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Yuan M, Chen G, Xiao Y, Qu Y, Ren Y. The mechanisms of yeast extracellular metabolites in stimulating microbial degradation of trichloroethylene: Physiological characteristics and omics analysis. ENVIRONMENTAL RESEARCH 2024; 255:119193. [PMID: 38777296 DOI: 10.1016/j.envres.2024.119193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The biodegradation of Trichloroethylene (TCE) is limited by low microbial metabolic capacity but can be enhanced through biostimulation strategies. This study explored the physiological effects and potential molecular mechanisms of the yeast Yarrowia lipolytica extracellular metabolites (YEMs) on the degradation of TCE by Acinetobacter LT1. Results indicated that YEMs stimulated the efficiency of strain LT1 by 50.28%. At the physiological level, YEMs exhibited protective effects on cell morphology, reduced oxidative stress, lessened membrane damage, and enhanced energy production and conversion. Analysis of omics results revealed that the regulation of various metabolic pathways by YEMs improved the degradation of TCE. Furthermore, RT-qPCR showed that the genes encoding YhhW protein in TCE stress and YEMs stimulation groups were 1.72 and 3.22 times the control group, respectively. Molecular docking results showed that the conformation of YhhW after binding to TCE changed into a more active form, which enhanced enzyme activity. Therefore, it is speculated that YhhW is the primary degradative enzyme involved in the process of YEMs stimulating strain LT1 to degrade TCE. These results reveal how YEMs induce strain LT1 to enhance TCE degradation.
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Affiliation(s)
- Meng Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Guotao Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yibo Xiao
- Protoga Biotechnology Co., Ltd., Shenzhen 518000, China; Microalgae Biosynthesis R&D Center, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, China
| | - Yujiao Qu
- Protoga Biotechnology Co., Ltd., Shenzhen 518000, China; Microalgae Biosynthesis R&D Center, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China; The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, Guangzhou 510006, China.
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2
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Martínez-Pérez C, Zweifel ST, Pioli R, Stocker R. Space, the final frontier: The spatial component of phytoplankton-bacterial interactions. Mol Microbiol 2024. [PMID: 38970428 DOI: 10.1111/mmi.15293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Microscale interactions between marine phytoplankton and bacteria shape the microenvironment of individual cells, impacting their physiology and ultimately influencing global-scale biogeochemical processes like carbon and nutrient cycling. In dilute environments such as the ocean water column, metabolic exchange between microorganisms likely requires close proximity between partners. However, the biological strategies to achieve this physical proximity remain an understudied aspect of phytoplankton-bacterial associations. Understanding the mechanisms by which these microorganisms establish and sustain spatial relationships and the extent to which spatial proximity is necessary for interactions to occur, is critical to learning how spatial associations influence the ecology of phytoplankton and bacterial communities. Here, we provide an overview of current knowledge on the role of space in shaping interactions among ocean microorganisms, encompassing behavioural and metabolic evidence. We propose that characterising phytoplankton-bacterial interactions from a spatial perspective can contribute to a mechanistic understanding of the establishment and maintenance of these associations and, consequently, an enhanced ability to predict the impact of microscale processes on ecosystem-wide phenomena.
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Affiliation(s)
- Clara Martínez-Pérez
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Sophie T Zweifel
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
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3
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Seymour JR, Brumley DR, Stocker R, Raina JB. Swimming towards each other: the role of chemotaxis in bacterial interactions. Trends Microbiol 2024; 32:640-649. [PMID: 38212193 DOI: 10.1016/j.tim.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
| | - Douglas R Brumley
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia.
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
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Huang Z, Wang D, Zhou J, He H, Wei C. Segregation of endosymbionts in complex symbiotic system of cicadas providing novel insights into microbial symbioses and evolutionary dynamics of symbiotic organs in sap-feeding insects. Front Zool 2024; 21:15. [PMID: 38863001 PMCID: PMC11165832 DOI: 10.1186/s12983-024-00536-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
The most extraordinary systems of symbiosis in insects are found in the suborder Auchenorrhyncha of Hemiptera, which provide unique perspectives for uncovering complicated insect-microbe symbiosis. We investigated symbionts associated with bacteriomes and fat bodies in six cicada species, and compared transmitted cell number ratio of related symbionts in ovaries among species. We reveal that Sulcia and Hodgkinia or a yeast-like fungal symbiont (YLS) are segregated from other host tissues by the bacteriomes in the nymphal stage, then some of them may migrate to other organs (i.e., fat bodies and ovaries) during host development. Particularly, YLS resides together with Sulcia in the "symbiont ball" of each egg and the bacteriomes of young-instar nymphs, but finally migrates to the fat bodies of adults in the majority of Hodgkinia-free cicadas, whereas it resides in both bacteriome sheath and fat bodies of adults in a few other species. The transmitted Sulcia/YLS or Sulcia/Hodgkinia cell number ratio in ovaries varies significantly among species, which could be related to the distribution and/or lineage splitting of symbiont(s). Rickettsia localizes to the nuclei of bacteriomes and fat bodies in some species, but it was not observed to be transmitted to the ovaries, indicating that this symbiont may be acquired from environments or from father to offspring. The considerable difference in the transovarial transmission process of symbionts suggests that cellular mechanisms underlying the symbiont transmission are complex. Our results may provide novel insights into insect-microbe symbiosis.
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Affiliation(s)
- Zhi Huang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dandan Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinrui Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong He
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Key Laboratory of Integrated Pest Management On Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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5
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Cao L, Yang H, Huang Z, Lu C, Chen F, Zhang J, Ye P, Yan J, Zhang H. Direct prediction of antimicrobial resistance in Pseudomonas aeruginosa by metagenomic next-generation sequencing. Front Microbiol 2024; 15:1413434. [PMID: 38903781 PMCID: PMC11187003 DOI: 10.3389/fmicb.2024.1413434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024] Open
Abstract
Objective Pseudomonas aeruginosa has strong drug resistance and can tolerate a variety of antibiotics, which is a major problem in the management of antibiotic-resistant infections. Direct prediction of multi-drug resistance (MDR) resistance phenotypes of P. aeruginosa isolates and clinical samples by genotype is helpful for timely antibiotic treatment. Methods In the study, whole genome sequencing (WGS) data of 494 P. aeruginosa isolates were used to screen key anti-microbial resistance (AMR)-associated genes related to imipenem (IPM), meropenem (MEM), piperacillin/tazobactam (TZP), and levofloxacin (LVFX) resistance in P. aeruginosa by comparing genes with copy number differences between resistance and sensitive strains. Subsequently, for the direct prediction of the resistance of P. aeruginosa to four antibiotics by the AMR-associated features screened, we collected 74 P. aeruginosa positive sputum samples to sequence by metagenomics next-generation sequencing (mNGS), of which 1 sample with low quality was eliminated. Then, we constructed the resistance prediction model. Results We identified 93, 88, 80, 140 AMR-associated features for IPM, MEM, TZP, and LVFX resistance in P. aeruginosa. The relative abundance of AMR-associated genes was obtained by matching mNGS and WGS data. The top 20 features with importance degree for IPM, MEM, TZP, and LVFX resistance were used to model, respectively. Then, we used the random forest algorithm to construct resistance prediction models of P. aeruginosa, in which the areas under the curves of the IPM, MEM, TZP, and LVFX resistance prediction models were all greater than 0.8, suggesting these resistance prediction models had good performance. Conclusion In summary, mNGS can predict the resistance of P. aeruginosa by directly detecting AMR-associated genes, which provides a reference for rapid clinical detection of drug resistance of pathogenic bacteria.
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Affiliation(s)
- Lichao Cao
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
| | - Huilin Yang
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Zhigang Huang
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Chang Lu
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Fang Chen
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
| | - Jiahao Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
| | - Peng Ye
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jinjin Yan
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Hezi Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong Province, China
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Yin Z, Liang J, Zhang M, Chen B, Yu Z, Tian X, Deng X, Peng L. Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172251. [PMID: 38604355 DOI: 10.1016/j.scitotenv.2024.172251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.
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Affiliation(s)
- Zhiqiu Yin
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Jiaxin Liang
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Mujie Zhang
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Baozhu Chen
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Zhanpeng Yu
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Xiaoyan Tian
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Xiaoyan Deng
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China.
| | - Liang Peng
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China; KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou 510180, Guangdong, China.
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7
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Cai C, Chen Y, Ohore OE, Cai G, Cai R, Wang H. A sonication-filtration method for acquisition of integrated bacterial communities from phycosphere. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106522. [PMID: 38685152 DOI: 10.1016/j.marenvres.2024.106522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Bacteria in phycosphere engage in intricate interactions with microalgae by exchanging organic and inorganic matter. However, elucidating the primary roles of bacteria in phycosphere has been a big challenge, due to the lack of adequate methods for separating tightly associated bacteria from microalgal cells. In this study we evaluated several isolation methods including centrifugation, filtration, sonication combined with filtration, and tween lysis followed by sonication and filtration, aiming to efficiently acquire complete bacterial communities from phycosphere. The results demonstrated that the sonication-filtration approach maximally preserves the original characteristics of the bacterial communities. This method will facilitate the acquisition and further analysis of future experimental data.
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Affiliation(s)
- Chao Cai
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, China
| | - Yuerong Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, China
| | - Okugbe Ebiotubo Ohore
- Key Laboratory of Tropical Diseases Control, National Health Commission, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Guanjing Cai
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, China
| | - Runlin Cai
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, China.
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Keren G, Yehezkel G, Satish L, Adamov Z, Barak Z, Ben-Shabat S, Kagan-Zur V, Sitrit Y. Root-secreted nucleosides: signaling chemoattractants of rhizosphere bacteria. FRONTIERS IN PLANT SCIENCE 2024; 15:1388384. [PMID: 38799096 PMCID: PMC11120975 DOI: 10.3389/fpls.2024.1388384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024]
Abstract
The rhizosphere is a complex ecosystem, consisting of a narrow soil zone influenced by plant roots and inhabited by soil-borne microorganisms. Plants actively shape the rhizosphere microbiome through root exudates. Some metabolites are signaling molecules specifically functioning as chemoattractants rather than nutrients. These elusive signaling molecules have been sought for several decades, and yet little progress has been made. Root-secreted nucleosides and deoxynucleosides were detected in exudates of various plants by targeted ultra-performance liquid chromatography-mass spectrometry/mass spectrometry. Rhizobacteria were isolated from the roots of Helianthemum sessiliflorum carrying the mycorrhizal desert truffle Terfezia boudieri. Chemotaxis was determined by a glass capillary assay or plate assays on semisolid agar and through a soil plate assay. Nucleosides were identified in root exudates of plants that inhabit diverse ecological niches. Nucleosides induced positive chemotaxis in plant beneficial bacteria Bacillus pumilus, Bacillus subtilis, Pseudomonas turukhanskensis spp., Serratia marcescens, and the pathogenic rhizobacterium Xanthomonas campestris and E coli. In a soil plate assay, nucleosides diffused to substantial distances and evoked chemotaxis under conditions as close as possible to natural environments. This study implies that root-secreted nucleosides are involved in the assembly of the rhizosphere bacterial community by inducing chemotaxis toward plant roots. In animals, nucleoside secretion known as "purinergic signaling" is involved in communication between cells, physiological processes, diseases, phagocytic cell migration, and bacterial activity. The coliform bacterium E. coli that inhabits the lower intestine of warm-blooded organisms also attracted to nucleosides, implying that nucleosides may serve as a common signal for bacterial species inhabiting distinct habitats. Taken together, all these may indicate that chemotaxis signaling by nucleosides is a conserved universal mechanism that encompasses living kingdoms and environments and should be given further attention in plant rhizosphere microbiome research.
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Affiliation(s)
- Guy Keren
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Galit Yehezkel
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lakkakula Satish
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Zahar Adamov
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ze’ev Barak
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shimon Ben-Shabat
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Varda Kagan-Zur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yaron Sitrit
- The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Katif Research Center for Research & Development, Netivot, Israel
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Xing W, Gai X, Xue L, Li S, Zhang X, Ju F, Chen G. Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas. Front Microbiol 2024; 15:1348054. [PMID: 38577689 PMCID: PMC10993014 DOI: 10.3389/fmicb.2024.1348054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.
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Affiliation(s)
- Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Liang Xue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Shaocui Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou, Zhejiang, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Dinango VN, Dhouib H, Wakam LN, Kouokap LK, Youmbi DY, Eke P, Driss F, Tounsi S, Boyom FF, Frikha-Gargouri O. Bacterial endophytes inhabiting desert plants provide protection against seed rot caused by Fusarium verticillioides and promote growth in maize. PEST MANAGEMENT SCIENCE 2024; 80:1206-1218. [PMID: 37886813 DOI: 10.1002/ps.7850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/05/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Fusarium maize ear and root rot disease caused by Fusarium verticillioides has become one of the most serious fungal diseases associated with maize production. Due to their abilities to promote plant development and manage diseases, bacterial endophytes provide a more promising approach for treating this vascular disease. RESULTS This work was undertaken for the selection and identification of promising isolates as plant growth promoters and biocontrol agents against F. verticillioides in maize agroecosystems. A screening procedure consisting of in vitro and in situ tests was applied to 27 endophytic strains originating from desert plants: Euphorbia antiquorum, Calotropis procera, and Alcasia albida. In vitro studies indicated that the bacteria exhibited variable results in biocontrol, endophytism, and plant growth-promoting traits. In addition, in situ plant growth promotion and biocontrol experiments allowed the identification of the most promising bacterial endophytes. In vitro and in situ comparative study results indicated a low correlation. Our data revealed that in situ screening must be used as the method of selection of biocontrol agents against Fusarium ear and root rot disease. Based on in situ results, seven potent strains were selected and identified as Bacillus subtilis, Bacillus velezensis, Bacillus tequilensis, Stenotrophomonas maltophilia, and Klebsiella pneumoniae. CONCLUSION The results of this study showed that the selected strains seem to be promising candidates to be exploited as biofertilizers and biocontrol agents against Fusarium maize ear and root rot disease. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Vanessa Nya Dinango
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Hanen Dhouib
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Louise Nana Wakam
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
- Soil Microbiology Laboratory, Biotechnology Centre, Yaoundé, Cameroon
| | - Lanvin Kepngop Kouokap
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Diane Yimta Youmbi
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Pierre Eke
- College of Technology, Department of Crop Production Technology, University of Bamenda, Bambili, Cameroon
| | - Fatma Driss
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Slim Tounsi
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Fabrice Fekam Boyom
- Antimicrobial & Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Olfa Frikha-Gargouri
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
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11
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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12
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Zhu S, Xie J, Yang J, Hou X, He L, Zhang Z. Seed-Borne Bacterial Diversity of Fescue ( Festuca ovina L.) and Properties Study. Microorganisms 2024; 12:329. [PMID: 38399732 PMCID: PMC10892014 DOI: 10.3390/microorganisms12020329] [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: 01/08/2024] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Rich endophytic bacterial communities exist in fescue (Festuca ovina L.) and play an important role in fescue growth, cold tolerance, drought tolerance and antibiotic tolerance. To screen for probiotics carried by fescue seeds, seven varieties were collected from three different regions of China for isolation by the milled seed method and analyzed for diversity and motility, biofilm and antibiotic resistance. A total of 91 bacterial isolates were obtained, and based on morphological characteristics, 36 representative dominant strains were selected for 16S rDNA sequencing analysis. The results showed that the 36 bacterial strains belonged to four phyla and nine genera. The Firmicutes was the dominant phylum, and Bacillus, Paenibacillus and Pseudomonas were the dominant genera. Most of the strains had motility (80%) and were biofilm-forming (91.7%). In this study, 15 strains were capable of Indole-3-acetic acid (IAA) production, 24 strains were capable of nitrogen fixation, and some strains possessed amylase and protease activities, suggesting their potential for growth promotion. Determination of the minimum inhibitory concentration (MIC) against the bacteria showed that the strains were not resistant to tetracycline and oxytetracycline. Pantoea (QY6, LH4, MS2) and Curtobacterium (YY4) showed resistance to five antibiotics (ampicillin, kanamycin, erythromycin, sulfadiazine and rifampicin). Using Pearson correlation analysis, a significant correlation was found between motility and biofilm, and between biofilm and sulfadiazine. In this study, we screened two strains of Pantoea (QY6, LH4) with excellent growth-promoting ability as well as broad-spectrum antibiotic resistance. which provided new perspectives for subsequent studies on the strong ecological adaptations of fescue, and mycorrhizal resources for endophytic bacteria and plant interactions.
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Affiliation(s)
| | | | | | | | | | - Zhenfen Zhang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China; (S.Z.); (J.X.); (J.Y.); (X.H.); (L.H.)
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13
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Aroney STN, Pini F, Kessler C, Poole PS, Sánchez-Cañizares C. The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS Ntr regulation. Environ Microbiol 2024; 26:e16570. [PMID: 38216524 DOI: 10.1111/1462-2920.16570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Motility and chemotaxis are crucial processes for soil bacteria and plant-microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled by two chemotaxis systems, Che1 and Che2. The Che1 cluster is particularly important in free-living motility prior to the establishment of the symbiosis, with a che1 mutant delayed in nodulation and reduced in nodulation competitiveness. The Che2 system alters bacteroid development and nodule maturation. In this work, we also identified 27 putative chemoreceptors encoded in the R. leguminosarum bv. viciae 3841 genome and characterized its motility in different growth conditions. We describe a metabolism-based taxis system in rhizobia that acts at high concentrations of dicarboxylates to halt motility independent of chemotaxis. Finally, we show how PTSNtr influences cell motility, with PTSNtr mutants exhibiting reduced swimming in different media. Motility is restored by the active forms of the PTSNtr output regulatory proteins, unphosphorylated ManX and phosphorylated PtsN. Overall, this work shows how rhizobia typify soil bacteria by having a high number of chemoreceptors and highlights the importance of the motility and chemotaxis mechanisms in a free-living cell in the rhizosphere, and at different stages of the symbiosis.
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Affiliation(s)
| | | | - Celia Kessler
- Department of Biology, University of Oxford, Oxford, UK
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14
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Ramoneda J, Fan K, Lucas JM, Chu H, Bissett A, Strickland MS, Fierer N. Ecological relevance of flagellar motility in soil bacterial communities. THE ISME JOURNAL 2024; 18:wrae067. [PMID: 38648266 PMCID: PMC11095265 DOI: 10.1093/ismejo/wrae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.
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Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), 17300 Blanes, Spain
| | - Kunkun Fan
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
| | - Jane M Lucas
- Cary Institute of Ecosystem Studies, 12545 Millbrook, NY, United States
| | - Haiyan Chu
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
- University of Chinese Academy of Sciences, 101408 Beijing, China
| | | | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, 83843 Moscow, ID, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, 80309 Boulder, CO, United States
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15
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Shi Y, Ma L, Zhou M, He Z, Zhao Y, Hong J, Zou X, Zhang L, Shu L. Copper stress shapes the dynamic behavior of amoebae and their associated bacteria. THE ISME JOURNAL 2024; 18:wrae100. [PMID: 38848278 PMCID: PMC11197307 DOI: 10.1093/ismejo/wrae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/15/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024]
Abstract
Amoeba-bacteria interactions are prevalent in both natural ecosystems and engineered environments. Amoebae, as essential consumers, hold significant ecological importance within ecosystems. Besides, they can establish stable symbiotic associations with bacteria. Copper plays a critical role in amoeba predation by either killing or restricting the growth of ingested bacteria in phagosomes. However, certain symbiotic bacteria have evolved mechanisms to persist within the phagosomal vacuole, evading antimicrobial defenses. Despite these insights, the impact of copper on the symbiotic relationships between amoebae and bacteria remains poorly understood. In this study, we investigated the effects of copper stress on amoebae and their symbiotic relationships with bacteria. Our findings revealed that elevated copper concentration adversely affected amoeba growth and altered cellular fate. Symbiont type significantly influenced the responses of the symbiotic relationships to copper stress. Beneficial symbionts maintained stability under copper stress, but parasitic symbionts exhibited enhanced colonization of amoebae. Furthermore, copper stress favored the transition of symbiotic relationships between amoebae and beneficial symbionts toward the host's benefit. Conversely, the pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress. This study sheds light on the intricate response mechanisms of soil amoebae and amoeba-bacteria symbiotic systems to copper stress, providing new insights into symbiotic dynamics under abiotic factors. Additionally, the results underscore the potential risks of copper accumulation in the environment for pathogen transmission and biosafety.
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Affiliation(s)
- Yijing Shi
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Lu Ma
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Zhou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanchen Zhao
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Junyue Hong
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xinyue Zou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
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Liu XJ, Zhu KL, Ye YQ, Han ZT, Tan XY, Du ZJ, Ye MQ. Phenotypic and genotypic characterization of Marinobacterium weihaiense sp. nov. and Marinobacterium marinum sp. nov., isolated from marine sediment, and genomic properties of the genus Marinobacterium. Microb Genom 2024; 10:001182. [PMID: 38265428 PMCID: PMC10868613 DOI: 10.1099/mgen.0.001182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
In this study, two novel bacterial strains were isolated from coastal sediment of Weihai, China. The two strains were Gram-stain-negative and facultatively aerobic, designated 3-1745T and A346T. Based on phenotypic, genetic and phylogenetic properties, strains 3-1745T and A346T represent two novel species of the genus Marinobacterium. The results of genome analysis revealed many central carbohydrate metabolism pathways such as gluconeogenesis, pyruvate oxidation, tricyclic acid cycle, pentose phosphate pathway and PRPP biosynthesis in the genus Marinobacterium. The ability of strains 3-1745T and A346T to utilize volatile fatty acids was experimentally confirmed. Polyhydroxyalkanoate synthases (PhaA, PhaB and PhaC) for the synthesis of polyhydroxyalkanoates were prevalent in the genus Marinobacterium. Multiple BGCs (biosynthetic gene clusters) including betalactone, ectoine, ranthipeptide, redox-cofactor, RiPPs (ribosomally synthesized post-translationally modified peptides) and T3PKS (polyketide synthases) in the genome of the genus Marinobacterium were found. Additional genome analyses suggested that the genus Marinobacterium contained diverse potential mechanisms of salt tolerance and mainly utilized oligosaccharides. This is the first report on broad genomic analyses of the genus Marinobacterium with the description of two novel species and potential ecological and biotechnological implications.
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Affiliation(s)
- Xin-Jiang Liu
- Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong, 518057, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ke-Lei Zhu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ze-Tian Han
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xin-Yun Tan
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, PR China
| | - Meng-Qi Ye
- Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong, 518057, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, PR China
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17
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Olander A, Raina JB, Lawson CA, Bartels N, Ueland M, Suggett DJ. Distinct emissions of biogenic volatile organic compounds from temperate benthic taxa. Metabolomics 2023; 20:9. [PMID: 38129550 DOI: 10.1007/s11306-023-02070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
INTRODUCTION Biogenic volatile organic compounds (BVOCs) are emitted by all organisms as intermediate or end-products of metabolic processes. Individual BVOCs perform important physiological, ecological and climatic functions, and collectively constitute the volatilome-which can be reflective of organism taxonomy and health. Although BVOC emissions of tropical benthic reef taxa have recently been the focus of multiple studies, emissions derived from their temperate counterparts have never been characterised. OBJECTIVES Characterise the volatilomes of key competitors for benthic space among Australian temperate reefs. METHODS Six fragments/fronds of a temperate coral (Plesiastrea versipora) and a macroalga (Ecklonia radiata) from a Sydney reef site were placed within modified incubation chambers filled with seawater. Organism-produced BVOCs were captured on thermal desorption tubes using a purge-and-trap methodology, and were then analysed using GC × GC - TOFMS and multivariate tests. RESULTS Analysis detected 55 and 63 BVOCs from P. versipora and E. radiata respectively, with 30 of these common between species. Each taxon was characterised by a similar relative composition of chemical classes within their volatilomes. However, 14 and 10 volatiles were distinctly emitted by either E. radiata or P. versipora respectively, including the halogenated compounds iodomethane, tribromomethane, carbon tetrachloride and trichloromonofluoromethane. While macroalgal cover was 3.7 times greater than coral cover at the sampling site, P. versipora produced on average 17 times more BVOCs per cm2 of live tissue, resulting in an estimated contribution to local BVOC emission that was 4.7 times higher than E. radiata. CONCLUSION Shifts in benthic community composition could disproportionately impact local marine chemistry and affect how ecosystems contribute to broader BVOC emissions.
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Affiliation(s)
- Axel Olander
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia.
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Caitlin A Lawson
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
| | - Natasha Bartels
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
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18
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de Oliveira KB, Goes AC, Silva AD, Vieira PC, Rodrigues A. Fungal Cultivars of Higher Attine Ants Promote Escovopsis Chemotropism. Curr Microbiol 2023; 81:37. [PMID: 38063979 DOI: 10.1007/s00284-023-03552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
In varied environments, microorganisms search for partners or nutritional resources using chemical signals. Microbes are drawn (chemotaxis) or grow directionally (chemotropism) towards the chemical source, enabling them to establish and maintain symbiosis. The hypocrealean fungi Escovopsis enhance their growth towards the basidiomycete fungus Leucoagaricus gongylophorus, which is cultivated by leaf-cutting attine ants for food. Although directional growth is well documented in this symbiosis, it is unclear whether non-volatile or volatile organic compounds participate in the interaction between cultivar and Escovopsis, and which specific chemical compounds might attract and induce chemotropism. In this study, we examined the growth responses of Escovopsis isolates to non-volatile and volatile organic compounds produced by fungal cultivars of higher attine ants. We also isolated and identified molecules released by the ant-cultivar and assessed the chemotropism of Escovopsis towards them. Our results indicate that the growth of Escovopsis is stimulated in the presence of both non-volatile and volatile compounds from fungal cultivars. We also identified three isomeric diketopiperazines molecules from crude extracts of the ant cultivar, suggesting that these might play a role in Escovopsis chemotropism. Our findings provide insights into the complex chemical interactions that govern the association between Escovopsis and fungal cultivars.
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Affiliation(s)
- Karina B de Oliveira
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Aryel C Goes
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP, Brazil
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Airton D Silva
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Paulo C Vieira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP, Brazil.
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Bongrand C, Foster JS. Modelled microgravity impacts Vibrio fischeri population structure in a mutualistic association with an animal host. Environ Microbiol 2023; 25:3269-3279. [PMID: 37828645 DOI: 10.1111/1462-2920.16522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Perturbations to host-microbe interactions, such as environmental stress, can alter and disrupt homeostasis. In this study, we examined the effects of a stressor, simulated microgravity, on beneficial bacteria behaviours when colonising their host. We studied the bacterium Vibrio fischeri, which establishes a mutualistic association in a symbiosis-specific organ within the bobtail squid, Euprymna scolopes. To elucidate how animal-microbe interactions are affected by the stress of microgravity, squid were inoculated with different bacterial strains exhibiting either a dominant- or sharing-colonisation behaviour in High Aspect Ratio Vessels, which simulate the low-shear environment of microgravity. The colonisation behaviours of the sharing and dominant strains under modelled microgravity conditions were determined by counting light-organ homogenate of squids as well as confocal microscopy to assess the partitioning of different strains within the light organ. The results indicated that although the colonisation behaviours of the strains did not change, the population levels of the sharing strains were at lower relative abundance in single-colonised animals exposed to modelled microgravity compared to unit gravity; in addition, there were shifts in the relative abundance of strains in co-colonised squids. Together these results suggest that the initiation of beneficial interactions between microbes and animals can be altered by environmental stress, such as simulated microgravity.
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Affiliation(s)
- Clotilde Bongrand
- Department of Microbiology and Cell Science, Space Life Sciences Lab, University of Florida, Merritt Island, Florida, USA
| | - Jamie S Foster
- Department of Microbiology and Cell Science, Space Life Sciences Lab, University of Florida, Merritt Island, Florida, USA
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20
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Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
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Altitinchi A, Schweizer A, Dean K, Lawson N, Sulaiman T, Fouad AF. An Ex-Vivo Model for Investigating Bacterial Extrusion from Infected Root Canals during Masticatory Function. J Endod 2023; 49:1553-1558. [PMID: 37611655 DOI: 10.1016/j.joen.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/24/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
INTRODUCTION The extrusion of bacteria from infected root canals may lead to increase in symptoms, expansion of periapical lesions, and contribution to systemic diseases. The aim of this study is to investigate a potential proof-of-concept model to study the extent to which bacteria can escape from infected root canals under dynamic loading (simulated chewing). METHODS The study was completed in 2 experiments performed at 2 institutions. Biofilms of Streptococcus intermedius in the first experiment and S. intermedius and Actinomyces naeslundii were allowed to grow in root canals of single-rooted extracted teeth for 3 weeks. The roots of the teeth were suspended in a small chamber containing dental transport medium and were mounted on a lower sample holder of a chewing simulator. In the experimental group, simulated chewing cycles equivalent to 1 year of function were conducted, and then bacterial migration was quantified and compared with stationary teeth. RESULTS All experimental samples of the loading group revealed bacterial penetration in both experiments. Several of the unloaded samples revealed no bacterial penetration. In the first experiment, a significantly higher number of bacteria were able to escape into the periapex of the loaded group compared with the unloaded group (P = .017). In the second experiment, there was no significant difference between the 2 bacterial species used in the amount of extruded bacteria; however, there was a highly significant effect for occlusal loading (P = .0001). CONCLUSIONS The potential for occlusal forces to enhance bacterial extrusion from infected root canals should be further explored.
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Affiliation(s)
- Ali Altitinchi
- Department of Endodontics, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Andrew Schweizer
- Department of Endodontics, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kimberly Dean
- Department of Endodontics, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel Lawson
- Division of Biomaterials, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Taiseer Sulaiman
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashraf F Fouad
- Department of Endodontics, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama.
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22
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Ho HVN, Dunigan DD, Salsbery ME, Agarkova IV, Al Ameeli Z, Van Etten JL, DeLong JP. Viral Chemotaxis of Paramecium Bursaria Altered by Algal Endosymbionts. MICROBIAL ECOLOGY 2023; 86:2904-2909. [PMID: 37650927 DOI: 10.1007/s00248-023-02292-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria's chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic algae (zoochlorellae) appeared to alter the movement of Paramecia toward chloroviruses, but it was not clear that ectosymbiotic viruses (chlorovirus) also had this effect. The change in behavior was consistent with a change in swimming speed, but a change in attraction remains possible. The potential costs and benefits of chemotactic movement toward chloroviruses for either the Paramecia hosts or its symbionts remain unclear.
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Affiliation(s)
- Huy V N Ho
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-2083, USA
| | - David D Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Miranda E Salsbery
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-2083, USA
| | - Irina V Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Zeina Al Ameeli
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722, USA
- Medical Technical Institutes, Middle Technical University, Baghdad, Iraq
| | - James L Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - John P DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-2083, USA.
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23
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Wang W, Xia J, Wang Z, Shao Z. Bacterial cell sensing and signaling pathway for external polycyclic aromatic hydrocarbons (PAHs). iScience 2023; 26:107912. [PMID: 37841585 PMCID: PMC10570129 DOI: 10.1016/j.isci.2023.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
The mechanism by which a bacterial cell senses external nutrients remains largely unknown. In this study, we identified a bacterial cell sensing system for polycyclic aromatic hydrocarbons (PAHs) in a common marine PAH-using bacterium, Cycloclasticus. It consists of an outer membrane receptor (PahS) and a periplasmic protein (PahP) in combination with a two-component sensing system (TCS) that ensures a rapid response to PAH occurrence by directly controlling serial reactions including chemotactic sensing and movement, PAH uptake and intracellular PAH metabolism. PahS protrudes from the cell and acts as a PAH sensor, transducing the PAH signal across the outer membrane to its periplasmic partner PahP, which in turn transduces the PAH signal across the periplasm to a specialized TCS. This sensing system plays a critical role in sensing and promoting the metabolism of PAHs, which can be scavenged by various hydrocarbon-degrading bacteria.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Jingyu Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zining Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
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24
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O'Banion BS, Jones P, Demetros AA, Kelley BR, Knoor LH, Wagner AS, Chen JG, Muchero W, Reynolds TB, Jacobson D, Lebeis SL. Plant myo-inositol transport influences bacterial colonization phenotypes. Curr Biol 2023; 33:3111-3124.e5. [PMID: 37419115 DOI: 10.1016/j.cub.2023.06.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/14/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023]
Abstract
Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites are consistently identified as important mediators of microbial interactions. We combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in seedlings of the model plant Arabidopsis thaliana to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions. While microbial catabolism of this compound has been linked to increased host colonization, we identify bacterial phenotypes that occur in both catabolism-dependent and -independent manners, suggesting that myo-inositol may additionally serve as a eukaryotic-derived signaling molecule to modulate microbial activities. Our data suggest host control of this compound and resulting microbial behavior are important mechanisms at play surrounding the host metabolite myo-inositol.
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Affiliation(s)
- Bridget S O'Banion
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Piet Jones
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - Alexander A Demetros
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Brittni R Kelley
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Leah H Knoor
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Andrew S Wagner
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Sarah L Lebeis
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 38824, USA.
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25
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Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
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Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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26
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Isenberg RY, Holschbach CS, Gao J, Mandel MJ. Functional analysis of cyclic diguanylate-modulating proteins in Vibrio fischeri. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550417. [PMID: 37546929 PMCID: PMC10402110 DOI: 10.1101/2023.07.24.550417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
As bacterial symbionts transition from a motile free-living state to a sessile biofilm state, they must coordinate behavior changes suitable to each lifestyle. Cyclic diguanylate (c-di-GMP) is an intracellular signaling molecule that can regulate this transition, and it is synthesized by diguanylate cyclase (DGC) enzymes and degraded by phosphodiesterase (PDE) enzymes. Generally, c-di-GMP inhibits motility and promotes biofilm formation. While c-di-GMP and the enzymes that contribute to its metabolism have been well-studied in pathogens, considerably less focus has been placed on c-di-GMP regulation in beneficial symbionts. Vibrio fischeri is the sole beneficial symbiont of the Hawaiian bobtail squid (Euprymna scolopes) light organ, and the bacterium requires both motility and biofilm formation to efficiently colonize. C-di-GMP regulates swimming motility and cellulose exopolysaccharide production in V. fischeri. The genome encodes 50 DGCs and PDEs, and while a few of these proteins have been characterized, the majority have not undergone comprehensive characterization. In this study, we use protein overexpression to systematically characterize the functional potential of all 50 V. fischeri proteins. All 28 predicted DGCs and 14 predicted PDEs displayed at least one phenotype consistent with their predicted function, and a majority of each displayed multiple phenotypes. Finally, active site mutant analysis of proteins with the potential for both DGC and PDE activities revealed potential activities for these proteins. This work presents a systems-level functional analysis of a family of signaling proteins in a tractable animal symbiont and will inform future efforts to characterize the roles of individual proteins during lifestyle transitions.
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Affiliation(s)
- Ruth Y. Isenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Chandler S. Holschbach
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
| | - Jing Gao
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mark J. Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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27
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Stehnach MR, Henshaw RJ, Floge SA, Guasto JS. Multiplexed microfluidic screening of bacterial chemotaxis. eLife 2023; 12:e85348. [PMID: 37486823 PMCID: PMC10365836 DOI: 10.7554/elife.85348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Microorganism sensing of and responding to ambient chemical gradients regulates a myriad of microbial processes that are fundamental to ecosystem function and human health and disease. The development of efficient, high-throughput screening tools for microbial chemotaxis is essential to disentangling the roles of diverse chemical compounds and concentrations that control cell nutrient uptake, chemorepulsion from toxins, and microbial pathogenesis. Here, we present a novel microfluidic multiplexed chemotaxis device (MCD) which uses serial dilution to simultaneously perform six parallel bacterial chemotaxis assays that span five orders of magnitude in chemostimulant concentration on a single chip. We first validated the dilution and gradient generation performance of the MCD, and then compared the measured chemotactic response of an established bacterial chemotaxis system (Vibrio alginolyticus) to a standard microfluidic assay. Next, the MCD's versatility was assessed by quantifying the chemotactic responses of different bacteria (Psuedoalteromonas haloplanktis, Escherichia coli) to different chemoattractants and chemorepellents. The MCD vastly accelerates the chemotactic screening process, which is critical to deciphering the complex sea of chemical stimuli underlying microbial responses.
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Affiliation(s)
- Michael R Stehnach
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Richard J Henshaw
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Sheri A Floge
- Department of Biology, Wake Forest University, Winston-Salem, United States
| | - Jeffrey S Guasto
- Department of Mechanical Engineering, Tufts University, Medford, United States
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28
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Peng M, Jiang Z, Zhou F, Wang Z. From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants. Front Microbiol 2023; 14:1169809. [PMID: 37426022 PMCID: PMC10327291 DOI: 10.3389/fmicb.2023.1169809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.
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Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Zhihui Jiang
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Fangzhen Zhou
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Zhiyong Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
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29
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Qi X, Zhang Y, Zhang Y, Luo F, Song K, Wang G, Ling F. Vitamin B 12 produced by Cetobacterium somerae improves host resistance against pathogen infection through strengthening the interactions within gut microbiota. MICROBIOME 2023; 11:135. [PMID: 37322528 PMCID: PMC10268390 DOI: 10.1186/s40168-023-01574-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Pathogen infections seriously affect host health, and the use of antibiotics increases the risk of the emergence of drug-resistant bacteria and also increases environmental and health safety risks. Probiotics have received much attention for their excellent ability to prevent pathogen infections. Particularly, explaining mechanism of action of probiotics against pathogen infections is important for more efficient and rational use of probiotics and the maintenance of host health. RESULTS Here, we describe the impacts of probiotic on host resistance to pathogen infections. Our findings revealed that (I) the protective effect of oral supplementation with B. velezensis against Aeromonas hydrophila infection was dependent on gut microbiota, specially the anaerobic indigenous gut microbe Cetobacterium; (II) Cetobacterium was a sensor of health, especially for fish infected with pathogenic bacteria; (III) the genome resolved the ability of Cetobacterium somerae CS2105-BJ to synthesize vitamin B12 de novo, while in vivo and in vitro metabolism assays also showed the ability of Cetobacterium somerae CS2105-BJ to produce vitamin B12; (IV) the addition of vitamin B12 significantly altered the gut redox status and the gut microbiome structure and function, and then improved the stability of the gut microbial ecological network, and enhanced the gut barrier tight junctions to prevent the pathogen infection. CONCLUSION Collectively, this study found that the effect of probiotics in enhancing host resistance to pathogen infections depended on function of B12 produced by an anaerobic indigenous gut microbe, Cetobacterium. Furthermore, as a gut microbial regulator, B12 exhibited the ability to strengthen the interactions within gut microbiota and gut barrier tight junctions, thereby improving host resistance against pathogen infection. Video Abstract.
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Affiliation(s)
- Xiaozhou Qi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yong Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yilin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Kaige Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Fei Ling
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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30
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Kong L, Zheng R, Feng Y, Du W, Xie C, Gu Y, Liu S. Anammox bacteria adapt to long-term light irradiation in photogranules. WATER RESEARCH 2023; 241:120144. [PMID: 37300965 DOI: 10.1016/j.watres.2023.120144] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/13/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Photogranules composed of algae, nitrifiers, and anammox bacteria are promising for nitrogen removal from wastewater with reduced aeration and carbon emissions. However, it is difficult to be achieved as the potential inhibition of anammox bacteria by light. In this study, a syntrophic algal-partial nitrification/anammox granular sludge process was developed, with a nitrogen removal rate of 294.5 mg N/(L·d). We found the symbiosis in the community promoted the adaptation of anammox bacteria under light, and cross-feeding played an important role. Microalgae in the outer layers of photogranules sheltered most of the light and supplied cofactors and amino acids to promote nitrogen removal. In particular, Myxococcota MYX1 degraded the extracellular proteins produced by microalgae, providing amino acids to the entire bacterial community, which helped anammox bacteria save metabolic energy and adapt to light. Notably, the anammox bacteria Candidatus Brocadia exhibited unique light-sensing potential and adaptations to light irradiation compared with Candidatus Jettenia, including diverse DNA repair, scavenging of reactive oxygen species, cell movement. The phytochrome-like proteins encoded by Candidatus Brocadia further facilitated their spatial positioning and niche partitioning in photogranules. This study provides insights into the response of anammox bacteria in the algae-bacteria symbiosis system and suggests its potential application for carbon-negative nitrogen removal.
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Affiliation(s)
- Lingrui Kong
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Ru Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Wenran Du
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Chen Xie
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yuanqi Gu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China.
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Cremin K, Duxbury SJN, Rosko J, Soyer OS. Formation and emergent dynamics of spatially organized microbial systems. Interface Focus 2023; 13:20220062. [PMID: 36789239 PMCID: PMC9912014 DOI: 10.1098/rsfs.2022.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 02/12/2023] Open
Abstract
Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.
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Affiliation(s)
- Kelsey Cremin
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Jerko Rosko
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Orkun S. Soyer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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32
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Tanabe Y, Yamaguchi H, Yoshida M, Kai A, Okazaki Y. Characterization of a bloom-associated alphaproteobacterial lineage, 'Candidatus Phycosocius': insights into freshwater algal-bacterial interactions. ISME COMMUNICATIONS 2023; 3:20. [PMID: 36906708 PMCID: PMC10008586 DOI: 10.1038/s43705-023-00228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/13/2023]
Abstract
Marine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage 'Candidatus Phycosocius' (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: 'Ca. Phycosocius spiralis.' Phylogenomic analyses indicated that the CaP clade is a deeply branching lineage in the Caulobacterales. Pangenome analyses revealed characteristic features of the CaP clade: aerobic anoxygenic photosynthesis and essential vitamin B auxotrophy. Genome size varies widely among members of the CaP clade (2.5-3.7 Mb), likely a result of independent genome reductions at each lineage. This includes a loss of tight adherence pilus genes (tad) in 'Ca. P. spiralis' that may reflect its adoption of a unique spiral cell shape and corkscrew-like burrowing activity at the algal surface. Notably, quorum sensing (QS) proteins showed incongruent phylogenies, suggesting that horizontal transfers of QS genes and QS-involved interactions with specific algal partners might drive CaP clade diversification. This study elucidates the ecophysiology and evolution of proteobacteria associated with freshwater algal blooms.
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Affiliation(s)
- Yuuhiko Tanabe
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, 305-8506, Japan.
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan.
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, 305-8506, Japan
| | - Masaki Yoshida
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Atsushi Kai
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
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Scarinci G, Sourjik V. Impact of direct physical association and motility on fitness of a synthetic interkingdom microbial community. THE ISME JOURNAL 2023; 17:371-381. [PMID: 36566339 PMCID: PMC9938286 DOI: 10.1038/s41396-022-01352-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Mutualistic exchange of metabolites can play an important role in microbial communities. Under natural environmental conditions, such exchange may be compromised by the dispersal of metabolites and by the presence of non-cooperating microorganisms. Spatial proximity between members during sessile growth on solid surfaces has been shown to promote stabilization of cross-feeding communities against these challenges. Nonetheless, many natural cross-feeding communities are not sessile but rather pelagic and exist in turbulent aquatic environments, where partner proximity is often achieved via direct cell-cell adhesion, and cooperation occurs between physically associated cells. Partner association in aquatic environments could be further enhanced by motility of individual planktonic microorganisms. In this work, we establish a model bipartite cross-feeding community between bacteria and yeast auxotrophs to investigate the impact of direct adhesion between prokaryotic and eukaryotic partners and of bacterial motility in a stirred mutualistic co-culture. We demonstrate that adhesion can provide fitness benefit to the bacterial partner, likely by enabling local metabolite exchange within co-aggregates, and that it counteracts invasion of the community by a non-cooperating cheater strain. In a turbulent environment and at low cell densities, fitness of the bacterial partner and its competitiveness against a non-cooperating strain are further increased by motility that likely facilitates partner encounters and adhesion. These results suggest that, despite their potential fitness costs, direct adhesion between partners and its enhancement by motility may play key roles as stabilization factors for metabolic communities in turbulent aquatic environments.
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Affiliation(s)
- Giovanni Scarinci
- grid.419554.80000 0004 0491 8361Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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Wisnoski NI, Lennon JT. Scaling up and down: movement ecology for microorganisms. Trends Microbiol 2023; 31:242-253. [PMID: 36280521 DOI: 10.1016/j.tim.2022.09.016] [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: 06/13/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at higher organizational levels, such as populations and communities. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements.
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Affiliation(s)
- Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, WY 82071, USA; Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Rhizobial migration toward roots mediated by FadL-ExoFQP modulation of extracellular long-chain AHLs. THE ISME JOURNAL 2023; 17:417-431. [PMID: 36627434 PMCID: PMC9938287 DOI: 10.1038/s41396-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Migration from rhizosphere to rhizoplane is a key selecting process in root microbiome assembly, but not fully understood. Rhizobiales members are overrepresented in the core root microbiome of terrestrial plants, and here we report a genome-wide transposon-sequencing of rhizoplane fitness genes of beneficial Sinorhizobium fredii on wild soybean, cultivated soybean, rice, and maize. There were few genes involved in broad-host-range rhizoplane colonization. The fadL mutant lacking a fatty acid transporter exhibited high colonization rates, while mutations in exoFQP (encoding membrane proteins directing exopolysaccharide polymerization and secretion), but not those in exo genes essential for exopolysaccharide biosynthesis, led to severely impaired colonization rates. This variation was not explainable by their rhizosphere and rhizoplane survivability, and associated biofilm and exopolysaccharide production, but consistent with their migration ability toward rhizoplane, and associated surface motility and the mixture of quorum-sensing AHLs (N-acylated-L-homoserine lactones). Genetics and physiology evidences suggested that FadL mediated long-chain AHL uptake while ExoF mediated the secretion of short-chain AHLs which negatively affected long-chain AHL biosynthesis. The fadL and exoF mutants had elevated and depleted extracellular long-chain AHLs, respectively. A synthetic mixture of long-chain AHLs mimicking that of the fadL mutant can improve rhizobial surface motility. When this AHL mixture was spotted into rhizosphere, the migration toward roots and rhizoplane colonization of S. fredii were enhanced in a diffusible way. This work adds novel parts managing extracellular AHLs, which modulate bacterial migration toward rhizoplane. The FadL-ExoFQP system is conserved in Alphaproteobacteria and may shape the "home life" of diverse keystone rhizobacteria.
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Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria. Nat Microbiol 2023; 8:510-521. [PMID: 36759754 DOI: 10.1038/s41564-023-01327-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023]
Abstract
Behaviours such as chemotaxis can facilitate metabolic exchanges between phytoplankton and heterotrophic bacteria, which ultimately regulate oceanic productivity and biogeochemistry. However, numerically dominant picophytoplankton have been considered too small to be detected by chemotactic bacteria, implying that cell-cell interactions might not be possible between some of the most abundant organisms in the ocean. Here we examined how bacterial behaviour influences metabolic exchanges at the single-cell level between the ubiquitous picophytoplankton Synechococcus and the heterotrophic bacterium Marinobacter adhaerens, using bacterial mutants deficient in motility and chemotaxis. Stable-isotope tracking revealed that chemotaxis increased nitrogen and carbon uptake of both partners by up to 4.4-fold. A mathematical model following thousands of cells confirmed that short periods of exposure to small but nutrient-rich microenvironments surrounding Synechococcus cells provide a considerable competitive advantage to chemotactic bacteria. These findings reveal that transient interactions mediated by chemotaxis can underpin metabolic relationships among the ocean's most abundant microorganisms.
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Duplicated Flagellins in Pseudomonas Divergently Contribute to Motility and Plant Immune Elicitation. Microbiol Spectr 2023; 11:e0362122. [PMID: 36629446 PMCID: PMC9927476 DOI: 10.1128/spectrum.03621-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Flagellins are the main constituents of the flagellar filaments that provide bacterial motility, chemotactic ability, and host immune elicitation ability. Although the functions of flagellins have been extensively studied in bacteria with a single flagellin-encoding gene, the function of multiple flagellin-encoding genes in a single bacterial species is largely unknown. Here, the model plant-growth-promoting bacterium Pseudomonas kilonensis F113 was used to decipher the divergent functions of duplicated flagellins. We demonstrate that the two flagellins (FliC-1 and FliC-2) in 12 Pseudomonas strains, including F113, are evolutionarily distinct. Only the fliC-1 gene but not the fliC-2 gene in strain F113 is responsible for flagellar biogenesis, motility, and plant immune elicitation. The transcriptional expression of fliC-2 was significantly lower than that of fliC-1 in medium and in planta, most likely due to variations in promoter activity. In silico prediction revealed that all fliC-2 genes in the 12 Pseudomonas strains have a poorly conserved promoter motif. Compared to the Flg22-2 epitope (relative to FliC-2), Flg22-1 (relative to FliC-1) induced stronger FLAGELLIN SENSING 2 (FLS2)-mediated microbe-associated molecular pattern-triggered immunity and significantly inhibited plant root growth. A change in the 19th amino acid in Flg22-2 reduced its binding affinity to the FLS2/brassinosteroid insensitive 1-associated kinase 1 complex. Also, Flg22-2 epitopes in the other 11 Pseudomonas strains were presumed to have low binding affinity due to the same change in the 19th amino acid. These findings suggest that Pseudomonas has evolved duplicate flagellins, with only FliC-1 contributing to motility and plant immune elicitation. IMPORTANCE Flagellins have emerged as important microbial patterns. This work focuses on flagellin duplication in some plant-associated Pseudomonas. Our findings on the divergence of duplicated flagellins provide a conceptual framework for better understanding the functional determinant flagellin and its peptide in multiple-flagellin plant-growth-promoting rhizobacteria.
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Synergy between microalgae and microbiome in polluted waters. Trends Microbiol 2023; 31:9-21. [PMID: 35985939 DOI: 10.1016/j.tim.2022.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.
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Ganesan R, Wierz JC, Kaltenpoth M, Flórez LV. How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts. Microbiol Mol Biol Rev 2022; 86:e0012621. [PMID: 36301103 PMCID: PMC9769632 DOI: 10.1128/mmbr.00126-21] [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] [Indexed: 01/01/2023] Open
Abstract
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.
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Affiliation(s)
- Ramya Ganesan
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jürgen C. Wierz
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Plant and Environmental Sciences, Section for Organismal Biology, University of Copenhagen, Copenhagen, Denmark
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40
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Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [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: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
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Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
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41
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Mars Brisbin M, Mitarai S, Saito MA, Alexander H. Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes. THE ISME JOURNAL 2022; 16:2255-2264. [PMID: 35764675 PMCID: PMC9381791 DOI: 10.1038/s41396-022-01263-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/11/2022] [Accepted: 05/31/2022] [Indexed: 05/29/2023]
Abstract
Phaeocystis is a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms, Phaeocystis species produce large carbon-rich colonies, creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton-e.g., they promote growth by producing phytohormones and vitamins-such interactions have not been shown for Phaeocystis. Therefore, we investigated the composition and function of P. globosa microbiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from four P. globosa strains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affect P. globosa growth under limiting conditions. Results illuminated a core colonial P. globosa microbiome-including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales-that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative that P. globosa microbiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions between Phaeocystis and bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals symbiotic and opportunistic interactions between Phaeocystis colonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.
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Affiliation(s)
- Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan.
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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43
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Motility Suppression and Trapping Bacteria by ZnO Nanostructures. CRYSTALS 2022. [DOI: 10.3390/cryst12081027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regulating the swimming motility of bacteria near surfaces is essential to suppress or avoid bacterial contamination and infection in catheters and medical devices with wall surfaces. However, the motility of bacteria near walls strongly depends on the combination of the local physicochemical properties of the surfaces. To unravel how nanostructures and their local chemical microenvironment dynamically affect the bacterial motility near surfaces, here, we directly visualize the bacterial swimming and systematically analyze the motility of Escherichia coli swimming on ZnO nanoparticle films and nanowire arrays with further ultraviolet irradiation. The results show that the ZnO nanowire arrays reduce the swimming motility, thus significantly enhancing the trapping ability for motile bacteria. Additionally, thanks to the wide bandgap nature of a ZnO semiconductor, the ultraviolet irradiation rapidly reduces the bacteria locomotion due to the hydroxyl and singlet oxygen produced by the photodynamic effects of ZnO nanowire arrays in an aqueous solution. The findings quantitatively reveal how the combination of geometrical nanostructured surfaces and local tuning of the steric microenvironment are able to regulate the motility of swimming bacteria and suggest the efficient inhibition of bacterial translocation and infection by nanostructured coatings.
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Renoz F, Ambroise J, Bearzatto B, Fakhour S, Parisot N, Ribeiro Lopes M, Gala JL, Calevro F, Hance T. The Di-Symbiotic Systems in the Aphids Sipha maydis and Periphyllus lyropictus Provide a Contrasting Picture of Recent Co-Obligate Nutritional Endosymbiosis in Aphids. Microorganisms 2022; 10:microorganisms10071360. [PMID: 35889078 PMCID: PMC9317480 DOI: 10.3390/microorganisms10071360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Dependence on multiple nutritional bacterial symbionts forming a metabolic unit has repeatedly evolved in many insect species that feed on nutritionally unbalanced diets such as plant sap. This is the case for aphids of the subfamilies Lachninae and Chaitophorinae, which have evolved di-symbiotic systems in which the ancient obligate nutritional symbiont Buchnera aphidicola is metabolically complemented by an additional nutritional symbiont acquired more recently. Deciphering how different symbionts integrate both metabolically and anatomically in such systems is crucial to understanding how complex nutritional symbiotic systems function and evolve. In this study, we sequenced and analyzed the genomes of the symbionts B. aphidicola and Serratia symbiotica associated with the Chaitophorinae aphids Sipha maydis and Periphyllus lyropictus. Our results show that, in these two species, B. aphidicola and S. symbiotica complement each other metabolically (and their hosts) for the biosynthesis of essential amino acids and vitamins, but with distinct metabolic reactions supported by each symbiont depending on the host species. Furthermore, the S. symbiotica symbiont associated with S. maydis appears to be strictly compartmentalized into the specialized host cells housing symbionts in aphids, the bacteriocytes, whereas the S. symbiotica symbiont associated with P. lyropictus exhibits a highly invasive phenotype, presumably because it is capable of expressing a larger set of virulence factors, including a complete flagellum for bacterial motility. Such contrasting levels of metabolic and anatomical integration for two S. symbiotica symbionts that were recently acquired as nutritional co-obligate partners reflect distinct coevolutionary processes specific to each association.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, Université Catholique de Louvain (UCLouvain), 1348 Louvain-la-Neuve, Belgium;
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, F-69621 Villeurbanne, France; (N.P.); (M.R.L.); (F.C.)
- Correspondence:
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), 1200 Woluwe-Saint-Lambert, Belgium; (J.A.); (B.B.); (J.-L.G.)
| | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), 1200 Woluwe-Saint-Lambert, Belgium; (J.A.); (B.B.); (J.-L.G.)
| | - Samir Fakhour
- Department of Plant Protection, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, Rabat 10090, Morocco;
| | - Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, F-69621 Villeurbanne, France; (N.P.); (M.R.L.); (F.C.)
| | - Mélanie Ribeiro Lopes
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, F-69621 Villeurbanne, France; (N.P.); (M.R.L.); (F.C.)
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), 1200 Woluwe-Saint-Lambert, Belgium; (J.A.); (B.B.); (J.-L.G.)
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, F-69621 Villeurbanne, France; (N.P.); (M.R.L.); (F.C.)
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, Université Catholique de Louvain (UCLouvain), 1348 Louvain-la-Neuve, Belgium;
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45
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Lynch JB, James N, McFall-Ngai M, Ruby EG, Shin S, Takagi D. Transitioning to confined spaces impacts bacterial swimming and escape response. Biophys J 2022; 121:2653-2662. [PMID: 35398019 PMCID: PMC9300662 DOI: 10.1016/j.bpj.2022.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/28/2021] [Accepted: 04/05/2022] [Indexed: 11/02/2022] Open
Abstract
Symbiotic bacteria often navigate complex environments before colonizing privileged sites in their host organism. Chemical gradients are known to facilitate directional taxis of these bacteria, guiding them toward their eventual destination. However, less is known about the role of physical features in shaping the path the bacteria take and defining how they traverse a given space. The flagellated marine bacterium Vibrio fischeri, which forms a binary symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, must navigate tight physical confinement during colonization, squeezing through a tissue bottleneck constricting to ∼2 μm in width on the way to its eventual home. Using microfluidic in vitro experiments, we discovered that V. fischeri cells alter their behavior upon entry into confined space, straightening their swimming paths and promoting escape from confinement. Using a computational model, we attributed this escape response to two factors: reduced directional fluctuation and a refractory period between reversals. Additional experiments in asymmetric capillary tubes confirmed that V. fischeri quickly escape from confined ends, even when drawn into the ends by chemoattraction. This avoidance was apparent down to a limit of confinement approaching the diameter of the cell itself, resulting in a balance between chemoattraction and evasion of physical confinement. Our findings demonstrate that nontrivial distributions of swimming bacteria can emerge from simple physical gradients in the level of confinement. Tight spaces may serve as an additional, crucial cue for bacteria while they navigate complex environments to enter specific habitats.
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Affiliation(s)
- Jonathan B Lynch
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawai'i.
| | - Nicholas James
- Department of Cell and Molecular Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Margaret McFall-Ngai
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Edward G Ruby
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Sangwoo Shin
- Department of Mechanical Engineering, University of Hawai'i at Mānoa, Honolulu, Hawai'i; Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, New York
| | - Daisuke Takagi
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawai'i; Department of Mechanical Engineering, University of Hawai'i at Mānoa, Honolulu, Hawai'i; Department of Mathematics, University of Hawai'i at Mānoa, Honolulu, Hawai'i
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46
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Ishikawa T. Bacterial behaviors in confined diorama environments. Biophys J 2022; 121:2487-2489. [PMID: 35690064 DOI: 10.1016/j.bpj.2022.05.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/02/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022] Open
Affiliation(s)
- Takuji Ishikawa
- Department of Biomedical Engineering, Tohoku University, Sendai, Japan.
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Bioactive Compounds for Quorum Sensing Signal-Response Systems in Marine Phycosphere. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10050699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Quorum sensing in the phycosphere refers to a sensor system in which bacteria secrete bioactive compounds to coordinate group behavior relying on cell density. It is an important way for algae and bacteria to communicate with each other and achieve interactions. It has been determined that quorum sensing is widely presented in the marine phycosphere, which involves a variety of bioactive compounds. Focused on these compounds in marine phycosphere, this review summarizes the types and structures of the compounds, describes the methods in detection and functional evaluation, discusses the ecological functions regulated by the compounds, such as modulating microbial colonization, achieving algae–bacteria mutualism or competition and contributing to marine biogeochemical cycles. Meanwhile, the application prospects of the compounds are also proposed, including controlling harmful algal blooms and producing biofuel. Future research should focus on improving detection techniques, developing more model systems and investigating the effects of climate change on the quorum-sensing pathway to further understand the mechanism and application potential of quorum sensing compounds. This review aims to present an overview of current research carried out in order to provide the reader with perspective on bioactive compounds involved in quorum sensing.
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48
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Du B, Wang S, Chen G, Wang G, Liu L. Nutrient starvation intensifies chlorine disinfection-stressed biofilm formation. CHEMOSPHERE 2022; 295:133827. [PMID: 35122818 DOI: 10.1016/j.chemosphere.2022.133827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/09/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Bacterial surface attachment and subsequent biofilm expansion represent an essential adaptation to environmental signals and stresses, which are of great concern for many natural and engineered ecosystems. Yet the underlying mechanisms and driving forces of biofilm formation in a chlorinated and nutrient-restricted system remain sketchy. In this study, we coupled an experimental investigation and modeling simulation to understand how chlorination and nutrient limitation conspire to form biofilm using Pseudomonas aeruginosa as a model bacterium. Experimental results showed that moderate chlorination at 1.0 mg/L led to biofilm development amplified to 2.6 times of those without chlorine, while additional nutrient limitation (of 1/50-diluted or 0.4 g/L LB broth culture) achieved 4.6 times increment as compared to those of undiluted scenarios (of 20 g/L LB broth culture) with absence of chlorination after 24 h exposure. Meanwhile, intermediate chlorination stimulated instant flagellar motility and subsequently extracellular polymeric substances (EPS) secretion, particularly under limited nutrient condition (of 1/50-diluted or 0.4 g/L LB broth culture) that retarded chlorine consumption and provoked bacterial nutrient-limitation response. From our simulations, chlorine and resource levels along with associated spatio-temporal variations collectively drove bacterial cell movement and EPS excretion. Our results demonstrated that restraining nutrient intensified chlorination-excited cell movement and EPS production that reinforced biological and cell-surface interactions, thereby encouraging bacterial surface attachment and subsequent biofilm development. The findings provide the insights into the linkage of disinfectant and nutrient-regulated bacterial functional responses with consequent micro-habitats and biofilm dynamics.
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Affiliation(s)
- Bang Du
- School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shudong Wang
- School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Guowei Chen
- School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Gang Wang
- Department of Soil and Water Sciences, China Agricultural University, Beijing, 100193, China
| | - Li Liu
- School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China.
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49
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Raina JB, Lambert BS, Parks DH, Rinke C, Siboni N, Bramucci A, Ostrowski M, Signal B, Lutz A, Mendis H, Rubino F, Fernandez VI, Stocker R, Hugenholtz P, Tyson GW, Seymour JR. Chemotaxis shapes the microscale organization of the ocean's microbiome. Nature 2022; 605:132-138. [PMID: 35444277 DOI: 10.1038/s41586-022-04614-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/04/2022] [Indexed: 01/04/2023]
Abstract
The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1-3, but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.
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Affiliation(s)
- Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Bennett S Lambert
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Center for Environmental Genomics, School of Oceanography, University of Washington, Seattle, WA, USA.,Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Anna Bramucci
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Martin Ostrowski
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Brandon Signal
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Adrian Lutz
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Himasha Mendis
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Francesco Rubino
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Vicente I Fernandez
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.,Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia.
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50
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King WL, Kaminsky LM, Richards SC, Bradley BA, Kaye JP, Bell TH. Farm-scale differentiation of active microbial colonizers. ISME COMMUNICATIONS 2022; 2:39. [PMID: 37938671 PMCID: PMC9723676 DOI: 10.1038/s43705-022-00120-9] [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: 12/10/2021] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 06/17/2023]
Abstract
Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Brosi A Bradley
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Kaye
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
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