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Pham TT, Nguyen TD, Nguyen TT, Pham MN, Nguyen PT, Nguyen TUT, Huynh TTN, Nguyen HT. Rhizosphere bacterial exopolysaccharides: composition, biosynthesis, and their potential applications. Arch Microbiol 2024; 206:388. [PMID: 39196410 DOI: 10.1007/s00203-024-04113-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 08/29/2024]
Abstract
Bacterial exopolysaccharides (EPS) are biopolymers of carbohydrates, often released from cells into the extracellular environment. Due to their distinctive physicochemical properties, biocompatibility, biodegradability, and non-toxicity, EPS finds applications in various industrial sectors. However, the need for alternative EPS has grown over the past few decades as lactic acid bacteria's (LAB) low-yield EPS is unable to meet the demand. In this case, rhizosphere bacteria with the diverse communities in soil leading to variations in composition and structure, are recognized as a potential source of EPS applicable in various industries. In addition, media components and cultivation conditions have an impact on EPS production, which ultimately affects the quantity, structure, and biological functions of the EPS. Therefore, scientists are currently working on manipulating bacterial EPS by developing cultures and applying abiotic and biotic stresses, so that better production of exopolysaccharides can be attained. This review highlights the composition, biosynthesis, and effects of environmental factors on EPS production along with the potential applications in different fields of industry. Ultimately, an overview of potential future paths and tactics for improving EPS implementation and commercialization is pointed out.
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Affiliation(s)
| | | | - Thi-Tho Nguyen
- Hutech Institute of Applied Science, HUTECH University, Ho Chi Minh City, Vietnam.
| | - Minh-Nhut Pham
- Hutech Institute of Applied Science, HUTECH University, Ho Chi Minh City, Vietnam
| | - Phu-Tho Nguyen
- An Giang University, An Giang, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - To-Uyen Thi Nguyen
- Graduate University of Sciences and Technology, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | | | - Huu-Thanh Nguyen
- An Giang University, An Giang, Vietnam.
- Vietnam National University, Ho Chi Minh City, Vietnam.
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Valenzuela JJ, Immanuel SRC, Wilson J, Turkarslan S, Ruiz M, Gibbons SM, Hunt KA, Stopnisek N, Auer M, Zemla M, Stahl DA, Baliga NS. Origin of biogeographically distinct ecotypes during laboratory evolution. Nat Commun 2024; 15:7451. [PMID: 39198408 PMCID: PMC11358416 DOI: 10.1038/s41467-024-51759-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
Resource partitioning is central to the incredible productivity of microbial communities, including gigatons in annual methane emissions through syntrophic interactions. Previous work revealed how a sulfate reducer (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification in a planktonic context, improving stability, cooperativity, and productivity within 300-1000 generations. Here, we show that mutations in just 15 Dv and 7 Mm genes within a minimal assemblage of this evolved community gave rise to co-existing ecotypes that were spatially enriched within a few days of culturing in a fluidized bed reactor. The spatially segregated communities partitioned resources in the simulated subsurface environment, with greater lactate utilization by attached Dv but partial utilization of resulting H2 by low affinity hydrogenases of Mm in the same phase. The unutilized H2 was scavenged by high affinity hydrogenases of planktonic Mm, producing copious amounts of methane. Our findings show how a few mutations can drive resource partitioning amongst niche-differentiated ecotypes, whose interplay synergistically improves productivity of the entire mutualistic community.
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Affiliation(s)
| | | | - James Wilson
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Maryann Ruiz
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- eScience Institute, University of Washington, Seattle, WA, 98195, USA
| | - Kristopher A Hunt
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Nejc Stopnisek
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Manfred Auer
- Department of Biomedical Engineering, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Marcin Zemla
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Biology, University of Washington, Seattle, WA, USA.
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
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3
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Zhao Y, Liang H, Zhang J, Chen Y, Dhital YP, Zhao T, Wang Z. Isolation and Characterization of Potassium-Solubilizing Rhizobacteria (KSR) Promoting Cotton Growth in Saline-Sodic Regions. Microorganisms 2024; 12:1474. [PMID: 39065241 PMCID: PMC11279176 DOI: 10.3390/microorganisms12071474] [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: 06/19/2024] [Revised: 07/06/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Cotton is highly sensitive to potassium, and Xinjiang, China's leading cotton-producing region, faces a severe challenge due to reduced soil potassium availability. Biofertilizers, particularly potassium-solubilizing rhizobacteria (KSR), convert insoluble potassium into plant-usable forms, offering a sustainable solution for evergreen agriculture. This study isolated and characterized KSR from cotton, elucidated their potassium solubilization mechanisms, and evaluated the effects of inoculating KSR strains on cotton seedlings. Twenty-three KSR strains were isolated from cotton rhizosphere soil using modified Aleksandrov medium. Their solubilizing capacities were assessed in a liquid medium. Strain A10 exhibited the highest potassium solubilization capacity (21.8 ppm) by secreting organic acids such as lactic, citric, acetic, and succinic acid, lowering the pH and facilitating potassium release. A growth curve analysis and potassium solubilization tests of A10 under alkali stress showed its vigorous growth and maintained solubilization ability at pH 8-9, with significant inhibition at pH 10. Furthermore, 16S rRNA sequencing identified strain A10 as Pseudomonas aeruginosa. Greenhouse pot experiments showed that inoculating cotton plants with strain A10 significantly increased plant height and promoted root growth. This inoculation also enhanced dry biomass accumulation in both the aerial parts and root systems of the plants, while reducing the root-shoot ratio. These results suggest that Pseudomonas aeruginosa A10 has potential as a biofertilizer, offering a new strategy for sustainable agriculture.
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Affiliation(s)
- Yue Zhao
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
| | - Hongbang Liang
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
| | - Jihong Zhang
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
| | - Yu Chen
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
| | - Yam Prasad Dhital
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
| | - Tao Zhao
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
| | - Zhenhua Wang
- College of Water Conservancy & Architectural Engineering, Shihezi University, Shihezi 832000, China; (Y.Z.); (H.L.); (J.Z.); (Y.C.); (Y.P.D.); (T.Z.)
- Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production & Construction Group, Shihezi University, Shihezi 832000, China
- Technology Innovation Center for Agricultural Water & Fertilizer Efficiency Equipment of Xinjiang Production & Construction Group, Shihezi 832000, China
- Key Laboratory of Northwest Oasis Water-Saving Agriculture, Ministry of Agriculture and Rural Affairs, Shihezi 832000, China
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Ji G, Huan C, Zeng Y, Lyu Q, Du Y, Liu Y, Xu L, He Y, Tian X, Yan Z. Microbiologically induced calcite precipitation (MICP) in situ remediated heavy metal contamination in sludge nutrient soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134600. [PMID: 38759409 DOI: 10.1016/j.jhazmat.2024.134600] [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: 02/21/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024]
Abstract
Microbiologically induced calcite precipitation (MICP), as a newly developing bioremediation technology, could redeem heavy metal contamination in diverse scenarios. In this study, MICP bacterium Sporosarcina ureilytica ML-2 was employed to suppress the pollution of Pb, Cd and Zn in municipal sludge nutrient soil. After MICP remediation, the exchangeable Cd and Zn in sludge nutrient soil were correspondingly reduced by 31.02 % and 6.09 %, while the carbonate-bound Pb, Cd and Zn as well as the residual fractions were increased by 16.12 %, 6.63 %, 13.09 % and 6.10 %, 45.70 %, 3.86 %, respectively. In addition, the extractable Pb, Cd and Zn either by diethylenetriaminepentaacetic acid (DTPA) or toxicity characteristic leaching procedure (TCLP) in sludge nutrient soil were significantly reduced. These results demonstrated that the bio-calcite generated via MICP helped to immobilize heavy metals. Furthermore, MICP treatment improved the abundance of functional microorganisms related to urea cycle, while reduced the overall abundance of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). This work confirmed the feasibility of MICP in remediation of heavy metal in sludge nutrient soil, which expanded the application field of MICP and provided a promising way for heavy metal pollution management.
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Affiliation(s)
- Gaosheng Ji
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Chenchen Huan
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang'an University, Xi'an, Shanxi Province 710064, China
| | - Yong Zeng
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Qingyang Lyu
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Yaling Du
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Xu
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Yue He
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; College of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Xueping Tian
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| | - Zhiying Yan
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
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Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 PMCID: PMC11237642 DOI: 10.1128/cmr.00104-23] [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] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
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Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Arabani M, Shalchian MM, Baghbani A. A state-of-the-art review on interactive mechanisms and multi-scale application of biopolymers (BPs) in geo-improvement and vegetation growth. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120905. [PMID: 38643623 DOI: 10.1016/j.jenvman.2024.120905] [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: 02/15/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/23/2024]
Abstract
The global trend toward sustainable development, coupled with growing concerns about environmental pollution and the depletion of fossil energy resources, has contributed to the widespread implementation of biopolymers (BPs) as bio-solutions for geo-infrastructures stabilization. In this respect, previous attempts proved that soil treatment with BP can guarantee the strength improvement of geo-materials by satisfying environmental standards. However, the applications, mechanisms, and interactions of BPs within geo-environments need more investigations on their suitability for specific sites, long-term durability, and economic viability. The present study aims to provide an in-depth and up-to-date analysis of BPs and outline potential future paths toward BP applications. To this end, after examining the process of producing BPs, we investigate bio-physicochemical behavior and their function mechanism within the soil matrix. In addition, the impact of environmental conditions on soil stabilization with BPs is evaluated. Finally, some recommendations are offered for selecting the types and doses of BPs to improve soil against erosion and to obtain high hydrodynamic resistance. The results outline that bio-chemical mechanisms (including bio-cementing, bio-clogging, bio-encapsulation, and bio-coating) play significant roles in stabilizing cohesive and non-cohesive soil properties. Besides, the findings suggest that the efficacy of BPs depends upon various factors, including the composition and concentration of BPs, soil characteristics, and the magnitude of electrostatic and van der Waals forces formed during bio-chemo-reaction, biocrystallization, and bio-gel production. Between various BPs, using Xanthan gum (XG) and Guar gum (GG) exhibited optimal efficacy, enhancing mechanical strength by up to 300%. Furthermore, BPs concurrently reduced permeability, erosion, compressibility, and shrinkage characteristics. Applying BPs in soils improves germination and vegetation growth, lowers the wilting rate, and reduces soil acidity (considering their natural origin). Overall, selecting suitable BPs was found to be dependent on key factors, including temperature, curing time, and pH. The findings from this study can provide a scientific foundation for planning, constructing and preserving of bio-geo-structures in various construction sites.
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Affiliation(s)
- Mahyar Arabani
- Department of Civil Engineering, University of Guilan, Rasht, Iran.
| | - Mohammad Mahdi Shalchian
- Department of Civil Engineering, University of Guilan, Rasht, Iran; Geotechnical Engineering, University of Guilan, Rasht, Iran.
| | - Abolfazl Baghbani
- Department of Civil Engineering, University of Guilan, Rasht, Iran; Geotechnical Engineering, 3School of Engineering, Deakin University, 3216, VIC, Australia.
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Kulkarni OS, Mazumder M, Kini S, Hill ED, Aow JSB, Phua SML, Elejalde U, Kjelleberg S, Swarup S. Volatile methyl jasmonate from roots triggers host-beneficial soil microbiome biofilms. Nat Chem Biol 2024; 20:473-483. [PMID: 37957272 PMCID: PMC10972745 DOI: 10.1038/s41589-023-01462-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 09/28/2023] [Indexed: 11/15/2023]
Abstract
The rhizosphere is a niche surrounding plant roots, where soluble and volatile molecules mediate signaling between plants and the associated microbiota. The preferred lifestyle of soil microorganisms is in the form of biofilms. However, less is known about whether root volatile organic compounds (rVOCs) can influence soil biofilms beyond the 2-10 mm rhizosphere zone influenced by root exudates. We report that rVOCs shift the microbiome composition and growth dynamics of complex soil biofilms. This signaling is evolutionarily conserved from ferns to higher plants. Methyl jasmonate (MeJA) is a bioactive signal of rVOCs that rapidly triggers both biofilm and microbiome changes. In contrast to the planktonic community, the resulting biofilm community provides ecological benefits to the host from a distance via growth enhancement. Thus, a volatile host defense signal, MeJA, is co-opted for assembling host-beneficial biofilms in the soil microbiota and extending the sphere of host influence in the rhizosphere.
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Affiliation(s)
- Omkar S Kulkarni
- Singapore Centre for Environmental Life Science Engineering (SCELSE), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Mrinmoy Mazumder
- Singapore Centre for Environmental Life Science Engineering (SCELSE), Singapore, Singapore
| | - Shruthi Kini
- Wilmar Innovation Center, Wilmar International Ltd., Singapore, Singapore
| | - Eric D Hill
- Singapore Centre for Environmental Life Science Engineering (SCELSE), Singapore, Singapore
| | - Johanan Shao Bing Aow
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Samantha Mun Lin Phua
- Singapore Centre for Environmental Life Science Engineering (SCELSE), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Untzizu Elejalde
- Wilmar Innovation Center, Wilmar International Ltd., Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Science Engineering (SCELSE), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Biological, Earth Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
| | - Sanjay Swarup
- Singapore Centre for Environmental Life Science Engineering (SCELSE), Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- NUS Environmental Research Institute, Singapore, Singapore.
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Pathak D, Suman A, Sharma P, Aswini K, Govindasamy V, Gond S, Anshika R. Community-forming traits play role in effective colonization of plant-growth-promoting bacteria and improved plant growth. FRONTIERS IN PLANT SCIENCE 2024; 15:1332745. [PMID: 38533409 PMCID: PMC10963436 DOI: 10.3389/fpls.2024.1332745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
Community-forming traits (CFts) play an important role in the effective colonization of plant-growth-promoting bacterial communities that influence host plants positively by modulating their adaptive functions. In this study, by considering plant-growth-promoting traits (PGPts) and community-forming traits (CFts), three communities were constructed, viz., SM1 (PGPts), SM2 (CFts), and SM3 (PGPts+CFts). Each category isolates were picked up on the basis of their catabolic diversity of different carbon sources. Results revealed a distinctive pattern in the colonization of the communities possessed with CF traits. It was observed that the community with CFts colonized inside the plant in groups or in large aggregations, whereas the community with only PGPts colonized as separate individual and small colonies inside the plant root and leaf. The effect of SM3 in the microcosm experiment was more significant than the uninoculated control by 22.12%, 27.19%, and 9.11% improvement in germination percentage, chlorophyll content, and plant biomass, respectively. The significant difference shown by the microbial community SM3 clearly demonstrates the integrated effect of CFts and PGPts on effective colonization vis-à-vis positive influence on the host plant. Further detailed characterization of the interaction will take this technology ahead in sustainable agriculture.
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Affiliation(s)
| | - Archna Suman
- Division of Microbiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Zhang B, Zhang J, Wang Y, Qu J, Jiang Z, Zhang X, Tao Y, Wang Y, Kang Z, Han S, Zhang J, Zhang Y. Biodegradation of atrazine with biochar-mediated functional bacterial biofilm: Construction, characterization and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133237. [PMID: 38113741 DOI: 10.1016/j.jhazmat.2023.133237] [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: 09/20/2023] [Revised: 11/05/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
The abuse and residue of herbicides in the black soil area had seriously affected the soil structure, function and crop growth, posing severe threats to agricultural soil environment and public health. Given the limitation of routine microbial remediation, innovative and eco-friendly functional bacterial biofilm which could adapt under adverse conditions was developed on the biochar to investigate its enhanced bioremediation and metabolic characteristics of typical herbicide atrazine. Results revealed that the atrazine degrading strain Acinetobacter lwoffii had competitive advantage in soil indigenous microorganisms and formed dense biofilms on the biochar which was beneficial to cell viability maintenance and aggregations. Metatranscriptomics and RT-qPCR analysis demonstrated that the biochar-mediated biofilm improved the frequency of intercellular communications through quorum sensing and two-component signal regulation systems, and enhanced the atrazine biodegradation efficiency through horizontal gene transfer in co-metabolism mode, providing important scientific basis for the biological remediation of farmland soil non-point source pollution.
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Affiliation(s)
- Bo Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jingdan Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yuping Wang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jianhua Qu
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhao Jiang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Xu Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yue Tao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yifan Wang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhonghui Kang
- Longjiang Environmental Protection Group Co.,Ltd., Harbin 150050, PR China
| | - Songting Han
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jingyi Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China.
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Huang XY, Ye XP, Hu YY, Tang ZX, Zhang T, Zhou H, Zhou T, Bai XL, Pi EX, Xie BH, Shi LE. Exopolysaccharides of Paenibacillus polymyxa: A review. Int J Biol Macromol 2024; 261:129663. [PMID: 38278396 DOI: 10.1016/j.ijbiomac.2024.129663] [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: 11/08/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of many metabolically active substances, including polypeptides, volatile organic compounds, phytohormone, hydrolytic enzymes, exopolysaccharide (EPS), etc. Due to the wide range of compounds that it produces, P. polymyxa has been extensively studied as a plant growth promoting bacterium which provides a direct benefit to plants through the improvement of N fixation from the atmosphere and enhancement of the solubilization of phosphorus and the uptake of iron in the soil, and phytohormones production. Among the metabolites from P. polymyxa, EPS exhibits many activities, for example, antioxidant, immunomodulating, anti-tumor and many others. EPS has various applications in food, agriculture, environmental protection. Particularly, in the field of sustainable agriculture, P. polymyxa EPS can be served as a biofilm to colonize microbes, and also can act as a nutrient sink on the roots of plants in the rhizosphere. Therefore, this paper would provide a comprehensive review of the advancements of diverse aspects of EPS from P. polymyxa, including the production, extraction, structure, biosynthesis, bioactivity and applications, etc. It would provide a direction for future research on P. polymyxa EPS.
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Affiliation(s)
- Xuan-Ya Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xin-Pei Ye
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yan-Yu Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Zhen-Xing Tang
- School of Culinary Art, Tourism College of Zhejiang, Hangzhou, Zhejiang 311231, China
| | - Tian Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Hai Zhou
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Ting Zhou
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xue-Lian Bai
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Er-Xu Pi
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Bing-Hua Xie
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
| | - Lu-E Shi
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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11
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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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12
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He F, Ma XK, Tu CK, Teng H, Shao X, Chen J, Hu MX. Lactobacillus reuteri biofilms formed on porous zein/cellulose scaffolds: Synbiotics to regulate intestinal microbiota. Int J Biol Macromol 2024; 262:130152. [PMID: 38365143 DOI: 10.1016/j.ijbiomac.2024.130152] [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: 10/08/2023] [Revised: 02/04/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Supplementing probiotics or indigestible carbohydrates is a usual strategy to prevent or revert unhealthy states of the gut by reshaping gut microbiota. One criterion that probiotics are efficacious is the capacity to survive in the gastrointestinal tract. Biofilm is the common growth mode of microorganisms with high tolerances toward harsh environments. Suitable scaffolds are crucial for successful biofilm culture and large-scale production of biofilm-phenotype probiotics. However, the role of scaffolds containing indigestible carbohydrates in biofilm formation has not been studied. In this study, porous zein/cellulose composite scaffolds provided nitrogen sources and carbon sources simultaneously at the solid/liquid interfaces, being beneficial to the biofilm formation of Lactobacillus reuteri. The biofilms showed 2.1-17.4 times higher tolerances in different gastrointestinal conditions. In human fecal fermentation, the biofilms combined with the zein/cellulose composite scaffolds act as the "synbiotics" positively modulating the gut microbiota and the short-chain fatty acids (SCFAs), where biofilms provide probiotics and scaffolds provide prebiotics. The "synbiotics" show a more positive regulation ability than planktonic L. reuteri, presenting potential applications in gut health interventions. These results provide an understanding of the synergistic effects of biofilm-phenotype probiotics and indigestible carbohydrates contained in the "synbiotics" in gut microbiota modulation.
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Affiliation(s)
- Fei He
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xue-Ke Ma
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Cheng-Kai Tu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Hui Teng
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xin Shao
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Jie Chen
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Meng-Xin Hu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.
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13
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Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [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: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
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Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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14
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Li Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167774. [PMID: 37848152 DOI: 10.1016/j.scitotenv.2023.167774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.
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Affiliation(s)
- Yujia Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai 602105, Tamil Nadu, India
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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15
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Lin D, Xu JY, Wang L, Du S, Zhu D. Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere. ENVIRONMENT INTERNATIONAL 2024; 183:108431. [PMID: 38217904 DOI: 10.1016/j.envint.2024.108431] [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: 09/18/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
Abstract
Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of a new environmental compartment, the plastisphere, which is a hotspot for the accumulation of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on the effects of long-term organic fertilizer application on the dispersal of ARGs and virulence factor genes (VFGs) in the plastisphere of farmland soil have been limited. Here, we performed a field culture experiment by burying nylon bags filled with MPs in paddy soil that had been treated with different fertilizers for over 30 years to explore the changes of ARGs and VFGs in soil plastisphere. Our results show that the soil plastisphere amplified the ARG and VFG pollution caused by organic fertilization by 1.5 and 1.4 times, respectively. And it also led to a 2.7-fold increase in the risk of horizontal gene transfer. Meanwhile, the plastisphere tended to promote deterministic process in the community assembly of HBPs, with an increase of 1.4 times. Network analysis found a significant correlation between ARGs, VFGs, and bacteria in plastisphere. Correlation analysis highlight the important role of mobile genetic elements (MGEs) and bacterial communities in shaping the abundance of ARGs and VFGs, respectively. Our findings provide new insights into the health risk associated with the soil plastisphere due ARGs and VFGs derived from organic fertilizers.
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Affiliation(s)
- Da Lin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jia-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Lu Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Shuai Du
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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16
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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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17
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Zhao G, Zhou J, Tian Y, Chen Q, Mao D, Zhu J, Huang X. Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122460. [PMID: 37634569 DOI: 10.1016/j.envpol.2023.122460] [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: 06/12/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.
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Affiliation(s)
- Guoqiang Zhao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Jing Zhou
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Yanning Tian
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Qifeng Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Dongmei Mao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Jianchun Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Xing Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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18
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Zhao Z, Sun Y, Wang H, Yu Q. Regulation of cadmium-induced biofilm formation by artificial polysaccharide-binding proteins for enhanced phytoremediation. CHEMOSPHERE 2023; 342:140156. [PMID: 37714481 DOI: 10.1016/j.chemosphere.2023.140156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/28/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023]
Abstract
Phytoremediation is an economic way to attenuate soil heavy metal pollution, but is frequently limited by its low pollutant-removing efficiency. Recently, we revealed the close relation between polysaccharide-based biofilm formation and cadmium removal. In this study, for improving the phytoremediation efficiency, an artificial polysaccharide-binding protein was designed by synthetic biology techniques to regulate biofilm formation. The artificial protein Syn contained two polysaccharide-binding domains from the Ruminococcus flavefaciens CttA and the Clostridium cellulolyticum CipC, preferentially binding polysaccharides exposed on both cadmium-treated bacteria and plant roots. Under cadmium stress, Syn remarkably promoted bacterial polysaccharide production from 99 mg/L to 237 mg/L, leading to 1.23-fold higher biofilm biomass. During treatment of the remediation plants with exogenous cadmium-capturing bacteria, Syn improved root biofilm formation, with the root surface polysaccharide contents increasing by 79%, and the Log10 CFU/g root increasing from 7.01 to 7.80. Meanwhile, Syn remodeled the rhizosphere microbiome, especially increasing the abundance of the bacterial groups involved in biofilm formation and stress tolerance, e.g., Pseudomonas, Enterobacter, etc. Consequently, Syn promoted plant cadmium adsorption, with the cadmium-removing efficiency increasing from 17.2% to 33.8%. This study sheds light on synthetic biology-based regulation of biofilm formation for enhanced phytoremediation.
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Affiliation(s)
- Zirun Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Ying Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Hairong Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
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19
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Li Y, Lu D, Xia Y, Xu X, Huang H, Mei X, Yang M, Li J, Zhu S, Liu Y, Zhang Z. Effects of allyl isothiocyanate fumigation on medicinal plant root knot disease control, plant survival, and the soil bacterial community. BMC Microbiol 2023; 23:278. [PMID: 37775764 PMCID: PMC10542678 DOI: 10.1186/s12866-023-02992-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/22/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Allyl isothiocyanate (AITC) is a natural product with high volatility that is used as a biofumigant to alleviate soil-borne plant diseases, and problems such as root knot nematodes (RKNs) that necessitate continuous cropping. However, little research has assessed the effects of AITC fumigation on medicinal plants. RESULTS AITC significantly reduced the population of RKNs in soil (p < 0.0001) and showed an excellent RKN disease control effect within 6 months after sowing Panax notoginseng (p < 0.0001). The seedling survival rate of 2-year-old P. notoginseng was approximately 1.7-fold higher after soil treatment with AITC (p = 0.1008). 16S rRNA sequencing indicated that the AITC treatment affected bacterial richness rather than diversity in consecutively cultivated (CC) soil. Furthermore, biomarkers with statistical differences between AITC-treated and untreated CC soil showed that Pirellulales (order), Pirellulaceae (family), Pseudomonadaceae (family), and Pseudomonas (genus) played important roles in the AITC-treated group. In addition, the microbiome functional phenotypes predicted using the BugBase tool suggested that AITC treatment is more conducive to improving CC soil through changes in the bacterial community structure. Crucially, our research also suggested that AITC soil treatment significantly increases soil organic matter (p = 0.0055), total nitrogen (p = 0.0054), and available potassium (p = 0.0373), which promotes the survival of a succeeding medicinal plant (Polygonatum kingianum). CONCLUSION AITC is an ecologically friendly soil treatment that affects the top 10 bacterial richness but not diversity. It could also provide a basis for a useful agricultural soil management measure to alleviate soil sickness.
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Affiliation(s)
- Yingbin Li
- Department of Pesticide Science, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Daqing Lu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yan Xia
- Department of Pesticide Science, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinjing Xu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinyue Mei
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jianqiang Li
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, 100193, China
| | - Shusheng Zhu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Zhiping Zhang
- Department of Horticulture, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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20
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Muñoz-Vega E, Schulz S, Rodriguez-Escales P, Behle V, Spada L, Vogel AL, Sanchez-Vila X, Schüth C. Role of Soil Biofilms in Clogging and Fate of Pharmaceuticals: A Laboratory-Scale Column Experiment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12398-12410. [PMID: 37558209 PMCID: PMC10448752 DOI: 10.1021/acs.est.3c02034] [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: 03/16/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
Contamination of groundwater with pharmaceutical active compounds (PhACs) increased over the last decades. Potential pathways of PhACs to groundwater include techniques such as irrigation, managed aquifer recharge, or bank filtration as well as natural processes such as losing streams of PhACs-loaded source waters. Usually, these systems are characterized by redox-active zones, where microorganisms grow and become immobilized by the formation of biofilms, structures that colonize the pore space and decrease the infiltration capacities, a phenomenon known as bioclogging. The goal of this work is to gain a deeper understanding of the influence of soil biofilms on hydraulic conductivity reduction and the fate of PhACs in the subsurface. For this purpose, we selected three PhACs with different physicochemical properties (carbamazepine, diclofenac, and metoprolol) and performed batch and column experiments using a natural soil, as it is and with the organic matter removed, under different biological conditions. We observed enhanced sorption and biodegradation for all PhACs in the system with higher biological activity. Bioclogging was more prevalent in the absence of organic matter. Our results differ from works using artificial porous media and thus reveal the importance of utilizing natural soils with organic matter in studies designed to assess the role of soil biofilms in bioclogging and the fate of PhACs in soils.
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Affiliation(s)
- Edinsson Muñoz-Vega
- Institute
of Applied Geosciences, Technische Universität
Darmstadt, Darmstadt 64287, Germany
| | - Stephan Schulz
- Institute
of Applied Geosciences, Technische Universität
Darmstadt, Darmstadt 64287, Germany
| | - Paula Rodriguez-Escales
- Department
of Civil and Environmental Engineering, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
- Hydrogeology
Group (UPC−CSIC), Barcelona 08034, Spain
| | - Vera Behle
- Department
of Civil and Environmental Engineering, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
| | - Lucas Spada
- Institute
for Atmospheric and Environmental Sciences, Goethe-University Frankfurt, Frankfurt
am Main 60438, Germany
| | - Alexander L. Vogel
- Institute
for Atmospheric and Environmental Sciences, Goethe-University Frankfurt, Frankfurt
am Main 60438, Germany
| | - Xavier Sanchez-Vila
- Department
of Civil and Environmental Engineering, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
- Hydrogeology
Group (UPC−CSIC), Barcelona 08034, Spain
| | - Christoph Schüth
- Institute
of Applied Geosciences, Technische Universität
Darmstadt, Darmstadt 64287, Germany
- Water
Resources Management Division, IWW Water
Centre, Mülheim
an der Ruhr 45476, Germany
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21
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Wu Y, Fu C, Peacock CL, Sørensen SJ, Redmile-Gordon MA, Xiao KQ, Gao C, Liu J, Huang Q, Li Z, Song P, Zhu Y, Zhou J, Cai P. Cooperative microbial interactions drive spatial segregation in porous environments. Nat Commun 2023; 14:4226. [PMID: 37454222 PMCID: PMC10349867 DOI: 10.1038/s41467-023-39991-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.
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Affiliation(s)
- Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Chengxia Fu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Caroline L Peacock
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marc A Redmile-Gordon
- Department of Environmental Horticulture, Royal Horticultural Society, Wisley, Surrey, GU23 6QB, UK
| | - Ke-Qing Xiao
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chunhui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jun Liu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Zixue Li
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyi Song
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, USA
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
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22
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Ahmad Ansari F, Ahmad I, Pichtel J. Synergistic effects of biofilm-producing PGPR strains on wheat plant colonization, growth and soil resilience under drought stress. Saudi J Biol Sci 2023; 30:103664. [PMID: 37213696 PMCID: PMC10193011 DOI: 10.1016/j.sjbs.2023.103664] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/23/2023] Open
Abstract
Drought stress substantially impedes crop productivity throughout the world. Microbial based approaches have been considered a potential possibility and are under study. Based on our prior screening examination, two distinct and novel biofilm-forming PGPR strains namely Bacillus subtilis-FAB1 and Pseudomonas azotoformans-FAP3 are encompassed in this research. Bacterial biofilm development on glass surface, microtiter plate and seedling roots were assessed and characterized quantitatively and qualitatively by light and scanning electron microscopy. Above two isolates were further evaluated for their consistent performance by inoculating on wheat plants in a pot-soil system under water stresses. Bacterial moderate tolerance to ten-day drought was recorded on the application of individual strains with wheat plants; however, the FAB1 + FAP3 consortium expressively improved wheat survival during drought. The strains FAB1 and FAP3 displayed distinct and multifunctional plant growth stimulating attributes as well as effective roots and rhizosphere colonization in combination which could provide sustained wheat growth during drought. FAB1 and FAP3-induced alterations cooperatively conferred improved plant drought tolerance by controlling physiological traits (gs, Ci, E, iWUE and PN), stress indicators (SOD, CAT, GR, proline and MDA content) and also maintained physico-chemical attributes and hydrolytic enzymes including DHA, urease, ALP, protease, ACP and β glucosidase in the soil. Our findings could support future efforts to enhance plant drought tolerance by engineering the rhizobacterial biofilms and associated attributes which requires in-depth exploration and exploiting potential native strains for local agricultural application.
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Affiliation(s)
- Firoz Ahmad Ansari
- Biofilm Research Lab., Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
- Corresponding author at: Department of Agricultural Microbiology Faculty of Agricultural Sciences AMU, Aligarh, India.
| | - Iqbal Ahmad
- Biofilm Research Lab., Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - John Pichtel
- Department of Environment, Geology and Natural Resources, Ball State University, Muncie, IN 47306, USA
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23
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Condinho M, Carvalho B, Cruz A, Pinto SN, Arraiano CM, Pobre V. The role of RNA regulators, quorum sensing and c-di-GMP in bacterial biofilm formation. FEBS Open Bio 2023; 13:975-991. [PMID: 35234364 PMCID: PMC10240345 DOI: 10.1002/2211-5463.13389] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/15/2022] [Accepted: 02/28/2022] [Indexed: 11/10/2022] Open
Abstract
Biofilms provide an ecological advantage against many environmental stressors, such as pH and temperature, making it the most common life-cycle stage for many bacteria. These protective characteristics make eradication of bacterial biofilms challenging. This is especially true in the health sector where biofilm formation on hospital or patient equipment, such as respirators, or catheters, can quickly become a source of anti-microbial resistant strains. Biofilms are complex structures encased in a self-produced polymeric matrix containing numerous components such as polysaccharides, proteins, signalling molecules, extracellular DNA and extracellular RNA. Biofilm formation is tightly controlled by several regulators, including quorum sensing (QS), cyclic diguanylate (c-di-GMP) and small non-coding RNAs (sRNAs). These three regulators in particular are fundamental in all stages of biofilm formation; in addition, their pathways overlap, and the significance of their role is strain-dependent. Currently, ribonucleases are also of interest for their potential role as biofilm regulators, and their relationships with QS, c-di-GMP and sRNAs have been investigated. This review article will focus on these four biofilm regulators (ribonucleases, QS, c-di-GMP and sRNAs) and the relationships between them.
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Affiliation(s)
- Manuel Condinho
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Beatriz Carvalho
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Adriana Cruz
- iBB‐Institute for Bioengineering and Biosciences (IBB)Instituto Superior TécnicoLisboaPortugal
- i4HB‐Institute for Health and BioeconomyInstituto Superior TécnicoLisboaPortugal
| | - Sandra N. Pinto
- iBB‐Institute for Bioengineering and Biosciences (IBB)Instituto Superior TécnicoLisboaPortugal
- i4HB‐Institute for Health and BioeconomyInstituto Superior TécnicoLisboaPortugal
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
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24
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Boubekri K, Soumare A, Lyamlouli K, Ouhdouch Y, Hafidi M, Kouisni L. Improving the efficiency of phosphate rocks combined with phosphate solubilizing Actinomycetota to increase wheat growth under alkaline and acidic soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1154372. [PMID: 37235036 PMCID: PMC10206120 DOI: 10.3389/fpls.2023.1154372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023]
Abstract
Low availability of phosphorus (P) in both acidic and alkaline soils is a major problem for sustainable improvement in wheat crops yield. Optimization of crops productivity can be achieved by increasing the bioavailability of P by phosphate solubilizing Actinomycetota (PSA). However, their effectiveness may vary with changing agro-climatic conditions. In this regard, a greenhouse experiment was conducted to assess the interaction inoculation of five potential PSA (P16-P18-BC3-BC10 and BC11) and RPs (RP1- RP2-RP3 and RP4) on the growth and yield of wheat crop in unsterilized P- deficient alkaline and acidic soils. Their performance was compared with single super phosphate (TSP) and reactive RP (BG4). The in-vitro tests showed that all PSA colonize wheat root and form a strong biofilm except Streptomyces anulatus strain P16. Our findings revealed that all PSA significantly improve the shoot/root dry weights, spike biomass, chlorophyll contents as well as nutrients uptake in plants fertilized with RP3 and RP4. However, the combined application of Nocardiopsis alba BC11 along with RP4 in alkaline soil, was effective in optimizing wheat yield attributes and improve the yield biomass up to 19.7% as compared to the triple superphosphate (TSP). This study supports the view that the inoculation with Nocardiopsis alba BC11 has a broad RP solubilization and could alleviate the agricultural losses due to P limitation in acidic and alkaline soils.
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Affiliation(s)
- Kenza Boubekri
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
- Laboratory of Microbial Biotechnologies Agrosciences and Environment (BioMAgE), Labelled Unit CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University (UCA), Marrakech, Morocco
| | - Abdoulaye Soumare
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
- Laboratory of Agroforestry and Ecology, Assane Seck University (UASZ-UFR ST), Ziguinchor, Senegal
| | - Karim Lyamlouli
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
- Laboratory of Microbial Biotechnologies Agrosciences and Environment (BioMAgE), Labelled Unit CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University (UCA), Marrakech, Morocco
| | - Yedir Ouhdouch
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
- Laboratory of Microbial Biotechnologies Agrosciences and Environment (BioMAgE), Labelled Unit CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University (UCA), Marrakech, Morocco
| | - Mohamed Hafidi
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
- Laboratory of Microbial Biotechnologies Agrosciences and Environment (BioMAgE), Labelled Unit CNRST N°4, Faculty of Sciences Semlalia, Cadi Ayyad University (UCA), Marrakech, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laayoune, Morocco
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25
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The effects of temperature, salt, and phosphate on biofilm and exopolysaccharide production by Azotobacter spp. Arch Microbiol 2023; 205:87. [PMID: 36781489 DOI: 10.1007/s00203-023-03428-9] [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: 12/06/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
Inoculation of agriculturally important biofilms to plants under stress conditions has been of great interest in recent years. Therefore, in this study, biofilm- and exopolysaccharide (EPS)-forming ability of Azotobacter spp. was examined under different temperatures, NaCl concentrations, and phosphate levels. Azotobacter strains formed varying levels of biofilm and EPS depending on the tested factors. The pattern of biofilm formation was similar to that of EPS production under the conditions tested. Biofilm and EPS production at 28 °C was consistently higher than at either 18 or 37 °C. Biofilm production significantly increased in A. chroococcum strains (SBS2, SBS4, and SBS12) and A. vinelandii SBS6 with increasing salinity. Furthermore, a strong negative correlation was observed between biofilm or EPS production and increasing phosphate concentrations. Higher phosphate concentrations decreased biofilm and EPS production. In conclusion, contrary to temperature and phosphate effect, salinity differently affected biofilm and EPS production by Azotobacter strains.
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26
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Duperron S, Foucault P, Duval C, Goto M, Gallet A, Colas S, Marie B. Multi-omics analyses from a single sample: prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types. FEMS Microbiol Lett 2023; 370:fnad125. [PMID: 37996396 DOI: 10.1093/femsle/fnad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Nontargeted metabolomics are a suitable tool to bridge this gap, yet extraction protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA gene sequencing after direct DNA extraction or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on nonaxenic cultures of cyanobacteria, lake water column, biofilm, and gut of wild and lab-reared fish indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.
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Affiliation(s)
- Sébastien Duperron
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Pierre Foucault
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
- UMR7618 iEES-Paris, Sorbonne Université, 4 place Jussieu, 75005 Paris, France
| | - Charlotte Duval
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Midoli Goto
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Alison Gallet
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Simon Colas
- Université de Pau et des Pays de l'Adour, E2S-UPPA, CNRS, IPREM, 2 Av. du Président Pierre Angot, 64053 Pau, France
| | - Benjamin Marie
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
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27
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Yan H, Liu C, Yu W, Zhu X, Chen B. The aggregate distribution of Pseudomonas aeruginosa on biochar facilitates quorum sensing and biofilm formation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159034. [PMID: 36167127 DOI: 10.1016/j.scitotenv.2022.159034] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Biochar when applied into soil, together with soil clay minerals, may provide habitats for soil microbes and shift soil microbial community structure. Although several mechanisms have been proposed to explain the effects of biochar on microbial community, the impact of biochar on quorum sensing (QS) and QS-regulated behavior is poorly understood. In this study, we compared the effects of biochar and three common soil minerals (i.e., montmorillonite, kaolinite, and goethite) on QS and biofilm formation. Pseudomonas aeruginosa PAO1 with complete QS systems was selected as a model organism. Our results showed that biochar and goethite effectively promoted microbial QS and biofilm formation, while montmorillonite and kaolinite posed no significant effect. Live/Dead staining, SEM and density-dependent QS activity indicated that biochar was beneficial to cell viability maintenance and cell aggregations, which improved the efficiency of intercellular communications through QS. QS mutant strain experiments confirmed that biochar enhanced PAO1 biofilm formation by promoting QS. Goethite promoted biofilm formation with a different mechanism that cell debris induced by iron ions and positive charge on goethite surface provided raw materials for bacterial biofilm formation. Our findings provide evidence that the presence of biochar can enhance QS and biofilm formation through a feedforward loop of the QS system. This contributes to better understand biochar-mediated microbial cell to cell communications through QS.
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Affiliation(s)
- Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
| | - Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
| | - Wentao Yu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
| | - Xiaomin Zhu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
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28
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Zeng Y, Chen Z, Lyu Q, Cheng Y, Huan C, Jiang X, Yan Z, Tan Z. Microbiologically induced calcite precipitation for in situ stabilization of heavy metals contributes to land application of sewage sludge. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129866. [PMID: 36063711 DOI: 10.1016/j.jhazmat.2022.129866] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Microbiologically induced calcite precipitation (MICP) has shed new light on solving the problem of in situ stabilization of heavy metals (HMs) in sewage sludge before land disposal. In this study, we examined whether MICP treatment can be integrated into a sewage sludge anaerobic digestion-land application process. Our results showed that MICP treatment not only prevented the transfer of ionic-state Cd from the sludge to the supernatant (98.46 % immobilization efficiency) but also reduced the soluble exchangeable Pb and Cd fractions by up to 100 % and 48.54 % and increased the residual fractions by 22.54 % and 81.77 %, respectively. In addition, the analysis of the stability of HMs in MICP-treated sludge revealed maximum reductions of 100 % and 89.56 % for TCLP-extractable Pb and Cd, respectively. Three-dimensional fluorescence, scanning electron microscopy-energy-dispersive X-ray spectroscopy, X-ray diffraction, and Fourier-transform infrared spectroscopy analyses confirmed the excellent performance of the ureolytic bacteria Sporosarcina ureilytica ML-2 in the sludge system. High-throughput sequencing showed that the relative abundance of Sporosarcina sp. reached 53.18 % in MICP-treated sludge, and the urease metabolism functional genes unit increased by a maximum of 239.3 %. The MICP technology may be a feasible method for permanently stabilizing HMs in sewage sludge before land disposal.
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Affiliation(s)
- Yong Zeng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China.
| | - Zezhi Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China.
| | - Qingyang Lyu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yapeng Cheng
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Chenchen Huan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Xinru Jiang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Zhiying Yan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
| | - Zhouliang Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
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Xiong BJ, Kleinsteuber S, Sträuber H, Dusny C, Harms H, Wick LY. Impact of Fungal Hyphae on Growth and Dispersal of Obligate Anaerobic Bacteria in Aerated Habitats. mBio 2022; 13:e0076922. [PMID: 35638736 PMCID: PMC9239063 DOI: 10.1128/mbio.00769-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/05/2022] [Indexed: 01/21/2023] Open
Abstract
Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes. Here, we analyzed whether and to which degree hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of the obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, microscopy, and metabolite analysis revealed the formation and persistence of anoxic circum hyphal niches, allowing for spore germination, growth, and fermentative activity of the obligate anaerobe in an otherwise inhabitable environment. Hypoxic liquid films containing 80% ± 10% of atmospheric oxygen saturation around single air-exposed hyphae thereby allowed for efficient clostridial dispersal amid spatially separated (>0.5 cm) anoxic sites. Hyphae hence may serve as good networks for the activity and spatial organization of obligate anaerobic bacteria in oxygenated heterogeneous environments such as soil. IMPORTANCE Although a few studies have reported on the presence of anoxic microniches in fungal biofilms, knowledge of the effects of fungal oxygen consumption on bacterial-fungal interactions is limited. Here, we demonstrate the existence and persistence of oxygen-free zones in air-exposed mycelia enabling spore germination, growth, fermentative activity, and dispersal of the obligate anaerobe. Our study points out a previously overlooked role of aerobic fungi in creating and bridging anoxic microniches in ambient oxic habitats. Air-exposed hyphae hence may act as a scaffold for activity and dispersal of strictly anaerobic microbes. Given the short-term tolerance of strict anaerobes to oxygen and reduced oxygen content in the mycosphere, hyphae can promote spatial organization of both obligate anaerobic and aerobic bacteria. Such finding may be important for a better understanding of previously observed co-occurrences of aerobes and anaerobes in well-aerated habitats such as upland soils.
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Affiliation(s)
- Bi-Jing Xiong
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Christian Dusny
- Department of Solar Materials, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Lukas Y. Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
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Criado Monleon AJ, Knappe J, Somlai C, Betancourth CO, Ali M, Curtis TP, Gill LW. Spatial Variation of the Microbial Community Structure of On-Site Soil Treatment Units in a Temperate Climate, and the Role of Pre-treatment of Domestic Effluent in the Development of the Biomat Community. Front Microbiol 2022; 13:915856. [PMID: 35814661 PMCID: PMC9263727 DOI: 10.3389/fmicb.2022.915856] [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: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022] Open
Abstract
The growth of microbial mats or "biomats" has been identified as an essential component in the attenuation of pollutants within the soil treatment unit (STU) of conventional on-site wastewater treatment systems (OWTSs). This study aimed to characterize the microbial community which colonizes these niches and to determine the influence of the pre-treatment of raw-domestic wastewater on these communities. This was achieved through a detailed sampling campaign of two OWTSs. At each site, the STU areas were split whereby half received effluent directly from septic tanks, and half received more highly treated effluents from packaged aerobic treatment systems [a coconut husk media filter on one site, and a rotating biodisc contactor (RBC) on the other site]. Effluents from the RBC had a higher level of pre-treatment [~90% Total Organic Carbon (TOC) removal], compared to the media filter (~60% TOC removal). A total of 92 samples were obtained from both STU locations and characterized by 16S rRNA gene sequencing analysis. The fully treated effluent from the RBC resulted in greater microbial community richness and diversity within the STUs compared to the STUs receiving partially treated effluents. The microbial community structure found within the STU receiving fully treated effluents was significantly different from its septic tank, primary effluent counterpart. Moreover, the distance along each STU appears to have a greater impact on the community structure than the depth in each STU. Our findings highlight the spatial variability of diversity, Phylum- and Genus-level taxa, and functional groups within the STUs, which supports the assumption that specialized biomes develop around the application of effluents under different degrees of treatment and distance from the source. This research indicates that the application of pre-treated effluents infers significant changes in the microbial community structure, which in turn has important implications for the functionality of the STU, and consequently the potential risks to public health and the environment.
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Affiliation(s)
- Alejandro Javier Criado Monleon
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, The University of Dublin College Green, Dublin, Ireland
| | - Jan Knappe
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, The University of Dublin College Green, Dublin, Ireland
- Mathematics Applications Consortium for Science and Industry (MASCI), Limerick University, Limerick, Ireland
| | - Celia Somlai
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, The University of Dublin College Green, Dublin, Ireland
| | | | - Muhammad Ali
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, The University of Dublin College Green, Dublin, Ireland
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas P. Curtis
- Department of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laurence William Gill
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, The University of Dublin College Green, Dublin, Ireland
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Ossai IC, Hamid FS, Hassan A. Micronised keratinous wastes as co-substrates, and source of nutrients and microorganisms for trichoremediation of petroleum hydrocarbon polluted soil. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Caldara M, Belgiovine C, Secchi E, Rusconi R. Environmental, Microbiological, and Immunological Features of Bacterial Biofilms Associated with Implanted Medical Devices. Clin Microbiol Rev 2022; 35:e0022120. [PMID: 35044203 PMCID: PMC8768833 DOI: 10.1128/cmr.00221-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spread of biofilms on medical implants represents one of the principal triggers of persistent and chronic infections in clinical settings, and it has been the subject of many studies in the past few years, with most of them focused on prosthetic joint infections. We review here recent works on biofilm formation and microbial colonization on a large variety of indwelling devices, ranging from heart valves and pacemakers to urological and breast implants and from biliary stents and endoscopic tubes to contact lenses and neurosurgical implants. We focus on bacterial abundance and distribution across different devices and body sites and on the role of environmental features, such as the presence of fluid flow and properties of the implant surface, as well as on the interplay between bacterial colonization and the response of the human immune system.
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Affiliation(s)
- Marina Caldara
- Interdepartmental Center on Safety, Technologies, and Agri-food Innovation (SITEIA.PARMA), University of Parma, Parma, Italy
| | - Cristina Belgiovine
- IRCCS Humanitas Research Hospital, Rozzano–Milan, Italy
- Scuola di Specializzazione in Microbiologia e Virologia, Università degli Studi di Pavia, Pavia, Italy
| | - Eleonora Secchi
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Roberto Rusconi
- IRCCS Humanitas Research Hospital, Rozzano–Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele–Milan, Italy
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OUIDIR T, GABRIEL B, CHABANE YNAIT. Overview of multi-species biofilms in different ecosystems: wastewater treatment, soil and oral cavity. J Biotechnol 2022; 350:67-74. [DOI: 10.1016/j.jbiotec.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
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Chen Y, Du J, Li Y, Tang H, Yin Z, Yang L, Ding X. Evolutions and Managements of Soil Microbial Community Structure Drove by Continuous Cropping. Front Microbiol 2022; 13:839494. [PMID: 35295291 PMCID: PMC8920486 DOI: 10.3389/fmicb.2022.839494] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Continuous cropping obstacles have increasingly become an important phenomenon affecting crop yield and quality. Its harm includes the deterioration of soil basic physical and chemical properties, changes of soil microbial community structure, accumulation of autotoxins, weakness of plant growth, and aggravation of diseases and pests. In this review, the evolutionary trend of soil microbial structure driven by continuous cropping was generalized, while drivers of these changes summed up as destruction of soil microbial living environment and competition within the community. We introduced a microorganism proliferation and working model with three basics and a vector, and four corresponding effective measures to reshape the structure were comprehensively expounded. According to the model, we also put forward three optimization strategies of the existing measures. In which, synthetic microbiology provides a new solution for improving soil community structure. Meanwhile, to ensure the survival and reproduction of soil microorganisms, it is necessary to consider their living space and carbon sources in soil fully. This review provided a comprehensive perspective for understanding the evolutionary trend of the soil microbial community under continuous cropping conditions and a summary of reshaping measures and their optimization direction.
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Affiliation(s)
- Yudong Chen
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Jianfeng Du
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Heng Tang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Long Yang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
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Gu M, Fang W, Li X, Yang W, Waigi MG, Kengara FO, Wu S, Han C, Zhang Y. Up-regulation of ribosomal and carbon metabolism proteins enhanced pyrene biodegradation in fulvic acid-induced biofilm system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118602. [PMID: 34856247 DOI: 10.1016/j.envpol.2021.118602] [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: 07/13/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
The polycyclic aromatic hydrocarbons (PAHs) that enter the aqueous phase usually coexist with fulvic acid (FA). Therefore, we initiated this investigation to explore the influences of FA on bacterial biofilm formation and its potential to biodegrade pyrene (PYR), using electron microscopic techniques and isobaric tags for relative and absolute quantification (iTRAQ). Our results revealed that FA stimulated biofilm formation and enhanced the biodegradation of PYR. First, FA favored the three-dimensional proliferation of bacteria, with an OD590/OD600 value of up to 14.78, and the extracellular surfaces covered by a layer of biomaterials. Distinctive intracellular morphologies of texture and organization were accompanied by reduced inter-bacterial distances of less than 0.31 μm. The biofilms formed displayed interactions between FA and surficial proteins, as noted by band shifts for the C-O and CO groups. Strikingly, FA triggered the upregulation of 130 proteins that were either operational in biofilm formation or in metabolic adjustments; with the changes supported by the increasing intensity of free amino acids and the newly generated N-O bonds. The results above revealed that the enhanced biodegradation was related to the up-regulation of the proteins functioned for ribosomal and carbon metabolism, and the ultra-structural changes in FA-induced biofilm system.
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Affiliation(s)
- Minfen Gu
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - WenWen Fang
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoning Li
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Weiben Yang
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, China
| | - Fredrick Orori Kengara
- School of Pure and Applied Sciences, Bomet University College, P.O. Box 701, 20400, Bomett, Kenya
| | - Shixi Wu
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Cheng Han
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Yinping Zhang
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China.
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36
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Liaqat I, Gulab B, Hanif U, Sultan A, Sadiqa A, Zafar U, Afzaal M, Naseem S, Akram S, Saleem G. Honey Potential as Antibiofilm, Antiquorum Sensing and Dispersal Agent against Multispecies Bacterial Biofilm. J Oleo Sci 2022; 71:425-434. [DOI: 10.5650/jos.ess21199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Iram Liaqat
- Microbiology Lab, Department of Zoology, GC University
| | - Babar Gulab
- Microbiology Lab, Department of Zoology, GC University
| | | | | | - Ayesha Sadiqa
- Department of Chemistry, University of Engineering and Technology
| | - Urooj Zafar
- Department of Microbiology, University of Karachi
| | | | - Sajida Naseem
- Department of Zoology, University of Education, Lower Mall Campu
| | - Sumia Akram
- Division of Science and Technology, University of Education
| | - Gulbeena Saleem
- Department of Pathology, University of Veterinary and Animal Sciences
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37
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Zuo X, Suo P, Li Y, Xu Q. Diversity and distribution of antibiotic resistance genes associated with road sediments transported in urban stormwater runoff. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118470. [PMID: 34748884 DOI: 10.1016/j.envpol.2021.118470] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/24/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, there were little data on the diversity and distribution of ARGs associated with road sediments transported in runoff. The investigation of ARGs diversity showed that sulfonamide resistance genes (sul2 and sul3) occupied 61.7%-82.3% of total ARGs in runoff. The analysis of ARGs distribution in particulate matter (PM) implied that both tetQ and trbC existed mainly in PM with size of 150-300 μm, but other ARGs and mobile genetic elements (MGEs) were dominant in PM with size <75 μm. The discussion of potential hosts indicated that target genes (ermF, blaOXA1/blaOXA30, ermC, qnrA, sul2, tnpA-01, intI2, tetW, intI1, sul3, trbC) had the strongest subordinate relationship with Proteobacteria at phylum level and Enterobacter at genus level. The effect evaluation of ARGs distribution suggested that 13 kinds of ARGs were positively correlated with Pr/PS and Zeta potential, resulting in the more ARGs in PM with smaller size (<75 μm).
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Affiliation(s)
- XiaoJun Zuo
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China.
| | - PengCheng Suo
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China
| | - Yang Li
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China
| | - Qiangqiang Xu
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Nanjing, 210044, China
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38
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Dynamic Changes in Soil Microbial Communities with Glucose Enrichment in Sediment Microbial Fuel Cells. Indian J Microbiol 2021; 61:497-505. [PMID: 34744205 DOI: 10.1007/s12088-021-00959-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/17/2021] [Indexed: 12/21/2022] Open
Abstract
To investigate soil microbial community dynamics in sediment microbial fuel cells (MFCs), this study applied nonhydric (D) and hydric (S) soils to single-chamber and mediator-free MFCs. Glucose was also used to enrich microorganisms in the soils. The voltage outputs of both the D and S sediment MFCs increased over time but differed from each other. The initial open circuit potentials were 345 and 264 mV for the D and S MFCs. The voltage output reached a maximum of 503 and 604 mV for D and S on days 125 and 131, respectively. The maximum power densities of the D and S MFCs were 2.74 and 2.12 mW m-2, analyzed on day 50. Clustering results revealed that the two groups did not cluster after glucose supplementation and 126 days of MFC function. The change in Geobacter abundance was consistent with the voltage output, indicating that these bacteria may act as the main exoelectrogens on the anode. Spearman correlation analysis demonstrated that, in the D soils, Geobacter was positively correlated with Dialister and negatively correlated with Bradyrhizobium, Kaistobacter, Pedomicrobium, and Phascolarctobacterium; in the S soils, Geobacter was positively correlated with Shewanella and negatively correlated with Blautia. The results suggested that different soil sources in the MFCs and the addition of glucose as a nutrient produced diverse microbial communities with varying voltage output efficiencies. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00959-x.
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39
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Formation and development of biofilm- an alarming concern in food safety perspectives. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Zhang X, Li Y, Ouyang D, Lei J, Tan Q, Xie L, Li Z, Liu T, Xiao Y, Farooq TH, Wu X, Chen L, Yan W. Systematical review of interactions between microplastics and microorganisms in the soil environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126288. [PMID: 34102358 DOI: 10.1016/j.jhazmat.2021.126288] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
Terrestrial ecosystems are widely contaminated by microplastics due to extensive usage and poor handling of plastic materials, but the subsequent fate and remediate strategy of these pollutants are far from fully understood. In soil environments, microplastics pose a potential threat to the survival, growth, and reproduction of soil microbiota that in turn threaten the biodiversity, function, and services of terrestrial ecosystems. Meanwhile, microorganisms are sensitive to microplastics due to the adaptability to changes in substrates and soil properties. Through the metabolic and mineralization processes, microorganisms are also crucial participator to the plastic biodegradation. In this review, we present current knowledges and research results of interactions between microplastics and microorganisms (both fungi and bacteria) in soil environments and mainly discuss the following: (1) effects of microplastics on microbial habitats via changes in soil physical, chemical, and biological properties; (2) effects of microplastics on soil microbial communities and functions; and (3) soil microbial-mediated plastic degradation with the likely mechanisms and potential remediation strategies. We aim to analyze the mechanisms driving these interactions and subsequent ecological effects, propose future directives for the study of microplastic in soils, and provide valuable information on the plastic bioremediation in contaminated soils.
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Affiliation(s)
- Xuyuan Zhang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; National Engineering Laboratory for Applied Forest Ecological Technology in Southern China, Changsha 410004, China
| | - Yong Li
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; National Engineering Laboratory for Applied Forest Ecological Technology in Southern China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha 410004, China.
| | - Dan Ouyang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Junjie Lei
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Qianlong Tan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lingli Xie
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ziqian Li
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ting Liu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yunmu Xiao
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Taimoor Hassan Farooq
- National Engineering Laboratory for Applied Forest Ecological Technology in Southern China, Changsha 410004, China; Bangor College China, a joint unit of Bangor University, Wales, UK and Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiaohong Wu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; National Engineering Laboratory for Applied Forest Ecological Technology in Southern China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha 410004, China
| | - Liang Chen
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; National Engineering Laboratory for Applied Forest Ecological Technology in Southern China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha 410004, China
| | - Wende Yan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; National Engineering Laboratory for Applied Forest Ecological Technology in Southern China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha 410004, China.
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Graddy CMR, Gomez MG, DeJong JT, Nelson DC. Native Bacterial Community Convergence in Augmented and Stimulated Ureolytic MICP Biocementation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10784-10793. [PMID: 34279077 DOI: 10.1021/acs.est.1c01520] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbially induced calcite precipitation is a biomineralization process with numerous civil engineering and ground improvement applications. In replicate soil columns, the efficacy and microbial composition of soil bioaugmented with the ureolytic bacterium Sporosarcina pasteurii were compared to a biostimulation method that enriches native ureolytic soil bacteria in situ under conditions analogous to field implementation. The selective enrichment resulting from sequential stimulation treatments strongly selected for Firmicutes (>97%), with Sporosarcina and Lysinibacillus comprising 60 to 94% of high-throughput 16S rDNA sequences in each suspended community sample. Seven species of the former and two of the latter were present in greater than 10% abundance at different times, demonstrating unexpected within-genus diversity and robustness in the suspended phase of this highly selective environment. Based on longer 16S sequences, it was inferred that augmented S. pasteurii competed poorly with natural bacteria, decreasing to below detection after nine treatments, while the native microbial community was enriched to approximately that present in the stimulated columns. These analyses were corroborated by the observed convergence in bulk ureolytic rates and calcite contents between techniques. However, a 10-fold discrepancy between the observed cell density and an activity-based estimate indicates the attached community, uncharacterized despite efforts, substantially contributes to bulk behavior.
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Affiliation(s)
- Charles M R Graddy
- Department of Microbiology and Molecular Genetics, University of California, Davis 95616, California, United States
| | - Michael G Gomez
- Department of Civil and Environmental Engineering, University of Washington, Seattle 98195-2700, Washington, United States
| | - Jason T DeJong
- Department of Civil and Environmental Engineering, University of California, Davis 95616, California, United States
| | - Douglas C Nelson
- Department of Microbiology and Molecular Genetics, University of California, Davis 95616, California, United States
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Xiao Z, Zhang L, Li ZL, Zhong J, Chen D, Huang H. Enhanced low-temperature denitrification by microbial consortium using solid-phase humin. ENVIRONMENTAL RESEARCH 2021; 196:110392. [PMID: 33129856 DOI: 10.1016/j.envres.2020.110392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/01/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Reducing the use of liquid organic carbon electron donors during biostimulation of heterotrophic denitrification is critical for sustainable groundwater remediation. Solid-phase humin isolated from natural sources can provide a cost-effective alternative to classical electron donors. In this study, the low-temperature denitrification capacity of an acetate-fed microbial community was enhanced using humin at 20 °C and 10 °C. These enhancements were not caused by faster acetate consumption and greater bacterial growth with the addition of humin. Estimation of the electron balance and first-order kinetics suggested that the enhancement in denitrification occurred mainly after acetate exhaustion. Humin may therefore have acted as an additional electron donor for the denitrifying microbial community, with the reduced quinone group in humin potentially responsible for electron donation. The addition of humin increased the richness and diversity of the denitrifying microbial community, in which Dechloromonas spp. played a critical role. Given the prevalence of humin and denitrifiers using humic substances, our results have important implications in the bioremediation of nitrate-contaminated groundwater using less liquid organic carbon electron donors.
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Affiliation(s)
- Zhixing Xiao
- College of Urban Construction, Nanjing Tech University, Nanjing, 211816, China
| | - Lei Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jicheng Zhong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dan Chen
- College of Urban Construction, Nanjing Tech University, Nanjing, 211816, China.
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
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43
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Qiu L, Wu J, Du W, Nafees M, Yin Y, Ji R, Banwart SA, Guo H. Response of soil bacterial communities to sulfadiazine present in manure: Protection and adaptation mechanisms of extracellular polymeric substances. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124887. [PMID: 33387717 DOI: 10.1016/j.jhazmat.2020.124887] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Extracellular polymeric substances (EPS) play a dominant role in protective biofilms. However, studies exploring the underlying protective mechanism of EPS have mainly focused on activated sludge, whereas their positive roles in protecting soil microbes from environmental stress have not been elucidated. In this study, we revealed the response of soil bacterial communities to various dosages of sulfadiazine (SDZ) present in manure, with a special emphasis on the role of EPS. Sequencing analysis showed that the bacterial community demonstrated stronger symbiotic relationships and weaker competitive interaction patterns to cope with disturbance induced by SDZ. EPS was mainly composed of tyrosine-like and tryptophan-like substances, and moreover, carboxyl, hydroxyl and ether groups were the main functional groups. An adaptation mechanism, namely the enhanced secretion of tryptophan-like substances, could help alleviate the SDZ stress effectively in the biofilms occurring in soil that experienced long-term manure application. Furthermore, the existence of EPS weakened the accumulation of antibiotic resistance genes (ARGs) in soil. Our results for the first time systematically uncover the joint action of biofilm tolerance and ARGs in resisting SDZ stress, which enhances understanding of the protective role of EPS and the underlying mechanisms governing biofilm functions in soil environments.
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Affiliation(s)
- Linlin Qiu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jingjing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wenchao Du
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Muhammad Nafees
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Steven A Banwart
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK; Global Food and Environment Institute, University of Leeds, Leeds LS2 9JT, UK
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
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44
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Flemming HC, Baveye P, Neu TR, Stoodley P, Szewzyk U, Wingender J, Wuertz S. Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond. NPJ Biofilms Microbiomes 2021; 7:10. [PMID: 33504794 PMCID: PMC7840925 DOI: 10.1038/s41522-020-00183-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Sessile microorganisms were described as early as the seventeenth century. However, the term biofilm arose only in the 1960s in wastewater treatment research and was adopted later in marine fouling and in medical and dental microbiology. The sessile mode of microbial life was gradually recognized to be predominant on Earth, and the term biofilm became established for the growth of microorganisms in aggregates, frequently associated with interfaces, although many, if not the majority, of them not being continuous "films" in the strict sense. In this sessile form of life, microorganisms live in close proximity in a matrix of extracellular polymeric substances (EPS). They share emerging properties, clearly distinct from solitary free floating planktonic microbial cells. Common characteristics include the formation of synergistic microconsortia, using the EPS matrix as an external digestion system, the formation of gradients and high biodiversity over microscopically small distances, resource capture and retention, facilitated gene exchange as well as intercellular communication, and enhanced tolerance to antimicrobials. Thus, biofilms belong to the class of collective systems in biology, like forests, beehives, or coral reefs, although the term film addresses only one form of the various manifestations of microbial aggregates. The uncertainty of this term is discussed, and it is acknowledged that it will not likely be replaced soon, but it is recommended to understand these communities in the broader sense of microbial aggregates.
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Affiliation(s)
- Hans-Curt Flemming
- grid.59025.3b0000 0001 2224 0361Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551 Singapore ,grid.5718.b0000 0001 2187 5445University of Duisburg-Essen, Biofilm Centre, Universitätsstrasse 5, 45131 Essen, Germany ,Water Academy, Schloss-Strasse 40, 88045 Friedrichshafen, Germany
| | - Philippe Baveye
- Saint Loup Research Institute, 7 rue des chênes, 79600 Saint Loup Lamairé, France
| | - Thomas R. Neu
- grid.7492.80000 0004 0492 3830Department of River Ecology, Helmholtz Centre for Environmental Research–UFZ, Magdeburg, Germany
| | - Paul Stoodley
- grid.261331.40000 0001 2285 7943Department of Microbial Infection and Immunity and the Department of Orthopaedics, The Ohio State University, Columbus, OH 43210 USA ,grid.5491.90000 0004 1936 9297National Centre for Advanced Tribology at Southampton (nCATS), National Biofilm Innovation Centre (NBIC), Mechanical Engineering, University of Southampton, Southampton, S017 1BJ UK
| | - Ulrich Szewzyk
- grid.7492.80000 0004 0492 3830Technical University of Berlin, Department of Environmental Microbiology, Ernst-Reuter-Platz 1, D-10587 Berlin, Germany
| | - Jost Wingender
- grid.5718.b0000 0001 2187 5445University of Duisburg-Essen, Biofilm Centre, Universitätsstrasse 5, 45131 Essen, Germany
| | - Stefan Wuertz
- grid.59025.3b0000 0001 2224 0361Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551 Singapore ,grid.59025.3b0000 0001 2224 0361School of Civil and Environmental Engineering, Nanyang Technological University Singapore, 50 Nanyang Avenue, Singapore, 639798 Singapore
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Rossi F. Beneficial biofilms for land rehabilitation and fertilization. FEMS Microbiol Lett 2020; 367:5974273. [PMID: 33175104 DOI: 10.1093/femsle/fnaa184] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
The acquisition of a biofilm lifestyle is common in nature for microorganisms. It increases their biotic and abiotic stress tolerance and their capability to provide ecosystem services. Although diminutive communities, soil beneficial biofilms are essential for nutrient cycling, soil stabilization and direct or indirect promotion of plant development. Some biofilms represent valid biotechnological tools to deal with problems related to soil degradation, which threat food quality and the maintenance of ecosystem functions. Three genres of biofilms: rhizobacterial biofilms, fungal-bacterial biofilms and biocrusts are reviewed, and their beneficial effects on the environment outlined. Their induction by microbial inoculation represents a potential eco-friendly and sustainable approach to restore lost ecosystem functions and counteract the effects of soil erosion. Yet, some existing knowledge and methodological gaps, that will be discussed here, still hamper the optimization of this technology, and its application at its full potential.
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Affiliation(s)
- Federico Rossi
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Cà Foscari University of Venice, Via Torino 155, 30172 Mestre, Venice, Italy
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46
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Yang L, Xiao S, Yang Q, Luan T, Tam NFY. Recovery of subtropical coastal intertidal system prokaryotes from a destruction event and the role of extracellular polymeric substances in the presence of endocrine disrupting chemicals. ENVIRONMENT INTERNATIONAL 2020; 144:106023. [PMID: 32822926 DOI: 10.1016/j.envint.2020.106023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Intertidal sediments constitute the micro-environment for the co-existence of endocrine disrupting chemicals (EDCs) and biofilms consisting of the microbial community and extracellular polymeric substances (EPS). However, the interactions and the resulting eco-function of this community are complex and poorly characterized, especially after a destruction event. This study evaluates the re-construction of biofilms in terms of the abundance of prokaryotic cells and related EPS characterization in two destroyed sedimentary matrices from subtropical environments simulated by sterilization in the presence of EDCs and investigates the role of EPS. The results show that benthic prokaryotes recover from the deposition of active prokaryotes in natural seawater and form biofilms after sterilization. Sterilization triggers the release of polysaccharides and protein from lysed native microbial cells and bound EPS in sedimentary organic matter, thus increasing their concentrations. The increased portion of EPS also acts as a persistent stress on re-colonizing prokaryotes and leads to the overproduction of sedimentary EPS. Due to the protective role mediated by EPS, the effect of EDCs on biofilm composition in sterilized sediment is not significant. The sedimentary matrix is the most important determinant of the composition of the biofilm and the occurrence of EDCs. At the end of an 84-day experiment, the abundance of prokaryotic cells and the concentrations of polysaccharides and protein in mangrove sediment are 1.6-1.8 times higher than those in sandflat sediment, regardless of EDCs. Sandflat sediment exhibits higher concentrations of nonylphenol and bisphenol A but a lower concentration of 17α-ethinylestradiol than mangrove sediment. This study enhances our understanding of the role of sedimentary biofilms and the fate of EDCs in intertidal systems and highlights the benefit of a destructive event in enhancing ecosystem function, particularly tolerance to EDC adversity due to EPS production.
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Affiliation(s)
- Lihua Yang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Sirui Xiao
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; State Key Laboratory of Biocontrol, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qian Yang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Nora F Y Tam
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region.
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Zhang L, Gadd GM, Li Z. Microbial biomodification of clay minerals. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:111-139. [PMID: 33934851 DOI: 10.1016/bs.aambs.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clay minerals are important reactive centers in the soil system. Their interactions with microorganisms are ubiquitous and wide-ranging, affecting growth and function, interactions with other organisms, including plants, biogeochemical processes and the fate of organic and inorganic pollutants. Clay minerals have a large specific surface area and cation exchange capacity (CEC) per unit mass, and are abundant in many soil systems, especially those of agricultural significance. They can adsorb microbial cells, exudates, and enzymes, organic and inorganic chemical species, nutrients, and contaminants, and stabilize soil organic matter. Bacterial modification of clays appears to be primarily due to biochemical mechanisms, while fungi can exhibit both biochemical and biomechanical mechanisms, the latter aided by their exploratory filamentous growth habit. Such interactions between microorganisms and clays regulate many critical environmental processes, such as soil development and transformation, the formation of soil aggregates, and the global cycling of multiple elements. Applications of biomodified clay minerals are of relevance to the fields of both agricultural management and environmental remediation. This review provides an overview of the interactions between bacteria, fungi and clay minerals, considers some important gaps in current knowledge, and indicates perspectives for future research.
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Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China; Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom; State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, College of Science and Environment, China University of Petroleum, Beijing, China
| | - Zhen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China; Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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48
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Exploring the Role of Bacterial Extracellular Polymeric Substances for Sustainable Development in Agriculture. Curr Microbiol 2020; 77:3224-3239. [PMID: 32876713 DOI: 10.1007/s00284-020-02169-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023]
Abstract
The incessant need to increase crop yields has led to the development of many chemical fertilizers containing NPK (nitrogen-phosphorous-potassium) which can degrade soil health in the long term. In addition, these fertilizers are often leached into nearby water bodies causing algal bloom and eutrophication. Bacterial secondary metabolites exuded into the extracellular space, termed extracellular polymeric substances (EPS) have gained commercial significance because of their biodegradability, non-toxicity, and renewability. In many habitats, bacterial communities faced with adversity will adhere together by production of EPS which also serves to bond them to surfaces. Typically, hygroscopic, EPS retain moisture in desiccating conditions and modulate nutrient exchange. Many plant growth-promoting bacteria (PGPR) combat harsh environmental conditions like salinity, drought, and attack of pathogens by producing EPS. The adhesive nature of EPS promotes soil aggregation and restores moisture thus combating soil erosion and promoting soil fertility. In addition, these molecules play vital roles in maintaining symbiosis and nitrogen fixation thus enhancing sustainability. Thus, along with other commercial applications, EPS show promising avenues for improving agricultural productivity thus helping to address land scarcity as well as minimizing environmental pollution.
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Ao X, Zhao J, Yan J, Liu S, Zhao K. Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells. PeerJ 2020; 8:e9639. [PMID: 32832272 PMCID: PMC7409786 DOI: 10.7717/peerj.9639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/09/2020] [Indexed: 12/26/2022] Open
Abstract
Background Lactiplantibacillus plantarum (L. plantarum), a dominant strain in traditional fermented foods, is widely used in fermentation industry because of its fast acid production. However, L. plantarum is easily inactivated due to acidity, high temperature and other factors. The formation of biofilm by bacteria can effectively increase environmental tolerance. Therefore, it is important to improve the environmental tolerance of L. plantarum by studying its biofilm formation conditions and regulatory mechanisms. Methods After determining a suitable NaCl concentration for promoting biofilm formation, L. plantarum was grown with 48 g L−1 NaCl. Differential gene expressions in L. plantarum biofilm vs. planktonic cells were analyzed using RNA sequencing and validated using qPCR. Result L. plantarum RS66CD biofilm formation formed highest amount of when grown at 48 g L−1 NaCl. Altogether 447 genes were up-regulated and 426 genes were down-regulated in the biofilm. KEGG pathway analysis showed that genes coding for D-Alanine metabolism, peptidoglycan biosynthesis, two-component system, carbon metabolism, bacterial secretion system, lysine biosynthesis and fatty acid metabolism were crucial for biofilm formation. In addition, eight other genes related to biofilm formation were differentially expressed. Our results provide insights into the differential gene expression involved in biofilm formation, which can help to reveal gene regulation during L. plantarum biofilm formation.
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Affiliation(s)
- Xiaolin Ao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Jiawei Zhao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Junling Yan
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Ke Zhao
- Colloge of Resources, Sichuan Agricultural University, Cheng'du', China
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50
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Achinas S, Yska SK, Charalampogiannis N, Krooneman J, Euverink GJW. A Technological Understanding of Biofilm Detection Techniques: A Review. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E3147. [PMID: 32679710 PMCID: PMC7412299 DOI: 10.3390/ma13143147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
Biofouling is a persistent problem in almost any water-based application in several industries. To eradicate biofouling-related problems in bioreactors, the detection of biofilms is necessary. The current literature does not provide clear supportive information on selecting biofilm detection techniques that can be applied to detect biofouling within bioreactors. Therefore, this research aims to review all available biofilm detection techniques and analyze their characteristic properties to provide a comparative assessment that researchers can use to find a suitable biofilm detection technique to investigate their biofilms. In addition, it discusses the confluence of common bioreactor fabrication materials in biofilm formation.
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Affiliation(s)
- Spyridon Achinas
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
| | - Stijn Keimpe Yska
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
| | | | - Janneke Krooneman
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
| | - Gerrit Jan Willem Euverink
- Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands; (S.K.Y.); (J.K.); (G.J.W.E.)
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