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Li Y, Hou F, Sun L, Lan J, Han Z, Li T, Wang Y, Zhao Z. Ecological effect of microplastics on soil microbe-driven carbon circulation and greenhouse gas emission: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 364:121429. [PMID: 38870791 DOI: 10.1016/j.jenvman.2024.121429] [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: 01/17/2024] [Revised: 05/09/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Soil organic carbon (SOC) pool, the largest part of terrestrial ecosystem, controls global terrestrial carbon balance and consequently presented carbon cycle-climate feedback in climate projections. Microplastics, (MPs, <5 mm) as common pollutants in soil ecosystems, have an obvious impact on soil-borne carbon circulation by affecting soil microbial processes, which play a central role in regulating SOC conversion. In this review, we initially presented the sources, properties and ecological risks of MPs in soil ecosystem, and then the differentiated effects of MPs on the component of SOC, including dissolved organic carbon, soil microbial biomass carbon and easily oxidized organic carbon varying with the types and concentrations of MPs, the soil types, etc. As research turns into a broader perspective, greenhouse gas emissions dominated by the mineralization of SOC coming into view since it can be significantly affected by MPs and is closely associated with soil microbial respiration. The pathways of MPs impacting soil microbes-driven carbon conversion include changing microbial community structure and composition, the functional enzyme's activity and the abundance and expression of functional genes. However, numerous uncertainties still exist regarding the microbial mechanisms in the deeper biochemical process. More comprehensive studies are necessary to explore the affected footprint and provide guidance for finding the evaluation criterion of MPs affecting climate change.
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Affiliation(s)
- Yaru Li
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Fangwei Hou
- College of Mechanical and Electrical Engineering, Qingdao University, Qingdao, 266071, China
| | - Lulu Sun
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Jing Lan
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Zhanghua Han
- Shandong Provincial Key Laboratory of Optics and Photonic Devices, Center of Light Manipulation and Applications, School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Tongtong Li
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Yiming Wang
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Zongshan Zhao
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China.
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2
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Devadhasan A, Kolodny O, Carja O. Competition for resources can reshape the evolutionary properties of spatial structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.13.589370. [PMID: 38659847 PMCID: PMC11042312 DOI: 10.1101/2024.04.13.589370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of interaction and replacement between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. Moreover, we show that this effect is a non-linear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations.
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Affiliation(s)
- Anush Devadhasan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oren Kolodny
- Department of Ecology, Evolution, and Behavior, E. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
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3
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Duckett M, Taylor MN, Bowman C, Vega NM. Parallel evolution of alternate morphotypes of Chryseobacterium gleum during experimental evolution with Caenorhabditis elegans. FEMS Microbiol Ecol 2024; 100:fiae039. [PMID: 38549432 PMCID: PMC11004935 DOI: 10.1093/femsec/fiae039] [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: 11/13/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities.
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Affiliation(s)
- Marissa Duckett
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
| | - Megan N Taylor
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
| | - Claire Bowman
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
| | - Nic M Vega
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA 30322, United States
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4
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Jin C, Sengupta A. Microbes in porous environments: from active interactions to emergent feedback. Biophys Rev 2024; 16:173-188. [PMID: 38737203 PMCID: PMC11078916 DOI: 10.1007/s12551-024-01185-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Microbes thrive in diverse porous environments-from soil and riverbeds to human lungs and cancer tissues-spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.
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Affiliation(s)
- Chenyu Jin
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
| | - Anupam Sengupta
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
- Institute for Advanced Studies, University of Luxembourg, 2 Avenue de l’Université, Esch-sur-Alzette, L-4365 Luxembourg
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5
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Copeland R, Zhang C, Hammer BK, Yunker PJ. Spatial constraints and stochastic seeding subvert microbial arms race. PLoS Comput Biol 2024; 20:e1011807. [PMID: 38277405 PMCID: PMC10849242 DOI: 10.1371/journal.pcbi.1011807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/07/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
Surface attached communities of microbes grow in a wide variety of environments. Often, the size of these microbial community is constrained by their physical surroundings. However, little is known about how size constraints of a colony impact the outcome of microbial competitions. Here, we use individual-based models to simulate contact killing between two bacterial strains with different killing rates in a wide range of community sizes. We found that community size has a substantial impact on outcomes; in fact, in some competitions the identity of the most fit strain differs in large and small environments. Specifically, when at a numerical disadvantage, the strain with the slow killing rate is more successful in smaller environments than in large environments. The improved performance in small spaces comes from finite size effects; stochastic fluctuations in the initial relative abundance of each strain in small environments lead to dramatically different outcomes. However, when the slow killing strain has a numerical advantage, it performs better in large spaces than in small spaces, where stochastic fluctuations now aid the fast killing strain in small communities. Finally, we experimentally validate these results by confining contact killing strains of Vibrio cholerae in transmission electron microscopy grids. The outcomes of these experiments are consistent with our simulations. When rare, the slow killing strain does better in small environments; when common, the slow killing strain does better in large environments. Together, this work demonstrates that finite size effects can substantially modify antagonistic competitions, suggesting that colony size may, at least in part, subvert the microbial arms race.
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Affiliation(s)
- Raymond Copeland
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christopher Zhang
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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6
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Fu F, Sun Y, Yang D, Zhao L, Li X, Weng L, Li Y. Combined pollution and soil microbial effect of pesticides and microplastics in greenhouse soil of suburban Tianjin, Northern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122898. [PMID: 37944885 DOI: 10.1016/j.envpol.2023.122898] [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: 07/31/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Current-used pesticides (CUPs) and plastic films are essential materials used in greenhouse cultivation, which can lead to the residual accumulation of CUPs and microplastics (MPs) over time. The impact of CUPs and MPs on soil quality and food safety cannot be overlooked. However, the combined pollution resulting from CUPs and MPs in greenhouse soil remains poorly understood. In this study, we conducted a survey at 30 greenhouse sites in the Wuqing District of Tianjin, China, to investigate the pollution levels and characteristics of CUPs and MPs using QuEChERS combined with LC-MS/MS, and density extraction, 30% H2O2 digestion and micro-fourier transform infrared spectroscopy, respectively. Additionally, we aimed to evaluate the interactions among these two pollutants, soil physicochemical properties, and the bacterial community in the soil. CUPs were frequently detected in the examined soil samples; however, they posed no significant ecological risks due to their low levels. Furthermore, MPs, which predominantly comprised fragmented and fibrous polyethylene (PE) and polypropylene (PP) particles smaller than 1.0 mm, could potentially degrade into nanoplastics, which might subsequently enter the food chain and pose a serious threat to human health. We observed no substantial correlations between CUPs and MPs, except for a negative correlation between dimethomorph and film MPs. The soil pH and total organic carbon (TOC) exhibited interactions with both types of pollutants, whereas soil clay content (CC) only correlated with CUPs, and soil available nitrogen (AN) only correlated with MPs. The variability of soil bacterial communities among the 30 sampling sites was minimal, with the dominant genus being Bacillus. Soil pH, TOC, and CC collectively exerted a strong influence on the microbial community across all samples; however, the effects of CUPs and MPs on the soil microbial structure were marginal. These results contribute to a comprehensive understanding of the environmental stress and ecological risks associated with the combined pollution of CUPs and MPs.
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Affiliation(s)
- Furong Fu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Yang Sun
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China.
| | - Dan Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Lixia Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Liping Weng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Yongtao Li
- College of Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
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7
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Hui C, Li Y, Yuan S, Zhang W. River connectivity determines microbial assembly processes and leads to alternative stable states in river networks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166797. [PMID: 37673267 DOI: 10.1016/j.scitotenv.2023.166797] [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: 05/09/2023] [Revised: 07/29/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023]
Abstract
River network is a common form of lotic ecosystems. Variances in river connection modes would form networks with significantly different structures, and further affect aquatic organisms. Microbial communities are vital organisms of river networks, they participate in numerous biogeochemical processes. Identifying associations between microbial community and structural features of river networks are essential for maintaining environmental quality. Thus, dendritic (DRN) and trellised river networks (TRN) were studied by combining molecular biological tools, ecological theory and hydrodynamic calculation. Results illustrated that river connectivity, a vital structural feature exhibiting mass transport ability of river network, increased relative importance of homogeneous selection processes in microbial assembly, which would further shape community with alternative stable states. Between the two researched river networks, DRN possessed higher connectivity, which made homogeneous selection as the driving force in community assembly. The microbial communities in DRN were consisted of species occupying similar ecological niche, and exhibited two alternative stable states, which can decrease influences of environmental disturbance on community composition. On the contrary, lower connectivity of TRN decreased proportions of homogeneous selection in community assembly, which further led to species occupying varied ecological niche. The microbial community exhibited only one stable state, and environmental disturbance would cause loss of ecological niche and significantly alter community composition. This study could provide useful information for the optimization of river connection engineering.
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Affiliation(s)
- Cizhang Hui
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Saiyu Yuan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Nanjing 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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8
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Osman DM, Yuan W, Shabaka S, Nyaga MP, Geng J, Yu Y, Yang Y. The threat of micro/nanoplastic to aquatic plants: current knowledge, gaps, and future perspectives. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 265:106771. [PMID: 38000132 DOI: 10.1016/j.aquatox.2023.106771] [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: 10/10/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023]
Abstract
Plastics have been recognized as an emerging pollutant and have raised global concerns due to their widespread distribution in the environment and potential harm to living systems. However, research on the threat of micro/nanoplastics (MPs/NPs) to the unique group of aquatic plants is far behind, necessitating a comprehensive review to summarize current research progress and identify future research needs. This review explores the sources and distribution patterns of MPs/NPs in aquatic environments, highlighting their uptake by aquatic plants through roots and leaves, and subsequent translocation via the vascular system facilitated by the transpiration stream. Exposure to MPs/NPs elicits diverse effects on the growth, physiology, and ecological interactions of aquatic plants, with variations influenced by plastic properties, plant species, and experimental conditions. Furthermore, the presence of MPs/NPs can impact the toxicity and bioavailability of other associated toxicants to aquatic plants. This review shows critical knowledge gaps and emphasizes the need for future research to bridge the current understanding of the limitations and challenges posed by MPs/NPs in aquatic ecosystems.
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Affiliation(s)
- Donia M Osman
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Soha Shabaka
- National Institute of Oceanography and Fisheries, NIOF, Egypt
| | - Muthii Patrick Nyaga
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Geng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxiang Yu
- Wuhan Institute of Technology, Wuhan 430205, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Liu B, Garza DR, Gonze D, Krzynowek A, Simoens K, Bernaerts K, Geirnaert A, Faust K. Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis. THE ISME JOURNAL 2023; 17:1940-1952. [PMID: 37670028 PMCID: PMC10579405 DOI: 10.1038/s41396-023-01501-1] [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: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact on the interactions between two abundant and prevalent human gut bacteria, the primary fermenter Bacteroides thetaiotaomicron and the butyrate producer Roseburia intestinalis. By combining machine learning and flow cytometry, we found that the number of viable B. thetaiotaomicron cells decreases with glucose consumption due to acid production, while R. intestinalis survives post-glucose depletion by entering a slow growth mode. Both species attach to mucin beads, but only viable cell counts of B. thetaiotaomicron increase significantly. The number of viable co-culture cells varies significantly over time compared to those of monocultures. A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption, whereas B. thetaiotaomicron survives glucose depletion and low pH by foraging on mucin sugars. In addition, most of the mucin monosaccharides we tested inhibited the growth of R. intestinalis but not B. thetaiotaomicron. We encoded these causal relationships in a kinetic model, which reproduced the observed dynamics. In summary, we explored how R. intestinalis and B. thetaiotaomicron respond to nutrient scarcity and how this affects their dynamics. We highlight the importance of understanding bacterial metabolic strategies to effectively modulate microbial dynamics in changing conditions.
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Affiliation(s)
- Bin Liu
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Daniel Rios Garza
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP 231, Université Libre de Bruxelles, Bvd du Triomphe, B-1050, Bruxelles, Belgium
| | - Anna Krzynowek
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Kenneth Simoens
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092, Zürich, Switzerland
| | - Karoline Faust
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium.
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10
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Ormaasen I, Rudi K, Diep DB, Snipen L. Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut. BMC Genomics 2023; 24:295. [PMID: 37259063 DOI: 10.1186/s12864-023-09388-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/18/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age. RESULTS We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (< 2 years) compared to adult-like metagenomes (2-107 years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities. CONCLUSIONS Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.
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Affiliation(s)
- Ida Ormaasen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
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11
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Chang SH, Lin CW, Cheng YS, Liu SH. Effects of biodegradation, biotoxicity and microbial community on biostimulation of sulfolane. CHEMOSPHERE 2023; 319:138047. [PMID: 36739988 DOI: 10.1016/j.chemosphere.2023.138047] [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: 11/22/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
To evaluate the effectiveness of biostimulation in remediating soil-free groundwater and groundwater with soil, experiments were conducted using soil and groundwater samples that were contaminated with sulfolane. The main objective was to characterize the differences in sulfolane removal efficiency and biotoxicity between in situ soil-free groundwater and groundwater with soil and different concentrations of dissolved oxygen (1 mg/L and 5 mg/L) and various nutrient salts (in situ and spiked). Optimizing the nutrient salt conditions improved the removal efficiency of sulfolane by 1.8-6.5 that under in situ nutrient salt conditions. Controlling the dissolved oxygen concentration enhanced the efficiency of removal of sulfolane by 1.5-4.5 times over that at the simulated in situ dissolved oxygen concentration, suggesting that the degradation of sulfolane by indigenous microorganisms requires nutrient salts more than it requires dissolved oxygen. Biotoxicity data showed that the luminescence inhibition of Aliivibrio fischeri by sulfolane was lower in the biostimulated samples than in the pre-treated samples. Biostimulation reduced the biotoxicity of the treated samples by 42-51%, revealing that it was effective in removing sulfolane and reducing biotoxicity. Microbial community analysis showed that the biostimulation did not change the dominant species in the original in situ community, and increased the proportion of sulfolane-degraders. The outcome of this study can be used to set parameters for the remediation of groundwater that is contaminated by sulfolane in oil refineries.
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Affiliation(s)
- Shao-Heng Chang
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC
| | - Chi-Wen Lin
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC; Graduate School of Engineering Science and Technology, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC
| | - Yu-Shen Cheng
- Department of Chemical and Materials Engineering, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC; Bachelor's Program in Industrial Technology, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC
| | - Shu-Hui Liu
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC.
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12
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Rong L, Wang Y, Meidl P, Wang L, Sun H. Microplastics affect soybean rhizosphere microbial composition and function during vegetative and reproductive stages. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114577. [PMID: 36709538 DOI: 10.1016/j.ecoenv.2023.114577] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/08/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Microplastics (MPs) are emerging contaminants in agricultural soil, whereas their effects on the rhizosphere microbial ecosystems and biogeochemical nitrogen cycles during plant growth remain unknown. Here, a 70-day greenhouse experiment was carried out with black and fluvo-aquic soil to evaluate the influence of polyamide (PA), polyethylene (PE), polyester (PES), and polyvinyl chloride (PVC) MPs on the bacterial communities and functions in the soybean rhizosphere. The PA treatment consistently affected the rhizobacterial alpha diversity in the fluvo-aquic soil at soybean vegetative and reproductive growth stages, whereas the PE, PES, and PVC treatments had a short-term effect on the bacterial alpha diversity. At two growth stages, 6 and 23 biomarkers were consistently abundant in the PA treatment in the black soil and fluvo-aquic soil, respectively, and order Rhizobiales was found to be a biomarker for PA MPs contamination in both soils. Additionally, PA treatment decreased bacterial network complexity and tightness, whereas the effects of the PE, PES, and PVC on bacterial co-occurrence patterns varied depending on the soil types. Furthermore, PES and PVC treatments inhibited ammonification processes in the soybean rhizosphere, and PE could temporarily inhibit ammonia oxidation and denitrification processes according to the variations of N-cycling gene abundances. These effects on soil N-cycling also varied with soil types and soybean growth stages. This study provides profound information for understanding of MPs residues on the assembly of the soybean rhizosphere communities and function during plant development.
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Affiliation(s)
- Lili Rong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China.
| | - Peter Meidl
- Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195 Berlin, Germany
| | - Lei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China.
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13
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Ding MQ, Yang SS, Ding J, Zhang ZR, Zhao YL, Dai W, Sun HJ, Zhao L, Xing D, Ren N, Wu WM. Gut Microbiome Associating with Carbon and Nitrogen Metabolism during Biodegradation of Polyethene in Tenebrio larvae with Crop Residues as Co-Diets. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3031-3041. [PMID: 36790312 DOI: 10.1021/acs.est.2c05009] [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] [Indexed: 06/18/2023]
Abstract
Tenebrio molitor and Tenebrio obscurus (Coleoptera: Tenebrionidae) larvae are two commercial insects that eat plant and crop residues as diets and also biodegrade synthetic plastics polyethylene (PE). We examined biodegradation of low-density PE (LDPE) foam (Mn = 28.9 kDa and Mw = 342.0 kDa) with and without respective co-diets, i.e., wheat brain (WB) or corn flour (CF), corn straw (CS), and rice straw (RS) at 4:1 (w/w), and their gut microbiome and genetic metabolic functional groups at 27.0 ± 0.5 °C after 28 days of incubation. The presence of co-diets enhanced LDPE consumption in both larvae and broad-depolymerized the ingested LDPE. The diet type shaped gut microbial diversity, potential pathways, and metabolic functions. The sequence of effectiveness of co-diets was WB or CF > CS > RS for larval development and LDPE degradation. Co-occurrence networks indicated that the larvae co-fed with LDPE displayed more complex correlations of gut microbiome than the larvae fed with single diets. The primary diet of WB or CF and crop residues CS and RS provided energy and nitrogen source to significantly enhance LDPE biodegradation with synergistic activities of the gut microbiota. For the larvae fed LDPE and LDPE plus co-diets, nitrogen fixation function was stimulated compared to normal diets and associated with LDPE biodegradation.
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Affiliation(s)
- Meng-Qi Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhi-Rong Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yi-Lin Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Dai
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han-Jun Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei-Min Wu
- Department of Civil and Environmental Engineering, Department of Chemistry, William & Cloy Codiga Resource Recovery Center, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, California 94305, United States
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14
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Doane MP, Johnson CJ, Johri S, Kerr EN, Morris MM, Desantiago R, Turnlund AC, Goodman A, Mora M, Lima LFO, Nosal AP, Dinsdale EA. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. MICROBIAL ECOLOGY 2023; 85:747-764. [PMID: 35129649 PMCID: PMC9957878 DOI: 10.1007/s00248-022-01969-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/06/2023]
Abstract
The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
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Affiliation(s)
- Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | - Colton J. Johnson
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA USA
| | - Emma N. Kerr
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | | | - Ric Desantiago
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Abigail C. Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD Australia
| | - Asha Goodman
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA USA
| | | | - Andrew P. Nosal
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA USA
- Scripps Institution of Oceanography, University of California – San Diego, CA La Jolla, USA
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15
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Wang H, Zhang W, Li Y, Gao Y, Niu L, Zhang H, Wang L. Hydrodynamics-driven community coalescence determines ecological assembly processes and shifts bacterial network stability in river bends. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159772. [PMID: 36309275 DOI: 10.1016/j.scitotenv.2022.159772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Community coalescence, i.e., the mixing and merging of microbial communities and their surrounding environments, is prevalent in various ecosystems and potentially acts on ecological processes. River bends are distinguished by significant cross-stream velocities and spiral flow. The flow in river bends causes the mixing of microbial communities, thus making the resultant community (after mixing) different from its precursors (before mixing) through ecological processes. However, so far, no studies have explored the effect of community coalescence on ecological processes and network stability under the hydrodynamic processes of river bends. Here, we explored bacterial community assembly and community coalescence in river bends by coupling hydrodynamic profiling, aqueous biogeochemistry, DNA sequencing, and ecological theory. The results showed that the water flow dominated the community coalescence by regulating the movement of suspended sediments. The main ecological process determining the bacterial community compositions in water was the dispersal process, whereas in sediments it was the selection process. Furthermore, the negative cohesion results showed that community coalescence determined the stability of bacterial networks through competition and predation. This study depicted the bacterial community coalescence in river bends and highlighted their associations with network stability, which might provide new insights into bacterial community assembly and coalescence under complex hydrodynamics in the aquatic environment.
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Affiliation(s)
- Haolan Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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16
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Li K, Jia W, Xu L, Zhang M, Huang Y. The plastisphere of biodegradable and conventional microplastics from residues exhibit distinct microbial structure, network and function in plastic-mulching farmland. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130011. [PMID: 36155295 DOI: 10.1016/j.jhazmat.2022.130011] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The inhomogeneity of plastisphere and soil may result in different microbial communities, thus potentially affecting soil functions. Biodegradable plastics offer an alternative to conventional plastics, nevertheless, the inadequate end-of-life treatment of biodegradable plastics may release more microplastics. Herein, we collected PE and PBAT/PLA microplastics in plastic-mulching farmland in Hebei, China. The bacterial communities of soil, PE and PBAT/PLA plastisphere were investigated using 16 S high-throughput sequencing. We found that the structure of bacterial communities in PBAT/PLA plastisphere were significantly distinct from PE plastisphere and soil. The alpha diversities in PBAT/PLA plastisphere were significantly lower than PE plastisphere and soil. Statistical analysis of differentially ASVs suggested that PBAT/PLA microplastics act as a filter, enriching taxa with the capability to degrade plastic polymers such as Proteobacteria and Actinobacteria. Compared to PE plastisphere, PBAT/PLA plastisphere has networks of less complexity, lower modularity, and more competitive interactions. Predicted metabolic pathways involved in human diseases, carbohydrate metabolism, amino acid metabolism, and xenobiotic biodegradation and metabolism were promoted in PBAT/PLA plastisphere, along with the facilitation in abundance of genes associated with carbon and nitrogen cycling. Our results highlighted the uniqueness of plastisphere of biodegradable microplastics from conventional microplastics and their potential impact on soil functions.
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Affiliation(s)
- Kang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Libo Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Mengjun Zhang
- Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
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17
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Wilbert SA, Newman DK. The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence. Curr Biol 2022; 32:5221-5234.e4. [PMID: 36306787 PMCID: PMC9772256 DOI: 10.1016/j.cub.2022.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 08/15/2022] [Accepted: 10/05/2022] [Indexed: 12/23/2022]
Abstract
Microbial assemblages are omnipresent in the biosphere, forming communities on the surfaces of roots and rocks and within living tissues. These communities can exhibit strikingly beautiful compositional structures, with certain members reproducibly occupying particular spatiotemporal microniches. Despite this reproducibility, we lack the ability to explain these spatial patterns. We hypothesize that certain spatial patterns in microbial communities may be explained by the exchange of redox-active metabolites whose biological function is sensitive to microenvironmental gradients. To test this, we developed a simple community consisting of synthetic Pseudomonas aeruginosa strains with a partitioned denitrification pathway: a strict consumer and strict producer of nitric oxide (NO), a key pathway intermediate. Because NO can be both toxic or beneficial depending on the amount of oxygen present, this system provided an opportunity to investigate whether dynamic oxygen gradients can tune metabolic cross-feeding and fitness outcomes in a predictable fashion. Using a combination of genetic analysis, controlled growth environments, and imaging, we show that oxygen availability dictates whether NO cross-feeding is deleterious or mutually beneficial and that this organizing principle maps to the microscale. More generally, this work underscores the importance of considering the double-edged and microenvironmentally tuned roles redox-active metabolites can play in shaping microbial communities.
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Affiliation(s)
- Steven A Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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18
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Islam MR, Ruponti SA, Rakib MA, Nguyen HQ, Mourshed M. Current scenario and challenges of plastic pollution in Bangladesh: a focus on farmlands and terrestrial ecosystems. FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2022; 17:66. [PMID: 36589210 PMCID: PMC9793393 DOI: 10.1007/s11783-023-1666-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 05/29/2023]
Abstract
Plastic is considered one of the most indispensable commodities in our daily life. At the end of life, the huge ever-growing pile of plastic waste (PW) causes serious concerns for our environment, including agricultural farmlands, groundwater quality, marine and land ecosystems, food toxicity and human health hazards. Lack of proper infrastructure, financial backup, and technological advancement turn this hazardous waste plastic management into a serious threat to developing countries, especially for Bangladesh. A comprehensive review of PW generation and its consequences on environment in both global and Bangladesh contexts is presented. The dispersion routes of PW from different sources in different forms (microplastic, macroplastic, nanoplastic) and its adverse effect on agriculture, marine life and terrestrial ecosystems are illustrated in this work. The key challenges to mitigate PW pollution and tackle down the climate change issue is discussed in this work. Moreover, way forward toward the design and implementation of proper PW management strategies are highlighted in this study.
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Affiliation(s)
- Md. Raihanul Islam
- Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706 Bangladesh
| | - Sumaiya Akter Ruponti
- Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706 Bangladesh
| | - Md. Abdur Rakib
- Department of Microbiology, Faculty of Biological Science and Technology, Jashore University of Science of Technology, Jashore, 7408 Bangladesh
| | - Huy Quoc Nguyen
- Faculty of Heat and Refrigeration Engineering, The University of Danang—University of Science and Technology, Danang, 550000 Vietnam
| | - Monjur Mourshed
- Mechanical and Automotive Engineering, School of Engineering, RMIT University, Bundoora, Victoria 3083 Australia
- Department of Mechanical Engineering, Rajshahi University of Engineering and Technology (RUET), Rajshahi, 6204 Bangladesh
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19
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Kuhn T, Mamin M, Bindschedler S, Bshary R, Estoppey A, Gonzalez D, Palmieri F, Junier P, Richter XYL. Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211592. [PMID: 36483758 PMCID: PMC9727664 DOI: 10.1098/rsos.211592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.
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Affiliation(s)
- Thierry Kuhn
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Marine Mamin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Redouan Bshary
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
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20
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Calleja-Solanas V, Khalil N, Gómez-Gardeñes J, Hernández-García E, Meloni S. Structured interactions as a stabilizing mechanism for competitive ecological communities. Phys Rev E 2022; 106:064307. [PMID: 36671121 DOI: 10.1103/physreve.106.064307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022]
Abstract
How large ecosystems can create and maintain the remarkable biodiversity we see in nature is probably one of the biggest open questions in science, attracting attention from different fields, from theoretical ecology to mathematics and physics. In this context, modeling the stable coexistence of species competing for limited resources is a particularly challenging task. From a mathematical point of view, coexistence in competitive dynamics can be achieved when dominance among species forms intransitive loops. However, these relationships usually lead to species' relative abundances neutrally cycling without converging to a stable equilibrium. Although in recent years several mechanisms have been proposed, models able to explain species coexistence in competitive communities are still limited. Here we identify locality in the interactions as one of the simplest mechanisms leading to stable species coexistence. We consider a simplified ecosystem where individuals of each species lay on a spatial network and interactions are possible only between nodes within a certain distance. Varying such distance allows to interpolate between local and global competition. Our results demonstrate, within the scope of our model, that species coexist reaching a stable equilibrium when two conditions are met: individuals are embedded in space and can only interact with other individuals within a short distance. On the contrary, when one of these ingredients is missing, large oscillations and neutral cycles emerge.
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Affiliation(s)
- Violeta Calleja-Solanas
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, 07122 Palma de Mallorca, Spain
| | - Nagi Khalil
- Complex Systems Group & GISC, Universidad Rey Juan Carlos, Móstoles 28933, Madrid, Spain
| | - Jesús Gómez-Gardeñes
- GOTHAM Lab., Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain.,Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain.,Center for Computational Social Science (CCSS), University of Kobe, 657-8501 Kobe, Japan
| | - Emilio Hernández-García
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, 07122 Palma de Mallorca, Spain
| | - Sandro Meloni
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, 07122 Palma de Mallorca, Spain
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21
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Roy T, Dey TK, Jamal M. Microplastic/nanoplastic toxicity in plants: an imminent concern. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:27. [PMID: 36279030 PMCID: PMC9589797 DOI: 10.1007/s10661-022-10654-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/10/2022] [Indexed: 05/04/2023]
Abstract
The toxic impact of microplastics/nanoplastics (MPs/NPs) in plants and the food chain has recently become a top priority. Several research articles highlighted the impact of MPs/NPs on the aquatic food chain; however, very little has been done in the terrestrial ecosystem. A number of studies revealed that MPs/NPs uptake and subsequent translocation in plants alter plant morphological, physiological, biochemical, and genetic properties to varying degrees. However, there is a research gap regarding MPs/NPs entry into plants, associated factors influencing phytotoxicity levels, and potential remediation plans in terms of food safety and security. To address these issues, all sources of MPs/NPs intrusion in agroecosystems should be revised to avoid these hazardous materials with special consideration as preventive measures. Furthermore, this review focuses on the routes of accumulation and transmission of MPs/NPs into plant tissues, related aspects influencing the intensity of plant stress, and potential solutions to improve food quality and quantity. This paper also concludes by providing an outlook approach of applying exogenous melatonin and introducing engineered plants that would enhance stress tolerance against MPs/NPs. In addition, an overview of inoculation of beneficial microorganisms and encapsulated enzymes in soil has been addressed, which would make the degradation of MPs/NPs faster.
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Affiliation(s)
- Tapati Roy
- Department of Agronomy, Faculty of Agriculture, Khulna Agricultural University, Khulna, Bangladesh
- Micropastics Solution Ltd., Incubation Centre, KUET Business Park, Khulna, Bangladesh
| | - Thuhin K Dey
- Department of Leather Engineering, Faculty of Mechanical Engineering, Khulna University of Engineering & Technology, Khulna, 9203, Bangladesh
- Micropastics Solution Ltd., Incubation Centre, KUET Business Park, Khulna, Bangladesh
| | - Mamun Jamal
- Department of Chemistry, Faculty of Civil Engineering, Khulna University of Engineering & Technology, Khulna, 9203, Bangladesh.
- Micropastics Solution Ltd., Incubation Centre, KUET Business Park, Khulna, Bangladesh.
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22
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Birt HWG, Tharp CL, Custer GF, Dini-Andreote F. Root phenotypes as modulators of microbial microhabitats. FRONTIERS IN PLANT SCIENCE 2022; 13:1003868. [PMID: 36212354 PMCID: PMC9539067 DOI: 10.3389/fpls.2022.1003868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/08/2022] [Indexed: 06/09/2023]
Abstract
Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems.
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23
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Lu Y, Shen C, Wu M, Du C, Shi L, Park J. Enhancing coexistence of mobile species in the cyclic competition system by wildlife refuge. CHAOS (WOODBURY, N.Y.) 2022; 32:081104. [PMID: 36049906 DOI: 10.1063/5.0093342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
We investigate evolving dynamics of cyclically competing species on spatially extended systems with considering a specific region, which is called the "wildlife refuge," one of the institutional ways to preserve species biodiversity. Through Monte-Carlo simulations, we found that the refuge can play not groundbreaking but an important role in species survival. Species coexistence is maintained at a moderate mobility regime, which traditionally leads to the collapse of coexistence, and eventually, the extinction is postponed depending on the competition rate rather than the portion of the refuge. Incorporating the extinction probability and Fourier transform supported our results in both stochastic and analogous ways. Our findings may provide valuable evidence to assist fields of ecological/biological sciences in understanding the presence and construction of refuges for wildlife with associated effects on species biodiversity.
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Affiliation(s)
- Yikang Lu
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, Yunnan 650221, China
| | - Chen Shen
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, Yunnan 650221, China
| | - Mengjie Wu
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, Yunnan 650221, China
| | - Chunpeng Du
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, Yunnan 650221, China
| | - Lei Shi
- School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, Yunnan 650221, China
| | - Junpyo Park
- Department of Applied Mathematics, Kyung Hee University, Yongin 17104, Republic of Korea
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24
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Eigentler L, Stanley‐Wall NR, Davidson FA. A theoretical framework for multi‐species range expansion in spatially heterogeneous landscapes. OIKOS 2022. [DOI: 10.1111/oik.09077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, Univ. of Dundee Dundee UK
- Mathematics, School of Science and Engineering, Univ. of Dundee Dundee UK
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25
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Liang Y, Ma A, Zhuang G. Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles. Front Microbiol 2022; 13:829717. [PMID: 35283862 PMCID: PMC8905317 DOI: 10.3389/fmicb.2022.829717] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 01/30/2023] Open
Abstract
In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.
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Affiliation(s)
- Yu Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
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26
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Junkins EN, McWhirter JB, McCall LI, Stevenson BS. Environmental structure impacts microbial composition and secondary metabolism. ISME COMMUNICATIONS 2022; 2:15. [PMID: 37938679 PMCID: PMC9723690 DOI: 10.1038/s43705-022-00097-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/03/2022] [Accepted: 01/18/2022] [Indexed: 05/11/2023]
Abstract
Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.
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Affiliation(s)
- Emily N Junkins
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Joseph B McWhirter
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Laura-Isobel McCall
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Department of Earth and Planetary Science, Northwestern University, Chicago, IL, USA
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27
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Teng L, Zhu Y, Li H, Song X, Shi L. The phytotoxicity of microplastics to the photosynthetic performance and transcriptome profiling of Nicotiana tabacum seedlings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113155. [PMID: 35007831 DOI: 10.1016/j.ecoenv.2021.113155] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/07/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Microplastics (MPs), as emerging "new generation" organic contaminants, have attracted extensive attention regarding their severe toxicity to aquatic and terrestrial organisms. However, the responses of plant photosynthesis to soil MP pollution are unclear. In this study, Nicotiana tabacum seedlings were grown in soils containing 0~1000 g·kg-1 polyethylene (PE)-MPs for 48 days. PE-MPs significantly increased the superoxide anion content by 15.3~44.8% but decreased the chlorophyll content and Rubisco activity by 4.3~14.0% and 4.23~30.9%, respectively. PE-MPs also inhibited RuBP carboxylation activation and regeneration, restrained light use efficiency, and prevented dark respiration, thereby reducing the light-saturated photosynthesis rate. The changed shape of OJIP transients indicated that PE-MP toxicity inhibited not only the primary photochemistry rate but also photoelectrochemical quenching, resulting in decreased quantum yields. RNA-Seq revealed thousands of differentially expressed genes (DEGs), among which 79 highly expressed DEGs were enriched in photosynthesis-related processes. Functional annotation revealed that the reduction in environment stress was mainly due to the repressed expression of light harvesting-, electron transport- and photosystem-related genes in chloroplasts. This study regarding the physiological and molecular responses of photosynthetic performance to soil PE-MP pollution provides a new viewpoint for exploring the plant photosynthesis regulating and protective mechanisms under soil MP stresses.
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Affiliation(s)
- Linhong Teng
- College of Life Sciences, Dezhou University, De'zhou 253023, China
| | - Yihao Zhu
- College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Haibin Li
- College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Xiliang Song
- College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China.
| | - Lianhui Shi
- College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China.
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28
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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: 97] [Impact Index Per Article: 32.3] [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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29
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Ullah R, Tsui MTK, Chen H, Chow A, Williams C, Ligaba-Osena A. Microplastics interaction with terrestrial plants and their impacts on agriculture. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:1024-1041. [PMID: 34245023 DOI: 10.1002/jeq2.20264] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/30/2021] [Indexed: 05/27/2023]
Abstract
Microplastics (MPs) are widespread in natural ecosystems and have attracted considerable attention from scientists all over the world because they are believed to threaten every life form. In addition to their potential physical and chemical effects on organisms, MPs may act as a carrier for many micropollutants, including antibiotics, heavy metals, and others. Over the last 10-15 yr, extensive research has been carried out on MPs in marine environments regarding their sources, fate, and toxicity. However, studies concerning their accumulation in the soil ecosystem, uptake, internalization, and impacts on photosynthetic components of the terrestrial ecosystem and risk assessments have been scanty. Thus, there is a large knowledge gap on the extent to which terrestrial environments, especially agroecosystems, are affected by MPs and their subsequent risks to human health. This review summarizes up-to-date findings about MPs on terrestrial environments and provides guidelines for future studies regarding the phytotoxic effects of MPs on plants; the mechanism of uptake and translocation in plant tissues; detection tools for MPs in plants; impacts on plant growth, plant development, and agricultural productivity; and, most important, the future prospects of MPs interaction and accumulation in plants.
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Affiliation(s)
- Raza Ullah
- Laboratory of Plant Molecular Biology and Biotechnology, Dep. of Biology, Univ. of North Carolina Greensboro, Greensboro, NC, 27402, USA
| | - Martin Tsz-Ki Tsui
- Laboratory of Plant Molecular Biology and Biotechnology, Dep. of Biology, Univ. of North Carolina Greensboro, Greensboro, NC, 27402, USA
- School of Life Sciences, the Chinese Univ. of Hong Kong, Hong Kong SAR, Shatin, New Territories, China
| | - Huan Chen
- Biogeochemistry & Environmental Quality Research Group, Clemson Univ., Clemson, SC, 29442, USA
- Dep. of Environmental Engineering and Earth Sciences, Clemson Univ., Clemson, SC, 29634, USA
| | - Alex Chow
- Biogeochemistry & Environmental Quality Research Group, Clemson Univ., Clemson, SC, 29442, USA
- Dep. of Environmental Engineering and Earth Sciences, Clemson Univ., Clemson, SC, 29634, USA
| | - Clinton Williams
- USDA-ARS, US Arid Land Agricultural Research Center, 21881 N. Cardon Ln, Maricopa, AZ, 85138, USA
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Dep. of Biology, Univ. of North Carolina Greensboro, Greensboro, NC, 27402, USA
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30
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Debray R, Herbert RA, Jaffe AL, Crits-Christoph A, Power ME, Koskella B. Priority effects in microbiome assembly. Nat Rev Microbiol 2021; 20:109-121. [PMID: 34453137 DOI: 10.1038/s41579-021-00604-w] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
Advances in next-generation sequencing have enabled the widespread measurement of microbiome composition across systems and over the course of microbiome assembly. Despite substantial progress in understanding the deterministic drivers of community composition, the role of historical contingency remains poorly understood. The establishment of new species in a community can depend on the order and/or timing of their arrival, a phenomenon known as a priority effect. Here, we review the mechanisms of priority effects and evidence for their importance in microbial communities inhabiting a range of environments, including the mammalian gut, the plant phyllosphere and rhizosphere, soil, freshwaters and oceans. We describe approaches for the direct testing and prediction of priority effects in complex microbial communities and illustrate these with re-analysis of publicly available plant and animal microbiome datasets. Finally, we discuss the shared principles that emerge across study systems, focusing on eco-evolutionary dynamics and the importance of scale. Overall, we argue that predicting when and how current community state impacts the success of newly arriving microbial taxa is crucial for the management of microbiomes to sustain ecological function and host health. We conclude by discussing outstanding conceptual and practical challenges that are faced when measuring priority effects in microbiomes.
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Affiliation(s)
- Reena Debray
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Robin A Herbert
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Mary E Power
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
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31
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Ramos CH, Rodríguez-Sánchez E, Del Angel JAA, Arzola AV, Benítez M, Escalante AE, Franci A, Volpe G, Rivera-Yoshida N. The environment topography alters the way to multicellularity in Myxococcus xanthus. SCIENCE ADVANCES 2021; 7:7/35/eabh2278. [PMID: 34433567 PMCID: PMC8386931 DOI: 10.1126/sciadv.abh2278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/02/2021] [Indexed: 05/10/2023]
Abstract
The social soil-dwelling bacterium Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physicochemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus In topographies realized by randomly placing silica particles over agar plates, we observe that the cells' interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size, and shape of the fruiting bodies and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological, and medical relevance.
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Affiliation(s)
- Corina H Ramos
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Edna Rodríguez-Sánchez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Juan Antonio Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, México
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alessio Franci
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
| | - Natsuko Rivera-Yoshida
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico.
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
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32
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Dubey M, Hadadi N, Pelet S, Carraro N, Johnson DR, van der Meer JR. Environmental connectivity controls diversity in soil microbial communities. Commun Biol 2021; 4:492. [PMID: 33888858 PMCID: PMC8062517 DOI: 10.1038/s42003-021-02023-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/24/2021] [Indexed: 01/03/2023] Open
Abstract
Interspecific interactions are thought to govern the stability and functioning of microbial communities, but the influence of the spatial environment and its structural connectivity on the potential of such interactions to unfold remain largely unknown. Here we studied the effects on community growth and microbial diversity as a function of environmental connectivity, where we define environmental connectivity as the degree of habitat fragmentation preventing microbial cells from living together. We quantitatively compared growth of a naturally-derived high microbial diversity community from soil in a completely mixed liquid suspension (high connectivity) to growth in a massively fragmented and poorly connected environment (low connectivity). The low connectivity environment consisted of homogenously-sized miniature agarose beads containing random single or paired founder cells. We found that overall community growth was the same in both environments, but the low connectivity environment dramatically reduced global community-level diversity compared to the high connectivity environment. Experimental observations were supported by community growth modeling. The model predicts a loss of diversity in the low connectivity environment as a result of negative interspecific interactions becoming more dominant at small founder species numbers. Counterintuitively for the low connectivity environment, growth of isolated single genotypes was less productive than that of random founder genotype cell pairs, suggesting that the community as a whole profited from emerging positive interspecific interactions. Our work demonstrates the importance of environmental connectivity for growth of natural soil microbial communities, which aids future efforts to intervene in or restore community composition to achieve engineering and biotechnological objectives. Manupriyam Dubey et al. use experimental systems with naturally derived soil microbiomes in liquid suspensions and encapsulated beads to compare community dynamics in well-connected and poorly connected environments. While their results show that microbial growth does not vary between conditions, they report that low connectivity led to reduced microbial diversity and suggest that these reductions in microbial diversity may be due to increased negative interspecific interactions.
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Affiliation(s)
- Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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33
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Eigentler L. Species coexistence in resource‐limited patterned ecosystems is facilitated by the interplay of spatial self‐organisation and intraspecific competition. OIKOS 2021. [DOI: 10.1111/oik.07880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- L. Eigentler
- Division of Molecular Microbiology, School of Life Sciences, Univ. of Dundee Dundee UK
- Maxwell Inst. for Mathematical Sciences, Dept of Mathematics, Heriot‐Watt Univ. Edinburgh UK
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34
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Borer B, Or D. Spatiotemporal metabolic modeling of bacterial life in complex habitats. Curr Opin Biotechnol 2021; 67:65-71. [PMID: 33493977 DOI: 10.1016/j.copbio.2021.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/21/2020] [Accepted: 01/07/2021] [Indexed: 01/04/2023]
Abstract
The combination of genome-scale metabolic networks with spatially explicit representation of microbial habitats (spatiotemporal metabolic network modeling) paves the way to predict complex metabolic landscapes to a hitherto unparalleled detail, thus providing new insights into trophic interactions occurring at different scales. Placing detailed bacterial metabolism in realistic physical environment highlights the roles of physical barriers and diffusional bottlenecks on bacterial community interactions, structure and stability. We review recent advances in spatiotemporal metabolic network modeling using a few illustrative examples that highlight the immense potential of these novel approaches to interpret and design metabolic mediated interactions in structures (natural and engineered) environments.
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Affiliation(s)
- Benedict Borer
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland; The Department for Earth, Atmospheric and Planetary Science, MIT, Boston, MA, USA.
| | - Dani Or
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland; Div. of Hydrologic Sciences, Desert Research Institute, Reno, NV, USA
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35
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Ursell T. Structured environments foster competitor coexistence by manipulating interspecies interfaces. PLoS Comput Biol 2021; 17:e1007762. [PMID: 33412560 PMCID: PMC7790539 DOI: 10.1371/journal.pcbi.1007762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/19/2020] [Indexed: 01/12/2023] Open
Abstract
Natural environments, like soils or the mammalian gut, frequently contain microbial consortia competing within a niche, wherein many species contain genetically encoded mechanisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize local competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that interfacial competition localizes to physical structures, stabilizing competitive ecological networks of many species, even with significant differences in the strength of competitive interactions between species. Within a limited range of parameter space, we show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physical environments with finer structure can sustain a broader spectrum of interspecific competition. These results highlight the potentially stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility.
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Affiliation(s)
- Tristan Ursell
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- Materials Science Institute, University of Oregon, Eugene, Oregon, United States of America
- Department of Physics, University of Oregon, Eugene, Oregon, United States of America
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Steinbach G, Crisan C, Ng SL, Hammer BK, Yunker PJ. Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms. J R Soc Interface 2020; 17:20200486. [PMID: 33292099 PMCID: PMC7811593 DOI: 10.1098/rsif.2020.0486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial communities are governed by a wide variety of social interactions, some of which are antagonistic with potential significance for bacterial warfare. Several antagonistic mechanisms, such as killing via the type VI secretion system (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defence of bacterial populations. However, we find that the efficacy of contact killing is severely limited by the material consequences of cell death. Through experiments with Vibrio cholerae strains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing physical contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as 106-fold, we find that, as a result of the formation of dead cell debris barriers, the impact of contact killing depends sensitively on the initial concentration of killer cells. Killer cells are incapable of invading or eliminating competitors on a community level. Instead, bacterial warfare itself can facilitate coexistence between nominally antagonistic strains. While a variety of defensive strategies against microbial warfare exist, the material consequences of cell death provide target cells with their first line of defence.
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Affiliation(s)
- Gabi Steinbach
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cristian Crisan
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Siu Lung Ng
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian K. Hammer
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter J. Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
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37
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Borer B, Ciccarese D, Johnson D, Or D. Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages. Commun Biol 2020; 3:685. [PMID: 33208809 PMCID: PMC7674409 DOI: 10.1038/s42003-020-01409-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Evidence suggests that bacterial community spatial organization affects their ecological function, yet details of the mechanisms that promote spatial patterns remain difficult to resolve experimentally. In contrast to bacterial communities in liquid cultures, surface-attached range expansion fosters genetic segregation of the growing population with preferential access to nutrients and reduced mechanical restrictions for cells at the expanding periphery. Here we elucidate how localized conditions in cross-feeding bacterial communities shape community spatial organization. We combine experiments with an individual based mathematical model to resolve how trophic dependencies affect localized growth rates and nucleate successful cell lineages. The model tracks individual cell lineages and attributes these with trophic dependencies that promote counterintuitive reproductive advantages and result in lasting influences on the community structure, and potentially, on its functioning. We examine persistence of lucky lineages in structured habitats where expansion is interrupted by physical obstacles to gain insights into patterns in porous domains.
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Affiliation(s)
- Benedict Borer
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland.
| | - Davide Ciccarese
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
| | - David Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
| | - Dani Or
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
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38
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Strain Background, Species Frequency, and Environmental Conditions Are Important in Determining Pseudomonas aeruginosa and Staphylococcus aureus Population Dynamics and Species Coexistence. Appl Environ Microbiol 2020; 86:AEM.00962-20. [PMID: 32651205 DOI: 10.1128/aem.00962-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/04/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial communities in the environment and in infections are typically diverse, yet we know little about the factors that determine interspecies interactions. Here, we apply concepts from ecological theory to understand how biotic and abiotic factors affect interaction patterns between the two opportunistic human pathogens Pseudomonas aeruginosa and Staphylococcus aureus, which often cooccur in polymicrobial infections. Specifically, we conducted a series of short- and long-term competition experiments between P. aeruginosa PAO1 (as our reference strain) and three different S. aureus strains (Cowan I, 6850, and JE2) at three starting frequencies and under three environmental (culturing) conditions. We found that the competitive ability of P. aeruginosa strongly depended on the strain background of S. aureus, whereby P. aeruginosa dominated against Cowan I and 6850 but not against JE2. In the latter case, both species could end up as winners depending on conditions. Specifically, we observed strong frequency-dependent fitness patterns, including positive frequency dependence, where P. aeruginosa could dominate JE2 only when common (not when rare). Finally, changes in environmental (culturing) conditions fundamentally altered the competitive balance between the two species in a way that P. aeruginosa dominance increased when moving from shaken to static environments. Altogether, our results highlight that ecological details can have profound effects on the competitive dynamics between coinfecting pathogens and determine whether two species can coexist or invade each others' populations from a state of rare frequency. Moreover, our findings might parallel certain dynamics observed in chronic polymicrobial infections.IMPORTANCE Bacterial infections are frequently caused by more than one species, and such polymicrobial infections are often considered more virulent and more difficult to treat than the respective monospecies infections. Pseudomonas aeruginosa and Staphylococcus aureus are among the most important pathogens in polymicrobial infections, and their cooccurrence is linked to worse disease outcome. There is great interest in understanding how these two species interact and what the consequences for the host are. While previous studies have mainly looked at molecular mechanisms implicated in interactions between P. aeruginosa and S. aureus, here we show that ecological factors, such as strain background, species frequency, and environmental conditions, are important elements determining population dynamics and species coexistence patterns. We propose that the uncovered principles also play major roles in infections and, therefore, proclaim that an integrative approach combining molecular and ecological aspects is required to fully understand polymicrobial infections.
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39
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Castledine M, Sierocinski P, Padfield D, Buckling A. Community coalescence: an eco-evolutionary perspective. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190252. [PMID: 32200752 PMCID: PMC7133537 DOI: 10.1098/rstb.2019.0252] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities-the type of species interaction that dominates the community-might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Meaghan Castledine
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
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40
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Ben Said S, Tecon R, Borer B, Or D. The engineering of spatially linked microbial consortia - potential and perspectives. Curr Opin Biotechnol 2020; 62:137-145. [PMID: 31678714 PMCID: PMC7208534 DOI: 10.1016/j.copbio.2019.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023]
Abstract
Traditional biotechnological applications of microorganisms employ mono-cultivation or co-cultivation in well-mixed vessels disregarding the potential of spatially organized cultures. Metabolic specialization and guided species interactions facilitated through spatial isolation would enable consortia of microbes to accomplish more complex functions than currently possible, for bioproduction as well as biodegradation processes. Here, we review concepts of spatially linked microbial consortia in which spatial arrangement is optimized to increase control and facilitate new species combinations. We highlight that genome-scale metabolic network models can inform the design and tuning of synthetic microbial consortia and suggest that a standardized assembly of such systems allows the combination of 'incompatibles', potentially leading to countless novel applications.
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Affiliation(s)
- Sami Ben Said
- Microbial Systems Ecology, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland.
| | - Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Benedict Borer
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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41
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König S, Vogel HJ, Harms H, Worrich A. Physical, Chemical and Biological Effects on Soil Bacterial Dynamics in Microscale Models. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Chacón JM, Shaw AK, Harcombe WR. Increasing growth rate slows adaptation when genotypes compete for diffusing resources. PLoS Comput Biol 2020; 16:e1007585. [PMID: 31910213 PMCID: PMC6946136 DOI: 10.1371/journal.pcbi.1007585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 11/18/2022] Open
Abstract
The rate at which a species responds to natural selection is a central predictor of the species’ ability to adapt to environmental change. It is well-known that spatially-structured environments slow the rate of adaptation due to increased intra-genotype competition. Here, we show that this effect magnifies over time as a species becomes better adapted and grows faster. Using a reaction-diffusion model, we demonstrate that growth rates are inextricably coupled with effective spatial scales, such that higher growth rates cause more localized competition. This has two effects: selection requires more generations for beneficial mutations to fix, and spatially-caused genetic drift increases. Together, these effects diminish the value of additional growth rate mutations in structured environments. What determines how quickly a beneficial mutation will spread through a population? The intuitive answer is that mutations that confer faster growth rates will spread at a rate that is relative to the size of the growth-rate benefit. Indeed, this is true in a well-mixed environment where all genotypes compete globally. But most organisms don’t live in a simple well-mixed environment. Many organisms, like bacteria, live in a structured environment, such as on the surface of a solid substrate. Does life on a surface change the expectation about the spread of faster-growing mutants? We developed a mathematical model to answer this question, and found that on a surface, the actual growth rates—not just the relative growth rates—were critical to determining how fast a faster-growing mutant spread through a population. When the simulated organisms grew slowly, competition was basically global and a faster-growing mutant could pre-empt resources from far-away competitors. In contrast, when organisms grew more quickly, competition became much more localized, and the faster-growing mutant could only steal resources from neighboring competitors. This result means that there are diminishing returns to series of mutations which confer growth-rate benefits. This idea will help us predict and understand future and past evolutionary trajectories.
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Affiliation(s)
- Jeremy M. Chacón
- University of Minnesota, Department of Ecology, Evolution, and Behavior, St. Paul, Minnesota, United States of America
- * E-mail:
| | - Allison K. Shaw
- University of Minnesota, Department of Ecology, Evolution, and Behavior, St. Paul, Minnesota, United States of America
| | - William R. Harcombe
- University of Minnesota, Department of Ecology, Evolution, and Behavior, St. Paul, Minnesota, United States of America
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43
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Ansari AF, Acharya NIS, Kumaran S, Ravindra K, Reddy YBS, Dixit NM, Raut J. 110th Anniversary: High-Order Interactions Can Eclipse Pairwise Interactions in Shaping the Structure of Microbial Communities. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aamir Faisal Ansari
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | | | | | | | | | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Janhavi Raut
- Unilever R&D India Pvt, Ltd., Bangalore 560066, India
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44
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Lee AM, Sæther B, Engen S. Spatial covariation of competing species in a fluctuating environment. Ecology 2019; 101:e02901. [DOI: 10.1002/ecy.2901] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/10/2019] [Accepted: 09/03/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Aline Magdalena Lee
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology 7491 Trondheim Norway
| | - Bernt‐Erik Sæther
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology 7491 Trondheim Norway
| | - Steinar Engen
- Centre for Biodiversity Dynamics Department of Mathematical Sciences Norwegian University of Science and Technology 7491 Trondheim Norway
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45
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Fuentes-Hernández A, Hernández-Koutoucheva A, Muñoz AF, Domínguez Palestino R, Peña-Miller R. Diffusion-driven enhancement of the antibiotic resistance selection window. J R Soc Interface 2019; 16:20190363. [PMID: 31506045 DOI: 10.1098/rsif.2019.0363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The current crisis of antimicrobial resistance in clinically relevant pathogens has highlighted our limited understanding of the ecological and evolutionary forces that drive drug resistance adaptation. For instance, although human tissues are highly heterogeneous, most of our mechanistic understanding about antibiotic resistance evolution is based on constant and well-mixed environmental conditions. A consequence of considering spatial heterogeneity is that, even if antibiotics are prescribed at high dosages, the penetration of drug molecules through tissues inevitably produces antibiotic gradients, exposing bacterial populations to a range of selective pressures and generating a dynamic fitness landscape that changes in space and time. In this paper, we will use a combination of mathematical modelling and computer simulations to study the population dynamics of susceptible and resistant strains competing for resources in a network of micro-environments with varying degrees of connectivity. Our main result is that highly connected environments increase diffusion of drug molecules, enabling resistant phenotypes to colonize a larger number of spatial locations. We validated this theoretical result by culturing fluorescently labelled Escherichia coli in 3D-printed devices that allow us to control the rate of diffusion of antibiotics between neighbouring compartments and quantify the spatio-temporal distribution of resistant and susceptible bacterial cells.
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Affiliation(s)
- Ayari Fuentes-Hernández
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - Anastasia Hernández-Koutoucheva
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - Alán F Muñoz
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - Raúl Domínguez Palestino
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - Rafael Peña-Miller
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
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46
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König S, Köhnke MC, Firle AL, Banitz T, Centler F, Frank K, Thullner M. Disturbance Size Can Be Compensated for by Spatial Fragmentation in Soil Microbial Ecosystems. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Rillig MC, Lehmann A, de Souza Machado AA, Yang G. Microplastic effects on plants. THE NEW PHYTOLOGIST 2019; 223:1066-1070. [PMID: 30883812 DOI: 10.1111/nph.15794] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/11/2019] [Indexed: 05/06/2023]
Abstract
Microplastic effects in terrestrial ecosystems have recently moved into focus, after about a decade of research being limited to aquatic systems. While effects on soil physical properties and soil biota are starting to become apparent, there is not much information on the consequences for plant performance. We here propose and discuss mechanistic pathways through which microplastics could impact plant growth, either positively or negatively. These effects will vary as a function of plant species, and plastic type, and thus are likely to translate to changes in plant community composition and perhaps primary production. Our mechanistic framework serves to guide ongoing and future research on this important topic.
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Affiliation(s)
- Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, 14195, Germany
| | - Anika Lehmann
- Institut für Biologie, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, 14195, Germany
| | - A Abel de Souza Machado
- Institut für Biologie, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, 14195, Germany
| | - Gaowen Yang
- Institut für Biologie, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, 14195, Germany
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48
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Worrich A, Musat N, Harms H. Associational effects in the microbial neighborhood. ISME JOURNAL 2019; 13:2143-2149. [PMID: 31114015 DOI: 10.1038/s41396-019-0444-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022]
Abstract
Even though "perfect" metagenomes or metatranscriptomes are close at hand, the implicit assumption of spatial homogeneity in the "omic" approaches makes it difficult if not impossible to relate those data to ecological processes occurring in natural and man-made ecosystems. In fact, the distribution of microbes in their habitats is far from being uniform and random. Microbial communities show a high degree of spatial organization that stems from environmental gradients and local interactions. These interactions can be very complex and may involve multiple species. Several studies highlighted the importance of indirect interactions for community stability, but the absence of a theoretical framework for microbial ecology restricts the possibilities to strike a balance between the investigation of simple communities with purely pairwise interactions and the attempts to understand interaction patterns in whole communities based on meta-omics studies. Here we suggest adapting the concept of Associational Effects (AE) from plant ecology, to better understand the link between ecological interactions, spatial arrangement, and stability in microbial communities. By bringing together a conceptual framework developed for plants and observations made for microbes, this perspective article fosters synthesis of related disciplines to yield novel insights into the advancing field of spatial microbial ecology. To promote the integration into microbial ecology, we (i) outline the theoretical background of AE, (ii) collect underlying mechanisms by literature synthesis, (iii) propose a three-point roadmap for the investigation of AE in microbial communities, and (iv) discuss its implications for microbial ecology research.
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Affiliation(s)
- Anja Worrich
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany.
| | - Niculina Musat
- Department of Isotope Biogeochemistry, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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