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Mukherjee S, Bhattacharjee S, Paul S, Nath S, Paul S. Biofilm-a Syntrophic Consortia of Microbial Cells: Boon or Bane? Appl Biochem Biotechnol 2023; 195:5583-5604. [PMID: 35829902 DOI: 10.1007/s12010-022-04075-4] [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: 03/21/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Biofilm is the conglomeration of microbial cells which is associated with a surface. In the recent times, the study of biofilm has gained popularity and vivid research is being done to know about the effects of biofilm and that it consists of many organisms which are symbiotic in nature, some of which are human pathogens. Here, in this study, we have discussed about biofilms, its formation, relevance of its presence in the biosphere, and the possible remediations to cope up with its negative effects. Since removal of biofilm is difficult, emphasis has been made to suggest ways to prevent biofilm formation and also to devise ways to utilize biofilm in an economically and environment-friendly method.
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Affiliation(s)
- Susmita Mukherjee
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Shreya Bhattacharjee
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Sharanya Paul
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Somava Nath
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India
| | - Sonali Paul
- Department of Biotechnology, University of Engineering and Management, University Area, Plot No. III - B/5, New Town, Action Area - III, Kolkata, West Bengal, 700160, India.
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2
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Fujiyoshi S, Yarimizu K, Fuenzalida G, Campos M, Rilling JI, Acuña JJ, Miranda PC, Cascales EK, Perera I, Espinoza-González O, Guzmán L, Jorquera MA, Maruyama F. Monitoring bacterial composition and assemblage in the Gulf of Corcovado, southern Chile: Bacteria associated with harmful algae. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100194. [PMID: 37346179 PMCID: PMC10279789 DOI: 10.1016/j.crmicr.2023.100194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Harmful Algal Blooms (HABs) have caused damage to the marine environment in Isla San Pedro in the Gulf of Corcovado, Chile. While rising water temperature and artificial eutrophication are the most discussed topics as a cause, marine bacteria is a recent attractive parameter as an algal bloom driver. This study monitored algal and bacterial compositions in the water of Isla San Pedro for one year using microscopy and 16S rRNA metabarcoding analysis, along with physicochemical parameters. The collected data were analyzed with various statistical tools to understand how the particle-associated bacteria (PA) and the free-living (FL) bacteria were possibly involved in algal blooms. Both FL and PA fractions maintained a stable bacterial composition: the FL fraction was dominated by Proteobacteria (α-Proteobacteria and γ-Proteobacteria), and Cyanobacteria dominated the PA fraction. The two fractions contained equivalent bacterial taxonomic richness (c.a. 8,000 Operational Taxonomic Units) and shared more than 50% of OTU; however, roughly 20% was exclusive to each fraction. The four most abundant algal genera in the Isla San Pedro water were Thalassiosira, Skeletonema, Chaetoceros, and Pseudo-nitzchia. Statistical analysis identified that the bacterial species Polycyclovorans algicola was correlated with Pseudo-nitzschia spp., and our monitoring data recorded a sudden increase of particle-associated Polycyclovorans algicola shortly after the increase of Pseudo-nitzschia, suggesting that P. algicola may have regression effect on Pseudo-nitzschia spp. The study also investigated the physicochemical parameter effect on algal-bacterial interactions. Oxygen concentration and chlorophyll-a showed a strong correlation with both FL and PA bacteria despite their assemblage differences, suggesting that the two groups had different mechanisms for interacting with algal species.
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Affiliation(s)
- So Fujiyoshi
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Kyoko Yarimizu
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Gonzalo Fuenzalida
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Buena Vecindad #91, Puerto Montt, Chile
| | - Marco Campos
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Joaquin-Ignacio Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Jacquelinne J. Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Pedro Calabrano Miranda
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Emma-Karin Cascales
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Ishara Perera
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 574, Puerto Montt 5480000, Chile
| | - Milko A. Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Quimicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile
| | - Fumito Maruyama
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
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3
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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4
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Iqbal MM, Nishimura M, Sano M, Yoshizawa S. Particle-attached Microbes in Eelgrass Vegetation Areas Differ in Community Structure Depending on the Distance from the Eelgrass Bed. Microbes Environ 2023; 38:ME23013. [PMID: 37661422 PMCID: PMC10522840 DOI: 10.1264/jsme2.me23013] [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: 02/04/2023] [Accepted: 06/01/2023] [Indexed: 09/05/2023] Open
Abstract
Zostera marina (eelgrass) is a submerged flowering plant often found in the coastal areas of Japan. Large amounts of suspended particles form in highly productive environments, such as eelgrass beds, and the behavior of these particles is expected to affect the surrounding microbial community. We investigated the microbial community structure of suspended particles in three eelgrass fields (Ikuno-Shima Is., Mutsu Bay, and Nanao Bay) and inferred the formation and dynamics of suspended particles from a microbial community structure ana-lysis. Seawater samples were collected directly above each eelgrass bed (eelgrass-covering) and from locations dozens of meters away from the eelgrass bed (bare-ground). In consideration of the two different lifestyles of marine microbes, microbial communities were obtained from particle-attached (PA) and free-living (FL) states. Differences in microbial diversity and community structures were observed between PA and FL in all eelgrass beds. The FL microbial community was similar between the two sampling points (eelgrass-covering and bare-ground), whereas a significant difference was noted in the microbial community structure of suspended particles between the two sampling points. This difference appeared to be due to the supply of organic matter from the eelgrass sea ground and leaf-attached detritus produced by microbial activity. In addition, the classes Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria were abundant in the PA and FL fractions. Furthermore, many sequences of the key groups (e.g., Planctomycetes and Verrucomicrobia) were exclusively detected in the PA fraction, in which they may circulate nutrients. The present results provide insights into the microbial communities of suspended particles and provide the first step towards understanding their biogeochemical impact on the eelgrass bed.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8563, Japan
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
| | - Masayoshi Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8563, Japan
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5
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Heins A, Harder J. Particle-associated bacteria in seawater dominate the colony-forming microbiome on ZoBell marine agar. FEMS Microbiol Ecol 2022; 99:6895545. [PMID: 36513318 PMCID: PMC9798892 DOI: 10.1093/femsec/fiac151] [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: 07/27/2022] [Revised: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution plating on marine agar 2216 (ZoBell marine agar) and microscopic counts indicated a cultivability of 0.7% (0.4%-1.2%) of bacteria in coastal seawater collected at Helgoland Roads, North Sea. Particle-associated bacteria presented a minority population in seawater, but had a larger cultivability of 25% (0.9%-100%) for populations collected by settlement of particles and 5.7% (0.9%-24%) for populations collected by filtration. Partial 16S rRNA gene sequences indicated that 84% of the cultured taxa were either enriched in particle-associated microbiomes or only found in these microbiomes, including Sulfitobacter and other Rhodobacteraceae, Pseudoalteromonas, Psychromonas, Arcobacter and many Flavobacteriaceae. Illumina-based 16S rRNA V3V4 amplicon sequences of plate communities revealed that nearly all operational taxonomic units had a cultivated and described strain in close phylogenetic proximity. This suggested that decades of strain isolation from seawater on ZoBell marine agar had achieved a very good coverage of cultivable genera abundant in nature. The majority belonged to particle-associated bacteria, complementing observations that abundant free-living seawater bacteria often require cultivation conditions closer to their natural habitat like liquid cultivation in oligotrophic medium.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr.1, D-28359 Bremen, Germany
| | - Jens Harder
- Corresponding author: Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr.1, D-28359 Bremen, Germany. E-mail:
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Zhang J, Shen H, Wang H, Zhang W, Deng X, Gao Q, Yang X, Chen J, Xie P. Salinity and seasonality shaping free-living and particle-associated bacterioplankton community assembly in lakeshores of the northeastern Qinghai-Tibet Plateau. ENVIRONMENTAL RESEARCH 2022; 214:113717. [PMID: 35760113 DOI: 10.1016/j.envres.2022.113717] [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: 02/27/2022] [Revised: 05/30/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms in lakeshore zones are essential for pollution interception and biodiversity maintenance. However, the biogeographic patterns of bacterioplankton communities in lakeshore zones and the mechanisms that driving them are poorly understood. We analyzed the 16 S rRNA gene sequences of particle-associated (PA) and free-living (FL) bacterioplankton communities in the lakeshore zones of 14 alpine lakes in two seasons on Qinghai-Tibet Plateau to investigate the bacterial diversity, composition and assembly processes. Our results revealed that PA and FL bacterioplankton communities were driven by both seasonality and salinity in the lakeshores on Qinghai-Tibet Plateau. Compared to FL bacterioplankton, PA bacterioplankton communities were more susceptible to seasonality than spatial salinity. FL bacterioplankton communities were more salinity constrained than the PA counterpart. Besides, the Stegen null model analyses have validated a quantitative bias on stochastic processes at different spatial scales. At a regional scale, stochasticity was the predominant assembly process in both PA and FL bacterioplankton. While at a subregional scale, dispersal limitation was the main contributor of stochastic processes for PA bacterioplankton in summer and heterogeneous selection was the dominant deterministic processes in winter, whereas the community assembly of FL bacterioplankton was more stochastic processes (i.e., dispersal limitation) dominated in the freshwater type but deterministic process (i.e., heterogeneous selection) increased with increasing salinity. Our study provides new insights into both significant spatiotemporal patterns and distinct assembly processes of PA and FL bacterioplankton in alpine lakeshores on the northeastern Qinghai-Tibet Plateau.
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Affiliation(s)
- Jia Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Shen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Huan Wang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
| | - Weizhen Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Xuwei Deng
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Xi Yang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China; Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
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7
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Li K, Guan W, He P, Li K. Comparison of bacterial communities on the surface of concrete breakwater structures and ambient bacterioplankton. Lett Appl Microbiol 2022; 75:1193-1202. [PMID: 35831926 DOI: 10.1111/lam.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/03/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Breakwater structures made of concrete are used widely around the world, and the bacteria living on these surfaces can cause the concrete to deteriorate. In this study, we collected bacterial biofilms from concrete breakwater structures located along the coast of an island, a mainland coast, and a freshwater riverbank as well as planktonic water samples from each site, and we analyzed their bacterial community structures using Illumina sequencing. At the phylum level, Proteobacteria and Actinobacteria dominated planktonic samples, whereas Cyanobacteria, Proteobacteria, and Bacteroidetes dominated the biofilm samples. High Cyanobacteria abundance was found in all biofilm samples. Bacterial communities significantly varied between planktonic and biofilm samples and between biofilm samples from seawater and freshwater. Only a small number of bacterial operational taxonomic units were shared by planktonic and biofilm samples from each sampling site. The permanganate index in ambient water had a more significant impact on biofilm bacterial communities than on planktonic samples. Additionally, ammonia nitrogen and total nitrogen contents were positively correlated and salinity was negatively correlated with bacterial beta diversity in biofilm samples.
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Affiliation(s)
- Kui Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Weibing Guan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kejun Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
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8
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Martínez-García S, Bunse C, Pontiller B, Baltar F, Israelsson S, Fridolfsson E, Lindh MV, Lundin D, Legrand C, Pinhassi J. Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent. Front Microbiol 2022; 13:834675. [PMID: 36212867 PMCID: PMC9533715 DOI: 10.3389/fmicb.2022.834675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 μm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05–0.27) of FL bacteria (defined as the size-fraction <3.0 μm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.
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Affiliation(s)
- Sandra Martínez-García
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Pontevedra, Spain
- *Correspondence: Sandra Martínez-García,
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Benjamin Pontiller
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Stina Israelsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Emil Fridolfsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Markus V. Lindh
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
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9
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Luo E, Leu AO, Eppley JM, Karl DM, DeLong EF. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. THE ISME JOURNAL 2022; 16:1627-1635. [PMID: 35236926 PMCID: PMC9122931 DOI: 10.1038/s41396-022-01202-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/15/2022]
Abstract
Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
- Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS 51, Woods Hole MA, 02543, Falmouth, USA.
| | - Andy O Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
- Australia Center for Ecogenomics, University of Queensland, St. Lucia QLD, 4072, Australia
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
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10
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Basili M, Techtmann SM, Zaggia L, Luna GM, Quero GM. Partitioning and sources of microbial pollution in the Venice Lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151755. [PMID: 34848267 DOI: 10.1016/j.scitotenv.2021.151755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/25/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Microbial pollutants are a serious threat to human and environmental health in coastal areas. Based on the hypothesis that pollution from multiple sources may produce a distinct microbial signature and that microbial pollutants seem to distribute between a free-living and a particle-attached fraction, we investigated the occurrence, partitioning and sources of microbial pollutants in water samples collected in the Venice Lagoon (Italy). The area was taken as a case study of an environment characterized by a long history of industrial pollution and by growing human pressure. We found a variety of pollutants from several sources, with sewage-associated and faecal bacteria accounting for up to 5.98% of microbial communities. Sewage-associated pollutants were most abundant close to the city centre. Faecal pollution was highest in the area of the industrial port and was dominated by human inputs, whereas contamination from animal faeces was mainly detected at the interface with the mainland. Microbial pollutants were almost exclusively associated with the particle-attached fraction. The samples also contained other potential pathogens. Our findings stress the need for monitoring and managing microbial pollution in highly urbanized lagoon and semi-enclosed systems and suggest that management plans to reduce microbial inputs to the waterways should include measures to reduce particulate matter inputs to the lagoon. Finally, High-Throughput Sequencing combined with computational approaches proved critical to assess water quality and appears to be a valuable tool to support the monitoring of waterborne diseases.
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Affiliation(s)
- Marco Basili
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, United States
| | - Luca Zaggia
- CNR IGG, National Research Council - Institute of Geosciences and Earth Resources, Via G. Gradenigo 6, 35131 Padova, Italy
| | - Gian Marco Luna
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Grazia Marina Quero
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125 Ancona, Italy.
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11
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Microbial Community Structure and Ecological Networks during Simulation of Diatom Sinking. Microorganisms 2022; 10:microorganisms10030639. [PMID: 35336213 PMCID: PMC8949005 DOI: 10.3390/microorganisms10030639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022] Open
Abstract
Microbial-mediated utilization of particulate organic matter (POM) during its downward transport from the surface to the deep ocean constitutes a critical component of the global ocean carbon cycle. However, it remains unclear as to how high hydrostatic pressure (HHP) and low temperature (LT) with the sinking particles affects community structure and network interactions of the particle-attached microorganisms (PAM) and those free-living microorganisms (FLM) in the surrounding water. In this study, we investigated microbial succession and network interactions in experiments simulating POM sinking in the ocean. Diatom-derived 13C- and 12C-labeled POM were used to incubate surface water microbial communities from the East China Sea (ECS) under pressure (temperature) of 0.1 (25 °C), 20 (4 °C), and 40 (4 °C) MPa (megapascal). Our results show that the diversity and species richness of the PAM and FLM communities decreased significantly with HHP and LT. Microbial community analysis indicated an increase in the relative abundance of Bacteroidetes at high pressure (40 MPa), mostly at the expense of Gammaproteobacteria, Alphaproteobacteria, and Gracilibacteria at atmospheric pressure. Hydrostatic pressure and temperature affected lifestyle preferences between particle-attached (PA) and free-living (FL) microbes. Ecological network analysis showed that HHP and LT enhanced microbial network interactions and resulted in higher vulnerability to networks of the PAM communities and more resilience of those of the FLM communities. Most interestingly, the PAM communities occupied most of the module hubs of the networks, whereas the FLM communities mainly served as connectors of the modules, suggesting their different ecological roles of the two groups of microbes. These results provided novel insights into how HHP and LT affected microbial community dynamics, ecological networks during POM sinking, and the implications for carbon cycling in the ocean.
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12
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Geisler E, Rahav E, Bar-Zeev E. Contribution of Heterotrophic Diazotrophs to N2 Fixation in a Eutrophic River: Free-Living vs. Aggregate-Associated. Front Microbiol 2022; 13:779820. [PMID: 35237246 PMCID: PMC8882987 DOI: 10.3389/fmicb.2022.779820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Recent studies have indicated that heterotrophic diazotrophs are highly diverse and fix N2 in aquatic environments with potentially adverse conditions for diazotrophy, such as oxic and rich in total nitrogen. In this study, we compared the activity and diversity of heterotrophic diazotrophs associated with aggregates (>12 μm) to free-living cells in the eutrophic Qishon River during the winter and summer seasons. Overall, measured heterotrophic N2 fixation rates in the Qishon River ranged between 2.6–3.5 nmol N L–1 d–1. Heterotrophic N2 fixation was mainly associated with aggregates in the summer samples (74 ± 24%), whereas during the winter the bulk diazotrophic activity was mostly ascribed to the free-living fraction (90 ± 6%). In addition, immunolabeled micrographs indicated the presence of aggregate-associated heterotrophic diazotrophs in both seasons, while phototrophic diazotrophs were also captured during the winter. The richness of free-living and aggregate-associated heterotrophic diazotrophs were overall similar, yet the evenness of the later was significantly smaller, suggesting that few of the species gained advantage from particle lifestyle. The differences in the activity, micro-localization and diversity of the diazotrophic community were mostly attributed to spatiotemporal changes in the ambient C:N ratios (total organic carbon, TOC: total nitrogen) and the TOC concentrations. Taken together, our results shed new light on the contribution of heterotrophic diazotroph associated with aggregates to total heterotrophic N2 fixation in oxic, highly eutrophic aquatic environments.
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Affiliation(s)
- Eyal Geisler
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
- *Correspondence: Eyal Rahav,
| | - Edo Bar-Zeev
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
- Edo Bar-Zeev,
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13
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Blais MA, Matveev A, Lovejoy C, Vincent WF. Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients. Front Microbiol 2022; 12:760282. [PMID: 35046910 PMCID: PMC8762315 DOI: 10.3389/fmicb.2021.760282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Alex Matveev
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Québec-Océan, Université Laval, Quebec City, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
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14
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Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics. Microorganisms 2021; 9:microorganisms9122621. [PMID: 34946222 PMCID: PMC8707726 DOI: 10.3390/microorganisms9122621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
The diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world’s oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. How the functioning of microbial communities is impacted by day and night periods in surface seawater remains to be elucidated. In this study, we compared the day and night metaproteomes of the free-living and the particle-attached bacterial fractions from picoplanktonic communities sampled from the northwest Mediterranean Sea surface. Our results showed similar taxonomic distribution of free-living and particle-attached bacterial populations, with Alphaproteobacteria, Gammaproteobacteria and Cyanobacteria being the most active members. Comparison of the day and night metaproteomes revealed that free-living and particle-attached bacteria were more active during the day and the night, respectively. Interestingly, protein diel variations were observed in the photoautotroph Synechococcales and in (photo)-heterotrophic bacteria such as Flavobacteriales, Pelagibacterales and Rhodobacterales. Moreover, our data demonstrated that diel cycle impacts light-dependent processes such as photosynthesis and UV-stress response in Synechococcales and Rhodobacterales, respectively, while the protein regulation from the ubiquitous Pelagibacterales remained stable over time. This study unravels, for the first time, the diel variation in the protein expression of major free-living and particle-attached microbial players at the sea surface, totaling an analysis of eight metaproteomes.
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15
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Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea. Microorganisms 2021; 9:microorganisms9122445. [PMID: 34946047 PMCID: PMC8704526 DOI: 10.3390/microorganisms9122445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.
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16
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Zhao D, Gao P, Xu L, Qu L, Han Y, Zheng L, Gong X. Disproportionate responses between free-living and particle-attached bacteria during the transition to oxygen-deficient zones in the Bohai Seawater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148097. [PMID: 34412405 DOI: 10.1016/j.scitotenv.2021.148097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/19/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
The Bohai Sea has recently suffered several seasonal oxygen-deficiency, even hypoxia events during the summer. To better understand effects of dissolved oxygen (DO) concentration on the bacterial composition in particle attached (PA) and free living (FL) fractions during the transition from oxic water to low oxygen conditions, the bacterial communities under three different oxygen levels, i.e., high oxygen (HO, close to 100% O2 saturation), medium oxygen (MO, close to 75% O2 saturation), and low oxygen (LO, close to 50% O2 saturation) in the Bohai Sea were investigated using 16S rRNA amplicon sequencing. Fourteen water samples from 5 stations were collected during a cruise from August to September in 2018. The results showed that the sequences of Proteobacteria and Actinobacteriota jointly accounted for up to 74% across all 14 samples. The Shannon index in HO samples were significantly higher than in LO samples (P < 0.05), especially in PA communities. The composition of bacterial communities varied by oxygen concentration in all samples, and the effect was more pronounced in the PA fraction, which indicates that the PA fraction was more sensitive to the change in oxygen concentration, possibly due to the tighter interactions in this community than in the FL fraction. This study provides novel insights into the distribution of bacterial communities, and clues for understanding the responses of bacterial communities in the Bohai Sea during the transition from the oxic to oxygen-deficient zones.
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Affiliation(s)
- Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ping Gao
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lingyun Qu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Yajing Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Liwen Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China.
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17
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Wang K, Mou X. Coordinated Diel Gene Expression of Cyanobacteria and Their Microbiome. Microorganisms 2021; 9:microorganisms9081670. [PMID: 34442749 PMCID: PMC8398468 DOI: 10.3390/microorganisms9081670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Diel rhythms have been well recognized in cyanobacterial metabolisms. However, whether this programmed activity of cyanobacteria could elicit coordinated diel gene expressions in microorganisms (microbiome) that co-occur with cyanobacteria and how such responses in turn impact cyanobacterial metabolism are unknown. To address these questions, a microcosm experiment was set up using Lake Erie water to compare the metatranscriptomic variations of Microcystis cells alone, the microbiome alone, and these two together (whole water) over two day-night cycles. A total of 1205 Microcystis genes and 4779 microbiome genes exhibited significant diel expression patterns in the whole-water microcosm. However, when Microcystis and the microbiome were separated, only 515 Microcystis genes showed diel expression patterns. A significant structural change was not observed for the microbiome communities between the whole-water and microbiome microcosms. Correlation analyses further showed that diel expressions of carbon, nitrogen, phosphorous, and micronutrient (iron and vitamin B12) metabolizing genes were significantly coordinated between Microcystis and the microbiome in the whole-water microcosm. Our results suggest that diel fluxes of organic carbon and vitamin B12 (cobalamin) in Microcystis could cause the diel expression of microbiome genes. Meanwhile, the microbiome communities may support the growth of Microcystis by supplying them with recycled nutrients, but compete with Microcystis for iron.
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18
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Roth Rosenberg D, Haber M, Goldford J, Lalzar M, Aharonovich D, Al-Ashhab A, Lehahn Y, Segrè D, Steindler L, Sher D. Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors. Environ Microbiol 2021; 23:4295-4308. [PMID: 34036706 DOI: 10.1111/1462-2920.15611] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/23/2021] [Indexed: 12/20/2022]
Abstract
In the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (2 years) in the ultra-oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free-living (FL) vs. particle-associated), followed by depth and finally season. The FL community was taxonomically richer and more stable than the particle-associated (PA) one, which was characterized by recurrent 'blooms' of heterotrophic bacteria such as Alteromonas and Ralstonia. The heterotrophic FL and PA communities were also correlated with different environmental parameters: the FL population correlated with depth and phytoplankton, whereas PA bacteria were correlated primarily with the time of sampling. A significant part of the variability in community structure could, however, not be explained by the measured parameters. The metabolic potential of the PA community, predicted from 16S rRNA amplicon data using PICRUSt, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in predicted pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Dalit Roth Rosenberg
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | | | - Maya Lalzar
- Bioinformatics Support Unit, University of Haifa, Haifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ashraf Al-Ashhab
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Microbial Metagenomics Division, Dead Sea and Arava Science Center, Masada, Israel
| | - Yoav Lehahn
- Department of Maritime Geosciences, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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19
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Heins A, Reintjes G, Amann RI, Harder J. Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria. Front Microbiol 2021; 12:643730. [PMID: 33868201 PMCID: PMC8047139 DOI: 10.3389/fmicb.2021.643730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day-1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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20
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Baker KD, Kellogg CTE, McClelland JW, Dunton KH, Crump BC. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons. Front Microbiol 2021; 12:601901. [PMID: 33643234 PMCID: PMC7906997 DOI: 10.3389/fmicb.2021.601901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
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Affiliation(s)
- Kristina D Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - James W McClelland
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Kenneth H Dunton
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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21
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Shahraki AH, Chaganti SR, Heath DD. Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario. MICROBIAL ECOLOGY 2021; 81:1-13. [PMID: 32621209 DOI: 10.1007/s00248-020-01539-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.
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Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
- Cooperative Institute for Great Lakes Research, School of Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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22
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Antunes JT, Sousa AGG, Azevedo J, Rego A, Leão PN, Vasconcelos V. Distinct Temporal Succession of Bacterial Communities in Early Marine Biofilms in a Portuguese Atlantic Port. Front Microbiol 2020; 11:1938. [PMID: 32849482 PMCID: PMC7432428 DOI: 10.3389/fmicb.2020.01938] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Marine biofilms are known to influence the corrosion of metal surfaces in the marine environment. Despite some recent research, the succession of bacterial communities colonizing artificial surfaces remains uncharacterized in some temporal settings. More specifically, it is not fully known if bacterial colonizers of artificial surfaces are similar or distinct in the different seasons of the year. In particular the study of early biofilms, in which the bacterial cells communities first adhere to artificial surfaces, are crucial for the development of the subsequent biofilm communities. In this work, we used amplicon-based NGS (next-generation sequencing) and universal 16S rRNA bacterial primers to characterize the early biofilm bacterial communities growing on 316 L stainless steel surfaces in a Northern Portugal port. Sampling spanned 30-day periods in two distinct seasons (spring and winter). Biofilm communities growing in steel surfaces covered with an anti-corrosion paint and planktonic communities from the same location were also characterized. Our results demonstrated that distinct temporal patterns were observed in the sampled seasons. Specifically, a significantly higher abundance of Gammaproteobacteria and Mollicutes was found on the first days of biofilm growth in spring (day 1 to day 4) and a higher abundance of Alphaproteobacteria during the same days of biofilm growth in winter. In the last sampled day (day 30), the spring biofilms significantly shifted toward a dominance of photoautotrophic groups (mostly diatoms) and were also colonized by some macrofouling communities, something not observed during the winter sampling. Our results revealed that bacterial composition in the biofilms was particularly affected by the sampled day of the specific season, more so than the overall effect of the season or overall sampling day of both seasons. Additionally, the application of a non-fouling-release anti-corrosion paint in the steel plates resulted in a significantly lower diversity compared with plates without paint, but this was only observed during spring. We suggest that temporal succession of marine biofilm communities should be taken in consideration for future antifouling/anti-biofilm applications.
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Affiliation(s)
- Jorge T. Antunes
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - António G. G. Sousa
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Joana Azevedo
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Adriana Rego
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Pedro N. Leão
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Vitor Vasconcelos
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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23
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Schultz D, Zühlke D, Bernhardt J, Francis TB, Albrecht D, Hirschfeld C, Markert S, Riedel K. An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:367-376. [PMID: 32281239 DOI: 10.1111/1758-2229.12842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to establish a robust and reliable metaproteomics protocol for an in-depth characterization of marine particle-associated (PA) bacteria. To this end, we compared six well-established protein extraction protocols together with different MS-sample preparation techniques using particles sampled during a North Sea spring algae bloom in 2009. In the final optimized workflow, proteins are extracted using a combination of SDS-containing lysis buffer and cell disruption by bead-beating, separated by SDS-PAGE, in-gel digested and analysed by LC-MS/MS, before MASCOT search against a metagenome-based database and data processing/visualization with the in-house-developed bioinformatics tools Prophane and Paver. As an application example, free-living (FL) and particulate communities sampled in April 2009 were analysed, resulting in an as yet unprecedented number of 9354 and 5034 identified protein groups for FL and PA bacteria, respectively. Our data suggest that FL and PA communities appeared similar in their taxonomic distribution, with notable exceptions: eukaryotic proteins and proteins assigned to Flavobacteriia, Cyanobacteria, and some proteobacterial genera were found more abundant on particles, whilst overall proteins belonging to Proteobacteria were more dominant in the FL fraction. Furthermore, our data points to functional differences including proteins involved in polysaccharide degradation, sugar- and phosphorus uptake, adhesion, motility, and stress response.
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Affiliation(s)
- Doreen Schultz
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Hirschfeld
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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24
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Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir. Sci Rep 2020; 10:11288. [PMID: 32647153 PMCID: PMC7347578 DOI: 10.1038/s41598-020-67774-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/22/2020] [Indexed: 02/01/2023] Open
Abstract
Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.
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25
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Zhang Y, Jing H, Peng X. Vertical shifts of particle-attached and free-living prokaryotes in the water column above the cold seeps of the South China Sea. MARINE POLLUTION BULLETIN 2020; 156:111230. [PMID: 32510376 DOI: 10.1016/j.marpolbul.2020.111230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Marine particle-attached (PA) and free-living (FL) microbes play important roles in the biogeochemical cycling of organic matter along the water column. Deep-sea cold seeps are highly productive and chemosynthetic ecosystems, their continuous emission of CH4, CO2, and H2S can reach up to 100 m in the above water, therefore would influence the distribution and potential metabolic functions of deep-sea prokaryotes. In this study, the vertical distribution profiles of both PA and FL microbes in the water column above two cold seeps of the South China Sea were investigated using Illumina sequencing and quantitative PCR (qPCR) based on 16S rRNA gene. Photosynthetic and heterotrophic prokaryotes were predominant in respective surface and deep layers below the photic zone. The typical cold seep chemosynthetic microbes, such as methanotrophs and sulfate-reducing bacteria were observed with low proportions in the two cold seeps as well. Distinct PA and FL microbial fractions were found in terms of abundance and diversity. FL fraction exposed to the bulk water was significantly affected by temperature and inorganic nutrients, whereas PA fraction relied more on the organic matter of the particles and less susceptible to the environmental variability. Our study highlights the importance of vertical geochemical gradients on the distribution and potential metabolic choice of marine microbes and extends our current knowledge of depth-associated microbial distribution patterns.
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Affiliation(s)
- Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Southern Marine Science and Engineering Guangdong Laboratory (ZhuHai), China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Southern Marine Science and Engineering Guangdong Laboratory (ZhuHai), China.
| | - Xiaotong Peng
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Southern Marine Science and Engineering Guangdong Laboratory (ZhuHai), China.
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26
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Xie R, Wang Y, Chen Q, Guo W, Jiao N, Zheng Q. Coupling Between Carbon and Nitrogen Metabolic Processes Mediated by Coastal Microbes in Synechococcus-Derived Organic Matter Addition Incubations. Front Microbiol 2020; 11:1041. [PMID: 32523578 PMCID: PMC7261836 DOI: 10.3389/fmicb.2020.01041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/27/2020] [Indexed: 11/20/2022] Open
Abstract
Phytoplankton are major contributors to labile organic matter in the upper ocean. Diverse heterotrophic bacteria successively metabolize these labile compounds and drive elemental biogeochemical cycling. We investigated the bioavailability of Synechococcus-derived organic matter (SOM) by estuarine and coastal microbes during 180-day dark incubations. Variations in organic carbon, inorganic nutrients, fluorescent dissolved organic matter (FDOM), and total/active microbial communities were monitored. The entire incubations could be partitioned into three phases (labeled I, II, and III) based on the total organic carbon (TOC) consumption rates of 6.38–7.01, 0.53–0.64, and 0.10–0.13 μmol C L–1 day–1, respectively. This corresponded with accumulation processes of NH4+, NO2–, and NO3–, respectively. One tryptophan-like (C1) and three humic-like (C2, C3, and C4) FDOM components were identified. The intensity variation of C1 followed bacterial growth activities, and C2, C3, and C4 displayed labile, semi-labile, and refractory DOM characteristics, respectively. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Actinobacteria dominated the quickly consumed process of SOM (phase I) coupled with a substantial amount of NH4+ generation. Thaumarchaeota became an abundant population with the highest activities in phase II, especially in the free-living size-fraction, and these organisms could perform chemoautotroph processes through the ammonia oxidation. Microbial populations frequently found in the dark ocean, even the deep sea, became abundant during phase III, in which Nitrospinae/Nitrospirae obtained energy through nitrite oxidation. Our results shed light on the transformation of different biological availability of organic carbon by coastal microorganisms which coupled with the regeneration of different form of inorganic nitrogen.
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Affiliation(s)
- Rui Xie
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 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, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Environment and Ecology, Xiamen University, Xiamen, China
| | - Qi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Weidong Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, Xiamen University, Xiamen, 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, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 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, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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27
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Liu Y, Fang J, Jia Z, Chen S, Zhang L, Gao W. DNA stable-isotope probing reveals potential key players for microbial decomposition and degradation of diatom-derived marine particulate matter. Microbiologyopen 2020; 9:e1013. [PMID: 32166910 PMCID: PMC7221439 DOI: 10.1002/mbo3.1013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 11/06/2022] Open
Abstract
Microbially mediated decomposition of particulate organic carbon (POC) is a central component of the oceanic carbon cycle, controlling the flux of organic carbon from the surface ocean to the deep ocean. Yet, the specific microbial taxa responsible for POC decomposition and degradation in the deep ocean are still unknown. To target the active microbial lineages involved in these processes, 13 C-labeled particulate organic matter (POM) was used as a substrate to incubate particle-attached (PAM) and free-living microbial (FLM) assemblages from the epi- and bathypelagic zones of the New Britain Trench (NBT). By combining DNA stable-isotope probing and Illumina Miseq high-throughput sequencing of bacterial 16S rRNA gene, we identified 14 active bacterial taxonomic groups that implicated in the decomposition of 13 C-labeled POM at low and high pressures under the temperature of 15°C. Our results show that both PAM and FLM were able to decompose POC and assimilate the released DOC. However, similar bacterial taxa in both the PAM and FLM assemblages were involved in POC decomposition and DOC degradation, suggesting the decoupling between microbial lifestyles and ecological functions. Microbial decomposition of POC and degradation of DOC were accomplished primarily by particle-attached bacteria at atmospheric pressure and by free-living bacteria at high pressures. Overall, the POC degradation rates were higher at atmospheric pressure (0.1 MPa) than at high pressures (20 and 40 MPa) under 15°C. Our results provide direct evidence linking the specific particle-attached and free-living bacterial lineages to decomposition and degradation of diatomic detritus at low and high pressures and identified the potential mediators of POC fluxes in the epi- and bathypelagic zones.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, USA
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Songze Chen
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Li Zhang
- State Key Laboratory of Geological Process and Mineral Resources, Faculty of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Wei Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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28
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Catão ECP, Pollet T, Misson B, Garnier C, Ghiglione JF, Barry-Martinet R, Maintenay M, Bressy C, Briand JF. Shear Stress as a Major Driver of Marine Biofilm Communities in the NW Mediterranean Sea. Front Microbiol 2019; 10:1768. [PMID: 31608016 PMCID: PMC6774042 DOI: 10.3389/fmicb.2019.01768] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
While marine biofilms depend on environmental conditions and substrate, little is known about the influence of hydrodynamic forces. We tested different immersion modes (dynamic, cyclic and static) in Toulon Bay (north-western Mediterranean Sea; NWMS). The static mode was also compared between Toulon and Banyuls Bays. In addition, different artificial surfaces designed to hamper cell attachment (self-polishing coating: SPC; and fouling-release coating: FRC) were compared to inert plastic. Prokaryotic community composition was affected by immersion mode, surface characteristics and site. Rhodobacteriaceae and Flavobacteriaceae dominated the biofilm community structure, with distinct genera according to surface type or immersion mode. Cell density increased with time, greatly limited by hydrodynamic forces, and supposed to delay biofilm maturation. After 1 year, a significant impact of shear stress on the taxonomic structure of the prokaryotic community developed on each surface type was observed. When surfaces contained no biocides, roughness and wettability shaped prokaryotic community structure, which was not enhanced by shear stress. Conversely, the biocidal effect of SPC surfaces, already major in static immersion mode, was amplified by the 15 knots speed. The biofilm community on SPC was 60% dissimilar to the biofilm on the other surfaces and was distinctly colonized by Sphingomonadaceae ((Alter)Erythrobacter). At Banyuls, prokaryotic community structures were more similar between the four surfaces tested than at Toulon, due possibly to a masking effect of environmental constraints, especially hydrodynamic, which was greater than in Toulon. Finally, predicted functions such as cell adhesion confirmed some of the hypotheses drawn regarding biofilm formation over the artificial surfaces tested here.
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Affiliation(s)
| | - Thomas Pollet
- Laboratoire MAPIEM (EA 4323), Université de Toulon, Toulon, France
- UMR BIPAR, INRA, ANSES, ENVA, Université Paris-Est, Maisons-Alfort, France
| | - Benjamin Misson
- CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, University of Toulon – Aix-Marseille University, La Garde, France
| | - Cédric Garnier
- CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, University of Toulon – Aix-Marseille University, La Garde, France
| | - Jean-Francois Ghiglione
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d’Océanographie Microbienne, Banyuls-sur-Mer, France
| | | | - Marine Maintenay
- Laboratoire MAPIEM (EA 4323), Université de Toulon, Toulon, France
| | - Christine Bressy
- Laboratoire MAPIEM (EA 4323), Université de Toulon, Toulon, France
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29
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The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea. Sci Rep 2019; 9:9176. [PMID: 31235719 PMCID: PMC6591218 DOI: 10.1038/s41598-019-45512-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/04/2019] [Indexed: 01/05/2023] Open
Abstract
To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.
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30
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Ijichi M, Itoh H, Hamasaki K. Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan. Arch Microbiol 2019; 201:1141-1146. [DOI: 10.1007/s00203-019-01680-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/14/2019] [Accepted: 05/21/2019] [Indexed: 11/30/2022]
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31
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Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India. Mol Biol Rep 2019; 46:3113-3127. [DOI: 10.1007/s11033-019-04766-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
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32
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Zoccarato L, Grossart HP. Relationship Between Lifestyle and Structure of Bacterial Communities and Their Functionality in Aquatic Systems. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2019. [DOI: 10.1007/978-3-030-16775-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Horton DJ, Cooper MJ, Wing AJ, Kourtev PS, Uzarski DG, Learman DR. Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands. FEMS Microbiol Lett 2018; 365:5184454. [PMID: 30445437 DOI: 10.1093/femsle/fny269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 11/12/2018] [Indexed: 01/21/2023] Open
Abstract
Oxygen (O2) concentrations often fluctuate over diel timescales within wetlands, driven by temperature, sunlight, photosynthesis and respiration. These daily fluxes have been shown to impact biogeochemical transformations (e.g. denitrification), which are mediated by the residing microbial community. However, little is known about how resident microbial communities respond to diel physical and chemical fluxes in freshwater wetland ecosystems. In this study, total microbial (bacterial and archaeal) community structure was significantly related to diel time points in just one out of four distinct freshwater wetlands sampled. This suggests that daily environmental shifts may influence wetlands differentially based upon the resident microbial community and specific physical and chemical conditions of a freshwater wetland. When exploring the microbial communities within each wetland at finer resolutions, subcommunities of taxa within two wetlands were found to correspond to fluctuating O2 levels. Microbial taxa that were found to be susceptible to fluctuating O2 levels within these subnetworks may have intimate ties to metabolism and/or diel redox cycles. This study highlights that freshwater wetland microbial communities are often stable in community structure when confronted with short-term O2 fluxes; however, specialist taxa may be sensitive to these same fluxes.
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Affiliation(s)
- Dean J Horton
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Matthew J Cooper
- Mary Griggs Burke Center for Freshwater Innovation, Northland College, Ashland, WI 54806, USA
| | - Anthony J Wing
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Peter S Kourtev
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Donald G Uzarski
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Deric R Learman
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
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34
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Xu H, Zhao D, Huang R, Cao X, Zeng J, Yu Z, Hooker KV, Hambright KD, Wu QL. Contrasting Network Features between Free-Living and Particle-Attached Bacterial Communities in Taihu Lake. MICROBIAL ECOLOGY 2018; 76:303-313. [PMID: 29318328 DOI: 10.1007/s00248-017-1131-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/18/2017] [Indexed: 05/22/2023]
Abstract
Free-living (FL) and particle-attached (PA) bacterial communities play critical roles in nutrient cycles, metabolite production, and as a food source in aquatic systems, and while their community composition, diversity, and functions have been well studied, we know little about their community interactions, co-occurrence patterns, and niche occupancy. In the present study, 13 sites in Taihu Lake were selected to study the differences of co-occurrence patterns and niches occupied between the FL and PA bacterial communities using correlation-based network analysis. The results show that both FL and PA bacterial community networks were non-random and significant differences of the network indexes (average path length, clustering coefficient, modularity) were found between the two groups. Furthermore, the PA bacterial community network consisted of more correlations between fewer OTUs, as well as higher average degree, making it more complex. The results of observed (O) to random (R) ratios of intra- or inter-phyla connections indicate more relationships such as cross-feeding, syntrophic, mutualistic, or competitive relationships in the PA bacterial community network. We also found that four OTUs (OTU00074, OTU00755, OTU00079, and OTU00454), which all had important influences on the nutrients cyclings, played different roles in the two networks as connectors or module hubs. Analysis of the relationships between the module eigengenes and environmental variables demonstrated that bacterial groups of the two networks favored quite different environmental conditions. These findings further confirmed the different ecological functions and niches occupied by the FL and PA bacterial communities in the aquatic ecosystem.
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Affiliation(s)
- Huimin Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xinyi Cao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Katherine V Hooker
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - K David Hambright
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
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35
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Reza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S. Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay. Gene 2018; 665:185-191. [PMID: 29705129 DOI: 10.1016/j.gene.2018.04.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 11/17/2022]
Abstract
The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.
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Affiliation(s)
- Md Shaheed Reza
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Atsushi Kobiyama
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Yuichiro Yamada
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Yuri Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Daisuke Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Nanami Mizusawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Kazuho Ikeo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Shigeru Sato
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Takehiko Ogata
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Mitsuru Jimbo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Toshiaki Kudo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Shinnosuke Kaga
- Iwate Fisheries Technology Center, Kamaishi 026-0001, Iwate, Japan
| | - Shiho Watanabe
- Iwate Fisheries Technology Center, Kamaishi 026-0001, Iwate, Japan
| | - Kimiaki Naiki
- Iwate Fisheries Technology Center, Kamaishi 026-0001, Iwate, Japan
| | - Yoshimasa Kaga
- Iwate Fisheries Technology Center, Kamaishi 026-0001, Iwate, Japan
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Vladimir Bajic
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia.
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan.
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Zhang C, Dang H, Azam F, Benner R, Legendre L, Passow U, Polimene L, Robinson C, Suttle CA, Jiao N. Evolving paradigms in biological carbon cycling in the ocean. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwy074] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.
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Affiliation(s)
- Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Benner
- Department of Biological Sciences and School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC 29208, USA
| | - Louis Legendre
- Sorbonne Université, Laboratoire d’Océanographie de Villefranche, LOV, 06230 Villefranche-sur-Mer, France
| | - Uta Passow
- Marine Science Institute, University of California Santa Barbara, CA 93106, USA
| | - Luca Polimene
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Carol Robinson
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Botany, and Microbiology and Immunology, and the Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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37
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Dussud C, Meistertzheim AL, Conan P, Pujo-Pay M, George M, Fabre P, Coudane J, Higgs P, Elineau A, Pedrotti ML, Gorsky G, Ghiglione JF. Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 236:807-816. [PMID: 29459335 DOI: 10.1016/j.envpol.2017.12.027] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 05/20/2023]
Abstract
Plastic pollution is widespread in ocean ecosystems worldwide, but it is unknown if plastic offers a unique habitat for bacteria compared to communities in the water column and attached to naturally-occurring organic particles. The large set of samples taken during the Tara-Mediterranean expedition revealed for the first time a clear niche partitioning between free-living (FL), organic particle-attached (PA) and the recently introduced plastic marine debris (PMD). Bacterial counts in PMD presented higher cell enrichment factors than generally observed for PA fraction, when compared to FL bacteria in the surrounding waters. Taxonomic diversity was also higher in the PMD communities, where higher evenness indicated a favorable environment for a very large number of species. Cyanobacteria were particularly overrepresented in PMD, together with essential functions for biofilm formation and maturation. The community distinction between the three habitats was consistent across the large-scale sampling in the Western Mediterranean basin. 'Plastic specific bacteria' recovered only on the PMD represented half of the OTUs, thus forming a distinct habitat that should be further considered for understanding microbial biodiversity in changing marine ecosystems.
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Affiliation(s)
- C Dussud
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - A L Meistertzheim
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - P Conan
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - M Pujo-Pay
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - M George
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - P Fabre
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - J Coudane
- Institut des Biomolécules Max Mousseron, CNRS UMR5247, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, BP 14491, F-34093, Montpellier cedex5, France
| | - P Higgs
- Symphony Environmental Ltd, Borehamwood, Hertfordshire WD6 1JD, UK
| | - A Elineau
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche, Villefranche sur mer, France
| | - M L Pedrotti
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche, Villefranche sur mer, France
| | - G Gorsky
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche, Villefranche sur mer, France
| | - J F Ghiglione
- Sorbonne Universités, CNRS, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Banyuls sur mer, France.
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38
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Liu R, Wang L, Liu Q, Wang Z, Li Z, Fang J, Zhang L, Luo M. Depth-Resolved Distribution of Particle-Attached and Free-Living Bacterial Communities in the Water Column of the New Britain Trench. Front Microbiol 2018; 9:625. [PMID: 29670597 PMCID: PMC5893722 DOI: 10.3389/fmicb.2018.00625] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/19/2018] [Indexed: 01/24/2023] Open
Abstract
Particle-attached (PA) and free-living (FL) microorganisms play significant but different roles in mineralization of organic matter (OM) in the ocean. Currently, little is known about PA and FL microbial communities in bathyal and abyssal pelagic waters, and understanding of their diversity and distribution in the water column and their interactions with environmental factors in the trench area is limited. We investigated for the first time the variations of abundance and diversities of the PA and FL bacterial communities in the epi-, bathy-, and abyssopelagic zones of the New Britain Trench (NBT). The PA communities showed decreasing species richness but increasing relative abundance with depth, suggesting the increasing ecological significance of the PA bacteria in the deep ocean. The abundance and diversity of PA and FL bacterial communities in the NBT water column appeared to be shaped by different sets of environment factors, which might be related to different micro-niches of the two communities. Analysis on species distribution suggested that the differences between PA and FL bacteria communities mainly resulted from the different relative abundance of the “shared taxa” in the two types of communities. These findings provide valuable information for understanding the relative ecological roles of the PA and FL bacterial communities and their interactions with environmental factors in different pelagic zones along the vertical profile of the NBT water column.
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Affiliation(s)
- Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qianfeng Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Zixuan Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Zhenzhen Li
- State Key Laboratory of Geological Process and Mineral Resources, Department of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, United States
| | - Li Zhang
- State Key Laboratory of Geological Process and Mineral Resources, Department of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Min Luo
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
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39
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Suter EA, Pachiadaki M, Taylor GT, Astor Y, Edgcomb VP. Free‐living chemoautotrophic and particle‐attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Environ Microbiol 2017; 20:693-712. [DOI: 10.1111/1462-2920.13997] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Elizabeth A. Suter
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
- Department of Biological SciencesWagner CollegeStaten Island NY 10301 USA
| | - Maria Pachiadaki
- Woods Hole Oceanographic InstitutionWoods Hole MA USA
- Bigelow Laboratory for Ocean SciencesEast Boothbay ME USA
| | - Gordon T. Taylor
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
| | - Yrene Astor
- Fundación La Salle de Ciencias Naturales, EDIMARPorlamar Nueva Esparta Venezuela
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40
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Herfort L, Crump BC, Fortunato CS, McCue LA, Campbell V, Simon HM, Baptista AM, Zuber P. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima. Microbiologyopen 2017; 6. [PMID: 28782284 PMCID: PMC5727365 DOI: 10.1002/mbo3.522] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/15/2017] [Accepted: 06/23/2017] [Indexed: 11/30/2022] Open
Abstract
Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production (3H‐leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1–24 PSU), but summer non‐ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free‐living (0.2–3 μm) assemblages of non‐ETM waters were similar to each other, indicating that particle‐attached (>3 μm) non‐ETM bacteria do not develop a distinct community. Brackish water type (ETM or non‐ETM) is thus a major factor affecting particle‐attached bacterial communities. Heterotrophic production was higher in particle‐attached than free‐living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM‐impacted waters). However, free‐living communities showed higher productivity prior to or after an ETM event (i.e., non‐ETM‐impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the existence of three particle types characterized by different bacterial communities in ETM, ETM‐impacted, and non‐ETM‐impacted brackish waters. Taxonomic analysis suggests that ETM key biological function is to remineralize organic matter.
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Affiliation(s)
- Lydie Herfort
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - Byron C Crump
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Caroline S Fortunato
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA
| | - Lee Ann McCue
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Victoria Campbell
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA
| | - Holly M Simon
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - António M Baptista
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - Peter Zuber
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
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41
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Zhao D, Xu H, Zeng J, Cao X, Huang R, Shen F, Yu Z. Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake. FEMS Microbiol Ecol 2017; 93:3814240. [DOI: 10.1093/femsec/fix062] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/09/2017] [Indexed: 11/12/2022] Open
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42
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Patterns of bacterial diversity in the marine planktonic particulate matter continuum. ISME JOURNAL 2017; 11:999-1010. [PMID: 28045454 DOI: 10.1038/ismej.2016.166] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022]
Abstract
Depending on their relationship with the pelagic particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to particles, and are generally separated using only one pore-size filter in a differential filtration. Nonetheless, particulate matter in the oceans appears in a continuum of sizes. Here we separated this continuum into six discrete size-fractions, from 0.2 to 200 μm, and described the prokaryotes associated to each of them. Each size-fraction presented different bacterial communities, with a range of 23-42% of unique (OTUs) in each size-fraction, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size-fractions, suggesting that increasingly larger particles contributed new niches. Our results show that a multiple size-fractionation provides a more exhaustive description of the bacterial diversity and community structure than the use of only one filter. In addition, and based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles, in which we differentiate the taxonomic groups with preference for the smaller fractions, those that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions.
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43
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Oberbeckmann S, Osborn AM, Duhaime MB. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris. PLoS One 2016; 11:e0159289. [PMID: 27487037 PMCID: PMC4972250 DOI: 10.1371/journal.pone.0159289] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 04/26/2016] [Indexed: 11/19/2022] Open
Abstract
Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET substrate. Future research is required to investigate microscale functional interactions at the plastic surface.
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Affiliation(s)
- Sonja Oberbeckmann
- Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, United Kingdom
- School of Life Sciences, University of Lincoln, Brayford Pool Lincoln LN6 7TS, United Kingdom
- Environmental Microbiology Working Group, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - A. Mark Osborn
- Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, United Kingdom
- School of Life Sciences, University of Lincoln, Brayford Pool Lincoln LN6 7TS, United Kingdom
- School of Applied Sciences, Royal Melbourne Institute of Technology University, PO Box 77, Bundoora, VIC3083, Australia
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Severin T, Sauret C, Boutrif M, Duhaut T, Kessouri F, Oriol L, Caparros J, Pujo-Pay M, Durrieu de Madron X, Garel M, Tamburini C, Conan P, Ghiglione JF. Impact of an intense water column mixing (0-1500 m) on prokaryotic diversity and activities during an open-ocean convection event in the NW Mediterranean Sea. Environ Microbiol 2016; 18:4378-4390. [DOI: 10.1111/1462-2920.13324] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatiana Severin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
| | - Caroline Sauret
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
| | - Mehdi Boutrif
- Aix-Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110; 13288 Marseille France
- Université du Sud Toulon-Var, Mediterranean Institute of Oceanography (MIO); 83957 La Garde Cedex France CNRS-INSU/IRD UM 110
| | - Thomas Duhaut
- LA, CNRS, Université de Toulouse; 14 avenue Edouard Belin 31400 Toulouse France
| | - Fayçal Kessouri
- LA, CNRS, Université de Toulouse; 14 avenue Edouard Belin 31400 Toulouse France
| | - Louise Oriol
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
| | - Jocelyne Caparros
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
| | - Mireille Pujo-Pay
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
| | | | - Marc Garel
- Aix-Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110; 13288 Marseille France
- Université du Sud Toulon-Var, Mediterranean Institute of Oceanography (MIO); 83957 La Garde Cedex France CNRS-INSU/IRD UM 110
| | - Christian Tamburini
- Aix-Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110; 13288 Marseille France
- Université du Sud Toulon-Var, Mediterranean Institute of Oceanography (MIO); 83957 La Garde Cedex France CNRS-INSU/IRD UM 110
| | - Pascal Conan
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
| | - Jean-François Ghiglione
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique; F-66650 Banyuls/mer France
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Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters. Appl Environ Microbiol 2016; 82:3431-3437. [PMID: 27037125 DOI: 10.1128/aem.00395-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/28/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED There is a growing recognition of the roles of marine microenvironments as reservoirs of biodiversity and as sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inhabiting free-living and particle-associated seawater microenvironments at the Pivers Island Coastal Observatory (PICO). 16S rRNA gene libraries from monthly samples (July 2013 to August 2014) were used to identify microbes in seawater in four size fractions: >63 μm (zooplankton and large particles), 63 to 5 μm (particles), 5 to 1 μm (small particles/dividing cells), and <1 μm (free-living prokaryotes). Analyses of microbial community composition highlight the importance of the microhabitat (e.g., particle-associated versus free-living lifestyle) as communities cluster by size fraction, and the microhabitat explains more of the community variability than measured environmental parameters, including pH, particle concentration, projected daily insolation, nutrients, and temperature. While temperature is statistically associated with community changes in the <1-μm and 5- to 1-μm fractions, none of the measured bulk seawater environmental variables are statistically significant in the larger-particle-associated fractions. These results, combined with high particle-associated community variability, especially in the largest size fraction (i.e., >63 μm), suggest that particle composition, including eukaryotes and their associated microbiomes, may be an important factor in selecting for specific particle-associated bacteria. IMPORTANCE By comparing levels of particle-associated and free-living bacterial diversity at a coastal location over the course of 14 months, we show that bacteria associated with particles are generally more diverse and appear to be less responsive to commonly measured environmental variables than free-living bacteria. These diverse and highly variable particle-associated communities are likely driven by differences in particle substrates both within the water column at a single time point and due to seasonal changes over the course of the year.
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Denef VJ, Fujimoto M, Berry MA, Schmidt ML. Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria. Front Microbiol 2016; 7:606. [PMID: 27199936 PMCID: PMC4850342 DOI: 10.3389/fmicb.2016.00606] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/12/2016] [Indexed: 11/24/2022] Open
Abstract
Relative abundance profiles of bacterial populations measured by sequencing DNA or RNA of marker genes can widely differ. These differences, made apparent when calculating ribosomal RNA:DNA ratios, have been interpreted as variable activities of bacterial populations. However, inconsistent correlations between ribosomal RNA:DNA ratios and metabolic activity or growth rates have led to a more conservative interpretation of this metric as the cellular protein synthesis potential (PSP). Little is known, particularly in freshwater systems, about how PSP varies for specific taxa across temporal and spatial environmental gradients and how conserved PSP is across bacterial phylogeny. Here, we generated 16S rRNA gene sequencing data using simultaneously extracted DNA and RNA from fractionated (free-living and particulate) water samples taken seasonally along a eutrophic freshwater estuary to oligotrophic pelagic transect in Lake Michigan. In contrast to previous reports, we observed frequent clustering of DNA and RNA data from the same sample. Analysis of the overlap in taxa detected at the RNA and DNA level indicated that microbial dormancy may be more common in the estuary, the particulate fraction, and during the stratified period. Across spatiotemporal gradients, PSP was often conserved at the phylum and class levels. PSPs for specific taxa were more similar across habitats in spring than in summer and fall. This was most notable for PSPs of the same taxa when located in the free-living or particulate fractions, but also when contrasting surface to deep, and estuary to Lake Michigan communities. Our results show that community composition assessed by RNA and DNA measurements are more similar than previously assumed in freshwater systems. However, the similarity between RNA and DNA measurements and taxa-specific PSPs that drive community-level similarities are conditional on spatiotemporal factors.
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Affiliation(s)
- Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
| | - Masanori Fujimoto
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
| | - Michelle A Berry
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
| | - Marian L Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
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Dynamics of size-fractionated bacterial communities during the coastal dispersal of treated municipal effluents. Appl Microbiol Biotechnol 2016; 100:5839-48. [PMID: 26944731 DOI: 10.1007/s00253-016-7408-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/13/2016] [Accepted: 02/20/2016] [Indexed: 10/22/2022]
Abstract
Everyday huge amount of treated municipal wastewater is discharged into the coastal seawater. However, microbial biomarkers for the municipal effluent instead of the fecal species from raw sewage have not been proposed. Meanwhile, bacterial taxa for degrading large amounts of input organics have not been fully understood. In this study, raw effluent and serial water samples were collected from the coastal dispersal of two sewage treatment plants in Xiamen, China. Free-living (FL) and particle-associated (PA) bacterial communities were analyzed via high-throughput sequencing of 16S rRNA gene and quantitative PCR to measure bacterial abundance. The PA bacterial communities in our samples exhibited higher cell abundance, alpha diversity, and population dynamics than the FL bacterial communities, which supports greater environmental significance of the PA bacterial communities. Two non-fecal but typical genera in activated sludge, Zoogloea and Dechloromonas, exhibited decreased but readily detectable abundance along the effluent dispersal distance. Furthermore, the dominating microbial species near the outfalls were related to well-known marine indigenous taxa, such as SAR11 clade, OM60 clade, low-GC Actinobacteria, and unclassified Flavobacteriales, as well as the less understood taxa like Pseudohongiella and Microbacteriaceae. It is interesting that these taxa exhibited two types of correlation patterns with COD concentration. Our study suggested Zoogloea as a potential indicator of municipal effluents and also proposed potential utilizers of residual effluent COD in marine environments.
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48
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Mayali X, Stewart B, Mabery S, Weber PK. Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:68-75. [PMID: 26525158 DOI: 10.1111/1758-2229.12352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 09/25/2015] [Accepted: 10/27/2015] [Indexed: 05/26/2023]
Abstract
We investigated bacterial carbon assimilation from stable isotope-labelled macromolecular substrates (proteins; lipids; and two types of polysaccharides, starch and cellobiose) while attached to killed diatom detrital particles during laboratory microcosms incubated for 17 days. Using Chip-SIP (secondary ion mass spectrometry analysis of RNA microarrays), we identified generalist operational taxonomic units (OTUs) from the Gammaproteobacteria, belonging to the genera Colwellia, Glaciecola, Pseudoalteromonas and Rheinheimera, and from the Bacteroidetes, genera Owenweeksia and Maribacter, that incorporated the four tested substrates throughout the incubation period. Many of these OTUs exhibited the highest isotope incorporation relative to the others, indicating that they were likely the most active. Additional OTUs from the Gammaproteobacteria, Bacteroidetes and Alphaproteobacteria exhibited generally (but not always) lower activity and did not incorporate all tested substrates at all times, showing species succession in organic carbon incorporation. We also found evidence to suggest that both generalist and specialist OTUs changed their relative substrate incorporation over time, presumably in response to changing substrate availability as the particles aged. This pattern was demonstrated by temporal succession from relatively higher starch incorporation early in the incubations, eventually switching to higher cellobiose incorporation after 2 weeks.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Benjamin Stewart
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Shalini Mabery
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
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49
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Schmidt ML, White JD, Denef VJ. Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla. Environ Microbiol 2016; 18:1212-26. [DOI: 10.1111/1462-2920.13143] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Marian L. Schmidt
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
| | - Jeffrey D. White
- Department of Biology; Framingham State University; Framingham MA 01701 USA
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
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50
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Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow. Appl Environ Microbiol 2016; 81:1463-71. [PMID: 25527538 DOI: 10.1128/aem.02570-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.
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