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Cowled MS, Phippen CBW, Kromphardt KJK, Clemmensen SE, Frandsen RJN, Frisvad JC, Larsen TO. Unveiling the fungal diversity and associated secondary metabolism on black apples. Appl Environ Microbiol 2024; 90:e0034224. [PMID: 38899884 PMCID: PMC11267942 DOI: 10.1128/aem.00342-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Black apples are the result of late-stage microbial decomposition after falling to the ground. This phenomenon is highly comparable from year to year, with the filamentous fungus Monilinia fructigena most commonly being the first invader, followed by Penicillium expansum. Motivated by the fact that only little chemistry has been reported from apple microbiomes, we set out to investigate the chemical diversity and potential ecological roles of secondary metabolites (SMs) in a total of 38 black apples. Metabolomics analyses were conducted on either whole apples or small excisions of fungal biomass derived from black apples. Annotation of fungal SMs in black apple extracts was aided by the cultivation of 15 recently isolated fungal strains on 9 different substrates in a One Strain Many Compounds (OSMAC) approach, leading to the identification of 3,319 unique chemical features. Only 6.4% were attributable to known compounds based on analysis of high-performance liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS/MS) data using spectral library matching tools. Of the 1,606 features detected in the black apple extracts, 32% could be assigned as fungal-derived, due to their presence in the OSMAC-based training data set. Notably, the detection of several antifungal compounds indicates the importance of such compounds for the invasion of and control of other microbial competitors on apples. In conclusion, the diversity and abundance of microbial SMs on black apples were found to be much higher than that typically observed for other environmental microbiomes. Detection of SMs known to be produced by the six fungal species tested also highlights a succession of fungal growth following the initial invader M. fructigena.IMPORTANCEMicrobial secondary metabolites constitute a significant reservoir of biologically potent and clinically valuable chemical scaffolds. However, their usefulness is hampered by rapidly developing resistance, resulting in reduced profitability of such research endeavors. Hence, the ecological role of such microbial secondary metabolites must be considered to understand how best to utilize such compounds as chemotherapeutics. Here, we explore an under-investigated environmental microbiome in the case of black apples; a veritable "low-hanging fruit," with relatively high abundances and diversity of microbially produced secondary metabolites. Using both a targeted and untargeted metabolomics approach, the interplay between metabolites, other microbes, and the apple host itself was investigated. This study highlights the surprisingly low incidence of known secondary metabolites in such a system, highlighting the need to study the functionality of secondary metabolites in microbial interactions and complex microbiomes.
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Affiliation(s)
- Michael S. Cowled
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christopher B. W. Phippen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kresten J. K. Kromphardt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sidsel E. Clemmensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas O. Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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2
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Hamrouni R, Regus F, Farnet Da Silva AM, Orsiere T, Boudenne JL, Laffont-Schwob I, Christen P, Dupuy N. Current status and future trends of microbial and nematode-based biopesticides for biocontrol of crop pathogens. Crit Rev Biotechnol 2024:1-20. [PMID: 38987982 DOI: 10.1080/07388551.2024.2370370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/26/2024] [Indexed: 07/12/2024]
Abstract
The increasing public demand to avoid the use of synthetic pesticides and fertilizers in agricultural production systems, causing serious environmental damages, has challenged industry to develop new and effective solutions to manage and control phytopathogens. Biopesticides, particularly microbial-based biopesticides, are a promising new alternative with high biodegradability, specificity, suitability for incorporation into integrated pest management practices, low likelihood of resistance development, and practically no known human health risks. However: expensive production methods, narrow action spectra, susceptibility to environmental conditions, short shelf life, poor storage stability, legislation registry constraints, and general lack of knowledge are slowing down their adoption. In addition to regulatory framework revisions and improved training initiatives, improved preservation methods, thoughtfully designed formulations, and field test validations are needed to offer new microbial- and nematode-based biopesticides with improved efficacy and increased shelf-life. During the last several years, substantial advancements in biopesticide production have been developed. The novelty part of this review written in 2023 is to summarize (i) mechanisms of action of beneficial microorganisms used to increase crop performance and (ii) successful formulation including commercial products for the biological control of phytopathogens based on microorganisms, nematode and/or metabolites.
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Affiliation(s)
- Rayhane Hamrouni
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Aix Marseille Univ, CNRS, LCE UMR 7376, 13331, Marseille, France
| | - Flor Regus
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Aix Marseille Univ, IRD, LPED, Marseille, France
| | | | - Thierry Orsiere
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | | | | | - Pierre Christen
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Nathalie Dupuy
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
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3
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Chouaia B, Dittmer J. A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis. Microorganisms 2024; 12:338. [PMID: 38399742 PMCID: PMC10893106 DOI: 10.3390/microorganisms12020338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Some bacteria (notably the genera Bacillus and Clostridium) have the capacity to form endospores that can survive for millions of years in isolated habitats. The genomes of such ancient bacteria provide unique opportunities to understand bacterial evolution and metabolic capabilities over longer time scales. Herein, we sequenced the genome of a 2000-year-old bacterial strain (Mal05) isolated from intact apple seeds recovered during archaeological excavations of a Roman villa in Italy. Phylogenomic analyses revealed that this strain belongs to the species Bacillus stercoris and that it is placed in an early-branching position compared to most other strains of this species. Similar to other Bacillus species, B. stercoris Mal05 had been previously shown to possess antifungal activity. Its genome encodes all the genes necessary for the biosynthesis of fengycin and surfactin, two cyclic lipopeptides known to play a role in the competition of Bacilli with other microorganisms due to their antimicrobial activity. Comparative genomics and analyses of selective pressure demonstrate that these genes are present in all sequenced B. stercoris strains, despite the fact that they are not under strong purifying selection. Hence, these genes may not be essential for the fitness of these bacteria, but they can still provide a competitive advantage against other microorganisms present in the same environment.
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Affiliation(s)
- Bessem Chouaia
- Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, 30172 Venice, Italy
| | - Jessica Dittmer
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy;
- UMR 1345, Institut Agro, INRAE, IRHS, SFR Quasav, Université d’Angers, 49070 Beaucouzé, France
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4
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Lozano-Andrade CN, Nogueira CG, Henriksen NNSE, Wibowo M, Jarmusch SA, Kovács ÁT. Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. ISME COMMUNICATIONS 2023; 3:110. [PMID: 37838789 PMCID: PMC10576751 DOI: 10.1038/s43705-023-00318-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS, and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.
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Affiliation(s)
| | - Carla G Nogueira
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | | | - Mario Wibowo
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ákos T Kovács
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark.
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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5
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Angelini LL, Dos Santos RAC, Fox G, Paruthiyil S, Gozzi K, Shemesh M, Chai Y. Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development. NPJ Biofilms Microbiomes 2023; 9:50. [PMID: 37468524 PMCID: PMC10356805 DOI: 10.1038/s41522-023-00418-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Pulcherrimin is an iron-binding reddish pigment produced by various bacterial and yeast species. In the soil bacterium Bacillus subtilis, this pigment is synthesized intracellularly as the colorless pulcherriminic acid by using two molecules of tRNA-charged leucine as the substrate; pulcherriminic acid molecules are then secreted and bind to ferric iron extracellularly to form the red-colored pigment pulcherrimin. The biological importance of pulcherrimin is not well understood. A previous study showed that secretion of pulcherrimin caused iron depletion in the surroundings and growth arrest on cells located at the edge of a B. subtilis colony biofilm. In this study, we identified that pulcherrimin is primarily produced under biofilm conditions and provides protection to cells in the biofilm against oxidative stress. We presented molecular evidence on how pulcherrimin lowers the level of reactive oxygen species (ROS) and alleviates oxidative stress and DNA damage caused by ROS accumulation in a mature biofilm. We also performed global transcriptome profiling to identify differentially expressed genes in the pulcherrimin-deficient mutant compared with the wild type, and further characterized the regulation of genes by pulcherrimin that are related to iron homeostasis, DNA damage response (DDR), and oxidative stress response. Based on our findings, we propose pulcherrimin as an important antioxidant that modulates B. subtilis biofilm development.
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Affiliation(s)
| | | | - Gabriel Fox
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Srinand Paruthiyil
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
- Medical Scientist Training Program (MSTP), Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO, 63110, USA
| | - Kevin Gozzi
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
- The Rowland Institute at Harvard, 100 Edwin H. Land Blvd., Cambridge, MA, 02142, USA
| | - Moshe Shemesh
- Department of Food Science, Agricultural Research Organization The Volcani Institute, Derech Hamacabim, POB 15159, Rishon LeZion, 7528809, Israel
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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6
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Poppeliers SW, Sánchez-Gil JJ, de Jonge R. Microbes to support plant health: understanding bioinoculant success in complex conditions. Curr Opin Microbiol 2023; 73:102286. [PMID: 36878082 DOI: 10.1016/j.mib.2023.102286] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.
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Affiliation(s)
- Sanne Wm Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
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7
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Miao S, Liang J, Xu Y, Yu G, Shao M. Bacillaene, sharp objects consist in the arsenal of antibiotics produced by Bacillus. J Cell Physiol 2023. [PMID: 36790954 DOI: 10.1002/jcp.30974] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Bacillus species act as plant growth-promoting rhizobacteria (PGPR) that can produce a large number of bioactive metabolites. Bacillaene, a linear polyketide/nonribosomal peptide produced by Bacillus strains, is synthesized by the trans-acyltransferase polyketide synthetase. The complexity of the chemical structure, particularity of biosynthesis, potent bioactivity, and the important role of competition make Bacillus an ideal antibiotic weapon to resist other microbes and maintain the optimal rhizosphere environment. This review provides an updated view of the structural features, biological activity, biosynthetic regulators of biosynthetic pathways, and the important competitive role of bacillaene during Bacillus survival.
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Affiliation(s)
- Shuang Miao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Jianhao Liang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Yuan Xu
- College of Pharmaceutical Engineering, XinYang College Of Agriculture And Forestry, Xinyang, P.R. China
| | - Guohui Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Mingwei Shao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
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8
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Henriksen NNSE, Schostag MD, Balder SR, Bech PK, Strube ML, Sonnenschein EC, Gram L. The ability of Phaeobacter inhibens to produce tropodithietic acid influences the community dynamics of a microalgal microbiome. ISME COMMUNICATIONS 2022; 2:109. [PMID: 37938341 PMCID: PMC9723703 DOI: 10.1038/s43705-022-00193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
Microbial secondary metabolites facilitate microbial interactions and are crucial for understanding the complexity of microbial community dynamics. The purpose of the present study was to determine how a secondary metabolite producing marine bacteria or its metabolite deficient mutant affected the microbiome of the marine microalgae Tetraselmis suecica during a 70 day long co-evolution experiment. Using 16S rRNA gene amplicon sequencing, we found that neither the tropodithietic acid (TDA)-producing Phaeobacter inhibens wildtype nor the TDA-deficient mutant had major impacts on the community composition. However, a subset of strains, displayed temporally different relative abundance trajectories depending on the presence of P. inhibens. In particular, a Winogradskyella strain displayed temporal higher relative abundance when the TDA-producing wildtype was present. Numbers of the TDA-producing wildtype were reduced significantly more than those of the mutant over time indicating that TDA production was not an advantage. In communities without the P. inhibens wildtype strain, an indigenous population of Phaeobacter increased over time, indicating that indigenous Phaeobacter populations cannot co-exist with the TDA-producing wildtype. Despite that TDA was not detected chemically, we detected transcripts of the tdaC gene indicating that TDA could be produced in the microbial community associated with the algae. Our work highlights the importance of deciphering longitudinal strain dynamics when addressing the ecological effect of secondary metabolites in a relevant natural community.
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Affiliation(s)
| | - Morten Dencker Schostag
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Simone Rosen Balder
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Eva Christina Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
- Department of Biosciences, Swansea University, Singleton Park, SA2 8PP, Swansea, United Kingdom
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark.
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9
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Gutierrez MM, Cameron-Harp MV, Chakraborty PP, Stallbaumer-Cyr EM, Morrow JA, Hansen RR, Derby MM. Investigating a microbial approach to water conservation: Effects of Bacillus subtilis and Surfactin on evaporation dynamics in loam and sandy loam soils. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.959591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Semi-arid regions faced with increasingly scarce freshwater resources must manage competing demands in the food-energy-water nexus. A possible solution modifies soil hydrologic properties using biosurfactants to reduce evaporation and improve water retention. In this study, two different soil textures representative of agricultural soils in Kansas were treated with a direct application of the biosurfactant, Surfactin, and an indirect application via inoculation of Bacillus subtilis. Evaporation rates of the wetted soils were measured when exposed to artificial sunlight (1000 W/m2) and compared to non-treated control soils. Experimental results indicate that both treatments alter soil moisture dynamics by increasing evaporation rates by when soil moisture is plentiful (i.e., constant rate period) and decreasing evaporation rates by when moisture is scarce (i.e., slower rate period). Furthermore, both treatments significantly reduced the soil moisture content at which the soil transitioned from constant rate to slower rate evaporation. Out of the two treatments, inoculation with B. subtilis generally produced greater changes in evaporation dynamics; for example, the treatment with B. subtilis in sandy loam soils increased constant rate periods of evaporation by 43% and decreased slower rate evaporation by 49%. In comparing the two soil textures, the sandy loam soil exhibited a larger treatment effect than the loam soil. To evaluate the potential significance of the treatment effects, a System Dynamics Model operationalized the evaporation rate results and simulated soil moisture dynamics under typical daily precipitation conditions. The results from this model indicate both treatment methods significantly altered soil moisture dynamics in the sandy loam soils and increased the probability of the soil exhibiting constant rate evaporation relative to the control soils. Overall, these findings suggest that the decrease in soil moisture threshold observed in the experimental setting could increase soil moisture availability by prolonging the constant rate stage of evaporation. As inoculation with B. subtilis in the sandy loam soil had the most pronounced effects in both the experimental and simulated contexts, future work should focus on testing this treatment in field trials with similar soil textures.
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10
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Jautzus T, van Gestel J, Kovács ÁT. Complex extracellular biology drives surface competition during colony expansion in Bacillus subtilis. THE ISME JOURNAL 2022; 16:2320-2328. [PMID: 35790818 PMCID: PMC9477810 DOI: 10.1038/s41396-022-01279-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 04/29/2023]
Abstract
Many bacteria grow on surfaces in nature, where they form cell collectives that compete for space. Within these collectives, cells often secrete molecules that benefit surface spreading by, for example, reducing surface tension or promoting filamentous growth. Although we have a detailed understanding of how these molecules are produced, much remains unknown about their role in surface competition. Here we examine sliding motility in Bacillus subtilis and compare how secreted molecules, essential for sliding, affect intraspecific cooperation and competition on a surface. We specifically examine (i) the lipopeptide surfactin, (ii) the hydrophobin protein BslA, and (iii) exopolysaccharides (EPS). We find that these molecules have a distinct effect on surface competition. Whereas surfactin acts like a common good, which is costly to produce and benefits cells throughout the surface, BslA and EPS are cost-free and act locally. Accordingly, surfactin deficient mutants can exploit the wild-type strain in competition for space, while BslA and EPS mutants cannot. Supported by a mathematical model, we show that three factors are important in predicting the outcome of surface competition: the costs of molecule synthesis, the private benefits of molecule production, and the diffusion rate. Our results underscore the intricate extracellular biology that can drive bacterial surface competition.
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Affiliation(s)
- Theresa Jautzus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Jordi van Gestel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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11
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Guo S, Tao C, Jousset A, Xiong W, Wang Z, Shen Z, Wang B, Xu Z, Gao Z, Liu S, Li R, Ruan Y, Shen Q, Kowalchuk GA, Geisen S. Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health. THE ISME JOURNAL 2022; 16:1932-1943. [PMID: 35461357 PMCID: PMC9296445 DOI: 10.1038/s41396-022-01244-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022]
Abstract
Plant health is strongly impacted by beneficial and pathogenic plant microbes, which are themselves structured by resource inputs. Organic fertilizer inputs may thus offer a means of steering soil-borne microbes, thereby affecting plant health. Concurrently, soil microbes are subject to top-down control by predators, particularly protists. However, little is known regarding the impact of microbiome predators on plant health-influencing microbes and the interactive links to plant health. Here, we aimed to decipher the importance of predator-prey interactions in influencing plant health. To achieve this goal, we investigated soil and root-associated microbiomes (bacteria, fungi and protists) over nine years of banana planting under conventional and organic fertilization regimes differing in Fusarium wilt disease incidence. We found that the reduced disease incidence and improved yield associated with organic fertilization could be best explained by higher abundances of protists and pathogen-suppressive bacteria (e.g. Bacillus spp.). The pathogen-suppressive actions of predatory protists and Bacillus spp. were mainly determined by their interactions that increased the relative abundance of secondary metabolite Q genes (e.g. nonribosomal peptide synthetase gene) within the microbiome. In a subsequent microcosm assay, we tested the interactions between predatory protists and pathogen-suppressive Bacillus spp. that showed strong improvements in plant defense. Our study shows how protistan predators stimulate disease-suppressive bacteria in the plant microbiome, ultimately enhancing plant health and yield. Thus, we suggest a new biological model useful for improving sustainable agricultural practices that is based on complex interactions between different domains of life.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Zhe Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Beibei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, PR China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhilei Gao
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shanshan Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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12
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Using Large-Scale Multi-Module NRPS to Heterologously Prepare Highly Efficient Lipopeptide Biosurfactants in Recombinant Escherichia coli. Enzyme Microb Technol 2022; 159:110068. [DOI: 10.1016/j.enzmictec.2022.110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022]
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13
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Mahapatra S, Yadav R, Ramakrishna W. Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde. J Appl Microbiol 2022; 132:3543-3562. [PMID: 35137494 DOI: 10.1111/jam.15480] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.
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14
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The Intertwined Roles of Specialized Metabolites within the Bacillus subtilis Biofilm. J Bacteriol 2021; 203:e0043121. [PMID: 34460313 DOI: 10.1128/jb.00431-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bacteria produce specialized metabolites with a range of functions. In this issue of the Journal of Bacteriology, Schoenborn et al. study the production and role of secondary metabolites during biofilm development and sporulation in Bacillus subtilis (A. A. Schoenborn, S. M. Yannarell, E. D. Wallace, H. Clapper, et al., J Bacteriol 203:e00337-21, 2021, https://doi.org/https://doi.org/10.1128/JB.00337-21). Most metabolites studied are produced during differentiation, and six are required for the development of biofilms and/or spores. The authors propose a model for the timing of production and role in differentiation exerted by each secondary metabolite.
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15
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Molina-Santiago C, de Vicente A, Romero D. Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials. Comput Struct Biotechnol J 2021; 19:2796-2805. [PMID: 34093994 PMCID: PMC8138678 DOI: 10.1016/j.csbj.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.
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Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
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