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Li X, Cheng X, Xu J, Wu J, Chan LL, Cai Z, Zhou J. Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms. Microbiol Res 2024; 286:127785. [PMID: 38851011 DOI: 10.1016/j.micres.2024.127785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/01/2024] [Accepted: 05/25/2024] [Indexed: 06/10/2024]
Abstract
Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.
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Affiliation(s)
- Xinyang Li
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Xueyu Cheng
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Junjie Xu
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Zhonghua Cai
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Jin Zhou
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China.
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Branscombe L, Harrison EL, Choong ZYD, Swink C, Keys M, Widdicombe C, Wilson WH, Cunliffe M, Helliwell K. Cryptic bacterial pathogens of diatoms peak during senescence of a winter diatom bloom. THE NEW PHYTOLOGIST 2024; 241:1292-1307. [PMID: 38037269 DOI: 10.1111/nph.19441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023]
Abstract
Diatoms are globally abundant microalgae that form extensive blooms in aquatic ecosystems. Certain bacteria behave antagonistically towards diatoms, killing or inhibiting their growth. Despite their crucial implications to diatom blooms and population health, knowledge of diatom antagonists in the environment is fundamentally lacking. We report systematic characterisation of the diversity and seasonal dynamics of bacterial antagonists of diatoms via plaque assay sampling in the Western English Channel (WEC), where diatoms frequently bloom. Unexpectedly, peaks in detection did not occur during characteristic spring diatom blooms, but coincided with a winter bloom of Coscinodiscus, suggesting that these bacteria likely influence distinct diatom host populations. We isolated multiple bacterial antagonists, spanning 4 classes and 10 bacterial orders. Notably, a diatom attaching Roseobacter Ponticoccus alexandrii was isolated multiple times, indicative of a persistent environmental presence. Moreover, many isolates had no prior reports of antagonistic activity towards diatoms. We verified diatom growth inhibitory effects of eight isolates. In all cases tested, these effects were activated by pre-exposure to diatom organic matter. Discovery of widespread 'cryptic' antagonistic activity indicates that bacterial pathogenicity towards diatoms is more prevalent than previously recognised. Finally, examination of the global biogeography of WEC antagonists revealed co-occurrence patterns with diatom host populations in marine waters globally.
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Affiliation(s)
- Laura Branscombe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Ellen L Harrison
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Zhi Yi Daniel Choong
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Courtney Swink
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Matthew Keys
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | | | - William H Wilson
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Michael Cunliffe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Katherine Helliwell
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
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Kim HJ, Jeoung G, Kim KE, Park JS, Kang D, Baek SH, Lee CY, Kim H, Cho S, Lee TK, Jung SW. Co-variance between free-living bacteria and Cochlodinium polykrikoides (Dinophyta) harmful algal blooms, South Korea. HARMFUL ALGAE 2023; 122:102371. [PMID: 36754457 DOI: 10.1016/j.hal.2022.102371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
To understand the co-variance between common free-living bacteria and Cochlodinium polykrikoides harmful algal blooms (HABs) and their metabolic functions, we investigated 110 sampling sites in the Southern Sea of South Korea. These sampling sites were divided into three groups based on environmental factors and phytoplankton data with a similarity of 85% using non-metric multidimensional scaling. One group represented high-severity C. polykrikoides blooms, while the other two represented low-severity or no blooms. In high-severity HABs, inorganic phosphorous and dissolved organic carbon concentrations were strongly correlated with C. polykrikoides density (p < 0.01). This may reflect the changes in biochemical cycling due to inorganic and organic substrates released by HAB cells (or by cell destruction). Furthermore, 88 common bacterial operational taxonomic units (OTUs, with mean relative abundance > 1%) were identified. These included Gammaproteobacteria (36 OTUs), Flavobacteriia (24), Alphaproteobacteria (18), and other taxa (11). When C. polykrikoides blooms intensified, the relative abundances of Gammaproteobacteria also increased. OTU #030 (Flavicella sp., Flavobacteria, 96%) was positively correlated with C. polykrikoides abundance (r = 0.77, p < 0.001). Functional analysis based on the dominant bacterial OTUs revealed that chemoheterotrophy-related functions were more common in high-severity sites of HABs than in other groups. Therefore, the occurrence of HABs highlighted their interactions with bacteria and affected the bacterial community structure and metabolic functions.
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Affiliation(s)
- Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea
| | - Gaeul Jeoung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea
| | - Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea; Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Joon Sang Park
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea
| | - Donhyug Kang
- Maritime Security and Safety Research Center, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Seung Ho Baek
- Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea; Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Chol Young Lee
- Marine Bigdata Center, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Hansoo Kim
- Maritime Security and Safety Research Center, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Sungho Cho
- Maritime Security and Safety Research Center, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea; Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea; Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea.
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Shao Q, Sun D, Fang C, Feng Y, Wang C. Microbial food webs share similar biogeographic patterns and driving mechanisms with depths in oligotrophic tropical western Pacific Ocean. Front Microbiol 2023; 14:1098264. [PMID: 36778869 PMCID: PMC9909095 DOI: 10.3389/fmicb.2023.1098264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Microbial food web (MFW) dominates the energy flow in oligotrophic tropical open ocean pelagic ecosystems. Understanding biogeographic patterns and driving mechanisms of key components of the MFW is one of the central topics in current marine ecology. Investigations were conducted along an 1,100-km horizontal gradient and in the full-water column vertical gradient of the oligotrophic tropical western Pacific Ocean. High-throughput sequencing and association networking methods were used to analyze the community structure and interspecies interactions of MFW. The structure of MFW significantly differed with depths, but not across horizontal gradients. Bacteria and microeukaryotes were interconnected and had more predominantly positive and negative linkages in the aphotic layers. Key components of MFW exhibited similar biogeographic patterns and driving mechanisms. Geographic distance exerted minimal effects on the distribution patterns of the microbial food web, while environmental factors played more important roles, especially for temperature and inorganic nutrients. Stochastic processes were more important in the microbial food webs of the 5-200 m layer than the >500 m layer, and drift explained the majority of stochastic processes. Moreover, only a weak but not significant driving force for North Equatorial Current on the east-west connectivity of the microbial food web was found in the upper layers. This knowledge is a critical fundamental data for future planning of marine protected areas targeting the protection of tuna fishing in the western Pacific Ocean.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Ningbo Institute of Oceanography, Ningbo, China
| | - Dong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Dong Sun, ✉
| | - Chen Fang
- College of Oceanography, Hohai University, Nanjing, China
| | - Yunzhi Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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Tsertou MI, Triga A, Droubogiannis S, Kokkari C, Anasi G, Katharios P. Isolation and characterization of a novel Tenacibaculum species and a corresponding bacteriophage from a Mediterranean fish hatchery: Description of Tenacibaculum larymnensis sp. nov. and Tenacibaculum phage Larrie. Front Microbiol 2023; 14:1078669. [PMID: 36925475 PMCID: PMC10013915 DOI: 10.3389/fmicb.2023.1078669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
Tenacibaculum larymnensis sp. nov., a novel species of the Tenacibaculum genus was isolated from a commercial fish hatchery in Greece. The novel species is phylogenetically close to T. discolor and was biochemically and genetically characterized. The genome of T. larymnensis has 3.66 Mbps length, 31.83% GC content and the genomic analysis demonstrated that it harbors a wide enzymatic repertoire suggestive of increased degrading capacity but also several virulence factors including hemolysins, secretion systems, transporters, siderophores, pili and extracellular proteins. Using the novel strain, a virulent bacteriophage designated as Tenacibaculum phage Larrie was isolated and characterized. Larrie is a novel Siphovirus with relatively large genome, 77.5 kbps with 111 ORFs, a GC content of 33.7% and an exclusively lytic lifestyle. The new phage-host system can serve as an efficient model to study microbial interactions in the aquatic environment which contribute to the nutrient cycling.
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Affiliation(s)
- Maria Ioanna Tsertou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.,Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Stavros Droubogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.,Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Constantina Kokkari
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | | | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
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Halary S, Duperron S, Demay J, Duval C, Hamlaoui S, Piquet B, Reinhardt A, Bernard C, Marie B. Metagenome-Based Exploration of Bacterial Communities Associated with Cyanobacteria Strains Isolated from Thermal Muds. Microorganisms 2022; 10:microorganisms10122337. [PMID: 36557590 PMCID: PMC9785279 DOI: 10.3390/microorganisms10122337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities.
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Affiliation(s)
- Sébastien Halary
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Sébastien Duperron
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Justine Demay
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
- Thermes de Balaruc-Les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France
| | - Charlotte Duval
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Sahima Hamlaoui
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Bérénice Piquet
- Electron Microscopy Platform, Muséum National d’Histoire Naturelle, CP 39, 12 rue Buffon, CEDEX 05, 75231 Paris, France
| | - Anita Reinhardt
- Thermes de Balaruc-Les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France
| | - Cécile Bernard
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Benjamin Marie
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
- Correspondence:
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Scicchitano D, Lo Martire M, Palladino G, Nanetti E, Fabbrini M, Dell’Anno A, Rampelli S, Corinaldesi C, Candela M. Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea). Sci Rep 2022; 12:16670. [PMID: 36198901 PMCID: PMC9535000 DOI: 10.1038/s41598-022-21182-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractBecause of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.
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Xie W, Yan Y, Hu J, Dong P, Hou D, Zhang H, Yao Z, Zhu X, Zhang D. Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China. MICROBIAL ECOLOGY 2022; 84:746-758. [PMID: 34665286 DOI: 10.1007/s00248-021-01899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.
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Affiliation(s)
- 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, 315832, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Jian Hu
- 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, 315832, China
| | - Pengsheng Dong
- 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, 315832, China
| | - Dandi 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, 315832, China
| | - 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, 315832, China.
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China
| | - Xiangyu Zhu
- 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, 315832, China.
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9
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Pontiller B, Martínez-García S, Joglar V, Amnebrink D, Pérez-Martínez C, González JM, Lundin D, Fernández E, Teira E, Pinhassi J. Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system. THE ISME JOURNAL 2022; 16:2360-2372. [PMID: 35804052 PMCID: PMC9478159 DOI: 10.1038/s41396-022-01273-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Coastal upwelling zones are hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM are not well understood. We therefore carried out comparative time-series metatranscriptome analyses of bacterioplankton in the Northwest Iberian upwelling system, using parallel sampling of seawater and mesocosms with in situ-like conditions. The mesocosm experiment uncovered a taxon-specific progression of transcriptional responses from bloom development (characterized by a diverse set of taxa in the orders Cellvibrionales, Rhodobacterales, and Pelagibacterales), over early decay (mainly taxa in the Alteromonadales and Flavobacteriales), to senescence phases (Flavobacteriales and Saprospirales taxa). Pronounced order-specific differences in the transcription of glycoside hydrolases, peptidases, and transporters were found, supporting that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of mesocosm and field samples revealed a high degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the labile DOM pool. Our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the time scales typical of upwelling-driven phytoplankton blooms.
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10
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Thiele S, Storesund JE, Fernández-Méndez M, Assmy P, Øvreås L. A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice. Microorganisms 2022; 10:1618. [PMID: 36014036 PMCID: PMC9414599 DOI: 10.3390/microorganisms10081618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.
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Affiliation(s)
- Stefan Thiele
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | | | - Mar Fernández-Méndez
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
- Biological Oceanography, GEOMAR Helmholtz Centre of Ocean Research, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
| | - Lise Øvreås
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
- Department of Arctic Biology, University Center in Svalbard, UNIS, 9171 Longyearbyen, Norway
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11
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Martínez-García S, Bunse C, Pontiller B, Baltar F, Israelsson S, Fridolfsson E, Lindh MV, Lundin D, Legrand C, Pinhassi J. Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent. Front Microbiol 2022; 13:834675. [PMID: 36212867 PMCID: PMC9533715 DOI: 10.3389/fmicb.2022.834675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 μm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05–0.27) of FL bacteria (defined as the size-fraction <3.0 μm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.
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Affiliation(s)
- Sandra Martínez-García
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Pontevedra, Spain
- *Correspondence: Sandra Martínez-García,
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Benjamin Pontiller
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Stina Israelsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Emil Fridolfsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Markus V. Lindh
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
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12
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Behzad H, Ohyanagi H, Alharbi B, Ibarra M, Alarawi M, Saito Y, Duarte CM, Bajic V, Mineta K, Gojobori T. A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota. BMC Genomics 2022; 23:277. [PMID: 35392799 PMCID: PMC8991508 DOI: 10.1186/s12864-022-08485-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters. RESULTS We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month. CONCLUSION Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.
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Affiliation(s)
- Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Hajime Ohyanagi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Badr Alharbi
- National Centre for Environmental Technology, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia
| | - Martin Ibarra
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yoshimoto Saito
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Marine Open Innovation (MaOI) Institute, Shizuoka, 424-0922, Japan
| | - Carlos M Duarte
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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13
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Ge Z, Li QP, Yang W, Liu X, Wu Z. Transparent exopolymer particle dynamics along a shelf-to-sea gradient and impacts on the regional carbon cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152117. [PMID: 34863747 DOI: 10.1016/j.scitotenv.2021.152117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/28/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Transparent exopolymer particles (TEPs) have drawn extensive attention in recent decades due to their crucial role in the biogeochemical and ecological processes of the ocean. However, TEP distribution and fluxes are relatively less addressed in the shelf-seas, where its variability can be affected by not only biology but also complex physical dynamics. Here, we present a comprehensive study of TEP from the coast to the basin (12 sampling sites) of the northern South China Sea (NSCS). We found a large TEP variability from 0.6 to 78.6 μg Xeq. L-1 with higher levels in the coastal waters than the offshore epipelagic waters and the deep waters. In addition, the spatial distribution of TEP was significantly correlated to the cross-shelf change of temperature, salinity, and chlorophyll-a, revealing the complex physical-biogeochemical controls on TEP variability. We found the TEP dynamics nearshore largely influenced by the sedimentation and transportation of TEP-rich aggregates from the river plume. The contribution of TEP to particulate organic carbon (POC) increased gradually when approaching the shore from the sea, suggesting an elevated role of TEP in the coastal carbon cycle. Finally, a good correlation of particle-attached bacteria (PAB) with TEP but not POC revealed a preferential utilization of TEP by PAB. Thus, TEP may play an essential role in the recycling of carbon and nitrogen in the shelf-sea. These findings are crucial for understanding of the TEP dynamics under a changing environment and the associated impacts on the oceanic carbon cycle.
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Affiliation(s)
- Zaiming Ge
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian P Li
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Weifeng Yang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Liu
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Zhengchao Wu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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14
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Water Column Microbial Communities Vary along Salinity Gradients in the Florida Coastal Everglades Wetlands. Microorganisms 2022; 10:microorganisms10020215. [PMID: 35208670 PMCID: PMC8874701 DOI: 10.3390/microorganisms10020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 01/04/2023] Open
Abstract
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This study provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) together with nutrient concentrations and environmental parameters at 14 sites along two transects covering two distinctly different drainages: the peat-based Shark River Slough (SRS) and marl-based Taylor Slough/Panhandle (TS/Ph). Both bacterial as well as eukaryotic community structures varied significantly along the salinity gradient. Although freshwater communities were relatively similar in both transects, bacterioplankton community composition at the ecotone (where freshwater and marine water mix) differed significantly. The most abundant taxa in the freshwater marshes include heterotrophic Polynucleobacter sp. and potentially phagotrophic cryptomonads of the genus Chilomonas, both of which could be key players in the transfer of detritus-based biomass to higher trophic levels.
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15
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Escalas A, Troussellier M, Melayah D, Bruto M, Nicolas S, Bernard C, Ader M, Leboulanger C, Agogué H, Hugoni M. Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake. FEMS Microbiol Ecol 2021; 97:6464137. [PMID: 34918080 DOI: 10.1093/femsec/fiab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the role of microbial interactions in the functioning of natural systems is often impaired by the levels of complexity they encompass. In this study, we used the relative simplicity of an hypersaline crater lake hosting only microbial organisms (Dziani Dzaha) to provide a detailed analysis of the microbial networks including the three domains of life. We identified two main ecological zones, one euphotic and oxic zone in surface, where two phytoplanktonic organisms produce a very high biomass, and one aphotic and anoxic deeper zone, where this biomass slowly sinks and undergoes anaerobic degradation. We highlighted strong differences in the structure of microbial communities from the two zones and between the microbial consortia associated with the two primary producers. Primary producers sedimentation was associated with a major reorganization of the microbial network at several levels: global properties, modules composition, nodes and links characteristics. We evidenced the potential dependency of Woesearchaeota to the primary producers' exudates in the surface zone, and their disappearance in the deeper anoxic zone, along with the restructuration of the networks in the anoxic zone toward the decomposition of the organic matter. Altogether, we provided an in-depth analysis of microbial association network and highlighted putative changes in microbial interactions supporting the functioning of the two ecological zones in this unique ecosystem.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Marc Troussellier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Delphine Melayah
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Sébastien Nicolas
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, CP 39, 75005 Paris, France
| | - Magali Ader
- Université de Paris, Institut de physique du globe de Paris, CNRS, 75005 Paris, France
| | - Christophe Leboulanger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Hélène Agogué
- Littoral Environnement et Sociétés (LIENSs) UMR 7266 CNRS -La Rochelle Université, 17000 La Rochelle, France
| | - Mylène Hugoni
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.,Institut Universitaire de France (IUF)
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16
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Matsumoto K, Sakami T, Watanabe T, Taniuchi Y, Kuwata A, Kakehi S, Engkong T, Igarashi Y, Kinoshita S, Asakawa S, Hattori M, Watabe S, Ishino Y, Kobayashi T, Gojobori T, Ikeo K. Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters. PLoS One 2021; 16:e0257862. [PMID: 34637433 PMCID: PMC8509957 DOI: 10.1371/journal.pone.0257862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/14/2021] [Indexed: 12/05/2022] Open
Abstract
The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.
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Affiliation(s)
- Kaoru Matsumoto
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail: (KM); (KI)
| | - Tomoko Sakami
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Tsuyoshi Watanabe
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Yukiko Taniuchi
- Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Akira Kuwata
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Shigeho Kakehi
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Tan Engkong
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yoji Igarashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takashi Gojobori
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail: (KM); (KI)
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17
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Cai YM. Non-surface Attached Bacterial Aggregates: A Ubiquitous Third Lifestyle. Front Microbiol 2020; 11:557035. [PMID: 33343514 PMCID: PMC7746683 DOI: 10.3389/fmicb.2020.557035] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/13/2020] [Indexed: 01/03/2023] Open
Abstract
Bacteria are now generally believed to adopt two main lifestyles: planktonic individuals, or surface-attached biofilms. However, in recent years medical microbiologists started to stress that suspended bacterial aggregates are a major form of bacterial communities in chronic infection sites. Despite sharing many similarities with surface-attached biofilms and are thus generally defined as biofilm-like aggregates, these non-attached clumps of cells in vivo show much smaller sizes and different formation mechanisms. Furthermore, ex vivo clinical isolates were frequently reported to be less attached to abiotic surfaces when compared to standard type strains. While this third lifestyle is starting to draw heavy attention in clinical studies, it has a long history in natural and environmental sciences. For example, marine gel particles formed by bacteria attachment to phytoplankton exopolymers have been well documented in oceans; large river and lake snows loaded with bacterial aggregates are frequently found in freshwater systems; multispecies bacterial "flocs" have long been used in wastewater treatment. This review focuses on non-attached aggregates found in a variety of natural and clinical settings, as well as some recent technical developments facilitating aggregate research. The aim is to summarise the characteristics of different types of bacterial aggregates, bridging the knowledge gap, provoking new perspectives for researchers from different fields, and highlighting the importance of more research input in this third lifestyle of bacteria closely relevant to our daily life.
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Affiliation(s)
- Yu-Ming Cai
- National Biofilms Innovation Centre, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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18
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Shibl AA, Isaac A, Ochsenkühn MA, Cárdenas A, Fei C, Behringer G, Arnoux M, Drou N, Santos MP, Gunsalus KC, Voolstra CR, Amin SA. Diatom modulation of select bacteria through use of two unique secondary metabolites. Proc Natl Acad Sci U S A 2020; 117:27445-27455. [PMID: 33067398 PMCID: PMC7959551 DOI: 10.1073/pnas.2012088117] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.
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Affiliation(s)
- Ahmed A Shibl
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- International Max Planck Research School of Marine Microbiology, University of Bremen, Bremen 28334, Germany
| | - Michael A Ochsenkühn
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz 78467, Germany
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Cong Fei
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Gregory Behringer
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Marc Arnoux
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Nizar Drou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Miraflor P Santos
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz 78467, Germany
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates;
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19
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Seasonality in Spatial Turnover of Bacterioplankton Along an Ecological Gradient in the East China Sea: Biogeographic Patterns, Processes and Drivers. Microorganisms 2020; 8:microorganisms8101484. [PMID: 32992545 PMCID: PMC7600760 DOI: 10.3390/microorganisms8101484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Seasonal succession in bacterioplankton is a common process in marine waters. However, seasonality in their spatial turnover is largely unknown. Here, we investigated spatial turnover of surface bacterioplankton along a nearshore-to-offshore gradient in the East China Sea across four seasons. Although seasonality overwhelmed spatial variability of bacterioplankton composition, we found significant spatial turnover of bacterioplankton along the gradient as well as overall seasonal consistency in biogeographic patterns (including distance-decay relationship and covariation of community composition with distance to shore) with subtle changes. Bacterioplankton assembly was consistently dominated by deterministic mechanisms across seasons, with changes in specific processes. We found overall seasonal consistency in abiotic factors (mainly salinity and nitrogen and phosphorus nutrients) shaping bacterioplankton composition, while phytoplankton showed a similar influence as abiotic factors only in spring. Although key taxa responsible for bacterioplankton spatial turnover showed certain season-specificity, seasonal switching between closely related taxa occurred within most dominant families. Moreover, many close relatives showed different responding patterns to the environmental gradients in different seasons, suggesting their differences in both seasonally climatic and spatially environmental preferences. Our results provide insights into seasonal consistency and variability in spatial turnover of bacterioplankton in terms of biogeographic patterns, ecological processes, and external and internal drivers.
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20
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Martinez-Varela A, Casas G, Piña B, Dachs J, Vila-Costa M. Large Enrichment of Anthropogenic Organic Matter Degrading Bacteria in the Sea-Surface Microlayer at Coastal Livingston Island (Antarctica). Front Microbiol 2020; 11:571983. [PMID: 33013806 PMCID: PMC7516020 DOI: 10.3389/fmicb.2020.571983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/14/2020] [Indexed: 01/04/2023] Open
Abstract
The composition of bacteria inhabiting the sea-surface microlayer (SML) is poorly characterized globally and yet undescribed for the Southern Ocean, despite their relevance for the biogeochemistry of the surface ocean. We report the abundances and diversity of bacteria inhabiting the SML and the subsurface waters (SSL) determined from a unique sample set from a polar coastal ecosystem (Livingston Island, Antarctica). From early to late austral summer (January–March 2018), we consistently found a higher abundance of bacteria in the SML than in the SSL. The SML was enriched in some Gammaproteobacteria genus such as Pseudoalteromonas, Pseudomonas, and Colwellia, known to degrade a wide range of semivolatile, hydrophobic, and surfactant-like organic pollutants. Hydrocarbons and other synthetic chemicals including surfactants, such as perfluoroalkyl substances (PFAS), reach remote marine environments by atmospheric transport and deposition and by oceanic currents, and are known to accumulate in the SML. Relative abundances of specific SML-enriched bacterial groups were significantly correlated to concentrations of PFASs, taken as a proxy of hydrophobic anthropogenic pollutants present in the SML and its stability. Our observations provide evidence for an important pollutant-bacteria interaction in the marine SML. Given that pollutant emissions have increased during the Anthropocene, our results point to the need to assess chemical pollution as a factor modulating marine microbiomes in the contemporaneous and future oceans.
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Affiliation(s)
- Alícia Martinez-Varela
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Gemma Casas
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Benjamin Piña
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
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21
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Mestre M, Höfer J, Sala MM, Gasol JM. Seasonal Variation of Bacterial Diversity Along the Marine Particulate Matter Continuum. Front Microbiol 2020; 11:1590. [PMID: 32793139 PMCID: PMC7385255 DOI: 10.3389/fmicb.2020.01590] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/17/2020] [Indexed: 11/13/2022] Open
Abstract
Seasonal dynamics of ocean prokaryotic communities in the free-living fraction have been widely described, but less is known about the seasonality of prokaryotes inhabiting marine particles. We describe the seasonality of bacterial communities in the particulate matter continuum by sampling monthly over two years in a temperate oligotrophic coastal ecosystem and using a serial filtration (including six size-fractions spanning from 0.2 to 200 μm). We observed that bacterial communities in the particulate matter continuum had annual changes following harmonic seasonal oscillations, where alpha, beta, and gamma diversity increased during the warm period and decreased during the cold period. Communities in each size-fraction changed gradually over time, being the communities in larger size-fractions the ones with stronger annual changes. Annual community changes were driven mainly by day length and sea surface temperature, and each size-fraction was additionally affected by other variables (e.g., smaller size-fractions by dissolved PO4 and larger size-fractions by turbidity). While some taxonomic groups mantained their preference for a given size fraction during most of the year, others varied their distribution into different size fractions over time, as e.g., SAR11, which increased its presence in particles during the cold period. Our results indicate that the size-fractionation scheme provides novel seasonal patterns that are not possible to unveil by analyzing only free-living bacteria, and that help to better understand the temporal dynamics of prokaryotes.
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Affiliation(s)
- Mireia Mestre
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centro de Investigación Oceanográfica COPAS Sur-Austral, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Juan Höfer
- Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - M Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centre for Marine Ecosystem Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
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22
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Transparent Exopolymer Particle (TEPs) Dynamics and Contribution to Particulate Organic Carbon (POC) in Jaran Bay, Korea. WATER 2020. [DOI: 10.3390/w12041057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Transparent exopolymer particles (TEPs) are defined as acidic polysaccharide particles and they are influenced by various biotic and abiotic processes that play significant roles in marine biogeochemical cycles. However, little information on their monthly variation, relationship and contribution to particulate organic carbon (POC) is currently available particularly in coastal regions. In this study, the water samples were collected monthly to determine TEP concentrations and POC concentrations in a southern coastal region of Korea, Jaran Bay from April 2016 to March 2017. The TEP concentrations varied from 26.5 to 1695.4 μg Xeq L−1 (mean ± standard deviation (S.D.) = 215.9 ± 172.2 μg Xeq L−1) and POC concentrations ranged from 109.9 to 1201.9 μg L−1 (mean ± S.D. = 399.1 ± 186.5 μg L−1) during our observation period. Based on the 13C stable isotope tracer technique, monthly carbon uptake rates of phytoplankton ranged from 3.0 to 274.1 mg C m−2 h−1 (mean ± S.D. = 34.5 ± 45.2 mg C m−2 h−1). The cross-correlation analysis showed a lag-time of 2 months between chlorophyll a and TEP concentrations (r = 0.86, p < 0.01; Pearson’s correlation coefficient). In addition, we observed a 2 month lag-phased correlation between TEP concentrations and primary production (r = 0.73, p < 0.05; Pearson’s correlation coefficient). In Jaran Bay, the TEP contribution was as high as 78.0% of the POC when the TEP-C content was high and declined to 2.4% of the POC when it was low. These results showed that TEP-C could be a significant contributor to the POC pool in Jaran Bay.
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23
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Hou F, Zhang H, Xie W, Zhou X, Zhu X, Zhang D. Co-occurrence patterns and assembly processes of microeukaryotic communities in an early-spring diatom bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134624. [PMID: 31818596 DOI: 10.1016/j.scitotenv.2019.134624] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/21/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
The interaction and assembly processes of microeukaryotic community compositions (MECs) are rarely elucidated in environment with strong disturbance such as harmful algal blooms. To fill this gap, we analyzed changes of MECs induced by a diatom bloom using 18S rRNA gene amplicon sequencing. The MECs were mainly dominated by Cercozoa (average relative abundance, 49.2%), Diatom (25.5%) and Dinoflagellata (15.6%). MECs changed significantly (ANOSIM P < 0.01) in four-bloom stages. Environmental factors including pH, DO, nitrate and phosphate, together with bacterial communities could significantly influence the variation of MECs. Co-occurrence network analysis revealed a complex interaction between microeukaryotic and bacterial communities. Most OTUs in modules of the co-occurrence network were specific to one particular bloom stage. Phylogenetic based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated microeukaryotic community assembly in the initial and after-bloom stage. However, microeukaryotic community assembly in middle and late stage of the bloom were driven by deterministic processes. In conclusion, both stochastic and deterministic processes play important roles in distinct bloom stages. These findings may expand current understandings of assembly mechanisms and microbial interactions underlying microeukaryotic dynamics in eutrophic aquatic ecosystems where harmful algal blooms occurred frequently.
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Affiliation(s)
- 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
| | - 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.
| | - 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
| | - Xiaoyan Zhou
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Xiangyu Zhu
- 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.
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24
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Macke E, Callens M, Massol F, Vanoverberghe I, De Meester L, Decaestecker E. Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities. Front Microbiol 2020; 11:380. [PMID: 32256467 PMCID: PMC7090131 DOI: 10.3389/fmicb.2020.00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/20/2020] [Indexed: 12/04/2022] Open
Abstract
In spite of the growing interest in the role of the gut microbiome (GM) in host physiology and health, the mechanisms governing its assembly and its effects on the environment are poorly understood. In this article, we show that the host genotype and the GM of Daphnia influence the community structure of the surrounding bacterioplankton (BPK). When Daphnia genotypes were placed in an identical environment, both the GM and BPK showed a genotype and diet-dependent taxonomic composition. Overall, the GM strongly differed from the BPK in taxonomic composition and was characterized by a lower α-diversity, suggesting a selective rejecting of bacteria from the regional species pool. In a microbiome transplant experiment, the assembly of both the GM and BPK was strongly affected by the host genotype and the inoculum to which germ-free Daphnia were exposed. The combination of these results suggests a strong interaction between the host genotype, its GM and free-living microbial communities. Currently, it is generally assumed that an animal’s diet has a strong effect on the animal’s GM, but only a negligible (if any) effect on the surrounding environment. However, our results indicate that the diet/microbiome inocula have a small effect on the gut community and a large effect on the community in the surrounding environment. This structuring genotype × microbiome × environment effect is an essential prerequisite that could indicate that microbiomes play an important role in eco-evolutionary processes.
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Affiliation(s)
- Emilie Macke
- Aquatic Biology, IRF Life Sciences, KU Leuven, Kortrijk, Belgium
| | - Martijn Callens
- Aquatic Biology, IRF Life Sciences, KU Leuven, Kortrijk, Belgium.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Francois Massol
- CNRS, Lille-Sciences et Technologies, UMR 8198 Evo-Eco-Paleo, SPICI Group, Villeneuve-d'Ascq, France.,University of Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | | | - Luc De Meester
- Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
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25
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Du XP, Cai ZH, Zuo P, Meng FX, Zhu JM, Zhou J. Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom. Microorganisms 2020; 8:microorganisms8010107. [PMID: 31940944 PMCID: PMC7023004 DOI: 10.3390/microorganisms8010107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 01/02/2023] Open
Abstract
Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.
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Affiliation(s)
- Xiao-Peng Du
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhong-Hua Cai
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ping Zuo
- The School of Geography and Ocean Science, Nanjing University, Nanjing 210000, China;
| | - Fan-Xu Meng
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310000, China
| | - Jian-Ming Zhu
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Zhou
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Correspondence:
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26
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Zamanillo M, Ortega-Retuerta E, Nunes S, Estrada M, Sala MM, Royer SJ, López-Sandoval DC, Emelianov M, Vaqué D, Marrasé C, Simó R. Distribution of transparent exopolymer particles (TEP) in distinct regions of the Southern Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:736-748. [PMID: 31325871 DOI: 10.1016/j.scitotenv.2019.06.524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 06/10/2023]
Abstract
Transparent exopolymer particles (TEP) are an abundant class of suspended organic particles, mainly formed by polysaccharides, which play important roles in biogeochemical and ecological processes in the ocean. In this study we investigated horizontal and vertical TEP distributions (within the euphotic layer, including the upper surface) and their short-term variability along with a suite of environmental and biological variables in four distinct regions of the Southern Ocean. TEP concentrations in the surface (4 m) averaged 102.3 ± 40.4 μg XG eq. L-1 and typically decreased with depth. Chlorophyll a (Chl a) concentration was a better predictor of TEP variability across the horizontal (R2 = 0.66, p < 0.001) and vertical (R2 = 0.74, p < 0.001) scales than prokaryotic heterotrophic abundance and production. Incubation experiments further confirmed the main role of phytoplankton as TEP producers. The highest surface TEP concentrations were found north of the South Orkney Islands (144.4 ± 21.7 μg XG eq. L-1), where the phytoplankton was dominated by cryptophytes and haptophytes; however, the highest TEP:Chl a ratios were found south of these islands (153.4 ± 29.8 μg XG eq (μg Chl a)-1, compared to a mean of 79.3 ± 54.9 μg XG eq (μg Chl a)-1 in the whole cruise, in association with haptophyte dominance, proximity of sea ice and high exposure to solar radiation. TEP were generally enriched in the upper surface (10 cm) respect to 4 m, despite a lack of biomass enrichment, suggesting either upward transport by positive buoyancy or bubble scavenging, or higher production at the upper surface by light stress or aggregation. TEP concentrations did not present any significant cyclic diel pattern. Altogether, our results suggest that photobiological stress, sea ice melt and turbulence add to phytoplankton productivity in driving TEP distribution across the Antarctic Peninsula area and Atlantic sector of the Southern Ocean.
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Affiliation(s)
- Marina Zamanillo
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - Eva Ortega-Retuerta
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain; CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Banyuls-sur-Mer, France
| | - Sdena Nunes
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - Marta Estrada
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - María Montserrat Sala
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - Sarah-Jeanne Royer
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain; Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daffne C López-Sandoval
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain; Red Sea Research Center (RSRC), King Abdullah University of Science and Techonolgy (KAUST), Thuwal, Saudi Arabia
| | - Mikhail Emelianov
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - Dolors Vaqué
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - Cèlia Marrasé
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | - Rafel Simó
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain.
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27
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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28
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de Sousa AGG, Tomasino MP, Duarte P, Fernández-Méndez M, Assmy P, Ribeiro H, Surkont J, Leite RB, Pereira-Leal JB, Torgo L, Magalhães C. Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. MICROBIAL ECOLOGY 2019; 78:388-408. [PMID: 30623212 DOI: 10.1007/s00248-018-01314-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.
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Affiliation(s)
- António Gaspar G de Sousa
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Maria Paola Tomasino
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | | | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | - Hugo Ribeiro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Jaroslaw Surkont
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Ricardo B Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - José B Pereira-Leal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Luís Torgo
- LIAAD - Laboratory of Artificial Intelligence and Decision Support, INESC Tec, Porto, Portugal
- Faculty of Computer Science, Dalhousie University, Halifax, Canada, USA
| | - Catarina Magalhães
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
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29
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Krüger K, Chafee M, Ben Francis T, Glavina Del Rio T, Becher D, Schweder T, Amann RI, Teeling H. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. ISME JOURNAL 2019; 13:2800-2816. [PMID: 31316134 PMCID: PMC6794258 DOI: 10.1038/s41396-019-0476-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 11/09/2022]
Abstract
We investigated Bacteroidetes during spring algae blooms in the southern North Sea in 2010–2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 Bacteroidetes MAGs covering ~120 mostly uncultivated species. We identified 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal polysaccharide degradation. The majority of PULs were predicted to target the diatom storage polysaccharide laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points in time revealed expression of SusC-like proteins from PULs targeting all of these substrates. Analyses of abundant key players and their PUL repertoires over time furthermore suggested that fewer and simpler polysaccharides dominated early bloom stages, and that more complex polysaccharides became available as blooms progressed.
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Affiliation(s)
- Karen Krüger
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Meghan Chafee
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - T Ben Francis
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | | | - Dörte Becher
- Institute for Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Felix-Hausdorff-Straße 3, 17487, Greifswald, Germany.,Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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30
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Zäncker B, Cunliffe M, Engel A. Bacterial Community Composition in the Sea Surface Microlayer Off the Peruvian Coast. Front Microbiol 2018; 9:2699. [PMID: 30498480 PMCID: PMC6249803 DOI: 10.3389/fmicb.2018.02699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/23/2018] [Indexed: 02/01/2023] Open
Abstract
The sea surface microlayer (SML) is located at the air-sea interface, with microorganisms and organic matter in the SML influencing air-sea exchange processes. Yet understanding of the SML bacterial (bacterioneuston) community composition and assembly remains limited. Availability of organic matter, UV radiation and wind speed have previously been suggested to influence the community composition of bacterioneuston. Another mechanism potentially controlling bacterioneuston dynamics is bacterioplankton attached to gel-like particles that ascend through the water column into the SML. We analyzed the bacterial community composition, Transparent Exopolymer Particles (TEP) abundance and nutrient concentrations in the surface waters of the Peruvian upwelling region. The bacterioneuston and bacterioplankton communities were similar, suggesting a close spatial coupling. Four Bacteroidetes families were significantly enriched in the SML, two of them, the Flavobacteriaceae and Cryomorphaceae, were found to comprise the majority of SML-enriched operational taxonomic units (OTUs). The enrichment of these families was controlled by a variety of environmental factors. The SML-enriched bacterial families were negatively correlated with water temperature and wind speed in the SML and positively correlated with nutrient concentrations, salinity and TEP in the underlying water (ULW). The correlations with nutrient concentrations and salinity suggest that the enriched bacterial families were more abundant at the upwelling stations.
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Affiliation(s)
- Birthe Zäncker
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, Plymouth, United Kingdom.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Plymouth, United Kingdom
| | - Anja Engel
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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31
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Zhu J, Hong Y, Zada S, Hu Z, Wang H. Spatial Variability and Co-acclimation of Phytoplankton and Bacterioplankton Communities in the Pearl River Estuary, China. Front Microbiol 2018; 9:2503. [PMID: 30405565 PMCID: PMC6206238 DOI: 10.3389/fmicb.2018.02503] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022] Open
Abstract
Phytoplankton and bacterioplankton play significant roles in estuarine systems. It is important to demonstrate the spatial variability of bacterial and microalgal communities and understand the co-acclimation of these organisms to different environmental factors. In this study, MiSeq sequencing and morphological identification were applied to analyze the variations in bacterial and microalgal communities in the Pearl River Estuary, respectively. Molecular ecological network analysis was used to investigate the potential interactions between microalgae and bacteria and illustrate the responses of these interactions to environmental gradients. The results revealed that microalgal/bacterial communities in freshwater samples were distinct from those in mesohaline water samples. Microalgae affiliated to the genus Skeletonema dominated the mesohaline water phytoplankton communities, while Melosira was the more abundant genus in freshwater communities. Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Acidimicrobiia dominated bacterial communities in freshwater samples, while Gammaproteobacteria, Bacilli, and Synechococcophycideae were more abundant in mesohaline water samples. Tightly correlations were observed between phytoplankton and bacterioplankton. These interactions were regarded to be key factors in shaping the community structures. Further, the KEGG database and PICRUSt were used to predict the functions of bacterioplankton in the process of nitrogen cycling. The results indicated that denitrification could play an important role in nitrogen loss and might alleviate the eutrophication in the Pearl River Estuary. Collectively, the results in this study revealed that substantial changes in phytoplankton and bacterioplankton communities were correlated with the gradients of environmental parameters in the Pearl River Estuary. The results also demonstrated that the interactions between phytoplankton and bacterioplankton were important for these organisms to acclimate to changing environments.
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Affiliation(s)
- Jianming Zhu
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Yiguo Hong
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou, China
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32
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Taylor JD, Bird KE, Widdicome CE, Cunliffe M. Active bacterioplankton community response to dissolved 'free' deoxyribonucleic acid (dDNA) in surface coastal marine waters. FEMS Microbiol Ecol 2018; 94:5053802. [PMID: 30010743 DOI: 10.1093/femsec/fiy132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/10/2018] [Indexed: 11/14/2022] Open
Abstract
Seawater contains dissolved 'free' DNA (dDNA) that is part of a larger <0.2 µm pool of DNA (D-DNA) including viruses and uncharacterised bound DNA. Previous studies have shown that bacterioplankton readily degrade dDNA, and culture-based approaches have identified several potential dDNA-utilising taxa. This study characterised the seasonal variation in D-DNA concentrations at Station L4, a coastal marine observatory in the Western English Channel, and linked changes in concentration to cognate physicochemical and biological factors. The impact of dDNA addition on active bacterioplankton communities at Station L4 was then determined using 16S rRNA high-throughput sequencing and RNA Stable Isotope Probing (RNA SIP) with 13C-labelled diatom-derived dDNA. Compared to other major bacterioplankton orders, the Rhodobacterales actively responded to dDNA additions in amended microcosms and RNA SIP identified two Rhodobacterales populations most closely associated with the genera Halocynthiibacter and Sulfitobacter that assimilated the 13C-labelled dDNA. Here we demonstrate that dDNA is a source of dissolved organic carbon for some members of the major bacterioplankton group the Marine Roseobacter Clade. This study enhances our understanding of roles of specific bacterioplankton taxa in dissolved organic matter cycling in coastal waters with potential implications for nitrogen and phosphorus regeneration processes.
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Kimberley E Bird
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth, UK
| | | | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth, UK
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33
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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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34
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Ortega-Retuerta E, Marrasé C, Muñoz-Fernández A, Sala MM, Simó R, Gasol JM. Seasonal dynamics of transparent exopolymer particles (TEP) and their drivers in the coastal NW Mediterranean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:180-190. [PMID: 29525702 DOI: 10.1016/j.scitotenv.2018.02.341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 05/26/2023]
Abstract
Transparent Exopolymer Particles (TEPs) are a subclass of organic particles with high impact in biogeochemical and ecological processes, such as the biological carbon pump, air-sea interactions, or the microbial loop. However, the complexity in production and consumption makes TEP dynamics hardly predictable, calling for the need of descriptive studies about the in situ dynamics of these particles. We followed monthly TEP dynamics and combined them with a dataset of environmental variables during three years in a coastal site of the oligotrophic North Western Mediterranean (Blanes Bay). TEP concentration, ranging from 11.3 to 289.1μgXGeqL-1 (average 81.7±11.7μgXGeqL-1), showed recurrent peaks in early summer (June-July). TEP were temporally disconnected from chlorophyll a maxima, that occurred in late winter and early spring (maxima 1.21μgL-1), but they were significantly related to the abundance of specific phytoplankton groups (diatoms and dinoflagellates) and also coincided with periods of low nutrient concentrations. The fraction of particulate organic carbon in the form of TEP (the TEP:POC and TEP:PM ratios) were also highest in early summer, indicating that TEP-enriched particles of low density accumulate in surface waters during stratified periods. We hypothesize that the accumulation of these particles affects the microbial food web by enhancing the activity of specific prokaryotic extracellular enzymes (esterase, β-glucosidase and alkaline phosphatase) and promoting the abundance of heterotrophic nanoflagellates.
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Affiliation(s)
- Eva Ortega-Retuerta
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain; Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Cèlia Marrasé
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Ana Muñoz-Fernández
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - M Montserrat Sala
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Rafel Simó
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
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35
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Zhou J, Richlen ML, Sehein TR, Kulis DM, Anderson DM, Cai Z. Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom. Front Microbiol 2018; 9:1201. [PMID: 29928265 PMCID: PMC5998739 DOI: 10.3389/fmicb.2018.01201] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
Interactions between microorganisms and algae during bloom events significantly impacts their physiology, alters ambient chemistry, and shapes ecosystem diversity. The potential role these interactions have in bloom development and decline are also of particular interest given the ecosystem impacts of algal blooms. We hypothesized that microbial community structure and succession is linked to specific bloom stages, and reflects complex interactions among taxa comprising the phycosphere environment. This investigation used pyrosequencing and correlation approaches to assess patterns and associations among bacteria, archaea, and microeukaryotes during a spring bloom of the dinoflagellate Alexandrium catenella. Within the bacterial community, Gammaproteobacteria and Bacteroidetes were predominant during the initial bloom stage, while Alphaproteobacteria, Cyanobacteria, and Actinobacteria were the most abundant taxa present during bloom onset and termination. In the archaea biosphere, methanogenic members were present during the early bloom period while the majority of species identified in the late bloom stage were ammonia-oxidizing archaea and Halobacteriales. Dinoflagellates were the major eukaryotic group present during most stages of the bloom, whereas a mixed assemblage comprising diatoms, green-algae, rotifera, and other microzooplankton were present during bloom termination. Temperature and salinity were key environmental factors associated with changes in bacterial and archaeal community structure, respectively, whereas inorganic nitrogen and inorganic phosphate were associated with eukaryotic variation. The relative contribution of environmental parameters measured during the bloom to variability among samples was 35.3%. Interaction analysis showed that Maxillopoda, Spirotrichea, Dinoflagellata, and Halobacteria were keystone taxa within the positive-correlation network, while Halobacteria, Dictyochophyceae, Mamiellophyceae, and Gammaproteobacteria were the main contributors to the negative-correlation network. The positive and negative relationships were the primary drivers of mutualist and competitive interactions that impacted algal bloom fate, respectively. Functional predictions showed that blooms enhance microbial carbohydrate and energy metabolism, and alter the sulfur cycle. Our results suggest that microbial community structure is strongly linked to bloom progression, although specific drivers of community interactions and responses are not well understood. The importance of considering biotic interactions (e.g., competition, symbiosis, and predation) when investigating the link between microbial ecological behavior and an algal bloom's trajectory is also highlighted.
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Affiliation(s)
- Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Mindy L. Richlen
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Taylor R. Sehein
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - David M. Kulis
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Donald M. Anderson
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
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36
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Wurl O, Bird K, Cunliffe M, Landing WM, Miller U, Mustaffa NIH, Ribas‐Ribas M, Witte C, Zappa CJ. Warming and Inhibition of Salinization at the Ocean's Surface by Cyanobacteria. GEOPHYSICAL RESEARCH LETTERS 2018; 45:4230-4237. [PMID: 29937608 PMCID: PMC6001423 DOI: 10.1029/2018gl077946] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
This paper describes high-resolution in situ observations of temperature and, for the first time, of salinity in the uppermost skin layer of the ocean, including the influence of large surface blooms of cyanobacteria on those skin properties. In the presence of the blooms, large anomalies of skin temperature and salinity of 0.95°C and -0.49 practical salinity unit were found, but a substantially cooler (-0.22°C) and saltier skin layer (0.19 practical salinity unit) was found in the absence of surface blooms. The results suggest that biologically controlled warming and inhibition of salinization of the ocean's surface occur. Less saline skin layers form during precipitation, but our observations also show that surface blooms of Trichodesmium sp. inhibit evaporation decreasing the salinity at the ocean's surface. This study has important implications in the assessment of precipitation over the ocean using remotely sensed salinity, but also for a better understanding of heat exchange and the hydrologic cycle on a regional scale.
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Affiliation(s)
- O. Wurl
- Institute for Chemistry and Biology of the Marine EnvironmentCarl von Ossietzky University OldenburgWilhelmshavenGermany
| | - K. Bird
- Marine Biological Association of the United KingdomPlymouthUK
| | - M. Cunliffe
- Marine Biological Association of the United KingdomPlymouthUK
- Marine Biology and Ecology Research Centre, School of Biological and Marine SciencesPlymouth University, Drake CircusPlymouthUK
| | - W. M. Landing
- Department of Earth, Ocean, and Atmospheric ScienceFlorida State UniversityTallahasseeFLUSA
| | - U. Miller
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNYUSA
| | - N. I. H. Mustaffa
- Institute for Chemistry and Biology of the Marine EnvironmentCarl von Ossietzky University OldenburgWilhelmshavenGermany
| | - M. Ribas‐Ribas
- Institute for Chemistry and Biology of the Marine EnvironmentCarl von Ossietzky University OldenburgWilhelmshavenGermany
| | - C. Witte
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNYUSA
| | - C. J. Zappa
- Lamont‐Doherty Earth ObservatoryColumbia UniversityPalisadesNYUSA
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37
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Liu J, Li C, Jing J, Zhao P, Luo Z, Cao M, Ma Z, Jia T, Chai B. Ecological patterns and adaptability of bacterial communities in alkaline copper mine drainage. WATER RESEARCH 2018; 133:99-109. [PMID: 29367051 DOI: 10.1016/j.watres.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/31/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Environmental gradient have strong effects on community assembly processes. In order to reveal the effects of alkaline mine drainage (AlkMD) on bacterial and denitrifying bacterial community compositions and diversity in tailings reservoir, here we conducted an experiment to examine all and core bacterial taxa and denitrifying functional genes's (nirS, nirK, nosZΙ) abundance along a chemical gradient in tailings water in Shibahe copper tailings in Zhongtiaoshan, China. Differences in bacterial and denitrifying bacterial community compositions in different habitats and their relationships with environmental parameters were analyzed. The results showed that the richness and diversity of bacterial community in downstream seeping water (SDSW) were the largest, while that in upstream tailings water (STW1) were the lowest. The diversity and abundance of bacterial communities tended to increase from STW1 to SDSW. The variation of bacterial community diversity was significantly related to electroconductibility (EC), nitrate (NO3-), nitrite (NO2-), total carbon (TC), inorganic carbon (IC) and sulfate (SO42-), but was not correlated with geographic distance in local scale. Core taxa from class to genus were all significantly related to NO3- and NO2-. Core taxa Rhodobacteraceae, Rhodobacter, Acinetobacter and Hydrogenophaga were typical denitrifying bacteria. The variation trends of these groups were consistent with the copy number of nirS, nirK and nosZΙ, demonstrating their importance in the process of nitrogen reduction. The copy number of nirK, nosZΙ and nirS/16S rDNA, nirK/16Sr DNA correlated strongly with NO3-, NO2- and IC, but nirS and nosZI/16SrDNA had no significant correlation with NO3- and NO2-. The copy numbers of denitrifying functional genes (nirS, nirK and nosZΙ) were negatively correlated with heavy metal plumbum (Pb) and zinc (Zn). It showed that heavy metal contamination was an important factor affecting the structure of denitrifying bacterial community in AlkMD. In this study we have identified the distribution pattern of bacterial community along physiochemical gradients in alkaline tailings reservoir and displayed the driving force of shaping the structure of bacterial community. The influence of NO3-, NO2-, IC and heavy metal Pb and Zn on bacterial community might via their influence on the functional groups involving nitrogen, carbon and metal metabolisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, 030006, China
| | - Juhui Jing
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Miaowen Cao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhuanzhuan Ma
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China.
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38
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Smale DA, Taylor JD, Coombs SH, Moore G, Cunliffe M. Community responses to seawater warming are conserved across diverse biological groupings and taxonomic resolutions. Proc Biol Sci 2018; 284:rspb.2017.0534. [PMID: 28878056 PMCID: PMC5597821 DOI: 10.1098/rspb.2017.0534] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/28/2017] [Indexed: 02/01/2023] Open
Abstract
Temperature variability is a major driver of ecological pattern, with recent changes in average and extreme temperatures having significant impacts on populations, communities and ecosystems. In the marine realm, very few experiments have manipulated temperature in situ, and current understanding of temperature effects on community dynamics is limited. We developed new technology for precise seawater temperature control to examine warming effects on communities of bacteria, microbial eukaryotes (protists) and metazoans. Despite highly contrasting phylogenies, size spectra and diversity levels, the three community types responded similarly to seawater warming treatments of +3°C and +5°C, highlighting the critical and overarching importance of temperature in structuring communities. Temperature effects were detectable at coarse taxonomic resolutions and many taxa responded positively to warming, leading to increased abundances at the community-level. Novel field-based experimental approaches are essential to improve mechanistic understanding of how ocean warming will alter the structure and functioning of diverse marine communities.
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Affiliation(s)
- Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Joe D Taylor
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Steve H Coombs
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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39
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Boniewicz-Szmyt K, Pogorzelski SJ. Evolution of natural sea surface films: a new quantification formalism based on multidimensional space vector. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:4826-4836. [PMID: 29198032 PMCID: PMC5846998 DOI: 10.1007/s11356-017-0788-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Spatial and temporal variability of natural surfactant sea surface film structural parameters were evaluated from force-area isotherms, film pressure-temperature isochors, dynamic surface tension-time relations performed on samples collected in Baltic Sea shallow coastal waters. The film structure state was postulated as a 10-D dimensionless vector created from the normalized thermodynamic, adsorptive, and viscoelastic film parameters. The normalization procedure is based on the concept of self-corresponding states known in thermodynamics. The values taken by all the reduced parameters indicated a significant deviation from the reference ideal-2D gas behavior. The exhibited deviations of the surface parameters from the background values of the same thermodynamic state of each film were independent on the film-collecting procedure, sample solvent treatment, and temperature. The structural similarity was expressed quantitatively as a (Cartesian, street, and Czebyszew) distance between two vectors of the analyzed film and the standard one from the database, and appeared to be related to environmental conditions, surface-active organic matter production, and migration in the studied coastal sea region. The most distinctive parameters differing the films were y, M w and E isoth, as established from Czebyszew function application. The proposed formalism is of universal concern and could be applied to any natural water surfactant system (seawater, inland water, rain water, and snowmelt water).
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Affiliation(s)
| | - Stanisław Józef Pogorzelski
- Institute of Experimental Physics, Faculty of Mathematics, Physics and Informatics, University of Gdansk, 80-308, Gdansk, Poland
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40
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Bioassessment of a Drinking Water Reservoir Using Plankton: High Throughput Sequencing vs. Traditional Morphological Method. WATER 2018. [DOI: 10.3390/w10010082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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41
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Li J, Jiang X, Jing Z, Li G, Chen Z, Zhou L, Zhao C, Liu J, Tan Y. Spatial and seasonal distributions of bacterioplankton in the Pearl River Estuary: The combined effects of riverine inputs, temperature, and phytoplankton. MARINE POLLUTION BULLETIN 2017; 125:199-207. [PMID: 28823423 DOI: 10.1016/j.marpolbul.2017.08.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 06/07/2023]
Abstract
In this study, we used flow cytometry and 16S rRNA gene pyrosequencing to investigate bacterioplankton (heterotrophic bacteria and picocyanobacteria) abundance and community structure in surface waters along the Pearl River Estuary. The results showed significant differences in bacterioplankton dynamics between fresh- and saltwater sites and between wet and dry season. Synechococcus constituted the majority of picocyanobacteria in both seasons. During the wet season, Synechococcus reached extremely high abundance at the mouth of the estuary, and heterotrophic bacteria were highly abundant (>106cellsml-1) throughout the studied region. At the same time, bacterioplankton decreased dramatically during the dry season. Pyrosequencing data indicated that salinity was a key parameter in shaping microbial community structure during both seasons. Phytoplankton was also an important factor; the proportion of Synechococcus and Rhodobacteriales was elevated at the frontal zone with higher chlorophyll a during the wet season, whereas Synechococcus were markedly reduced during the dry season.
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Affiliation(s)
- Jiajun Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xin Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhiyou Jing
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zuozhi Chen
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Linbin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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42
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Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.08.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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43
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Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone. Appl Environ Microbiol 2017; 83:AEM.00494-17. [PMID: 28667110 DOI: 10.1128/aem.00494-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for <0.1% of the total sequence abundance), the majority of which were unique to each site. The relationship between 16S rRNA and the 16S rRNA gene, i.e., between potential metabolic activity and abundance, was positive for the whole community. However, analysis of individual OTUs revealed high rRNA-to-rRNA gene ratios for most (71.6% ± 16.7%) of the rare taxa, suggesting that these low-abundance organisms were potentially active and hence might be playing an important role in ecosystem diversity and functioning in the GON.IMPORTANCE The study of bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of different environmental factors leading to their heterogeneous distribution, with the rare taxa contributing to a major proportion of diversity and shifts in community composition and potentially holding a key role in ecosystem functioning.
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44
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Marine Bacterioplankton Seasonal Succession Dynamics. Trends Microbiol 2017; 25:494-505. [DOI: 10.1016/j.tim.2016.12.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023]
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45
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Kegler HF, Lukman M, Teichberg M, Plass-Johnson J, Hassenrück C, Wild C, Gärdes A. Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia. Front Microbiol 2017; 8:662. [PMID: 28473810 PMCID: PMC5397486 DOI: 10.3389/fmicb.2017.00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/31/2017] [Indexed: 12/04/2022] Open
Abstract
Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.
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Affiliation(s)
- Hauke F Kegler
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Muhammad Lukman
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin UniversitySouth Sulawesi, Indonesia
| | - Mirta Teichberg
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany
| | - Jeremiah Plass-Johnson
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Centre for Ocean Life, National Institute of Aquatic Resources (DTU-Aqua), Technical University of DenmarkCharlottenlund, Denmark
| | - Christiane Hassenrück
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany
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46
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Taylor JD, Cunliffe M. Coastal bacterioplankton community response to diatom-derived polysaccharide microgels. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:151-157. [PMID: 27943607 DOI: 10.1111/1758-2229.12513] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Phytoplankton-derived polysaccharide microgels, including transparent exopolymer particles (TEP), are a major component of the marine organic carbon pool. Previous studies have made correlative links between phytoplankton material and bacterioplankton, and performed experiments that assess general responses to phytoplankton, yet there is a lack of direct empirical evidence of specific bacterioplankton responses to natural phytoplankton polysaccharide microgels. In this study, we used diatom produced TEP in controlled incubation experiments to determine the impact of polysaccharide microgels on a coastal bacterioplankton community. Quantification of bacterial 16S rRNA gene transcripts showed that the addition of TEP caused an increase in bacterioplankton activity. Similarly, high-throughput sequencing of RT-PCR amplified bacterial 16S rRNA gene transcripts showed that active bacterioplankton community structure and diversity also changed in response to microgels. Alteromonadales and Rhodobacterales increased in abundance in response to TEP, suggesting that both bacterioplankton taxa utilize diatom-derived microgels. However, through assessing 13 C-labelled TEP uptake via RNA Stable Isotope Probing, we show that only the Alteromonadales (genus Alteromonas) assimilated the TEP carbon. This study adds utilization of diatom-derived TEP to the metabolic repertoire of the archetypal copiotrophic bacterioplankton Alteromonas, and indicates that the Rhodobacterales may utilize TEP for other purposes (e.g. attachment sites).
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Affiliation(s)
- Joe D Taylor
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Plymouth, UK
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47
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Ortega-Retuerta E, Sala MM, Borrull E, Mestre M, Aparicio FL, Gallisai R, Antequera C, Marrasé C, Peters F, Simó R, Gasol JM. Horizontal and Vertical Distributions of Transparent Exopolymer Particles (TEP) in the NW Mediterranean Sea Are Linked to Chlorophyll a and O 2 Variability. Front Microbiol 2017; 7:2159. [PMID: 28197126 PMCID: PMC5281620 DOI: 10.3389/fmicb.2016.02159] [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: 09/12/2016] [Accepted: 12/22/2016] [Indexed: 11/13/2022] Open
Abstract
Transparent Exopolymer Particles (TEP) are relevant in particle and carbon fluxes in the ocean, and have economic impact in the desalination industry affecting reverse osmosis membrane fouling. However, general models of their occurrence and dynamics are not yet possible because of the poorly known co-variations with other physical and biological variables. Here, we describe TEP distributions in the NW Mediterranean Sea during late spring 2012, along perpendicular and parallel transects to the Catalan coast. The stations in the parallel transect were sampled at the surface, while the stations in the perpendicular transect were sampled from the surface to the bathypelagic, including the bottom nepheloid layers. We also followed the short-term TEP dynamics along a 2-day cycle in offshore waters. TEP concentrations in the area ranged from 4.9 to 122.8 and averaged 31.4 ± 12.0 μg XG eq L−1. The distribution of TEP measured in transects parallel to the Catalan Coast correlated those of chlorophyll a (Chla) in May but not in June, when higher TEP-values with respect to Chla were observed. TEP horizontal variability in epipelagic waters from the coast to the open sea also correlated to that of Chla, O2 (that we interpret as a proxy of primary production) and bacterial production (BP). In contrast, the TEP vertical distributions in epipelagic waters were uncoupled from those of Chla, as TEP maxima were located above the deep chlorophyll maxima. The vertical distribution of TEP in the epipelagic zone was correlated with O2 and BP, suggesting combined phytoplankton (through primary production) and bacterial (through carbon reprocessing) TEP sources. However, no clear temporal patterns arose during the 2-day cycle. In meso- and bathypelagic waters, where phytoplanktonic sources are minor, TEP concentrations (10.1 ± 4.3 μg XG eq l−1) were half those in the epipelagic, but we observed relative TEP increments coinciding with the presence of nepheloid layers. These TEP increases were not paralleled by increases in particulate organic carbon, indicating that TEP are likely to act as aggregating agents of the mostly inorganic particles present in these bottom nepheloid layers.
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Affiliation(s)
- Eva Ortega-Retuerta
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Maria M Sala
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Encarna Borrull
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Mireia Mestre
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Fran L Aparicio
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Rachele Gallisai
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Carolina Antequera
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Cèlia Marrasé
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Francesc Peters
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Rafel Simó
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
| | - Josep M Gasol
- Biologia Marina i Oceanografia, Consejo Superior de Investigaciones Científicas, Institut de Ciències del Mar Barcelona, Spain
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48
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Tang K, Lin Y, Han Y, Jiao N. Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach. Front Microbiol 2017; 8:220. [PMID: 28261179 PMCID: PMC5306329 DOI: 10.3389/fmicb.2017.00220] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/31/2017] [Indexed: 01/26/2023] Open
Abstract
Members of phylum Bacteroidetes are distributed across diverse marine niches and Flavobacteria is often the predominant bacterial class decomposing algae-derived polysaccharides. Here, we report the complete genome of Gramella flava JLT2011 (Flavobacteria) isolated from surface water of the southeastern Pacific. A remarkable genomic feature is that the number of glycoside hydrolase (GH) genes in the genome of G. flava JLT2011 is more than 2-fold higher than that of other Gramella species. The functional profiles of the GHs suggest extensive variation in Gramella species. Growth experiments revealed that G. flava JLT2011 has the ability to utilize a wide range of polysaccharides for growth such as xylan and homogalacturonan in pectin. Nearly half of all GH genes were located on the multi-gene polysaccharide utilization loci (PUL) or PUL-like systems in G. flava JLT2011. This species was also found to harbor the two xylan PULs and a pectin PUL, respectively. Gene expression data indicated that more GHs and sugar-specific outer-membrane susC-susD systems were found in the presence of xylan than in the presence of pectin, suggesting a different strategy for heteropolymeric xylan and homoglacturonan utilization. Multi-omics data (transcriptomics, proteomics, and metabolomics) indicated that xylan PULs and pectin PUL are respectively involved in the catabolism of their corresponding polysaccharides. This work presents a comparison of polysaccharide decomposition within a genus and expands current knowledge on the diversity and function of PULs in marine Bacteroidetes, thereby deepening our understanding of their ecological role in polysaccharide remineralization in the marine system.
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Affiliation(s)
- Kai Tang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
| | - Yingfan Lin
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
| | - Yu Han
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen, China
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49
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Sperling M, Piontek J, Engel A, Wiltshire KH, Niggemann J, Gerdts G, Wichels A. Combined Carbohydrates Support Rich Communities of Particle-Associated Marine Bacterioplankton. Front Microbiol 2017; 8:65. [PMID: 28197132 PMCID: PMC5281597 DOI: 10.3389/fmicb.2017.00065] [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: 09/14/2016] [Accepted: 01/10/2017] [Indexed: 11/13/2022] Open
Abstract
Carbohydrates represent an important fraction of labile and semi-labile marine organic matter that is mainly comprised of exopolymeric substances derived from phytoplankton exudation and decay. This study investigates the composition of total combined carbohydrates (tCCHO; >1 kDa) and the community development of free-living (0.2-3 μm) and particle-associated (PA) (3-10 μm) bacterioplankton during a spring phytoplankton bloom in the southern North Sea. Furthermore, rates were determined for the extracellular enzymatic hydrolysis that catalyzes the initial step in bacterial organic matter remineralization. Concentrations of tCCHO greatly increased during bloom development, while the composition showed only minor changes over time. The combined concentration of glucose, galactose, fucose, rhamnose, galactosamine, glucosamine, and glucuronic acid in tCCHO was a significant factor shaping the community composition of the PA bacteria. The richness of PA bacteria greatly increased in the post-bloom phase. At the same time, the increase in extracellular β-glucosidase activity was sufficient to explain the observed decrease in tCCHO, indicating the efficient utilization of carbohydrates by the bacterioplankton community during the post-bloom phase. Our results suggest that carbohydrate concentration and composition are important factors in the multifactorial environmental control of bacterioplankton succession and the enzymatic hydrolysis of organic matter during phytoplankton blooms.
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Affiliation(s)
- Martin Sperling
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine ResearchBremerhaven, Germany; Biologische Anstalt Helgoland, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine ResearchHelgoland, Germany; Biological Oceanography, Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research KielKiel, Germany
| | - Judith Piontek
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine ResearchBremerhaven, Germany; Biological Oceanography, Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research KielKiel, Germany
| | - Anja Engel
- Biological Oceanography, Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel Kiel, Germany
| | - Karen H Wiltshire
- Biologische Anstalt Helgoland, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research Helgoland, Germany
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Gunnar Gerdts
- Biologische Anstalt Helgoland, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research Helgoland, Germany
| | - Antje Wichels
- Biologische Anstalt Helgoland, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research Helgoland, Germany
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50
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Jackrel SL, Owens SM, Gilbert JA, Pfister CA. Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery. Mol Ecol Resour 2017; 17:931-942. [PMID: 27997751 DOI: 10.1111/1755-0998.12645] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/09/2016] [Accepted: 12/14/2016] [Indexed: 11/26/2022]
Abstract
Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal-associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast-blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14-bp sequence in the Proteobacteria that matches the 17-bp chloroplast-blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14-bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle-blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n-mer oligonucleotides of each PNA sequence.
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Affiliation(s)
- Sara L Jackrel
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL, 60439, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL, 60439, USA
- The Microbiome Center, Department of Surgery, The University of Chicago, 5841 S Maryland Ave, Chicago, IL, 60637, USA
| | - Catherine A Pfister
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA
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