51
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Zhang H, Hou F, Xie W, Wang K, Zhou X, Zhang D, Zhu X. Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process. Environ Microbiol 2019; 22:1707-1719. [PMID: 31599072 DOI: 10.1111/1462-2920.14820] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 02/01/2023]
Abstract
Diatom blooms can significantly influence the dynamics of microbial communities, yet little is known about the interaction and assembly mechanisms of abundant and rare taxa during bloom process. Here, using 16S rRNA gene amplicon sequencing, we investigated the co-occurrence patterns and assembly processes of abundant and rare microbial communities during an early spring diatom bloom in Xiangshan bay. Our results showed that α-diversity indices in the rare subcommunity (RS) were significantly higher than those in the abundant and common subcommunities. β-Diversity of the RS was the highest among three subcommunities, and the variation of β-diversity in the three subcommunities was mainly induced by species turnover, which was also the highest in the RS. The assembly of microbial communities was mainly driven by the neutral processes, but the roles of neutral processes might differ in each subcommunity. Co-occurrence network analysis revealed that abundant and common operational taxonomic units were more often located in central positions within the network. Most of the modules in the network were specific to a particular bloom stage, owing to the succession of Skeletonema costatum. Overall, these findings expand current understanding of the microbial interaction and assembly mechanisms in marine environment suffering harmful algal bloom disturbance.
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Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Fanrong Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Weijuan Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiaoyan Zhou
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
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52
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Hattenrath-Lehmann TK, Jankowiak J, Koch F, Gobler CJ. Prokaryotic and eukaryotic microbiomes associated with blooms of the ichthyotoxic dinoflagellate Cochlodinium (Margalefidinium) polykrikoides in New York, USA, estuaries. PLoS One 2019; 14:e0223067. [PMID: 31697694 PMCID: PMC6837389 DOI: 10.1371/journal.pone.0223067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/12/2019] [Indexed: 12/19/2022] Open
Abstract
While harmful algal blooms caused by the ichthyotoxic dinoflagellate, Cochlodinium (Margalefidinium) polykrikoides, are allelopathic and may have unique associations with bacteria, a comprehensive assessment of the planktonic communities associated with these blooms has been lacking. Here, we used high-throughput amplicon sequencing to assess size fractionated (0.2 and 5 μm) bacterial (16S) and phytoplankton assemblages (18S) associated with blooms of C. polykrikoides during recurrent blooms in NY, USA. Over a three-year period, samples were collected inside (‘patch’) and outside (‘non-patch’) dense accumulations of C. polykrikoides to assess the microbiome associated with these blooms. Eukaryotic plankton communities of blooms had significantly lower diversity than non-bloom samples, and non-bloom samples hosted 30 eukaryotic operational taxonomic units (OTUs) not found within blooms, suggesting they may have been allelopathically excluded from blooms. Differential abundance analyses revealed that C. polykrikoides blooms were significantly enriched in dinoflagellates (p<0.001) and the experimental enrichment of C. polykrikoides led to a significant increase in the relative abundance of eight genera of dinoflagellates but a significant decline in other eukaryotic plankton. Amoebophrya co-dominated both within- and near- C. polykrikoides blooms and was more abundant in bloom patches. The core bacterial microbiome of the >0.2μm fraction of blooms was dominated by an uncultured bacterium from the SAR11 clade, while the >5μm size fraction was co-dominated by an uncultured bacterium from Rhodobacteraceae and Coraliomargarita. Two bacterial lineages within the >0.2μm fraction, as well as the Gammaproteobacterium, Halioglobus, from the >5μm fraction were unique to the microbiome of blooms, while there were 154 bacterial OTUs only found in non-bloom waters. Collectively, these findings reveal the unique composition and potential function of eukaryotic and prokaryotic communities associated with C. polykrikoides blooms.
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Affiliation(s)
| | - Jennifer Jankowiak
- Stony Brook University, School of Marine and Atmospheric Sciences, Southampton, NY, United States of America
| | - Florian Koch
- Stony Brook University, School of Marine and Atmospheric Sciences, Southampton, NY, United States of America
| | - Christopher J Gobler
- Stony Brook University, School of Marine and Atmospheric Sciences, Southampton, NY, United States of America
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53
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Wang H, Zhu R, Zhang X, Li Y, Ni L, Xie P, Shen H. Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake. AMB Express 2019; 9:170. [PMID: 31673822 PMCID: PMC6823470 DOI: 10.1186/s13568-019-0889-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.
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54
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Wang S, Zhao D, Zeng J, Xu H, Huang R, Jiao C, Guo L. Variations of bacterial community during the decomposition of Microcystis under different temperatures and biomass. BMC Microbiol 2019; 19:207. [PMID: 31484494 PMCID: PMC6727399 DOI: 10.1186/s12866-019-1585-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 08/28/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The decomposition of Microcystis can dramatically change the physicochemical properties of freshwater ecosystems. Bacteria play an important role in decomposing organic matters and accelerating the cycling of materials within freshwater lakes. However, actions of the bacterial community are greatly influenced by temperature and the amount of organic matter available to decompose during a bloom. Therefore, it is vital to understand how different temperatures and biomass levels affect the bacterial community during the decomposition of Microcystis. RESULTS Microcystis addition reduced the diversity of bacterial community. The composition of bacterial community differed markedly between samples with different biomass of Microcystis (no addition, low biomass addition: 0.17 g/L, and high biomass addition: 0.33 g/L). In contrast, temperature factor did not contribute much to the different bacterial community composition. Total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), ammonia nitrogen (NH4+-N) and oxidation-reduction potential (ORP) were the key measured environmental variables shaping the composition of bacterial community. CONCLUSIONS Decomposition of Microcystis changed the physicochemical characteristics of the water and controlled the diversity and composition of the bacterial community. Microcystis biomass rather than temperature was the dominant factor affecting the diversity and composition of the bacterial community.
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Affiliation(s)
- Shuren Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Xikang Road 1, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Xikang Road 1, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
| | - Huimin Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Xikang Road 1, Nanjing, 210098, China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Xikang Road 1, Nanjing, 210098, China
| | - Congcong Jiao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Xikang Road 1, Nanjing, 210098, China
| | - Lin Guo
- Department of Biological and Environmental Sciences, Texas A&M University, Commerce, TX, 76129, USA
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55
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Happel EM, Markussen T, Teikari JE, Huchaiah V, Alneberg J, Andersson AF, Sivonen K, Middelboe M, Kisand V, Riemann L. Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites. FEMS Microbiol Ecol 2019; 95:5545591. [PMID: 31397876 DOI: 10.1093/femsec/fiz123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.
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Affiliation(s)
- Elisabeth M Happel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Trine Markussen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jonna E Teikari
- University of Helsinki, Department of Microbiology, Helsinki, Finland
| | - Vimala Huchaiah
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Johannes Alneberg
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Kaarina Sivonen
- University of Helsinki, Department of Microbiology, Helsinki, Finland
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Veljo Kisand
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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56
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Tiwari PK, Samanta S, Bona F, Venturino E, Misra AK. The time delays influence on the dynamical complexity of algal blooms in the presence of bacteria. ECOLOGICAL COMPLEXITY 2019. [DOI: 10.1016/j.ecocom.2019.100769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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57
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Debeljak P, Toulza E, Beier S, Blain S, Obernosterer I. Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. Environ Microbiol 2019; 21:2360-2374. [PMID: 30958628 PMCID: PMC6618146 DOI: 10.1111/1462-2920.14621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Iron (Fe) is a limiting nutrient in large regions of the ocean, but the strategies of prokaryotes to cope with this micronutrient are poorly known. Using a gene-specific approach from metatranscriptomics data, we investigated seven Fe-related metabolic pathways in microbial communities from high nutrient low chlorophyll and naturally Fe-fertilized waters in the Southern Ocean. We observed major differences in the contribution of prokaryotic groups at different taxonomic levels to transcripts encoding Fe-uptake mechanisms, intracellular Fe storage and replacement and Fe-related pathways in the tricarboxylic acid (TCA) cycle. The composition of the prokaryotic communities contributing to the transcripts of a given Fe-related pathway was overall independent of the in situ Fe supply, indicating that microbial taxa utilize distinct Fe-related metabolic processes. Only a few prokaryotic groups contributed to the transcripts of more than one Fe-uptake mechanism, suggesting limited metabolic versatility. Taxa-specific expression of individual genes varied among prokaryotic groups and was substantially higher for all inspected genes in Fe-limited as compared to naturally fertilized waters, indicating the link between transcriptional state and Fe regime. Different metabolic strategies regarding low Fe concentrations in the Southern Ocean are discussed for two abundant prokaryotic groups, Pelagibacteraceae and Flavobacteriaceae.
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Affiliation(s)
- Pavla Debeljak
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
- Department of Limnology and Bio‐OceanographyUniversity of Vienna, A‐1090ViennaAustria
| | - Eve Toulza
- Université Perpignan Via DomitiaIHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F‐66860PerpignanFrance
| | - Sara Beier
- Leibniz Institute for Baltic Sea ResearchWarnemündeGermany
| | - Stephane Blain
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
| | - Ingrid Obernosterer
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
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58
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Cirri E, Pohnert G. Algae-bacteria interactions that balance the planktonic microbiome. THE NEW PHYTOLOGIST 2019; 223:100-106. [PMID: 30825329 DOI: 10.1111/nph.15765] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/19/2019] [Indexed: 05/10/2023]
Abstract
Phytoplankton communities within the photic zones of the oceans and lakes are characterised by highly complex assemblages of unicellular microalgae and associated bacteria. The interconnected evolutionary history of algae and bacteria allowed the formation of a wide spectrum of associations defined by orchestrated nutrient exchange, mutual support with growth factors, quorum sensing mediation, and episodic killing of the partners to obtain more resources. In this review, we discuss how these cross-kingdom interactions shape plankton communities that undergo annual, seasonal switching between alternative states with balanced multispecies consortia. We illustrate how these microscopic interactions can have consequences that scale up to influence global element cycling.
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Affiliation(s)
- Emilio Cirri
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743, Jena, Germany
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743, Jena, Germany
- Microverse Cluster Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany
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59
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Ávila MP, Brandão LPM, Brighenti LS, Tonetta D, Reis MP, Stæhr PA, Asmala E, Amado AM, Barbosa FAR, Bezerra-Neto JF, Nascimento AMA. Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:990-1003. [PMID: 30981171 DOI: 10.1016/j.scitotenv.2019.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.
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Affiliation(s)
- Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Luciana P M Brandão
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ludmila S Brighenti
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Denise Tonetta
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - Peter A Stæhr
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark
| | - Eero Asmala
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark; Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, 10900 Hanko, Finland
| | - André M Amado
- Limnology Laboratory, Department of Oceanography and Limnology, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - José F Bezerra-Neto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
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60
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Abed RMM, Al Fahdi D, Muthukrishnan T. Short-term succession of marine microbial fouling communities and the identification of primary and secondary colonizers. BIOFOULING 2019; 35:526-540. [PMID: 31216872 DOI: 10.1080/08927014.2019.1622004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Microbial succession during the initial stages of marine biofouling has been rarely studied, especially in the Arabian Gulf. This study was undertaken to follow temporal shifts in biofouling communities in order to identify primary and secondary colonizers. Quantitative analysis revealed a significant increase in total biomass, coverage of macrofoulers, chlorophyll a concentrations, and bacterial counts with time. The relative abundance of the adnate diatoms increased with time, whereas it decreased in the case of the plocon diatoms. Non-metric multidimensional scaling (NMDS) ordination based on MiSeq data placed the bacterial communities in three distinct clusters, depending on the time of sampling. While the relative abundance of Alphaproteobacteria and Flavobacteriia decreased with time, suggesting their role as primary colonizers, the relative abundance of Actinobacteria and Planctomycetia increased with time, suggesting their role as secondary colonizers. Biofouling is a dynamic process that involves temporal quantitative and qualitative shifts in the micro- and macrofouling communities.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University , Al Khoud , Sultanate of Oman
| | - Dhikra Al Fahdi
- Biology Department, College of Science, Sultan Qaboos University , Al Khoud , Sultanate of Oman
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61
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Ruiz-González C, Logares R, Sebastián M, Mestre M, Rodríguez-Martínez R, Galí M, Sala MM, Acinas SG, Duarte CM, Gasol JM. Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Mol Ecol 2019; 28:1930-1945. [PMID: 30663830 DOI: 10.1111/mec.15026] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/21/2018] [Accepted: 01/14/2019] [Indexed: 01/21/2023]
Abstract
Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal-like"- abundant and ubiquitous; "logistic"- globally rare, present in few sites; and "bimodal"- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal-like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal-like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.
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Affiliation(s)
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Mireia Mestre
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Raquel Rodríguez-Martínez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Martí Galí
- Unité Mixte Internationale Takuvik (Université Laval-CNRS) and Québec-Océan, Département de Biologie, Université Laval, Québec City, Québec, Canada.,Barcelona Supercomputing Centre (BSC), Barcelona, Catalonia, Spain
| | | | - Silvia G Acinas
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centre for Marine Ecosystem Research, Edith Cowan University, Joondalup, Western Australia, Australia
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62
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Liu Y, Debeljak P, Rembauville M, Blain S, Obernosterer I. Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean. Environ Microbiol 2019; 21:1452-1465. [DOI: 10.1111/1462-2920.14579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/21/2019] [Accepted: 03/03/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Liu
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
| | - Pavla Debeljak
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
- Department of Limnology and Bio‐OceanographyUniversity of Vienna, 1090 Vienna Austria
| | - Mathieu Rembauville
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
| | - Stéphane Blain
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
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63
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Tsagaraki TM, Pree B, Leiknes Ø, Larsen A, Bratbak G, Øvreås L, Egge JK, Spanek R, Paulsen ML, Olsen Y, Vadstein O, Thingstad TF. Bacterial community composition responds to changes in copepod abundance and alters ecosystem function in an Arctic mesocosm study. THE ISME JOURNAL 2018; 12:2694-2705. [PMID: 29991763 PMCID: PMC6194086 DOI: 10.1038/s41396-018-0217-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 05/24/2018] [Accepted: 06/11/2018] [Indexed: 01/30/2023]
Abstract
Combining a minimum food web model with Arctic microbial community dynamics, we have suggested that top-down control by copepods can affect the food web down to bacterial consumption of organic carbon. Pursuing this hypothesis further, we used the minimum model to design and analyse a mesocosm experiment, studying the effect of high (+Z) and low (-Z) copepod density on resource allocation, along an organic-C addition gradient. In the Arctic, both effects are plausible due to changes in advection patterns (affecting copepods) and meltwater inputs (affecting carbon). The model predicts a trophic cascade from copepods via ciliates to flagellates, which was confirmed experimentally. Auto- and heterotrophic flagellates affect bacterial growth rate and abundance via competition for mineral nutrients and predation, respectively. In +Z, the model predicts low bacterial abundance and activity, and little response to glucose; as opposed to clear glucose consumption effects in -Z. We observed a more resilient bacterial response to high copepods and demonstrate this was due to changes in bacterial community equitability. Species able to use glucose to improve their competitive and/or defensive properties, became predominant. The observed shift from a SAR11-to a Psychromonodaceae - dominated community suggests the latter was pivotal in this modification of ecosystem function. We argue that this group used glucose to improve its defensive or its competitive abilities (or both). Adding such flexibility in bacterial traits to the model, we show how it creates the observed resilience to top-down manipulations observed in our experiment.
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Affiliation(s)
| | - Bernadette Pree
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Øystein Leiknes
- Department of Biology, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Aud Larsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Uni Research Environment, Uni Research AS, Bergen, Norway
| | - Gunnar Bratbak
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- The University Centre in Svalbard, Longyearbyen, Norway
| | - Jorun K Egge
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Roman Spanek
- The Institute of Mechatronics and Computer Engineering, Technical University of Liberec, Liberec, Czech Republic
| | - Maria L Paulsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Yngvar Olsen
- Department of Biology, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - T F Thingstad
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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64
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Kolmakova OV, Gladyshev MI, Fonvielle JA, Ganzert L, Hornick T, Grossart HP. Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling. Environ Microbiol 2018; 21:34-49. [PMID: 30246449 DOI: 10.1111/1462-2920.14418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 11/27/2022]
Abstract
Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh 13 C-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.
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Affiliation(s)
- Olesya V Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia.,Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michail I Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jérémy André Fonvielle
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Lars Ganzert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,GFZ German Research Centre for Geosciencess, Section 5.3 Geomicrobiology, Potsdam, Germany.,Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, Germany
| | - Thomas Hornick
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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65
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Hernández-Ruiz M, Barber-Lluch E, Prieto A, Álvarez-Salgado XA, Logares R, Teira E. Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system. Environ Microbiol 2018; 20:2955-2973. [DOI: 10.1111/1462-2920.14313] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/12/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Marta Hernández-Ruiz
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | - Esther Barber-Lluch
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | - Antero Prieto
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | | | - Ramiro Logares
- Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC); Barcelona, 08003 Spain
| | - Eva Teira
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
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66
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Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay. Appl Environ Microbiol 2018; 84:AEM.01000-18. [PMID: 30006403 DOI: 10.1128/aem.01000-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/09/2018] [Indexed: 11/20/2022] Open
Abstract
Harmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes. Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae were the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyll a contents, which were affected mainly by Skeletonema costatum Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCE Harmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.
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67
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Landa M, Blain S, Harmand J, Monchy S, Rapaport A, Obernosterer I. Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter. FEMS Microbiol Ecol 2018; 94:4935155. [DOI: 10.1093/femsec/fiy034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 03/13/2018] [Indexed: 02/05/2023] Open
Affiliation(s)
- Marine Landa
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
| | - Stéphane Blain
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
| | | | - Sébastien Monchy
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 59 000 Lille, France
| | - Alain Rapaport
- MISTEA, Univ. Montpellier, INRA, Montpellier SupAgro, 2, pl. Viala 34060 Montpellier, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
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68
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Zhang H, Jia J, Chen S, Huang T, Wang Y, Zhao Z, Feng J, Hao H, Li S, Ma X. Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15020361. [PMID: 29463021 PMCID: PMC5858430 DOI: 10.3390/ijerph15020361] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 11/24/2022]
Abstract
The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Jingyu Jia
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Tinglin Huang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Zhenfang Zhao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Ji Feng
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Huiyan Hao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Sulin Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Xinxin Ma
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
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69
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Yu X, Cai G, Wang H, Hu Z, Zheng W, Lei X, Zhu X, Chen Y, Chen Q, Din H, Xu H, Tian Y, Fu L, Zheng T. Fast-growing algicidal Streptomyces sp. U3 and its potential in harmful algal bloom controls. JOURNAL OF HAZARDOUS MATERIALS 2018; 341:138-149. [PMID: 28777959 DOI: 10.1016/j.jhazmat.2017.06.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/18/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
To find the potential algicidal microorganisms and apply them to prevent and terminate harmful algal blooms (HABs), we isolated an actinomycete U3 from Mangrove, which had a potent algicidal effect on the harmful alga Heterosigma akashiwo. It could completely lyse the algal cells by producing active compounds, which were highly sensitive to high temperature and strong alkaline, but resistant to acid. One μg/mL of crude extract of the fermentation supernatant could kill 70% of H. akashiwo cells in 3 d. Unlike most of the other known algicidal Streptomyces, U3 showed strong ability of proliferation with the algal inclusion as the nutrient source. The washed mycelial pellets also gradually exhibited significant algicidal effect during the visible growth in the algal culture. It suggests that U3 could efficiently absorb nutrients from algal culture to support its growth and produce algicidal compounds that might cause the autophagy of algal cells. Therefore, applying U3, as a long-term and environmentally friendly bio-agent to control the harmful blooms of H. akashiwo, would be effective and promising. And the decrease of bioavailable DOM and increase of bio-refractory DOM during the algicidal process of U3 provided new insights into the ecological influence of algicial microorganisms on marine ecosystem.
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Affiliation(s)
- Xiaoqi Yu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Guanjing Cai
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Wang
- Biology Department, College of Life Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Biology Department, College of Life Science, Shantou University, Shantou 515063, China
| | - Wei Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xueqian Lei
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoying Zhu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yao Chen
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qiuliang Chen
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hongyan Din
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hong Xu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Lijun Fu
- Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants, Putian University, Putian 351100, China.
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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70
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Kaur A, Hernandez-Fernaud JR, Aguilo-Ferretjans MDM, Wellington EM, Christie-Oleza JA. 100 Days of marine Synechococcus-Ruegeria pomeroyi interaction: A detailed analysis of the exoproteome. Environ Microbiol 2017; 20:785-799. [PMID: 29194907 PMCID: PMC5839243 DOI: 10.1111/1462-2920.14012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/23/2017] [Indexed: 12/03/2022]
Abstract
Marine phototroph and heterotroph interactions are vital in maintaining the nutrient balance in the oceans as essential nutrients need to be rapidly cycled before sinking to aphotic layers. The aim of this study was to highlight the molecular mechanisms that drive these interactions. For this, we generated a detailed exoproteomic time‐course analysis of a 100‐day co‐culture between the model marine picocyanobacterium Synechococcus sp. WH7803 and the Roseobacter strain Ruegeria pomeroyi DSS‐3, both in nutrient‐enriched and natural oligotrophic seawater. The proteomic data showed a transition between the initial growth phase and stable‐state phase that, in the case of the heterotroph, was caused by a switch in motility attributed to organic matter availability. The phototroph adapted to seawater oligotrophy by reducing its selective leakiness, increasing the acquisition of essential nutrients and secreting conserved proteins of unknown function. We also report a surprisingly high abundance of extracellular superoxide dismutase produced by Synechococcus and a dynamic secretion of potential hydrolytic enzyme candidates used by the heterotroph to cleave organic groups and hydrolase polymeric organic matter produced by the cyanobacterium. The time course dataset we present here will become a reference for understanding the molecular processes underpinning marine phototroph‐heterotroph interactions.
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Affiliation(s)
- Amandeep Kaur
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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71
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Luria CM, Amaral-Zettler LA, Ducklow HW, Repeta DJ, Rhyne AL, Rich JJ. Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula. Front Microbiol 2017; 8:2117. [PMID: 29163409 PMCID: PMC5675858 DOI: 10.3389/fmicb.2017.02117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
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Affiliation(s)
- Catherine M. Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Linda A. Amaral-Zettler
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, United States
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Hugh W. Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Andrew L. Rhyne
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, RI, United States
| | - Jeremy J. Rich
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, United States
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72
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Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T. Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol 2017; 40:370-382. [PMID: 28641923 DOI: 10.1016/j.syapm.2017.05.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B12 was produced by 70% of the isolates. Since growth of F. spiralis depends on B12 supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Laura Wolter
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Nils Bergen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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73
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Goldberg SJ, Nelson CE, Viviani DA, Shulse CN, Church MJ. Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean. Environ Microbiol 2017; 19:3450-3464. [PMID: 28618153 DOI: 10.1111/1462-2920.13825] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022]
Abstract
Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean.
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Affiliation(s)
- S J Goldberg
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - C E Nelson
- Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - D A Viviani
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - C N Shulse
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - M J Church
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
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74
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Wang Y, Zhang R, He Z, Van Nostrand JD, Zheng Q, Zhou J, Jiao N. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment. Front Microbiol 2017; 8:1153. [PMID: 28680420 PMCID: PMC5478683 DOI: 10.3389/fmicb.2017.01153] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 06/07/2017] [Indexed: 01/28/2023] Open
Abstract
Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C), nitrogen (N), and phosphorus (P) cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS) is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip), we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D)] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT) showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH), transformation of hydroxylamine to nitrite (hao) and ammonification (gdh) genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated with salinity, temperature, and chlorophyll based on canonical correspondence analysis, suggesting a significant influence of hydrologic conditions on water microbial communities. Our data provide new insights into better understanding of the functional potential of microbial communities in the complex estuarine-coastal environmental gradient of the ECS.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Zhili He
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States.,School of Environment, Tsinghua UniversityBeijing, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
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75
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Sipler RE, Kellogg CTE, Connelly TL, Roberts QN, Yager PL, Bronk DA. Microbial Community Response to Terrestrially Derived Dissolved Organic Matter in the Coastal Arctic. Front Microbiol 2017. [PMID: 28649233 PMCID: PMC5465303 DOI: 10.3389/fmicb.2017.01018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Warming at nearly twice the global rate, higher than average air temperatures are the new ‘normal’ for Arctic ecosystems. This rise in temperature has triggered hydrological and geochemical changes that increasingly release carbon-rich water into the coastal ocean via increased riverine discharge, coastal erosion, and the thawing of the semi-permanent permafrost ubiquitous in the region. To determine the biogeochemical impacts of terrestrially derived dissolved organic matter (tDOM) on marine ecosystems we compared the nutrient stocks and bacterial communities present under ice-covered and ice-free conditions, assessed the lability of Arctic tDOM to coastal microbial communities from the Chukchi Sea, and identified bacterial taxa that respond to rapid increases in tDOM. Once thought to be predominantly refractory, we found that ∼7% of dissolved organic carbon and ∼38% of dissolved organic nitrogen from tDOM was bioavailable to receiving marine microbial communities on short 4 – 6 day time scales. The addition of tDOM shifted bacterial community structure toward more copiotrophic taxa and away from more oligotrophic taxa. Although no single order was found to respond universally (positively or negatively) to the tDOM addition, this study identified 20 indicator species as possible sentinels for increased tDOM. These data suggest the true ecological impact of tDOM will be widespread across many bacterial taxa and that shifts in coastal microbial community composition should be anticipated.
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Affiliation(s)
- Rachel E Sipler
- The Virginia Institute of Marine Science, College of William & Mary, Gloucester PointVA, United States
| | - Colleen T E Kellogg
- Department of Microbiology & Immunology, University of British Columbia, VancouverBC, Canada
| | - Tara L Connelly
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Quinn N Roberts
- The Virginia Institute of Marine Science, College of William & Mary, Gloucester PointVA, United States
| | - Patricia L Yager
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Deborah A Bronk
- The Virginia Institute of Marine Science, College of William & Mary, Gloucester PointVA, United States
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76
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Herlemann DPR, Manecki M, Dittmar T, Jürgens K. Differential responses of marine, mesohaline and oligohaline bacterial communities to the addition of terrigenous carbon. Environ Microbiol 2017; 19:3098-3117. [PMID: 28474480 DOI: 10.1111/1462-2920.13784] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 04/13/2017] [Accepted: 04/26/2017] [Indexed: 12/21/2022]
Abstract
In response to global warming, increasing quantities of tDOM are transported through estuaries from land to the sea. In this study, we investigated microbial responses to increased tDOM concentrations in three salinity regimes (salinity: 32, 7 and 3) characteristic of the Baltic Sea. Mesocosm experiments performed in May and November revealed low (0-6%) dissolved organic carbon (DOC) utilisation. Molecular DOM analyses using ultrahigh-resolution mass spectrometry identified the terrigenous signal in the tDOM manipulation, but the molecular changes in DOM levels over the course of the experiment were subtle. However, tDOM had significant stimulatory effects on bacterial production in the oligohaline mesocosms. The shift in the bacterial community composition was especially prominent in the tDOM-amended marine and mesohaline mesocosms, but not in the oligohaline mesocosms after 7 and 11 days of incubation. These results suggested the inherent ability of oligohaline bacterial communities to adapt to high tDOM concentrations and therefore to use tDOM. The higher rates of bacterial activity and DOC removal in mesocosms containing UV-pretreated tDOM supported the increased bioavailability of photoinduced, modified tDOM. The overall low rates of microbial tDOM utilisation highlights the importance of abiotic factors in determining the distribution and dynamics of tDOM in estuaries.
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Affiliation(s)
- D P R Herlemann
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Biological Oceanography, Seestrasse 15, Rostock, D-18119, Germany
| | - M Manecki
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Str, Oldenburg, 9-11 D-26129, Germany.,Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Marine Chemistry, Seestrasse 15, Rostock, D-18119, Germany
| | - T Dittmar
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Str, Oldenburg, 9-11 D-26129, Germany
| | - K Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Biological Oceanography, Seestrasse 15, Rostock, D-18119, Germany
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77
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Zhao D, Cao X, Huang R, Zeng J, Wu QL. Variation of bacterial communities in water and sediments during the decomposition of Microcystis biomass. PLoS One 2017; 12:e0176397. [PMID: 28437480 PMCID: PMC5402945 DOI: 10.1371/journal.pone.0176397] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/10/2017] [Indexed: 12/14/2022] Open
Abstract
The bacterial community composition in water and sediment samples during the decomposition of Microcystis biomass were analyzed using the 454 pyrosequencing technique. We found dramatic shifts in the bacterial community composition of water and sediments after the addition of Microcystis biomass. Among all the detected phyla, only Firmicutes was found to be dominant in both water and sediment samples. The genus Clostridium sensu stricto was the absolutely dominant group in Firmicutes and showed drastic variations with incubation time during the decomposition process. Peak values in relative abundance of Clostridium sensu stricto appeared in the first few days for water and sediment samples. Environmental factors such as pH, dissolved oxygen (DO), and dissolved organic carbon (DOC) in water samples showed drastic variations during the decomposing process, which might be the prominent forces driving the variation of bacterial communities. The abundant genus, Clostridium sensu stricto, were thought to be well adapted to higher DOC and turbidity and lower pH and DO conditions. Compared with the sediment samples, the decomposition of Microcystis biomass had greater influence on the bacterial community composition in water and Clostridium sensu stricto might play important roles in the process of Microcystis biomass decomposition.
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Affiliation(s)
- Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Xinyi Cao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Qinglong L. Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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78
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Sun Y, Zhang Y, Hollibaugh JT, Luo H. Ecotype diversification of an abundant Roseobacter lineage. Environ Microbiol 2017; 19:1625-1638. [PMID: 28142225 DOI: 10.1111/1462-2920.13683] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/21/2016] [Accepted: 01/11/2017] [Indexed: 11/29/2022]
Abstract
The Roseobacter DC5-80-3 cluster (also known as the RCA clade) is among the most abundant bacterial lineages in temperate and polar oceans. Previous studies revealed two phylotypes within this cluster that are distinctly distributed in the Antarctic and other ocean provinces. Here, we report a nearly complete genome co-assembly of three closely related single cells co-occurring in the Antarctic, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies.
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Affiliation(s)
- Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiang'an, Xiamen, 361101, China
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China.,Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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79
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Sison-Mangus MP, Jiang S, Kudela RM, Mehic S. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events. Front Microbiol 2016; 7:1433. [PMID: 27672385 PMCID: PMC5018474 DOI: 10.3389/fmicb.2016.01433] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6–65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12–86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental variables such as nitrate and phosphate and temperature appear to influence some low abundant bacterial groups as well. Our results suggest that phytoplankton-associated bacterial communities are strongly affected not just by phytoplankton bloom in general, but also by the type of algal species that dominates in the natural bloom.
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Affiliation(s)
- Marilou P Sison-Mangus
- Department of Ocean Sciences and Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA USA
| | - Sunny Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA USA
| | - Raphael M Kudela
- Department of Ocean Sciences and Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA USA
| | - Sanjin Mehic
- Department of Ocean Sciences and Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA USA
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80
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Lasbleiz M, Leblanc K, Armand LK, Christaki U, Georges C, Obernosterer I, Quéguiner B. Composition of diatom communities and their contribution to plankton biomass in the naturally iron-fertilized region of Kerguelen in the Southern Ocean. FEMS Microbiol Ecol 2016; 92:fiw171. [PMID: 27515734 DOI: 10.1093/femsec/fiw171] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 12/25/2022] Open
Abstract
In the naturally iron-fertilized surface waters of the northern Kerguelen Plateau region, the early spring diatom community composition and contribution to plankton carbon biomass were investigated and compared with the high nutrient, low chlorophyll (HNLC) surrounding waters. The large iron-induced blooms were dominated by small diatom species belonging to the genera Chaetoceros (Hyalochaete) and Thalassiosira, which rapidly responded to the onset of favorable light-conditions in the meander of the Polar Front. In comparison, the iron-limited HNLC area was typically characterized by autotrophic nanoeukaryote-dominated communities and by larger and more heavily silicified diatom species (e.g. Fragilariopsis spp.). Our results support the hypothesis that diatoms are valuable vectors of carbon export to depth in naturally iron-fertilized systems of the Southern Ocean. Furthermore, our results corroborate observations of the exported diatom assemblage from a sediment trap deployed in the iron-fertilized area, whereby the dominant Chaetoceros (Hyalochaete) cells were less efficiently exported than the less abundant, yet heavily silicified, cells of Thalassionema nitzschioides and Fragilariopsis kerguelensis Our observations emphasize the strong influence of species-specific diatom cell properties combined with trophic interactions on matter export efficiency, and illustrate the tight link between the specific composition of phytoplankton communities and the biogeochemical properties characterizing the study area.
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Affiliation(s)
- Marine Lasbleiz
- Aix-Marseille Université, Université de Toulon, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, Cedex 09, France
| | - Karine Leblanc
- Aix-Marseille Université, Université de Toulon, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, Cedex 09, France
| | - Leanne K Armand
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, 2109, Australia
| | - Urania Christaki
- INSU-CNRS, UMR8187 LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral Côte d'Opale, ULCO, 32 avenue Foch, 62930 Wimereux, France
| | - Clément Georges
- INSU-CNRS, UMR8187 LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral Côte d'Opale, ULCO, 32 avenue Foch, 62930 Wimereux, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Bernard Quéguiner
- Aix-Marseille Université, Université de Toulon, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, Cedex 09, France
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81
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Fuentes JL, Garbayo I, Cuaresma M, Montero Z, González-Del-Valle M, Vílchez C. Impact of Microalgae-Bacteria Interactions on the Production of Algal Biomass and Associated Compounds. Mar Drugs 2016; 14:md14050100. [PMID: 27213407 PMCID: PMC4882574 DOI: 10.3390/md14050100] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/29/2022] Open
Abstract
A greater insight on the control of the interactions between microalgae and other microorganisms, particularly bacteria, should be useful for enhancing the efficiency of microalgal biomass production and associated valuable compounds. Little attention has been paid to the controlled utilization of microalgae-bacteria consortia. However, the studies of microalgal-bacterial interactions have revealed a significant impact of the mutualistic or parasitic relationships on algal growth. The algal growth, for instance, has been shown to be enhanced by growth promoting factors produced by bacteria, such as indole-3-acetic acid. Vitamin B12 produced by bacteria in algal cultures and bacterial siderophores are also known to be involved in promoting faster microalgal growth. More interestingly, enhancement in the intracellular levels of carbohydrates, lipids and pigments of microalgae coupled with algal growth stimulation has also been reported. In this sense, massive algal production might occur in the presence of bacteria, and microalgae-bacteria interactions can be beneficial to the massive production of microalgae and algal products. This manuscript reviews the recent knowledge on the impact of the microalgae-bacteria interactions on the production of microalgae and accumulation of valuable compounds, with an emphasis on algal species having application in aquaculture.
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Affiliation(s)
- Juan Luis Fuentes
- Algal Biotechnology Group, Ciderta and Faculty of Sciences, University of Huelva and Marine International Campus of Excellence (CEIMAR), Huelva 21007, Spain.
| | - Inés Garbayo
- Algal Biotechnology Group, Ciderta and Faculty of Sciences, University of Huelva and Marine International Campus of Excellence (CEIMAR), Huelva 21007, Spain.
| | - María Cuaresma
- Algal Biotechnology Group, Ciderta and Faculty of Sciences, University of Huelva and Marine International Campus of Excellence (CEIMAR), Huelva 21007, Spain.
| | - Zaida Montero
- Algal Biotechnology Group, Ciderta and Faculty of Sciences, University of Huelva and Marine International Campus of Excellence (CEIMAR), Huelva 21007, Spain.
| | | | - Carlos Vílchez
- Algal Biotechnology Group, Ciderta and Faculty of Sciences, University of Huelva and Marine International Campus of Excellence (CEIMAR), Huelva 21007, Spain.
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82
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Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel HA, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nat Microbiol 2016; 1:16063. [PMID: 27572966 DOI: 10.1038/nmicrobiol.2016.63] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/05/2016] [Indexed: 12/13/2022]
Abstract
The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer. The first sequenced genome of a CHAB-I-5 organism comprises 3.6 Mbp and exhibits features of an oligotrophic lifestyle. In a metatranscriptome of North Sea surface waters, 98% of the encoded genes were present, and genes encoding various ABC transporters, glutamate synthase and CO oxidation were particularly upregulated. Phylogenetic gene content analyses of 41 genomes of the Roseobacter group revealed a unique cluster of pelagic organisms distinct from other lineages of this group, highlighting the adaptation to life in nutrient-depleted environments.
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Affiliation(s)
- Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Sonja Voget
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Lyngby DK-2800 Kgs, Denmark
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida 32514, USA
| | - Rolf Daniel
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
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Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. Appl Environ Microbiol 2016; 82:2100-2111. [PMID: 26826224 DOI: 10.1128/aem.03678-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/20/2016] [Indexed: 01/28/2023] Open
Abstract
Members of the marine Roseobacter clade are major participants in global carbon and sulfur cycles. While roseobacters are well represented in cultures, several abundant pelagic lineages, including SAG-O19, DC5-80-3, and NAC11-7, remain largely uncultivated and show evidence of genome streamlining. Here, we analyzed the partial genomes of three single cells affiliated with CHAB-I-5, another abundant but exclusively uncultivated Roseobacter lineage. Members of this lineage encode several metabolic potentials that are absent in streamlined genomes. Examples are quorum sensing and type VI secretion systems, which enable them to effectively interact with host and other bacteria. Further analysis of the CHAB-I-5 single-cell amplified genomes (SAGs) predicted that this lineage comprises members with relatively large genomes (4.1 to 4.4 Mbp) and a high fraction of noncoding DNA (10 to 12%), which is similar to what is observed in many cultured, nonstreamlined Roseobacter lineages. The four uncultured lineages, while exhibiting highly variable geographic distributions, together represent >60% of the global pelagic roseobacters. They are consistently enriched in genes encoding the capabilities of light harvesting, oxidation of "energy-rich" reduced sulfur compounds and methylated amines, uptake and catabolism of various carbohydrates and osmolytes, and consumption of abundant exudates from phytoplankton. These traits may define the global prevalence of the four lineages among marine bacterioplankton.
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