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Liu S, Chen Q, Liu L, Dong C, Qiu X, Tang K. Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174845. [PMID: 39053558 DOI: 10.1016/j.scitotenv.2024.174845] [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: 05/21/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024]
Abstract
Marine organic matter fuels the growth of microbial communities, shaping the composition of bacteria that specialize in its breakdown. However, responses of free-living (FL) and particle-associated (PA) bacterial communities to the changing pools of dissolved organic matter (DOM) and particulate organic matter (POM) remained unclear. This study investigates the composition of size-fractionated bacterial communities, DOM and POM in coastal waters over a 22-day period that includes a diatom bloom. Co-occurrence analysis showed that the FL bacterial communities were significantly less stable than PA communities. During the diatom bloom, we observed a significant increase in DOM molecules, particularly those derived from amino acids and peptides. In contrast, the relative intensities of major POM molecule classes remained stable despite the algal bloom's influence. Our study revealed a strong negative correlation between bacterial alpha-diversity and the amount of molecules in the organic matter pool. Similarly, bacterial community beta-diversity was found to be related to the composition of organic matter pool. However, the composition of organic matter was more strongly related to the composition of FL bacterial communities compared to PA communities. This suggests that FL bacteria exhibit greater variations in temporal dynamics and higher sensitivity to the specific structure of organic matter molecules.
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Affiliation(s)
- Shujing Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Changjie Dong
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Xuanyun Qiu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China.
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2
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Yang S, Zu J, Feng Y, Ding L, Zhang Q, Zhang H. A functional-group-based perspective on the response of marine phytoplankton to mesoscale eddies. MARINE POLLUTION BULLETIN 2024; 207:116864. [PMID: 39180965 DOI: 10.1016/j.marpolbul.2024.116864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
This study analyzed the response of marine phytoplankton to environmental changes induced by mesoscale warm eddies through the lens of functional groups, highlighting the complex interactions within the ecosystem. It was found that warm eddies significantly affected phytoplankton distribution, with cell abundance in the center being only 75.60 cells/L, compared to 1095.00 cells/L in the periphery. Vertical transport within warm eddies altered light conditions, affecting photophilic diatoms more, while increased temperatures favored the growth of warm-water dinoflagellates. This study also emphasized that ocean currents were significant factors, showing correlations with various functional groups and playing a key role in material transport and phytoplankton distribution. Additionally, the distinct responses of different functional groups to temperature and salinity underscored their unique adaptations to environmental changes. In periods without warm eddies, phytoplankton primarily congregated in shallower water layers.
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Affiliation(s)
- Shimin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiying Zu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Youfei Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lichi Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qinchao Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Huiling Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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3
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Behrendt L, Alcolombri U, Hunter JE, Smriga S, Mincer T, Lowenstein DP, Yawata Y, Peaudecerf FJ, Fernandez VI, Fredricks HF, Almblad H, Harrison JJ, Stocker R, Van Mooy BAS. Microbial dietary preference and interactions affect the export of lipids to the deep ocean. Science 2024; 385:eaab2661. [PMID: 39265021 DOI: 10.1126/science.aab2661] [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: 12/08/2023] [Accepted: 07/09/2024] [Indexed: 09/14/2024]
Abstract
Lipids comprise a significant fraction of sinking organic matter in the ocean and play a crucial role in the carbon cycle. Despite this, our understanding of the processes that control lipid degradation is limited. We combined nanolipidomics and imaging to study the bacterial degradation of diverse algal lipid droplets and found that bacteria isolated from marine particles exhibited distinct dietary preferences, ranging from selective to promiscuous degraders. Dietary preference was associated with a distinct set of lipid degradation genes rather than with taxonomic origin. Using synthetic communities composed of isolates with distinct dietary preferences, we showed that lipid degradation is modulated by microbial interactions. A particle export model incorporating these dynamics indicates that metabolic specialization and community dynamics may influence lipid transport efficiency in the ocean's mesopelagic zone.
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Affiliation(s)
- Lars Behrendt
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan E Hunter
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Steven Smriga
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Tracy Mincer
- Florida Atlantic University, Wilkes Honors College, Jupiter, FL, USA
| | - Daniel P Lowenstein
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Yutaka Yawata
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - François J Peaudecerf
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
- University of Rennes, CNRS, Institut de Physique de Rennes, Rennes, France
| | - Vicente I Fernandez
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Henrik Almblad
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
| | - Joe J Harrison
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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4
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Cai S, Lao Q, Cai M, Silva DPTT, Lu X, Zhou X, Jin G, Chen C, Chen F. Water residence time controls seasonal nitrous oxide budget in a semi-enclosed bay: Insights from an improvement estimation method. MARINE POLLUTION BULLETIN 2024; 206:116701. [PMID: 38991612 DOI: 10.1016/j.marpolbul.2024.116701] [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: 05/30/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
This study developed an estimation method for the N2O budget using 15N stable isotope labeling techniques, a dual-layer model and a box model, which was used to elucidate the underlying dynamics of N2O accumulation in Zhanjiang Bay. The results showed that although the net input of N2O during the rainy season was 2.36 times higher than that during the dry season, the overall N2O concentration was only 66.6 % of that during the dry season due to the extended water residence time in the dry season. Our findings highlighted that water residence time was the key factor for the N2O emission, and a longer water residence time was unfavorable for the efflux of N2O through hydrodynamic processes and was more conducive to the production and accumulation of N2O within the bay. This research enhanced our comprehension of N2O dynamics and provided crucial insights for refining nitrogen management strategies and mitigation efforts.
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Affiliation(s)
- Shangjun Cai
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qibin Lao
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Minggang Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Dickwelle P T T Silva
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xuan Lu
- Polar and Marine Research Institute, College of Harbor and Coastal Engineering, Jimei University, Xiamen 361021, China
| | - Xin Zhou
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Guangzhe Jin
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chunqing Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fajin Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang 524088, China.
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5
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Saha M, Dittami SM, Chan CX, Raina JB, Stock W, Ghaderiardakani F, Valathuparambil Baby John AM, Corr S, Schleyer G, Todd J, Cardini U, Bengtsson MM, Prado S, Skillings D, Sonnenschein EC, Engelen AH, Wang G, Wichard T, Brodie J, Leblanc C, Egan S. Progress and future directions for seaweed holobiont research. THE NEW PHYTOLOGIST 2024. [PMID: 39137959 DOI: 10.1111/nph.20018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed-microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.
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Affiliation(s)
- Mahasweta Saha
- Plymouth Marine Laboratory, Marine Ecology and Biodiversity, Prospect Place, Plymouth, PL1 3DH, UK
| | - Simon M Dittami
- CNRS, Integrative Biology of Marine Models Laboratory (LBI2M, UMR 8227), Station Biologique de Roscoff, Place Georges Teissier, Sorbonne Université, Roscoff, 29680, France
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Willem Stock
- Phycology Research Group, Ghent University, Krijgslaan 281 Sterre S8, Ghent, 9000, Belgium
| | - Fatemeh Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07743, Germany
| | | | - Shauna Corr
- Plymouth Marine Laboratory, Marine Ecology and Biodiversity, Prospect Place, Plymouth, PL1 3DH, UK
| | - Guy Schleyer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, Jena, 07745, Germany
| | - Jonathan Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ulisse Cardini
- Department of Integrative Marine Ecology (EMI), Genoa Marine Centre, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Genoa, 16126, Italy
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, Greifswald, 17489, Germany
| | - Soizic Prado
- National Museum of Natural History, Unit Molecules of Communication and Adaptation of Microorganisms (UMR 7245), Paris, France
| | - Derek Skillings
- Department of Philosophy, University of North Carolina Greensboro, Greensboro, NC, 27402, USA
| | - Eva C Sonnenschein
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | | | - Gaoge Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- MoE Key Laboratory of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07743, Germany
| | - Juliet Brodie
- Natural History Museum, Research, Cromwell Road, London, SW7 5BD, UK
| | - Catherine Leblanc
- CNRS, Integrative Biology of Marine Models Laboratory (LBI2M, UMR 8227), Station Biologique de Roscoff, Place Georges Teissier, Sorbonne Université, Roscoff, 29680, France
| | - Suhelen Egan
- Centre for Marine Science and Innovation (CMSI), School of Biological, Earth and Environmental Sciences (BEES), UNSW Sydney, Sydney, NSW, 2052, Australia
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6
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Xu J, Wang Y, Liu L, Wang X, Xiao S, Chen J, Jiao N, Zheng Q. Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174883. [PMID: 39034013 DOI: 10.1016/j.scitotenv.2024.174883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.
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Affiliation(s)
- Jinxin Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Lu Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Xiaomeng Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Shicong Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Jiaxin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China.
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7
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Freckelton ML, Nedved BT, Hadfield MG. Bacterial envelope polysaccharide cues settlement and metamorphosis in the biofouling tubeworm Hydroides elegans. Commun Biol 2024; 7:883. [PMID: 39030323 PMCID: PMC11271524 DOI: 10.1038/s42003-024-06585-9] [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: 08/24/2023] [Accepted: 07/15/2024] [Indexed: 07/21/2024] Open
Abstract
Metamorphosis for many marine invertebrates is triggered by external cues, commonly produced by bacteria. For larvae of Hydroides elegans, lipopolysaccharide (LPS) from the biofilm-dwelling bacterium Cellulophaga lytica induces metamorphosis. To determine whether bacterial LPS is a common metamorphosis-inducing factor for this species, we compare larval responses to LPS from 3 additional inductive Gram-negative marine biofilm bacteria with commercially available LPS from 3 bacteria not known to induce metamorphosis. LPS from all the inductive bacteria trigger metamorphosis, while LPS from non-inductive isolated marine bacteria do not. We then ask, which part of the LPS is the inductive element, the lipid (Lipid-A) or the polysaccharide (O-antigen), and find it is the latter for all four inductive bacteria. Finally, we examine the LPS subunits from two strains of the same bacterial species, one inductive and the other not, and find the LPS and O-antigen to be inductive from only the inductive bacterial strain.
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Affiliation(s)
| | - Brian T Nedved
- Kewalo Marine Laboratory, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Michael G Hadfield
- Kewalo Marine Laboratory, University of Hawai'i, Honolulu, HI, 96813, USA.
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8
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Held NA, Manhart M. Are microbes colimited by multiple resources? Curr Opin Microbiol 2024; 80:102509. [PMID: 38991468 DOI: 10.1016/j.mib.2024.102509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/03/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024]
Abstract
Resource colimitation - the dependence of growth on multiple resources simultaneously - has become an important topic in microbiology due both to the development of systems approaches to cell physiology and ecology and to the relevance of colimitation to environmental science, biotechnology, and human health. Empirical tests of colimitation in microbes suggest that it may be common in nature. However, recent theoretical and empirical work has demonstrated the need for systematic measurements across resource conditions, in contrast to the factorial supplementation experiments used in most previous studies. The mechanistic causes of colimitation remain unclear in most cases and are an important challenge for future work, but we identify the alignment of resource consumption with the environment, interactions between resources, and biological and environmental heterogeneity as major factors. On the other hand, the consequences of colimitation are widespread for microbial physiology and ecology, especially the prediction and control of microbial growth, motivating continued consideration of this state in microbiology.
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Affiliation(s)
- Noelle A Held
- Department of Biological Sciences, Marine and Enviornmental Biology Section, University of Southern California, Los Angeles, CA, USA.
| | - Michael Manhart
- Center for Advanced Biotechnology and Medicine and Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
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9
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Sun J, Zhou H, Cheng H, Chen Z, Wang Y. Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106624. [PMID: 38943698 DOI: 10.1016/j.marenvres.2024.106624] [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: 04/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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10
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Dannenmann M, Le Moigne A, Hofer C, Pernthaler J. Centimetre scale functional dispersal limitation of freshwater copiotrophs. Environ Microbiol 2024; 26:e16682. [PMID: 39128858 DOI: 10.1111/1462-2920.16682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024]
Abstract
The freshwater microbiome harbours numerous copiotrophic bacteria that rapidly respond to elevated substrate concentrations. We hypothesized that their high centimetre-scale beta diversity in lake water translates into pronounced metabolic variability, and that a large fraction of microbial 'metabolic potential' originates from point sources such as fragile organic aggregates. Three experiments were conducted in pre-alpine Lake Zurich over the course of a harmful cyanobacterial bloom: Spatially explicit 9 ml 'syringe' samples were collected in situ at centimetre distances along with equally sized 'mixed' samples drawn from pre-homogenized lake water and incubated in BIOLOG EcoPlate substrate arrays. Fewer compounds promoted bacterial growth in the syringe than in the mixed samples, in particular during the pre- and late bloom periods. Community analysis of enrichments on three frequently utilized substrates revealed both pronounced heterogeneity and functional redundancy. Bacterial consortia had higher richness in mixed than in syringe samples and differed in composition. Members of the Enterobacter cloacae complex dominated the EcoPlate assemblages during the mid-bloom period irrespective of treatment or substrate. We conclude that small-scale functional dispersal limitation among free-living copiotrophs in lake water reduces local biotransformation potential, and that lacustrine blooms of harmful cyanobacteria can be environmental reservoirs for metabolically versatile potential pathogens.
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Affiliation(s)
- Marie Dannenmann
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Institute of Geological Sciences, Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Alizée Le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, Québec, Canada
| | - Cyrill Hofer
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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11
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Seymour JR, Brumley DR, Stocker R, Raina JB. Swimming towards each other: the role of chemotaxis in bacterial interactions. Trends Microbiol 2024; 32:640-649. [PMID: 38212193 DOI: 10.1016/j.tim.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
| | - Douglas R Brumley
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia.
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
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12
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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. WATER RESEARCH 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [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: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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13
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Smith WJM, Liu Y, Simpson SL, Bivins A, Ahmed W. Assessment of nucleic acid extraction protocols for antibiotic resistance genes (ARGs) quantification in aircraft wastewater. Hum Genomics 2024; 18:54. [PMID: 38816866 PMCID: PMC11138010 DOI: 10.1186/s40246-024-00617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
This study evaluated ten nucleic acid extraction protocols (EP1 to EP10) for measuring five endogenous antibiotic resistance genes (ARGs) in four aircraft wastewater samples (AWW1 to AWW4). The targeted ARGs, including blaCTX-M, blaNDM-1, ermB, qnrS, and tetA, encompassed highly and minimally abundant ARGs. TetA and ermB were consistently detected across four aircraft wastewater samples using the DNeasy Blood and Tissue Kit and the AllPrep PowerViral DNA/RNA kit. QnrS displayed high detection rates with specific extraction protocols and aliquot volumes. Concentrations of ARGs varied across aircraft wastewater samples, with differing extraction protocols influencing quantitative results. The concentrations of tetA, ermB, and qnrS in AWW1 were distinct, while AWW2 to AWW4 exhibited a broader range for tetA, ermB, qnrS, blaCTX-M, and blaNDM-1. EP1 consistently produced the highest concentrations for several ARGs. Collective data analysis revealed varying ARG concentrations across the ten extraction protocols, suggesting the importance of careful extraction protocol selection in ARG monitoring in aircraft wastewater samples. Based on the results, we suggest that a small sample volume (as low as 0.2 mL) may be sufficient for ARG characterization in aircraft wastewater samples. The findings also emphasize the need for considering toilet paper removal without compromising nucleic acid extraction efficiency. The study highlights promising prospects for aircraft wastewater monitoring of ARGs, calling for further investigation into the import and spread of unique ARGs through transport hubs.
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Affiliation(s)
- Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Stuart L Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia.
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14
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Chen S, Xie ZX, Yan KQ, Chen JW, Li DX, Wu PF, Peng L, Lin L, Dong CM, Zhao Z, Fan GY, Liu SQ, Herndl GJ, Wang DZ. Functional vertical connectivity of microbial communities in the ocean. SCIENCE ADVANCES 2024; 10:eadj8184. [PMID: 38781332 PMCID: PMC11114224 DOI: 10.1126/sciadv.adj8184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16S rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.
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Affiliation(s)
- Shi Chen
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Zhang-Xian Xie
- School of Resource and Environmental Sciences, Quanzhou Normal University, Quanzhou 362000, China
| | - Ke-Qiang Yan
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Wei Chen
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Ling Peng
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Chun-Ming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen 361005, Fujian, China
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guang-Yi Fan
- BGI-Shenzhen, Shenzhen 518083, China
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Si-Qi Liu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, Netherlands
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
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15
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Karthäuser C, Fucile PD, Maas AE, Blanco-Bercial L, Gossner H, Lowenstein DP, Niimi YJ, Van Mooy BAS, Bernhard JM, Buesseler KO, Sievert SM. RotoBOD─Quantifying Oxygen Consumption by Suspended Particles and Organisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8760-8770. [PMID: 38717860 PMCID: PMC11112748 DOI: 10.1021/acs.est.4c03186] [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: 03/30/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Sinking or floating is the natural state of planktonic organisms and particles in the ocean. Simulating these conditions is critical when making measurements, such as respirometry, because they allow the natural exchange of substrates and products between sinking particles and water flowing around them and prevent organisms that are accustomed to motion from changing their metabolism. We developed a rotating incubator, the RotoBOD (named after its capability to rotate and determine biological oxygen demand, BOD), that uniquely enables automated oxygen measurements in small volumes while keeping the samples in their natural state of suspension. This allows highly sensitive rate measurements of oxygen utilization and subsequent characterization of single particles or small planktonic organisms, such as copepods, jellyfish, or protists. As this approach is nondestructive, it can be combined with several further measurements during and after the incubation, such as stable isotope additions and molecular analyses. This makes the instrument useful for ecologists, biogeochemists, and potentially other user groups such as aquaculture facilities. Here, we present the technical background of our newly developed apparatus and provide examples of how it can be utilized to determine oxygen production and consumption in small organisms and particles.
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Affiliation(s)
- Clarissa Karthäuser
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Paul D. Fucile
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Amy E. Maas
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Leocadio Blanco-Bercial
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Hannah Gossner
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Daniel P. Lowenstein
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Yuuki J. Niimi
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Benjamin A. S. Van Mooy
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Joan M. Bernhard
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Ken O. Buesseler
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Stefan M. Sievert
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
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16
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Cai S, Lao Q, Chen C, Zhu Q, Chen F. The impact of algal blooms on promoting in-situ N 2O emissions: A case in Zhanjiang bay, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120935. [PMID: 38648725 DOI: 10.1016/j.jenvman.2024.120935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Under the influence of many factors, such as climate change, anthropogenic eutrophication, and the development of aquaculture, the area and frequency of algal blooms have showed an increasing trend worldwide, which has become a challenging issue at present. However, the coupled relationship between nitrous oxide (N2O) and algal blooms and the underlying mechanisms remain unclear. To address this issue, 15N isotope cultures and quantitative polymerase chain reaction (qPCR) experiments were conducted in Zhanjiang Bay during algal and non-algal bloom periods. The results showed that denitrification and nitrification-denitrification were the two processes responsible for the in-situ production of N2O during algal and non-algal bloom periods. Stable isotope rate cultivation experiments indicated that denitrification and nitrification-denitrification were promoted in the water during the algal bloom period. The in-situ production of N2O during the algal bloom period was three-fold that during the non-algal bloom period. This may be because fresh particulate organic matter (POM) from the organisms responsible for the algal bloom provides the necessary anaerobic and hypoxic environment for denitrification and nitrification-denitrification in the degradation environment. Additionally, a positive linear correlation between N2O concentrations and ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (nirK and nirS) also supported the significant denitrification and nitrification-denitrification occurring in the water during the algal bloom period. However, the algal bloom changed the main process for the in-situ production of N2O, wherein it shifted from denitrification during the non-algal bloom period to nitrification-denitrification during the algal bloom period. The results of our study will improve our understanding of the processes responsible for the in-situ production of N2O during the algal bloom period, and can help formulate effective policies to mitigate N2O emissions in the bay.
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Affiliation(s)
- Shangjun Cai
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qibin Lao
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chunqing Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qingmei Zhu
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Fajin Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, 524088, China.
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17
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Salek MM, Carrara F, Zhou J, Stocker R, Jimenez‐Martinez J. Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310121. [PMID: 38445967 PMCID: PMC11132056 DOI: 10.1002/advs.202310121] [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: 12/22/2023] [Indexed: 03/07/2024]
Abstract
Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.
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Affiliation(s)
- M. Mehdi Salek
- Department of Biological Engineering, School of EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Francesco Carrara
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Jiande Zhou
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Microsystems LaboratoryInstitute of MicroengineeringSchool of EngineeringEPFLLausanneSwitzerland
| | - Roman Stocker
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Joaquin Jimenez‐Martinez
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Department of Water Resources and Drinking WaterEawagDubendorfSwitzerland
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18
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Picoche C, Young WR, Barraquand F. Local intraspecific aggregation in phytoplankton model communities: spatial scales of occurrence and implications for coexistence. J Math Biol 2024; 88:68. [PMID: 38661851 DOI: 10.1007/s00285-024-02067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/17/2023] [Accepted: 02/20/2024] [Indexed: 04/26/2024]
Abstract
The coexistence of multiple phytoplankton species despite their reliance on similar resources is often explained with mean-field models assuming mixed populations. In reality, observations of phytoplankton indicate spatial aggregation at all scales, including at the scale of a few individuals. Local spatial aggregation can hinder competitive exclusion since individuals then interact mostly with other individuals of their own species, rather than competitors from different species. To evaluate how microscale spatial aggregation might explain phytoplankton diversity maintenance, an individual-based, multispecies representation of cells in a hydrodynamic environment is required. We formulate a three-dimensional and multispecies individual-based model of phytoplankton population dynamics at the Kolmogorov scale. The model is studied through both simulations and the derivation of spatial moment equations, in connection with point process theory. The spatial moment equations show a good match between theory and simulations. We parameterized the model based on phytoplankters' ecological and physical characteristics, for both large and small phytoplankton. Defining a zone of potential interactions as the overlap between nutrient depletion volumes, we show that local species composition-within the range of possible interactions-depends on the size class of phytoplankton. In small phytoplankton, individuals remain in mostly monospecific clusters. Spatial structure therefore favours intra- over inter-specific interactions for small phytoplankton, contributing to coexistence. Large phytoplankton cell neighbourhoods appear more mixed. Although some small-scale self-organizing spatial structure remains and could influence coexistence mechanisms, other factors may need to be explored to explain diversity maintenance in large phytoplankton.
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Affiliation(s)
- Coralie Picoche
- Institute of Mathematics of Bordeaux, University of Bordeaux and CNRS, Talence, France
| | | | - Frédéric Barraquand
- Institute of Mathematics of Bordeaux, University of Bordeaux and CNRS, Talence, France.
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19
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Diver P, Ward BA, Cunliffe M. Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean. FEMS Microbiol Ecol 2024; 100:fiae053. [PMID: 38599628 PMCID: PMC11062419 DOI: 10.1093/femsec/fiae053] [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: 08/09/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024] Open
Abstract
Yeasts are prevalent in the open ocean, yet we have limited understanding of their ecophysiological adaptations, including their response to nitrogen availability, which can have a major role in determining the ecological potential of other planktonic microbes. In this study, we characterized the nitrogen uptake capabilities and growth responses of marine-occurring yeasts. Yeast isolates from the North Atlantic Ocean were screened for growth on diverse nitrogen substrates, and across a concentration gradient of three environmentally relevant nitrogen substrates: nitrate, ammonium, and urea. Three strains grew with enriched nitrate while two did not, demonstrating that nitrate utilization is present but not universal in marine yeasts, consistent with existing knowledge of nonmarine yeast strains. Naganishia diffluens MBA_F0213 modified the key functional trait of cell size in response to nitrogen concentration, suggesting yeast cell morphology changes along chemical gradients in the marine environment. Meta-analysis of the reference DNA barcode in public databases revealed that the genus Naganishia has a global ocean distribution, strengthening the environmental applicability of the culture-based observations. This study provides novel quantitative understanding of the ecophysiological and morphological responses of marine-derived yeasts to variable nitrogen availability in vitro, providing insight into the functional ecology of yeasts within pelagic open ocean environments.
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Affiliation(s)
- Poppy Diver
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, United Kingdom
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Ben A Ward
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, United Kingdom
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20
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Han D, Park KT, Kim H, Kim TH, Jeong MK, Nam SI. Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding. FEMS Microbiol Ecol 2024; 100:fiae059. [PMID: 38621717 PMCID: PMC11067963 DOI: 10.1093/femsec/fiae059] [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: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024] Open
Abstract
The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.
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Affiliation(s)
- Dukki Han
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Ki-Tae Park
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Environmental Sciences and Biotechnology, Hallym University, Chuncheon 24252, Republic of Korea
| | - Haryun Kim
- East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin 36315, Republic of Korea
| | - Tae-Hoon Kim
- Department of Oceanography, Faculty of Earth Systems and Environmental Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Ki Jeong
- Department of Smart Fisheries Resources Management, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Seung-Il Nam
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
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21
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Kajan K, Fuchs BM, Orlić S. Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre. Microbiol Spectr 2024; 12:e0301623. [PMID: 38334383 PMCID: PMC10913754 DOI: 10.1128/spectrum.03016-23] [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: 08/04/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.
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Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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22
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Genitsaris S, Stefanidou N, Hatzinikolaou D, Kourkoutmani P, Michaloudi E, Voutsa D, Gros M, García-Gómez E, Petrović M, Ntziachristos L, Moustaka-Gouni M. Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38415986 DOI: 10.1002/etc.5834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/29/2024]
Abstract
The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;00:1-18. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Savvas Genitsaris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitris Hatzinikolaou
- Department of Botany, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Polyxeni Kourkoutmani
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Michaloudi
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Voutsa
- Environmental Pollution Control Laboratory, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Meritxell Gros
- Catalan Institute for Water Research (ICRA), Girona, Spain
- University of Girona (UdG), Girona, Spain
| | - Elisa García-Gómez
- Catalan Institute for Water Research (ICRA), Girona, Spain
- University of Girona (UdG), Girona, Spain
| | - Mira Petrović
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Leonidas Ntziachristos
- Department of Mechanical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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23
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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24
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Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [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: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
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25
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Cram JA, Hollins A, McCarty AJ, Martinez G, Cui M, Gomes ML, Fuchsman CA. Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay. Environ Microbiol 2024; 26:e16557. [PMID: 38173306 DOI: 10.1111/1462-2920.16557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
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Affiliation(s)
- Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Ashley Hollins
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- Marine Advisory Program, Virginia Institute of Marine Science, Gloucester, Virginia, USA
| | | | - Minming Cui
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya L Gomes
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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26
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Wan XS, Sheng HX, Liu L, Shen H, Tang W, Zou W, Xu MN, Zheng Z, Tan E, Chen M, Zhang Y, Ward BB, Kao SJ. Particle-associated denitrification is the primary source of N 2O in oxic coastal waters. Nat Commun 2023; 14:8280. [PMID: 38092778 PMCID: PMC10719265 DOI: 10.1038/s41467-023-43997-3] [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: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (N2O) emission to the atmosphere. The processes underpinning the N2O flux, however, remain poorly understood, leading to large uncertainties in assessing global N2O budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to N2O production throughout the estuarine-coastal gradient, sustaining intensive N2O flux to the atmosphere. Unexpectedly, denitrification, rather than ammonia oxidation as previously assumed, constitutes the major source of N2O in well-oxygenated coastal waters. Size-fractionated manipulation experiments with gene analysis further reveal niche partitioning of ammonia oxidizers and denitrifiers across the particle size spectrum; denitrification dominated on large particles and ammonia oxidizers on small particles. Total N2O production rate increases with substrate and particle concentrations, suggesting a crucial interplay between nutrients and particles in controlling N2O production. The controlling factors identified here may help understand climate feedback mechanisms between human activity and coastal oceans.
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Affiliation(s)
- Xianhui S Wan
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
| | - Hua-Xia Sheng
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Li Liu
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Hui Shen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Weiyi Tang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Wenbin Zou
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Min N Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Zhenzhen Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China
| | - Mingming Chen
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Yao Zhang
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Shuh-Ji Kao
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570208, China.
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27
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Liu Y, Smith W, Gebrewold M, Wang X, Simpson SL, Bivins A, Ahmed W. Comparison of concentration and extraction workflows for qPCR quantification of intI1 and vanA in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166442. [PMID: 37604373 DOI: 10.1016/j.scitotenv.2023.166442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) measurement of antibiotic resistance genes (ARGs) in untreated municipal wastewater may prove useful in combating the antimicrobial resistance crisis. However, harmonizing and optimizing qPCR-based workflows is essential to facilitate comparisons across studies, and includes achieving highly-effective ARG capture through efficient concentration and extraction procedures. In the current study, combinations of sample volume, membrane types and DNA extraction kits within filtration and centrifugation-based workflows were used to quantify 16S ribosomal RNA (16S rRNA), class 1 integron-integrase gene (intI1) and an ARG encoding resistance to vancomycin (vanA) in untreated wastewater sampled from three wastewater treatment plants (WWTPs). Highly abundant 16S rRNA and intI1 were detected in 100 % of samples from all three WWTPs using both 2 and 20 mL sample volumes, while lower prevalence vanA was only detected when using the 20 mL volume. When filtering 2 mL of wastewater, workflows with 0.20-/0.40-μm polycarbonate (PC) membranes generally yielded greater concentrations of the three targets than workflows with 0.22-/0.45-μm mixed cellulose ester (MCE) membranes. The improved performance was diminished when the sample volume was increased to 20 mL. Consistently greater concentrations of 16S rRNA, intI1 and vanA were yielded by filtration-based workflows using PC membranes combined with a DNeasy PowerWater (DPW) Kit, regardless of the sample volume used, and centrifugation-based workflows with DNeasy Blood & Tissue Kit for 2-mL wastewater extractions. Within the filtration-based workflows, the DPW kit yielded more detection and quantifiable results for less abundant vanA than the DNeasy PowerSoil Pro Kit and FastDNA™ SPIN Kit for Soil. These findings indicate that the performance of qPCR-based workflows for surveillance of ARGs in wastewater varies across targets, sample volumes, concentration methods and extraction kits. Workflows must be carefully considered and validated considering the target ARGs to be monitored.
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Affiliation(s)
- Yawen Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Xinhong Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70809, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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28
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Clerc EE, Raina JB, Keegstra JM, Landry Z, Pontrelli S, Alcolombri U, Lambert BS, Anelli V, Vincent F, Masdeu-Navarro M, Sichert A, De Schaetzen F, Sauer U, Simó R, Hehemann JH, Vardi A, Seymour JR, Stocker R. Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP. Nat Commun 2023; 14:8080. [PMID: 38057294 DOI: 10.1038/s41467-023-43143-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many bacteria are chemotactic towards small metabolites, marine organic matter is predominantly composed of large molecules and polymers. Yet, the signalling role of these large molecules is largely unknown. Using in situ and laboratory-based chemotaxis assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharides laminarin and alginate. Unexpectedly, these polysaccharides elicited stronger chemoattraction than their oligo- and monosaccharide constituents. Furthermore, chemotaxis towards laminarin was strongly enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. We demonstrate that marine bacteria are capable of strong chemotaxis towards large soluble polysaccharides and uncover a new ecological role for DMSP in enhancing this attraction. These navigation behaviours may contribute to the rapid turnover of polymers in the ocean, with important consequences for marine carbon cycling.
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Affiliation(s)
- Estelle E Clerc
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Johannes M Keegstra
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Zachary Landry
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Uria Alcolombri
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
- Institute for Life Sciences, Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bennett S Lambert
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Valerio Anelli
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Developmental Biology Unit, European Molecular Biological Laboratory, Heidelberg, 69117, Germany
| | | | - Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frédéric De Schaetzen
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | | | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
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29
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Frank B, Antonietti M, Giusto P, Zeininger L. Photocharging of Carbon Nitride Thin Films for Controllable Manipulation of Droplet Force Gradient Sensors. J Am Chem Soc 2023; 145. [PMID: 37934048 PMCID: PMC10655103 DOI: 10.1021/jacs.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Intentional generation, amplification, and discharging of chemical gradients is central to many nano- and micromanipulative technologies. We describe a straightforward strategy to direct chemical gradients inside a solution via local photoelectric surface charging of organic semiconducting thin films. We observed that the irradiation of carbon nitride thin films with ultraviolet light generates local and sustained surface charges in illuminated regions, inducing chemical gradients in adjacent solutions via charge-selective immobilization of surfactants onto the substrate. We studied these gradients using droplet force gradient sensors, complex emulsions with simultaneous and independent responsive modalities to transduce information on transient gradients in temperature, chemistry, and concentration via tilting, morphological reconfiguration, and chemotaxis. Fine control over the interaction between local, photoelectrically patterned, semiconducting carbon nitride thin films and their environment yields a new method to design chemomechanically responsive materials, potentially applicable to micromanipulative technologies including microfluidics, lab-on-a-chip devices, soft robotics, biochemical assays, and the sorting of colloids and cells.
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Affiliation(s)
- Bradley
D. Frank
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Markus Antonietti
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Paolo Giusto
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Lukas Zeininger
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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30
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Ros-Rocher N, Brunet T. What is it like to be a choanoflagellate? Sensation, processing and behavior in the closest unicellular relatives of animals. Anim Cogn 2023; 26:1767-1782. [PMID: 37067637 PMCID: PMC10770216 DOI: 10.1007/s10071-023-01776-z] [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: 01/12/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Given that the single-celled ancestors of the animal kingdom are extinct, the only way to reconstruct how these features evolved is by comparing the biology and genomic content of extant animals to their closest living relatives. Here, we reconstruct the Umwelt (the subjective, perceptive world) inhabited by choanoflagellates, a group of unicellular (or facultatively multicellular) aquatic microeukaryotes that are the closest living relatives of animals. Although behavioral research on choanoflagellates remains patchy, existing evidence shows that they are capable of chemosensation, photosensation and mechanosensation. These processes often involve specialized sensorimotor cellular appendages (cilia, microvilli, and/or filopodia) that resemble those that underlie perception in most animal sensory cells. Furthermore, comparative genomics predicts an extensive "sensory molecular toolkit" in choanoflagellates, which both provides a potential basis for known behaviors and suggests the existence of a largely undescribed behavioral complexity that presents exciting avenues for future research. Finally, we discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process.
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Affiliation(s)
- Núria Ros-Rocher
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Thibaut Brunet
- Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3691, 25-28 Rue du Docteur Roux, 75015, Paris, France.
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31
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Shoup D, Ursell T. Bacterial bioconvection confers context-dependent growth benefits and is robust under varying metabolic and genetic conditions. J Bacteriol 2023; 205:e0023223. [PMID: 37787517 PMCID: PMC10601612 DOI: 10.1128/jb.00232-23] [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: 07/26/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
Microbes often respond to environmental cues by adopting collective behaviors-like biofilms or swarming-that benefit the population. During "bioconvection," microbes gather in dense groups and plume downward through fluid environments, driving flow and mixing on the scale of millions of cells. Though bioconvection was observed a century ago, the effects of differing physical and chemical inputs and its potential selective advantages for different species of microbes remain largely unexplored. In Bacillus subtilis, vertical oxygen gradients that originate from air-liquid interfaces create cell-density inversions that drive bioconvection. Here, we develop Escherichia coli as a complementary model for the study of bioconvection. In the context of a still fluid, we found that motile and chemotactic genotypes of both E. coli and B. subtilis bioconvect and show increased growth compared to immotile or non-chemotactic genotypes, whereas in a well-mixed fluid, there is no growth advantage to motility or chemotaxis. We found that fluid depth, cell concentration, and carbon availability affect the emergence and timing of bioconvective patterns. Also, whereas B. subtilis requires oxygen gradients to bioconvect, E. coli deficient in aerotaxis (Δaer) or energy-taxis (Δtsr) still bioconvects, as do cultures that lack an air-liquid interface. Thus, in two distantly related microbes, bioconvection may confer context-dependent growth benefits, and E. coli bioconvection is robustly elicited by multiple types of chemotaxis. These results greatly expand the set of physical and metabolic conditions in which this striking collective behavior can be expected and demonstrate its potential to be a generic force for behavioral selection across ecological contexts. IMPORTANCE Individual microorganisms frequently move in response to gradients in their fluid environment, with corresponding metabolic benefits. At a population level, such movements can create density variations in a fluid that couple to gravity and drive large-scale convection and mixing called bioconvection. In this work, we provide evidence that this collective behavior confers a selective benefit on two distantly related species of bacteria. We develop new methods for quantifying this behavior and show that bioconvection in Escherichia coli is surprisingly robust to changes in cell concentration, fluid depth, interface conditions, metabolic sensing, and carbon availability. These results greatly expand the set of conditions known to elicit this collective behavior and indicate its potential to be a selective pressure across ecological contexts.
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Affiliation(s)
- Daniel Shoup
- Department of Physics, University of Oregon, Eugene, Oregon, USA
- Rocky Mountain National Laboratories (NIH), Hamilton, Montana, USA
| | - Tristan Ursell
- Department of Physics, University of Oregon, Eugene, Oregon, USA
- Material Science Institute, Eugene, Oregon, USA
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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32
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Shao Q, Zhu Z, Zhou C. Alteration in Community Dynamics of Chaetoceros curvisetus and Bacterioplankton Communities in Response to Surfactin Exposure. Microorganisms 2023; 11:2596. [PMID: 37894254 PMCID: PMC10609649 DOI: 10.3390/microorganisms11102596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The use of surfactin is a promising method to mitigate algal blooms. However, little is known about surfactin toxicity to algae and bacterioplankton. Here, we treated Chaetoceros curvisetus, the dominant species of algal blooms in the East China Sea, with 0, 0.5, 1, 2, 3, and 4 mg/L of surfactin for 96 h to investigate temporal variability. Our results showed that low concentrations of surfactin (<2 mg/L) changed the cell morphology of C. curvisetus, and higher concentrations (>3 mg/L) had lethal effects. Meanwhile, we examined the community dynamics of the free-living (FL, 0.22-5 μm) and particle-attached (PA, >5 μm) bacterioplankton of C. curvisetus in response to different surfactin concentrations and cultivation periods. Both PA and FL bacterioplankton were mainly composed of Proteobacteria, Actinobacteria, and Bacteroidetes, while FL bacterioplankton were more diverse than PA bacterioplankton. The variations of FL and PA bacterioplankton were significantly constrained by the surfactin concentration. Surfactin changed the lifestyle of some bacterioplankton from FL to PA, which mainly belonged to abundant bacterioplankton. Furthermore, we identified some surfactin-sensitive species/taxa. Our study will help enhance the ability to predict marine microbial responses under the effect of surfactin, providing a research foundation for this new harmful algal bloom mitigation method.
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Affiliation(s)
- Qianwen Shao
- Ningbo Institute of Oceanography, Ningbo 315832, China;
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Zhujun Zhu
- Ningbo Institute of Oceanography, Ningbo 315832, China;
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China;
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33
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Ciccarese D, Tantawi O, Zhang IH, Plata D, Babbin AR. Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:275. [PMID: 38665198 PMCID: PMC11041763 DOI: 10.1038/s43247-023-00935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/18/2023] [Indexed: 04/28/2024]
Abstract
Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms-important primary producers for global carbon export-support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle's boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification.
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Affiliation(s)
- Davide Ciccarese
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Omar Tantawi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Irene H. Zhang
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Desiree Plata
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
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34
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Stehnach MR, Henshaw RJ, Floge SA, Guasto JS. Multiplexed microfluidic screening of bacterial chemotaxis. eLife 2023; 12:e85348. [PMID: 37486823 PMCID: PMC10365836 DOI: 10.7554/elife.85348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Microorganism sensing of and responding to ambient chemical gradients regulates a myriad of microbial processes that are fundamental to ecosystem function and human health and disease. The development of efficient, high-throughput screening tools for microbial chemotaxis is essential to disentangling the roles of diverse chemical compounds and concentrations that control cell nutrient uptake, chemorepulsion from toxins, and microbial pathogenesis. Here, we present a novel microfluidic multiplexed chemotaxis device (MCD) which uses serial dilution to simultaneously perform six parallel bacterial chemotaxis assays that span five orders of magnitude in chemostimulant concentration on a single chip. We first validated the dilution and gradient generation performance of the MCD, and then compared the measured chemotactic response of an established bacterial chemotaxis system (Vibrio alginolyticus) to a standard microfluidic assay. Next, the MCD's versatility was assessed by quantifying the chemotactic responses of different bacteria (Psuedoalteromonas haloplanktis, Escherichia coli) to different chemoattractants and chemorepellents. The MCD vastly accelerates the chemotactic screening process, which is critical to deciphering the complex sea of chemical stimuli underlying microbial responses.
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Affiliation(s)
- Michael R Stehnach
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Richard J Henshaw
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Sheri A Floge
- Department of Biology, Wake Forest University, Winston-Salem, United States
| | - Jeffrey S Guasto
- Department of Mechanical Engineering, Tufts University, Medford, United States
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35
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. THE ISME JOURNAL 2023; 17:952-966. [PMID: 37041326 PMCID: PMC10284905 DOI: 10.1038/s41396-023-01405-0] [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: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
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36
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Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
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Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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37
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Abada A, Beiralas R, Narvaez D, Sperfeld M, Duchin-Rapp Y, Lipsman V, Yuda L, Cohen B, Carmieli R, Ben-Dor S, Rocha J, Huang Zhang I, Babbin AR, Segev E. Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse. THE ISME JOURNAL 2023:10.1038/s41396-023-01427-8. [PMID: 37173383 DOI: 10.1038/s41396-023-01427-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions between Phaeobacter inhibens bacteria and Gephyrocapsa huxleyi algae are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiratory mechanism. The bacterial NO is involved in triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of inorganic nitrogen species in oxygenated environments is a potentially significant route of microbial communication within and across kingdoms.
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Affiliation(s)
- Adi Abada
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Roni Beiralas
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Delia Narvaez
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Martin Sperfeld
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yemima Duchin-Rapp
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Valeria Lipsman
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Yuda
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bar Cohen
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Raanan Carmieli
- Depertment of Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Science Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Jorge Rocha
- CIDEA Consortium Conacyt-Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Irene Huang Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Einat Segev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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38
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Słomka J, Alcolombri U, Carrara F, Foffi R, Peaudecerf FJ, Zbinden M, Stocker R. Encounter rates prime interactions between microorganisms. Interface Focus 2023; 13:20220059. [PMID: 36789236 PMCID: PMC9912013 DOI: 10.1098/rsfs.2022.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/03/2023] [Indexed: 02/12/2023] Open
Abstract
Properties of microbial communities emerge from the interactions between microorganisms and between microorganisms and their environment. At the scale of the organisms, microbial interactions are multi-step processes that are initiated by cell-cell or cell-resource encounters. Quantification and rational design of microbial interactions thus require quantification of encounter rates. Encounter rates can often be quantified through encounter kernels-mathematical formulae that capture the dependence of encounter rates on cell phenotypes, such as cell size, shape, density or motility, and environmental conditions, such as turbulence intensity or viscosity. While encounter kernels have been studied for over a century, they are often not sufficiently considered in descriptions of microbial populations. Furthermore, formulae for kernels are known only in a small number of canonical encounter scenarios. Yet, encounter kernels can guide experimental efforts to control microbial interactions by elucidating how encounter rates depend on key phenotypic and environmental variables. Encounter kernels also provide physically grounded estimates for parameters that are used in ecological models of microbial populations. We illustrate this encounter-oriented perspective on microbial interactions by reviewing traditional and recently identified kernels describing encounters between microorganisms and between microorganisms and resources in aquatic systems.
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Affiliation(s)
- Jonasz Słomka
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Uria Alcolombri
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Francesco Carrara
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Riccardo Foffi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - François J. Peaudecerf
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Matti Zbinden
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
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39
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:6491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
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40
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Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone. mSystems 2023; 8:e0109522. [PMID: 36920198 PMCID: PMC10134851 DOI: 10.1128/msystems.01095-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.
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Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar Drugs 2023; 21:md21030165. [PMID: 36976214 PMCID: PMC10054348 DOI: 10.3390/md21030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.
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42
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Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria. Nat Microbiol 2023; 8:510-521. [PMID: 36759754 DOI: 10.1038/s41564-023-01327-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023]
Abstract
Behaviours such as chemotaxis can facilitate metabolic exchanges between phytoplankton and heterotrophic bacteria, which ultimately regulate oceanic productivity and biogeochemistry. However, numerically dominant picophytoplankton have been considered too small to be detected by chemotactic bacteria, implying that cell-cell interactions might not be possible between some of the most abundant organisms in the ocean. Here we examined how bacterial behaviour influences metabolic exchanges at the single-cell level between the ubiquitous picophytoplankton Synechococcus and the heterotrophic bacterium Marinobacter adhaerens, using bacterial mutants deficient in motility and chemotaxis. Stable-isotope tracking revealed that chemotaxis increased nitrogen and carbon uptake of both partners by up to 4.4-fold. A mathematical model following thousands of cells confirmed that short periods of exposure to small but nutrient-rich microenvironments surrounding Synechococcus cells provide a considerable competitive advantage to chemotactic bacteria. These findings reveal that transient interactions mediated by chemotaxis can underpin metabolic relationships among the ocean's most abundant microorganisms.
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43
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Noell SE, Brennan E, Washburn Q, Davis EW, Hellweger FL, Giovannoni SJ. Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility. Environ Microbiol 2023. [PMID: 36826469 DOI: 10.1111/1462-2920.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14 C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth Brennan
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Oregon, USA
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Krishnamurthy D, Pepper R, Prakash M. Active sinking particles: sessile suspension feeders significantly alter the flow and transport to sinking aggregates. J R Soc Interface 2023; 20:20220537. [PMID: 36751929 PMCID: PMC9905981 DOI: 10.1098/rsif.2022.0537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/04/2023] [Indexed: 02/09/2023] Open
Abstract
Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in wastewater treatment plants. In both these contexts, the sinking aggregates are 'active', since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories and mass transfer to these 'active sinking particles' has not previously been studied. Here, we use a novel scale-free vertical tracking microscope (a.k.a. gravity machine; Krishnamurthy et al. 2020 Nat. Methods 17, 1040-1051 (doi:10.1038/s41592-020-0924-7)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached V. convallaria causes significant changes to the flow around aggregates in a dynamic manner and reshapes mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking modify the encounter and plume cross-sections of the aggregate and induce sustained aggregate rotations. Overall, our work shows the important role of biological activity in shaping the near-field flows around aggregates with potentially important effects on aggregate fate and material fluxes.
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Affiliation(s)
- Deepak Krishnamurthy
- Department of Bioengineering, University of California, Berkeley, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rachel Pepper
- Department of Physics, University of Puget Sound, Tacoma, WA, USA
| | - Manu Prakash
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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45
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Abad N, Uranga A, Ayo B, Arrieta JM, Baña Z, Azúa I, Artolozaga I, Iriberri J, González-Rojí SJ, Unanue M. Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters. Environ Microbiol 2023; 25:548-561. [PMID: 36478509 PMCID: PMC10108013 DOI: 10.1111/1462-2920.16297] [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: 07/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
In this study, we hypothesized that shifts in the kinetic parameters of extracellular hydrolytic enzymes may occur as a consequence of seasonal environmental disturbances and would reflect the level of adaptation of the bacterial community to the organic matter of the ecosystem. We measured the activities of enzymes that play a key role in the bacterial growth (leucine aminopeptidase, β- and α-glucosidases) in surface coastal waters of the Eastern Cantabrian Sea and determined their kinetic parameters by computing kinetic models of distinct complexity. Our results revealed the existence of two clearly distinct enzymatic systems operating at different substrate concentrations: a high-affinity system prevailing at low substrate concentrations and a low-affinity system characteristic of high substrate concentrations. These findings could be the result of distinct functional bacterial assemblages growing concurrently under sharp gradients of high-molecular-weight compounds. We constructed an ecological network based on contemporaneous and time-delayed correlations to explore the associations between the kinetic parameters and the environmental variables. The analysis revealed that the recurring phytoplankton blooms registered throughout the seasonal cycle trigger the wax and wane of those members of the bacterial community able to synthesize and secrete specific enzymes.
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Affiliation(s)
- Naiara Abad
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Alava, Spain
| | - Ainhoa Uranga
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
| | - Begoña Ayo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Jesús Maria Arrieta
- Canary Islands Oceanographic Center, Spanish Institute of Oceanography (IEO-CSIC), Santa Cruz, Spain
| | - Zuriñe Baña
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Iñigo Azúa
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Itxaso Artolozaga
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
| | - Juan Iriberri
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | - Santos J González-Rojí
- Oeschger Centre for Climate Change Research (OCCR), University of Bern, Bern, Switzerland
- Climate and Environmental Physics (CEP), University of Bern, Bern, Switzerland
| | - Marian Unanue
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Leioa, Spain
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Barak-Gavish N, Dassa B, Kuhlisch C, Nussbaum I, Brandis A, Rosenberg G, Avraham R, Vardi A. Bacterial lifestyle switch in response to algal metabolites. eLife 2023; 12:e84400. [PMID: 36691727 PMCID: PMC9873259 DOI: 10.7554/elife.84400] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in the biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly recognized that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during its interaction with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. To unravel the bacterial lifestyle switch, we analyzed bacterial transcriptomes in response to exudates derived from algae in exponential growth and stationary phase, which supported the Sulfitobacter D7 coexistence and pathogenicity lifestyles, respectively. In pathogenic mode, Sulfitobacter D7 upregulated flagellar motility and diverse transport systems, presumably to maximize assimilation of E. huxleyi-derived metabolites released by algal cells upon cell death. Algal dimethylsulfoniopropionate (DMSP) was a pivotal signaling molecule that mediated the transition between the lifestyles, supporting our previous findings. However, the coexisting and pathogenic lifestyles were evident only in the presence of additional algal metabolites. Specifically, we discovered that algae-produced benzoate promoted the growth of Sulfitobacter D7 and hindered the DMSP-induced lifestyle switch to pathogenicity, demonstrating that benzoate is important for maintaining the coexistence of algae and bacteria. We propose that bacteria can sense the physiological state of the algal host through changes in the metabolic composition, which will determine the bacterial lifestyle during interaction.
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Affiliation(s)
- Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Inbal Nussbaum
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
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47
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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48
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Gong J, Shaik VA, Elfring GJ. Active particles crossing sharp viscosity gradients. Sci Rep 2023; 13:596. [PMID: 36631505 PMCID: PMC9834246 DOI: 10.1038/s41598-023-27423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Active particles (living or synthetic) often move through inhomogeneous environments, such as gradients in light, heat or nutrient concentration, that can lead to directed motion (or taxis). Recent research has explored inhomogeneity in the rheological properties of a suspending fluid, in particular viscosity, as a mechanical (rather than biological) mechanism for taxis. Theoretical and experimental studies have shown that gradients in viscosity can lead to reorientation due to asymmetric viscous forces. In particular, recent experiments with Chlamydomonas Reinhardtii algae swimming across sharp viscosity gradients have observed that the microorganisms are redirected and scattered due to the viscosity change. Here we develop a simple theoretical model to explain these experiments. We model the swimmers as spherical squirmers and focus on small, but sharp, viscosity changes. We derive a law, analogous to Snell's law of refraction, that governs the orientation of active particles in the presence of a viscosity interface. Theoretical predictions show good agreement with experiments and provide a mechanistic understanding of the observed reorientation process.
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Affiliation(s)
- Jiahao Gong
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada
| | - Vaseem A Shaik
- Department of Mechanical Engineering, Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Gwynn J Elfring
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada. .,Department of Mechanical Engineering, Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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49
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Zhang Y, Wei D, Wang X, Wang B, Li M, Fang H, Peng Y, Fan Q, Ye F. Run-and-Tumble Dynamics and Mechanotaxis Discovered in Microglial Migration. RESEARCH (WASHINGTON, D.C.) 2023; 6:0063. [PMID: 36939442 PMCID: PMC10013966 DOI: 10.34133/research.0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023]
Abstract
Microglia are resident macrophage cells in the central nervous system that search for pathogens or abnormal neural activities and migrate to resolve the issues. The effective search and targeted motion of macrophages mean dearly to maintaining a healthy brain, yet little is known about their migration dynamics. In this work, we study microglial motion with and without the presence of external mechanostimuli. We discover that the cells are promptly attracted by the applied forces (i.e., mechanotaxis), which is a tactic behavior as yet unconfirmed in microglia. Meanwhile, in both the explorative and the targeted migration, microglia display dynamics that is strikingly analogous to bacterial run-and-tumble motion. A closer examination reveals that microglial run-and-tumble is more sophisticated, e.g., they display a short-term memory when tumbling and rely on active steering during runs to achieve mechanotaxis, probably via the responses of mechanosensitive ion channels. These differences reflect the sharp contrast between microglia and bacteria cells (eukaryotes vs. prokaryotes) and their environments (compact tissue vs. fluid). Further analyses suggest that the reported migration dynamics has an optimal search efficiency and is shared among a subset of immune cells (human monocyte and macrophage). This work reveals a fruitful analogy between the locomotion of 2 remote systems and provides a framework for studying immune cells exploring complex environments.
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Affiliation(s)
- Yiyu Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Da Wei
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaochen Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Boyi Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Haiping Fang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School of Science,
East China University of Science and Technology, Shanghai 200237, China
| | - Yi Peng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
- Address correspondence to: (F.Y.); (Y.P.); (Q.F.)
| | - Qihui Fan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- Address correspondence to: (F.Y.); (Y.P.); (Q.F.)
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences,
University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325000, China
- Address correspondence to: (F.Y.); (Y.P.); (Q.F.)
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50
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Taniguchi A, Kuroyanagi Y, Aoki R, Eguchi M. Community Structure and Predicted Functions of Actively Growing Bacteria Responsive to Released Coral Mucus in Surrounding Seawater. Microbes Environ 2023; 38:ME23024. [PMID: 37704450 PMCID: PMC10522842 DOI: 10.1264/jsme2.me23024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/31/2023] [Indexed: 09/15/2023] Open
Abstract
A direct relationship exists between diverse corals and fish farming in Keten Bay, Amami-Oshima, Japan. The release of coral mucus has a significant impact on the microbial activity of surrounding seawater. To obtain a more detailed understanding of biogeochemical cycles in this environment, the effects of coral mucus on the community structure and function of bacteria in surrounding seawater need to be elucidated. We herein used a bromodeoxyuridine approach to investigate the structures and functions of bacterial communities growing close to mucus derived from two different Acropora corals, AC1 and AC2. The alpha diversities of actively growing bacteria (AGB) were lower in mucus-containing seawater than in control seawater and their community structures significantly differed, suggesting that the growth of specific bacteria was modulated by coral mucus. Rhodobacteraceae and Cryomorphaceae species were the most dominant AGB in response to the mucus of Acropora AC1 and AC2, respectively. In contrast, the growth of Actinomarinaceae, Alteromonadaceae, Flavobacteriaceae, and SAR86 clade bacteria was inhibited by coral mucus. The results of a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) ana-lysis suggested that the predicted functions of AGB in mucus-containing seawater differed from those in seawater. These functions were related to the biosynthesis and degradation of the constituents of coral mucus, such as polysaccharides, sugar acids, and aromatic compounds. The present study demonstrated that complex bacterial community structures and functions may be shaped by coral mucus, suggesting that corals foster diverse bacterial communities that enhance the ecological resilience of this fish farming area.
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Affiliation(s)
- Akito Taniguchi
- Faculty of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
| | - Yuki Kuroyanagi
- Graduate School of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
| | - Ryuichiro Aoki
- Graduate School of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
| | - Mitsuru Eguchi
- Faculty of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
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