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Vass M, Székely AJ, Carlsson-Graner U, Wikner J, Andersson A. Microeukaryote community coalescence strengthens community stability and elevates diversity. FEMS Microbiol Ecol 2024; 100:fiae100. [PMID: 39003240 PMCID: PMC11287207 DOI: 10.1093/femsec/fiae100] [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: 02/21/2024] [Revised: 06/19/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024] Open
Abstract
Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities, and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e. one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.
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Affiliation(s)
- Máté Vass
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
- Division of Systems and Synthetic Biology, Department of Life Sciences, Science for Life Laboratory, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Anna J Székely
- Division of Microbial Ecology, Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Ulla Carlsson-Graner
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, SE-90571 Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, SE-90571 Hörnefors, Sweden
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Bagra K, Kneis D, Padfield D, Szekeres E, Teban-Man A, Coman C, Singh G, Berendonk TU, Klümper U. Contrary effects of increasing temperatures on the spread of antimicrobial resistance in river biofilms. mSphere 2024; 9:e0057323. [PMID: 38323843 PMCID: PMC10900892 DOI: 10.1128/msphere.00573-23] [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: 10/10/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
River microbial communities regularly act as the first barrier of defense against the spread of antimicrobial resistance genes (ARGs) that enter environmental microbiomes through wastewater. However, how the invasion dynamics of wastewater-borne ARGs into river biofilm communities will shift due to climate change with increasing average and peak temperatures remains unknown. Here, we aimed to elucidate the effects of increasing temperatures on the naturally occurring river biofilm resistome, as well as the invasion success of foreign ARGs entering through wastewater. Natural biofilms were grown in a low-anthropogenic impact river and transferred to artificial laboratory recirculation flume systems operated at three different temperatures (20°C, 25°C, and 30°C). After 1 week of temperature acclimatization, significant increases in the abundance of the naturally occurring ARGs in biofilms were detected at higher temperatures. After this acclimatization period, biofilms were exposed to a single pulse of wastewater, and the invasion dynamics of wastewater-borne ARGs were analyzed over 2 weeks. After 1 day, wastewater-borne ARGs were able to invade the biofilms successfully with no observable effect of temperature on their relative abundance. However, thereafter, ARGs were lost at a far increased rate at 30°C, with ARG levels dropping to the initial natural levels after 14 days. Contrary to the lower temperatures, ARGs were either lost at slower rates or even able to establish themselves in biofilms with stable relative abundances above natural levels. Hence, higher temperatures come with contrary effects on river biofilm resistomes: naturally occurring ARGs increase in abundance, while foreign, invading ARGs are lost at elevated speeds.IMPORTANCEInfections with bacteria that gained resistance to antibiotics are taking millions of lives annually, with the death toll predicted to increase. River microbial communities act as a first defense barrier against the spread of antimicrobial resistance genes (ARGs) that enter the environment through wastewater after enrichment in human and animal microbiomes. The global increase in temperature due to climate change might disrupt this barrier effect by altering microbial community structure and functions. We consequently explored how increasing temperatures alter ARG spread in river microbial communities. At higher temperatures, naturally occurring ARGs increased in relative abundance. However, this coincided with a decreased success rate of invading foreign ARGs from wastewater to establish themselves in the communities. Therefore, to predict the effects of climate change on ARG spread in river microbiomes, it is imperative to consider if the river ecosystem and its resistome are dominated by naturally occurring or invading foreign ARGs.
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Affiliation(s)
- Kenyum Bagra
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
- Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - David Kneis
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Daniel Padfield
- Environment and Sustainability Institute, University of Exeter, Exeter, United Kingdom
| | - Edina Szekeres
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
| | - Adela Teban-Man
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
| | - Cristian Coman
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
| | - Gargi Singh
- Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Thomas U. Berendonk
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
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Lumpi T, Guo X, Lindström ES. Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence. Environ Microbiol 2023; 25:2289-2302. [PMID: 37381117 DOI: 10.1111/1462-2920.16450] [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: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.
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Affiliation(s)
- Theresa Lumpi
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Xin Guo
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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Márton Z, Csitári B, Felföldi T, Hidas A, Jordán F, Szabó A, Székely AJ. Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes. FEMS Microbiol Ecol 2023; 99:fiad095. [PMID: 37586889 PMCID: PMC10449373 DOI: 10.1093/femsec/fiad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. However, departures from usual seasonal trends are often reported. To understand the role of local stressors in modifying seasonal succession, we sampled fortnightly, throughout three seasons, five nearby shallow soda lakes exposed to identical seasonal and meteorological changes. We characterised their microeukaryotic and bacterial communities by amplicon sequencing of the 16S and 18S rRNA gene, respectively. Biological interactions were inferred by analyses of synchronous and time-shifted interaction networks, and the keystone taxa of the communities were topologically identified. The lakes showed similar succession patterns during the study period with spring being characterised by the relevance of trophic interactions and a certain level of community stability followed by a more dynamic and variable summer-autumn period. Adaptation to general seasonal changes happened through shared core microbiome of the lakes. Stochastic events such as desiccation disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. Our results demonstrated that, despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet local stressors such as droughts instigate deviations from prevalent trends to a greater extent for microeukaryotic than for bacterial communities.
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Affiliation(s)
- Zsuzsanna Márton
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- National Multidisciplinary Laboratory for Climate Change, Centre for Ecological Research, H-1113 Budapest, Hungary
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Bianka Csitári
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
- Karolinska Institutet, 171 65 Stockholm, Sweden
- Uppsala University, 752 36 Uppsala, Sweden
| | - Tamás Felföldi
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - András Hidas
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Ferenc Jordán
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anna J Székely
- Uppsala University, 752 36 Uppsala, Sweden
- Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Wan W, Gadd GM, He D, Liu W, Xiong X, Ye L, Cheng Y, Yang Y. Abundance and diversity of eukaryotic rather than bacterial community relate closely to the trophic level of urban lakes. Environ Microbiol 2023; 25:661-674. [PMID: 36527341 DOI: 10.1111/1462-2920.16317] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Scientific understanding of biotic effects on the water trophic level is lacking for urban lakes during algal bloom development stage. Based on the Illumina MiSeq sequencing, quantitative polymerase chain reaction (PCR), and multiple statistical analyses, we estimated distribution patterns and ecological roles of planktonic bacteria and eukaryotes in urban lakes during algal bloom development stage (i.e., April, May, and June). Cyanobacteria and Chlorophyta mainly dominated algal blooms. Bacteria exhibited significantly higher absolute abundance and community diversity than eukaryotes, whereas abundance and diversity of eukaryotic rather than bacterial community relate closely to the water trophic level. Multinutrient cycling (MNC) index was significantly correlated with eukaryotic diversity rather than bacterial diversity. Stronger species replacement, broader environmental breadth, and stronger phylogenetic signal were found for eukaryotic community than for bacterial community. In contrast, bacterial community displayed stronger community stability and environmental constraint than eukaryotic community. Stochastic and differentiating processes contributed more to community assemblies of bacteria and eukaryotes. Our results emphasized that a strong linkage between planktonic diversity and MNC ensured a close relationship between planktonic diversity and the water trophic level of urban lakes. Our findings could be useful to guide the formulation and implementation of environmental lake protection measures.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, People's Republic of China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, People's Republic of China
| | - Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan, People's Republic of China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, People's Republic of China
| | - Xiang Xiong
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, People's Republic of China
| | - Luping Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, People's Republic of China
| | - Yarui Cheng
- College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, People's Republic of China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, People's Republic of China
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Top-down and bottom-up cohesiveness in microbial community coalescence. Proc Natl Acad Sci U S A 2022; 119:2111261119. [PMID: 35105804 PMCID: PMC8832967 DOI: 10.1073/pnas.2111261119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2021] [Indexed: 12/13/2022] Open
Abstract
In the microbial world, it is common for previously isolated communities to come in contact with one another. This phenomenon is known as community coalescence. Despite it being a key process in the assembly of microbial communities, little is known about the mechanisms that determine its outcomes. Here we present an experimental system that allowed us to study over 100 coalescence events between previously segregated microbiomes. Our results, predicted by a mathematical model, provide direct evidence of ecological coselection: the situation where members of a community recruit one another during coalescence. Our combined experimental and theoretical framework represents a powerful tool to predict the outcomes and interrogate the mechanisms of community coalescence. Microbial communities frequently invade one another as a whole, a phenomenon known as community coalescence. Despite its potential importance for the assembly, dynamics, and stability of microbial consortia, as well as its prospective utility for microbiome engineering, our understanding of the processes that govern it is still very limited. Theory has suggested that microbial communities may exhibit cohesiveness in the face of invasions emerging from collective metabolic interactions across microbes and their environment. This cohesiveness may lead to correlated invasional outcomes, where the fate of a given taxon is determined by that of other members of its community—a hypothesis known as ecological coselection. Here, we have performed over 100 invasion and coalescence experiments with microbial communities of various origins assembled in two different synthetic environments. We show that the dominant members of the primary communities can recruit their rarer partners during coalescence (top-down coselection) and also be recruited by them (bottom-up coselection). With the aid of a consumer-resource model, we found that the emergence of top-down or bottom-up cohesiveness is modulated by the structure of the underlying cross-feeding networks that sustain the coalesced communities. The model also predicts that these two forms of ecological coselection cannot co-occur under our conditions, and we have experimentally confirmed that one can be strong only when the other is weak. Our results provide direct evidence that collective invasions can be expected to produce ecological coselection as a result of cross-feeding interactions at the community level.
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Lechón-Alonso P, Clegg T, Cook J, Smith TP, Pawar S. The role of competition versus cooperation in microbial community coalescence. PLoS Comput Biol 2021; 17:e1009584. [PMID: 34748540 PMCID: PMC8601617 DOI: 10.1371/journal.pcbi.1009584] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/18/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023] Open
Abstract
New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed "community coalescence". Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because of their superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities.
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Affiliation(s)
- Pablo Lechón-Alonso
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Tom Clegg
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Jacob Cook
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
| | - Thomas P. Smith
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Samraat Pawar
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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