽

Resistance Determinants ◽

A Genome

Current treatment options for visceral leishmaniasis have several drawbacks, and clinicians are confronted with an increasing number of treatment failures. To overcome this, the Drugs for Neglected Diseases initiative (DNDi) has invested in the development of novel antileishmanial leads, including a very promising class of oxaboroles. The mode of action/resistance of this series to Leishmania is still unknown and may be important for its further development and implementation. Repeated in vivo drug exposure and an in vitro selection procedure on both extracellular promastigote and intracellular amastigote stages were both unable to select for resistance. The use of specific inhibitors for ABC-transporters could not demonstrate the putative involvement of efflux pumps. Selection experiments and inhibitor studies, therefore, suggest that resistance to oxaboroles may not emerge readily in the field. The selection of a genome-wide cosmid library coupled to next-generation sequencing (Cos-seq) was used to identify resistance determinants and putative targets. This resulted in the identification of a highly enriched cosmid, harboring genes of chromosome 2 that confer a subtly increased resistance to the oxaboroles tested. Moderately enriched cosmids encompassing a region of chromosome 34 contained the cleavage and polyadenylation specificity factor (cpsf) gene, encoding the molecular target of several related benzoxaboroles in other organisms.

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Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance

Communications Biology ◽

10.1038/s42003-021-02372-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Fatemeh Ostadhossein ◽

Parikshit Moitra ◽

Esra Altun ◽

Debapriya Dutta ◽

Dinabandhu Sar ◽

...

Keyword(s):

Streptococcus Mutans ◽

Ex Vivo ◽

Bacterial Species ◽

Reactive Oxygen Species Generation ◽

Biofilm Inhibition ◽

16S Rrna Analysis ◽

Dental Biofilm ◽

Dental Plaques

AbstractDental plaques are biofilms that cause dental caries by demineralization with acidogenic bacteria. These bacteria reside inside a protective sheath which makes any curative treatment challenging. We propose an antibiotic-free strategy to disrupt the biofilm by engineered clustered carbon dot nanoparticles that function in the acidic environment of the biofilms. In vitro and ex vivo studies on the mature biofilms of Streptococcus mutans revealed >90% biofilm inhibition associated with the contact-mediated interaction of nanoparticles with the bacterial membrane, excessive reactive oxygen species generation, and DNA fragmentation. An in vivo examination showed that these nanoparticles could effectively suppress the growth of S. mutans. Importantly, 16S rRNA analysis of the dental microbiota showed that the diversity and richness of bacterial species did not substantially change with nanoparticle treatment. Overall, this study presents a safe and effective approach to decrease the dental biofilm formation without disrupting the ecological balance of the oral cavity.

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A novel design of wound bandage using heparin-polyvinylpyrrolidone/TiO2 nanocomposite to improved antibacterial treatment and burn wound healing effect: In vitro and in vivo evaluation

Materials Express ◽

10.1166/mex.2021.1877 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1808-1818

Author(s):

Xiuli Li ◽

Jigang Wang ◽

Xin Li ◽

Xiaoqian Hou ◽

Hao Wang ◽

...

Keyword(s):

Electron Microscope ◽

Dermal Fibroblast ◽

Synergistic Effects ◽

Bacterial Species ◽

Human Dermal Fibroblast ◽

Burn Wound ◽

In Vivo Evaluation ◽

Closure Rate

In our current study, porous heparin-polyvinylpyrrolidone/TiO2 nanocomposite (HpPVP/TiO2) bandage were prepared via the incorporation of TiO2 into HpPVP hydrogels for biomedical applications such as burn infection. The effect of the HpPVP hydrogels and the nanoparticles of TiO2 composition on the functional group and the surface properties of the as-fabricated bandages were characterized by Fourier transform infrared spectroscopy (FTIR) and X-ray diffractometry (XRD). The presence of TiO2 nanoparticles created the internal structure of the HpPVP hydrogel that aids in a homogeneous porous structure, as indicated by the scanning electron microscope (SEM). The size distribution of the TiO2 nanoparticles was measured using a transmission electron microscope (TEM). The studies on the mechanical properties of the HpPVP hydrogel indicate that the addition of TiO2 nanoparticles increases its strength. The prepared HpPVP/TiO2 nanocomposite dressing has excellent antimicrobial activity were tested against bacterial species (Staphylococcus aureus and Escherichia coli) and has good biocompatibility against human dermal fibroblast cells (HFFF2) for biological applications. In addition, in vivo evaluations in Kunming mice exposed that the as-fabricated HpPVP/TiO2 nanocomposite bandages increased the wound curing and facilitated accelerate skin cell construction along with collagen development. The synergistic effects of the HpPVP/TiO2 nanocomposite hydrogel dressing material, such as its excellent hydrophilic nature, good bactericidal activity, biocompatibility and wound closure rate through in vivo test makes it a suitable candidate for burn infections.

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Antimicrobial Activity of Non-steroidal Anti-inflammatory Drugs on Biofilm: Current Evidence and Potential for Drug Repurposing

Frontiers in Microbiology ◽

10.3389/fmicb.2021.707629 ◽

2021 ◽

Vol 12 ◽

Author(s):

Rodrigo Cuiabano Paes Leme ◽

Raquel Bandeira da Silva

Keyword(s):

Bacterial Species ◽

Drug Repurposing ◽

Current Evidence ◽

Pharmacokinetic Studies ◽

Bacterial Populations ◽

Human Pharmacokinetic ◽

Inflammatory Drugs ◽

Anti Inflammatory

It has been demonstrated that some non-steroidal anti-inflammatory drugs (NSAIDs), like acetylsalicylic acid, diclofenac, and ibuprofen, have anti-biofilm activity in concentrations found in human pharmacokinetic studies, which could fuel an interest in repurposing these well tolerated drugs as adjunctive therapies for biofilm-related infections. Here we sought to review the currently available data on the anti-biofilm activity of NSAIDs and its relevance in a clinical context. We performed a systematic literature review to identify the most commonly tested NSAIDs drugs in the last 5 years, the bacterial species that have demonstrated to be responsive to their actions, and the emergence of resistance to these molecules. We found that most studies investigating NSAIDs’ activity against biofilms were in vitro, and frequently tested non-clinical bacterial isolates, which may not adequately represent the bacterial populations that cause clinically-relevant biofilm-related infections. Furthermore, studies concerning NSAIDs and antibiotic resistance are scarce, with divergent outcomes. Although the potential to use NSAIDs to control biofilm-related infections seems to be an exciting avenue, there is a paucity of studies that tested these drugs using appropriate in vivo models of biofilm infections or in controlled human clinical trials to support their repurposing as anti-biofilm agents.

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Structural insights into a novel family of integral membrane siderophore reductases

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2101952118 ◽

2021 ◽

Vol 118 (34) ◽

pp. e2101952118

Author(s):

Inokentijs Josts ◽

Katharina Veith ◽

Vincent Normant ◽

Isabelle J. Schalk ◽

Henning Tidow

Keyword(s):

Iron Uptake ◽

Bacterial Species ◽

Gram Negative Bacteria ◽

Inner Membrane ◽

Gram Negative ◽

Inner Membrane Protein ◽

Uptake Studies ◽

Structural Insights

Gram-negative bacteria take up the essential ion Fe3+ as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (from Pseudomonas aeruginosa) that is involved in Fe-siderophore uptake. The structure revealed a fold with two tightly bound heme molecules. In combination with in vitro reduction assays and in vivo iron uptake studies, these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.

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Identification of Functional LsrB-Like Autoinducer-2 Receptors

Journal of Bacteriology ◽

10.1128/jb.00976-09 ◽

2009 ◽

Vol 191 (22) ◽

pp. 6975-6987 ◽

Cited By ~ 51

Author(s):

Catarina S. Pereira ◽

Anna K. de Regt ◽

Patrícia H. Brito ◽

Stephen T. Miller ◽

Karina B. Xavier

Keyword(s):

Structure Prediction ◽

Molecular Mechanisms ◽

Bacterial Species ◽

Autoinducer 2 ◽

Communication Signal ◽

Independent Events ◽

Key Species ◽

Serovar Typhimurium

ABSTRACT Although a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (AI-2) to regulate multiple behaviors, the molecular mechanisms of AI-2 recognition and signal transduction remain poorly understood. To date, two types of AI-2 receptors have been identified: LuxP, present in Vibrio spp., and LsrB, first identified in Salmonella enterica serovar Typhimurium. In S. Typhimurium, LsrB is the ligand binding protein of a transport system that enables the internalization of AI-2. Here, using both sequence analysis and structure prediction, we establish a set of criteria for identifying functional AI-2 receptors. We test our predictions experimentally, assaying key species for their abilities to import AI-2 in vivo, and test their LsrB orthologs for AI-2 binding in vitro. Using these experimental approaches, we were able to identify AI-2 receptors in organisms belonging to phylogenetically distinct families such as the Enterobacteriaceae, Rhizobiaceae, and Bacillaceae. Phylogenetic analysis of LsrB orthologs indicates that this pattern could result from one single origin of the functional LsrB gene in a gammaproteobacterium, suggesting possible posterior independent events of lateral gene transfer to the Alphaproteobacteria and Firmicutes. Finally, we used mutagenesis to show that two AI-2-interacting residues are essential for the AI-2 binding ability. These two residues are conserved in the binding sites of all the functional AI-2 binding proteins but not in the non-AI-2-binding orthologs. Together, these results strongly support our ability to identify functional LsrB-type AI-2 receptors, an important step in investigations of this interspecies signal.

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Root Bacteria Recruited by Phragmites australis in Constructed Wetlands Have the Potential to Enhance Azo-Dye Phytodepuration

Microorganisms ◽

10.3390/microorganisms7100384 ◽

2019 ◽

Vol 7 (10) ◽

pp. 384 ◽

Cited By ~ 7

Author(s):

Valentina Riva ◽

Francesca Mapelli ◽

Evdokia Syranidou ◽

Elena Crotti ◽

Redouane Choukrallah ◽

...

Keyword(s):

Plant Growth ◽

Phragmites Australis ◽

Textile Industry ◽

Azo Dye ◽

Growth Promotion ◽

Wide Spectrum ◽

Reactive Black 5 ◽

Potential Use

The microbiome associated with plants used in phytodepuration systems can boost plant growth and services, especially in ecosystems dealing with recalcitrant compounds, hardly removed via traditional wastewater (WW) treatments, such as azo-dyes used in textile industry. In this context, we aimed to study the cultivable microbiome selected by Phragmites australis plants in a Constructed Wetland (CW) in Morocco, in order to obtain candidate inoculants for the phytodepuration of azo-dye contaminated WW. A collection of 152 rhizospheric and endophytic bacteria was established. The strains were phylogenetically identified and characterized for traits of interest in the phytodepuration context. All strains showed Plant Growth Promotion potential in vitro and 67% of them significantly improved the growth of a model plant in vivo compared to the non bacterized control plants. Moreover, most of the isolates were able to grow in presence of several model micropollutants typically found in WW, indicating their potential use in phytodepuration of a wide spectrum of effluents. The six most promising strains of the collection were tested in CW microcosms alone or as consortium: the consortium and two single inocula demonstrated to significantly increase the removal of the model azo-dye Reactive Black 5 compared to the non bacterized controls.

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